From 7257de1722318226e7e621054e7009eed5400285 Mon Sep 17 00:00:00 2001
From: Alexandru Mahmoud <almahmoud@jhu.edu>
Date: Mon, 14 Jun 2021 16:57:02 -0400
Subject: [PATCH 001/218] Temporary fix for keycloak OIDC

---
 lib/galaxy/authnz/custos_authnz.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/authnz/custos_authnz.py b/lib/galaxy/authnz/custos_authnz.py
index f2a22191dd3..e5eef15b196 100644
--- a/lib/galaxy/authnz/custos_authnz.py
+++ b/lib/galaxy/authnz/custos_authnz.py
@@ -87,6 +87,7 @@ class CustosAuthnz(IdentityProvider):
         else:
             userinfo = self._get_userinfo(oauth2_session)
         email = userinfo['email']
+        username = userinfo.get('preferred_username', self._generate_username(trans, email))
         user_id = userinfo['sub']
 
         # Create or update custos_authnz_token record
@@ -110,9 +111,13 @@ class CustosAuthnz(IdentityProvider):
                         message = "There already exists a user with email %s.  To associate this external login, you must first be logged in as that existing account." % email
                         log.exception(message)
                         raise exceptions.AuthenticationFailed(message)
-                else:
-                    login_redirect_url = login_redirect_url + 'root/login?confirm=true&custos_token=' + json.dumps(token)
+                elif self.config['provider'] == 'custos':
+                    login_redirect_url = f"{login_redirect_url}root/login?confirm=true&custos_token={json.dumps(token)}"
                     return login_redirect_url, None
+                else:
+                    user = trans.app.user_manager.create(email=email, username=username)
+                    if trans.app.config.user_activation_on:
+                        trans.app.user_manager.send_activation_email(trans, email, username)
 
             custos_authnz_token = CustosAuthnzToken(user=user,
                                    external_user_id=user_id,
@@ -130,7 +135,7 @@ class CustosAuthnz(IdentityProvider):
             custos_authnz_token.refresh_expiration_time = refresh_expiration_time
         trans.sa_session.add(custos_authnz_token)
         trans.sa_session.flush()
-        return login_redirect_url, custos_authnz_token.user
+        return "/", custos_authnz_token.user
 
     def create_user(self, token, trans, login_redirect_url):
         token_dict = json.loads(token)

From 3c88705c4bc1f6231999b436cbd9dd0c734fb586 Mon Sep 17 00:00:00 2001
From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
Date: Thu, 22 Jul 2021 15:53:15 +0530
Subject: [PATCH 002/218] Some refactoring of interactive tool handling in k8s

---
 lib/galaxy/jobs/runners/kubernetes.py | 93 ++++++++++++++++-----------
 1 file changed, 57 insertions(+), 36 deletions(-)

diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py
index 9e0c089a2ba..ca8561354b9 100644
--- a/lib/galaxy/jobs/runners/kubernetes.py
+++ b/lib/galaxy/jobs/runners/kubernetes.py
@@ -150,36 +150,24 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             log.exception(f"({job_wrapper.get_id_tag()}) failure writing job script")
             return
 
-        # Construction of the Kubernetes Job object follows: http://kubernetes.io/docs/user-guide/persistent-volumes/
+        # Construction of Kubernetes objects follow: https://kubernetes.io/docs/concepts/workloads/controllers/job/
+        if self.__is_interactive_tool(ajs):
+            try:
+                self.__configure_interactive_tool_services(ajs)
+            except HTTPError:
+                log.exception("Kubernetes failed to create interactive tool services, HTTP exception encountered")
+                ajs.runner_state = JobState.runner_states.UNKNOWN_ERROR
+                ajs.fail_message = "Kubernetes failed to create interactive tool services."
+                self.mark_as_failed(ajs)
+                return
+
         k8s_job_prefix = self.__produce_k8s_job_prefix()
-        guest_ports = ajs.job_wrapper.guest_ports
-        ports_dict = {}
-        for guest_port in guest_ports:
-            ports_dict[str(guest_port)] = dict(host='manual', port=guest_port, protocol="https")
-        eps = None
-        if ajs.job_wrapper.guest_ports:
-            k8s_job_name = self.__get_k8s_job_name(k8s_job_prefix, ajs.job_wrapper)
-            log.debug(f'Configuring entry points and deploying service/ingress for job with ID {ajs.job_id}')
-            k8s_service_obj = service_object_dict(
-                self.runner_params,
-                k8s_job_name,
-                self.__get_k8s_service_spec(ajs)
-            )
-            eps = self.app.interactivetool_manager.configure_entry_points(ajs.job_wrapper.get_job(), ports_dict)
-            k8s_ingress_obj = ingress_object_dict(
-                self.runner_params,
-                k8s_job_name,
-                self.__get_k8s_ingress_spec(ajs, eps)
-            )
-            service = Service(self._pykube_api, k8s_service_obj)
-            service.create()
-            ingress = Ingress(self._pykube_api, k8s_ingress_obj)
-            ingress.create()
         k8s_job_obj = job_object_dict(
             self.runner_params,
             k8s_job_prefix,
-            self.__get_k8s_job_spec(ajs, eps)
+            self.__get_k8s_job_spec(ajs)
         )
+
         job = Job(self._pykube_api, k8s_job_obj)
         try:
             job.create()
@@ -203,6 +191,37 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         job_wrapper.set_external_id(job_id)
         self.monitor_queue.put(ajs)
 
+    def __is_interactive_tool(self, ajs):
+        return bool(ajs.job_wrapper.guest_ports)
+
+    def __configure_interactive_tool_services(self, ajs):
+        # Configure interactive tool entry points first
+        guest_ports = ajs.job_wrapper.guest_ports
+        ports_dict = {}
+        for guest_port in guest_ports:
+            ports_dict[str(guest_port)] = dict(host='manual', port=guest_port, protocol="https")
+        self.app.interactivetool_manager.configure_entry_points(ajs.job_wrapper.get_job(), ports_dict)
+
+        # Configure additional k8s service and ingress for interactive tool
+        k8s_job_prefix = self.__produce_k8s_job_prefix()
+        k8s_job_name = self.__get_k8s_job_name(k8s_job_prefix, ajs.job_wrapper)
+        log.debug(f'Configuring entry points and deploying service/ingress for job with ID {ajs.job_id}')
+        k8s_service_obj = service_object_dict(
+            self.runner_params,
+            k8s_job_name,
+            self.__get_k8s_service_spec(ajs)
+        )
+
+        k8s_ingress_obj = ingress_object_dict(
+            self.runner_params,
+            k8s_job_name,
+            self.__get_k8s_ingress_spec(ajs)
+        )
+        service = Service(self._pykube_api, k8s_service_obj)
+        service.create()
+        ingress = Ingress(self._pykube_api, k8s_ingress_obj)
+        ingress.create()
+
     def __get_overridable_params(self, job_wrapper, param_key):
         dest_params = self.__get_destination_params(job_wrapper)
         return dest_params.get(param_key, self.runner_params[param_key])
@@ -265,10 +284,10 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         instance_id = self._galaxy_instance_id or ''
         return produce_k8s_job_prefix(app_prefix='gxy', instance_id=instance_id)
 
-    def __get_k8s_job_spec(self, ajs, eps=None):
+    def __get_k8s_job_spec(self, ajs):
         """Creates the k8s Job spec. For a Job spec, the only requirement is to have a .spec.template.
         If the job hangs around unlimited it will be ended after k8s wall time limit, which sets activeDeadlineSeconds"""
-        k8s_job_spec = {"template": self.__get_k8s_job_spec_template(ajs, eps),
+        k8s_job_spec = {"template": self.__get_k8s_job_spec_template(ajs),
                         "activeDeadlineSeconds": int(self.runner_params['k8s_walltime_limit'])}
         job_ttl = self.runner_params["k8s_job_ttl_secs_after_finished"]
         if self.runner_params["k8s_cleanup_job"] != "never" and job_ttl is not None:
@@ -289,7 +308,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             label_val += 'x'
         return label_val
 
-    def __get_k8s_job_spec_template(self, ajs, eps=None):
+    def __get_k8s_job_spec_template(self, ajs):
         """The k8s spec template is nothing but a Pod spec, except that it is nested and does not have an apiversion
         nor kind. In addition to required fields for a Pod, a pod template in a job must specify appropriate labels
         (see pod selector) and an appropriate restart policy."""
@@ -314,7 +333,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             "spec": {
                 "volumes": self.runner_params['k8s_mountable_volumes'],
                 "restartPolicy": self.__get_k8s_restart_policy(ajs.job_wrapper),
-                "containers": self.__get_k8s_containers(ajs, eps),
+                "containers": self.__get_k8s_containers(ajs),
                 "priorityClassName": self.runner_params['k8s_pod_priority_class'],
                 "tolerations": yaml.safe_load(self.runner_params['k8s_tolerations'] or "[]"),
                 "affinity": yaml.safe_load(self.__get_overridable_params(ajs.job_wrapper,
@@ -363,19 +382,20 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         }
         return k8s_spec_template
 
-    def __get_k8s_ingress_spec(self, ajs, eps=None):
+    def __get_k8s_ingress_spec(self, ajs):
         """The k8s spec template is nothing but a Ingress spec, except that it is nested and does not have an apiversion
         nor kind."""
         guest_ports = ajs.job_wrapper.guest_ports
         if len(guest_ports) > 0:
             entry_points = []
-            for entry_point in eps.get('configured', []):
+            configured_eps = [ep for ep in ajs.job_wrapper.get_job().interactivetool_entry_points if ep.configured]
+            for entry_point in configured_eps:
                 # sending in self.app as `trans` since it's only used for `.security` so seems to work
                 entry_point_path = self.app.interactivetool_manager.get_entry_point_path(self.app, entry_point)
                 if '?' in entry_point_path:
                     # Removing all the parameters from the ingress path, but they will still be in the database
                     # so the link that the user clicks on will still have them
-                    log.warn("IT urls including parameters (eg: /myit?mykey=myvalue) are only experimentally supported on K8S")
+                    log.warning("IT urls including parameters (eg: /myit?mykey=myvalue) are only experimentally supported on K8S")
                     entry_point_path = entry_point_path.split('?')[0]
                 entry_point_domain = f'{self.app.config.interactivetools_proxy_host}'
                 if entry_point.requires_domain:
@@ -432,7 +452,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         """The default Kubernetes restart policy for Jobs"""
         return "Never"
 
-    def __get_k8s_containers(self, ajs, eps=None):
+    def __get_k8s_containers(self, ajs):
         """Fills in all required for setting up the docker containers to be used, including setting a pull policy if
            this has been set.
            $GALAXY_VIRTUAL_ENV is set to None to avoid the galaxy virtualenv inside the tool container.
@@ -480,14 +500,15 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             extra_envs = yaml.safe_load(self.__get_overridable_params(ajs.job_wrapper, 'k8s_extra_job_envs') or "{}")
             for key in extra_envs:
                 envs.append({'name': key, 'value': extra_envs[key]})
-            if eps:
-                for entry_point in eps.get('configured', []):
+            if self.__is_interactive_tool(ajs):
+                configured_eps = [ep for ep in ajs.job_wrapper.get_job().interactivetool_entry_points if ep.configured]
+                for entry_point in configured_eps:
                     # sending in self.app as `trans` since it's only used for `.security` so seems to work
                     entry_point_path = self.app.interactivetool_manager.get_entry_point_path(self.app, entry_point)
                     if '?' in entry_point_path:
                         # Removing all the parameters from the ingress path, but they will still be in the database
                         # so the link that the user clicks on will still have them
-                        log.warn("IT urls including parameters (eg: /myit?mykey=myvalue) are only experimentally supported on K8S")
+                        log.warning("IT urls including parameters (eg: /myit?mykey=myvalue) are only experimentally supported on K8S")
                         entry_point_path = entry_point_path.split('?')[0]
                     entry_point_domain = f'{self.app.config.interactivetools_proxy_host}'
                     if entry_point.requires_domain:

From 08dc137ccb126bddda3226f7909de882bf72a698 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 16 Jun 2021 13:11:42 -0400
Subject: [PATCH 003/218] Add workflow parameters to workflow run component

---
 .../Workflow/Run/WorkflowRunForm.vue          | 23 ++++++++++++++++++-
 client/src/mvc/tool/tool-form-composite.js    |  2 +-
 2 files changed, 23 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index c645ed2cae3..9f81a779394 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -1,11 +1,24 @@
 <template>
-    <div ref="form" />
+    <div>
+        <FormCard v-if="wpInputsAvailable" title="Workflow Parameters" icon="">
+            <template v-slot:body>
+                <Form :inputs="wpInputsArray" :options="model" />
+            </template>
+        </FormCard>
+        <div ref="form" />
+    </div>
 </template>
 
 <script>
 import ToolFormComposite from "mvc/tool/tool-form-composite";
+import Form from "components/Form/Form";
+import FormCard from "components/Form/FormCard";
 
 export default {
+    components: {
+        Form,
+        FormCard,
+    },
     props: {
         model: {
             type: Object,
@@ -21,6 +34,14 @@ export default {
             runForm: null,
         };
     },
+    computed: {
+        wpInputsAvailable() {
+            return this.wpInputsArray.length > 0;
+        },
+        wpInputsArray() {
+            return Object.keys(this.model.wpInputs).map((k) => this.model.wpInputs[k]);
+        },
+    },
     mounted() {
         this.$nextTick(() => {
             const el = this.$refs["form"];
diff --git a/client/src/mvc/tool/tool-form-composite.js b/client/src/mvc/tool/tool-form-composite.js
index a68b8dae6f2..abff56d190d 100644
--- a/client/src/mvc/tool/tool-form-composite.js
+++ b/client/src/mvc/tool/tool-form-composite.js
@@ -62,7 +62,7 @@ var View = Backbone.View.extend({
                     });
                 },
             });
-            this._append(this.$el.empty(), this.wp_form.$el);
+            //this._append(this.$el.empty(), this.wp_form.$el);
         }
     },
 

From 5ee3dd7c8ad0831e049dbf068a60cc5b851e0c47 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 16 Jun 2021 13:18:49 -0400
Subject: [PATCH 004/218] Add history options to workflow run component

---
 client/src/components/Form/FormCard.vue       |  2 +-
 .../Workflow/Run/WorkflowRunForm.vue          | 36 +++++++++++++++++--
 2 files changed, 34 insertions(+), 4 deletions(-)

diff --git a/client/src/components/Form/FormCard.vue b/client/src/components/Form/FormCard.vue
index 1562b2e8161..69399b90a83 100644
--- a/client/src/components/Form/FormCard.vue
+++ b/client/src/components/Form/FormCard.vue
@@ -29,7 +29,7 @@ export default {
         },
         icon: {
             type: String,
-            default: "fa-wrench",
+            default: "",
         },
     },
 };
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 9f81a779394..6fc700674ac 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -1,8 +1,13 @@
 <template>
     <div>
-        <FormCard v-if="wpInputsAvailable" title="Workflow Parameters" icon="">
+        <FormCard v-if="wpInputsAvailable" title="Workflow Parameters">
             <template v-slot:body>
-                <Form :inputs="wpInputsArray" :options="model" />
+                <Form :inputs="wpInputsArray" />
+            </template>
+        </FormCard>
+        <FormCard title="History Options">
+            <template v-slot:body>
+                <Form :inputs="historyInputs" />
             </template>
         </FormCard>
         <div ref="form" />
@@ -31,7 +36,32 @@ export default {
     },
     data() {
         return {
-            runForm: null,
+            historyInputs: [
+                {
+                    type: "conditional",
+                    name: "new_history",
+                    test_param: {
+                        name: "check",
+                        label: "Send results to a new history",
+                        type: "boolean",
+                        value: "false",
+                        help: "",
+                    },
+                    cases: [
+                        {
+                            value: "true",
+                            inputs: [
+                                {
+                                    name: "name",
+                                    label: "History name",
+                                    type: "text",
+                                    value: this.model.name,
+                                },
+                            ],
+                        },
+                    ],
+                },
+            ],
         };
     },
     computed: {

From 0e9ffe230bba000cf91d0fd75d6f220e6db4ca1b Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 16 Jun 2021 14:20:34 -0400
Subject: [PATCH 005/218] Add chached jobs form to run workflow component

---
 .../Workflow/Run/WorkflowRunForm.vue          | 56 +++++++++++++++++--
 client/src/mvc/tool/tool-form-composite.js    |  2 +-
 2 files changed, 52 insertions(+), 6 deletions(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 6fc700674ac..06624d69446 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -2,7 +2,7 @@
     <div>
         <FormCard v-if="wpInputsAvailable" title="Workflow Parameters">
             <template v-slot:body>
-                <Form :inputs="wpInputsArray" />
+                <Form :inputs="wpInputs" />
             </template>
         </FormCard>
         <FormCard title="History Options">
@@ -10,11 +10,22 @@
                 <Form :inputs="historyInputs" />
             </template>
         </FormCard>
+        <FormCard v-if="cacheInputsAvailable" title="Job re-use Options">
+            <template v-slot:body>
+                <Form :inputs="cacheInputs" />
+            </template>
+        </FormCard>
+        <FormCard v-if="resourceInputsAvailable" title="Workflow Resource Options">
+            <template v-slot:body>
+                <Form :inputs="resourceInputs" />
+            </template>
+        </FormCard>
         <div ref="form" />
     </div>
 </template>
 
 <script>
+import { getGalaxyInstance } from "app";
 import ToolFormComposite from "mvc/tool/tool-form-composite";
 import Form from "components/Form/Form";
 import FormCard from "components/Form/FormCard";
@@ -65,11 +76,43 @@ export default {
         };
     },
     computed: {
-        wpInputsAvailable() {
-            return this.wpInputsArray.length > 0;
+        cacheInputsAvailable() {
+            const Galaxy = getGalaxyInstance();
+            var extra_user_preferences = {};
+            if (Galaxy.user.attributes.preferences && "extra_user_preferences" in Galaxy.user.attributes.preferences) {
+                extra_user_preferences = JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences);
+            }
+            return;
+            "use_cached_job|use_cached_job_checkbox" in extra_user_preferences
+                ? extra_user_preferences["use_cached_job|use_cached_job_checkbox"] === "true"
+                : false;
         },
-        wpInputsArray() {
-            return Object.keys(this.model.wpInputs).map((k) => this.model.wpInputs[k]);
+        cacheInputs() {
+            return [
+                {
+                    type: "conditional",
+                    name: "use_cached_job",
+                    test_param: {
+                        name: "check",
+                        label: "Attempt to reuse jobs with identical parameters?",
+                        type: "boolean",
+                        value: "false",
+                        help: "This may skip executing jobs that you have already run.",
+                    },
+                },
+            ];
+        },
+        resourceInputsAvailable() {
+            return this.resourceInputs.length > 0;
+        },
+        resourceInputs() {
+            return this.toArray(this.model.workflowResourceParameters);
+        },
+        wpInputsAvailable() {
+            return this.wpInputs.length > 0;
+        },
+        wpInputs() {
+            return this.toArray(this.model.wpInputs);
         },
     },
     mounted() {
@@ -91,6 +134,9 @@ export default {
         handleInvocations(invocations) {
             this.$emit("submissionSuccess", invocations);
         },
+        toArray(obj) {
+            return obj ? Object.keys(obj).map((k) => obj[k]) : [];
+        },
     },
 };
 </script>
diff --git a/client/src/mvc/tool/tool-form-composite.js b/client/src/mvc/tool/tool-form-composite.js
index abff56d190d..57043fcfb8d 100644
--- a/client/src/mvc/tool/tool-form-composite.js
+++ b/client/src/mvc/tool/tool-form-composite.js
@@ -98,7 +98,7 @@ var View = Backbone.View.extend({
                 },
             ],
         });
-        this._append(this.$el, this.history_form.$el);
+        //this._append(this.$el, this.history_form.$el);
     },
 
     /** Render Workflow Options */

From a37fef2aa9ebfa4faf07afd19cc1af48a4ca3f9a Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 16 Jun 2021 15:52:22 -0400
Subject: [PATCH 006/218] Add initial components for data and tool steps to
 workflow run component

---
 .../Workflow/Run/WorkflowRunDefaultStep.vue   | 57 ++++++++++++++++++
 .../Workflow/Run/WorkflowRunForm.vue          | 12 ++++
 .../Workflow/Run/WorkflowRunToolStep.vue      | 60 +++++++++++++++++++
 client/src/mvc/tool/tool-form-composite.js    |  8 +--
 4 files changed, 133 insertions(+), 4 deletions(-)
 create mode 100644 client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
 create mode 100644 client/src/components/Workflow/Run/WorkflowRunToolStep.vue

diff --git a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
new file mode 100644
index 00000000000..0d878cafb7a
--- /dev/null
+++ b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
@@ -0,0 +1,57 @@
+<template>
+    <div>
+        <FormCard :title="model.fixed_title">
+            <template v-slot:body>
+                <Form :inputs="inputs" />
+            </template>
+        </FormCard>
+    </div>
+</template>
+
+<script>
+import { getGalaxyInstance } from "app";
+import Form from "components/Form/Form";
+import FormCard from "components/Form/FormCard";
+
+export default {
+    components: {
+        Form,
+        FormCard,
+    },
+    props: {
+        model: {
+            type: Object,
+            required: true,
+        },
+    },
+    data() {
+        return {};
+    },
+    computed: {
+        isSimpleInput() {
+            return (
+                this.model.step_type.startsWith("data_input") ||
+                this.model.step_type.startsWith("data_collection_input")
+            );
+        },
+        inputs() {
+            this.model.inputs.forEach((input) => {
+                input.flavor = "module";
+                input.hide_label = this.isSimpleInput;
+            });
+            if (this.model.inputs && this.model.inputs.length > 0) {
+                return this.model.inputs;
+            } else {
+                return [
+                    {
+                        type: "hidden",
+                        name: "No options available.",
+                        ignore: null,
+                    },
+                ];
+            }
+        },
+    },
+    methods: {},
+};
+</script>
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 06624d69446..bd04fc61cb5 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -21,6 +21,14 @@
             </template>
         </FormCard>
         <div ref="form" />
+        <div v-for="step in model.steps">
+            <div v-if="step.step_type.startsWith('data_input') || step.step_type.startsWith('data_collection_input')">
+                <WorkflowRunDefaultStep :model="step" />
+            </div>
+            <div v-else>
+                <WorkflowRunToolStep :model="step" />
+            </div>
+        </div>
     </div>
 </template>
 
@@ -29,11 +37,15 @@ import { getGalaxyInstance } from "app";
 import ToolFormComposite from "mvc/tool/tool-form-composite";
 import Form from "components/Form/Form";
 import FormCard from "components/Form/FormCard";
+import WorkflowRunDefaultStep from "./WorkflowRunDefaultStep";
+import WorkflowRunToolStep from "./WorkflowRunToolStep";
 
 export default {
     components: {
         Form,
         FormCard,
+        WorkflowRunDefaultStep,
+        WorkflowRunToolStep,
     },
     props: {
         model: {
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
new file mode 100644
index 00000000000..09195fa97ac
--- /dev/null
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -0,0 +1,60 @@
+<template>
+    <div>
+        <FormCard title="model.label">
+            <template v-slot:body>
+                <Form :inputs="inputs" />
+            </template>
+        </FormCard>
+    </div>
+</template>
+
+<script>
+import { getGalaxyInstance } from "app";
+import Form from "components/Form/Form";
+import FormCard from "components/Form/FormCard";
+
+export default {
+    components: {
+        Form,
+        FormCard,
+    },
+    props: {
+        model: {
+            type: Object,
+            required: true,
+        },
+    },
+    data() {
+        return {};
+    },
+    created() {
+        console.log(this.model);
+    },
+    computed: {
+        isSimpleInput() {
+            return (
+                this.model.step_type.startsWith("data_input") ||
+                this.model.step_type.startsWith("data_collection_input")
+            );
+        },
+        inputs() {
+            this.model.inputs.forEach((input) => {
+                input.flavor = "module";
+                input.hide_label = this.isSimpleInput;
+            });
+            if (this.model.inputs && this.model.inputs.length > 0) {
+                return this.model.inputs;
+            } else {
+                return [
+                    {
+                        type: "hidden",
+                        name: "No options available.",
+                        ignore: null,
+                    },
+                ];
+            }
+        },
+    },
+    methods: {},
+};
+</script>
diff --git a/client/src/mvc/tool/tool-form-composite.js b/client/src/mvc/tool/tool-form-composite.js
index 57043fcfb8d..aee5bede902 100644
--- a/client/src/mvc/tool/tool-form-composite.js
+++ b/client/src/mvc/tool/tool-form-composite.js
@@ -37,13 +37,13 @@ var View = Backbone.View.extend({
 
     render: function () {
         this.deferred.reset();
-        this._renderParameters();
+        /*this._renderParameters();
         this._renderHistory();
         this._renderUseCachedJob();
         this._renderResourceParameters();
         _.each(this.steps, (step) => {
             this._renderStep(step);
-        });
+        });*/
     },
 
     /** Render workflow parameters */
@@ -62,7 +62,7 @@ var View = Backbone.View.extend({
                     });
                 },
             });
-            //this._append(this.$el.empty(), this.wp_form.$el);
+            this._append(this.$el.empty(), this.wp_form.$el);
         }
     },
 
@@ -98,7 +98,7 @@ var View = Backbone.View.extend({
                 },
             ],
         });
-        //this._append(this.$el, this.history_form.$el);
+        this._append(this.$el, this.history_form.$el);
     },
 
     /** Render Workflow Options */

From 62a1475d6a4e0e30c874b681ab5c9543617612ee Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 17 Jun 2021 03:26:07 -0400
Subject: [PATCH 007/218] Add correct tool form title to workflow steps

---
 client/src/components/Tool/ToolCard.vue       |  6 +---
 .../Workflow/Run/WorkflowRunToolStep.vue      | 28 ++++---------------
 2 files changed, 7 insertions(+), 27 deletions(-)

diff --git a/client/src/components/Tool/ToolCard.vue b/client/src/components/Tool/ToolCard.vue
index 850cfd2050a..8c276fb16cd 100644
--- a/client/src/components/Tool/ToolCard.vue
+++ b/client/src/components/Tool/ToolCard.vue
@@ -143,10 +143,6 @@ export default {
             type: String,
             required: false,
         },
-        sustainVersion: {
-            type: Boolean,
-            default: false,
-        },
         options: {
             type: Object,
             required: true,
@@ -179,7 +175,7 @@ export default {
             return !!this.user.email && !this.isFavorite;
         },
         showVersions() {
-            return !this.sustainVersion && this.versions && this.versions.length > 1;
+            return this.versions && this.versions.length > 1;
         },
         availableVersions() {
             const versions = this.versions.slice();
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index 09195fa97ac..1d5d7448120 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -1,8 +1,8 @@
 <template>
     <div>
-        <FormCard title="model.label">
+        <FormCard :title="title">
             <template v-slot:body>
-                <Form :inputs="inputs" />
+                <Form :inputs="model.inputs" />
             </template>
         </FormCard>
     </div>
@@ -31,27 +31,11 @@ export default {
         console.log(this.model);
     },
     computed: {
-        isSimpleInput() {
-            return (
-                this.model.step_type.startsWith("data_input") ||
-                this.model.step_type.startsWith("data_collection_input")
-            );
-        },
-        inputs() {
-            this.model.inputs.forEach((input) => {
-                input.flavor = "module";
-                input.hide_label = this.isSimpleInput;
-            });
-            if (this.model.inputs && this.model.inputs.length > 0) {
-                return this.model.inputs;
+        title() {
+            if (this.model.fixed_title) {
+                return this.model.fixed_title;
             } else {
-                return [
-                    {
-                        type: "hidden",
-                        name: "No options available.",
-                        ignore: null,
-                    },
-                ];
+                return `${this.model.name} ${this.model.description} (Galaxy Version ${this.model.version})`;
             }
         },
     },

From 3b002cd15e9712202b066e2bfbd2137ed9210c3a Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 17 Jun 2021 03:29:04 -0400
Subject: [PATCH 008/218] Fix step type selector in workflow run component

---
 client/src/components/Workflow/Run/WorkflowRunForm.vue | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index bd04fc61cb5..964f917a238 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -22,12 +22,8 @@
         </FormCard>
         <div ref="form" />
         <div v-for="step in model.steps">
-            <div v-if="step.step_type.startsWith('data_input') || step.step_type.startsWith('data_collection_input')">
-                <WorkflowRunDefaultStep :model="step" />
-            </div>
-            <div v-else>
-                <WorkflowRunToolStep :model="step" />
-            </div>
+            <WorkflowRunToolStep v-if="step.step_type == 'tool'" :model="step" />
+            <WorkflowRunDefaultStep v-else :model="step" />
         </div>
     </div>
 </template>

From 8cc89b1159ddd72e8ad5760d818edcc05558ce73 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 17 Jun 2021 03:42:53 -0400
Subject: [PATCH 009/218] Add corresponding icons to workflow steps

---
 .../src/components/Workflow/Run/WorkflowRunDefaultStep.vue  | 6 +++++-
 client/src/components/Workflow/Run/WorkflowRunToolStep.vue  | 2 +-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
index 0d878cafb7a..224f0eaf702 100644
--- a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
@@ -1,6 +1,6 @@
 <template>
     <div>
-        <FormCard :title="model.fixed_title">
+        <FormCard :title="model.fixed_title" :icon="icon">
             <template v-slot:body>
                 <Form :inputs="inputs" />
             </template>
@@ -10,6 +10,7 @@
 
 <script>
 import { getGalaxyInstance } from "app";
+import WorkflowIcons from "components/Workflow/icons";
 import Form from "components/Form/Form";
 import FormCard from "components/Form/FormCard";
 
@@ -28,6 +29,9 @@ export default {
         return {};
     },
     computed: {
+        icon() {
+            return WorkflowIcons[this.model.step_type];
+        },
         isSimpleInput() {
             return (
                 this.model.step_type.startsWith("data_input") ||
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index 1d5d7448120..76da6aae14f 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -1,6 +1,6 @@
 <template>
     <div>
-        <FormCard :title="title">
+        <FormCard :title="title" icon="fa-wrench">
             <template v-slot:body>
                 <Form :inputs="model.inputs" />
             </template>

From 8f3d4f18f3a80324fad0127fc34b71bb4dd256d7 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 17 Jun 2021 11:09:27 -0400
Subject: [PATCH 010/218] Remove unused fixed title condition for tool steps

---
 client/src/components/Workflow/Run/WorkflowRunToolStep.vue | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index 76da6aae14f..ee2200bf77b 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -32,11 +32,7 @@ export default {
     },
     computed: {
         title() {
-            if (this.model.fixed_title) {
-                return this.model.fixed_title;
-            } else {
-                return `${this.model.name} ${this.model.description} (Galaxy Version ${this.model.version})`;
-            }
+            return `${this.model.name} ${this.model.description} (Galaxy Version ${this.model.version})`;
         },
     },
     methods: {},

From 5c67e7e6c71bdd4d1a47c6066f1c4c51a8abcfe0 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 17 Jun 2021 12:35:08 -0400
Subject: [PATCH 011/218] Allow workflow steps to be collapsed

---
 client/src/components/Form/FormCard.vue       | 38 +++++++++++++++++--
 .../Workflow/Run/WorkflowRunDefaultStep.vue   |  2 +-
 .../Workflow/Run/WorkflowRunToolStep.vue      |  2 +-
 3 files changed, 37 insertions(+), 5 deletions(-)

diff --git a/client/src/components/Form/FormCard.vue b/client/src/components/Form/FormCard.vue
index 69399b90a83..95a88fdc53a 100644
--- a/client/src/components/Form/FormCard.vue
+++ b/client/src/components/Form/FormCard.vue
@@ -3,15 +3,28 @@
         <div class="portlet-header">
             <div class="portlet-operations">
                 <slot name="operations" />
+                <b-button
+                    v-if="collapsible"
+                    role="button"
+                    title="Collapse/Expand"
+                    variant="link"
+                    size="sm"
+                    class="float-right py-0"
+                    v-b-tooltip.hover
+                    @click="onCollapse"
+                >
+                    <span v-if="collapsed" class="fa fa-eye" />
+                    <span v-else class="fa fa-eye-slash" />
+                </b-button>
             </div>
-            <div class="portlet-title">
+            <a class="portlet-title" @click="onCollapse" :href="href">
                 <i :class="['portlet-title-icon fa mr-1', icon]" style="display: inline"></i>
                 <span class="portlet-title-text">
                     <b itemprop="name">{{ title }}</b> <span itemprop="description">{{ description }}</span>
                 </span>
-            </div>
+            </a>
         </div>
-        <div class="portlet-content">
+        <div v-if="!collapsed" class="portlet-content">
             <slot name="body" />
         </div>
     </div>
@@ -31,6 +44,25 @@ export default {
             type: String,
             default: "",
         },
+        collapsible: {
+            type: Boolean,
+            default: false,
+        },
+    },
+    data() {
+        return {
+            collapsed: this.collapsible,
+        };
+    },
+    computed: {
+        href() {
+            return this.collapsible ? "#" : null;
+        },
+    },
+    methods: {
+        onCollapse() {
+            this.collapsed = this.collapsible && !this.collapsed;
+        },
     },
 };
 </script>
diff --git a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
index 224f0eaf702..9176bbf68e4 100644
--- a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
@@ -1,6 +1,6 @@
 <template>
     <div>
-        <FormCard :title="model.fixed_title" :icon="icon">
+        <FormCard :title="model.fixed_title" :icon="icon" :collapsible="true">
             <template v-slot:body>
                 <Form :inputs="inputs" />
             </template>
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index ee2200bf77b..a1a835ed8b1 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -1,6 +1,6 @@
 <template>
     <div>
-        <FormCard :title="title" icon="fa-wrench">
+        <FormCard :title="title" icon="fa-wrench" :collapsible="true">
             <template v-slot:body>
                 <Form :inputs="model.inputs" />
             </template>

From 788d9c49a4dac06dce8c4ece618c44abd69aa483 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 17 Jun 2021 14:32:44 -0400
Subject: [PATCH 012/218] Remove legacy run workflow form view from run
 component

---
 .../components/Workflow/Run/WorkflowRunForm.vue    | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 964f917a238..8582f29de7a 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -20,7 +20,6 @@
                 <Form :inputs="resourceInputs" />
             </template>
         </FormCard>
-        <div ref="form" />
         <div v-for="step in model.steps">
             <WorkflowRunToolStep v-if="step.step_type == 'tool'" :model="step" />
             <WorkflowRunDefaultStep v-else :model="step" />
@@ -30,7 +29,6 @@
 
 <script>
 import { getGalaxyInstance } from "app";
-import ToolFormComposite from "mvc/tool/tool-form-composite";
 import Form from "components/Form/Form";
 import FormCard from "components/Form/FormCard";
 import WorkflowRunDefaultStep from "./WorkflowRunDefaultStep";
@@ -123,18 +121,6 @@ export default {
             return this.toArray(this.model.wpInputs);
         },
     },
-    mounted() {
-        this.$nextTick(() => {
-            const el = this.$refs["form"];
-            const formProps = {
-                el,
-                model: this.model,
-                setRunButtonStatus: this.setRunButtonStatus,
-                handleInvocations: this.handleInvocations,
-            };
-            this.runForm = new ToolFormComposite.View(formProps);
-        });
-    },
     methods: {
         execute() {
             this.runForm.execute();

From 3cad3daf11eddbdd2fc171eb131d36da03bfb136 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 17 Jun 2021 14:34:53 -0400
Subject: [PATCH 013/218] Remove legacy tool form base and tool composite form
 views

---
 client/src/mvc/tool/tool-form-base.js      | 289 -------------
 client/src/mvc/tool/tool-form-composite.js | 475 ---------------------
 2 files changed, 764 deletions(-)
 delete mode 100644 client/src/mvc/tool/tool-form-base.js
 delete mode 100644 client/src/mvc/tool/tool-form-composite.js

diff --git a/client/src/mvc/tool/tool-form-base.js b/client/src/mvc/tool/tool-form-base.js
deleted file mode 100644
index 5648e664f78..00000000000
--- a/client/src/mvc/tool/tool-form-base.js
+++ /dev/null
@@ -1,289 +0,0 @@
-/**
-    This is the base class of the tool form plugin. This class is e.g. inherited by the regular and the workflow tool form.
-*/
-import $ from "jquery";
-import { getAppRoot } from "onload/loadConfig";
-import { getGalaxyInstance } from "app";
-import _l from "utils/localization";
-import ariaAlert from "utils/ariaAlert";
-import Deferred from "utils/deferred";
-import Ui from "mvc/ui/ui-misc";
-import FormBase from "mvc/form/form-view";
-import Webhooks from "mvc/webhooks";
-import ToolFooter from "components/Tool/ToolFooter.vue";
-import Vue from "vue";
-import axios from "axios";
-import { copy } from "utils/clipboard";
-
-export default FormBase.extend({
-    initialize: function (options) {
-        const Galaxy = getGalaxyInstance();
-        var self = this;
-        this.deferred = new Deferred();
-        FormBase.prototype.initialize.call(this, options);
-
-        // optional model update
-        this._update();
-
-        // listen to history panel
-        if (this.model.get("listen_to_history") && Galaxy.currHistoryPanel) {
-            this.listenTo(Galaxy.currHistoryPanel.collection, "change", () => {
-                self.model.get("onchange")();
-            });
-        }
-        // destroy dom elements
-        this.$el.on("remove", () => {
-            self._destroy();
-        });
-    },
-
-    /** Allows tool form variation to update tool model */
-    _update: function () {
-        var self = this;
-        var callback = this.model.get("buildmodel");
-        if (callback) {
-            this.deferred.reset();
-            this.deferred.execute((process) => {
-                callback(process, self);
-                process.then(() => {
-                    self._render();
-                });
-            });
-        } else {
-            this._render();
-        }
-    },
-
-    /** Wait for deferred build processes before removal */
-    _destroy: function () {
-        var self = this;
-        this.$el.off().hide();
-        this.deferred.execute(() => {
-            FormBase.prototype.remove.call(self);
-            const Galaxy = getGalaxyInstance();
-            Galaxy.emit.debug("tool-form-base::_destroy()", "Destroy view.");
-        });
-    },
-
-    /** Build form */
-    _render: function () {
-        var self = this;
-        var options = this.model.attributes;
-        if (options.setupToolMicrodata) {
-            this.$el.attr("itemscope", "itemscope");
-            this.$el.attr("itemtype", "https://schema.org/CreativeWork");
-        }
-        this.model.set({
-            title:
-                options.fixed_title ||
-                `<b itemprop="name">${options.name}</b> <span itemprop="description">${options.description}</span> (Galaxy Version ${options.version})`,
-            operations: !options.hide_operations && this._operations(),
-            onchange: function () {
-                self.deferred.reset();
-                self.deferred.execute((process) => {
-                    self.model.get("postchange")(process, self);
-                });
-            },
-        });
-        this.render();
-        if (!this.model.get("collapsible")) {
-            this.$el.append($("<div/>").addClass("mt-2").append(this._footer()));
-        }
-        options.tool_errors &&
-            this.message.update({
-                status: "danger",
-                message: options.tool_errors,
-                persistent: true,
-            });
-        this.show_message &&
-            this.message.update({
-                status: "success",
-                message: `Now you are using '${options.name}' version ${options.version}, id '${options.id}'.`,
-                persistent: false,
-            });
-        this.show_message = true;
-    },
-
-    /** Create tool operation menu */
-    _operations: function () {
-        var self = this;
-        var options = this.model.attributes;
-        const Galaxy = getGalaxyInstance();
-
-        // Buttons for adding and removing favorite.
-        const in_favorites = Galaxy.user.getFavorites().tools.indexOf(options.id) >= 0;
-        var favorite_button = new Ui.Button({
-            icon: "fa-star-o",
-            title: options.narrow ? null : "Favorite",
-            tooltip: "Add to favorites",
-            visible: !Galaxy.user.isAnonymous() && !in_favorites,
-            onclick: () => {
-                axios
-                    .put(`${Galaxy.root}api/users/${Galaxy.user.id}/favorites/tools`, { object_id: options.id })
-                    .then((response) => {
-                        favorite_button.hide();
-                        remove_favorite_button.show();
-                        Galaxy.user.updateFavorites("tools", response.data);
-                        ariaAlert("added to favorites");
-                    });
-            },
-        });
-
-        var remove_favorite_button = new Ui.Button({
-            icon: "fa-star",
-            title: options.narrow ? null : "Added",
-            tooltip: "Remove from favorites",
-            visible: !Galaxy.user.isAnonymous() && in_favorites,
-            onclick: () => {
-                axios
-                    .delete(
-                        `${Galaxy.root}api/users/${Galaxy.user.id}/favorites/tools/${encodeURIComponent(options.id)}`
-                    )
-                    .then((response) => {
-                        remove_favorite_button.hide();
-                        favorite_button.show();
-                        Galaxy.user.updateFavorites("tools", response.data);
-                        ariaAlert("removed from favorites");
-                    });
-            },
-        });
-
-        // button for version selection
-        var versions_button = new Ui.ButtonMenu({
-            icon: "fa-cubes",
-            cls: "btn btn-secondary float-right tool-versions",
-            title: options.narrow ? null : "Versions",
-            tooltip: "Select another tool version",
-        });
-
-        if (!options.sustain_version && options.versions && options.versions.length > 1) {
-            for (var i in options.versions.reverse()) {
-                var version = options.versions[i];
-                if (version != options.version) {
-                    versions_button.addMenu({
-                        title: `Switch to ${version}`,
-                        version: version,
-                        icon: "fa-cube",
-                        onclick: function () {
-                            // here we update the tool version (some tools encode the version also in the id)
-                            self.model.set("id", options.id.replace(options.version, this.version));
-                            self.model.set("version", this.version);
-                            self.model.get("onchange")();
-                            self._update();
-                        },
-                    });
-                }
-            }
-        } else {
-            versions_button.$el.hide();
-        }
-
-        // button for options e.g. search, help
-        var menu_button = new Ui.ButtonMenu({
-            id: "options",
-            icon: "fa-caret-down",
-            title: options.narrow ? null : "Options",
-            tooltip: "View available options",
-        });
-        menu_button.addMenu({
-            icon: "fa-chain",
-            title: _l("Copy link"),
-            onclick: function () {
-                copy(
-                    `${window.location.origin + getAppRoot()}root?tool_id=${options.id}`,
-                    "Link was copied to your clipboard"
-                );
-            },
-        });
-        menu_button.addMenu({
-            icon: "fa-files-o",
-            title: _l("Copy Tool ID"),
-            onclick: function () {
-                copy(`${options.id}`, "Tool ID was copied to your clipboard");
-            },
-        });
-
-        // add admin operations
-        if (Galaxy.user && Galaxy.user.get("is_admin")) {
-            menu_button.addMenu({
-                icon: "fa-download",
-                title: _l("Download"),
-                onclick: function () {
-                    window.location.href = `${getAppRoot()}api/tools/${options.id}/download`;
-                },
-            });
-        }
-
-        // add toolshed url
-        if (options.sharable_url) {
-            menu_button.addMenu({
-                icon: "fa-external-link",
-                title: _l("See in Tool Shed"),
-                onclick: function () {
-                    window.open(options.sharable_url);
-                },
-            });
-        }
-
-        // add tool menu webhooks
-        Webhooks.load({
-            type: "tool-menu",
-            callback: function (webhooks) {
-                webhooks.each((model) => {
-                    var webhook = model.toJSON();
-                    if (webhook.activate && webhook.config.function) {
-                        menu_button.addMenu({
-                            icon: webhook.config.icon,
-                            title: webhook.config.title,
-                            onclick: function () {
-                                var func = new Function("options", webhook.config.function);
-                                func(options);
-                            },
-                        });
-                    }
-                });
-            },
-        });
-
-        return {
-            menu: menu_button,
-            versions: versions_button,
-            favorite: favorite_button,
-            remove_favorite: remove_favorite_button,
-        };
-    },
-
-    /** Create footer */
-    _footer: function () {
-        const options = this.model.attributes;
-        const $el = $("<div/>").append(this._templateHelp(options));
-        const toolFooterInstance = Vue.extend(ToolFooter);
-        const vm = document.createElement("div");
-        $el.append(vm);
-        const propsData = {
-            id: options.id,
-            hasCitations: options.citations,
-            xrefs: options.xrefs,
-            license: options.license,
-            creators: options.creator,
-            requirements: options.requirements,
-        };
-        new toolFooterInstance({
-            propsData,
-        }).$mount(vm);
-        return $el;
-    },
-
-    /** Templates */
-    _templateHelp: function (options) {
-        var $tmpl = $("<div/>").addClass("form-help form-text mt-4").append(options.help);
-        $tmpl.find("a").attr("target", "_blank");
-        $tmpl.find("img").each(function () {
-            var img_src = $(this).attr("src");
-            if (img_src.indexOf("admin_toolshed") !== -1) {
-                $(this).attr("src", getAppRoot() + img_src);
-            }
-        });
-        return $tmpl;
-    },
-});
diff --git a/client/src/mvc/tool/tool-form-composite.js b/client/src/mvc/tool/tool-form-composite.js
deleted file mode 100644
index aee5bede902..00000000000
--- a/client/src/mvc/tool/tool-form-composite.js
+++ /dev/null
@@ -1,475 +0,0 @@
-/** This is the run workflow tool form view. */
-import _ from "underscore";
-import $ from "jquery";
-import Backbone from "backbone";
-import { getAppRoot } from "onload/loadConfig";
-import { getGalaxyInstance } from "app";
-import _l from "utils/localization";
-import Utils from "utils/utils";
-import Deferred from "utils/deferred";
-import Form from "mvc/form/form-view";
-import { isDataStep, invokeWorkflow } from "components/Workflow/Run";
-
-import ToolFormBase from "mvc/tool/tool-form-base";
-import Modal from "mvc/ui/ui-modal";
-
-var View = Backbone.View.extend({
-    initialize: function (options) {
-        const Galaxy = getGalaxyInstance();
-        this.modal = Galaxy.modal || new Modal.View();
-        this.runWorkflowModel = options.model;
-        this.deferred = new Deferred();
-        this.setRunButtonStatus = options.setRunButtonStatus;
-        this.handleInvocations = options.handleInvocations;
-        this.setElement(options.el);
-        this._configure();
-        this.render();
-    },
-
-    /** Configures form/step options for each workflow step */
-    _configure: function () {
-        this.forms = [];
-        this.steps = this.runWorkflowModel.steps;
-        this.links = this.runWorkflowModel.links;
-        this.parms = this.runWorkflowModel.parms;
-        this.wp_inputs = this.runWorkflowModel.wpInputs;
-    },
-
-    render: function () {
-        this.deferred.reset();
-        /*this._renderParameters();
-        this._renderHistory();
-        this._renderUseCachedJob();
-        this._renderResourceParameters();
-        _.each(this.steps, (step) => {
-            this._renderStep(step);
-        });*/
-    },
-
-    /** Render workflow parameters */
-    _renderParameters: function () {
-        this.wp_form = null;
-        if (!_.isEmpty(this.wp_inputs)) {
-            this.wp_form = new Form({
-                title: "<b>Workflow Parameters</b>",
-                inputs: this.wp_inputs,
-                cls: "ui-portlet-section",
-                onchange: () => {
-                    _.each(this.wp_form.input_list, (input_def, i) => {
-                        _.each(input_def.links, (step) => {
-                            this._refreshStep(step);
-                        });
-                    });
-                },
-            });
-            this._append(this.$el.empty(), this.wp_form.$el);
-        }
-    },
-
-    /** Render workflow parameters */
-    _renderHistory: function () {
-        this.history_form = new Form({
-            cls: "ui-portlet-section",
-            title: "<b>History Options</b>",
-            inputs: [
-                {
-                    type: "conditional",
-                    name: "new_history",
-                    test_param: {
-                        name: "check",
-                        label: "Send results to a new history",
-                        type: "boolean",
-                        value: "false",
-                        help: "",
-                    },
-                    cases: [
-                        {
-                            value: "true",
-                            inputs: [
-                                {
-                                    name: "name",
-                                    label: "History name",
-                                    type: "text",
-                                    value: this.runWorkflowModel.name,
-                                },
-                            ],
-                        },
-                    ],
-                },
-            ],
-        });
-        this._append(this.$el, this.history_form.$el);
-    },
-
-    /** Render Workflow Options */
-    _renderResourceParameters: function () {
-        this.workflow_resource_parameters_form = null;
-        if (!_.isEmpty(this.runWorkflowModel.workflowResourceParameters)) {
-            this.workflow_resource_parameters_form = new Form({
-                cls: "ui-portlet-section",
-                title: "<b>Workflow Resource Options</b>",
-                inputs: this.runWorkflowModel.workflowResourceParameters,
-            });
-            this._append(this.$el, this.workflow_resource_parameters_form.$el);
-        }
-    },
-
-    /** Render job caching option */
-    _renderUseCachedJob: function () {
-        const Galaxy = getGalaxyInstance();
-        var extra_user_preferences = {};
-        if (Galaxy.user.attributes.preferences && "extra_user_preferences" in Galaxy.user.attributes.preferences) {
-            extra_user_preferences = JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences);
-        }
-        var display_use_cached_job_checkbox =
-            "use_cached_job|use_cached_job_checkbox" in extra_user_preferences
-                ? extra_user_preferences["use_cached_job|use_cached_job_checkbox"]
-                : false;
-        this.display_use_cached_job_checkbox = display_use_cached_job_checkbox === "true";
-        if (this.display_use_cached_job_checkbox) {
-            this.job_options_form = new Form({
-                cls: "ui-portlet-section",
-                title: "<b>Job re-use Options</b>",
-                inputs: [
-                    {
-                        type: "conditional",
-                        name: "use_cached_job",
-                        test_param: {
-                            name: "check",
-                            label: "BETA: Attempt to reuse jobs with identical parameters?",
-                            type: "boolean",
-                            value: "false",
-                            help: "This may skip executing jobs that you have already run.",
-                        },
-                    },
-                ],
-            });
-            this._append(this.$el, this.job_options_form.$el);
-        }
-    },
-
-    /** Render step */
-    _renderStep: function (step) {
-        const Galaxy = getGalaxyInstance();
-        var form = null;
-        this.deferred.execute((promise) => {
-            this.$el.addClass("ui-steps");
-            if (step.step_type == "tool") {
-                step.postchange = function (process, form) {
-                    var current_state = {
-                        tool_id: step.id,
-                        tool_version: step.version,
-                        inputs: $.extend(true, {}, form.data.create()),
-                    };
-                    form.wait(true);
-                    Galaxy.emit.debug("tool-form-composite::postchange()", "Sending current state.", current_state);
-                    Utils.request({
-                        type: "POST",
-                        url: `${getAppRoot()}api/tools/${step.id}/build`,
-                        data: current_state,
-                        success: function (data) {
-                            form.update(data);
-                            form.wait(false);
-                            Galaxy.emit.debug("tool-form-composite::postchange()", "Received new model.", data);
-                            process.resolve();
-                        },
-                        error: function (response) {
-                            Galaxy.emit.debug("tool-form-composite::postchange()", "Refresh request failed.", response);
-                            process.reject();
-                        },
-                    });
-                };
-                form = new ToolFormBase(step);
-                if (step.post_job_actions && step.post_job_actions.length) {
-                    form.portlet.append(
-                        $("<div/>")
-                            .addClass("ui-form-element-disabled")
-                            .append($("<div/>").addClass("ui-form-title").html("<b>Job Post Actions</b>"))
-                            .append(
-                                $("<div/>")
-                                    .addClass("ui-form-preview")
-                                    .html(
-                                        _.reduce(
-                                            step.post_job_actions,
-                                            (memo, value) => `${memo} ${value.short_str}`,
-                                            ""
-                                        )
-                                    )
-                            )
-                    );
-                }
-            } else {
-                var is_simple_input = ["data_input", "data_collection_input"].indexOf(step.step_type) != -1;
-                _.each(step.inputs, (input) => {
-                    input.flavor = "module";
-                    input.hide_label = is_simple_input;
-                });
-                form = new Form(
-                    Utils.merge(
-                        {
-                            title: step.fixed_title,
-                            onchange: () => {
-                                _.each(this.links[step.index], (link) => {
-                                    this._refreshStep(link);
-                                });
-                            },
-                            inputs:
-                                step.inputs && step.inputs.length > 0
-                                    ? step.inputs
-                                    : [
-                                          {
-                                              type: "hidden",
-                                              name: "No options available.",
-                                              ignore: null,
-                                          },
-                                      ],
-                        },
-                        step
-                    )
-                );
-                if (step.step_label) {
-                    form.$el.attr("step-label", step.step_label);
-                }
-            }
-            this.forms[step.index] = form;
-            this._append(this.$el, form.$el);
-            if (step.needs_refresh) {
-                this._refreshStep(step);
-            }
-            form.portlet[!this.show_progress ? "enable" : "disable"]();
-            if (this.show_progress) {
-                const percentage = ((step.index + 1) * 100.0) / this.steps.length;
-                this.setRunButtonStatus(false, "Preparing...", percentage);
-            }
-            Galaxy.emit.debug("tool-form-composite::initialize()", `${step.index} : Workflow step state ready.`, step);
-            window.setTimeout(() => {
-                promise.resolve();
-            }, 0);
-        });
-    },
-
-    /** Refreshes step values from source step values */
-    _refreshStep: function (step) {
-        var form = this.forms[step.index];
-        if (form) {
-            _.each(this.parms[step.index], (input, name) => {
-                if (input.step_linked || input.wp_linked) {
-                    var field = form.field_list[form.data.match(name)];
-                    if (field) {
-                        var new_value;
-                        if (input.step_linked) {
-                            new_value = { values: [] };
-                            _.each(input.step_linked, (source_step) => {
-                                if (isDataStep(source_step)) {
-                                    var value = this.forms[source_step.index].data.create().input;
-                                    if (value) {
-                                        _.each(value.values, (v) => {
-                                            new_value.values.push(v);
-                                        });
-                                    }
-                                }
-                            });
-                            if (!input.multiple && new_value.values.length > 0) {
-                                new_value = {
-                                    values: [new_value.values[0]],
-                                };
-                            }
-                        } else if (input.wp_linked) {
-                            new_value = input.value;
-                            var re = /\$\{(.+?)\}/g;
-                            var match;
-                            while ((match = re.exec(input.value))) {
-                                var wp_field = this.wp_form.field_list[this.wp_form.data.match(match[1])];
-                                var wp_value = wp_field && wp_field.value();
-                                if (wp_value) {
-                                    new_value = new_value.split(match[0]).join(wp_value);
-                                }
-                            }
-                        }
-                        if (new_value !== undefined) {
-                            field.value(new_value);
-                        }
-                    }
-                }
-            });
-            form.trigger("change");
-        } else {
-            step.needs_refresh = true;
-        }
-    },
-
-    /** Build remaining steps */
-    execute: function () {
-        this.show_progress = true;
-        this._enabled(false);
-        this.deferred.execute((promise) => {
-            window.setTimeout(() => {
-                promise.resolve();
-                this._submit();
-            }, 0);
-        });
-    },
-
-    /** Validate and submit workflow */
-    _submit: function () {
-        const Galaxy = getGalaxyInstance();
-        var history_form_data = this.history_form.data.create();
-        var job_def = {
-            new_history_name: history_form_data["new_history|name"] ? history_form_data["new_history|name"] : null,
-            history_id: !history_form_data["new_history|name"] ? this.runWorkflowModel.historyId : null,
-            resource_params: this.workflow_resource_parameters_form
-                ? this.workflow_resource_parameters_form.data.create()
-                : {},
-            replacement_params: this.wp_form ? this.wp_form.data.create() : {},
-            parameters: {},
-            // Tool form will submit flat maps for each parameter
-            // (e.g. "repeat_0|cond|param": "foo" instead of nested
-            // data structures).
-            parameters_normalized: true,
-            // Tool form always wants a list of invocations back
-            // so that inputs can be batched.
-            batch: true,
-        };
-        if (this.display_use_cached_job_checkbox) {
-            job_def.use_cached_job = this.job_options_form.data.create()["use_cached_job|check"] === "true";
-        }
-        var validated = true;
-        for (var i in this.forms) {
-            var form = this.forms[i];
-            var job_inputs = form.data.create();
-            var step = this.steps[i];
-            var step_index = step.step_index;
-            form.trigger("reset");
-            for (var job_input_id in job_inputs) {
-                var input_value = job_inputs[job_input_id];
-                var input_id = form.data.match(job_input_id);
-                var input_def = form.input_list[input_id];
-                if (!input_def.step_linked) {
-                    if (isDataStep(step)) {
-                        validated = input_value && input_value.values && input_value.values.length > 0;
-                        if (!validated && input_def.optional) {
-                            validated = true;
-                        }
-                    } else {
-                        validated =
-                            input_def.optional ||
-                            (input_def.is_workflow && input_value !== "") ||
-                            (!input_def.is_workflow && input_value !== null);
-                    }
-                    if (!validated) {
-                        if (input_def.type == "hidden") {
-                            this.modal.show({
-                                title: _l("Workflow submission failed"),
-                                body: `Step ${step_index}: ${
-                                    step.step_label || step.step_name
-                                } is in an invalid state. Please remove and re-add this step in the Workflow Editor.`,
-                                buttons: {
-                                    Close: () => {
-                                        this.modal.hide();
-                                    },
-                                },
-                            });
-                        }
-                        form.highlight(input_id);
-                        break;
-                    }
-                    job_def.parameters[step_index] = job_def.parameters[step_index] || {};
-                    job_def.parameters[step_index][job_input_id] = job_inputs[job_input_id];
-                }
-            }
-            if (!validated) {
-                break;
-            }
-        }
-        if (!validated) {
-            this._enabled(true);
-            Galaxy.emit.debug("tool-form-composite::submit()", "Validation failed.", job_def);
-        } else {
-            Galaxy.emit.debug("tool-form-composite::submit()", "Validation complete.", job_def);
-            invokeWorkflow(this.runWorkflowModel.workflowId, job_def)
-                .then((invocations) => {
-                    Galaxy.emit.debug("tool-form-composite::submit", "Submission successful.", invocations);
-                    if (Array.isArray(invocations) && invocations.length > 0) {
-                        this.handleInvocations(invocations);
-                    } else {
-                        this.submissionErrorModal(job_def, invocations);
-                    }
-                    this._enabled(true);
-                })
-                .catch((response) => {
-                    // TODO: Is this the same response as the Utils post would
-                    // have had?
-                    Galaxy.emit.debug("tool-form-composite::submit", "Submission failed.", response);
-                    var input_found = false;
-                    if (response && response.err_data) {
-                        for (var i in this.forms) {
-                            var form = this.forms[i];
-                            var step_related_errors = response.err_data[form.model.get("step_index")];
-                            if (step_related_errors) {
-                                var error_messages = form.data.matchResponse(step_related_errors);
-                                for (var input_id in error_messages) {
-                                    form.highlight(input_id, error_messages[input_id]);
-                                    input_found = true;
-                                    break;
-                                }
-                            }
-                        }
-                    }
-                    if (!input_found) {
-                        this.submissionErrorModal(job_def, response);
-                    }
-                    this._enabled(true);
-                });
-        }
-    },
-
-    /** Append new dom to body */
-    _append: function ($container, $el) {
-        $container.append("<p/>").append($el);
-    },
-
-    /** Set enabled/disabled state */
-    _enabled: function (enabled) {
-        this.setRunButtonStatus(enabled, "Sending...", -1);
-        if (this.wp_form) {
-            this.wp_form.portlet[enabled ? "enable" : "disable"]();
-        }
-        if (this.history_form) {
-            this.history_form.portlet[enabled ? "enable" : "disable"]();
-        }
-        _.each(this.forms, (form) => {
-            if (form) {
-                form.portlet[enabled ? "enable" : "disable"]();
-            }
-        });
-    },
-
-    submissionErrorModal: function (job_def, response) {
-        this.modal.show({
-            title: _l("Workflow submission failed"),
-            body: this._templateError(job_def, response && response.err_msg),
-            buttons: {
-                Close: () => {
-                    this.modal.hide();
-                },
-            },
-        });
-    },
-
-    /** Templates */
-    _templateError: function (response, err_msg) {
-        return $("<div/>")
-            .addClass("errormessagelarge")
-            .append(
-                $("<p/>").text(
-                    `The server could not complete the request. Please contact the Galaxy Team if this error persists. ${
-                        JSON.stringify(err_msg) || ""
-                    }`
-                )
-            )
-            .append($("<pre/>").text(JSON.stringify(response, null, 4)));
-    },
-});
-export default {
-    View: View,
-};

From d1c4a69fe87f4ac56682d544724d5904a5859e41 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 21 Jun 2021 15:55:12 -0400
Subject: [PATCH 014/218] Update workflow parameters in form

---
 client/src/components/Form/FormDisplay.vue    | 35 +++++++++++++++++++
 .../Workflow/Run/WorkflowRunForm.vue          |  8 +++--
 .../Workflow/Run/WorkflowRunToolStep.vue      | 13 ++++---
 3 files changed, 47 insertions(+), 9 deletions(-)

diff --git a/client/src/components/Form/FormDisplay.vue b/client/src/components/Form/FormDisplay.vue
index 09d42bd6f16..af63a90c0df 100644
--- a/client/src/components/Form/FormDisplay.vue
+++ b/client/src/components/Form/FormDisplay.vue
@@ -4,6 +4,7 @@
 
 <script>
 import Form from "mvc/form/form-view";
+import FormData from "mvc/form/form-data";
 
 export default {
     props: {
@@ -39,6 +40,10 @@ export default {
             type: Object,
             default: null,
         },
+        placeholderParams: {
+            type: Object,
+            default: null,
+        },
     },
     data() {
         return {
@@ -70,6 +75,9 @@ export default {
                 }
             });
         },
+        placeholderParams() {
+            this.onPlaceholderParams();
+        },
     },
     mounted() {
         this.onRender();
@@ -125,6 +133,32 @@ export default {
         },
     },
     methods: {
+        onPlaceholderParams() {
+            this.params = {};
+            FormData.visitInputs(this.inputs, (input, name) => {
+                this.params[name] = input;
+            });
+            _.each(this.params, (input, name) => {
+                if (input.wp_linked) {
+                    var field = this.form.field_list[this.form.data.match(name)];
+                    if (field) {
+                        var new_value;
+                        new_value = input.value;
+                        var re = /\$\{(.+?)\}/g;
+                        var match;
+                        while ((match = re.exec(input.value))) {
+                            var wp_value = this.placeholderParams[match[1]];
+                            if (wp_value) {
+                                new_value = new_value.split(match[0]).join(wp_value);
+                            }
+                        }
+                    }
+                    if (new_value !== undefined) {
+                        field.value(new_value);
+                    }
+                }
+            });
+        },
         onChange() {
             this.formData = this.form.data.create();
             this.$emit("onChange", this.formData);
@@ -142,6 +176,7 @@ export default {
                         this.onChange();
                     },
                 });
+                this.onPlaceholderParams();
                 this.onChange();
             });
         },
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 8582f29de7a..133fcbf25cc 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -2,7 +2,7 @@
     <div>
         <FormCard v-if="wpInputsAvailable" title="Workflow Parameters">
             <template v-slot:body>
-                <Form :inputs="wpInputs" />
+                <Form :inputs="wpInputs" @onChange="onWpInputs" />
             </template>
         </FormCard>
         <FormCard title="History Options">
@@ -21,7 +21,7 @@
             </template>
         </FormCard>
         <div v-for="step in model.steps">
-            <WorkflowRunToolStep v-if="step.step_type == 'tool'" :model="step" />
+            <WorkflowRunToolStep v-if="step.step_type == 'tool'" :model="step" :placeholderParams="wpData" />
             <WorkflowRunDefaultStep v-else :model="step" />
         </div>
     </div>
@@ -53,6 +53,7 @@ export default {
     },
     data() {
         return {
+            wpData: {},
             historyInputs: [
                 {
                     type: "conditional",
@@ -122,6 +123,9 @@ export default {
         },
     },
     methods: {
+        onWpInputs(data) {
+            this.wpData = data;
+        },
         execute() {
             this.runForm.execute();
         },
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index a1a835ed8b1..6efab0c1f58 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -1,15 +1,14 @@
 <template>
     <div>
-        <FormCard :title="title" icon="fa-wrench" :collapsible="true">
+        <FormCard :title="title" icon="fa-wrench" :collapsible="false">
             <template v-slot:body>
-                <Form :inputs="model.inputs" />
+                <Form :inputs="model.inputs" :placeholderParams="placeholderParams" />
             </template>
         </FormCard>
     </div>
 </template>
 
 <script>
-import { getGalaxyInstance } from "app";
 import Form from "components/Form/Form";
 import FormCard from "components/Form/FormCard";
 
@@ -23,18 +22,18 @@ export default {
             type: Object,
             required: true,
         },
+        placeholderParams: {
+            type: Object,
+            default: null,
+        },
     },
     data() {
         return {};
     },
-    created() {
-        console.log(this.model);
-    },
     computed: {
         title() {
             return `${this.model.name} ${this.model.description} (Galaxy Version ${this.model.version})`;
         },
     },
-    methods: {},
 };
 </script>

From adc3e6e821666c9a6df2f63e4b57f917ab34a57f Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 21 Jun 2021 15:57:38 -0400
Subject: [PATCH 015/218] Trigger change when workflow parameters change

---
 client/src/components/Form/FormDisplay.vue | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/src/components/Form/FormDisplay.vue b/client/src/components/Form/FormDisplay.vue
index af63a90c0df..f3e6ef26015 100644
--- a/client/src/components/Form/FormDisplay.vue
+++ b/client/src/components/Form/FormDisplay.vue
@@ -77,6 +77,7 @@ export default {
         },
         placeholderParams() {
             this.onPlaceholderParams();
+            this.onChange();
         },
     },
     mounted() {

From 454037ba5fc9221f1bfd0ff7d5dc76accf5b0107 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 21 Jun 2021 16:39:30 -0400
Subject: [PATCH 016/218] Preliminary update mechanism for tool steps

---
 client/src/components/Form/FormCard.vue       |  2 +-
 client/src/components/Form/FormDisplay.vue    | 58 ++++++++++++++-----
 .../Workflow/Run/WorkflowRunDefaultStep.vue   |  8 ++-
 .../Workflow/Run/WorkflowRunForm.vue          | 15 ++++-
 .../Workflow/Run/WorkflowRunToolStep.vue      | 13 ++++-
 5 files changed, 76 insertions(+), 20 deletions(-)

diff --git a/client/src/components/Form/FormCard.vue b/client/src/components/Form/FormCard.vue
index 95a88fdc53a..3cd4a54a44b 100644
--- a/client/src/components/Form/FormCard.vue
+++ b/client/src/components/Form/FormCard.vue
@@ -24,7 +24,7 @@
                 </span>
             </a>
         </div>
-        <div v-if="!collapsed" class="portlet-content">
+        <div v-show="!collapsed" class="portlet-content">
             <slot name="body" />
         </div>
     </div>
diff --git a/client/src/components/Form/FormDisplay.vue b/client/src/components/Form/FormDisplay.vue
index f3e6ef26015..aa54f1d9d4e 100644
--- a/client/src/components/Form/FormDisplay.vue
+++ b/client/src/components/Form/FormDisplay.vue
@@ -5,6 +5,7 @@
 <script>
 import Form from "mvc/form/form-view";
 import FormData from "mvc/form/form-data";
+import { isDataStep } from "components/Workflow/Run/model";
 
 export default {
     props: {
@@ -40,7 +41,11 @@ export default {
             type: Object,
             default: null,
         },
-        placeholderParams: {
+        replaceParams: {
+            type: Object,
+            default: null,
+        },
+        replaceData: {
             type: Object,
             default: null,
         },
@@ -75,8 +80,12 @@ export default {
                 }
             });
         },
-        placeholderParams() {
-            this.onPlaceholderParams();
+        replaceParams() {
+            this.onReplaceParams();
+            this.onChange();
+        },
+        replaceData() {
+            this.onReplaceParams();
             this.onChange();
         },
     },
@@ -134,23 +143,46 @@ export default {
         },
     },
     methods: {
-        onPlaceholderParams() {
+        onReplaceParams() {
             this.params = {};
             FormData.visitInputs(this.inputs, (input, name) => {
                 this.params[name] = input;
             });
             _.each(this.params, (input, name) => {
-                if (input.wp_linked) {
+                if (input.wp_linked || input.step_linked) {
                     var field = this.form.field_list[this.form.data.match(name)];
                     if (field) {
                         var new_value;
-                        new_value = input.value;
-                        var re = /\$\{(.+?)\}/g;
-                        var match;
-                        while ((match = re.exec(input.value))) {
-                            var wp_value = this.placeholderParams[match[1]];
-                            if (wp_value) {
-                                new_value = new_value.split(match[0]).join(wp_value);
+                        if (input.step_linked) {
+                            new_value = { values: [] };
+                            _.each(input.step_linked, (source_step) => {
+                                if (isDataStep(source_step)) {
+                                    console.log(this.replaceData);
+                                    console.log(source_step.index);
+                                    var value = this.replaceData[source_step.index].input;
+                                    console.log(value);
+                                    if (value) {
+                                        _.each(value.values, (v) => {
+                                            new_value.values.push(v);
+                                        });
+                                    }
+                                }
+                            });
+                            if (!input.multiple && new_value.values.length > 0) {
+                                new_value = {
+                                    values: [new_value.values[0]],
+                                };
+                            }
+                        }
+                        if (input.wp_linked) {
+                            new_value = input.value;
+                            var re = /\$\{(.+?)\}/g;
+                            var match;
+                            while ((match = re.exec(input.value))) {
+                                var wp_value = this.replaceParams[match[1]];
+                                if (wp_value) {
+                                    new_value = new_value.split(match[0]).join(wp_value);
+                                }
                             }
                         }
                     }
@@ -177,7 +209,7 @@ export default {
                         this.onChange();
                     },
                 });
-                this.onPlaceholderParams();
+                this.onReplaceParams();
                 this.onChange();
             });
         },
diff --git a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
index 9176bbf68e4..2d18e9ba279 100644
--- a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
@@ -2,7 +2,7 @@
     <div>
         <FormCard :title="model.fixed_title" :icon="icon" :collapsible="true">
             <template v-slot:body>
-                <Form :inputs="inputs" />
+                <Form :inputs="inputs" @onChange="onChange" />
             </template>
         </FormCard>
     </div>
@@ -56,6 +56,10 @@ export default {
             }
         },
     },
-    methods: {},
+    methods: {
+        onChange(data) {
+            this.$emit("onChange", this.model.index, data);
+        },
+    },
 };
 </script>
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 133fcbf25cc..c34516453c7 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -21,13 +21,20 @@
             </template>
         </FormCard>
         <div v-for="step in model.steps">
-            <WorkflowRunToolStep v-if="step.step_type == 'tool'" :model="step" :placeholderParams="wpData" />
-            <WorkflowRunDefaultStep v-else :model="step" />
+            <WorkflowRunToolStep
+                v-if="step.step_type == 'tool'"
+                :model="step"
+                :replaceData="stepData"
+                :replaceParams="wpData"
+                @onChange="onStepInputs"
+            />
+            <WorkflowRunDefaultStep v-else :model="step" @onChange="onStepInputs" />
         </div>
     </div>
 </template>
 
 <script>
+import Vue from "vue";
 import { getGalaxyInstance } from "app";
 import Form from "components/Form/Form";
 import FormCard from "components/Form/FormCard";
@@ -53,6 +60,7 @@ export default {
     },
     data() {
         return {
+            stepData: {},
             wpData: {},
             historyInputs: [
                 {
@@ -123,6 +131,9 @@ export default {
         },
     },
     methods: {
+        onStepInputs(stepId, data) {
+            Vue.set(this.stepData, stepId, data);
+        },
         onWpInputs(data) {
             this.wpData = data;
         },
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index 6efab0c1f58..f294e5f83db 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -2,7 +2,7 @@
     <div>
         <FormCard :title="title" icon="fa-wrench" :collapsible="false">
             <template v-slot:body>
-                <Form :inputs="model.inputs" :placeholderParams="placeholderParams" />
+                <Form :inputs="model.inputs" :replaceParams="replaceParams" :replaceData="replaceData" @onChange="onChange" />
             </template>
         </FormCard>
     </div>
@@ -22,7 +22,11 @@ export default {
             type: Object,
             required: true,
         },
-        placeholderParams: {
+        replaceParams: {
+            type: Object,
+            default: null,
+        },
+        replaceData: {
             type: Object,
             default: null,
         },
@@ -35,5 +39,10 @@ export default {
             return `${this.model.name} ${this.model.description} (Galaxy Version ${this.model.version})`;
         },
     },
+    methods: {
+        onChange(data) {
+            this.$emit("onChange", this.model.index, data);
+        },
+    },
 };
 </script>

From 9ebe3925fef802b44e8dee49c5b834859f30e6c2 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 22 Jun 2021 20:33:24 -0400
Subject: [PATCH 017/218] Handle connected input change triggers to tool step
 states

---
 client/src/components/Form/FormDisplay.vue    |  3 ---
 .../Workflow/Run/WorkflowRunForm.vue          | 10 ++++++---
 .../Workflow/Run/WorkflowRunToolStep.vue      | 22 +++++++++++++++++--
 .../src/components/Workflow/Run/services.js   | 19 ++++++++++++++++
 4 files changed, 46 insertions(+), 8 deletions(-)

diff --git a/client/src/components/Form/FormDisplay.vue b/client/src/components/Form/FormDisplay.vue
index aa54f1d9d4e..bbb5b056cef 100644
--- a/client/src/components/Form/FormDisplay.vue
+++ b/client/src/components/Form/FormDisplay.vue
@@ -157,10 +157,7 @@ export default {
                             new_value = { values: [] };
                             _.each(input.step_linked, (source_step) => {
                                 if (isDataStep(source_step)) {
-                                    console.log(this.replaceData);
-                                    console.log(source_step.index);
                                     var value = this.replaceData[source_step.index].input;
-                                    console.log(value);
                                     if (value) {
                                         _.each(value.values, (v) => {
                                             new_value.values.push(v);
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index c34516453c7..e3ec4a3a42f 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -26,9 +26,9 @@
                 :model="step"
                 :replaceData="stepData"
                 :replaceParams="wpData"
-                @onChange="onStepInputs"
+                @onChange="onToolStepInputs"
             />
-            <WorkflowRunDefaultStep v-else :model="step" @onChange="onStepInputs" />
+            <WorkflowRunDefaultStep v-else :model="step" @onChange="onDefaultStepInputs" />
         </div>
     </div>
 </template>
@@ -131,8 +131,12 @@ export default {
         },
     },
     methods: {
-        onStepInputs(stepId, data) {
+        onDefaultStepInputs(stepId, data) {
             Vue.set(this.stepData, stepId, data);
+            this.stepData = Object.assign({}, this.stepData);
+        },
+        onToolStepInputs(stepId, data) {
+            this.stepData[stepId] = data;
         },
         onWpInputs(data) {
             this.wpData = data;
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index f294e5f83db..817d2a1967a 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -2,7 +2,13 @@
     <div>
         <FormCard :title="title" icon="fa-wrench" :collapsible="false">
             <template v-slot:body>
-                <Form :inputs="model.inputs" :replaceParams="replaceParams" :replaceData="replaceData" @onChange="onChange" />
+                <Form
+                    :inputs="model.inputs"
+                    :form-config="formConfig"
+                    :replaceParams="replaceParams"
+                    :replaceData="replaceData"
+                    @onChange="onChange"
+                />
             </template>
         </FormCard>
     </div>
@@ -11,6 +17,7 @@
 <script>
 import Form from "components/Form/Form";
 import FormCard from "components/Form/FormCard";
+import { getTool } from "./services";
 
 export default {
     components: {
@@ -32,7 +39,9 @@ export default {
         },
     },
     data() {
-        return {};
+        return {
+            formConfig: {},
+        };
     },
     computed: {
         title() {
@@ -41,6 +50,15 @@ export default {
     },
     methods: {
         onChange(data) {
+            getTool(this.model.id, this.model.version, data).then(
+                (formConfig) => {
+                    this.formConfig = formConfig;
+                },
+                (response) => {
+                    //Galaxy.emit.debug("tool-form-composite::postchange()", "Refresh request failed.", response);
+                    //process.reject();
+                }
+            );
             this.$emit("onChange", this.model.index, data);
         },
     },
diff --git a/client/src/components/Workflow/Run/services.js b/client/src/components/Workflow/Run/services.js
index 58122884002..a70a1c342ec 100644
--- a/client/src/components/Workflow/Run/services.js
+++ b/client/src/components/Workflow/Run/services.js
@@ -31,3 +31,22 @@ export async function invokeWorkflow(workflowId, invocationData) {
     const response = await axios.post(url, invocationData);
     return response.data;
 }
+
+/**
+ * Request tool step data.
+ *
+ * @param {String} workflowId - (Stored?) Workflow ID to fetch data for.
+ */
+export async function getTool(toolId, toolVersion, toolInputs) {
+    const requestData = {
+        tool_id: toolId,
+        tool_version: toolVersion,
+        inputs: $.extend(true, {}, toolInputs),
+    };
+    try {
+        const { data } = await axios.post(`${getAppRoot()}api/tools/${toolId}/build`, requestData);
+        return data;
+    } catch (e) {
+        rethrowSimple(e);
+    }
+}

From 24bd44a737b791b8866e9dfd5df85369dc2d7ba2 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 22 Jun 2021 20:42:11 -0400
Subject: [PATCH 018/218] Add error handling, adjust form message style

---
 client/src/components/Form/FormMessage.vue               | 2 +-
 client/src/components/Tool/ToolCard.vue                  | 4 ++--
 .../src/components/Workflow/Editor/Forms/FormDefault.vue | 2 +-
 .../src/components/Workflow/Run/WorkflowRunToolStep.vue  | 9 ++++++---
 4 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/client/src/components/Form/FormMessage.vue b/client/src/components/Form/FormMessage.vue
index 3d8b65ac7ed..2cffe77fc4f 100644
--- a/client/src/components/Form/FormMessage.vue
+++ b/client/src/components/Form/FormMessage.vue
@@ -1,5 +1,5 @@
 <template>
-    <b-alert :variant="variant" :show="showAlert">
+    <b-alert class="mt-2" :variant="variant" :show="showAlert">
         {{ message | l }}
     </b-alert>
 </template>
diff --git a/client/src/components/Tool/ToolCard.vue b/client/src/components/Tool/ToolCard.vue
index 8c276fb16cd..1f06b2b9e85 100644
--- a/client/src/components/Tool/ToolCard.vue
+++ b/client/src/components/Tool/ToolCard.vue
@@ -88,8 +88,8 @@
                 </div>
             </div>
             <div class="portlet-content">
-                <FormMessage class="mt-2" :message="errorText" variant="danger" :persistent="true" />
-                <FormMessage class="mt-2" :message="messageText" :variant="messageVariant" />
+                <FormMessage :message="errorText" variant="danger" :persistent="true" />
+                <FormMessage :message="messageText" :variant="messageVariant" />
                 <slot name="body" />
             </div>
         </div>
diff --git a/client/src/components/Workflow/Editor/Forms/FormDefault.vue b/client/src/components/Workflow/Editor/Forms/FormDefault.vue
index 226b2a11a82..f4637d50bbd 100644
--- a/client/src/components/Workflow/Editor/Forms/FormDefault.vue
+++ b/client/src/components/Workflow/Editor/Forms/FormDefault.vue
@@ -27,7 +27,7 @@
             </b-button>
         </template>
         <template v-slot:body>
-            <FormMessage class="mt-2" :message="errorText" variant="danger" :persistent="true" />
+            <FormMessage :message="errorText" variant="danger" :persistent="true" />
             <FormElement
                 id="__label"
                 :value="node.label"
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index 817d2a1967a..7c4e1f227c2 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -2,6 +2,7 @@
     <div>
         <FormCard :title="title" icon="fa-wrench" :collapsible="false">
             <template v-slot:body>
+                <FormMessage :message="errorText" variant="danger" :persistent="true" />
                 <Form
                     :inputs="model.inputs"
                     :form-config="formConfig"
@@ -16,6 +17,7 @@
 
 <script>
 import Form from "components/Form/Form";
+import FormMessage from "components/Form/FormMessage";
 import FormCard from "components/Form/FormCard";
 import { getTool } from "./services";
 
@@ -23,6 +25,7 @@ export default {
     components: {
         Form,
         FormCard,
+        FormMessage,
     },
     props: {
         model: {
@@ -41,6 +44,7 @@ export default {
     data() {
         return {
             formConfig: {},
+            errorText: null,
         };
     },
     computed: {
@@ -54,9 +58,8 @@ export default {
                 (formConfig) => {
                     this.formConfig = formConfig;
                 },
-                (response) => {
-                    //Galaxy.emit.debug("tool-form-composite::postchange()", "Refresh request failed.", response);
-                    //process.reject();
+                (errorText) => {
+                    this.errorText = errorText;
                 }
             );
             this.$emit("onChange", this.model.index, data);

From dbba34b53df105bf97fd3ef9686ab7d89f9f56cc Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 22 Jun 2021 20:45:10 -0400
Subject: [PATCH 019/218] Allow collapsing tool steps

---
 client/src/components/Workflow/Run/WorkflowRunToolStep.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index 7c4e1f227c2..97886cff31a 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -1,6 +1,6 @@
 <template>
     <div>
-        <FormCard :title="title" icon="fa-wrench" :collapsible="false">
+        <FormCard :title="title" icon="fa-wrench" :collapsible="true">
             <template v-slot:body>
                 <FormMessage :message="errorText" variant="danger" :persistent="true" />
                 <Form

From ae7e7ab4975167a419524b76442e92a24ccb13d1 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 23 Jun 2021 10:29:29 -0400
Subject: [PATCH 020/218] Refactor parameter replacement handling

---
 client/src/components/Form/FormDisplay.vue    | 57 +++++--------------
 .../Workflow/Run/WorkflowRunForm.vue          |  2 +-
 .../Workflow/Run/WorkflowRunToolStep.vue      | 39 ++++++++++++-
 3 files changed, 52 insertions(+), 46 deletions(-)

diff --git a/client/src/components/Form/FormDisplay.vue b/client/src/components/Form/FormDisplay.vue
index bbb5b056cef..42f4476f56d 100644
--- a/client/src/components/Form/FormDisplay.vue
+++ b/client/src/components/Form/FormDisplay.vue
@@ -85,7 +85,7 @@ export default {
             this.onChange();
         },
         replaceData() {
-            this.onReplaceParams();
+            //this.onReplaceParams();
             this.onChange();
         },
     },
@@ -144,50 +144,19 @@ export default {
     },
     methods: {
         onReplaceParams() {
-            this.params = {};
-            FormData.visitInputs(this.inputs, (input, name) => {
-                this.params[name] = input;
-            });
-            _.each(this.params, (input, name) => {
-                if (input.wp_linked || input.step_linked) {
-                    var field = this.form.field_list[this.form.data.match(name)];
-                    if (field) {
-                        var new_value;
-                        if (input.step_linked) {
-                            new_value = { values: [] };
-                            _.each(input.step_linked, (source_step) => {
-                                if (isDataStep(source_step)) {
-                                    var value = this.replaceData[source_step.index].input;
-                                    if (value) {
-                                        _.each(value.values, (v) => {
-                                            new_value.values.push(v);
-                                        });
-                                    }
-                                }
-                            });
-                            if (!input.multiple && new_value.values.length > 0) {
-                                new_value = {
-                                    values: [new_value.values[0]],
-                                };
-                            }
-                        }
-                        if (input.wp_linked) {
-                            new_value = input.value;
-                            var re = /\$\{(.+?)\}/g;
-                            var match;
-                            while ((match = re.exec(input.value))) {
-                                var wp_value = this.replaceParams[match[1]];
-                                if (wp_value) {
-                                    new_value = new_value.split(match[0]).join(wp_value);
-                                }
-                            }
-                        }
+            if (this.replaceParams) {
+                this.params = {};
+                FormData.visitInputs(this.inputs, (input, name) => {
+                    this.params[name] = input;
+                });
+                _.each(this.params, (input, name) => {
+                    const newValue = this.replaceParams[name];
+                    if (newValue) {
+                        const field = this.form.field_list[this.form.data.match(name)];
+                        field.value(newValue);
                     }
-                    if (new_value !== undefined) {
-                        field.value(new_value);
-                    }
-                }
-            });
+                });
+            }
         },
         onChange() {
             this.formData = this.form.data.create();
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index e3ec4a3a42f..68ce88851cd 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -25,7 +25,7 @@
                 v-if="step.step_type == 'tool'"
                 :model="step"
                 :replaceData="stepData"
-                :replaceParams="wpData"
+                :wpData="wpData"
                 @onChange="onToolStepInputs"
             />
             <WorkflowRunDefaultStep v-else :model="step" @onChange="onDefaultStepInputs" />
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index 97886cff31a..5d479c665d9 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -19,6 +19,7 @@
 import Form from "components/Form/Form";
 import FormMessage from "components/Form/FormMessage";
 import FormCard from "components/Form/FormCard";
+import FormData from "mvc/form/form-data";
 import { getTool } from "./services";
 
 export default {
@@ -32,7 +33,7 @@ export default {
             type: Object,
             required: true,
         },
-        replaceParams: {
+        wpData: {
             type: Object,
             default: null,
         },
@@ -44,15 +45,50 @@ export default {
     data() {
         return {
             formConfig: {},
+            formData: {},
+            replaceParams: {},
             errorText: null,
         };
     },
+    watch: {
+        wpData() {
+            this.onReplaceParams();
+        },
+    },
     computed: {
         title() {
             return `${this.model.name} ${this.model.description} (Galaxy Version ${this.model.version})`;
         },
     },
     methods: {
+        onReplaceParams() {
+            const params = {};
+            FormData.visitInputs(this.model.inputs, (input, name) => {
+                params[name] = input;
+            });
+            const values = this.formData;
+            this.replaceParams = {};
+            _.each(params, (input, name) => {
+                if (input.wp_linked) {
+                    let new_value;
+                    if (input.wp_linked) {
+                        new_value = input.value;
+                        var re = /\$\{(.+?)\}/g;
+                        var match;
+                        while ((match = re.exec(input.value))) {
+                            var wp_value = this.wpData[match[1]];
+                            if (wp_value) {
+                                new_value = new_value.split(match[0]).join(wp_value);
+                            }
+                        }
+                    }
+                    if (new_value !== undefined) {
+                        this.replaceParams[name] = new_value;
+                    }
+                }
+            });
+            console.log(this.replaceParams);
+        },
         onChange(data) {
             getTool(this.model.id, this.model.version, data).then(
                 (formConfig) => {
@@ -62,6 +98,7 @@ export default {
                     this.errorText = errorText;
                 }
             );
+            this.formData = data;
             this.$emit("onChange", this.model.index, data);
         },
     },

From 1697f1ecd09e5422cea23a7d09cc215175b9ec2a Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 23 Jun 2021 10:43:55 -0400
Subject: [PATCH 021/218] Add linked dataset to revised parameter replacement
 handling

---
 client/src/components/Form/FormDisplay.vue    |  9 -----
 .../Workflow/Run/WorkflowRunForm.vue          |  4 +-
 .../Workflow/Run/WorkflowRunToolStep.vue      | 39 ++++++++++++++-----
 3 files changed, 32 insertions(+), 20 deletions(-)

diff --git a/client/src/components/Form/FormDisplay.vue b/client/src/components/Form/FormDisplay.vue
index 42f4476f56d..2cda9dd8409 100644
--- a/client/src/components/Form/FormDisplay.vue
+++ b/client/src/components/Form/FormDisplay.vue
@@ -5,7 +5,6 @@
 <script>
 import Form from "mvc/form/form-view";
 import FormData from "mvc/form/form-data";
-import { isDataStep } from "components/Workflow/Run/model";
 
 export default {
     props: {
@@ -45,10 +44,6 @@ export default {
             type: Object,
             default: null,
         },
-        replaceData: {
-            type: Object,
-            default: null,
-        },
     },
     data() {
         return {
@@ -84,10 +79,6 @@ export default {
             this.onReplaceParams();
             this.onChange();
         },
-        replaceData() {
-            //this.onReplaceParams();
-            this.onChange();
-        },
     },
     mounted() {
         this.onRender();
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 68ce88851cd..763caa0b7c9 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -24,8 +24,8 @@
             <WorkflowRunToolStep
                 v-if="step.step_type == 'tool'"
                 :model="step"
-                :replaceData="stepData"
-                :wpData="wpData"
+                :step-data="stepData"
+                :wp-data="wpData"
                 @onChange="onToolStepInputs"
             />
             <WorkflowRunDefaultStep v-else :model="step" @onChange="onDefaultStepInputs" />
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index 5d479c665d9..dcd93bbecd2 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -6,8 +6,7 @@
                 <Form
                     :inputs="model.inputs"
                     :form-config="formConfig"
-                    :replaceParams="replaceParams"
-                    :replaceData="replaceData"
+                    :replace-params="replaceParams"
                     @onChange="onChange"
                 />
             </template>
@@ -20,6 +19,7 @@ import Form from "components/Form/Form";
 import FormMessage from "components/Form/FormMessage";
 import FormCard from "components/Form/FormCard";
 import FormData from "mvc/form/form-data";
+import { isDataStep } from "components/Workflow/Run/model";
 import { getTool } from "./services";
 
 export default {
@@ -37,7 +37,7 @@ export default {
             type: Object,
             default: null,
         },
-        replaceData: {
+        stepData: {
             type: Object,
             default: null,
         },
@@ -51,6 +51,9 @@ export default {
         };
     },
     watch: {
+        stepData() {
+            this.onReplaceParams();
+        },
         wpData() {
             this.onReplaceParams();
         },
@@ -69,21 +72,39 @@ export default {
             const values = this.formData;
             this.replaceParams = {};
             _.each(params, (input, name) => {
-                if (input.wp_linked) {
-                    let new_value;
+                if (input.wp_linked || input.step_linked) {
+                    let newValue;
+                    if (input.step_linked) {
+                        newValue = { values: [] };
+                        _.each(input.step_linked, (source_step) => {
+                            if (isDataStep(source_step)) {
+                                var value = this.stepData[source_step.index].input;
+                                if (value) {
+                                    _.each(value.values, (v) => {
+                                        newValue.values.push(v);
+                                    });
+                                }
+                            }
+                        });
+                        if (!input.multiple && newValue.values.length > 0) {
+                            newValue = {
+                                values: [newValue.values[0]],
+                            };
+                        }
+                    }
                     if (input.wp_linked) {
-                        new_value = input.value;
+                        newValue = input.value;
                         var re = /\$\{(.+?)\}/g;
                         var match;
                         while ((match = re.exec(input.value))) {
                             var wp_value = this.wpData[match[1]];
                             if (wp_value) {
-                                new_value = new_value.split(match[0]).join(wp_value);
+                                newValue = newValue.split(match[0]).join(wp_value);
                             }
                         }
                     }
-                    if (new_value !== undefined) {
-                        this.replaceParams[name] = new_value;
+                    if (newValue !== undefined) {
+                        this.replaceParams[name] = newValue;
                     }
                 }
             });

From 3fbf3ff929bbf406e62710c26527c3dafa0d8f19 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 23 Jun 2021 10:47:35 -0400
Subject: [PATCH 022/218] Remove debug statements, trigger change event for
 replacement values conditionally

---
 client/src/components/Form/FormDisplay.vue                 | 3 +--
 client/src/components/Workflow/Run/WorkflowRunToolStep.vue | 1 -
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/client/src/components/Form/FormDisplay.vue b/client/src/components/Form/FormDisplay.vue
index 2cda9dd8409..620da634c24 100644
--- a/client/src/components/Form/FormDisplay.vue
+++ b/client/src/components/Form/FormDisplay.vue
@@ -77,7 +77,6 @@ export default {
         },
         replaceParams() {
             this.onReplaceParams();
-            this.onChange();
         },
     },
     mounted() {
@@ -147,6 +146,7 @@ export default {
                         field.value(newValue);
                     }
                 });
+                this.onChange();
             }
         },
         onChange() {
@@ -166,7 +166,6 @@ export default {
                         this.onChange();
                     },
                 });
-                this.onReplaceParams();
                 this.onChange();
             });
         },
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index dcd93bbecd2..3466e0bbc83 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -108,7 +108,6 @@ export default {
                     }
                 }
             });
-            console.log(this.replaceParams);
         },
         onChange(data) {
             getTool(this.model.id, this.model.version, data).then(

From 86001732d7df73598b1d9e7f6f2daf9b1036658b Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 23 Jun 2021 10:55:00 -0400
Subject: [PATCH 023/218] Move input visitor helper to Form component utilities

---
 client/src/components/Form/FormDisplay.vue    |  4 +-
 client/src/components/Form/utilities.js       | 42 +++++++++++++++++
 .../Workflow/Run/WorkflowRunToolStep.vue      |  4 +-
 client/src/mvc/form/form-data.js              | 46 +------------------
 4 files changed, 47 insertions(+), 49 deletions(-)
 create mode 100644 client/src/components/Form/utilities.js

diff --git a/client/src/components/Form/FormDisplay.vue b/client/src/components/Form/FormDisplay.vue
index 620da634c24..85e2f754a2c 100644
--- a/client/src/components/Form/FormDisplay.vue
+++ b/client/src/components/Form/FormDisplay.vue
@@ -4,7 +4,7 @@
 
 <script>
 import Form from "mvc/form/form-view";
-import FormData from "mvc/form/form-data";
+import { visitInputs } from "components/Form/utilities";
 
 export default {
     props: {
@@ -136,7 +136,7 @@ export default {
         onReplaceParams() {
             if (this.replaceParams) {
                 this.params = {};
-                FormData.visitInputs(this.inputs, (input, name) => {
+                visitInputs(this.inputs, (input, name) => {
                     this.params[name] = input;
                 });
                 _.each(this.params, (input, name) => {
diff --git a/client/src/components/Form/utilities.js b/client/src/components/Form/utilities.js
new file mode 100644
index 00000000000..669c07f18db
--- /dev/null
+++ b/client/src/components/Form/utilities.js
@@ -0,0 +1,42 @@
+/** Visits tool inputs
+ * @param{dict}   inputs    - Nested dictionary of input elements
+ * @param{dict}   callback  - Called with the mapped dictionary object and corresponding model node
+ */
+ export var visitInputs = (inputs, callback, prefix, context) => {
+    context = $.extend({}, context);
+    _.each(inputs, (input) => {
+        if (input && input.type && input.name) {
+            context[input.name] = input;
+        }
+    });
+    for (var key in inputs) {
+        var node = inputs[key];
+        node.name = node.name || key;
+        var name = prefix ? `${prefix}|${node.name}` : node.name;
+        switch (node.type) {
+            case "repeat":
+                _.each(node.cache, (cache, j) => {
+                    visitInputs(cache, callback, `${name}_${j}`, context);
+                });
+                break;
+            case "conditional":
+                if (node.test_param) {
+                    callback(node.test_param, `${name}|${node.test_param.name}`, context);
+                    var selectedCase = matchCase(node, node.test_param.value);
+                    if (selectedCase != -1) {
+                        visitInputs(node.cases[selectedCase].inputs, callback, name, context);
+                    } else {
+                        console.debug(`Form.utilities::visitInputs() - Invalid case for ${name}.`);
+                    }
+                } else {
+                    console.debug(`Form.utilities::visitInputs() - Conditional test parameter missing for ${name}.`);
+                }
+                break;
+            case "section":
+                visitInputs(node.inputs, callback, name, context);
+                break;
+            default:
+                callback(node, name, context);
+        }
+    }
+};
\ No newline at end of file
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index 3466e0bbc83..374754d4688 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -18,7 +18,7 @@
 import Form from "components/Form/Form";
 import FormMessage from "components/Form/FormMessage";
 import FormCard from "components/Form/FormCard";
-import FormData from "mvc/form/form-data";
+import { visitInputs } from "components/Form/utilities";
 import { isDataStep } from "components/Workflow/Run/model";
 import { getTool } from "./services";
 
@@ -66,7 +66,7 @@ export default {
     methods: {
         onReplaceParams() {
             const params = {};
-            FormData.visitInputs(this.model.inputs, (input, name) => {
+            visitInputs(this.model.inputs, (input, name) => {
                 params[name] = input;
             });
             const values = this.formData;
diff --git a/client/src/mvc/form/form-data.js b/client/src/mvc/form/form-data.js
index 61f0778b8f8..63c68919716 100644
--- a/client/src/mvc/form/form-data.js
+++ b/client/src/mvc/form/form-data.js
@@ -1,7 +1,7 @@
 import _ from "underscore";
 import $ from "jquery";
 import Backbone from "backbone";
-import { getGalaxyInstance } from "app";
+import { visitInputs } from "components/Form/utilities";
 
 /* This class maps the form dom to an api compatible javascript dictionary. */
 export var Manager = Backbone.Model.extend({
@@ -202,50 +202,6 @@ export var matchCase = (input, value) => {
     return -1;
 };
 
-/** Visits tool inputs
- * @param{dict}   inputs    - Nested dictionary of input elements
- * @param{dict}   callback  - Called with the mapped dictionary object and corresponding model node
- */
-export var visitInputs = (inputs, callback, prefix, context) => {
-    context = $.extend({}, context);
-    _.each(inputs, (input) => {
-        if (input && input.type && input.name) {
-            context[input.name] = input;
-        }
-    });
-    for (var key in inputs) {
-        const Galaxy = getGalaxyInstance();
-        var node = inputs[key];
-        node.name = node.name || key;
-        var name = prefix ? `${prefix}|${node.name}` : node.name;
-        switch (node.type) {
-            case "repeat":
-                _.each(node.cache, (cache, j) => {
-                    visitInputs(cache, callback, `${name}_${j}`, context);
-                });
-                break;
-            case "conditional":
-                if (node.test_param) {
-                    callback(node.test_param, `${name}|${node.test_param.name}`, context);
-                    var selectedCase = matchCase(node, node.test_param.value);
-                    if (selectedCase != -1) {
-                        visitInputs(node.cases[selectedCase].inputs, callback, name, context);
-                    } else {
-                        Galaxy.emit.debug(`form-data::visitInputs() - Invalid case for ${name}.`);
-                    }
-                } else {
-                    Galaxy.emit.debug(`form-data::visitInputs() - Conditional test parameter missing for ${name}.`);
-                }
-                break;
-            case "section":
-                visitInputs(node.inputs, callback, name, context);
-                break;
-            default:
-                callback(node, name, context);
-        }
-    }
-};
-
 export default {
     Manager: Manager,
     visitInputs: visitInputs,

From 1dcac7dea1eed709594af38fe083f9bcd47c0a64 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 23 Jun 2021 12:23:47 -0400
Subject: [PATCH 024/218] Restore initial collapsible state as in the current
 run form

---
 client/src/components/Form/FormCard.vue       |  6 +++++-
 client/src/components/Form/FormDisplay.vue    |  2 +-
 client/src/components/Form/utilities.js       |  4 ++--
 .../Workflow/Run/WorkflowRunDefaultStep.vue   |  2 +-
 .../Workflow/Run/WorkflowRunForm.vue          |  3 +--
 .../Workflow/Run/WorkflowRunToolStep.vue      | 20 ++++++++++---------
 6 files changed, 21 insertions(+), 16 deletions(-)

diff --git a/client/src/components/Form/FormCard.vue b/client/src/components/Form/FormCard.vue
index 3cd4a54a44b..c24d65cffcf 100644
--- a/client/src/components/Form/FormCard.vue
+++ b/client/src/components/Form/FormCard.vue
@@ -48,10 +48,14 @@ export default {
             type: Boolean,
             default: false,
         },
+        initialCollapse: {
+            type: Boolean,
+            default: false,
+        },
     },
     data() {
         return {
-            collapsed: this.collapsible,
+            collapsed: this.initialCollapse,
         };
     },
     computed: {
diff --git a/client/src/components/Form/FormDisplay.vue b/client/src/components/Form/FormDisplay.vue
index 85e2f754a2c..b4415e5a4df 100644
--- a/client/src/components/Form/FormDisplay.vue
+++ b/client/src/components/Form/FormDisplay.vue
@@ -146,7 +146,7 @@ export default {
                         field.value(newValue);
                     }
                 });
-                this.onChange();
+                this.form.trigger("change");
             }
         },
         onChange() {
diff --git a/client/src/components/Form/utilities.js b/client/src/components/Form/utilities.js
index 669c07f18db..64f90c463c4 100644
--- a/client/src/components/Form/utilities.js
+++ b/client/src/components/Form/utilities.js
@@ -2,7 +2,7 @@
  * @param{dict}   inputs    - Nested dictionary of input elements
  * @param{dict}   callback  - Called with the mapped dictionary object and corresponding model node
  */
- export var visitInputs = (inputs, callback, prefix, context) => {
+export var visitInputs = (inputs, callback, prefix, context) => {
     context = $.extend({}, context);
     _.each(inputs, (input) => {
         if (input && input.type && input.name) {
@@ -39,4 +39,4 @@
                 callback(node, name, context);
         }
     }
-};
\ No newline at end of file
+};
diff --git a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
index 2d18e9ba279..eb7f368c8d1 100644
--- a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
@@ -1,6 +1,6 @@
 <template>
     <div>
-        <FormCard :title="model.fixed_title" :icon="icon" :collapsible="true">
+        <FormCard :title="model.fixed_title" :icon="icon" :collapsible="true" :initial-collapse="false">
             <template v-slot:body>
                 <Form :inputs="inputs" @onChange="onChange" />
             </template>
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 763caa0b7c9..147a73baf6f 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -34,7 +34,6 @@
 </template>
 
 <script>
-import Vue from "vue";
 import { getGalaxyInstance } from "app";
 import Form from "components/Form/Form";
 import FormCard from "components/Form/FormCard";
@@ -132,7 +131,7 @@ export default {
     },
     methods: {
         onDefaultStepInputs(stepId, data) {
-            Vue.set(this.stepData, stepId, data);
+            this.stepData[stepId] = data;
             this.stepData = Object.assign({}, this.stepData);
         },
         onToolStepInputs(stepId, data) {
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index 374754d4688..ede56f55bc8 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -1,6 +1,6 @@
 <template>
     <div>
-        <FormCard :title="title" icon="fa-wrench" :collapsible="true">
+        <FormCard :title="title" icon="fa-wrench" :collapsible="true" :initial-collapse="model.collapsed">
             <template v-slot:body>
                 <FormMessage :message="errorText" variant="danger" :persistent="true" />
                 <Form
@@ -52,6 +52,7 @@ export default {
     },
     watch: {
         stepData() {
+            console.log(this.model.id);
             this.onReplaceParams();
         },
         wpData() {
@@ -76,9 +77,10 @@ export default {
                     let newValue;
                     if (input.step_linked) {
                         newValue = { values: [] };
-                        _.each(input.step_linked, (source_step) => {
-                            if (isDataStep(source_step)) {
-                                var value = this.stepData[source_step.index].input;
+                        _.each(input.step_linked, (sourceStep) => {
+                            if (isDataStep(sourceStep)) {
+                                const sourceData = this.stepData[sourceStep.index];
+                                const value = sourceData && sourceData.input;
                                 if (value) {
                                     _.each(value.values, (v) => {
                                         newValue.values.push(v);
@@ -94,12 +96,12 @@ export default {
                     }
                     if (input.wp_linked) {
                         newValue = input.value;
-                        var re = /\$\{(.+?)\}/g;
-                        var match;
+                        const re = /\$\{(.+?)\}/g;
+                        let match;
                         while ((match = re.exec(input.value))) {
-                            var wp_value = this.wpData[match[1]];
-                            if (wp_value) {
-                                newValue = newValue.split(match[0]).join(wp_value);
+                            const wpValue = this.wpData[match[1]];
+                            if (wpValue) {
+                                newValue = newValue.split(match[0]).join(wpValue);
                             }
                         }
                     }

From 370f8a0b0a91b4890e1a0338e21972297745c40d Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 23 Jun 2021 12:59:40 -0400
Subject: [PATCH 025/218] Consolidate redundant run button component, refactor
 without using references

---
 client/src/components/WaitButton.vue          | 67 -------------------
 .../components/Workflow/Run/WorkflowRun.vue   | 60 ++---------------
 .../Workflow/Run/WorkflowRunForm.vue          | 14 ++--
 .../Workflow/Run/WorkflowRunFormSimple.vue    | 15 +++--
 client/src/style/scss/base.scss               |  5 --
 5 files changed, 24 insertions(+), 137 deletions(-)
 delete mode 100644 client/src/components/WaitButton.vue

diff --git a/client/src/components/WaitButton.vue b/client/src/components/WaitButton.vue
deleted file mode 100644
index dd19137cedd..00000000000
--- a/client/src/components/WaitButton.vue
+++ /dev/null
@@ -1,67 +0,0 @@
-/** Button variant with waiting and progress tracking. */
-<template>
-    <button class="ui-button-default" :class="buttonClass" type="button" @click="$emit('click')">
-        <i class="icon fa" :class="iconClass"> </i>
-        <span class="title"> {{ currentText }} </span>
-        <div class="progress" v-if="percentage != -1">
-            <div class="progress-bar" :style="{ width: progressWidth }"></div>
-        </div>
-    </button>
-</template>
-
-<script>
-export default {
-    props: {
-        title: {
-            type: String,
-            default: "",
-        },
-        icon: {
-            type: String,
-            default: "fa-play",
-        },
-        percentage: {
-            type: Number,
-            default: -1,
-        },
-        waiting: {
-            type: Boolean,
-            default: false,
-        },
-        waitText: {
-            type: String,
-            default: "Sending...",
-        },
-        variant: {
-            type: String,
-            default: "info",
-        },
-    },
-    computed: {
-        progressWidth() {
-            return `${this.percentage}%`;
-        },
-        buttonClass() {
-            if (this.waiting) {
-                return "disabled";
-            } else {
-                return `btn btn-${this.variant}`;
-            }
-        },
-        iconClass() {
-            if (this.waiting) {
-                return "fa-spinner fa-spin mr-1";
-            } else {
-                return this.icon + " mr-1";
-            }
-        },
-        currentText() {
-            if (this.waiting) {
-                return this.waitText;
-            } else {
-                return this.title;
-            }
-        },
-    },
-};
-</script>
diff --git a/client/src/components/Workflow/Run/WorkflowRun.vue b/client/src/components/Workflow/Run/WorkflowRun.vue
index c7d1ee31425..d90fb2242e9 100644
--- a/client/src/components/Workflow/Run/WorkflowRun.vue
+++ b/client/src/components/Workflow/Run/WorkflowRun.vue
@@ -7,11 +7,7 @@
             <b-alert v-if="loading" variant="info" show>
                 <loading-span message="Loading workflow run data" />
             </b-alert>
-            <workflow-run-success
-                v-else-if="invocations != null"
-                :invocations="invocations"
-                :workflow-name="workflowName"
-            />
+            <workflow-run-success v-else-if="!!invocations" :invocations="invocations" :workflow-name="workflowName" />
             <div v-else class="ui-form-composite">
                 <div class="ui-form-composite-messages mb-4">
                     <b-alert v-if="hasUpgradeMessages" variant="warning" show>
@@ -29,41 +25,15 @@
                         Workflow submission failed: {{ submissionError }}
                     </b-alert>
                 </div>
-                <!-- h4 as a class here looks odd but it was in the Backbone -->
-                <div class="ui-form-composite-header h4">
-                    <b>Workflow: {{ workflowName }}</b>
-                    <wait-button
-                        title="Run Workflow"
-                        id="run-workflow"
-                        variant="primary"
-                        :disabled="!runButtonEnabled"
-                        :waiting="!runButtonEnabled"
-                        :wait-text="runButtonWaitText"
-                        :percentage="runButtonPercentage"
-                        @click="execute"
-                    >
-                    </wait-button>
-                </div>
-                <workflow-run-form
-                    ref="runform"
+                <workflow-run-form-simple
+                    v-if="simpleForm"
                     :model="model"
-                    v-if="!simpleForm"
-                    :set-run-button-status="setRunButtonStatus"
+                    :target-history="simpleFormTargetHistory"
+                    :use-job-cache="simpleFormUseJobCache"
                     @submissionSuccess="handleInvocations"
+                    @showAdvanced="showAdvanced"
                 />
-                <div v-else>
-                    <workflow-run-form-simple
-                        ref="runform"
-                        :model="model"
-                        :set-run-button-status="setRunButtonStatus"
-                        :target-history="simpleFormTargetHistory"
-                        :use-job-cache="simpleFormUseJobCache"
-                        @submissionSuccess="handleInvocations"
-                        @submissionError="handleSubmissionError"
-                    />
-                    <!-- Options to default one way or the other, disable if admins want, etc.. -->
-                    <a href="#" @click="showAdvanced">Expand to full workflow form.</a>
-                </div>
+                <workflow-run-form v-else :model="model" @submissionSuccess="handleInvocations" />
             </div>
         </span>
     </span>
@@ -71,7 +41,6 @@
 
 <script>
 import { getRunData } from "./services";
-import WaitButton from "components/WaitButton";
 import LoadingSpan from "components/LoadingSpan";
 import WorkflowRunSuccess from "./WorkflowRunSuccess";
 import WorkflowRunForm from "./WorkflowRunForm";
@@ -82,7 +51,6 @@ import { errorMessageAsString } from "utils/simple-error";
 export default {
     components: {
         LoadingSpan,
-        WaitButton,
         WorkflowRunSuccess,
         WorkflowRunForm,
         WorkflowRunFormSimple,
@@ -109,10 +77,6 @@ export default {
             hasUpgradeMessages: false,
             hasStepVersionChanges: false,
             workflowName: "",
-            runForm: null,
-            runButtonEnabled: true,
-            runButtonWaitText: "",
-            runButtonPercentage: -1,
             invocations: null,
             simpleForm: null,
             submissionError: null,
@@ -158,20 +122,10 @@ export default {
                 this.loading = false;
             })
             .catch((response) => {
-                console.log(response);
                 this.error = errorMessageAsString(response);
             });
     },
     methods: {
-        execute() {
-            this.$refs.runform.execute();
-            this.submissionError = null;
-        },
-        setRunButtonStatus(enabled, waitText, percentage) {
-            this.runButtonEnabled = enabled;
-            this.runButtonWaitText = waitText;
-            this.runButtonPercentage = percentage;
-        },
         handleInvocations(invocations) {
             this.invocations = invocations;
         },
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 147a73baf6f..dbc52458623 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -1,5 +1,9 @@
 <template>
     <div>
+        <div class="h4 clearfix mb-3">
+            <b>Workflow: {{ model.name }}</b>
+            <ButtonSpinner class="float-right" title="Run Workflow" id="run-workflow" @click="onExecute" />
+        </div>
         <FormCard v-if="wpInputsAvailable" title="Workflow Parameters">
             <template v-slot:body>
                 <Form :inputs="wpInputs" @onChange="onWpInputs" />
@@ -37,6 +41,7 @@
 import { getGalaxyInstance } from "app";
 import Form from "components/Form/Form";
 import FormCard from "components/Form/FormCard";
+import ButtonSpinner from "components/Common/ButtonSpinner";
 import WorkflowRunDefaultStep from "./WorkflowRunDefaultStep";
 import WorkflowRunToolStep from "./WorkflowRunToolStep";
 
@@ -44,6 +49,7 @@ export default {
     components: {
         Form,
         FormCard,
+        ButtonSpinner,
         WorkflowRunDefaultStep,
         WorkflowRunToolStep,
     },
@@ -52,10 +58,6 @@ export default {
             type: Object,
             required: true,
         },
-        setRunButtonStatus: {
-            type: Function,
-            required: true,
-        },
     },
     data() {
         return {
@@ -140,9 +142,7 @@ export default {
         onWpInputs(data) {
             this.wpData = data;
         },
-        execute() {
-            this.runForm.execute();
-        },
+        onExecute() {},
         handleInvocations(invocations) {
             this.$emit("submissionSuccess", invocations);
         },
diff --git a/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue b/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
index b3809a92104..738da40c544 100644
--- a/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
@@ -1,22 +1,28 @@
 <template>
+    <div class="h4 clearfix mb-3">
+        <b>Workflow: {{ model.name }}</b>
+        <ButtonSpinner class="float-right" title="Run Workflow" id="run-workflow" @click="execute" />
+    </div>
     <div ref="form"></div>
+    <!-- Options to default one way or the other, disable if admins want, etc.. -->
+    <a href="#" @click="$emit('showAdvanced')">Expand to full workflow form.</a>
 </template>
 
 <script>
 import Form from "mvc/form/form-view";
+import ButtonSpinner from "components/Common/ButtonSpinner";
 import { invokeWorkflow } from "./services";
 import { isWorkflowInput } from "components/Workflow/constants";
 
 export default {
+    components: {
+        ButtonSpinner,
+    },
     props: {
         model: {
             type: Object,
             required: true,
         },
-        setRunButtonStatus: {
-            type: Function,
-            required: true,
-        },
         targetHistory: {
             type: String,
             default: "current",
@@ -32,7 +38,6 @@ export default {
             inputTypes: {},
         };
     },
-    computed: {},
     created() {
         this.form = new Form(this.formDefinition());
         this.$nextTick(() => {
diff --git a/client/src/style/scss/base.scss b/client/src/style/scss/base.scss
index f7b71f82d12..d516c1c8523 100644
--- a/client/src/style/scss/base.scss
+++ b/client/src/style/scss/base.scss
@@ -587,11 +587,6 @@ div.form-row-input label {
     margin-top: 5px;
 }
 
-#run-workflow {
-    @extend .float-right;
-    @extend .mt-3;
-}
-
 .form-row {
     select,
     textarea,

From e781bb4f32887217be1eee6ab40b0b25bacf9ba6 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 23 Jun 2021 13:35:09 -0400
Subject: [PATCH 026/218] Use vue components in refactored simplified workflow
 run form, restore config parsing

---
 .../Workflow/Run/WorkflowRunFormSimple.vue    | 50 ++++++++-----------
 lib/galaxy/managers/configuration.py          |  1 +
 2 files changed, 23 insertions(+), 28 deletions(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue b/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
index 738da40c544..557da05e287 100644
--- a/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
@@ -1,15 +1,17 @@
 <template>
-    <div class="h4 clearfix mb-3">
-        <b>Workflow: {{ model.name }}</b>
-        <ButtonSpinner class="float-right" title="Run Workflow" id="run-workflow" @click="execute" />
+    <div>
+        <div class="h4 clearfix mb-3">
+            <b>Workflow: {{ model.name }}</b>
+            <ButtonSpinner class="float-right" title="Run Workflow" id="run-workflow" @click="onExecute" />
+        </div>
+        <Form :inputs="formInputs" @onChange="onChange" />
+        <!-- Options to default one way or the other, disable if admins want, etc.. -->
+        <a href="#" @click="$emit('showAdvanced')">Expand to full workflow form.</a>
     </div>
-    <div ref="form"></div>
-    <!-- Options to default one way or the other, disable if admins want, etc.. -->
-    <a href="#" @click="$emit('showAdvanced')">Expand to full workflow form.</a>
 </template>
 
 <script>
-import Form from "mvc/form/form-view";
+import Form from "components/Form/Form";
 import ButtonSpinner from "components/Common/ButtonSpinner";
 import { invokeWorkflow } from "./services";
 import { isWorkflowInput } from "components/Workflow/constants";
@@ -17,6 +19,7 @@ import { isWorkflowInput } from "components/Workflow/constants";
 export default {
     components: {
         ButtonSpinner,
+        Form,
     },
     props: {
         model: {
@@ -34,21 +37,13 @@ export default {
     },
     data() {
         return {
-            form: null,
+            formData: {},
             inputTypes: {},
         };
     },
-    created() {
-        this.form = new Form(this.formDefinition());
-        this.$nextTick(() => {
-            const el = this.$refs["form"];
-            el.appendChild(this.form.$el[0]);
-        });
-    },
-    methods: {
-        formDefinition() {
+    computed: {
+        formInputs() {
             const inputs = [];
-
             // Add workflow parameters.
             Object.values(this.model.wpInputs).forEach((input) => {
                 const inputCopy = Object.assign({}, input);
@@ -57,7 +52,6 @@ export default {
                 inputs.push(inputCopy);
                 this.inputTypes[inputCopy.name] = "replacement_parameter";
             });
-
             // Add actual input modules.
             this.model.steps.forEach((step, i) => {
                 if (!isWorkflowInput(step.step_type)) {
@@ -73,18 +67,18 @@ export default {
                 inputs.push(stepAsInput);
                 this.inputTypes[stepName] = step.step_type;
             });
-
-            const def = {
-                inputs: inputs,
-            };
-            return def;
+            return inputs;
         },
-        execute() {
+    },
+    methods: {
+        onChange(data) {
+            this.formData = data;
+        },
+        onExecute() {
             const replacementParams = {};
             const inputs = {};
-            const formData = this.form.data.create();
-            for (const inputName in formData) {
-                const value = formData[inputName];
+            for (const inputName in this.formData) {
+                const value = this.formData[inputName];
                 const inputType = this.inputTypes[inputName];
                 if (inputType == "replacement_parameter") {
                     replacementParams[inputName] = value;
diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py
index 38aca4485cb..3e43f4320c4 100644
--- a/lib/galaxy/managers/configuration.py
+++ b/lib/galaxy/managers/configuration.py
@@ -172,6 +172,7 @@ class ConfigSerializer(base.ModelSerializer):
             'simplified_workflow_run_ui': _use_config,
             'simplified_workflow_run_ui_target_history': _use_config,
             'simplified_workflow_run_ui_job_cache': _use_config,
+            'simplified_workflow_run_ui': _use_config,
             'has_user_tool_filters': _defaults_to(False),
             # TODO: is there no 'correct' way to get an api url? controller='api', action='tools' is a hack
             # at any rate: the following works with path_prefix but is still brittle

From c9a496f5459460995538ee80be96ffde169b575c Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 23 Jun 2021 13:59:30 -0400
Subject: [PATCH 027/218] Add error handling to simplified workflow form

---
 client/src/components/Workflow/Run/WorkflowRun.vue     |  2 +-
 .../components/Workflow/Run/WorkflowRunFormSimple.vue  | 10 +++++++---
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRun.vue b/client/src/components/Workflow/Run/WorkflowRun.vue
index d90fb2242e9..c5410e918ea 100644
--- a/client/src/components/Workflow/Run/WorkflowRun.vue
+++ b/client/src/components/Workflow/Run/WorkflowRun.vue
@@ -86,6 +86,7 @@ export default {
     created() {
         getRunData(this.workflowId)
             .then((runData) => {
+                this.loading = false;
                 const model = new WorkflowRunModel(runData);
                 let simpleForm = this.preferSimpleForm;
                 if (simpleForm) {
@@ -119,7 +120,6 @@ export default {
                 this.hasUpgradeMessages = model.hasUpgradeMessages;
                 this.hasStepVersionChanges = model.hasStepVersionChanges;
                 this.workflowName = this.model.name;
-                this.loading = false;
             })
             .catch((response) => {
                 this.error = errorMessageAsString(response);
diff --git a/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue b/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
index 557da05e287..19ff3de2d78 100644
--- a/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
@@ -2,8 +2,11 @@
     <div>
         <div class="h4 clearfix mb-3">
             <b>Workflow: {{ model.name }}</b>
-            <ButtonSpinner class="float-right" title="Run Workflow" id="run-workflow" @click="onExecute" />
+            <ButtonSpinner class="float-right" title="Run Workflow" id="run-workflow" @onClick="onExecute" />
         </div>
+        <b-alert v-if="errorText" class="mt-2" variant="danger" show>
+            {{ errorText | l }}
+        </b-alert>
         <Form :inputs="formInputs" @onChange="onChange" />
         <!-- Options to default one way or the other, disable if admins want, etc.. -->
         <a href="#" @click="$emit('showAdvanced')">Expand to full workflow form.</a>
@@ -15,6 +18,7 @@ import Form from "components/Form/Form";
 import ButtonSpinner from "components/Common/ButtonSpinner";
 import { invokeWorkflow } from "./services";
 import { isWorkflowInput } from "components/Workflow/constants";
+import { errorMessageAsString } from "utils/simple-error";
 
 export default {
     components: {
@@ -39,6 +43,7 @@ export default {
         return {
             formData: {},
             inputTypes: {},
+            errorText: null,
         };
     },
     computed: {
@@ -103,8 +108,7 @@ export default {
                     this.$emit("submissionSuccess", invocations);
                 })
                 .catch((error) => {
-                    console.log(error);
-                    this.$emit("submissionError", error);
+                    this.errorText = errorMessageAsString(error);
                 });
         },
     },

From 2865171fe4a205e3ca6c258df138d19c53fe12f9 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 23 Jun 2021 15:04:24 -0400
Subject: [PATCH 028/218] Add execution handler for regular run workflow form

---
 .../Workflow/Run/WorkflowRunForm.vue          | 125 +++++++++++++++++-
 1 file changed, 120 insertions(+), 5 deletions(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index dbc52458623..9f789c0eafc 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -2,7 +2,7 @@
     <div>
         <div class="h4 clearfix mb-3">
             <b>Workflow: {{ model.name }}</b>
-            <ButtonSpinner class="float-right" title="Run Workflow" id="run-workflow" @click="onExecute" />
+            <ButtonSpinner class="float-right" title="Run Workflow" id="run-workflow" @onClick="onExecute" />
         </div>
         <FormCard v-if="wpInputsAvailable" title="Workflow Parameters">
             <template v-slot:body>
@@ -11,17 +11,17 @@
         </FormCard>
         <FormCard title="History Options">
             <template v-slot:body>
-                <Form :inputs="historyInputs" />
+                <Form :inputs="historyInputs" @onChange="onHistoryInputs" />
             </template>
         </FormCard>
         <FormCard v-if="cacheInputsAvailable" title="Job re-use Options">
             <template v-slot:body>
-                <Form :inputs="cacheInputs" />
+                <Form :inputs="cacheInputs" @onChange="onCacheInputs" />
             </template>
         </FormCard>
         <FormCard v-if="resourceInputsAvailable" title="Workflow Resource Options">
             <template v-slot:body>
-                <Form :inputs="resourceInputs" />
+                <Form :inputs="resourceInputs" @onChange="onResourceInputs" />
             </template>
         </FormCard>
         <div v-for="step in model.steps">
@@ -63,6 +63,8 @@ export default {
         return {
             stepData: {},
             wpData: {},
+            historyData: {},
+            cacheData: {},
             historyInputs: [
                 {
                     type: "conditional",
@@ -139,10 +141,123 @@ export default {
         onToolStepInputs(stepId, data) {
             this.stepData[stepId] = data;
         },
+        onHistoryInputs(data) {
+            this.historyData = data;
+        },
+        onResourceInputs(data) {
+            this.resourceData = data;
+        },
         onWpInputs(data) {
             this.wpData = data;
         },
-        onExecute() {},
+        onCacheInputs(data) {
+            this.cacheData = data;
+        },
+        onExecute() {
+            const Galaxy = getGalaxyInstance();
+            const job_def = {
+                new_history_name: this.historyData["new_history|name"] ? this.historyData["new_history|name"] : null,
+                history_id: !this.historyData["new_history|name"] ? this.model.historyId : null,
+                resource_params: this.resourceData,
+                replacement_params: this.wpData,
+                use_cached_job: this.cacheData["use_cached_job|check"] === "true",
+                parameters: {},
+                // Tool form will submit flat maps for each parameter
+                // (e.g. "repeat_0|cond|param": "foo" instead of nested
+                // data structures).
+                parameters_normalized: true,
+                // Tool form always wants a list of invocations back
+                // so that inputs can be batched.
+                batch: true,
+            };
+            var validated = true;
+            /*for (var i in this.forms) {
+                var form = this.forms[i];
+                var job_inputs = form.data.create();
+                var step = this.steps[i];
+                var step_index = step.step_index;
+                form.trigger("reset");
+                for (var job_input_id in job_inputs) {
+                    var input_value = job_inputs[job_input_id];
+                    var input_id = form.data.match(job_input_id);
+                    var input_def = form.input_list[input_id];
+                    if (!input_def.step_linked) {
+                        if (isDataStep(step)) {
+                            validated = input_value && input_value.values && input_value.values.length > 0;
+                            if (!validated && input_def.optional) {
+                                validated = true;
+                            }
+                        } else {
+                            validated =
+                                input_def.optional ||
+                                (input_def.is_workflow && input_value !== "") ||
+                                (!input_def.is_workflow && input_value !== null);
+                        }
+                        if (!validated) {
+                            if (input_def.type == "hidden") {
+                                this.modal.show({
+                                    title: _l("Workflow submission failed"),
+                                    body: `Step ${step_index}: ${
+                                        step.step_label || step.step_name
+                                    } is in an invalid state. Please remove and re-add this step in the Workflow Editor.`,
+                                    buttons: {
+                                        Close: () => {
+                                            this.modal.hide();
+                                        },
+                                    },
+                                });
+                            }
+                            form.highlight(input_id);
+                            break;
+                        }
+                        job_def.parameters[step_index] = job_def.parameters[step_index] || {};
+                        job_def.parameters[step_index][job_input_id] = job_inputs[job_input_id];
+                    }
+                }
+                if (!validated) {
+                    break;
+                }
+            }
+            if (!validated) {
+                this._enabled(true);
+                Galaxy.emit.debug("tool-form-composite::submit()", "Validation failed.", job_def);
+            } else {
+                Galaxy.emit.debug("tool-form-composite::submit()", "Validation complete.", job_def);
+                invokeWorkflow(this.runWorkflowModel.workflowId, job_def)
+                    .then((invocations) => {
+                        Galaxy.emit.debug("tool-form-composite::submit", "Submission successful.", invocations);
+                        if (Array.isArray(invocations) && invocations.length > 0) {
+                            this.handleInvocations(invocations);
+                        } else {
+                            this.submissionErrorModal(job_def, invocations);
+                        }
+                        this._enabled(true);
+                    })
+                    .catch((response) => {
+                        // TODO: Is this the same response as the Utils post would
+                        // have had?
+                        Galaxy.emit.debug("tool-form-composite::submit", "Submission failed.", response);
+                        var input_found = false;
+                        if (response && response.err_data) {
+                            for (var i in this.forms) {
+                                var form = this.forms[i];
+                                var step_related_errors = response.err_data[form.model.get("step_index")];
+                                if (step_related_errors) {
+                                    var error_messages = form.data.matchResponse(step_related_errors);
+                                    for (var input_id in error_messages) {
+                                        form.highlight(input_id, error_messages[input_id]);
+                                        input_found = true;
+                                        break;
+                                    }
+                                }
+                            }
+                        }
+                        if (!input_found) {
+                            this.submissionErrorModal(job_def, response);
+                        }
+                        this._enabled(true);
+                    });*/
+        },
         handleInvocations(invocations) {
             this.$emit("submissionSuccess", invocations);
         },

From 61268ed38d872b9bc7c927ebe3154c9288337b78 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 8 Jul 2021 14:45:20 -0400
Subject: [PATCH 029/218] Adjust to renaming Form to FormDisplay component

---
 .../Workflow/Run/WorkflowRunDefaultStep.vue          |  6 +++---
 .../src/components/Workflow/Run/WorkflowRunForm.vue  | 12 ++++++------
 .../Workflow/Run/WorkflowRunFormSimple.vue           |  6 +++---
 .../components/Workflow/Run/WorkflowRunToolStep.vue  |  7 +++----
 4 files changed, 15 insertions(+), 16 deletions(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
index eb7f368c8d1..9acbf2aa660 100644
--- a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
@@ -2,7 +2,7 @@
     <div>
         <FormCard :title="model.fixed_title" :icon="icon" :collapsible="true" :initial-collapse="false">
             <template v-slot:body>
-                <Form :inputs="inputs" @onChange="onChange" />
+                <FormDisplay :inputs="inputs" @onChange="onChange" />
             </template>
         </FormCard>
     </div>
@@ -11,12 +11,12 @@
 <script>
 import { getGalaxyInstance } from "app";
 import WorkflowIcons from "components/Workflow/icons";
-import Form from "components/Form/Form";
+import FormDisplay from "components/Form/FormDisplay";
 import FormCard from "components/Form/FormCard";
 
 export default {
     components: {
-        Form,
+        FormDisplay,
         FormCard,
     },
     props: {
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 9f789c0eafc..0acdaaf1962 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -6,22 +6,22 @@
         </div>
         <FormCard v-if="wpInputsAvailable" title="Workflow Parameters">
             <template v-slot:body>
-                <Form :inputs="wpInputs" @onChange="onWpInputs" />
+                <FormDisplay :inputs="wpInputs" @onChange="onWpInputs" />
             </template>
         </FormCard>
         <FormCard title="History Options">
             <template v-slot:body>
-                <Form :inputs="historyInputs" @onChange="onHistoryInputs" />
+                <FormDisplay :inputs="historyInputs" @onChange="onHistoryInputs" />
             </template>
         </FormCard>
         <FormCard v-if="cacheInputsAvailable" title="Job re-use Options">
             <template v-slot:body>
-                <Form :inputs="cacheInputs" @onChange="onCacheInputs" />
+                <FormDisplay :inputs="cacheInputs" @onChange="onCacheInputs" />
             </template>
         </FormCard>
         <FormCard v-if="resourceInputsAvailable" title="Workflow Resource Options">
             <template v-slot:body>
-                <Form :inputs="resourceInputs" @onChange="onResourceInputs" />
+                <FormDisplay :inputs="resourceInputs" @onChange="onResourceInputs" />
             </template>
         </FormCard>
         <div v-for="step in model.steps">
@@ -39,7 +39,7 @@
 
 <script>
 import { getGalaxyInstance } from "app";
-import Form from "components/Form/Form";
+import FormDisplay from "components/Form/FormDisplay";
 import FormCard from "components/Form/FormCard";
 import ButtonSpinner from "components/Common/ButtonSpinner";
 import WorkflowRunDefaultStep from "./WorkflowRunDefaultStep";
@@ -47,7 +47,7 @@ import WorkflowRunToolStep from "./WorkflowRunToolStep";
 
 export default {
     components: {
-        Form,
+        FormDisplay,
         FormCard,
         ButtonSpinner,
         WorkflowRunDefaultStep,
diff --git a/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue b/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
index 19ff3de2d78..82b373f08c9 100644
--- a/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
@@ -7,14 +7,14 @@
         <b-alert v-if="errorText" class="mt-2" variant="danger" show>
             {{ errorText | l }}
         </b-alert>
-        <Form :inputs="formInputs" @onChange="onChange" />
+        <FormDisplay :inputs="formInputs" @onChange="onChange" />
         <!-- Options to default one way or the other, disable if admins want, etc.. -->
         <a href="#" @click="$emit('showAdvanced')">Expand to full workflow form.</a>
     </div>
 </template>
 
 <script>
-import Form from "components/Form/Form";
+import FormDisplay from "components/Form/FormDisplay";
 import ButtonSpinner from "components/Common/ButtonSpinner";
 import { invokeWorkflow } from "./services";
 import { isWorkflowInput } from "components/Workflow/constants";
@@ -23,7 +23,7 @@ import { errorMessageAsString } from "utils/simple-error";
 export default {
     components: {
         ButtonSpinner,
-        Form,
+        FormDisplay,
     },
     props: {
         model: {
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index ede56f55bc8..26fc1cc45af 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -3,7 +3,7 @@
         <FormCard :title="title" icon="fa-wrench" :collapsible="true" :initial-collapse="model.collapsed">
             <template v-slot:body>
                 <FormMessage :message="errorText" variant="danger" :persistent="true" />
-                <Form
+                <FormDisplay
                     :inputs="model.inputs"
                     :form-config="formConfig"
                     :replace-params="replaceParams"
@@ -15,7 +15,7 @@
 </template>
 
 <script>
-import Form from "components/Form/Form";
+import FormDisplay from "components/Form/FormDisplay";
 import FormMessage from "components/Form/FormMessage";
 import FormCard from "components/Form/FormCard";
 import { visitInputs } from "components/Form/utilities";
@@ -24,7 +24,7 @@ import { getTool } from "./services";
 
 export default {
     components: {
-        Form,
+        FormDisplay,
         FormCard,
         FormMessage,
     },
@@ -52,7 +52,6 @@ export default {
     },
     watch: {
         stepData() {
-            console.log(this.model.id);
             this.onReplaceParams();
         },
         wpData() {

From 2cc675c218de67daf8bcda684bd638eb1ebc1112 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 8 Jul 2021 15:31:50 -0400
Subject: [PATCH 030/218] Use fortawesome to load collapsible icons in tool
 card component

---
 client/src/components/Form/FormCard.vue | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Form/FormCard.vue b/client/src/components/Form/FormCard.vue
index c24d65cffcf..8966a29c6c8 100644
--- a/client/src/components/Form/FormCard.vue
+++ b/client/src/components/Form/FormCard.vue
@@ -13,8 +13,8 @@
                     v-b-tooltip.hover
                     @click="onCollapse"
                 >
-                    <span v-if="collapsed" class="fa fa-eye" />
-                    <span v-else class="fa fa-eye-slash" />
+                    <font-awesome-icon v-if="collapsed" icon="eye-slash" class="fa-fw" />
+                    <font-awesome-icon v-else icon="eye" class="fa-fw" />
                 </b-button>
             </div>
             <a class="portlet-title" @click="onCollapse" :href="href">
@@ -30,7 +30,17 @@
     </div>
 </template>
 <script>
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faEye, faEyeSlash } from "@fortawesome/free-solid-svg-icons";
+
+library.add(faEye);
+library.add(faEyeSlash);
+
 export default {
+    components: {
+        FontAwesomeIcon,
+    },
     props: {
         title: {
             type: String,

From 255bf69e9b4854eb51d8b56a204a73146a301b26 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 8 Jul 2021 15:42:10 -0400
Subject: [PATCH 031/218] Fix tooltip orientation

---
 client/src/components/Form/FormCard.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Form/FormCard.vue b/client/src/components/Form/FormCard.vue
index 8966a29c6c8..736ab9ef34e 100644
--- a/client/src/components/Form/FormCard.vue
+++ b/client/src/components/Form/FormCard.vue
@@ -10,7 +10,7 @@
                     variant="link"
                     size="sm"
                     class="float-right py-0"
-                    v-b-tooltip.hover
+                    v-b-tooltip.hover.bottom
                     @click="onCollapse"
                 >
                     <font-awesome-icon v-if="collapsed" icon="eye-slash" class="fa-fw" />

From 386502e7971e98b23ab48029bbc17abbad5a9b9e Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 12 Jul 2021 11:23:05 -0400
Subject: [PATCH 032/218] Migrate form conditional case matching helper from
 backbone utilities

---
 client/src/components/Form/utilities.js | 20 ++++++++++++++++++++
 client/src/mvc/form/form-data.js        | 23 ++---------------------
 2 files changed, 22 insertions(+), 21 deletions(-)

diff --git a/client/src/components/Form/utilities.js b/client/src/components/Form/utilities.js
index 64f90c463c4..5c863cda8aa 100644
--- a/client/src/components/Form/utilities.js
+++ b/client/src/components/Form/utilities.js
@@ -40,3 +40,23 @@ export var visitInputs = (inputs, callback, prefix, context) => {
         }
     }
 };
+
+/** Match conditional values to selected cases
+ * @param{dict}   input     - Definition of conditional input parameter
+ * @param{dict}   value     - Current value
+ */
+export var matchCase = (input, value) => {
+    if (input.test_param.type == "boolean") {
+        if (value == "true") {
+            value = input.test_param.truevalue || "true";
+        } else {
+            value = input.test_param.falsevalue || "false";
+        }
+    }
+    for (var i in input.cases) {
+        if (input.cases[i].value == value) {
+            return i;
+        }
+    }
+    return -1;
+};
diff --git a/client/src/mvc/form/form-data.js b/client/src/mvc/form/form-data.js
index 63c68919716..12c7848fb7c 100644
--- a/client/src/mvc/form/form-data.js
+++ b/client/src/mvc/form/form-data.js
@@ -1,7 +1,7 @@
 import _ from "underscore";
 import $ from "jquery";
 import Backbone from "backbone";
-import { visitInputs } from "components/Form/utilities";
+import { matchCase, visitInputs } from "components/Form/utilities";
 
 /* This class maps the form dom to an api compatible javascript dictionary. */
 export var Manager = Backbone.Model.extend({
@@ -182,27 +182,8 @@ export var Manager = Backbone.Model.extend({
     },
 });
 
-/** Match conditional values to selected cases
- * @param{dict}   input     - Definition of conditional input parameter
- * @param{dict}   value     - Current value
- */
-export var matchCase = (input, value) => {
-    if (input.test_param.type == "boolean") {
-        if (value == "true") {
-            value = input.test_param.truevalue || "true";
-        } else {
-            value = input.test_param.falsevalue || "false";
-        }
-    }
-    for (var i in input.cases) {
-        if (input.cases[i].value == value) {
-            return i;
-        }
-    }
-    return -1;
-};
-
 export default {
     Manager: Manager,
+    matchCase: matchCase,
     visitInputs: visitInputs,
 };

From 45e571d7dc4b6fd5a29855bcb5579a48aafeb28c Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 13 Jul 2021 15:26:55 -0400
Subject: [PATCH 033/218] Fix submission error handling

---
 client/src/components/Workflow/Run/WorkflowRun.vue        | 8 +++++++-
 .../src/components/Workflow/Run/WorkflowRunFormSimple.vue | 6 +-----
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRun.vue b/client/src/components/Workflow/Run/WorkflowRun.vue
index c5410e918ea..18d4e8f5e54 100644
--- a/client/src/components/Workflow/Run/WorkflowRun.vue
+++ b/client/src/components/Workflow/Run/WorkflowRun.vue
@@ -31,9 +31,15 @@
                     :target-history="simpleFormTargetHistory"
                     :use-job-cache="simpleFormUseJobCache"
                     @submissionSuccess="handleInvocations"
+                    @submissionError="handleSubmissionError"
                     @showAdvanced="showAdvanced"
                 />
-                <workflow-run-form v-else :model="model" @submissionSuccess="handleInvocations" />
+                <workflow-run-form
+                    v-else
+                    :model="model"
+                    @submissionSuccess="handleInvocations"
+                    @submissionError="handleSubmissionError"
+                />
             </div>
         </span>
     </span>
diff --git a/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue b/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
index 82b373f08c9..1683ee3e8cf 100644
--- a/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
@@ -4,9 +4,6 @@
             <b>Workflow: {{ model.name }}</b>
             <ButtonSpinner class="float-right" title="Run Workflow" id="run-workflow" @onClick="onExecute" />
         </div>
-        <b-alert v-if="errorText" class="mt-2" variant="danger" show>
-            {{ errorText | l }}
-        </b-alert>
         <FormDisplay :inputs="formInputs" @onChange="onChange" />
         <!-- Options to default one way or the other, disable if admins want, etc.. -->
         <a href="#" @click="$emit('showAdvanced')">Expand to full workflow form.</a>
@@ -43,7 +40,6 @@ export default {
         return {
             formData: {},
             inputTypes: {},
-            errorText: null,
         };
     },
     computed: {
@@ -108,7 +104,7 @@ export default {
                     this.$emit("submissionSuccess", invocations);
                 })
                 .catch((error) => {
-                    this.errorText = errorMessageAsString(error);
+                    this.$emit("submissionError", errorMessageAsString(error));
                 });
         },
     },

From 60fb69ce9f760c99f9cda6cac5657b694353e7e4 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 19 Jul 2021 15:46:02 -0400
Subject: [PATCH 034/218] Preliminary handling of validation errors and
 highlighting in workflow steps

---
 client/src/components/Form/FormDisplay.vue    |  7 +++--
 .../Workflow/Run/WorkflowRunDefaultStep.vue   | 25 ++++++++++++++++--
 .../Workflow/Run/WorkflowRunForm.vue          | 26 ++++++++++++++++++-
 .../Workflow/Run/WorkflowRunToolStep.vue      | 15 +++++++++++
 client/src/style/scss/ui.scss                 |  1 +
 5 files changed, 69 insertions(+), 5 deletions(-)

diff --git a/client/src/components/Form/FormDisplay.vue b/client/src/components/Form/FormDisplay.vue
index b4415e5a4df..d1137ec2049 100644
--- a/client/src/components/Form/FormDisplay.vue
+++ b/client/src/components/Form/FormDisplay.vue
@@ -94,10 +94,13 @@ export default {
                 const input_id = this.form.data.match(job_input_id);
                 const input_field = this.form.field_list[input_id];
                 const input_def = this.form.input_list[input_id];
-                if (!input_id || !input_def || !input_field) {
+                if (!input_id || !input_def || !input_field || input_def.step_linked) {
                     continue;
                 }
-                if (!input_def.optional && input_value == null && input_def.type != "hidden") {
+                if (input_value && input_value.values && input_value.values.length == 0 && !input_def.optional) {
+                    return [input_id, "Please provide data for this input."];
+                }
+                if (!input_value && !input_def.optional && input_def.type != "hidden") {
                     return [input_id, "Please provide a value for this option."];
                 }
                 if (input_field.validate) {
diff --git a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
index 9acbf2aa660..3c1293d1a00 100644
--- a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
@@ -2,7 +2,12 @@
     <div>
         <FormCard :title="model.fixed_title" :icon="icon" :collapsible="true" :initial-collapse="false">
             <template v-slot:body>
-                <FormDisplay :inputs="inputs" @onChange="onChange" />
+                <FormDisplay
+                    :inputs="inputs"
+                    :validation-scroll-to="validationScrollTo"
+                    @onChange="onChange"
+                    @onValidation="onValidation"
+                />
             </template>
         </FormCard>
     </div>
@@ -24,9 +29,22 @@ export default {
             type: Object,
             required: true,
         },
+        stepScrollTo: {
+            type: Object,
+            required: true,
+        },
     },
     data() {
-        return {};
+        return {
+            validationScrollTo: [],
+        };
+    },
+    watch: {
+        stepScrollTo() {
+            if (this.stepScrollTo && this.stepScrollTo.stepId == this.model.index) {
+                this.validationScrollTo = this.stepScrollTo.validation;
+            }
+        },
     },
     computed: {
         icon() {
@@ -60,6 +78,9 @@ export default {
         onChange(data) {
             this.$emit("onChange", this.model.index, data);
         },
+        onValidation(validation) {
+            this.$emit("onValidation", this.model.index, validation);
+        },
     },
 };
 </script>
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 0acdaaf1962..d58f78f4a3f 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -29,10 +29,18 @@
                 v-if="step.step_type == 'tool'"
                 :model="step"
                 :step-data="stepData"
+                :step-scroll-to="stepScrollTo"
                 :wp-data="wpData"
                 @onChange="onToolStepInputs"
+                @onValidation="onValidation"
+            />
+            <WorkflowRunDefaultStep
+                v-else
+                :model="step"
+                :step-scroll-to="stepScrollTo"
+                @onChange="onDefaultStepInputs"
+                @onValidation="onValidation"
             />
-            <WorkflowRunDefaultStep v-else :model="step" @onChange="onDefaultStepInputs" />
         </div>
     </div>
 </template>
@@ -62,6 +70,8 @@ export default {
     data() {
         return {
             stepData: {},
+            stepValidation: {},
+            stepScrollTo: {},
             wpData: {},
             historyData: {},
             cacheData: {},
@@ -153,7 +163,20 @@ export default {
         onCacheInputs(data) {
             this.cacheData = data;
         },
+        onValidation(stepId, validation) {
+            this.stepValidation[stepId] = validation;
+        },
         onExecute() {
+            for (const [stepId, stepValidation] of Object.entries(this.stepValidation)) {
+                if (stepValidation) {
+                    const validation = stepValidation.slice();
+                    this.stepScrollTo = {
+                        stepId,
+                        validation,
+                    };
+                    return;
+                }
+            }
             const Galaxy = getGalaxyInstance();
             const job_def = {
                 new_history_name: this.historyData["new_history|name"] ? this.historyData["new_history|name"] : null,
@@ -170,6 +193,7 @@ export default {
                 // so that inputs can be batched.
                 batch: true,
             };
+
             var validated = true;
             /*for (var i in this.forms) {
                 var form = this.forms[i];
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index 26fc1cc45af..1b023e50446 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -7,7 +7,9 @@
                     :inputs="model.inputs"
                     :form-config="formConfig"
                     :replace-params="replaceParams"
+                    :validation-scroll-to="validationScrollTo"
                     @onChange="onChange"
+                    @onValidation="onValidation"
                 />
             </template>
         </FormCard>
@@ -41,6 +43,10 @@ export default {
             type: Object,
             default: null,
         },
+        stepScrollTo: {
+            type: Object,
+            required: true,
+        },
     },
     data() {
         return {
@@ -48,9 +54,15 @@ export default {
             formData: {},
             replaceParams: {},
             errorText: null,
+            validationScrollTo: [],
         };
     },
     watch: {
+        stepScrollTo() {
+            if (this.stepScrollTo && this.stepScrollTo.stepId == this.model.index) {
+                this.validationScrollTo = this.stepScrollTo.validation;
+            }
+        },
         stepData() {
             this.onReplaceParams();
         },
@@ -122,6 +134,9 @@ export default {
             this.formData = data;
             this.$emit("onChange", this.model.index, data);
         },
+        onValidation(validation) {
+            this.$emit("onValidation", this.model.index, validation);
+        },
     },
 };
 </script>
diff --git a/client/src/style/scss/ui.scss b/client/src/style/scss/ui.scss
index a752574eb50..3099d91631e 100644
--- a/client/src/style/scss/ui.scss
+++ b/client/src/style/scss/ui.scss
@@ -195,6 +195,7 @@ $ui-margin-horizontal-large: $margin-v * 2;
         background: $portlet-bg-color;
         border-color: transparent;
         .portlet-title {
+            @extend .my-1;
             .portlet-title-text.collapsible {
                 cursor: pointer;
                 text-decoration: underline;

From a63874b870d471cfd022555fbff06324e074ba79 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 19 Jul 2021 16:02:33 -0400
Subject: [PATCH 035/218] Add workflow run submission protocol to workflow
 component

---
 .../Workflow/Run/WorkflowRunForm.vue          | 133 ++++++------------
 1 file changed, 42 insertions(+), 91 deletions(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index d58f78f4a3f..2ca72019c74 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -2,7 +2,13 @@
     <div>
         <div class="h4 clearfix mb-3">
             <b>Workflow: {{ model.name }}</b>
-            <ButtonSpinner class="float-right" title="Run Workflow" id="run-workflow" @onClick="onExecute" />
+            <ButtonSpinner
+                id="run-workflow"
+                class="float-right"
+                title="Run Workflow"
+                :wait="disableExecution"
+                @onClick="onExecute"
+            />
         </div>
         <FormCard v-if="wpInputsAvailable" title="Workflow Parameters">
             <template v-slot:body>
@@ -52,6 +58,7 @@ import FormCard from "components/Form/FormCard";
 import ButtonSpinner from "components/Common/ButtonSpinner";
 import WorkflowRunDefaultStep from "./WorkflowRunDefaultStep";
 import WorkflowRunToolStep from "./WorkflowRunToolStep";
+import { invokeWorkflow } from "./services";
 
 export default {
     components: {
@@ -69,6 +76,7 @@ export default {
     },
     data() {
         return {
+            disableExecution: false,
             stepData: {},
             stepValidation: {},
             stepScrollTo: {},
@@ -177,14 +185,14 @@ export default {
                     return;
                 }
             }
-            const Galaxy = getGalaxyInstance();
-            const job_def = {
+
+            const jobDef = {
                 new_history_name: this.historyData["new_history|name"] ? this.historyData["new_history|name"] : null,
                 history_id: !this.historyData["new_history|name"] ? this.model.historyId : null,
                 resource_params: this.resourceData,
                 replacement_params: this.wpData,
                 use_cached_job: this.cacheData["use_cached_job|check"] === "true",
-                parameters: {},
+                parameters: this.stepData,
                 // Tool form will submit flat maps for each parameter
                 // (e.g. "repeat_0|cond|param": "foo" instead of nested
                 // data structures).
@@ -194,96 +202,39 @@ export default {
                 batch: true,
             };
 
-            var validated = true;
-            /*for (var i in this.forms) {
-                var form = this.forms[i];
-                var job_inputs = form.data.create();
-                var step = this.steps[i];
-                var step_index = step.step_index;
-                form.trigger("reset");
-                for (var job_input_id in job_inputs) {
-                    var input_value = job_inputs[job_input_id];
-                    var input_id = form.data.match(job_input_id);
-                    var input_def = form.input_list[input_id];
-                    if (!input_def.step_linked) {
-                        if (isDataStep(step)) {
-                            validated = input_value && input_value.values && input_value.values.length > 0;
-                            if (!validated && input_def.optional) {
-                                validated = true;
-                            }
-                        } else {
-                            validated =
-                                input_def.optional ||
-                                (input_def.is_workflow && input_value !== "") ||
-                                (!input_def.is_workflow && input_value !== null);
-                        }
-                        if (!validated) {
-                            if (input_def.type == "hidden") {
-                                this.modal.show({
-                                    title: _l("Workflow submission failed"),
-                                    body: `Step ${step_index}: ${
-                                        step.step_label || step.step_name
-                                    } is in an invalid state. Please remove and re-add this step in the Workflow Editor.`,
-                                    buttons: {
-                                        Close: () => {
-                                            this.modal.hide();
-                                        },
-                                    },
-                                });
-                            }
-                            form.highlight(input_id);
-                            break;
-                        }
-                        job_def.parameters[step_index] = job_def.parameters[step_index] || {};
-                        job_def.parameters[step_index][job_input_id] = job_inputs[job_input_id];
-                    }
-                }
-                if (!validated) {
-                    break;
-                }
-            }
-            if (!validated) {
-                this._enabled(true);
-                Galaxy.emit.debug("tool-form-composite::submit()", "Validation failed.", job_def);
-            } else {
-                Galaxy.emit.debug("tool-form-composite::submit()", "Validation complete.", job_def);
-                invokeWorkflow(this.runWorkflowModel.workflowId, job_def)
-                    .then((invocations) => {
-                        Galaxy.emit.debug("tool-form-composite::submit", "Submission successful.", invocations);
-                        if (Array.isArray(invocations) && invocations.length > 0) {
-                            this.handleInvocations(invocations);
-                        } else {
-                            this.submissionErrorModal(job_def, invocations);
-                        }
-                        this._enabled(true);
-                    })
-                    .catch((response) => {
-                        // TODO: Is this the same response as the Utils post would
-                        // have had?
-                        Galaxy.emit.debug("tool-form-composite::submit", "Submission failed.", response);
-                        var input_found = false;
-                        if (response && response.err_data) {
-                            for (var i in this.forms) {
-                                var form = this.forms[i];
-                                var step_related_errors = response.err_data[form.model.get("step_index")];
-                                if (step_related_errors) {
-                                    var error_messages = form.data.matchResponse(step_related_errors);
-                                    for (var input_id in error_messages) {
-                                        form.highlight(input_id, error_messages[input_id]);
-                                        input_found = true;
-                                        break;
-                                    }
+            console.debug("WorkflowRunForm::onExecute()", "Ready for submission.", jobDef);
+            this.disableExecution = true;
+            invokeWorkflow(this.model.workflowId, jobDef)
+                .then((invocations) => {
+                    console.debug("WorkflowRunForm::onExecute()", "Submission successful.", invocations);
+                    this.disableExecution = false;
+                    this.$emit("submissionSuccess", invocations);
+                })
+                .catch((response) => {
+                    // TODO: Is this the same response as the Utils post would
+                    // have had?
+                    console.debug("WorkflowRunForm::onExecute()", "Submission failed.", response);
+                    /*var input_found = false;
+                    if (response && response.err_data) {
+                        for (var i in this.forms) {
+                            var form = this.forms[i];
+                            var step_related_errors = response.err_data[form.model.get("step_index")];
+                            if (step_related_errors) {
+                                var error_messages = form.data.matchResponse(step_related_errors);
+                                for (var input_id in error_messages) {
+                                    form.highlight(input_id, error_messages[input_id]);
+                                    input_found = true;
+                                    break;
                                 }
                             }
                         }
-                        if (!input_found) {
-                            this.submissionErrorModal(job_def, response);
-                        }
-                        this._enabled(true);
-                    });*/
-        },
-        handleInvocations(invocations) {
-            this.$emit("submissionSuccess", invocations);
+                    }
+                    if (!input_found) {
+                        this.submissionErrorModal(jobDef, response);
+                    }*/
+                    this.$emit("submissionError", response);
+                    this.disableExecution = false;
+                });
         },
         toArray(obj) {
             return obj ? Object.keys(obj).map((k) => obj[k]) : [];

From 803f02083b49d284ceb710b2a2c70659abc37120 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 19 Jul 2021 22:41:56 -0400
Subject: [PATCH 036/218] Handle validation highlighting and workflow step
 collapse handling

---
 client/src/components/Form/FormCard.vue       |  8 +++-----
 .../Workflow/Run/WorkflowRunDefaultStep.vue   | 19 ++++++++++++-------
 .../Workflow/Run/WorkflowRunForm.vue          | 15 ++++++++++-----
 .../Workflow/Run/WorkflowRunToolStep.vue      | 18 +++++++++---------
 4 files changed, 34 insertions(+), 26 deletions(-)

diff --git a/client/src/components/Form/FormCard.vue b/client/src/components/Form/FormCard.vue
index 736ab9ef34e..ae104920783 100644
--- a/client/src/components/Form/FormCard.vue
+++ b/client/src/components/Form/FormCard.vue
@@ -58,15 +58,13 @@ export default {
             type: Boolean,
             default: false,
         },
-        initialCollapse: {
+        collapsed: {
             type: Boolean,
             default: false,
         },
     },
     data() {
-        return {
-            collapsed: this.initialCollapse,
-        };
+        return {};
     },
     computed: {
         href() {
@@ -75,7 +73,7 @@ export default {
     },
     methods: {
         onCollapse() {
-            this.collapsed = this.collapsible && !this.collapsed;
+            this.$emit("update:collapsed", !this.collapsed);
         },
     },
 };
diff --git a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
index 3c1293d1a00..9b1628e2004 100644
--- a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
@@ -1,6 +1,11 @@
 <template>
     <div>
-        <FormCard :title="model.fixed_title" :icon="icon" :collapsible="true" :initial-collapse="false">
+        <FormCard
+            :title="model.fixed_title"
+            :icon="icon"
+            :collapsible="true"
+            :collapsed.sync="collapsed"
+        >
             <template v-slot:body>
                 <FormDisplay
                     :inputs="inputs"
@@ -29,20 +34,20 @@ export default {
             type: Object,
             required: true,
         },
-        stepScrollTo: {
-            type: Object,
+        validationScrollTo: {
+            type: Array,
             required: true,
         },
     },
     data() {
         return {
-            validationScrollTo: [],
+            collapsed: this.model.collapsed,
         };
     },
     watch: {
-        stepScrollTo() {
-            if (this.stepScrollTo && this.stepScrollTo.stepId == this.model.index) {
-                this.validationScrollTo = this.stepScrollTo.validation;
+        validationScrollTo() {
+            if (this.validationScrollTo.length > 0) {
+                this.collapsed = false;
             }
         },
     },
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 2ca72019c74..945f5803157 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -35,7 +35,7 @@
                 v-if="step.step_type == 'tool'"
                 :model="step"
                 :step-data="stepData"
-                :step-scroll-to="stepScrollTo"
+                :validation-scroll-to="getValidationScrollTo(step.index)"
                 :wp-data="wpData"
                 @onChange="onToolStepInputs"
                 @onValidation="onValidation"
@@ -43,7 +43,7 @@
             <WorkflowRunDefaultStep
                 v-else
                 :model="step"
-                :step-scroll-to="stepScrollTo"
+                :validation-scroll-to="getValidationScrollTo(step.index)"
                 @onChange="onDefaultStepInputs"
                 @onValidation="onValidation"
             />
@@ -152,6 +152,12 @@ export default {
         },
     },
     methods: {
+        getValidationScrollTo(stepId) {
+            if (this.stepScrollTo.stepId == stepId) {
+                return this.stepScrollTo.stepValidation;
+            }
+            return [];
+        },
         onDefaultStepInputs(stepId, data) {
             this.stepData[stepId] = data;
             this.stepData = Object.assign({}, this.stepData);
@@ -177,10 +183,9 @@ export default {
         onExecute() {
             for (const [stepId, stepValidation] of Object.entries(this.stepValidation)) {
                 if (stepValidation) {
-                    const validation = stepValidation.slice();
                     this.stepScrollTo = {
-                        stepId,
-                        validation,
+                        stepId: stepId,
+                        stepValidation: stepValidation.slice(),
                     };
                     return;
                 }
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index 1b023e50446..2f92939a3ed 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -1,6 +1,6 @@
 <template>
     <div>
-        <FormCard :title="title" icon="fa-wrench" :collapsible="true" :initial-collapse="model.collapsed">
+        <FormCard :title="title" icon="fa-wrench" :collapsible="true" :collapsed.sync="collapsed">
             <template v-slot:body>
                 <FormMessage :message="errorText" variant="danger" :persistent="true" />
                 <FormDisplay
@@ -43,32 +43,32 @@ export default {
             type: Object,
             default: null,
         },
-        stepScrollTo: {
-            type: Object,
+        validationScrollTo: {
+            type: Array,
             required: true,
         },
     },
     data() {
         return {
+            collapsed: this.model.collapsed,
             formConfig: {},
             formData: {},
             replaceParams: {},
             errorText: null,
-            validationScrollTo: [],
         };
     },
     watch: {
-        stepScrollTo() {
-            if (this.stepScrollTo && this.stepScrollTo.stepId == this.model.index) {
-                this.validationScrollTo = this.stepScrollTo.validation;
-            }
-        },
         stepData() {
             this.onReplaceParams();
         },
         wpData() {
             this.onReplaceParams();
         },
+        validationScrollTo() {
+            if (this.validationScrollTo.length > 0) {
+                this.collapsed = false;
+            }
+        },
     },
     computed: {
         title() {

From 2b7bdd60a4d108a1819a6f65f4876590f75c6c7b Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 20 Jul 2021 00:50:44 -0400
Subject: [PATCH 037/218] Fix workflow parameter handling and validation

---
 client/src/components/Form/FormDisplay.vue                 | 3 +++
 client/src/components/Tool/ToolCard.vue                    | 2 +-
 .../src/components/Workflow/Run/WorkflowRunDefaultStep.vue | 7 +------
 client/src/components/Workflow/Run/model.js                | 1 +
 client/src/style/scss/ui.scss                              | 1 -
 5 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/client/src/components/Form/FormDisplay.vue b/client/src/components/Form/FormDisplay.vue
index d1137ec2049..24e240f59a1 100644
--- a/client/src/components/Form/FormDisplay.vue
+++ b/client/src/components/Form/FormDisplay.vue
@@ -103,6 +103,9 @@ export default {
                 if (!input_value && !input_def.optional && input_def.type != "hidden") {
                     return [input_id, "Please provide a value for this option."];
                 }
+                if (input_def.wp_linked && input_def.text_value == input_value) {
+                    return [input_id, "Please provide a value for this workflow parameter."];
+                }
                 if (input_field.validate) {
                     const message = input_field.validate();
                     if (message) {
diff --git a/client/src/components/Tool/ToolCard.vue b/client/src/components/Tool/ToolCard.vue
index 1f06b2b9e85..68fa050ee22 100644
--- a/client/src/components/Tool/ToolCard.vue
+++ b/client/src/components/Tool/ToolCard.vue
@@ -79,7 +79,7 @@
                         <span class="fa fa-star" />
                     </b-button>
                 </div>
-                <div class="portlet-title">
+                <div class="portlet-title my-1">
                     <i class="portlet-title-icon fa mr-1 fa-wrench" style="display: inline"></i>
                     <span class="portlet-title-text">
                         <b itemprop="name">{{ title }}</b> <span itemprop="description">{{ description }}</span> (Galaxy
diff --git a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
index 9b1628e2004..d478e40290c 100644
--- a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
@@ -1,11 +1,6 @@
 <template>
     <div>
-        <FormCard
-            :title="model.fixed_title"
-            :icon="icon"
-            :collapsible="true"
-            :collapsed.sync="collapsed"
-        >
+        <FormCard :title="model.fixed_title" :icon="icon" :collapsible="true" :collapsed.sync="collapsed">
             <template v-slot:body>
                 <FormDisplay
                     :inputs="inputs"
diff --git a/client/src/components/Workflow/Run/model.js b/client/src/components/Workflow/Run/model.js
index a35ba4eeccb..c0b66ec5ab5 100644
--- a/client/src/components/Workflow/Run/model.js
+++ b/client/src/components/Workflow/Run/model.js
@@ -123,6 +123,7 @@ export class WorkflowRunModel {
                 color: `hsl( ${++wp_count * 100}, 70%, 30% )`,
                 style: "ui-form-wp-source",
                 links: [],
+                optional: true,
             });
         };
 
diff --git a/client/src/style/scss/ui.scss b/client/src/style/scss/ui.scss
index 3099d91631e..a752574eb50 100644
--- a/client/src/style/scss/ui.scss
+++ b/client/src/style/scss/ui.scss
@@ -195,7 +195,6 @@ $ui-margin-horizontal-large: $margin-v * 2;
         background: $portlet-bg-color;
         border-color: transparent;
         .portlet-title {
-            @extend .my-1;
             .portlet-title-text.collapsible {
                 cursor: pointer;
                 text-decoration: underline;

From 275a7b92fadd35eb8970b0d51b69a563bdf312f8 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 20 Jul 2021 11:16:05 -0400
Subject: [PATCH 038/218] Refine client-side input validation of forms

---
 client/src/components/Form/FormDisplay.vue | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Form/FormDisplay.vue b/client/src/components/Form/FormDisplay.vue
index 24e240f59a1..cb813858ad4 100644
--- a/client/src/components/Form/FormDisplay.vue
+++ b/client/src/components/Form/FormDisplay.vue
@@ -97,10 +97,15 @@ export default {
                 if (!input_id || !input_def || !input_field || input_def.step_linked) {
                     continue;
                 }
-                if (input_value && input_value.values && input_value.values.length == 0 && !input_def.optional) {
+                if (
+                    input_value &&
+                    Array.isArray(input_value.values) &&
+                    input_value.values.length == 0 &&
+                    !input_def.optional
+                ) {
                     return [input_id, "Please provide data for this input."];
                 }
-                if (!input_value && !input_def.optional && input_def.type != "hidden") {
+                if (input_value == null && !input_def.optional && input_def.type != "hidden") {
                     return [input_id, "Please provide a value for this option."];
                 }
                 if (input_def.wp_linked && input_def.text_value == input_value) {

From 9ceb33e696e8729f7e574163cb047e19e92bf1b5 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 20 Jul 2021 11:50:36 -0400
Subject: [PATCH 039/218] Add server side validation error handling to run form
 client component

---
 .../Workflow/Run/WorkflowRunForm.vue          | 62 ++++++++++---------
 .../Workflow/Run/WorkflowRunToolStep.vue      |  5 ++
 2 files changed, 37 insertions(+), 30 deletions(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 945f5803157..420be9fb3f7 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -6,7 +6,7 @@
                 id="run-workflow"
                 class="float-right"
                 title="Run Workflow"
-                :wait="disableExecution"
+                :wait="showExecuting"
                 @onClick="onExecute"
             />
         </div>
@@ -36,6 +36,7 @@
                 :model="step"
                 :step-data="stepData"
                 :validation-scroll-to="getValidationScrollTo(step.index)"
+                :validation-errors="getValidationErrors(step.index)"
                 :wp-data="wpData"
                 @onChange="onToolStepInputs"
                 @onValidation="onValidation"
@@ -76,10 +77,11 @@ export default {
     },
     data() {
         return {
-            disableExecution: false,
+            showExecuting: false,
             stepData: {},
-            stepValidation: {},
+            stepValidations: {},
             stepScrollTo: {},
+            stepErrors: {},
             wpData: {},
             historyData: {},
             cacheData: {},
@@ -154,10 +156,16 @@ export default {
     methods: {
         getValidationScrollTo(stepId) {
             if (this.stepScrollTo.stepId == stepId) {
-                return this.stepScrollTo.stepValidation;
+                return this.stepScrollTo.details;
             }
             return [];
         },
+        getValidationErrors(stepId) {
+            if (this.stepErrors.stepId == stepId) {
+                return this.stepErrors.details;
+            }
+            return {};
+        },
         onDefaultStepInputs(stepId, data) {
             this.stepData[stepId] = data;
             this.stepData = Object.assign({}, this.stepData);
@@ -178,14 +186,14 @@ export default {
             this.cacheData = data;
         },
         onValidation(stepId, validation) {
-            this.stepValidation[stepId] = validation;
+            this.stepValidations[stepId] = validation;
         },
         onExecute() {
-            for (const [stepId, stepValidation] of Object.entries(this.stepValidation)) {
+            for (const [stepId, stepValidation] of Object.entries(this.stepValidations)) {
                 if (stepValidation) {
                     this.stepScrollTo = {
                         stepId: stepId,
-                        stepValidation: stepValidation.slice(),
+                        details: stepValidation.slice(),
                     };
                     return;
                 }
@@ -208,37 +216,31 @@ export default {
             };
 
             console.debug("WorkflowRunForm::onExecute()", "Ready for submission.", jobDef);
-            this.disableExecution = true;
+            this.showExecuting = true;
             invokeWorkflow(this.model.workflowId, jobDef)
                 .then((invocations) => {
                     console.debug("WorkflowRunForm::onExecute()", "Submission successful.", invocations);
-                    this.disableExecution = false;
+                    this.showExecuting = false;
                     this.$emit("submissionSuccess", invocations);
                 })
-                .catch((response) => {
-                    // TODO: Is this the same response as the Utils post would
-                    // have had?
-                    console.debug("WorkflowRunForm::onExecute()", "Submission failed.", response);
-                    /*var input_found = false;
-                    if (response && response.err_data) {
-                        for (var i in this.forms) {
-                            var form = this.forms[i];
-                            var step_related_errors = response.err_data[form.model.get("step_index")];
-                            if (step_related_errors) {
-                                var error_messages = form.data.matchResponse(step_related_errors);
-                                for (var input_id in error_messages) {
-                                    form.highlight(input_id, error_messages[input_id]);
-                                    input_found = true;
-                                    break;
-                                }
+                .catch((e) => {
+                    console.debug("WorkflowRunForm::onExecute()", "Submission failed.", e);
+                    this.showExecuting = false;
+                    const errorData = e && e.response && e.response.data && e.response.data.err_data;
+                    if (errorData) {
+                        for (const stepId in errorData) {
+                            const stepError = errorData[stepId];
+                            if (stepError) {
+                                this.stepError = {
+                                    stepId: stepId,
+                                    details: stepError,
+                                };
+                                return;
                             }
                         }
+                    } else {
+                        this.$emit("submissionError", response);
                     }
-                    if (!input_found) {
-                        this.submissionErrorModal(jobDef, response);
-                    }*/
-                    this.$emit("submissionError", response);
-                    this.disableExecution = false;
                 });
         },
         toArray(obj) {
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index 2f92939a3ed..a2e0f7f25b8 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -8,6 +8,7 @@
                     :form-config="formConfig"
                     :replace-params="replaceParams"
                     :validation-scroll-to="validationScrollTo"
+                    :validation-errors="validationErrors"
                     @onChange="onChange"
                     @onValidation="onValidation"
                 />
@@ -47,6 +48,10 @@ export default {
             type: Array,
             required: true,
         },
+        validationErrors: {
+            type: Object,
+            default: null,
+        },
     },
     data() {
         return {

From 28a374f8b9360b8640b50a3f2722b42294185763 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 20 Jul 2021 12:23:06 -0400
Subject: [PATCH 040/218] Unify handling of client and server side validation

---
 client/src/components/Form/FormDisplay.vue    | 25 ++++++-------------
 client/src/components/Tool/ToolForm.vue       |  4 +--
 .../Workflow/Run/WorkflowRunForm.vue          | 16 +++---------
 .../Workflow/Run/WorkflowRunToolStep.vue      |  5 ----
 4 files changed, 14 insertions(+), 36 deletions(-)

diff --git a/client/src/components/Form/FormDisplay.vue b/client/src/components/Form/FormDisplay.vue
index cb813858ad4..4708451b6fc 100644
--- a/client/src/components/Form/FormDisplay.vue
+++ b/client/src/components/Form/FormDisplay.vue
@@ -32,10 +32,6 @@ export default {
             type: Array,
             default: null,
         },
-        validationErrors: {
-            type: Object,
-            default: null,
-        },
         formConfig: {
             type: Object,
             default: null,
@@ -61,12 +57,6 @@ export default {
             this.onHighlight(this.validation, true);
             this.$emit("onValidation", this.validation);
         },
-        validationErrors() {
-            const matchedErrors = Object.entries(this.form.data.matchResponse(this.validationErrors));
-            if (matchedErrors.length > 0) {
-                this.onHighlight(matchedErrors[0]);
-            }
-        },
         formConfig() {
             this.$nextTick(() => {
                 this.form.update(this.formConfig);
@@ -103,18 +93,18 @@ export default {
                     input_value.values.length == 0 &&
                     !input_def.optional
                 ) {
-                    return [input_id, "Please provide data for this input."];
+                    return [job_input_id, "Please provide data for this input."];
                 }
                 if (input_value == null && !input_def.optional && input_def.type != "hidden") {
-                    return [input_id, "Please provide a value for this option."];
+                    return [job_input_id, "Please provide a value for this option."];
                 }
                 if (input_def.wp_linked && input_def.text_value == input_value) {
-                    return [input_id, "Please provide a value for this workflow parameter."];
+                    return [job_input_id, "Please provide a value for this workflow parameter."];
                 }
                 if (input_field.validate) {
                     const message = input_field.validate();
                     if (message) {
-                        return [input_id, message];
+                        return [job_input_id, message];
                     }
                 }
                 if (input_value && input_value.batch) {
@@ -125,7 +115,7 @@ export default {
                             batch_src = src;
                         } else if (batch_src !== src) {
                             return [
-                                input_id,
+                                job_input_id,
                                 "Please select either dataset or dataset list fields for all batch mode fields.",
                             ];
                         }
@@ -134,7 +124,7 @@ export default {
                         batch_n = n;
                     } else if (batch_n !== n) {
                         return [
-                            input_id,
+                            job_input_id,
                             `Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>${n}</b> selection(s) while a previous field contains <b>${batch_n}</b>.`,
                         ];
                     }
@@ -183,7 +173,8 @@ export default {
         onHighlight(validation, silent = false) {
             this.form.trigger("reset");
             if (validation && validation.length == 2) {
-                this.form.highlight(validation[0], validation[1], silent);
+                const input_id = this.form.data.match(validation[0]);
+                this.form.highlight(input_id, validation[1], silent);
             }
         },
     },
diff --git a/client/src/components/Tool/ToolForm.vue b/client/src/components/Tool/ToolForm.vue
index 29f5de66e28..47865f9cca7 100644
--- a/client/src/components/Tool/ToolForm.vue
+++ b/client/src/components/Tool/ToolForm.vue
@@ -42,7 +42,6 @@
                             <FormDisplay
                                 :id="formConfig.id"
                                 :inputs="inputs"
-                                :validation-errors="validationErrors"
                                 :validation-scroll-to="validationScrollTo"
                                 :form-config="formConfig"
                                 @onChange="onChange"
@@ -301,7 +300,8 @@ export default {
                     this.showExecuting = false;
                     const errorData = e && e.response && e.response.data && e.response.data.err_data;
                     if (errorData) {
-                        this.validationErrors = errorData;
+                        const errorEntries = Object.entries(errorData);
+                        this.validationScrollTo = errorEntries[0];
                     } else {
                         this.showError = true;
                         this.showForm = false;
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 420be9fb3f7..75c04be4970 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -36,7 +36,6 @@
                 :model="step"
                 :step-data="stepData"
                 :validation-scroll-to="getValidationScrollTo(step.index)"
-                :validation-errors="getValidationErrors(step.index)"
                 :wp-data="wpData"
                 @onChange="onToolStepInputs"
                 @onValidation="onValidation"
@@ -81,7 +80,6 @@ export default {
             stepData: {},
             stepValidations: {},
             stepScrollTo: {},
-            stepErrors: {},
             wpData: {},
             historyData: {},
             cacheData: {},
@@ -160,12 +158,6 @@ export default {
             }
             return [];
         },
-        getValidationErrors(stepId) {
-            if (this.stepErrors.stepId == stepId) {
-                return this.stepErrors.details;
-            }
-            return {};
-        },
         onDefaultStepInputs(stepId, data) {
             this.stepData[stepId] = data;
             this.stepData = Object.assign({}, this.stepData);
@@ -228,12 +220,12 @@ export default {
                     this.showExecuting = false;
                     const errorData = e && e.response && e.response.data && e.response.data.err_data;
                     if (errorData) {
-                        for (const stepId in errorData) {
-                            const stepError = errorData[stepId];
+                        for (const [stepId, stepError] of Object.entries(errorData)) {
                             if (stepError) {
-                                this.stepError = {
+                                const errorEntries = Object.entries(stepError);
+                                this.stepScrollTo = {
                                     stepId: stepId,
-                                    details: stepError,
+                                    details: errorEntries[0],
                                 };
                                 return;
                             }
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index a2e0f7f25b8..2f92939a3ed 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -8,7 +8,6 @@
                     :form-config="formConfig"
                     :replace-params="replaceParams"
                     :validation-scroll-to="validationScrollTo"
-                    :validation-errors="validationErrors"
                     @onChange="onChange"
                     @onValidation="onValidation"
                 />
@@ -48,10 +47,6 @@ export default {
             type: Array,
             required: true,
         },
-        validationErrors: {
-            type: Object,
-            default: null,
-        },
     },
     data() {
         return {

From 676cae5d44360aa456a6010cd7472058c15a111d Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 20 Jul 2021 13:05:58 -0400
Subject: [PATCH 041/218] Catch potential errors in server response formatting

---
 client/src/components/Tool/ToolForm.vue       |  9 +++++--
 .../Workflow/Run/WorkflowRunForm.vue          | 27 +++++++++++--------
 2 files changed, 23 insertions(+), 13 deletions(-)

diff --git a/client/src/components/Tool/ToolForm.vue b/client/src/components/Tool/ToolForm.vue
index 47865f9cca7..558848a0fc4 100644
--- a/client/src/components/Tool/ToolForm.vue
+++ b/client/src/components/Tool/ToolForm.vue
@@ -298,11 +298,16 @@ export default {
                 },
                 (e) => {
                     this.showExecuting = false;
+                    let genericError = true;
                     const errorData = e && e.response && e.response.data && e.response.data.err_data;
                     if (errorData) {
                         const errorEntries = Object.entries(errorData);
-                        this.validationScrollTo = errorEntries[0];
-                    } else {
+                        if (errorEntries.length > 0) {
+                            this.validationScrollTo = errorEntries[0];
+                            genericError = false;
+                        }
+                    }
+                    if (genericError) {
                         this.showError = true;
                         this.showForm = false;
                         this.errorTitle = "Job submission failed";
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 75c04be4970..a057a6795a1 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -154,7 +154,7 @@ export default {
     methods: {
         getValidationScrollTo(stepId) {
             if (this.stepScrollTo.stepId == stepId) {
-                return this.stepScrollTo.details;
+                return this.stepScrollTo.stepError;
             }
             return [];
         },
@@ -185,7 +185,7 @@ export default {
                 if (stepValidation) {
                     this.stepScrollTo = {
                         stepId: stepId,
-                        details: stepValidation.slice(),
+                        stepError: stepValidation.slice(),
                     };
                     return;
                 }
@@ -220,15 +220,20 @@ export default {
                     this.showExecuting = false;
                     const errorData = e && e.response && e.response.data && e.response.data.err_data;
                     if (errorData) {
-                        for (const [stepId, stepError] of Object.entries(errorData)) {
-                            if (stepError) {
-                                const errorEntries = Object.entries(stepError);
-                                this.stepScrollTo = {
-                                    stepId: stepId,
-                                    details: errorEntries[0],
-                                };
-                                return;
-                            }
+                        try {
+                            const errorEntries = Object.entries(errorData);
+                            this.stepScrollTo = {
+                                stepId: errorEntries[0][0],
+                                stepError: Object.entries(errorEntries[0][1])[0],
+                            };
+                        } catch (e) {
+                            console.debug(
+                                e,
+                                "WorkflowRunForm::onExecute()",
+                                "Invalid server error response.",
+                                errorData
+                            );
+                            this.$emit("submissionError", response);
                         }
                     } else {
                         this.$emit("submissionError", response);

From d22de0cf9aa17bc58b33431d279e3c7ce3f9a1cc Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 20 Jul 2021 13:22:21 -0400
Subject: [PATCH 042/218] Fix error parameter naming

---
 client/src/components/Workflow/Run/WorkflowRunForm.vue | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index a057a6795a1..37885311f9c 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -226,17 +226,17 @@ export default {
                                 stepId: errorEntries[0][0],
                                 stepError: Object.entries(errorEntries[0][1])[0],
                             };
-                        } catch (e) {
+                        } catch (errorFormatting) {
                             console.debug(
-                                e,
+                                errorFormatting,
                                 "WorkflowRunForm::onExecute()",
-                                "Invalid server error response.",
+                                "Invalid server error response format.",
                                 errorData
                             );
-                            this.$emit("submissionError", response);
+                            this.$emit("submissionError", e);
                         }
                     } else {
-                        this.$emit("submissionError", response);
+                        this.$emit("submissionError", e);
                     }
                 });
         },

From 87b2c5db8282c9fcb55d9eb4b6d3e763c3e249d1 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 20 Jul 2021 14:19:25 -0400
Subject: [PATCH 043/218] Remove unnecessary jquery usage in form utilities

---
 client/src/components/Form/utilities.js        | 4 +++-
 client/src/components/Workflow/Run/model.js    | 6 +++---
 client/src/components/Workflow/Run/services.js | 2 +-
 3 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/client/src/components/Form/utilities.js b/client/src/components/Form/utilities.js
index 5c863cda8aa..cac83e9ff82 100644
--- a/client/src/components/Form/utilities.js
+++ b/client/src/components/Form/utilities.js
@@ -1,9 +1,11 @@
+import _ from "underscore";
+
 /** Visits tool inputs
  * @param{dict}   inputs    - Nested dictionary of input elements
  * @param{dict}   callback  - Called with the mapped dictionary object and corresponding model node
  */
 export var visitInputs = (inputs, callback, prefix, context) => {
-    context = $.extend({}, context);
+    context = Object.assign({}, context);
     _.each(inputs, (input) => {
         if (input && input.type && input.name) {
             context[input.name] = input;
diff --git a/client/src/components/Workflow/Run/model.js b/client/src/components/Workflow/Run/model.js
index c0b66ec5ab5..a9c4bbc447b 100644
--- a/client/src/components/Workflow/Run/model.js
+++ b/client/src/components/Workflow/Run/model.js
@@ -1,6 +1,6 @@
 import _ from "underscore";
 
-import FormData from "mvc/form/form-data";
+import { visitInputs } from "components/Form/utilities";
 import WorkflowIcons from "components/Workflow/icons";
 import Utils from "utils/utils";
 
@@ -73,7 +73,7 @@ export class WorkflowRunModel {
 
         // build linear index of step input pairs
         _.each(this.steps, (step, i) => {
-            FormData.visitInputs(step.inputs, (input, name) => {
+            visitInputs(step.inputs, (input, name) => {
                 this.parms[i][name] = input;
             });
         });
@@ -159,7 +159,7 @@ export class WorkflowRunModel {
         _.each(this.steps, (step, i) => {
             if (step.step_type == "tool") {
                 var data_resolved = true;
-                FormData.visitInputs(step.inputs, (input, name, context) => {
+                visitInputs(step.inputs, (input, name, context) => {
                     var is_runtime_value = input.value && input.value.__class__ == "RuntimeValue";
                     var is_data_input = ["data", "data_collection"].indexOf(input.type) != -1;
                     var data_ref = context[input.data_ref];
diff --git a/client/src/components/Workflow/Run/services.js b/client/src/components/Workflow/Run/services.js
index a70a1c342ec..5ae80968a0a 100644
--- a/client/src/components/Workflow/Run/services.js
+++ b/client/src/components/Workflow/Run/services.js
@@ -41,7 +41,7 @@ export async function getTool(toolId, toolVersion, toolInputs) {
     const requestData = {
         tool_id: toolId,
         tool_version: toolVersion,
-        inputs: $.extend(true, {}, toolInputs),
+        inputs: JSON.parse(JSON.stringify(toolInputs)),
     };
     try {
         const { data } = await axios.post(`${getAppRoot()}api/tools/${toolId}/build`, requestData);

From 9c1046559e5b1b53141f81cd502396d8d0740061 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 20 Jul 2021 16:42:40 -0400
Subject: [PATCH 044/218] Remove unused import in form component, add step
 labels for selenium tests

---
 client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue | 2 +-
 client/src/components/Workflow/Run/WorkflowRunToolStep.vue    | 2 +-
 client/src/mvc/form/form-data.js                              | 1 -
 3 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
index d478e40290c..5f08564525f 100644
--- a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
@@ -1,5 +1,5 @@
 <template>
-    <div>
+    <div :step-label="model.step_label">
         <FormCard :title="model.fixed_title" :icon="icon" :collapsible="true" :collapsed.sync="collapsed">
             <template v-slot:body>
                 <FormDisplay
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index 2f92939a3ed..15b817a1396 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -1,5 +1,5 @@
 <template>
-    <div>
+    <div :step-label="model.step_label">
         <FormCard :title="title" icon="fa-wrench" :collapsible="true" :collapsed.sync="collapsed">
             <template v-slot:body>
                 <FormMessage :message="errorText" variant="danger" :persistent="true" />
diff --git a/client/src/mvc/form/form-data.js b/client/src/mvc/form/form-data.js
index 12c7848fb7c..ae7f5732d6a 100644
--- a/client/src/mvc/form/form-data.js
+++ b/client/src/mvc/form/form-data.js
@@ -1,4 +1,3 @@
-import _ from "underscore";
 import $ from "jquery";
 import Backbone from "backbone";
 import { matchCase, visitInputs } from "components/Form/utilities";

From c9b2627b1d5227ae9b91eeeffa0a0cc3be415a17 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 20 Jul 2021 16:48:57 -0400
Subject: [PATCH 045/218] Remove unused global galaxy object in default
 workflow step component

---
 client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue | 1 -
 1 file changed, 1 deletion(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
index 5f08564525f..215b05ee3ee 100644
--- a/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
@@ -14,7 +14,6 @@
 </template>
 
 <script>
-import { getGalaxyInstance } from "app";
 import WorkflowIcons from "components/Workflow/icons";
 import FormDisplay from "components/Form/FormDisplay";
 import FormCard from "components/Form/FormCard";

From 497bcfdfc1d062ec4593e1f42d9a00f6266289b8 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 20 Jul 2021 17:20:26 -0400
Subject: [PATCH 046/218] Fix linting, place use job cache preference into
 utilities, use user provider

---
 client/src/components/Tool/ToolForm.vue       |  10 +-
 client/src/components/Tool/utilities.js       |  11 ++
 .../Workflow/Run/WorkflowRunForm.vue          | 118 +++++++++---------
 .../Workflow/Run/WorkflowRunToolStep.vue      |   2 +-
 4 files changed, 71 insertions(+), 70 deletions(-)

diff --git a/client/src/components/Tool/ToolForm.vue b/client/src/components/Tool/ToolForm.vue
index 558848a0fc4..79261cf89ec 100644
--- a/client/src/components/Tool/ToolForm.vue
+++ b/client/src/components/Tool/ToolForm.vue
@@ -92,6 +92,7 @@
 import Scroller from "vue-scrollto";
 import { getGalaxyInstance } from "app";
 import { getToolFormData, updateToolFormData, submitJob } from "./services";
+import { reuseCachedJobs } from "./utilities";
 import ToolCard from "./ToolCard";
 import ButtonSpinner from "components/Common/ButtonSpinner";
 import CurrentUser from "components/providers/CurrentUser";
@@ -207,14 +208,7 @@ export default {
             return config.server_mail_configured && !user.isAnonymous;
         },
         reuseAllowed(user) {
-            if (user.preferences && "extra_user_preferences" in user.preferences) {
-                const extra_user_preferences = JSON.parse(user.preferences.extra_user_preferences);
-                const keyCached = "use_cached_job|use_cached_job_checkbox";
-                const hasCachedJobs = keyCached in extra_user_preferences;
-                return hasCachedJobs ? extra_user_preferences[keyCached] : false;
-            } else {
-                return false;
-            }
+            return reuseCachedJobs(user.preferences);
         },
         onValidation(validationInternal) {
             this.validationInternal = validationInternal;
diff --git a/client/src/components/Tool/utilities.js b/client/src/components/Tool/utilities.js
index d0d4e736c5b..5100338a473 100644
--- a/client/src/components/Tool/utilities.js
+++ b/client/src/components/Tool/utilities.js
@@ -12,3 +12,14 @@ export function downloadTool(toolId) {
 export function openLink(url) {
     window.open(url);
 }
+
+export function reuseCachedJobs(userPreferences) {
+    if (userPreferences && "extra_user_preferences" in userPreferences) {
+        const extra_user_preferences = JSON.parse(userPreferences.extra_user_preferences);
+        const keyCached = "use_cached_job|use_cached_job_checkbox";
+        const hasCachedJobs = keyCached in extra_user_preferences;
+        return hasCachedJobs ? ["true", true].includes(extra_user_preferences[keyCached]) : false;
+    } else {
+        return false;
+    }
+}
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 37885311f9c..6ffa3275d5a 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -1,67 +1,71 @@
 <template>
-    <div>
-        <div class="h4 clearfix mb-3">
-            <b>Workflow: {{ model.name }}</b>
-            <ButtonSpinner
-                id="run-workflow"
-                class="float-right"
-                title="Run Workflow"
-                :wait="showExecuting"
-                @onClick="onExecute"
-            />
+    <CurrentUser v-slot="{ user }">
+        <div>
+            <div class="h4 clearfix mb-3">
+                <b>Workflow: {{ model.name }}</b>
+                <ButtonSpinner
+                    id="run-workflow"
+                    class="float-right"
+                    title="Run Workflow"
+                    :wait="showExecuting"
+                    @onClick="onExecute"
+                />
+            </div>
+            <FormCard v-if="wpInputsAvailable" title="Workflow Parameters">
+                <template v-slot:body>
+                    <FormDisplay :inputs="wpInputs" @onChange="onWpInputs" />
+                </template>
+            </FormCard>
+            <FormCard title="History Options">
+                <template v-slot:body>
+                    <FormDisplay :inputs="historyInputs" @onChange="onHistoryInputs" />
+                </template>
+            </FormCard>
+            <FormCard v-if="cacheInputsAvailable(user)" title="Job re-use Options">
+                <template v-slot:body>
+                    <FormDisplay :inputs="cacheInputs" @onChange="onCacheInputs" />
+                </template>
+            </FormCard>
+            <FormCard v-if="resourceInputsAvailable" title="Workflow Resource Options">
+                <template v-slot:body>
+                    <FormDisplay :inputs="resourceInputs" @onChange="onResourceInputs" />
+                </template>
+            </FormCard>
+            <div v-for="step in model.steps" :key="step.index">
+                <WorkflowRunToolStep
+                    v-if="step.step_type == 'tool'"
+                    :model="step"
+                    :step-data="stepData"
+                    :validation-scroll-to="getValidationScrollTo(step.index)"
+                    :wp-data="wpData"
+                    @onChange="onToolStepInputs"
+                    @onValidation="onValidation"
+                />
+                <WorkflowRunDefaultStep
+                    v-else
+                    :model="step"
+                    :validation-scroll-to="getValidationScrollTo(step.index)"
+                    @onChange="onDefaultStepInputs"
+                    @onValidation="onValidation"
+                />
+            </div>
         </div>
-        <FormCard v-if="wpInputsAvailable" title="Workflow Parameters">
-            <template v-slot:body>
-                <FormDisplay :inputs="wpInputs" @onChange="onWpInputs" />
-            </template>
-        </FormCard>
-        <FormCard title="History Options">
-            <template v-slot:body>
-                <FormDisplay :inputs="historyInputs" @onChange="onHistoryInputs" />
-            </template>
-        </FormCard>
-        <FormCard v-if="cacheInputsAvailable" title="Job re-use Options">
-            <template v-slot:body>
-                <FormDisplay :inputs="cacheInputs" @onChange="onCacheInputs" />
-            </template>
-        </FormCard>
-        <FormCard v-if="resourceInputsAvailable" title="Workflow Resource Options">
-            <template v-slot:body>
-                <FormDisplay :inputs="resourceInputs" @onChange="onResourceInputs" />
-            </template>
-        </FormCard>
-        <div v-for="step in model.steps">
-            <WorkflowRunToolStep
-                v-if="step.step_type == 'tool'"
-                :model="step"
-                :step-data="stepData"
-                :validation-scroll-to="getValidationScrollTo(step.index)"
-                :wp-data="wpData"
-                @onChange="onToolStepInputs"
-                @onValidation="onValidation"
-            />
-            <WorkflowRunDefaultStep
-                v-else
-                :model="step"
-                :validation-scroll-to="getValidationScrollTo(step.index)"
-                @onChange="onDefaultStepInputs"
-                @onValidation="onValidation"
-            />
-        </div>
-    </div>
+    </CurrentUser>
 </template>
 
 <script>
-import { getGalaxyInstance } from "app";
+import CurrentUser from "components/providers/CurrentUser";
 import FormDisplay from "components/Form/FormDisplay";
 import FormCard from "components/Form/FormCard";
 import ButtonSpinner from "components/Common/ButtonSpinner";
 import WorkflowRunDefaultStep from "./WorkflowRunDefaultStep";
 import WorkflowRunToolStep from "./WorkflowRunToolStep";
 import { invokeWorkflow } from "./services";
+import { reuseCachedJobs } from "components/Tool/utilities";
 
 export default {
     components: {
+        CurrentUser,
         FormDisplay,
         FormCard,
         ButtonSpinner,
@@ -112,17 +116,6 @@ export default {
         };
     },
     computed: {
-        cacheInputsAvailable() {
-            const Galaxy = getGalaxyInstance();
-            var extra_user_preferences = {};
-            if (Galaxy.user.attributes.preferences && "extra_user_preferences" in Galaxy.user.attributes.preferences) {
-                extra_user_preferences = JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences);
-            }
-            return;
-            "use_cached_job|use_cached_job_checkbox" in extra_user_preferences
-                ? extra_user_preferences["use_cached_job|use_cached_job_checkbox"] === "true"
-                : false;
-        },
         cacheInputs() {
             return [
                 {
@@ -152,6 +145,9 @@ export default {
         },
     },
     methods: {
+        cacheInputsAvailable(user) {
+            return reuseCachedJobs(user.preferences);
+        },
         getValidationScrollTo(stepId) {
             if (this.stepScrollTo.stepId == stepId) {
                 return this.stepScrollTo.stepError;
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index 15b817a1396..41b440dc6d8 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -17,6 +17,7 @@
 </template>
 
 <script>
+import _ from "underscore";
 import FormDisplay from "components/Form/FormDisplay";
 import FormMessage from "components/Form/FormMessage";
 import FormCard from "components/Form/FormCard";
@@ -81,7 +82,6 @@ export default {
             visitInputs(this.model.inputs, (input, name) => {
                 params[name] = input;
             });
-            const values = this.formData;
             this.replaceParams = {};
             _.each(params, (input, name) => {
                 if (input.wp_linked || input.step_linked) {

From 545a1b5e27c898c3ea17ff4a85bc875c5dd407f4 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 20 Jul 2021 17:32:10 -0400
Subject: [PATCH 047/218] Revise handling of using cached job option

---
 client/src/components/Tool/ToolForm.vue       | 10 ++---
 client/src/components/Tool/utilities.js       |  2 +-
 .../Workflow/Run/WorkflowRunForm.vue          | 39 +++++++------------
 3 files changed, 20 insertions(+), 31 deletions(-)

diff --git a/client/src/components/Tool/ToolForm.vue b/client/src/components/Tool/ToolForm.vue
index 79261cf89ec..a88ddf01d73 100644
--- a/client/src/components/Tool/ToolForm.vue
+++ b/client/src/components/Tool/ToolForm.vue
@@ -69,7 +69,7 @@
                                 title="Attempt to re-use jobs with identical parameters?"
                                 help="This may skip executing jobs that you have already run."
                                 type="boolean"
-                                v-model="reuse"
+                                v-model="useCachedJobs"
                             />
                         </template>
                         <template v-slot:buttons>
@@ -92,7 +92,7 @@
 import Scroller from "vue-scrollto";
 import { getGalaxyInstance } from "app";
 import { getToolFormData, updateToolFormData, submitJob } from "./services";
-import { reuseCachedJobs } from "./utilities";
+import { allowCachedJobs } from "./utilities";
 import ToolCard from "./ToolCard";
 import ButtonSpinner from "components/Common/ButtonSpinner";
 import CurrentUser from "components/providers/CurrentUser";
@@ -151,7 +151,7 @@ export default {
             errorContent: null,
             messageVariant: "",
             messageText: "",
-            reuse: false,
+            useCachedJobs: false,
             email: false,
             remap: false,
             entryPoints: [],
@@ -208,7 +208,7 @@ export default {
             return config.server_mail_configured && !user.isAnonymous;
         },
         reuseAllowed(user) {
-            return reuseCachedJobs(user.preferences);
+            return allowCachedJobs(user.preferences);
         },
         onValidation(validationInternal) {
             this.validationInternal = validationInternal;
@@ -261,7 +261,7 @@ export default {
             if (this.remap) {
                 jobDef.inputs["rerun_remap_job_id"] = this.job_id;
             }
-            if (this.reuse) {
+            if (this.useCachedJobs) {
                 jobDef.inputs["use_cached_job"] = true;
             }
             console.debug("toolForm::onExecute()", jobDef);
diff --git a/client/src/components/Tool/utilities.js b/client/src/components/Tool/utilities.js
index 5100338a473..c503f61141b 100644
--- a/client/src/components/Tool/utilities.js
+++ b/client/src/components/Tool/utilities.js
@@ -13,7 +13,7 @@ export function openLink(url) {
     window.open(url);
 }
 
-export function reuseCachedJobs(userPreferences) {
+export function allowCachedJobs(userPreferences) {
     if (userPreferences && "extra_user_preferences" in userPreferences) {
         const extra_user_preferences = JSON.parse(userPreferences.extra_user_preferences);
         const keyCached = "use_cached_job|use_cached_job_checkbox";
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 6ffa3275d5a..b2ec4ffdf40 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -21,9 +21,14 @@
                     <FormDisplay :inputs="historyInputs" @onChange="onHistoryInputs" />
                 </template>
             </FormCard>
-            <FormCard v-if="cacheInputsAvailable(user)" title="Job re-use Options">
+            <FormCard v-if="reuseAllowed(user)" title="Job re-use Options">
                 <template v-slot:body>
-                    <FormDisplay :inputs="cacheInputs" @onChange="onCacheInputs" />
+                    <FormElement
+                        title="Attempt to re-use jobs with identical parameters?"
+                        help="This may skip executing jobs that you have already run."
+                        type="boolean"
+                        v-model="useCachedJobs"
+                    />
                 </template>
             </FormCard>
             <FormCard v-if="resourceInputsAvailable" title="Workflow Resource Options">
@@ -57,17 +62,19 @@
 import CurrentUser from "components/providers/CurrentUser";
 import FormDisplay from "components/Form/FormDisplay";
 import FormCard from "components/Form/FormCard";
+import FormElement from "components/Form/FormElement";
 import ButtonSpinner from "components/Common/ButtonSpinner";
 import WorkflowRunDefaultStep from "./WorkflowRunDefaultStep";
 import WorkflowRunToolStep from "./WorkflowRunToolStep";
 import { invokeWorkflow } from "./services";
-import { reuseCachedJobs } from "components/Tool/utilities";
+import { allowCachedJobs } from "components/Tool/utilities";
 
 export default {
     components: {
         CurrentUser,
         FormDisplay,
         FormCard,
+        FormElement,
         ButtonSpinner,
         WorkflowRunDefaultStep,
         WorkflowRunToolStep,
@@ -86,7 +93,7 @@ export default {
             stepScrollTo: {},
             wpData: {},
             historyData: {},
-            cacheData: {},
+            useCachedJobs: false,
             historyInputs: [
                 {
                     type: "conditional",
@@ -116,21 +123,6 @@ export default {
         };
     },
     computed: {
-        cacheInputs() {
-            return [
-                {
-                    type: "conditional",
-                    name: "use_cached_job",
-                    test_param: {
-                        name: "check",
-                        label: "Attempt to reuse jobs with identical parameters?",
-                        type: "boolean",
-                        value: "false",
-                        help: "This may skip executing jobs that you have already run.",
-                    },
-                },
-            ];
-        },
         resourceInputsAvailable() {
             return this.resourceInputs.length > 0;
         },
@@ -145,8 +137,8 @@ export default {
         },
     },
     methods: {
-        cacheInputsAvailable(user) {
-            return reuseCachedJobs(user.preferences);
+        reuseAllowed(user) {
+            return allowCachedJobs(user.preferences);
         },
         getValidationScrollTo(stepId) {
             if (this.stepScrollTo.stepId == stepId) {
@@ -170,9 +162,6 @@ export default {
         onWpInputs(data) {
             this.wpData = data;
         },
-        onCacheInputs(data) {
-            this.cacheData = data;
-        },
         onValidation(stepId, validation) {
             this.stepValidations[stepId] = validation;
         },
@@ -192,7 +181,7 @@ export default {
                 history_id: !this.historyData["new_history|name"] ? this.model.historyId : null,
                 resource_params: this.resourceData,
                 replacement_params: this.wpData,
-                use_cached_job: this.cacheData["use_cached_job|check"] === "true",
+                use_cached_job: useCachedJobs,
                 parameters: this.stepData,
                 // Tool form will submit flat maps for each parameter
                 // (e.g. "repeat_0|cond|param": "foo" instead of nested

From 5b845a263b6c767676c5c85a4de95046dbcbab3f Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 20 Jul 2021 17:52:46 -0400
Subject: [PATCH 048/218] Fix missing underscore import, fix option parsing

---
 client/src/components/Form/FormDisplay.vue             | 1 +
 client/src/components/Workflow/Run/WorkflowRunForm.vue | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/client/src/components/Form/FormDisplay.vue b/client/src/components/Form/FormDisplay.vue
index 4708451b6fc..68f4a5cafdf 100644
--- a/client/src/components/Form/FormDisplay.vue
+++ b/client/src/components/Form/FormDisplay.vue
@@ -3,6 +3,7 @@
 </template>
 
 <script>
+import _ from "underscore";
 import Form from "mvc/form/form-view";
 import { visitInputs } from "components/Form/utilities";
 
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index b2ec4ffdf40..54a343355f9 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -181,7 +181,7 @@ export default {
                 history_id: !this.historyData["new_history|name"] ? this.model.historyId : null,
                 resource_params: this.resourceData,
                 replacement_params: this.wpData,
-                use_cached_job: useCachedJobs,
+                use_cached_job: this.useCachedJobs,
                 parameters: this.stepData,
                 // Tool form will submit flat maps for each parameter
                 // (e.g. "repeat_0|cond|param": "foo" instead of nested

From 43f15d3d853568aca85c9ca3c3a09eaec4de7f71 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 20 Jul 2021 22:40:13 -0400
Subject: [PATCH 049/218] Filter connected inputs from workflow request payload

---
 .../src/components/Workflow/Run/WorkflowRunForm.vue | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 54a343355f9..d4bfc32bbe8 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -176,13 +176,24 @@ export default {
                 }
             }
 
+            const parameters = {};
+            Object.entries(this.stepData).forEach(([stepId, stepData]) => {
+                const stepDataFiltered = {};
+                Object.entries(stepData).forEach(([inputName, inputValue]) => {
+                    if (typeof inputValue !== "object" || inputValue.__class__ != "ConnectedValue") {
+                        stepDataFiltered[inputName] = inputValue;
+                    }
+                });
+                parameters[stepId] = stepDataFiltered;
+            });
+
             const jobDef = {
                 new_history_name: this.historyData["new_history|name"] ? this.historyData["new_history|name"] : null,
                 history_id: !this.historyData["new_history|name"] ? this.model.historyId : null,
                 resource_params: this.resourceData,
                 replacement_params: this.wpData,
                 use_cached_job: this.useCachedJobs,
-                parameters: this.stepData,
+                parameters: parameters,
                 // Tool form will submit flat maps for each parameter
                 // (e.g. "repeat_0|cond|param": "foo" instead of nested
                 // data structures).

From f4690f255dac13866d27c03109a7f193841b54d9 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 20 Jul 2021 23:02:32 -0400
Subject: [PATCH 050/218] Show input help for connected and collapsed inputs

---
 client/src/components/Workflow/Run/model.js |  2 +-
 client/src/mvc/form/form-input.js           | 10 +++-------
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/client/src/components/Workflow/Run/model.js b/client/src/components/Workflow/Run/model.js
index a9c4bbc447b..c425c3f1cdc 100644
--- a/client/src/components/Workflow/Run/model.js
+++ b/client/src/components/Workflow/Run/model.js
@@ -104,7 +104,7 @@ export class WorkflowRunModel {
                     if (connection) {
                         input.type = "hidden";
                         input.help = input.step_linked ? `${input.help}, ` : "";
-                        input.help += `Output dataset '${connection.output_name}' from step ${parseInt(i) + 1}`;
+                        input.help += `Connected to '${connection.output_name}' from Step ${parseInt(i) + 1}`;
                         input.step_linked = input.step_linked || [];
                         input.step_linked.push({ index: step.index, step_type: step.step_type });
                     }
diff --git a/client/src/mvc/form/form-input.js b/client/src/mvc/form/form-input.js
index a4f84d75328..14de94a9db7 100644
--- a/client/src/mvc/form/form-input.js
+++ b/client/src/mvc/form/form-input.js
@@ -201,12 +201,8 @@ export default Backbone.View.extend({
                     )
                     .append($("<span/>").addClass("ui-form-title-text"))
             )
-            .append(
-                $("<div/>")
-                    .addClass("ui-form-field")
-                    .append($("<span/>").addClass("ui-form-info form-text text-muted mt-2"))
-                    .append($("<div/>").addClass("ui-form-backdrop"))
-            )
-            .append($("<div/>").addClass("ui-form-preview"));
+            .append($("<div/>").addClass("ui-form-field").append($("<div/>").addClass("ui-form-backdrop")))
+            .append($("<div/>").addClass("ui-form-preview"))
+            .append($("<span/>").addClass("ui-form-info form-text text-muted mb-2"));
     },
 });

From ed530564040d8a2ed4104b689e7b049652838eb8 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 21 Jul 2021 00:06:11 -0400
Subject: [PATCH 051/218] Use connected value test as used in form-input

---
 client/src/components/Workflow/Run/WorkflowRunForm.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index d4bfc32bbe8..019078bee62 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -180,7 +180,7 @@ export default {
             Object.entries(this.stepData).forEach(([stepId, stepData]) => {
                 const stepDataFiltered = {};
                 Object.entries(stepData).forEach(([inputName, inputValue]) => {
-                    if (typeof inputValue !== "object" || inputValue.__class__ != "ConnectedValue") {
+                    if (JSON.stringify(inputValue) != JSON.stringify({ __class__: "ConnectedValue" })) {
                         stepDataFiltered[inputName] = inputValue;
                     }
                 });

From 7e9610f139be40d3d3fdf0355a25c4b6b009eea7 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 21 Jul 2021 00:09:54 -0400
Subject: [PATCH 052/218] Test connected values without json parsing

---
 client/src/components/Workflow/Run/WorkflowRunForm.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 019078bee62..8d7f72de26c 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -180,7 +180,7 @@ export default {
             Object.entries(this.stepData).forEach(([stepId, stepData]) => {
                 const stepDataFiltered = {};
                 Object.entries(stepData).forEach(([inputName, inputValue]) => {
-                    if (JSON.stringify(inputValue) != JSON.stringify({ __class__: "ConnectedValue" })) {
+                    if (!inputValue || typeof inputValue !== "object" || inputValue.__class__ != "ConnectedValue") {
                         stepDataFiltered[inputName] = inputValue;
                     }
                 });

From 32e7f92867f506246c0f650b7397af9900234f8b Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 21 Jul 2021 00:21:25 -0400
Subject: [PATCH 053/218] Fix job remap handling, parse history id on tool form
 data updates, use consistent option naming, fix appearance

---
 client/src/components/Form/FormCard.vue |  6 ++++--
 client/src/components/Tool/ToolCard.vue |  2 +-
 client/src/components/Tool/ToolForm.vue | 27 ++++++++++++-------------
 client/src/components/Tool/services.js  |  3 ++-
 client/src/mvc/form/form-view.js        |  1 -
 client/src/style/scss/ui.scss           | 11 +++-------
 6 files changed, 23 insertions(+), 27 deletions(-)

diff --git a/client/src/components/Form/FormCard.vue b/client/src/components/Form/FormCard.vue
index ae104920783..88fca17d454 100644
--- a/client/src/components/Form/FormCard.vue
+++ b/client/src/components/Form/FormCard.vue
@@ -9,7 +9,7 @@
                     title="Collapse/Expand"
                     variant="link"
                     size="sm"
-                    class="float-right py-0"
+                    class="float-right"
                     v-b-tooltip.hover.bottom
                     @click="onCollapse"
                 >
@@ -73,7 +73,9 @@ export default {
     },
     methods: {
         onCollapse() {
-            this.$emit("update:collapsed", !this.collapsed);
+            if (this.collapsible) {
+                this.$emit("update:collapsed", !this.collapsed);
+            }
         },
     },
 };
diff --git a/client/src/components/Tool/ToolCard.vue b/client/src/components/Tool/ToolCard.vue
index 68fa050ee22..1f06b2b9e85 100644
--- a/client/src/components/Tool/ToolCard.vue
+++ b/client/src/components/Tool/ToolCard.vue
@@ -79,7 +79,7 @@
                         <span class="fa fa-star" />
                     </b-button>
                 </div>
-                <div class="portlet-title my-1">
+                <div class="portlet-title">
                     <i class="portlet-title-icon fa mr-1 fa-wrench" style="display: inline"></i>
                     <span class="portlet-title-text">
                         <b itemprop="name">{{ title }}</b> <span itemprop="description">{{ description }}</span> (Galaxy
diff --git a/client/src/components/Tool/ToolForm.vue b/client/src/components/Tool/ToolForm.vue
index a88ddf01d73..b6b36b3cacb 100644
--- a/client/src/components/Tool/ToolForm.vue
+++ b/client/src/components/Tool/ToolForm.vue
@@ -53,7 +53,7 @@
                                 title="Email notification"
                                 help="Send an email notification when the job completes."
                                 type="boolean"
-                                v-model="email"
+                                v-model="useEmail"
                             />
                             <FormElement
                                 v-if="remapAllowed"
@@ -61,7 +61,7 @@
                                 :title="remapTitle"
                                 :help="remapHelp"
                                 type="boolean"
-                                v-model="remap"
+                                v-model="useJobRemapping"
                             />
                             <FormElement
                                 v-if="reuseAllowed(user)"
@@ -147,13 +147,14 @@ export default {
             error: null,
             formConfig: {},
             formData: {},
+            remapAllowed: false,
             errorTitle: null,
             errorContent: null,
             messageVariant: "",
             messageText: "",
             useCachedJobs: false,
-            email: false,
-            remap: false,
+            useEmail: false,
+            useJobRemapping: false,
             entryPoints: [],
             jobDef: {},
             jobResponse: {},
@@ -185,18 +186,15 @@ export default {
         inputs() {
             return this.formConfig.inputs;
         },
-        remapAllowed() {
-            return this.job_id && this.formConfig.job_remap;
-        },
         remapTitle() {
-            if (this.formConfig.job_remap === "job_produced_collection_elements") {
-                return "Replace elements in collection ?";
+            if (this.remapAllowed === "job_produced_collection_elements") {
+                return "Replace elements in collection?";
             } else {
-                return "Resume dependencies from this job ?";
+                return "Resume dependencies from this job?";
             }
         },
         remapHelp() {
-            if (this.formConfig.job_remap === "job_produced_collection_elements") {
+            if (this.remapAllowed === "job_produced_collection_elements") {
                 return "The previous run of this tool failed. Use this option to replace the failed element(s) in the dataset collection that were produced during the previous tool run.";
             } else {
                 return "The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run.";
@@ -218,7 +216,7 @@ export default {
             this.onUpdate();
         },
         onUpdate() {
-            updateToolFormData(this.formConfig.id, this.currentVersion, this.formData).then((data) => {
+            updateToolFormData(this.formConfig.id, this.currentVersion, this.history_id, this.formData).then((data) => {
                 this.formConfig = data;
             });
         },
@@ -232,6 +230,7 @@ export default {
             this.currentVersion = newVersion || this.currentVersion;
             getToolFormData(this.id, this.currentVersion, this.job_id, this.history_id).then((data) => {
                 this.formConfig = data;
+                this.remapAllowed = this.job_id && data.job_remap;
                 this.showLoading = false;
                 this.showForm = true;
                 if (newVersion) {
@@ -255,10 +254,10 @@ export default {
                     ...this.formData,
                 },
             };
-            if (this.email) {
+            if (this.useEmail) {
                 jobDef.inputs["send_email_notification"] = true;
             }
-            if (this.remap) {
+            if (this.useJobRemapping) {
                 jobDef.inputs["rerun_remap_job_id"] = this.job_id;
             }
             if (this.useCachedJobs) {
diff --git a/client/src/components/Tool/services.js b/client/src/components/Tool/services.js
index f8df815e275..ad5a5720bc8 100644
--- a/client/src/components/Tool/services.js
+++ b/client/src/components/Tool/services.js
@@ -2,11 +2,12 @@ import axios from "axios";
 import { rethrowSimple } from "utils/simple-error";
 import { getAppRoot } from "onload/loadConfig";
 
-export async function updateToolFormData(tool_id, tool_version, inputs) {
+export async function updateToolFormData(tool_id, tool_version, history_id, inputs) {
     const current_state = {
         tool_id: tool_id,
         tool_version: tool_version,
         inputs: inputs,
+        history_id: history_id,
     };
     const url = `${getAppRoot()}api/tools/${tool_id}/build`;
     try {
diff --git a/client/src/mvc/form/form-view.js b/client/src/mvc/form/form-view.js
index fe0bc26a869..93ac9c7956d 100644
--- a/client/src/mvc/form/form-view.js
+++ b/client/src/mvc/form/form-view.js
@@ -32,7 +32,6 @@ export default Backbone.View.extend({
             if (field.update) {
                 field.update(node);
                 field.trigger("change");
-                console.debug("form-view::update()", `Updating input: ${input_id}`);
             }
         });
     },
diff --git a/client/src/style/scss/ui.scss b/client/src/style/scss/ui.scss
index a752574eb50..afa56414df5 100644
--- a/client/src/style/scss/ui.scss
+++ b/client/src/style/scss/ui.scss
@@ -194,15 +194,10 @@ $ui-margin-horizontal-large: $margin-v * 2;
         @extend .rounded;
         background: $portlet-bg-color;
         border-color: transparent;
-        .portlet-title {
-            .portlet-title-text.collapsible {
-                cursor: pointer;
-                text-decoration: underline;
-            }
-        }
         .portlet-operations {
             button {
                 @extend .ml-1;
+                @extend .py-0;
             }
         }
     }
@@ -239,11 +234,11 @@ $ui-margin-horizontal-large: $margin-v * 2;
         background: $portlet-bg-color;
         @extend .rounded-0;
         border-top-right-radius: $border-radius-large !important;
-        padding: 5px;
+        @extend .py-1;
+        @extend .px-2;
     }
     > .portlet-content {
         @extend .pl-2;
-        @extend .pr-0;
     }
 }
 

From 20c83278ea2440c0078d07339867533f802e0d46 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 21 Jul 2021 03:25:42 -0400
Subject: [PATCH 054/218] Increase padding of form headers

---
 client/src/style/scss/ui.scss | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/client/src/style/scss/ui.scss b/client/src/style/scss/ui.scss
index afa56414df5..4ce0c217def 100644
--- a/client/src/style/scss/ui.scss
+++ b/client/src/style/scss/ui.scss
@@ -231,11 +231,10 @@ $ui-margin-horizontal-large: $margin-v * 2;
     border-left: solid 3px $portlet-bg-color;
     border-radius: $border-radius-large;
     .portlet-header:first-child {
-        background: $portlet-bg-color;
         @extend .rounded-0;
+        @extend .p-2;
+        background: $portlet-bg-color;
         border-top-right-radius: $border-radius-large !important;
-        @extend .py-1;
-        @extend .px-2;
     }
     > .portlet-content {
         @extend .pl-2;

From 6dad2344829e9143a8a6263c119156e7f91ec81b Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 21 Jul 2021 03:41:59 -0400
Subject: [PATCH 055/218] Restore style for sub-sections

---
 client/src/style/scss/ui.scss | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/client/src/style/scss/ui.scss b/client/src/style/scss/ui.scss
index 4ce0c217def..4e347bba16a 100644
--- a/client/src/style/scss/ui.scss
+++ b/client/src/style/scss/ui.scss
@@ -194,6 +194,12 @@ $ui-margin-horizontal-large: $margin-v * 2;
         @extend .rounded;
         background: $portlet-bg-color;
         border-color: transparent;
+        .portlet-title {
+            .portlet-title-text.collapsible {
+                cursor: pointer;
+                text-decoration: underline;
+            }
+        }
         .portlet-operations {
             button {
                 @extend .ml-1;

From dc2112af3c08a380ead6d8211c65cc3460041f2f Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 23 Jul 2021 08:01:08 -0400
Subject: [PATCH 056/218] Adjust selenium test to properly select control
 element in filter testing

---
 lib/galaxy/selenium/navigation.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index c470af05574..11fc8a5c98c 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -84,7 +84,7 @@ toolbox_filters:
   selectors:
     input:
       type: xpath
-      selector: "//span[contains(. ,'${description}')]/../div/div[@class=\"custom-control\"]"
+      selector: "//span[contains(. ,'${description}')]/../div/div/div[@class=\"custom-control\"]"
     submit: '#submit'
 
 change_user_email:

From 8f975dcd4bed66f403618223ae69b1dd5ff98395 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 23 Jul 2021 10:11:48 -0400
Subject: [PATCH 057/218] Refactor streaming to util so toolbox.base doesn't
 depend on datatype code.

---
 lib/galaxy/datatypes/sniff.py    | 32 --------------------------------
 lib/galaxy/tools/toolbox/base.py |  4 ++--
 lib/galaxy/util/__init__.py      | 32 ++++++++++++++++++++++++++++++++
 3 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py
index 2e9323b3ee0..a899be82b5c 100644
--- a/lib/galaxy/datatypes/sniff.py
+++ b/lib/galaxy/datatypes/sniff.py
@@ -61,38 +61,6 @@ def stream_url_to_file(path, file_sources=None):
         return temp_name
 
 
-def stream_to_open_named_file(stream, fd, filename, source_encoding=None, source_error='strict', target_encoding=None, target_error='strict'):
-    """Writes a stream to the provided file descriptor, returns the file name. Closes file descriptor"""
-    # signature and behavor is somewhat odd, due to backwards compatibility, but this can/should be done better
-    CHUNK_SIZE = 1048576
-    try:
-        codecs.lookup(target_encoding)
-    except Exception:
-        target_encoding = util.DEFAULT_ENCODING  # utf-8
-    use_source_encoding = source_encoding is not None
-    while True:
-        chunk = stream.read(CHUNK_SIZE)
-        if not chunk:
-            break
-        if use_source_encoding:
-            # If a source encoding is given we use it to convert to the target encoding
-            try:
-                if not isinstance(chunk, str):
-                    chunk = chunk.decode(source_encoding, source_error)
-                os.write(fd, chunk.encode(target_encoding, target_error))
-            except UnicodeDecodeError:
-                use_source_encoding = False
-                os.write(fd, chunk)
-        else:
-            # Compressed files must be encoded after they are uncompressed in the upload utility,
-            # while binary files should not be encoded at all.
-            if isinstance(chunk, str):
-                chunk = chunk.encode(target_encoding, target_error)
-            os.write(fd, chunk)
-    os.close(fd)
-    return filename
-
-
 def stream_to_file(stream, suffix='', prefix='', dir=None, text=False, **kwd):
     """Writes a stream to a temporary file, returns the temporary file's name"""
     fd, temp_name = tempfile.mkstemp(suffix=suffix, prefix=prefix, dir=dir, text=text)
diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index d99b43557d9..ce32b202369 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -10,7 +10,6 @@ from urllib.parse import urlparse
 
 from markupsafe import escape
 
-from galaxy.datatypes import sniff
 from galaxy.exceptions import (
     ConfigurationError,
     MessageException,
@@ -28,6 +27,7 @@ from galaxy.util import (
     listify,
     parse_xml,
     string_as_bool,
+    stream_to_open_named_file,
     unicodify,
 )
 from galaxy.util.bunch import Bunch
@@ -141,7 +141,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             log.debug('EDAM ontology file not present, downloading')
 
             page = urllib.request.urlopen('https://edamontology.org/EDAM.tsv')
-            sniff.stream_to_open_named_file(page, os.open(self.app.config.beta_edam_toolbox_ontology_path, os.O_WRONLY | os.O_CREAT), None, source_encoding=get_charset_from_http_headers(page.headers))
+            stream_to_open_named_file(page, os.open(self.app.config.beta_edam_toolbox_ontology_path, os.O_WRONLY | os.O_CREAT), None, source_encoding=get_charset_from_http_headers(page.headers))
 
         log.debug('Processing EDAM Terms')
         with open(self.app.config.beta_edam_toolbox_ontology_path, 'r') as handle:
diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index b4cb2253378..640ade67e7e 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -1674,6 +1674,38 @@ def download_to_file(url, dest_file_path, timeout=30, chunk_size=2 ** 20):
                 f.write(chunk)
 
 
+def stream_to_open_named_file(stream, fd, filename, source_encoding=None, source_error='strict', target_encoding=None, target_error='strict'):
+    """Writes a stream to the provided file descriptor, returns the file name. Closes file descriptor"""
+    # signature and behavor is somewhat odd, due to backwards compatibility, but this can/should be done better
+    CHUNK_SIZE = 1048576
+    try:
+        codecs.lookup(target_encoding)
+    except Exception:
+        target_encoding = util.DEFAULT_ENCODING  # utf-8
+    use_source_encoding = source_encoding is not None
+    while True:
+        chunk = stream.read(CHUNK_SIZE)
+        if not chunk:
+            break
+        if use_source_encoding:
+            # If a source encoding is given we use it to convert to the target encoding
+            try:
+                if not isinstance(chunk, str):
+                    chunk = chunk.decode(source_encoding, source_error)
+                os.write(fd, chunk.encode(target_encoding, target_error))
+            except UnicodeDecodeError:
+                use_source_encoding = False
+                os.write(fd, chunk)
+        else:
+            # Compressed files must be encoded after they are uncompressed in the upload utility,
+            # while binary files should not be encoded at all.
+            if isinstance(chunk, str):
+                chunk = chunk.encode(target_encoding, target_error)
+            os.write(fd, chunk)
+    os.close(fd)
+    return filename
+
+
 class classproperty:
 
     def __init__(self, f):

From 038045a600aad4d1b26eebd6711e9a73301e5f33 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Fri, 23 Jul 2021 14:55:54 -0400
Subject: [PATCH 058/218] Add a GDPR-friendly user purge to pgcleanup.

---
 scripts/cleanup_datasets/pgcleanup.py | 125 +++++++++++++++++++++++++-
 1 file changed, 124 insertions(+), 1 deletion(-)

diff --git a/scripts/cleanup_datasets/pgcleanup.py b/scripts/cleanup_datasets/pgcleanup.py
index 21cb488e5b1..a4498a5d438 100755
--- a/scripts/cleanup_datasets/pgcleanup.py
+++ b/scripts/cleanup_datasets/pgcleanup.py
@@ -12,6 +12,7 @@ import logging
 import os
 import string
 import sys
+import time
 from collections import namedtuple
 from functools import partial
 
@@ -105,6 +106,7 @@ class Action:
         self._debug = app.args.debug
         self._update_time = app.args.update_time
         self._force_retry = app.args.force_retry
+        self._epoch_time = str(int(time.time()))
         self._days = app.args.days
         self._config = app.config
         self._update = app._update
@@ -141,6 +143,7 @@ class Action:
         self.__log.propagate = False
         m = ('==== Log opened: %s ' % datetime.datetime.now().isoformat()).ljust(72, '=')
         self.__log.info(m)
+        self.__log.info(f'Epoch time for this action: {self._epoch_time}')
 
     def __close_log(self):
         m = ('==== Log closed: %s ' % datetime.datetime.now().isoformat()).ljust(72, '=')
@@ -188,6 +191,7 @@ class Action:
         return self._action_sql.format(
             update_time_sql=self._update_time_sql,
             force_retry_sql=self._force_retry_sql,
+            epoch_time=self._epoch_time,
         )
 
     @property
@@ -334,11 +338,13 @@ class PurgesHDAs:
         _purge_hda_dependencies_sql = self._purge_hda_dependencies_sql.format(
             update_time_sql=self._update_time_sql,
             force_retry_sql=self._force_retry_sql,
+            epoch_time=self._epoch_time,
         )
         return self._action_sql.format(
             purge_hda_dependencies_sql=_purge_hda_dependencies_sql,
             update_time_sql=self._update_time_sql,
             force_retry_sql=self._force_retry_sql,
+            epoch_time=self._epoch_time,
         )
 
 
@@ -525,6 +531,7 @@ class DeleteInactiveUsers(Action):
 class PurgeDeletedUsers(PurgesHDAs, RemovesMetadataFiles, Action):
     """
     - Mark purged all users that are older than the specified number of days.
+    - Set User.disk_usage = 0 for all users purged in this step.
     - Mark purged all Histories whose user_ids are purged in this step.
     - Mark purged all HistoryDatasetAssociations whose history_ids are purged in this step.
     - Delete all UserGroupAssociations whose user_ids are purged in this step.
@@ -655,6 +662,121 @@ class PurgeDeletedUsers(PurgesHDAs, RemovesMetadataFiles, Action):
         self.log.info('zero_disk_usage user_ids: %s', ' '.join(str(i) for i in user_ids))
 
 
+class PurgeDeletedUsersGDPR(PurgesHDAs, RemovesMetadataFiles, Action):
+    """
+    - Perform all steps in the PurgeDeletedUsers/purge_deleted_users action
+    - Obfuscate User.email and User.username for all users purged in this step.
+
+    NOTE: Your database must have the pgcrypto extension installed e.g. with:
+      CREATE EXTENSION IF NOT EXISTS pgcrypto;
+    """
+    _action_sql = """
+        WITH purged_user_ids
+          AS (     UPDATE galaxy_user
+                      SET purged = true,
+                          disk_usage = 0,
+                          email = encode(digest(email || '{epoch_time}', 'sha1'), 'hex'),
+                          username = encode(digest(username || '{epoch_time}', 'sha1'), 'hex'){update_time_sql}
+                    WHERE deleted{force_retry_sql}
+                          AND update_time < (NOW() AT TIME ZONE 'utc' - interval '%(days)s days')
+                RETURNING id),
+             deleted_uga_ids
+          AS (DELETE FROM user_group_association
+                    USING purged_user_ids
+                    WHERE user_group_association.user_id = purged_user_ids.id
+                RETURNING user_group_association.user_id AS user_id,
+                          user_group_association.id AS id),
+             deleted_ura_ids
+          AS (DELETE FROM user_role_association
+                    USING role
+                    WHERE role.id = user_role_association.role_id
+                          AND role.type != 'private'
+                          AND user_role_association.user_id IN
+                            (SELECT id
+                               FROM purged_user_ids)
+                RETURNING user_role_association.user_id AS user_id,
+                          user_role_association.id AS id),
+             deleted_ua_ids
+          AS (DELETE FROM user_address
+                    USING purged_user_ids
+                    WHERE user_address.user_id = purged_user_ids.id
+                RETURNING user_address.user_id AS user_id,
+                          user_address.id AS id),
+             user_events
+          AS (INSERT INTO cleanup_event_user_association
+                          (create_time, cleanup_event_id, user_id)
+                   SELECT NOW() AT TIME ZONE 'utc', %(event_id)s, id
+                     FROM purged_user_ids),
+             purged_history_ids
+          AS (     UPDATE history
+                      SET purged = true{update_time_sql}
+                     FROM purged_user_ids
+                    WHERE purged_user_ids.id = history.user_id
+                          AND NOT history.purged
+                RETURNING history.user_id AS user_id,
+                          history.id AS id),
+             history_events
+          AS (INSERT INTO cleanup_event_history_association
+                          (create_time, cleanup_event_id, history_id)
+                   SELECT NOW() AT TIME ZONE 'utc', %(event_id)s, id
+                     FROM purged_history_ids),
+             purged_hda_ids
+          AS (     UPDATE history_dataset_association
+                      SET purged = true, deleted = true{update_time_sql}
+                     FROM purged_history_ids
+                    WHERE purged_history_ids.id = history_dataset_association.history_id
+                          AND NOT history_dataset_association.purged
+                RETURNING history_dataset_association.history_id AS history_id,
+                          history_dataset_association.id AS id),
+             hda_events
+          AS (INSERT INTO cleanup_event_hda_association
+                          (create_time, cleanup_event_id, hda_id)
+                   SELECT NOW() AT TIME ZONE 'utc', %(event_id)s, id
+                     FROM purged_hda_ids),
+             {purge_hda_dependencies_sql}
+      SELECT purged_user_ids.id AS purged_user_id,
+             purged_user_ids.id AS zero_disk_usage_user_id,
+             purged_history_ids.id AS purged_history_id,
+             purged_hda_ids.id AS purged_hda_id,
+             deleted_metadata_file_ids.id AS deleted_metadata_file_id,
+             deleted_metadata_file_ids.object_store_id AS object_store_id,
+             deleted_icda_ids.id AS deleted_icda_id,
+             deleted_icda_ids.hda_id AS deleted_icda_hda_id,
+             deleted_uga_ids.id AS deleted_uga_id,
+             deleted_ura_ids.id AS deleted_ura_id,
+             deleted_ua_ids.id AS deleted_ua_id
+        FROM purged_user_ids
+             LEFT OUTER JOIN purged_history_ids
+                             ON purged_user_ids.id = purged_history_ids.user_id
+             LEFT OUTER JOIN purged_hda_ids
+                             ON purged_history_ids.id = purged_hda_ids.history_id
+             LEFT OUTER JOIN deleted_metadata_file_ids
+                             ON deleted_metadata_file_ids.hda_id = purged_hda_ids.id
+             LEFT OUTER JOIN deleted_icda_ids
+                             ON deleted_icda_ids.hda_parent_id = purged_hda_ids.id
+             LEFT OUTER JOIN deleted_uga_ids
+                             ON purged_user_ids.id = deleted_uga_ids.user_id
+             LEFT OUTER JOIN deleted_ura_ids
+                             ON purged_user_ids.id = deleted_ura_ids.user_id
+             LEFT OUTER JOIN deleted_ua_ids
+                             ON purged_user_ids.id = deleted_ua_ids.user_id
+    ORDER BY purged_user_ids.id
+    """
+    causals = (
+        ('purged_user_id', 'purged_history_id'),
+        ('purged_history_id', 'purged_hda_id'),
+        ('purged_hda_id', 'deleted_metadata_file_id', 'object_store_id'),
+        ('purged_hda_id', 'deleted_icda_id', 'deleted_icda_hda_id'),
+        ('purged_user_id', 'deleted_uga_id'),
+        ('purged_user_id', 'deleted_ura_id'),
+        ('purged_user_id', 'deleted_ua_id'),
+    )
+
+    @classmethod
+    def name_c(cls):
+        return 'purge_deleted_users_gdpr'
+
+
 class PurgeDeletedHDAs(PurgesHDAs, RemovesMetadataFiles, RequiresDiskUsageRecalculation, Action):
     """
     - Mark purged all HistoryDatasetAssociations currently marked deleted that are older than the
@@ -1103,7 +1225,8 @@ class Cleanup:
 
     def _execute(self, sql, args):
         cur = self.conn.cursor()
-        log.debug("SQL is: %s", cur.mogrify(sql, args))
+        sql_str = cur.mogrify(sql, args).decode('utf-8')
+        log.debug(f"SQL is: {sql_str}")
         log.info("Executing SQL")
         cur.execute(sql, args)
         log.info('Database status: %s', cur.statusmessage)

From 356ecd4281410bbbe267bdf456317ca711806b11 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 23 Jul 2021 18:21:03 -0400
Subject: [PATCH 059/218] Move options from workflow model to Vue props

---
 client/src/components/Form/FormDisplay.vue         | 14 ++++++++++++++
 .../Workflow/Run/WorkflowRunToolStep.vue           |  2 ++
 client/src/components/Workflow/Run/model.js        |  9 ---------
 3 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/client/src/components/Form/FormDisplay.vue b/client/src/components/Form/FormDisplay.vue
index 68f4a5cafdf..23f95003bef 100644
--- a/client/src/components/Form/FormDisplay.vue
+++ b/client/src/components/Form/FormDisplay.vue
@@ -17,6 +17,18 @@ export default {
             type: Array,
             required: true,
         },
+        sustainRepeats: {
+            type: Boolean,
+            default: false,
+        },
+        sustainConditionals: {
+            type: Boolean,
+            default: false,
+        },
+        hideOperations: {
+            type: Boolean,
+            default: false,
+        },
         textEnable: {
             type: String,
             default: null,
@@ -164,6 +176,8 @@ export default {
                     initial_errors: this.initialErrors,
                     text_enable: this.textEnable,
                     text_disable: this.textDisable,
+                    sustain_repeats: this.sustainRepeats,
+                    sustain_conditionals: this.sustainConditionals,
                     onchange: () => {
                         this.onChange();
                     },
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index 41b440dc6d8..76328b9cf93 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -6,6 +6,8 @@
                 <FormDisplay
                     :inputs="model.inputs"
                     :form-config="formConfig"
+                    :sustainRepeats="true"
+                    :sustainConditionals="true"
                     :replace-params="replaceParams"
                     :validation-scroll-to="validationScrollTo"
                     @onChange="onChange"
diff --git a/client/src/components/Workflow/Run/model.js b/client/src/components/Workflow/Run/model.js
index c425c3f1cdc..5219c4db584 100644
--- a/client/src/components/Workflow/Run/model.js
+++ b/client/src/components/Workflow/Run/model.js
@@ -44,20 +44,11 @@ export class WorkflowRunModel {
                     citations: null,
                     collapsible: true,
                     collapsed: i > 0 && !isDataStep(step),
-                    sustain_version: true,
-                    sustain_repeats: true,
-                    sustain_conditionals: true,
-                    narrow: true,
                     text_enable: "Edit",
                     text_disable: "Undo",
                     cls_enable: "fa fa-edit",
                     cls_disable: "fa fa-undo",
                     errors: step.messages,
-                    initial_errors: true,
-                    cls: "ui-portlet-section",
-                    hide_operations: true,
-                    needs_refresh: false,
-                    always_refresh: step.step_type != "tool",
                 },
                 step
             );

From 8f384a8197f27e02cf69840cf755c0d97a957148 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 23 Jul 2021 18:37:07 -0400
Subject: [PATCH 060/218] Hyphenate form props

---
 client/src/components/Workflow/Run/WorkflowRunToolStep.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index 76328b9cf93..5dc2fc97d56 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -6,8 +6,8 @@
                 <FormDisplay
                     :inputs="model.inputs"
                     :form-config="formConfig"
-                    :sustainRepeats="true"
-                    :sustainConditionals="true"
+                    :sustain-repeats="true"
+                    :sustain-conditionals="true"
                     :replace-params="replaceParams"
                     :validation-scroll-to="validationScrollTo"
                     @onChange="onChange"

From 2a23d8ba1df9a15fb6b34e2c32b4e7497bae29ac Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 23 Jul 2021 21:46:22 -0400
Subject: [PATCH 061/218] Add additional wait for transiently failing history
 selenium test

---
 lib/galaxy_test/selenium/test_history_panel.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy_test/selenium/test_history_panel.py b/lib/galaxy_test/selenium/test_history_panel.py
index d6008255a24..01206979646 100644
--- a/lib/galaxy_test/selenium/test_history_panel.py
+++ b/lib/galaxy_test/selenium/test_history_panel.py
@@ -187,6 +187,7 @@ class HistoryPanelTestCase(SeleniumTestCase):
         self.history_panel_ensure_showing_item_details(hid=1)
         self.history_panel_item_body_component(1, wait=True)
         self.history_panel_refresh_click()
+        self.wait_for_history()
 
         # After the refresh, verify the details are still open.
         self.sleep_for(self.wait_types.UX_TRANSITION)

From 47dc4e6d282b943b3a3e931a8544ff87bb75ca7c Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Sun, 25 Jul 2021 15:00:44 -0400
Subject: [PATCH 062/218] Correctly pass along user param from admin user
 management

---
 client/src/components/User/UserPreferencesModel.js | 13 +++++++------
 client/src/entry/analysis/AnalysisRouter.js        |  3 +--
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/client/src/components/User/UserPreferencesModel.js b/client/src/components/User/UserPreferencesModel.js
index 16e69b87847..110bfc4cbd4 100644
--- a/client/src/components/User/UserPreferencesModel.js
+++ b/client/src/components/User/UserPreferencesModel.js
@@ -1,15 +1,16 @@
 import { getGalaxyInstance } from "app";
 import _l from "utils/localization";
 
-export const getUserPreferencesModel = () => {
+export const getUserPreferencesModel = (user_id) => {
     const Galaxy = getGalaxyInstance();
     const config = Galaxy.config;
+    user_id = user_id || Galaxy.user.id;
     return {
         information: {
             title: _l("Manage Information"),
             id: "edit-preferences-information",
             description: "Edit your email, addresses and custom parameters or change your public name.",
-            url: `api/users/${Galaxy.user.id}/information/inputs`,
+            url: `api/users/${user_id}/information/inputs`,
             icon: "fa-user",
             redirect: "user",
             shouldRender: !config.use_remote_user,
@@ -19,7 +20,7 @@ export const getUserPreferencesModel = () => {
             id: "edit-preferences-password",
             description: _l("Allows you to change your login credentials."),
             icon: "fa-unlock-alt",
-            url: `api/users/${Galaxy.user.id}/password/inputs`,
+            url: `api/users/${user_id}/password/inputs`,
             submit_title: "Save Password",
             redirect: "user",
             shouldRender: !config.use_remote_user,
@@ -38,7 +39,7 @@ export const getUserPreferencesModel = () => {
             id: "edit-preferences-permissions",
             description:
                 "Grant others default access to newly created histories. Changes made here will only affect histories created after these settings have been stored.",
-            url: `api/users/${Galaxy.user.id}/permissions/inputs`,
+            url: `api/users/${user_id}/permissions/inputs`,
             icon: "fa-users",
             submit_title: "Save Permissions",
             redirect: "user",
@@ -55,7 +56,7 @@ export const getUserPreferencesModel = () => {
             title: _l("Manage API Key"),
             id: "edit-preferences-api-key",
             description: _l("Access your current API key or create a new one."),
-            url: `api/users/${Galaxy.user.id}/api_key/inputs`,
+            url: `api/users/${user_id}/api_key/inputs`,
             icon: "fa-key",
             submit_title: "Create a new Key",
             submit_icon: "fa-check",
@@ -72,7 +73,7 @@ export const getUserPreferencesModel = () => {
             title: _l("Manage Toolbox Filters"),
             id: "edit-preferences-toolbox-filters",
             description: _l("Customize your Toolbox by displaying or omitting sets of Tools."),
-            url: `api/users/${Galaxy.user.id}/toolbox_filters/inputs`,
+            url: `api/users/${user_id}/toolbox_filters/inputs`,
             icon: "fa-filter",
             submit_title: "Save Filters",
             redirect: "user",
diff --git a/client/src/entry/analysis/AnalysisRouter.js b/client/src/entry/analysis/AnalysisRouter.js
index b409c8374fc..e78327b9d62 100644
--- a/client/src/entry/analysis/AnalysisRouter.js
+++ b/client/src/entry/analysis/AnalysisRouter.js
@@ -152,8 +152,7 @@ export const getAnalysisRouter = (Galaxy) => {
 
         show_user_form: function (form_id) {
             const Galaxy = getGalaxyInstance();
-            const model = getUserPreferencesModel();
-            model.user_id = Galaxy.params.id;
+            const model = getUserPreferencesModel(Galaxy.params.id);
             this.page.display(new FormWrapper.View(_.extend(model[form_id], { active_tab: "user" })));
         },
 

From 99ede0da11978c9b1cdbbdb086e2762654429514 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Sun, 25 Jul 2021 15:01:38 -0400
Subject: [PATCH 063/218] Drop Galaxy object dependency here; use parsed params
 from router

---
 client/src/entry/analysis/AnalysisRouter.js | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/client/src/entry/analysis/AnalysisRouter.js b/client/src/entry/analysis/AnalysisRouter.js
index e78327b9d62..3ce25839b94 100644
--- a/client/src/entry/analysis/AnalysisRouter.js
+++ b/client/src/entry/analysis/AnalysisRouter.js
@@ -150,9 +150,8 @@ export const getAnalysisRouter = (Galaxy) => {
             });
         },
 
-        show_user_form: function (form_id) {
-            const Galaxy = getGalaxyInstance();
-            const model = getUserPreferencesModel(Galaxy.params.id);
+        show_user_form: function (form_id, params) {
+            const model = getUserPreferencesModel(params.id);
             this.page.display(new FormWrapper.View(_.extend(model[form_id], { active_tab: "user" })));
         },
 

From fbd2fb10ff115399c31e46e59da133f7bfe9de88 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 23 Jul 2021 10:19:56 -0400
Subject: [PATCH 064/218] Refactor base toolbox code de-coupled from app &
 config into tool_util.

This was originally decoupled by me for this purpose and this code was in galaxy-lib years ago, but it just never made it into galaxy-tool-util. This commit clears up that oversight I think.
---
 lib/galaxy/config_watchers.py                                 | 2 +-
 lib/galaxy/datatypes/sniff.py                                 | 3 +--
 lib/galaxy/tool_shed/galaxy_install/tool_migration_manager.py | 4 ++--
 lib/galaxy/{tools => tool_util}/toolbox/__init__.py           | 0
 lib/galaxy/{tools => tool_util}/toolbox/base.py               | 2 +-
 lib/galaxy/{tools => tool_util}/toolbox/filters/__init__.py   | 2 +-
 .../{tools => tool_util}/toolbox/filters/examples.py.sample   | 0
 lib/galaxy/{tools => tool_util}/toolbox/integrated_panel.py   | 0
 lib/galaxy/{tools => tool_util}/toolbox/lineages/__init__.py  | 0
 lib/galaxy/{tools => tool_util}/toolbox/lineages/factory.py   | 0
 lib/galaxy/{tools => tool_util}/toolbox/lineages/interface.py | 0
 lib/galaxy/{tools => tool_util}/toolbox/panel.py              | 0
 lib/galaxy/{tools => tool_util}/toolbox/parser.py             | 0
 lib/galaxy/{tools => tool_util}/toolbox/tags.py               | 0
 lib/galaxy/{tools => tool_util}/toolbox/watcher.py            | 0
 lib/galaxy/tools/__init__.py                                  | 2 +-
 lib/galaxy/tools/cache.py                                     | 2 +-
 lib/galaxy/tools/filters/__init__.py                          | 2 +-
 lib/galaxy/util/__init__.py                                   | 3 ++-
 lib/galaxy/util/odict.py                                      | 2 +-
 lib/galaxy/util/watcher.py                                    | 2 +-
 lib/galaxy/webapps/galaxy/api/users.py                        | 2 +-
 lib/galaxy/webapps/galaxy/config_schema.yml                   | 2 +-
 packages/app/requirements.txt                                 | 1 -
 packages/app/setup.py                                         | 3 ---
 packages/tool_util/requirements.txt                           | 1 +
 packages/tool_util/setup.py                                   | 3 +++
 test/unit/tool_util/toolbox/__init__.py                       | 0
 test/unit/{tools => tool_util/toolbox}/test_tool_panel.py     | 2 +-
 .../unit/{tools => tool_util/toolbox}/test_toolbox_filters.py | 2 +-
 test/unit/{tools => tool_util/toolbox}/test_watcher.py        | 2 +-
 test/unit/tools/conftest.py                                   | 2 +-
 32 files changed, 23 insertions(+), 23 deletions(-)
 rename lib/galaxy/{tools => tool_util}/toolbox/__init__.py (100%)
 rename lib/galaxy/{tools => tool_util}/toolbox/base.py (100%)
 rename lib/galaxy/{tools => tool_util}/toolbox/filters/__init__.py (98%)
 rename lib/galaxy/{tools => tool_util}/toolbox/filters/examples.py.sample (100%)
 rename lib/galaxy/{tools => tool_util}/toolbox/integrated_panel.py (100%)
 rename lib/galaxy/{tools => tool_util}/toolbox/lineages/__init__.py (100%)
 rename lib/galaxy/{tools => tool_util}/toolbox/lineages/factory.py (100%)
 rename lib/galaxy/{tools => tool_util}/toolbox/lineages/interface.py (100%)
 rename lib/galaxy/{tools => tool_util}/toolbox/panel.py (100%)
 rename lib/galaxy/{tools => tool_util}/toolbox/parser.py (100%)
 rename lib/galaxy/{tools => tool_util}/toolbox/tags.py (100%)
 rename lib/galaxy/{tools => tool_util}/toolbox/watcher.py (100%)
 create mode 100644 test/unit/tool_util/toolbox/__init__.py
 rename test/unit/{tools => tool_util/toolbox}/test_tool_panel.py (92%)
 rename test/unit/{tools => tool_util/toolbox}/test_toolbox_filters.py (98%)
 rename test/unit/{tools => tool_util/toolbox}/test_watcher.py (98%)

diff --git a/lib/galaxy/config_watchers.py b/lib/galaxy/config_watchers.py
index c20ed8651e5..4601319deba 100644
--- a/lib/galaxy/config_watchers.py
+++ b/lib/galaxy/config_watchers.py
@@ -3,7 +3,7 @@ from os.path import dirname
 
 from galaxy.queue_worker import job_rule_modules
 from galaxy.structured_app import StructuredApp
-from galaxy.tools.toolbox.watcher import (
+from galaxy.tool_util.toolbox.watcher import (
     get_tool_conf_watcher,
     get_tool_watcher,
 )
diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py
index a899be82b5c..e67725ce893 100644
--- a/lib/galaxy/datatypes/sniff.py
+++ b/lib/galaxy/datatypes/sniff.py
@@ -3,7 +3,6 @@ File format detector
 """
 
 import bz2
-import codecs
 import gzip
 import io
 import logging
@@ -17,7 +16,7 @@ import urllib.request
 import zipfile
 
 from galaxy import util
-from galaxy.util import compression_utils
+from galaxy.util import compression_utils, stream_to_open_named_file
 from galaxy.util.checkers import (
     check_binary,
     check_bz2,
diff --git a/lib/galaxy/tool_shed/galaxy_install/tool_migration_manager.py b/lib/galaxy/tool_shed/galaxy_install/tool_migration_manager.py
index 8e39c3fe002..f7e49548d50 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tool_migration_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tool_migration_manager.py
@@ -23,8 +23,8 @@ from galaxy.tool_shed.util.basic_util import remove_dir, strip_path
 from galaxy.tool_shed.util.hg_util import clone_repository, get_config_from_disk
 from galaxy.tool_shed.util.repository_util import create_or_update_tool_shed_repository
 from galaxy.tool_shed.util.tool_dependency_util import create_tool_dependency_objects
-from galaxy.tools.toolbox import ToolSection
-from galaxy.tools.toolbox.parser import ensure_tool_conf_item
+from galaxy.tool_util.toolbox import ToolSection
+from galaxy.tool_util.toolbox.parser import ensure_tool_conf_item
 from galaxy.util import RW_R__R__
 from galaxy.util.tool_shed import common_util
 from galaxy.util.tool_shed.xml_util import parse_xml
diff --git a/lib/galaxy/tools/toolbox/__init__.py b/lib/galaxy/tool_util/toolbox/__init__.py
similarity index 100%
rename from lib/galaxy/tools/toolbox/__init__.py
rename to lib/galaxy/tool_util/toolbox/__init__.py
diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
similarity index 100%
rename from lib/galaxy/tools/toolbox/base.py
rename to lib/galaxy/tool_util/toolbox/base.py
index ce32b202369..4728139c2ff 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -26,8 +26,8 @@ from galaxy.util import (
     get_charset_from_http_headers,
     listify,
     parse_xml,
-    string_as_bool,
     stream_to_open_named_file,
+    string_as_bool,
     unicodify,
 )
 from galaxy.util.bunch import Bunch
diff --git a/lib/galaxy/tools/toolbox/filters/__init__.py b/lib/galaxy/tool_util/toolbox/filters/__init__.py
similarity index 98%
rename from lib/galaxy/tools/toolbox/filters/__init__.py
rename to lib/galaxy/tool_util/toolbox/filters/__init__.py
index 87bb8d696a2..3bdefbc98d6 100644
--- a/lib/galaxy/tools/toolbox/filters/__init__.py
+++ b/lib/galaxy/tool_util/toolbox/filters/__init__.py
@@ -22,7 +22,7 @@ class FilterFactory:
         self.default_filters = dict(tool=[_not_hidden, _handle_authorization], section=[], label=[])
         # Add dynamic filters to these default filters.
         config = toolbox.app.config
-        self.__base_modules = listify(getattr(config, "toolbox_filter_base_modules", "galaxy.tools.filters"))
+        self.__base_modules = listify(getattr(config, "toolbox_filter_base_modules", "galaxy.tool_util.filters"))
         self.__init_filters("tool", getattr(config, "tool_filters", ""), self.default_filters)
         self.__init_filters("section", getattr(config, "tool_section_filters", ""), self.default_filters)
         self.__init_filters("label", getattr(config, "tool_label_filters", ""), self.default_filters)
diff --git a/lib/galaxy/tools/toolbox/filters/examples.py.sample b/lib/galaxy/tool_util/toolbox/filters/examples.py.sample
similarity index 100%
rename from lib/galaxy/tools/toolbox/filters/examples.py.sample
rename to lib/galaxy/tool_util/toolbox/filters/examples.py.sample
diff --git a/lib/galaxy/tools/toolbox/integrated_panel.py b/lib/galaxy/tool_util/toolbox/integrated_panel.py
similarity index 100%
rename from lib/galaxy/tools/toolbox/integrated_panel.py
rename to lib/galaxy/tool_util/toolbox/integrated_panel.py
diff --git a/lib/galaxy/tools/toolbox/lineages/__init__.py b/lib/galaxy/tool_util/toolbox/lineages/__init__.py
similarity index 100%
rename from lib/galaxy/tools/toolbox/lineages/__init__.py
rename to lib/galaxy/tool_util/toolbox/lineages/__init__.py
diff --git a/lib/galaxy/tools/toolbox/lineages/factory.py b/lib/galaxy/tool_util/toolbox/lineages/factory.py
similarity index 100%
rename from lib/galaxy/tools/toolbox/lineages/factory.py
rename to lib/galaxy/tool_util/toolbox/lineages/factory.py
diff --git a/lib/galaxy/tools/toolbox/lineages/interface.py b/lib/galaxy/tool_util/toolbox/lineages/interface.py
similarity index 100%
rename from lib/galaxy/tools/toolbox/lineages/interface.py
rename to lib/galaxy/tool_util/toolbox/lineages/interface.py
diff --git a/lib/galaxy/tools/toolbox/panel.py b/lib/galaxy/tool_util/toolbox/panel.py
similarity index 100%
rename from lib/galaxy/tools/toolbox/panel.py
rename to lib/galaxy/tool_util/toolbox/panel.py
diff --git a/lib/galaxy/tools/toolbox/parser.py b/lib/galaxy/tool_util/toolbox/parser.py
similarity index 100%
rename from lib/galaxy/tools/toolbox/parser.py
rename to lib/galaxy/tool_util/toolbox/parser.py
diff --git a/lib/galaxy/tools/toolbox/tags.py b/lib/galaxy/tool_util/toolbox/tags.py
similarity index 100%
rename from lib/galaxy/tools/toolbox/tags.py
rename to lib/galaxy/tool_util/toolbox/tags.py
diff --git a/lib/galaxy/tools/toolbox/watcher.py b/lib/galaxy/tool_util/toolbox/watcher.py
similarity index 100%
rename from lib/galaxy/tools/toolbox/watcher.py
rename to lib/galaxy/tool_util/toolbox/watcher.py
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index c6e71906154..a62ddf0e7f0 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -46,6 +46,7 @@ from galaxy.tool_util.parser import (
 )
 from galaxy.tool_util.parser.xml import XmlPageSource
 from galaxy.tool_util.provided_metadata import parse_tool_provided_metadata
+from galaxy.tool_util.toolbox import BaseGalaxyToolBox
 from galaxy.tools import expressions
 from galaxy.tools.actions import DefaultToolAction
 from galaxy.tools.actions.data_manager import DataManagerToolAction
@@ -80,7 +81,6 @@ from galaxy.tools.parameters.input_translation import ToolInputTranslator
 from galaxy.tools.parameters.meta import expand_meta_parameters
 from galaxy.tools.parameters.wrapped_json import json_wrap
 from galaxy.tools.test import parse_tests
-from galaxy.tools.toolbox import BaseGalaxyToolBox
 from galaxy.util import (
     in_directory,
     listify,
diff --git a/lib/galaxy/tools/cache.py b/lib/galaxy/tools/cache.py
index dfdde299f8c..69617e5eda5 100644
--- a/lib/galaxy/tools/cache.py
+++ b/lib/galaxy/tools/cache.py
@@ -17,7 +17,7 @@ from sqlitedict import SqliteDict
 
 from galaxy.model.tool_shed_install import ToolShedRepository
 from galaxy.structured_app import MinimalManagerApp
-from galaxy.tools.toolbox.base import ToolConfRepository
+from galaxy.tool_util.toolbox.base import ToolConfRepository
 from galaxy.util import unicodify
 from galaxy.util.hash_util import md5_hash_file
 
diff --git a/lib/galaxy/tools/filters/__init__.py b/lib/galaxy/tools/filters/__init__.py
index c984816ff30..32b2b02421b 100644
--- a/lib/galaxy/tools/filters/__init__.py
+++ b/lib/galaxy/tools/filters/__init__.py
@@ -1,5 +1,5 @@
 """Deprecated module for toolbox filters.
 
 Filters placed in this module will still work - but filters should be
-moved to lib/galaxy/tools/toolbox/filters.
+moved to lib/galaxy/tool_util/toolbox/filters.
 """
diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index 640ade67e7e..4c236fadfe7 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -4,6 +4,7 @@ Utility functions used systemwide.
 """
 
 import binascii
+import codecs
 import collections
 import errno
 import importlib
@@ -1681,7 +1682,7 @@ def stream_to_open_named_file(stream, fd, filename, source_encoding=None, source
     try:
         codecs.lookup(target_encoding)
     except Exception:
-        target_encoding = util.DEFAULT_ENCODING  # utf-8
+        target_encoding = DEFAULT_ENCODING  # utf-8
     use_source_encoding = source_encoding is not None
     while True:
         chunk = stream.read(CHUNK_SIZE)
diff --git a/lib/galaxy/util/odict.py b/lib/galaxy/util/odict.py
index b28de5642b4..ca284dfb459 100644
--- a/lib/galaxy/util/odict.py
+++ b/lib/galaxy/util/odict.py
@@ -2,7 +2,7 @@
 Ordered dictionary implementation with `insert` functionality.
 
 This is only used in one specific place in the codebase:
-    galaxy.tools.toolbox.panel
+    galaxy.tool_util.toolbox.panel
 
 Whenever possible the stdlib `collections.OrderedDict` should be used instead of
 this custom implementation.
diff --git a/lib/galaxy/util/watcher.py b/lib/galaxy/util/watcher.py
index 4c3de5ef198..1ed77c21512 100644
--- a/lib/galaxy/util/watcher.py
+++ b/lib/galaxy/util/watcher.py
@@ -1,4 +1,4 @@
-# TODO: this is largely copied from galaxy.tools.toolbox.galaxy and generalized, the tool-oriented watchers in that
+# TODO: this is largely copied from galaxy.tool_util.toolbox.galaxy and generalized, the tool-oriented watchers in that
 # module should probably be updated to use this where possible
 
 
diff --git a/lib/galaxy/webapps/galaxy/api/users.py b/lib/galaxy/webapps/galaxy/api/users.py
index 25233326d73..607e8236ca9 100644
--- a/lib/galaxy/webapps/galaxy/api/users.py
+++ b/lib/galaxy/webapps/galaxy/api/users.py
@@ -30,7 +30,7 @@ from galaxy.security.validate_user_input import (
     validate_password,
     validate_publicname
 )
-from galaxy.tools.toolbox.filters import FilterFactory
+from galaxy.tool_util.toolbox.filters import FilterFactory
 from galaxy.util import (
     docstring_trim,
     listify
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 26bb3c91639..be85ddc24ef 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -3231,7 +3231,7 @@ mapping:
 
       toolbox_filter_base_modules:
         type: str
-        default: galaxy.tools.filters,galaxy.tools.toolbox.filters
+        default: galaxy.tools.filters,galaxy.tools.toolbox.filters,galaxy.tool_util.toolbox.filters
         required: false
         desc: |
           The base module(s) that are searched for modules for toolbox filtering
diff --git a/packages/app/requirements.txt b/packages/app/requirements.txt
index c7ff5fbe1b6..4faa725a7df 100644
--- a/packages/app/requirements.txt
+++ b/packages/app/requirements.txt
@@ -14,7 +14,6 @@ gxformat2
 Mako
 sqlitedict
 svgwrite
-sortedcontainers
 Markdown
 refgenconf>=0.7.0,<0.10.0 # https://github.com/galaxyproject/galaxy/issues/11601
 Fabric3
diff --git a/packages/app/setup.py b/packages/app/setup.py
index a69668442c4..f0b961fea2a 100644
--- a/packages/app/setup.py
+++ b/packages/app/setup.py
@@ -61,9 +61,6 @@ PACKAGES = [
     'galaxy.tools.imp_exp',
     'galaxy.tools.parameters',
     'galaxy.tools.search',
-    'galaxy.tools.toolbox',
-    'galaxy.tools.toolbox.filters',
-    'galaxy.tools.toolbox.lineages',
     'galaxy.tools.util',
     'galaxy.tools.util.galaxyops',
     'galaxy.tool_shed',
diff --git a/packages/tool_util/requirements.txt b/packages/tool_util/requirements.txt
index 19aaeae66b0..f0ac0b2b776 100644
--- a/packages/tool_util/requirements.txt
+++ b/packages/tool_util/requirements.txt
@@ -1,3 +1,4 @@
 galaxy-util>=20.1.0.dev0
 galaxy-containers
 lxml
+sortedcontainers
diff --git a/packages/tool_util/setup.py b/packages/tool_util/setup.py
index d4c98ed57eb..2d3a6a349ad 100644
--- a/packages/tool_util/setup.py
+++ b/packages/tool_util/setup.py
@@ -40,6 +40,9 @@ PACKAGES = [
     'galaxy.tool_util.linters',
     'galaxy.tool_util.locations',
     'galaxy.tool_util.parser',
+    'galaxy.tool_util.toolbox',
+    'galaxy.tool_util.toolbox.filters',
+    'galaxy.tool_util.toolbox.lineages',
     'galaxy.tool_util.verify',
     'galaxy.tool_util.verify.asserts',
 ]
diff --git a/test/unit/tool_util/toolbox/__init__.py b/test/unit/tool_util/toolbox/__init__.py
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/test/unit/tools/test_tool_panel.py b/test/unit/tool_util/toolbox/test_tool_panel.py
similarity index 92%
rename from test/unit/tools/test_tool_panel.py
rename to test/unit/tool_util/toolbox/test_tool_panel.py
index c58eb8046ca..3beca3b57be 100644
--- a/test/unit/tools/test_tool_panel.py
+++ b/test/unit/tool_util/toolbox/test_tool_panel.py
@@ -1,4 +1,4 @@
-from galaxy.tools.toolbox import ToolSection
+from galaxy.tool_util.toolbox import ToolSection
 from galaxy.util import etree
 
 
diff --git a/test/unit/tools/test_toolbox_filters.py b/test/unit/tool_util/toolbox/test_toolbox_filters.py
similarity index 98%
rename from test/unit/tools/test_toolbox_filters.py
rename to test/unit/tool_util/toolbox/test_toolbox_filters.py
index f6212bf4337..55219d4f4fd 100644
--- a/test/unit/tools/test_toolbox_filters.py
+++ b/test/unit/tool_util/toolbox/test_toolbox_filters.py
@@ -1,4 +1,4 @@
-from galaxy.tools.toolbox.filters import FilterFactory
+from galaxy.tool_util.toolbox.filters import FilterFactory
 from galaxy.util.bunch import Bunch
 
 
diff --git a/test/unit/tools/test_watcher.py b/test/unit/tool_util/toolbox/test_watcher.py
similarity index 98%
rename from test/unit/tools/test_watcher.py
rename to test/unit/tool_util/toolbox/test_watcher.py
index be74e071bdf..827113c2217 100644
--- a/test/unit/tools/test_watcher.py
+++ b/test/unit/tool_util/toolbox/test_watcher.py
@@ -6,7 +6,7 @@ from shutil import rmtree
 
 import pytest
 
-from galaxy.tools.toolbox import watcher
+from galaxy.tool_util.toolbox import watcher
 from galaxy.util import bunch
 
 
diff --git a/test/unit/tools/conftest.py b/test/unit/tools/conftest.py
index ab8d702131e..4e6ff369dfb 100644
--- a/test/unit/tools/conftest.py
+++ b/test/unit/tools/conftest.py
@@ -4,8 +4,8 @@ import pytest
 
 from galaxy.model import tool_shed_install
 from galaxy.model.tool_shed_install import mapping
+from galaxy.tool_util.toolbox.base import ToolConfRepository
 from galaxy.tools.cache import ToolShedRepositoryCache
-from galaxy.tools.toolbox.base import ToolConfRepository
 from galaxy.util import bunch
 
 

From 7469d674f98e2d9b8f8a4d656399f799f1a87352 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 27 Jul 2021 00:15:37 +0100
Subject: [PATCH 065/218] Fix unit tests after toolbox code move

---
 lib/galaxy/tool_util/toolbox/filters/__init__.py             | 2 +-
 .../{tools => tool_util/toolbox}/filter_modules/__init__.py  | 0
 .../{tools => tool_util/toolbox}/filter_modules/filtermod.py | 0
 test/unit/tool_util/toolbox/test_toolbox_filters.py          | 5 +++--
 test/unit/tools/test_toolbox.py                              | 2 +-
 5 files changed, 5 insertions(+), 4 deletions(-)
 rename test/unit/{tools => tool_util/toolbox}/filter_modules/__init__.py (100%)
 rename test/unit/{tools => tool_util/toolbox}/filter_modules/filtermod.py (100%)

diff --git a/lib/galaxy/tool_util/toolbox/filters/__init__.py b/lib/galaxy/tool_util/toolbox/filters/__init__.py
index 3bdefbc98d6..922323b5733 100644
--- a/lib/galaxy/tool_util/toolbox/filters/__init__.py
+++ b/lib/galaxy/tool_util/toolbox/filters/__init__.py
@@ -22,7 +22,7 @@ class FilterFactory:
         self.default_filters = dict(tool=[_not_hidden, _handle_authorization], section=[], label=[])
         # Add dynamic filters to these default filters.
         config = toolbox.app.config
-        self.__base_modules = listify(getattr(config, "toolbox_filter_base_modules", "galaxy.tool_util.filters"))
+        self.__base_modules = listify(getattr(config, "toolbox_filter_base_modules", "galaxy.tool_util.toolbox.filters"))
         self.__init_filters("tool", getattr(config, "tool_filters", ""), self.default_filters)
         self.__init_filters("section", getattr(config, "tool_section_filters", ""), self.default_filters)
         self.__init_filters("label", getattr(config, "tool_label_filters", ""), self.default_filters)
diff --git a/test/unit/tools/filter_modules/__init__.py b/test/unit/tool_util/toolbox/filter_modules/__init__.py
similarity index 100%
rename from test/unit/tools/filter_modules/__init__.py
rename to test/unit/tool_util/toolbox/filter_modules/__init__.py
diff --git a/test/unit/tools/filter_modules/filtermod.py b/test/unit/tool_util/toolbox/filter_modules/filtermod.py
similarity index 100%
rename from test/unit/tools/filter_modules/filtermod.py
rename to test/unit/tool_util/toolbox/filter_modules/filtermod.py
diff --git a/test/unit/tool_util/toolbox/test_toolbox_filters.py b/test/unit/tool_util/toolbox/test_toolbox_filters.py
index 55219d4f4fd..a803cd2fe68 100644
--- a/test/unit/tool_util/toolbox/test_toolbox_filters.py
+++ b/test/unit/tool_util/toolbox/test_toolbox_filters.py
@@ -32,7 +32,7 @@ def test_custom_filters():
     tool_filters = filters["tool"]
     # TODO: the fact that -1 is the custom filter is an implementation
     # detail that should not be tested here.
-    assert tool_filters[-1].__doc__ == "Test Filter Tool"
+    assert tool_filters[-1].__doc__ == "Test Filter Tool", tool_filters
 
     section_filters = filters["section"]
     assert section_filters[0].__doc__ == "Test Filter Section"
@@ -50,7 +50,8 @@ def filter_factory(config_dict=None):
             tool_label_filters=["filtermod:filter_label_1", "filtermod:filter_label_2"],
         )
     config = Bunch(**config_dict)
-    config.toolbox_filter_base_modules = "galaxy.tools.filters,unit.tools.filter_modules"
+    parent_module_name = '.'.join(__name__.split('.')[:-1])
+    config.toolbox_filter_base_modules = f"galaxy.tool_util.toolbox.filters,{parent_module_name}.filter_modules"
     app = Bunch(config=config)
     toolbox = Bunch(app=app)
     return FilterFactory(toolbox)
diff --git a/test/unit/tools/test_toolbox.py b/test/unit/tools/test_toolbox.py
index 9004cfde49a..13ef949bd0f 100644
--- a/test/unit/tools/test_toolbox.py
+++ b/test/unit/tools/test_toolbox.py
@@ -15,7 +15,7 @@ from galaxy.model import tool_shed_install
 from galaxy.model.tool_shed_install import mapping
 from galaxy.tools import ToolBox
 from galaxy.tools.cache import ToolCache
-from .test_toolbox_filters import mock_trans
+from ..tool_util.toolbox.test_toolbox_filters import mock_trans
 from ..tools_support import UsesApp, UsesTools
 from ..unittest_utils.sample_data import SIMPLE_MACRO, SIMPLE_TOOL_WITH_MACRO
 

From 544903e7dde86e81ec4c3bc46d7902c2583c9ea7 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 28 Jul 2021 13:55:58 +0200
Subject: [PATCH 066/218] Allow lists and comma separated strings when
 filtering history item types

---
 lib/galaxy/webapps/galaxy/api/history_contents.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
index eb6ded8120d..0f6dfdeff2c 100644
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -141,12 +141,12 @@ class HistoryContentsIndexLegacyParams(HistoryContentsIndexLegacyParamsBase):
             "specific datasets will be provided. Also, setting this value will set `dataset_details` to `all`."
         ),
     )
-    types: Optional[str] = Field(
+    types: Optional[Union[List[HistoryContentType], str]] = Field(
         default=None,
         alias="type",  # Legacy alias
         title="Types",
         description=(
-            "A comma separated list of kinds of contents to return "
+            "A list or comma separated list of kinds of contents to return "
             "(currently just `dataset` and `dataset_collection` are available)."
         ),
     )

From 9ea3b87569b92d4b4bff52cbc7ab45a386fca928 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 28 Jul 2021 13:57:22 +0200
Subject: [PATCH 067/218] Fix model population only working on field alias

---
 lib/galaxy/schema/schema.py | 13 +++----------
 1 file changed, 3 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index b0c6f4ae6ea..8c31eb11ada 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -166,6 +166,7 @@ class Model(BaseModel):
     """Base model definition with common configuration used by all derived models."""
     class Config:
         use_enum_values = True  # when using .dict()
+        allow_population_by_field_name = True
 
 
 class UserModel(Model):
@@ -2089,11 +2090,7 @@ class DatasetPermissionAction(str, Enum):
     remove_restrictions = "remove_restrictions"
 
 
-class LibraryPermissionsPayloadBase(BaseModel):
-    class Config:
-        use_enum_values = True  # When using .dict()
-        allow_population_by_alias = True
-
+class LibraryPermissionsPayloadBase(Model):
     add_ids: Optional[RoleIdList] = Field(
         [],
         alias="add_ids[]",
@@ -2281,11 +2278,7 @@ class DatasetAssociationRoles(Model):
     )
 
 
-class UpdateDatasetPermissionsPayload(BaseModel):
-    class Config:
-        use_enum_values = True  # When using .dict()
-        allow_population_by_alias = True
-
+class UpdateDatasetPermissionsPayload(Model):
     action: Optional[DatasetPermissionAction] = Field(
         ...,
         title="Action",

From a73cf9e0d9bd42e9e28282fb355cff1344be878e Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 28 Jul 2021 14:24:23 +0200
Subject: [PATCH 068/218] Add API test for filtering history content by type

---
 lib/galaxy_test/api/test_history_contents.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/lib/galaxy_test/api/test_history_contents.py b/lib/galaxy_test/api/test_history_contents.py
index 7f349dd7f74..831c2122585 100644
--- a/lib/galaxy_test/api/test_history_contents.py
+++ b/lib/galaxy_test/api/test_history_contents.py
@@ -621,3 +621,18 @@ class HistoryContentsApiTestCase(ApiTestCase):
                 if any(c for c in update if c['history_content_type'] == 'dataset_collection' and c['populated_state'] == 'ok'):
                     return
             raise Exception(f"History content update time query did not include populated_state update for dynamic nested collection {collection_id}")
+
+    def test_index_filter_by_type(self):
+        history_id = self.dataset_populator.new_history()
+        self.dataset_populator.new_dataset(history_id)
+        self.dataset_collection_populator.create_list_in_history(history_id=history_id)
+
+        contents_response = self._get(f"histories/{history_id}/contents").json()
+        num_items = len(contents_response)
+        expected_num_collections = 1
+        expected_num_datasets = num_items - expected_num_collections
+
+        contents_response = self._get(f"histories/{history_id}/contents?types=dataset").json()
+        assert len(contents_response) == expected_num_datasets
+        contents_response = self._get(f"histories/{history_id}/contents?types=dataset_collection").json()
+        assert len(contents_response) == expected_num_collections

From e5964432e840e97924380e77313340a4c6a9323d Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 28 Jul 2021 10:40:05 -0400
Subject: [PATCH 069/218] Add history provider to run workflow form, parse
 history id to tool step build request

---
 client/src/components/Tool/ToolForm.vue       |   2 +-
 .../Workflow/Run/WorkflowRunForm.vue          | 115 +++++++++---------
 .../Workflow/Run/WorkflowRunToolStep.vue      |   6 +-
 .../src/components/Workflow/Run/services.js   |   7 +-
 4 files changed, 71 insertions(+), 59 deletions(-)

diff --git a/client/src/components/Tool/ToolForm.vue b/client/src/components/Tool/ToolForm.vue
index b6b36b3cacb..7990e82fadb 100644
--- a/client/src/components/Tool/ToolForm.vue
+++ b/client/src/components/Tool/ToolForm.vue
@@ -76,7 +76,7 @@
                             <ButtonSpinner
                                 id="execute"
                                 title="Execute"
-                                @onClick="onExecute(config, currentHistory.id)"
+                                @onClick="onExecute(config, currentHistory && currentHistory.id)"
                                 :wait="showExecuting"
                                 :tooltip="tooltip"
                             />
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 8d7f72de26c..644b4ae2417 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -1,69 +1,73 @@
 <template>
     <CurrentUser v-slot="{ user }">
-        <div>
-            <div class="h4 clearfix mb-3">
-                <b>Workflow: {{ model.name }}</b>
-                <ButtonSpinner
-                    id="run-workflow"
-                    class="float-right"
-                    title="Run Workflow"
-                    :wait="showExecuting"
-                    @onClick="onExecute"
-                />
-            </div>
-            <FormCard v-if="wpInputsAvailable" title="Workflow Parameters">
-                <template v-slot:body>
-                    <FormDisplay :inputs="wpInputs" @onChange="onWpInputs" />
-                </template>
-            </FormCard>
-            <FormCard title="History Options">
-                <template v-slot:body>
-                    <FormDisplay :inputs="historyInputs" @onChange="onHistoryInputs" />
-                </template>
-            </FormCard>
-            <FormCard v-if="reuseAllowed(user)" title="Job re-use Options">
-                <template v-slot:body>
-                    <FormElement
-                        title="Attempt to re-use jobs with identical parameters?"
-                        help="This may skip executing jobs that you have already run."
-                        type="boolean"
-                        v-model="useCachedJobs"
+        <UserHistories v-if="user" :user="user" v-slot="{ currentHistory }">
+            <div>
+                <div class="h4 clearfix mb-3">
+                    <b>Workflow: {{ model.name }}</b>
+                    <ButtonSpinner
+                        id="run-workflow"
+                        class="float-right"
+                        title="Run Workflow"
+                        :wait="showExecuting"
+                        @onClick="onExecute"
                     />
-                </template>
-            </FormCard>
-            <FormCard v-if="resourceInputsAvailable" title="Workflow Resource Options">
-                <template v-slot:body>
-                    <FormDisplay :inputs="resourceInputs" @onChange="onResourceInputs" />
-                </template>
-            </FormCard>
-            <div v-for="step in model.steps" :key="step.index">
-                <WorkflowRunToolStep
-                    v-if="step.step_type == 'tool'"
-                    :model="step"
-                    :step-data="stepData"
-                    :validation-scroll-to="getValidationScrollTo(step.index)"
-                    :wp-data="wpData"
-                    @onChange="onToolStepInputs"
-                    @onValidation="onValidation"
-                />
-                <WorkflowRunDefaultStep
-                    v-else
-                    :model="step"
-                    :validation-scroll-to="getValidationScrollTo(step.index)"
-                    @onChange="onDefaultStepInputs"
-                    @onValidation="onValidation"
-                />
+                </div>
+                <FormCard v-if="wpInputsAvailable" title="Workflow Parameters">
+                    <template v-slot:body>
+                        <FormDisplay :inputs="wpInputs" @onChange="onWpInputs" />
+                    </template>
+                </FormCard>
+                <FormCard title="History Options">
+                    <template v-slot:body>
+                        <FormDisplay :inputs="historyInputs" @onChange="onHistoryInputs" />
+                    </template>
+                </FormCard>
+                <FormCard v-if="reuseAllowed(user)" title="Job re-use Options">
+                    <template v-slot:body>
+                        <FormElement
+                            title="Attempt to re-use jobs with identical parameters?"
+                            help="This may skip executing jobs that you have already run."
+                            type="boolean"
+                            v-model="useCachedJobs"
+                        />
+                    </template>
+                </FormCard>
+                <FormCard v-if="resourceInputsAvailable" title="Workflow Resource Options">
+                    <template v-slot:body>
+                        <FormDisplay :inputs="resourceInputs" @onChange="onResourceInputs" />
+                    </template>
+                </FormCard>
+                <div v-for="step in model.steps" :key="step.index">
+                    <WorkflowRunToolStep
+                        v-if="step.step_type == 'tool'"
+                        :model="step"
+                        :step-data="stepData"
+                        :validation-scroll-to="getValidationScrollTo(step.index)"
+                        :wp-data="wpData"
+                        :history-id="currentHistory && currentHistory.id"
+                        @onChange="onToolStepInputs"
+                        @onValidation="onValidation"
+                    />
+                    <WorkflowRunDefaultStep
+                        v-else
+                        :model="step"
+                        :validation-scroll-to="getValidationScrollTo(step.index)"
+                        @onChange="onDefaultStepInputs"
+                        @onValidation="onValidation"
+                    />
+                </div>
             </div>
-        </div>
+        </UserHistories>
     </CurrentUser>
 </template>
 
 <script>
+import ButtonSpinner from "components/Common/ButtonSpinner";
 import CurrentUser from "components/providers/CurrentUser";
 import FormDisplay from "components/Form/FormDisplay";
 import FormCard from "components/Form/FormCard";
 import FormElement from "components/Form/FormElement";
-import ButtonSpinner from "components/Common/ButtonSpinner";
+import UserHistories from "components/History/providers/UserHistories";
 import WorkflowRunDefaultStep from "./WorkflowRunDefaultStep";
 import WorkflowRunToolStep from "./WorkflowRunToolStep";
 import { invokeWorkflow } from "./services";
@@ -71,11 +75,12 @@ import { allowCachedJobs } from "components/Tool/utilities";
 
 export default {
     components: {
+        ButtonSpinner,
         CurrentUser,
         FormDisplay,
         FormCard,
         FormElement,
-        ButtonSpinner,
+        UserHistories,
         WorkflowRunDefaultStep,
         WorkflowRunToolStep,
     },
diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index 5dc2fc97d56..c1f616f070d 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -50,6 +50,10 @@ export default {
             type: Array,
             required: true,
         },
+        historyId: {
+            type: String,
+            default: null,
+        },
     },
     data() {
         return {
@@ -125,7 +129,7 @@ export default {
             });
         },
         onChange(data) {
-            getTool(this.model.id, this.model.version, data).then(
+            getTool(this.model.id, this.model.version, data, this.historyId).then(
                 (formConfig) => {
                     this.formConfig = formConfig;
                 },
diff --git a/client/src/components/Workflow/Run/services.js b/client/src/components/Workflow/Run/services.js
index 5ae80968a0a..862269ce058 100644
--- a/client/src/components/Workflow/Run/services.js
+++ b/client/src/components/Workflow/Run/services.js
@@ -35,13 +35,16 @@ export async function invokeWorkflow(workflowId, invocationData) {
 /**
  * Request tool step data.
  *
- * @param {String} workflowId - (Stored?) Workflow ID to fetch data for.
+ * @param {String} toolId - Tool ID to fetch data for.
+ * @param {String} toolVersion - Corresponding tool version.
+ * @param {Object} toolInputs - Current tool state.
  */
-export async function getTool(toolId, toolVersion, toolInputs) {
+export async function getTool(toolId, toolVersion, toolInputs, historyId) {
     const requestData = {
         tool_id: toolId,
         tool_version: toolVersion,
         inputs: JSON.parse(JSON.stringify(toolInputs)),
+        history_id: historyId,
     };
     try {
         const { data } = await axios.post(`${getAppRoot()}api/tools/${toolId}/build`, requestData);

From 1be22d6bbcea469fc855857951b56530374d37a4 Mon Sep 17 00:00:00 2001
From: Aysam Guerler <aysam.guerler@gmail.com>
Date: Wed, 28 Jul 2021 10:42:36 -0400
Subject: [PATCH 070/218] Update client/src/components/Tool/ToolForm.vue

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
---
 client/src/components/Tool/ToolForm.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Tool/ToolForm.vue b/client/src/components/Tool/ToolForm.vue
index 7990e82fadb..675b93a156f 100644
--- a/client/src/components/Tool/ToolForm.vue
+++ b/client/src/components/Tool/ToolForm.vue
@@ -76,7 +76,7 @@
                             <ButtonSpinner
                                 id="execute"
                                 title="Execute"
-                                @onClick="onExecute(config, currentHistory && currentHistory.id)"
+                                @onClick="onExecute(config, currentHistory?.id)"
                                 :wait="showExecuting"
                                 :tooltip="tooltip"
                             />

From 8fb22e23937c3b44dd485c34207ac83dd38577b4 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 28 Jul 2021 10:44:08 -0400
Subject: [PATCH 071/218] Add doc line to get tool helper

---
 client/src/components/Workflow/Run/WorkflowRunForm.vue | 2 +-
 client/src/components/Workflow/Run/services.js         | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 644b4ae2417..59c494bb0bc 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -44,7 +44,7 @@
                         :step-data="stepData"
                         :validation-scroll-to="getValidationScrollTo(step.index)"
                         :wp-data="wpData"
-                        :history-id="currentHistory && currentHistory.id"
+                        :history-id="currentHistory?.id"
                         @onChange="onToolStepInputs"
                         @onValidation="onValidation"
                     />
diff --git a/client/src/components/Workflow/Run/services.js b/client/src/components/Workflow/Run/services.js
index 862269ce058..b090b20a3fb 100644
--- a/client/src/components/Workflow/Run/services.js
+++ b/client/src/components/Workflow/Run/services.js
@@ -38,6 +38,7 @@ export async function invokeWorkflow(workflowId, invocationData) {
  * @param {String} toolId - Tool ID to fetch data for.
  * @param {String} toolVersion - Corresponding tool version.
  * @param {Object} toolInputs - Current tool state.
+ * @param {Object} historyId - History ID to populate data selection fields.
  */
 export async function getTool(toolId, toolVersion, toolInputs, historyId) {
     const requestData = {

From f6d8e4b9ebf92e960fd31f1c8633e88e8294b47b Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 28 Jul 2021 10:49:51 -0400
Subject: [PATCH 072/218] Wait until history provider resolves current history
 in tool and workflow run forms

---
 client/src/components/Tool/ToolForm.vue                | 4 ++--
 client/src/components/Workflow/Run/WorkflowRunForm.vue | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/client/src/components/Tool/ToolForm.vue b/client/src/components/Tool/ToolForm.vue
index 675b93a156f..04bd7fe7209 100644
--- a/client/src/components/Tool/ToolForm.vue
+++ b/client/src/components/Tool/ToolForm.vue
@@ -2,7 +2,7 @@
     <ConfigProvider v-slot="{ config }">
         <CurrentUser v-slot="{ user }">
             <UserHistories v-if="user" :user="user" v-slot="{ currentHistory }">
-                <div>
+                <div v-if="currentHistory">
                     <LoadingSpan v-if="showLoading" message="Loading Tool" />
                     <div v-if="showEntryPoints">
                         <ToolEntryPoints v-for="job in entryPoints" :job-id="job.id" :key="job.id" />
@@ -76,7 +76,7 @@
                             <ButtonSpinner
                                 id="execute"
                                 title="Execute"
-                                @onClick="onExecute(config, currentHistory?.id)"
+                                @onClick="onExecute(config, currentHistory.id)"
                                 :wait="showExecuting"
                                 :tooltip="tooltip"
                             />
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 59c494bb0bc..5225b4d88cf 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -1,7 +1,7 @@
 <template>
     <CurrentUser v-slot="{ user }">
         <UserHistories v-if="user" :user="user" v-slot="{ currentHistory }">
-            <div>
+            <div v-if="currentHistory">
                 <div class="h4 clearfix mb-3">
                     <b>Workflow: {{ model.name }}</b>
                     <ButtonSpinner
@@ -44,7 +44,7 @@
                         :step-data="stepData"
                         :validation-scroll-to="getValidationScrollTo(step.index)"
                         :wp-data="wpData"
-                        :history-id="currentHistory?.id"
+                        :history-id="currentHistory.id"
                         @onChange="onToolStepInputs"
                         @onValidation="onValidation"
                     />

From 81b0e5371cf0b0bfab4a570b10bd7b389682fbf8 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 28 Jul 2021 11:04:50 -0400
Subject: [PATCH 073/218] Use currentHistoryId slot in tool and run workflow
 forms

---
 client/src/components/Tool/ToolForm.vue                | 6 +++---
 client/src/components/Workflow/Run/WorkflowRunForm.vue | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/client/src/components/Tool/ToolForm.vue b/client/src/components/Tool/ToolForm.vue
index 04bd7fe7209..33aadafb650 100644
--- a/client/src/components/Tool/ToolForm.vue
+++ b/client/src/components/Tool/ToolForm.vue
@@ -1,8 +1,8 @@
 <template>
     <ConfigProvider v-slot="{ config }">
         <CurrentUser v-slot="{ user }">
-            <UserHistories v-if="user" :user="user" v-slot="{ currentHistory }">
-                <div v-if="currentHistory">
+            <UserHistories v-if="user" :user="user" v-slot="{ currentHistoryId }">
+                <div v-if="currentHistoryId">
                     <LoadingSpan v-if="showLoading" message="Loading Tool" />
                     <div v-if="showEntryPoints">
                         <ToolEntryPoints v-for="job in entryPoints" :job-id="job.id" :key="job.id" />
@@ -76,7 +76,7 @@
                             <ButtonSpinner
                                 id="execute"
                                 title="Execute"
-                                @onClick="onExecute(config, currentHistory.id)"
+                                @onClick="onExecute(config, currentHistoryId)"
                                 :wait="showExecuting"
                                 :tooltip="tooltip"
                             />
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index 5225b4d88cf..212f9ec54f1 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -1,7 +1,7 @@
 <template>
     <CurrentUser v-slot="{ user }">
-        <UserHistories v-if="user" :user="user" v-slot="{ currentHistory }">
-            <div v-if="currentHistory">
+        <UserHistories v-if="user" :user="user" v-slot="{ currentHistoryId }">
+            <div v-if="currentHistoryId">
                 <div class="h4 clearfix mb-3">
                     <b>Workflow: {{ model.name }}</b>
                     <ButtonSpinner
@@ -44,7 +44,7 @@
                         :step-data="stepData"
                         :validation-scroll-to="getValidationScrollTo(step.index)"
                         :wp-data="wpData"
-                        :history-id="currentHistory.id"
+                        :history-id="currentHistoryId"
                         @onChange="onToolStepInputs"
                         @onValidation="onValidation"
                     />

From a9ced37c3dc82794811beff18418cfca8653c090 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 28 Jul 2021 11:10:49 -0400
Subject: [PATCH 074/218] Modify history provider to parse history identifier
 without accessing the history model

---
 .../components/History/providers/UserHistories/UserHistories.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/History/providers/UserHistories/UserHistories.js b/client/src/components/History/providers/UserHistories/UserHistories.js
index 56b3f761ebe..e9547e7db02 100644
--- a/client/src/components/History/providers/UserHistories/UserHistories.js
+++ b/client/src/components/History/providers/UserHistories/UserHistories.js
@@ -65,7 +65,7 @@ export default {
 
             // currently selected history object, should be a full object not just a summary
             currentHistory: this.currentHistoryModel,
-            currentHistoryId: this.currentHistoryModel?.id || null,
+            currentHistoryId: this.currentHistoryId,
 
             handlers: {
                 // Updates the history in the store without a trip to the server, in the event that a

From 1f7604c84bc77b67d48cf0143883e274dec7e0a1 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 28 Jul 2021 18:51:11 +0200
Subject: [PATCH 075/218] reword history import button text

Import from file seems outdated.
---
 lib/galaxy/selenium/navigation.yml               | 2 +-
 lib/galaxy/webapps/galaxy/controllers/history.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index 8c7b6f29617..86b5dcffe29 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -290,7 +290,7 @@ collection_builders:
 
 histories:
   labels:
-    import_button: 'Import from file'
+    import_button: 'Import history'
 
   sharing:
     selectors:
diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py
index b613d8cfdf2..610786a63c8 100644
--- a/lib/galaxy/webapps/galaxy/controllers/history.py
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -118,7 +118,7 @@ class HistoryListGrid(grids.Grid):
             key="free-text-search", visible=False, filterable="standard")
     )
     global_actions = [
-        grids.GridAction("Import from file", dict(controller="", action="histories/import"))
+        grids.GridAction("Import history", dict(controller="", action="histories/import"))
     ]
     operations = [
         grids.GridOperation("Switch", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=True),

From 02cb253f7a9bb5faf85702a754ca01034d93ef3e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 29 Jul 2021 12:59:28 +0200
Subject: [PATCH 076/218] Fix order of dataset instances

---
 lib/galaxy/model/__init__.py          |  4 ++-
 test/unit/data/test_galaxy_mapping.py | 37 +++++++++++++++++++++++++++
 2 files changed, 40 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 7a818541c37..14e50ddfe63 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -4302,17 +4302,19 @@ class DatasetCollection(Dictifiable, UsesAnnotations, RepresentById):
 
             depth_collection_type = self.collection_type
             select_from = dc.outerjoin(de, de.c.dataset_collection_id == dc.c.id)
+            order_by_columns = [de.c.element_index]
 
             while ":" in depth_collection_type:
                 child_collection = alias(DatasetCollection.table)
                 child_collection_element = alias(DatasetCollectionElement.table)
                 select_from = select_from.outerjoin(child_collection, child_collection.c.id == de.c.child_collection_id)
                 select_from = select_from.outerjoin(child_collection_element, child_collection_element.c.dataset_collection_id == child_collection.c.id)
+                order_by_columns.append(child_collection_element.c.element_index)
 
                 de = child_collection_element
                 depth_collection_type = depth_collection_type.split(":", 1)[1]
             select_from = select_from.outerjoin(hda, hda.c.id == de.c.hda_id)
-            select_stmt = select([hda]).select_from(select_from).where(dc.c.id == self.id).distinct()
+            select_stmt = select([hda]).select_from(select_from).where(dc.c.id == self.id).distinct(*order_by_columns).order_by(*order_by_columns)
             return db_session.query(HistoryDatasetAssociation).select_entity_from(select_stmt).filter(HistoryDatasetAssociation.id.isnot(None)).all()
         else:
             # Sessionless context
diff --git a/test/unit/data/test_galaxy_mapping.py b/test/unit/data/test_galaxy_mapping.py
index 12788b63ebf..ca7514de342 100644
--- a/test/unit/data/test_galaxy_mapping.py
+++ b/test/unit/data/test_galaxy_mapping.py
@@ -1,5 +1,6 @@
 import collections
 import os
+import random
 import unittest
 import uuid
 
@@ -288,6 +289,42 @@ class MappingTests(BaseModelTestCase):
         for i in range(elements):
             assert c1[i] == dces[i]
 
+    def test_dataset_instance_order(self):
+        model = self.model
+        u = model.User(email="mary@example.com", password="password")
+        h1 = model.History(name="History 1", user=u)
+        elements = []
+        list_pair = model.DatasetCollection(collection_type="list:paired")
+        for i in range(20):
+            pair = model.DatasetCollection(collection_type="pair")
+            forward = model.HistoryDatasetAssociation(extension="txt", history=h1, name=f"forward_{i}", create_dataset=True, sa_session=model.session)
+            reverse = model.HistoryDatasetAssociation(extension="bam", history=h1, name=f"reverse_{i}", create_dataset=True, sa_session=model.session)
+            dce1 = model.DatasetCollectionElement(collection=pair, element=forward, element_identifier=f"forward_{i}", element_index=1)
+            dce2 = model.DatasetCollectionElement(collection=pair, element=reverse, element_identifier=f"reverse_{i}", element_index=2)
+            to_persist = [(forward, reverse), (dce1, dce2)]
+            self.persist(pair)
+            for item in to_persist:
+                if i % 2:
+                    self.persist(item[0])
+                    self.persist(item[1])
+                else:
+                    self.persist(item[1])
+                    self.persist(item[0])
+            elements.append(model.DatasetCollectionElement(collection=list_pair, element=pair, element_index=i, element_identifier=str(i)))
+        self.persist(list_pair)
+        random.shuffle(elements)
+        for item in elements:
+            self.persist(item)
+        forward = []
+        reverse = []
+        for i, dataset_instance in enumerate(list_pair.dataset_instances):
+            if i % 2:
+                reverse.append(dataset_instance)
+            else:
+                forward.append(dataset_instance)
+        assert all(d.name == f"forward_{i}" for i, d in enumerate(forward))
+        assert all(d.name == f"reverse_{i}" for i, d in enumerate(reverse))
+
     def test_collections_in_histories(self):
         model = self.model
 

From fee4c39371ee8ae3fc0ddafc6f2876484fb5556b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 29 Jul 2021 20:03:38 +0200
Subject: [PATCH 077/218] Fix repository_update test

---
 test/integration/test_repository_operations.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/test/integration/test_repository_operations.py b/test/integration/test_repository_operations.py
index de17c8a9b56..d3a5e45bad4 100644
--- a/test/integration/test_repository_operations.py
+++ b/test/integration/test_repository_operations.py
@@ -59,7 +59,7 @@ class TestRepositoryInstallIntegrationTestCase(integration_util.IntegrationTestC
 
     def test_repository_update(self):
         response = self._install_repository(revision=REVISION_4, version="0.0.3")[0]
-        assert response['ctx_rev'] == '4'
+        assert int(response['ctx_rev']) >= 4
         repo_response = self._get("/api/tool_shed_repositories/%s" % response['id']).json()
         assert repo_response['tool_shed_status']['revision_update'] == 'False'  # that should really be a boolean
         # now checkout revision 3 and attempt an update
@@ -108,7 +108,8 @@ class TestRepositoryInstallIntegrationTestCase(integration_util.IntegrationTestC
         response = self._install_repository(revision=REVISION_4, version="0.0.3", verify_tool_absent=False)[0]
         assert response['changeset_revision'] == REVISION_4
         assert response['installed_changeset_revision'] == REVISION_3
-        assert response['ctx_rev'] == '4'
+        # should be 4 or newer
+        assert int(response['ctx_rev']) >= 4
 
     def _uninstall_repository(self):
         tool = self._get('/api/tools/collection_column_join').json()

From 8aea13ce2e61fc990149190a2b97c9a9e9385209 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 30 Jul 2021 11:18:59 +0200
Subject: [PATCH 078/218] Fix test_repository_update

for real this time.
---
 test/integration/test_repository_operations.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/test/integration/test_repository_operations.py b/test/integration/test_repository_operations.py
index d3a5e45bad4..5ba8c2ad58d 100644
--- a/test/integration/test_repository_operations.py
+++ b/test/integration/test_repository_operations.py
@@ -60,11 +60,12 @@ class TestRepositoryInstallIntegrationTestCase(integration_util.IntegrationTestC
     def test_repository_update(self):
         response = self._install_repository(revision=REVISION_4, version="0.0.3")[0]
         assert int(response['ctx_rev']) >= 4
+        latest_revision = response['changeset_revision']
         repo_response = self._get("/api/tool_shed_repositories/%s" % response['id']).json()
         assert repo_response['tool_shed_status']['revision_update'] == 'False'  # that should really be a boolean
         # now checkout revision 3 and attempt an update
         path_components = [
-            self._app.config.shed_tools_dir,
+            os.path.dirname(self._app.config.shed_tool_config_file),
             'toolshed.g2.bx.psu.edu',
             'repos',
             REPO.owner,
@@ -73,25 +74,25 @@ class TestRepositoryInstallIntegrationTestCase(integration_util.IntegrationTestC
             REPO.name
         ]
         revision_3_path = os.path.join(*path_components[:6])
-        revision_4_path = os.path.join(*path_components[:5] + [REVISION_4])
+        latest_revision_path = os.path.join(*path_components[:5] + [latest_revision])
         repository_path = os.path.join(*path_components)
         # Move repo to location expected before minor update
-        os.rename(revision_4_path, revision_3_path)
+        os.rename(latest_revision_path, revision_3_path)
         # Checkout revision 3
         hg_util.update_repository(repository_path, ctx_rev='3')
         # change repo to revision 3 in database
         model = self._app.install_model
         tsr = model.context.query(model.ToolShedRepository).first()
         assert tsr.name == REPO.name
-        assert tsr.changeset_revision == REVISION_4
-        assert tsr.ctx_rev == '4'
+        assert tsr.changeset_revision == latest_revision
+        assert int(tsr.ctx_rev) >= 4
         tsr.ctx_rev = '3'
         tsr.installed_changeset_revision = REVISION_3
         tsr.changeset_revision = REVISION_3
         model.context.flush()
         # update shed_tool_conf.xml to look like revision 3 was the installed_changeset_revision
         with open(self._app.config.shed_tool_config_file) as shed_config:
-            shed_text = shed_config.read().replace(REVISION_4, REVISION_3)
+            shed_text = shed_config.read().replace(latest_revision, REVISION_3)
         with open(self._app.config.shed_tool_config_file, 'w') as shed_config:
             shed_config.write(shed_text)
         self._get(
@@ -106,7 +107,7 @@ class TestRepositoryInstallIntegrationTestCase(integration_util.IntegrationTestC
         assert repo_response['ctx_rev'] == '3'
         # now install revision 4 (a.k.a a minor update)
         response = self._install_repository(revision=REVISION_4, version="0.0.3", verify_tool_absent=False)[0]
-        assert response['changeset_revision'] == REVISION_4
+        assert response['changeset_revision'] == latest_revision
         assert response['installed_changeset_revision'] == REVISION_3
         # should be 4 or newer
         assert int(response['ctx_rev']) >= 4

From b8cd3381f8e69ccce4ac88f76e03eea8e9c300af Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 30 Jul 2021 10:46:59 +0200
Subject: [PATCH 079/218] Add webdriver setup

How did this work before ? Preloaded webdriver ?
---
 .github/workflows/integration_selenium.yaml | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/.github/workflows/integration_selenium.yaml b/.github/workflows/integration_selenium.yaml
index 4d0e3b1d706..2bc331c14f6 100644
--- a/.github/workflows/integration_selenium.yaml
+++ b/.github/workflows/integration_selenium.yaml
@@ -2,8 +2,6 @@ name: Integration Selenium
 on: [push, pull_request]
 env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
-  GALAXY_TEST_SELENIUM_REMOTE: '1'
-  GALAXY_TEST_SELENIUM_REMOTE_PORT: "4444"
   GALAXY_SKIP_CLIENT_BUILD: '0'
   GALAXY_TEST_SELENIUM_RETRIES: 1
 jobs:
@@ -22,10 +20,6 @@ jobs:
           POSTGRES_DB: postgres
         ports:
           - 5432:5432
-      selenium:
-        image: selenium/standalone-chrome:3.141.59
-        ports:
-          - 4444:4444
     steps:
       - name: Prune unused docker image, volumes and containers
         run: docker system prune -a -f
@@ -41,6 +35,7 @@ jobs:
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - uses: nanasess/setup-chromedriver@master
       - name: Run tests
         run: './run_tests.sh -integration test/integration_selenium'
         working-directory: 'galaxy root'

From cb8d157f24380ba59652b6321d157b9d5f71b8b2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 30 Jul 2021 15:50:13 +0200
Subject: [PATCH 080/218] Fix repo test setUp / tearDown

---
 test/integration/test_repository_operations.py | 4 +++-
 test/integration/uses_shed.py                  | 6 +++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/test/integration/test_repository_operations.py b/test/integration/test_repository_operations.py
index 5ba8c2ad58d..e27193b4395 100644
--- a/test/integration/test_repository_operations.py
+++ b/test/integration/test_repository_operations.py
@@ -26,10 +26,12 @@ class TestRepositoryInstallIntegrationTestCase(integration_util.IntegrationTestC
 
     def setUp(self):
         super().setUp()
+        self.setup_shed_config()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
 
     def tearDown(self):
         self.reset_shed_tools()
+        return super().tearDown()
 
     def test_repository_installation(self):
         """
@@ -105,7 +107,7 @@ class TestRepositoryInstallIntegrationTestCase(integration_util.IntegrationTestC
         assert repo_response['tool_shed_status']['revision_update'] == 'True'
         assert repo_response['changeset_revision'] == REVISION_3
         assert repo_response['ctx_rev'] == '3'
-        # now install revision 4 (a.k.a a minor update)
+        # now install revision 4 (or newer) (a.k.a a minor update)
         response = self._install_repository(revision=REVISION_4, version="0.0.3", verify_tool_absent=False)[0]
         assert response['changeset_revision'] == latest_revision
         assert response['installed_changeset_revision'] == REVISION_3
diff --git a/test/integration/uses_shed.py b/test/integration/uses_shed.py
index f43550c3e71..8125a0fb59f 100644
--- a/test/integration/uses_shed.py
+++ b/test/integration/uses_shed.py
@@ -59,13 +59,17 @@ class UsesShed:
         config["conda_auto_install"] = True
         config["conda_prefix"] = os.environ.get('GALAXY_TEST_CONDA_PREFIX') or os.path.join(cls.conda_tmp_prefix, 'conda')
 
-    def reset_shed_tools(self):
+    def setup_shed_config(self):
         shutil.rmtree(self._app.config.shed_tools_dir, ignore_errors=True)
         os.makedirs(self._app.config.shed_tools_dir)
+        self._app.config.shed_tools_dir = self.shed_tools_dir
         with open(self._app.config.shed_tool_config_file, "w") as tool_conf_file:
             tool_conf_file.write(SHED_TOOL_CONF.substitute(shed_tools_path=self._app.config.shed_tools_dir))
         # deleting the containing folder doesn't trigger a toolbox reload, so signal it now and wait until it's done
         self._app.queue_worker.send_control_task('reload_toolbox', get_response=True)
+
+    def reset_shed_tools(self):
+        self.setup_shed_config()
         model = self._app.install_model
         models_to_delete = [
             model.RepositoryRepositoryDependencyAssociation,

From fb6522121cbb7d1dcf956e77f59e95d47c9d61b3 Mon Sep 17 00:00:00 2001
From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
Date: Sat, 31 Jul 2021 18:50:29 +0530
Subject: [PATCH 081/218] [21.05] Make authnz end session endpoint optional to
 support various providers

---
 lib/galaxy/authnz/custos_authnz.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/authnz/custos_authnz.py b/lib/galaxy/authnz/custos_authnz.py
index 73c5aa1d2c9..b9ed90c4aa8 100644
--- a/lib/galaxy/authnz/custos_authnz.py
+++ b/lib/galaxy/authnz/custos_authnz.py
@@ -310,7 +310,7 @@ class CustosAuthnz(IdentityProvider):
         self.config['authorization_endpoint'] = well_known_oidc_config['authorization_endpoint']
         self.config['token_endpoint'] = well_known_oidc_config['token_endpoint']
         self.config['userinfo_endpoint'] = well_known_oidc_config['userinfo_endpoint']
-        self.config['end_session_endpoint'] = well_known_oidc_config['end_session_endpoint']
+        self.config['end_session_endpoint'] = well_known_oidc_config.get('end_session_endpoint')
 
     def _get_verify_param(self):
         """Return 'ca_bundle' if 'verify_ssl' is true and 'ca_bundle' is configured."""

From cfce1aa2cb8d8d5266e7695a6ad3ce52de75cb11 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Sun, 1 Aug 2021 12:02:59 +0200
Subject: [PATCH 082/218] allow HTML in DatasetStorage view

---
 client/src/components/Dataset/DatasetStorage/DatasetStorage.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Dataset/DatasetStorage/DatasetStorage.vue b/client/src/components/Dataset/DatasetStorage/DatasetStorage.vue
index 7232d97e508..83589c5ce76 100644
--- a/client/src/components/Dataset/DatasetStorage/DatasetStorage.vue
+++ b/client/src/components/Dataset/DatasetStorage/DatasetStorage.vue
@@ -66,7 +66,7 @@ export default {
             const description = storageInfo.description;
             this.storageInfo = storageInfo;
             if (description) {
-                this.descriptionRendered = MarkdownIt().render(storageInfo.description);
+                this.descriptionRendered = MarkdownIt({html: true}).render(storageInfo.description);
             } else {
                 this.descriptionRendered = null;
             }

From 1fee6893248169c17dc69ad3c4961a4d0313b338 Mon Sep 17 00:00:00 2001
From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
Date: Mon, 26 Jul 2021 16:52:29 +0530
Subject: [PATCH 083/218] Allow absolute or relative url in assertion

---
 test/unit/authnz/test_custos_authnz.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/unit/authnz/test_custos_authnz.py b/test/unit/authnz/test_custos_authnz.py
index 2b71f40d16b..4cf04f52215 100644
--- a/test/unit/authnz/test_custos_authnz.py
+++ b/test/unit/authnz/test_custos_authnz.py
@@ -313,7 +313,7 @@ class CustosAuthnzTestCase(unittest.TestCase):
         self.assertTrue(self._create_oauth2_session_called)
         self.assertTrue(self._fetch_token_called)
         self.assertTrue(self._get_userinfo_called)
-        self.assertEqual(login_redirect_url, "http://localhost:8000/")
+        self.assertEqual(login_redirect_url, "/")
         self.assertIsNotNone(user)
 
     def test_callback_nonce_validation_with_bad_nonce(self):

From f2413b1c0781e6a850251ff860eb2676923940e0 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 30 Jul 2021 11:20:14 +0200
Subject: [PATCH 084/218] add output linter test

making sure that an output collection with statically defined
elements that use `format_source` are accepted (which is not the case
yet)
---
 test/unit/tool_util/test_tool_linters.py | 23 +++++++++++++++++++++--
 1 file changed, 21 insertions(+), 2 deletions(-)

diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
index 5323ea820a8..fa65480507c 100644
--- a/test/unit/tool_util/test_tool_linters.py
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -1,7 +1,7 @@
 import pytest
 
 from galaxy.tool_util.lint import LintContext
-from galaxy.tool_util.linters import general, inputs
+from galaxy.tool_util.linters import general, inputs, outputs
 from galaxy.tool_util.parser.xml import XmlToolSource
 from galaxy.util import etree
 
@@ -134,6 +134,19 @@ VALIDATOR_INCOMPATIBILITIES = """
 </tool>
 """
 
+OUTPUTS_COLLECTION_FORMAT_SOURCE = """
+<tool name="BWA Mapper" id="bwa" version="1.0.1" is_multi_byte="true" display_interface="true" require_login="true" hidden="true">
+    <description>The BWA Mapper</description>
+    <version_command interpreter="python">bwa.py --version</version_command>
+    <outputs>
+        <collection name="output_collection" type="paired">
+            <data name="forward" format_source="input_readpair" />
+            <data name="reverse" format_source="input_readpair" />
+        </collection>
+    </outputs>
+</tool>
+"""
+
 TESTS = [
     (
         NO_SECTIONS_XML, inputs.lint_inputs,
@@ -202,6 +215,11 @@ TESTS = [
             and "Parameter [param_name]: 'regex' validators need to define an 'expression' attribute" in x.error_messages
             and len(x.warn_messages) == 1 and len(x.error_messages) == 4
     ),
+    (
+        OUTPUTS_COLLECTION_FORMAT_SOURCE, outputs.lint_output,
+        lambda x:
+            len(x.warn_messages) == 0 and len(x.error_messages) == 0
+    ),
 ]
 
 TEST_IDS = [
@@ -212,7 +230,8 @@ TEST_IDS = [
     'select deprecations',
     'select option definitions',
     'hazardous whitespace',
-    'validator imcompatibilities'
+    'validator imcompatibilities',
+    'outputs collection static elements with format_source'
 ]
 
 

From d945f57efa7e8492597d177bddcc86687a5d73f4 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 30 Jul 2021 13:16:26 +0200
Subject: [PATCH 085/218] linter support for format_source in static collection
 elements

add support for linting `format_source` in static collection elements.
also warn for using `format_source` and `ext`/`format`.
---
 lib/galaxy/tool_util/linters/outputs.py  | 10 ++++++----
 test/unit/tool_util/test_tool_linters.py |  5 +++--
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/tool_util/linters/outputs.py b/lib/galaxy/tool_util/linters/outputs.py
index 42e5ca68ea8..6b5dfff886b 100644
--- a/lib/galaxy/tool_util/linters/outputs.py
+++ b/lib/galaxy/tool_util/linters/outputs.py
@@ -38,8 +38,6 @@ def lint_output(tool_xml, lint_ctx):
                 lint_ctx.warn("Collection output with undefined 'type' found.")
             if "structured_like" in output.attrib and "inherit_format" in output.attrib:
                 format_set = True
-        if "format_source" in output.attrib:
-            format_set = True
         for sub in output:
             if __check_pattern(sub):
                 format_set = True
@@ -54,12 +52,16 @@ def lint_output(tool_xml, lint_ctx):
 
 def __check_format(node, lint_ctx, allow_ext=False):
     """
-    check if format/ext attribute is set in a given node
+    check if format/ext/format_source attribute is set in a given node
     issue a warning if the value is input
     return true (node defines format/ext) / false (else)
     """
-    fmt = None
+    if "format_source" in node.attrib and ("ext" in node.attrib or "format" in node.attrib):
+        lint_ctx.warn(f"Tool {node.tag} output {node.attrib.get('name', 'with missing name')} should use either format_source or format/ext")
+    if "format_source" in node.attrib:
+        return True
     # if allowed (e.g. for discover_datasets), ext takes precedence over format
+    fmt = None
     if allow_ext:
         fmt = node.attrib.get("ext")
     if fmt is None:
diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
index fa65480507c..2a15b99023c 100644
--- a/test/unit/tool_util/test_tool_linters.py
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -141,7 +141,7 @@ OUTPUTS_COLLECTION_FORMAT_SOURCE = """
     <outputs>
         <collection name="output_collection" type="paired">
             <data name="forward" format_source="input_readpair" />
-            <data name="reverse" format_source="input_readpair" />
+            <data name="reverse" format_source="input_readpair" format="fastq"/>
         </collection>
     </outputs>
 </tool>
@@ -218,7 +218,8 @@ TESTS = [
     (
         OUTPUTS_COLLECTION_FORMAT_SOURCE, outputs.lint_output,
         lambda x:
-            len(x.warn_messages) == 0 and len(x.error_messages) == 0
+            "Tool data output reverse should use either format_source or format/ext" in x.warn_messages
+            and len(x.warn_messages) == 1 and len(x.error_messages) == 0
     ),
 ]
 

From a00c50f49e65e820c24f79978aa6a4efeb93d740 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 2 Aug 2021 15:39:08 +0200
Subject: [PATCH 086/218] xsd: document the delta attribute of has_size assert

---
 lib/galaxy/tool_util/xsd/galaxy.xsd | 21 ++++++++++++++++-----
 1 file changed, 16 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
index 578e6067ef1..719962630b6 100644
--- a/lib/galaxy/tool_util/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -2027,14 +2027,25 @@ module.
       </xs:element>
       <xs:element name="has_archive_member" type="AssertHasArchiveMember">
       </xs:element>
-      <xs:element name="has_size" type="xs:anyType">
-        <xs:annotation>
-          <xs:documentation xml:lang="en"><![CDATA[Asserts the output has a size (in bytes) of the specified ``value``; if the size is allowed to deviate from this value, the maximum difference can be optionally specified with ``delta`` (e.g. ``<has_size value="10000" delta="100" />``).]]>
-          </xs:documentation>
-        </xs:annotation>
+      <xs:element name="has_size" type="AssertHasSize">
       </xs:element>
     </xs:choice>
   </xs:group>
+  <xs:complexType name="AssertHasSize">
+    <xs:annotation>
+      <xs:documentation xml:lang="en"><![CDATA[Asserts the output has specific size (in bytes), e.g. ``<has_size value="10000" delta="100" />``.]]></xs:documentation>
+    </xs:annotation>
+    <xs:attribute name="value" type="xs:string">
+      <xs:annotation>
+        <xs:documentation xml:lang="en">Desired size of the outpyt (in bytes)</xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+    <xs:attribute name="delta" type="xs:integer" use="optional">
+      <xs:annotation>
+        <xs:documentation xml:lang="en">Maximum allowed size difference (default is 0).</xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+  </xs:complexType>
   <xs:complexType name="AssertHasH5Keys">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[Asserts HDF5 output has a set of attributes (``keys``), specified as a comma-separated list (e.g. ``<has_h5_keys keys="bins,chroms,indexes,pixels,chroms/lengths" />``).]]></xs:documentation>

From 6c477eb7c3a420381e2211c9a73849bc6245c11d Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 25 Jul 2021 14:47:22 -0400
Subject: [PATCH 087/218] Replace form views in charts with mounted FormDisplay
 component

---
 .../mvc/visualization/chart/views/groups.js    | 18 ++++++++----------
 .../mvc/visualization/chart/views/settings.js  | 17 ++++++++---------
 client/src/utils/mountVueComponent.js          |  8 ++++++++
 3 files changed, 24 insertions(+), 19 deletions(-)

diff --git a/client/src/mvc/visualization/chart/views/groups.js b/client/src/mvc/visualization/chart/views/groups.js
index 18651df6096..d26259fcba8 100644
--- a/client/src/mvc/visualization/chart/views/groups.js
+++ b/client/src/mvc/visualization/chart/views/groups.js
@@ -5,9 +5,10 @@ import $ from "jquery";
 import Backbone from "backbone";
 import { getAppRoot } from "onload/loadConfig";
 import Utils from "utils/utils";
-import Form from "mvc/form/form-view";
 import Repeat from "mvc/form/form-repeat";
 import FormData from "mvc/form/form-data";
+import FormDisplay from "components/Form/FormDisplay";
+import { appendVueComponent } from "utils/mountVueComponent";
 
 var GroupView = Backbone.View.extend({
     initialize: function (app, options) {
@@ -66,18 +67,15 @@ var GroupView = Backbone.View.extend({
                             value: data_columns,
                         });
                         self.chart.state("ok", "Metadata initialized...");
-                        self.form = new Form({
+                        const instance = appendVueComponent(self.$el, FormDisplay, {
                             inputs: inputs,
-                            onchange: function () {
-                                self.group.set(self.form.data.create());
-                                self.chart.set("modified", true);
-                                self.chart.trigger("redraw");
-                            },
                         });
-                        self.group.set(self.form.data.create());
-                        self.$el.empty().append(self.form.$el);
+                        instance.$on("onChange", (data) => {
+                            self.group.set(data);
+                            self.chart.set("modified", true);
+                            self.chart.trigger("redraw");
+                        });
                         process.resolve();
-                        self.chart.trigger("redraw");
                     },
                 });
             });
diff --git a/client/src/mvc/visualization/chart/views/settings.js b/client/src/mvc/visualization/chart/views/settings.js
index 1cebb8b7f51..dcd4c7f49f0 100644
--- a/client/src/mvc/visualization/chart/views/settings.js
+++ b/client/src/mvc/visualization/chart/views/settings.js
@@ -2,11 +2,12 @@
 import _ from "underscore";
 import Backbone from "backbone";
 import Utils from "utils/utils";
-import Form from "mvc/form/form-view";
+import FormDisplay from "components/Form/FormDisplay";
 import FormData from "mvc/form/form-data";
+import { appendVueComponent } from "utils/mountVueComponent";
 
 export default Backbone.View.extend({
-    initialize: function (app, options) {
+    initialize: function (app) {
         var self = this;
         this.chart = app.chart;
         this.setElement("<div/>");
@@ -37,15 +38,13 @@ export default Backbone.View.extend({
                     input.value = model_value;
                 }
             });
-            this.form = new Form({
+            const instance = appendVueComponent(this.$el, FormDisplay, {
                 inputs: inputs,
-                onchange: function () {
-                    self.chart.settings.set(self.form.data.create());
-                    self.chart.trigger("redraw");
-                },
             });
-            this.chart.settings.set(this.form.data.create());
-            this.$el.append(this.form.$el);
+            instance.$on("onChange", (data) => {
+                this.chart.settings.set(data);
+                this.chart.trigger("redraw");
+            });
         }
     },
 });
diff --git a/client/src/utils/mountVueComponent.js b/client/src/utils/mountVueComponent.js
index 3c8a0df173f..8f685614822 100644
--- a/client/src/utils/mountVueComponent.js
+++ b/client/src/utils/mountVueComponent.js
@@ -28,3 +28,11 @@ export const mountVueComponent = (ComponentDefinition) => {
     const component = Vue.extend(ComponentDefinition);
     return (propsData, el) => new component({ store, propsData, el });
 };
+
+export const appendVueComponent = ($el, ComponentDefinition, propsData = {}) => {
+    const container = document.createElement("div");
+    $el.empty().append(container);
+    const component = Vue.extend(ComponentDefinition);
+    const mountFn = (propsData, el) => new component({ propsData, el });
+    return mountFn(propsData, container);
+};

From ea10fbe89bc7f67cfcd8eb81042126772029b88e Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 25 Jul 2021 21:37:15 -0400
Subject: [PATCH 088/218] Make colors optional in nvd3 visualizations

---
 client/src/mvc/dataset/dataset-edit-attributes.js               | 1 -
 client/src/mvc/visualization/chart/views/settings.js            | 2 +-
 .../plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml | 1 +
 3 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/src/mvc/dataset/dataset-edit-attributes.js b/client/src/mvc/dataset/dataset-edit-attributes.js
index 9d32f43a5d3..f14bfaad0ee 100644
--- a/client/src/mvc/dataset/dataset-edit-attributes.js
+++ b/client/src/mvc/dataset/dataset-edit-attributes.js
@@ -5,7 +5,6 @@ import Backbone from "backbone";
 import { getAppRoot } from "onload/loadConfig";
 import { getGalaxyInstance } from "app";
 import _l from "utils/localization";
-// import Utils from "utils/utils";
 import Tabs from "mvc/ui/ui-tabs";
 import Ui from "mvc/ui/ui-misc";
 import Form from "mvc/form/form-view";
diff --git a/client/src/mvc/visualization/chart/views/settings.js b/client/src/mvc/visualization/chart/views/settings.js
index dcd4c7f49f0..e78404b223d 100644
--- a/client/src/mvc/visualization/chart/views/settings.js
+++ b/client/src/mvc/visualization/chart/views/settings.js
@@ -2,8 +2,8 @@
 import _ from "underscore";
 import Backbone from "backbone";
 import Utils from "utils/utils";
-import FormDisplay from "components/Form/FormDisplay";
 import FormData from "mvc/form/form-data";
+import FormDisplay from "components/Form/FormDisplay";
 import { appendVueComponent } from "utils/mountVueComponent";
 
 export default Backbone.View.extend({
diff --git a/config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml b/config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml
index c96f4104468..c218842603b 100644
--- a/config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml
@@ -26,6 +26,7 @@
             <label>Pick a series color</label>
             <name>color</name>
             <type>color</type>
+            <optional>true</optional>
         </input>
         <input>
             <label>Column of data point labels</label>

From eb2e064fc7c6039027e9ff90adb31fa03a5e4e32 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 2 Aug 2021 11:20:10 -0400
Subject: [PATCH 089/218] prettier.

---
 client/src/components/Dataset/DatasetStorage/DatasetStorage.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Dataset/DatasetStorage/DatasetStorage.vue b/client/src/components/Dataset/DatasetStorage/DatasetStorage.vue
index 83589c5ce76..37f661fe0a1 100644
--- a/client/src/components/Dataset/DatasetStorage/DatasetStorage.vue
+++ b/client/src/components/Dataset/DatasetStorage/DatasetStorage.vue
@@ -66,7 +66,7 @@ export default {
             const description = storageInfo.description;
             this.storageInfo = storageInfo;
             if (description) {
-                this.descriptionRendered = MarkdownIt({html: true}).render(storageInfo.description);
+                this.descriptionRendered = MarkdownIt({ html: true }).render(storageInfo.description);
             } else {
                 this.descriptionRendered = null;
             }

From e540ef5775f9f8257aa4620d798bf710d416c6a4 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 2 Aug 2021 17:27:50 +0200
Subject: [PATCH 090/218] Continue handler startup even if job working
 directory can't be recovered

---
 lib/galaxy/jobs/handler.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/lib/galaxy/jobs/handler.py b/lib/galaxy/jobs/handler.py
index 4c5fa582025..7326a3dc02c 100644
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -21,6 +21,7 @@ from sqlalchemy.sql.expression import (
 )
 
 from galaxy import model
+from galaxy.exceptions import ObjectNotFound
 from galaxy.jobs import (
     JobDestination,
     JobWrapper,
@@ -1087,6 +1088,10 @@ class DefaultJobDispatcher:
         except KeyError:
             log.error(f'recover(): ({job_wrapper.job_id}) Invalid job runner: {runner_name}')
             job_wrapper.fail(DEFAULT_JOB_PUT_FAILURE_MESSAGE)
+        except ObjectNotFound:
+            msg = "Could not recover job working directory after Galaxy restart"
+            log.exception(f"recover(): ({job_wrapper.job_id}) {msg}")
+            job_wrapper.fail(msg)
 
     def shutdown(self):
         failures = []

From 2667d79f4f3bf1329e55074cb4bafbf90f660c8d Mon Sep 17 00:00:00 2001
From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
Date: Tue, 3 Aug 2021 17:54:26 +0530
Subject: [PATCH 091/218] Default k8s_unschedulable_walltime_limit to None and
 allow for unlimited queue wait time

---
 lib/galaxy/jobs/runners/kubernetes.py | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py
index 57c6a950fdb..7cb7923f6e0 100644
--- a/lib/galaxy/jobs/runners/kubernetes.py
+++ b/lib/galaxy/jobs/runners/kubernetes.py
@@ -83,7 +83,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             k8s_cleanup_job=dict(map=str, valid=lambda s: s in {"onsuccess", "always", "never"}, default="always"),
             k8s_pod_retries=dict(map=int, valid=lambda x: int(x) >= 0, default=3),
             k8s_walltime_limit=dict(map=int, valid=lambda x: int(x) >= 0, default=172800),
-            k8s_unschedulable_walltime_limit=dict(map=int, valid=lambda x: int(x) >= 0, default=1800),
+            k8s_unschedulable_walltime_limit=dict(map=int, valid=lambda x: not x or int(x) >= 0, default=None),
             k8s_interactivetools_use_ssl=dict(map=bool, default=False),
             k8s_interactivetools_ingress_annotations=dict(map=str),)
 
@@ -676,11 +676,16 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             elif active > 0 and failed <= max_pod_retries:
                 if not job_state.running:
                     if self.__job_pending_due_to_unschedulable_pod(job_state):
-                        creation_time_str = job.obj['metadata'].get('creationTimestamp')
-                        creation_time = datetime.strptime(creation_time_str, '%Y-%m-%dT%H:%M:%SZ')
-                        elapsed_seconds = (datetime.utcnow() - creation_time).total_seconds()
-                        if elapsed_seconds > self.runner_params['k8s_unschedulable_walltime_limit']:
-                            return self._handle_unschedulable_job(job, job_state)
+                        if self.runner_params.get('k8s_unschedulable_walltime_limit'):
+                            creation_time_str = job.obj['metadata'].get('creationTimestamp')
+                            creation_time = datetime.strptime(creation_time_str, '%Y-%m-%dT%H:%M:%SZ')
+                            elapsed_seconds = (datetime.utcnow() - creation_time).total_seconds()
+                            if elapsed_seconds > self.runner_params['k8s_unschedulable_walltime_limit']:
+                                return self._handle_unschedulable_job(job, job_state)
+                            else:
+                                pass
+                        else:
+                            pass
                     else:
                         job_state.running = True
                         job_state.job_wrapper.change_state(model.Job.states.RUNNING)

From 36ef4ab1d960c57d894130049e00cd064d5a5f85 Mon Sep 17 00:00:00 2001
From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
Date: Tue, 3 Aug 2021 19:18:48 +0530
Subject: [PATCH 092/218] Added documentation on
 k8s_unschedulable_walltime_limit parameter

---
 lib/galaxy/config/sample/job_conf.xml.sample_advanced | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/lib/galaxy/config/sample/job_conf.xml.sample_advanced b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
index 795998ed9be..fa78f51f8f7 100644
--- a/lib/galaxy/config/sample/job_conf.xml.sample_advanced
+++ b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
@@ -322,6 +322,9 @@
             <!-- Whether to enabled HTTPS access in the k8s ingress spec generated for each interactive tools -->
             <!-- <param id="k8s_interactivetools_ingress_annotations">{'cert-manager.io/cluster-issuer': 'letsencrypt-prod'}</param> -->
             <!-- Annotations to add to the metadata section in the k8s ingress generated for each interactive tools -->
+            <!-- <param id="k8s_unschedulable_walltime_limit">172800</param> -->
+            <!-- The amount of time (in seconds) to let a job remain in an unschedulable state before being flagged
+                 as having failed. The default is None (unlimited time). -->
 
         </plugin>
         <plugin id="godocker" type="runner" load="galaxy.jobs.runners.godocker:GodockerJobRunner">

From fbb7c0dad70b880b5cbdb111954b3411d11ad2a8 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Thu, 29 Jul 2021 21:55:27 +0200
Subject: [PATCH 093/218] fix recursive

---
 lib/galaxy/files/sources/posix.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/files/sources/posix.py b/lib/galaxy/files/sources/posix.py
index dcdd53fbe82..3dcbf08ea77 100644
--- a/lib/galaxy/files/sources/posix.py
+++ b/lib/galaxy/files/sources/posix.py
@@ -39,7 +39,8 @@ class PosixFilesSource(BaseFilesSource):
         if recursive:
             res = []
             for (p, dirs, files) in safe_walk(dir_path, allowlist=self._allowlist):
-                rel_dir = os.path.relpath(p, dir_path)
+                dir_path_root = os.path.split(dir_path)[0]
+                rel_dir = os.path.relpath(p, dir_path_root)
                 to_dict = functools.partial(self._resource_info_to_dict, rel_dir, user_context=user_context)
                 res.extend(map(to_dict, dirs))
                 res.extend(map(to_dict, files))

From 93218821048f547fe5fc99b7332c0e57706fdb36 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Fri, 30 Jul 2021 16:57:49 +0200
Subject: [PATCH 094/218] use root path

---
 lib/galaxy/files/sources/posix.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/galaxy/files/sources/posix.py b/lib/galaxy/files/sources/posix.py
index 3dcbf08ea77..aab43fce6f1 100644
--- a/lib/galaxy/files/sources/posix.py
+++ b/lib/galaxy/files/sources/posix.py
@@ -39,8 +39,7 @@ class PosixFilesSource(BaseFilesSource):
         if recursive:
             res = []
             for (p, dirs, files) in safe_walk(dir_path, allowlist=self._allowlist):
-                dir_path_root = os.path.split(dir_path)[0]
-                rel_dir = os.path.relpath(p, dir_path_root)
+                rel_dir = os.path.relpath(p, self.root)
                 to_dict = functools.partial(self._resource_info_to_dict, rel_dir, user_context=user_context)
                 res.extend(map(to_dict, dirs))
                 res.extend(map(to_dict, files))

From 1e04bf91ecaba0031010c10c3e4a6e84597bfa32 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Tue, 3 Aug 2021 18:47:17 +0200
Subject: [PATCH 095/218] fix integration test

---
 lib/galaxy/files/sources/posix.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/files/sources/posix.py b/lib/galaxy/files/sources/posix.py
index aab43fce6f1..43bc1d95d9f 100644
--- a/lib/galaxy/files/sources/posix.py
+++ b/lib/galaxy/files/sources/posix.py
@@ -38,8 +38,9 @@ class PosixFilesSource(BaseFilesSource):
             raise exceptions.ObjectNotFound(f'The specified directory does not exist [{dir_path}].')
         if recursive:
             res = []
+            effective_root = self._effective_root(user_context)
             for (p, dirs, files) in safe_walk(dir_path, allowlist=self._allowlist):
-                rel_dir = os.path.relpath(p, self.root)
+                rel_dir = os.path.relpath(p, effective_root)
                 to_dict = functools.partial(self._resource_info_to_dict, rel_dir, user_context=user_context)
                 res.extend(map(to_dict, dirs))
                 res.extend(map(to_dict, files))

From 28394f006827fc848f710a87c551a0da7496d473 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 4 Aug 2021 12:48:25 +0200
Subject: [PATCH 096/218] make linter accept from_tool_provided_metadata

as means to specify the format for discovered datasets
---
 lib/galaxy/tool_util/linters/outputs.py  |  7 ++++++-
 test/unit/tool_util/test_tool_linters.py | 22 +++++++++++++++++++++-
 2 files changed, 27 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tool_util/linters/outputs.py b/lib/galaxy/tool_util/linters/outputs.py
index 6b5dfff886b..8d0b7fe858f 100644
--- a/lib/galaxy/tool_util/linters/outputs.py
+++ b/lib/galaxy/tool_util/linters/outputs.py
@@ -1,4 +1,5 @@
 """This module contains a linting functions for tool outputs."""
+from galaxy.util import string_as_bool
 from ._util import is_valid_cheetah_placeholder
 
 
@@ -73,10 +74,14 @@ def __check_format(node, lint_ctx, allow_ext=False):
 
 def __check_pattern(node):
     """
-    check if pattern attribute is set and defines the extension
+    check if
+    - pattern attribute is set and defines the extension or
+    - from_tool_provided_metadata is true
     """
     if node.tag != "discover_datasets":
         return False
+    if "from_tool_provided_metadata" in node.attrib and string_as_bool(node.attrib.get("from_tool_provided_metadata", "false")):
+        return True
     if "pattern" not in node.attrib:
         return False
     if node.attrib["pattern"] == "__default__":
diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
index 2a15b99023c..0dab32dba2e 100644
--- a/test/unit/tool_util/test_tool_linters.py
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -134,6 +134,8 @@ VALIDATOR_INCOMPATIBILITIES = """
 </tool>
 """
 
+# check that linter accepts format source for collection elements as means to specify format
+# and that the linter warns if format and format_source are used
 OUTPUTS_COLLECTION_FORMAT_SOURCE = """
 <tool name="BWA Mapper" id="bwa" version="1.0.1" is_multi_byte="true" display_interface="true" require_login="true" hidden="true">
     <description>The BWA Mapper</description>
@@ -147,6 +149,18 @@ OUTPUTS_COLLECTION_FORMAT_SOURCE = """
 </tool>
 """
 
+# check that linter does not complain about missing format if from_tool_provided_metadata is used
+OUTPUTS_DISCOVER_TOOL_PROVIDED_METADATA = """
+<tool name="BWA Mapper" id="bwa" version="1.0.1" is_multi_byte="true" display_interface="true" require_login="true" hidden="true">
+    <description>The BWA Mapper</description>
+    <version_command interpreter="python">bwa.py --version</version_command>
+    <outputs>
+        <data name="output">
+            <discover_datasets from_tool_provided_metadata="true"/>
+        </data>
+    </outputs>
+</tool>
+"""
 TESTS = [
     (
         NO_SECTIONS_XML, inputs.lint_inputs,
@@ -221,6 +235,11 @@ TESTS = [
             "Tool data output reverse should use either format_source or format/ext" in x.warn_messages
             and len(x.warn_messages) == 1 and len(x.error_messages) == 0
     ),
+    (
+        OUTPUTS_DISCOVER_TOOL_PROVIDED_METADATA, outputs.lint_output,
+        lambda x:
+            len(x.warn_messages) == 0 and len(x.error_messages) == 0
+    ),
 ]
 
 TEST_IDS = [
@@ -232,7 +251,8 @@ TEST_IDS = [
     'select option definitions',
     'hazardous whitespace',
     'validator imcompatibilities',
-    'outputs collection static elements with format_source'
+    'outputs collection static elements with format_source',
+    'outputs discover datatsets with tool provided metadata'
 ]
 
 

From a7bba11208924186245ca31f2cf166f191cab992 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 26 Jul 2021 15:28:27 -0400
Subject: [PATCH 097/218] Use modified SingleQueryProvider (thx @nerdinacan) to
 Vueify Dataset Error display

---
 client/package.json                           |  1 +
 .../DatasetInformation/DatasetError.vue       | 84 +++++++++++++++++++
 .../src/components/providers/JobProvider.js   | 18 ++++
 .../providers/SingleQueryProvider.js          | 40 +++++++--
 client/src/entry/analysis/AnalysisRouter.js   |  7 +-
 client/yarn.lock                              |  5 ++
 6 files changed, 144 insertions(+), 11 deletions(-)
 create mode 100644 client/src/components/DatasetInformation/DatasetError.vue
 create mode 100644 client/src/components/providers/JobProvider.js

diff --git a/client/package.json b/client/package.json
index bf6b816241c..2c70f9711bf 100644
--- a/client/package.json
+++ b/client/package.json
@@ -55,6 +55,7 @@
     "markdown-it": "^11.0.0",
     "markdown-it-regexp": "^0.4.0",
     "moment": "2.26.0",
+    "object-hash": "^2.2.0",
     "popper.js": "^1.16.1",
     "pouchdb": "^7.2.2",
     "pouchdb-adapter-memory": "^7.2.2",
diff --git a/client/src/components/DatasetInformation/DatasetError.vue b/client/src/components/DatasetInformation/DatasetError.vue
new file mode 100644
index 00000000000..255fc27a7b0
--- /dev/null
+++ b/client/src/components/DatasetInformation/DatasetError.vue
@@ -0,0 +1,84 @@
+<template>
+    <DatasetProvider :id="datasetId" v-slot="{ item: dataset, loading }">
+        <div v-if="!loading">
+            <JobDetailsProvider :jobid="dataset.creating_job" v-slot="{ result, loading }">
+                <div v-if="!loading">
+                    <div class="page-container edit-attr">
+                        <div class="response-message"></div>
+                    </div>
+                    <h2>Dataset Error Report</h2>
+                    <p>
+                        An error occurred while running the tool <b>{{ result.tool_id }}</b
+                        >.
+                    </p>
+                    <div v-if="result.tool_stderr || result.job_stderr || result.job_messages">
+                        <h3>Details</h3>
+                    </div>
+                    <div v-if="result.job_messages">
+                        <p>Execution resulted in the following messages:</p>
+                        <div v-for="job_message in result.job_messages">
+                            <pre class="rounded code">{{ job_message["desc"] }}</pre>
+                        </div>
+                    </div>
+                    <div v-if="result.tool_stderr">
+                        <p>Tool generated the following standard error:</p>
+                        <pre class="rounded code">{{ result.tool_stderr }}</pre>
+                    </div>
+                    <div v-if="result.job_stderr">
+                        <p>Galaxy job runner generated the following standard error:</p>
+                        <pre class="rounded code">{{ result.job_stderr }}</pre>
+                    </div>
+                </div>
+            </JobDetailsProvider>
+            <JobProblemProvider :jobid="dataset.creating_job" v-slot="{ result, loading }">
+                <h3 class="common_problems"></h3>
+            </JobProblemProvider>
+            <h3>Troubleshooting</h3>
+            <p>
+                There are a number of helpful resources to self diagnose and correct problems.
+                <br />
+                Start here:
+                <b>
+                    <a href="https://galaxyproject.org/support/tool-error/" target="_blank">
+                        My job ended with an error. What can I do?
+                    </a>
+                </b>
+            </p>
+            <h3>Issue Report</h3>
+        </div>
+    </DatasetProvider>
+</template>
+
+<script>
+import { DatasetProvider } from "components/WorkflowInvocationState/providers";
+import { JobDetailsProvider, JobProblemProvider } from "components/providers/JobProvider";
+import FormDisplay from "components/Form/FormDisplay";
+import FormCard from "components/Form/FormCard";
+
+export default {
+    components: {
+        DatasetProvider,
+        FormDisplay,
+        FormCard,
+        JobDetailsProvider,
+        JobProblemProvider,
+    },
+    props: {
+        datasetId: {
+            type: String,
+            required: true,
+        },
+    },
+    data() {
+        return {};
+    },
+    computed: {
+        inputs() {
+            return [];
+        },
+    },
+    methods: {
+        onChange(data) {},
+    },
+};
+</script>
diff --git a/client/src/components/providers/JobProvider.js b/client/src/components/providers/JobProvider.js
new file mode 100644
index 00000000000..913af215cc4
--- /dev/null
+++ b/client/src/components/providers/JobProvider.js
@@ -0,0 +1,18 @@
+import axios from "axios";
+import { getAppRoot } from "onload/loadConfig";
+import { SingleQueryProvider } from "components/providers/SingleQueryProvider";
+
+async function jobDetails({ jobid }) {
+    const url = `${getAppRoot()}api/jobs/${jobid}?full=True`;
+    const { data } = await axios.get(url);
+    return data;
+}
+
+async function jobProblems({ jobid }) {
+    const url = `${getAppRoot()}api/jobs/${jobid}/common_problems`;
+    const { data } = await axios.get(url);
+    return data;
+}
+
+export const JobDetailsProvider = SingleQueryProvider(jobDetails);
+export const JobProblemProvider = SingleQueryProvider(jobProblems);
diff --git a/client/src/components/providers/SingleQueryProvider.js b/client/src/components/providers/SingleQueryProvider.js
index 2bea088d34e..5327ac4e506 100644
--- a/client/src/components/providers/SingleQueryProvider.js
+++ b/client/src/components/providers/SingleQueryProvider.js
@@ -1,7 +1,16 @@
-export const SingleQueryProvider = (cfg = {}) => {
-    const { resultName = "result", lookup } = cfg;
+import hash from "object-hash";
 
-    let cached_result;
+/**
+ * Builds a provider that gets its result from a single promise-based query function and
+ * caches the result of lookup for subsequent instantitations.
+ *
+ * @param   {Function}  lookup  async function that loads the result, paramters will be an object
+ *                              whose properties are the attributes assigned to the provider component
+ * @return  {VueComponentOptions} Vue component options definition
+ */
+export const SingleQueryProvider = (lookup) => {
+    const promiseCache = new Map();
+    const resultCache = new Map();
 
     return {
         data() {
@@ -13,17 +22,32 @@ export const SingleQueryProvider = (cfg = {}) => {
             loading() {
                 return this.result === undefined;
             },
+            cacheKey() {
+                hash(this.$attrs || {});
+            },
         },
-        async created() {
-            if (undefined === cached_result) {
-                cached_result = await lookup();
+        mounted() {
+            const cachedResult = resultCache.get(this.cacheKey);
+            if (cachedResult) {
+                this.result = cachedResult;
+                return;
             }
-            this.result = cached_result;
+
+            let lookupPromise = promiseCache.get(this.cacheKey);
+            if (!lookupPromise) {
+                lookupPromise = lookup(this.$attrs);
+                promiseCache.set(this.cacheKey, lookupPromise);
+            }
+
+            lookupPromise.then((result) => {
+                resultCache.set(this.cacheKey, result);
+                this.result = result;
+            });
         },
         render() {
             return this.$scopedSlots.default({
                 loading: this.loading,
-                [resultName]: this.result,
+                result: this.result,
             });
         },
     };
diff --git a/client/src/entry/analysis/AnalysisRouter.js b/client/src/entry/analysis/AnalysisRouter.js
index d0e31fa7618..1e34faef65a 100644
--- a/client/src/entry/analysis/AnalysisRouter.js
+++ b/client/src/entry/analysis/AnalysisRouter.js
@@ -41,7 +41,7 @@ import ToolsJson from "components/ToolsView/ToolsSchemaJson/ToolsJson.vue";
 import HistoryList from "mvc/history/history-list";
 import PluginList from "components/PluginList.vue";
 import QueryStringParsing from "utils/query-string-parsing";
-import DatasetError from "mvc/dataset/dataset-error";
+import DatasetError from "components/DatasetInformation/DatasetError";
 import DatasetEditAttributes from "mvc/dataset/dataset-edit-attributes";
 import Citations from "components/Citation/Citations.vue";
 import DisplayStructure from "components/DisplayStructured.vue";
@@ -389,8 +389,9 @@ export const getAnalysisRouter = (Galaxy) => {
             this.page.display(new DatasetEditAttributes.View());
         },
 
-        show_dataset_error: function () {
-            this.page.display(new DatasetError.View());
+        show_dataset_error: function (params) {
+            const datasetId = params.dataset_id;
+            this._display_vue_helper(DatasetError, { datasetId: datasetId });
         },
 
         /**  */
diff --git a/client/yarn.lock b/client/yarn.lock
index cdc734cab1e..829749ec72d 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -10333,6 +10333,11 @@ object-copy@^0.1.0:
     define-property "^0.2.5"
     kind-of "^3.0.3"
 
+object-hash@^2.2.0:
+  version "2.2.0"
+  resolved "https://registry.yarnpkg.com/object-hash/-/object-hash-2.2.0.tgz#5ad518581eefc443bd763472b8ff2e9c2c0d54a5"
+  integrity sha512-gScRMn0bS5fH+IuwyIFgnh9zBdo4DV+6GhygmWM9HyNJSgS0hScp1f5vjtm7oIIOiT9trXrShAkLFSc2IqKNgw==
+
 object-inspect@^1.8.0:
   version "1.9.0"
   resolved "https://registry.yarnpkg.com/object-inspect/-/object-inspect-1.9.0.tgz#c90521d74e1127b67266ded3394ad6116986533a"

From 00418f138ae7057e5a01808a81a53b0061199dbd Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 26 Jul 2021 15:37:49 -0400
Subject: [PATCH 098/218] Add common job problem section to dataset error
 component

---
 .../components/DatasetInformation/DatasetError.vue   | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/client/src/components/DatasetInformation/DatasetError.vue b/client/src/components/DatasetInformation/DatasetError.vue
index 255fc27a7b0..12134ca3585 100644
--- a/client/src/components/DatasetInformation/DatasetError.vue
+++ b/client/src/components/DatasetInformation/DatasetError.vue
@@ -31,7 +31,17 @@
                 </div>
             </JobDetailsProvider>
             <JobProblemProvider :jobid="dataset.creating_job" v-slot="{ result, loading }">
-                <h3 class="common_problems"></h3>
+                <div v-if="result.has_duplicate_inputs || result.has_empty_inputs">
+                    <h3 class="common_problems">Detected Common Potential Problems</h3>
+                    <p v-if="result.has_empty_inputs">
+                        The tool was executed with one or more empty input datasets. This frequently
+                        results in tool errors due to problematic input choices.
+                    <p>
+                    <p v-if="result.has_duplicate_inputs">
+                        The tool was executed with one or more duplicate input datasets. This frequently
+                        results in tool errors due to problematic input choices.
+                    <p>
+                </div>
             </JobProblemProvider>
             <h3>Troubleshooting</h3>
             <p>

From 7dd797d8ce86b8fd3d2ee2787d235146a6ff40cf Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 27 Jul 2021 18:02:05 -0400
Subject: [PATCH 099/218] Remove legacy dataset error backbone module, replace
 with Vue component

---
 .../DatasetInformation/DatasetError.vue       | 166 +++++++-----
 client/src/mvc/dataset/dataset-error.js       | 244 ------------------
 2 files changed, 100 insertions(+), 310 deletions(-)
 delete mode 100644 client/src/mvc/dataset/dataset-error.js

diff --git a/client/src/components/DatasetInformation/DatasetError.vue b/client/src/components/DatasetInformation/DatasetError.vue
index 12134ca3585..56109288092 100644
--- a/client/src/components/DatasetInformation/DatasetError.vue
+++ b/client/src/components/DatasetInformation/DatasetError.vue
@@ -1,75 +1,98 @@
 <template>
-    <DatasetProvider :id="datasetId" v-slot="{ item: dataset, loading }">
-        <div v-if="!loading">
-            <JobDetailsProvider :jobid="dataset.creating_job" v-slot="{ result, loading }">
-                <div v-if="!loading">
-                    <div class="page-container edit-attr">
-                        <div class="response-message"></div>
-                    </div>
-                    <h2>Dataset Error Report</h2>
-                    <p>
-                        An error occurred while running the tool <b>{{ result.tool_id }}</b
-                        >.
-                    </p>
-                    <div v-if="result.tool_stderr || result.job_stderr || result.job_messages">
-                        <h3>Details</h3>
-                    </div>
-                    <div v-if="result.job_messages">
-                        <p>Execution resulted in the following messages:</p>
-                        <div v-for="job_message in result.job_messages">
-                            <pre class="rounded code">{{ job_message["desc"] }}</pre>
+    <CurrentUser v-slot="{ user }">
+        <DatasetProvider :id="datasetId" v-slot="{ item: dataset, loading }">
+            <div v-if="!loading">
+                <JobDetailsProvider :jobid="dataset.creating_job" v-slot="{ result, loading }">
+                    <div v-if="!loading">
+                        <div class="page-container edit-attr">
+                            <div class="response-message"></div>
+                        </div>
+                        <h2>Dataset Error Report</h2>
+                        <p>
+                            An error occurred while running the tool <b>{{ result.tool_id }}</b
+                            >.
+                        </p>
+                        <div v-if="result.tool_stderr || result.job_stderr || result.job_messages">
+                            <h3>Details</h3>
+                        </div>
+                        <div v-if="result.job_messages">
+                            <p>Execution resulted in the following messages:</p>
+                            <div v-for="job_message in result.job_messages">
+                                <pre class="rounded code">{{ job_message["desc"] }}</pre>
+                            </div>
+                        </div>
+                        <div v-if="result.tool_stderr">
+                            <p>Tool generated the following standard error:</p>
+                            <pre class="rounded code">{{ result.tool_stderr }}</pre>
+                        </div>
+                        <div v-if="result.job_stderr">
+                            <p>Galaxy job runner generated the following standard error:</p>
+                            <pre class="rounded code">{{ result.job_stderr }}</pre>
                         </div>
                     </div>
-                    <div v-if="result.tool_stderr">
-                        <p>Tool generated the following standard error:</p>
-                        <pre class="rounded code">{{ result.tool_stderr }}</pre>
+                </JobDetailsProvider>
+                <JobProblemProvider :jobid="dataset.creating_job" v-slot="{ result, loading }">
+                    <div v-if="result && (result.has_duplicate_inputs || result.has_empty_inputs)">
+                        <h3 class="common_problems">Detected Common Potential Problems</h3>
+                        <p v-if="result.has_empty_inputs">
+                            The tool was executed with one or more empty input datasets. This frequently results in tool
+                            errors due to problematic input choices.
+                        </p>
+                        <p v-if="result && result.has_duplicate_inputs">
+                            The tool was executed with one or more duplicate input datasets. This frequently results in
+                            tool errors due to problematic input choices.
+                        </p>
                     </div>
-                    <div v-if="result.job_stderr">
-                        <p>Galaxy job runner generated the following standard error:</p>
-                        <pre class="rounded code">{{ result.job_stderr }}</pre>
-                    </div>
-                </div>
-            </JobDetailsProvider>
-            <JobProblemProvider :jobid="dataset.creating_job" v-slot="{ result, loading }">
-                <div v-if="result.has_duplicate_inputs || result.has_empty_inputs">
-                    <h3 class="common_problems">Detected Common Potential Problems</h3>
-                    <p v-if="result.has_empty_inputs">
-                        The tool was executed with one or more empty input datasets. This frequently
-                        results in tool errors due to problematic input choices.
-                    <p>
-                    <p v-if="result.has_duplicate_inputs">
-                        The tool was executed with one or more duplicate input datasets. This frequently
-                        results in tool errors due to problematic input choices.
-                    <p>
-                </div>
-            </JobProblemProvider>
-            <h3>Troubleshooting</h3>
-            <p>
-                There are a number of helpful resources to self diagnose and correct problems.
-                <br />
-                Start here:
-                <b>
-                    <a href="https://galaxyproject.org/support/tool-error/" target="_blank">
-                        My job ended with an error. What can I do?
-                    </a>
-                </b>
-            </p>
-            <h3>Issue Report</h3>
-        </div>
-    </DatasetProvider>
+                </JobProblemProvider>
+                <h3>Troubleshooting</h3>
+                <p>
+                    There are a number of helpful resources to self diagnose and correct problems.
+                    <br />
+                    Start here:
+                    <b>
+                        <a href="https://galaxyproject.org/support/tool-error/" target="_blank">
+                            My job ended with an error. What can I do?
+                        </a>
+                    </b>
+                </p>
+                <h3 class="mb-2">Issue Report</h3>
+                <b-alert v-if="errorMessage" variant="danger" show>{{ errorMessage }}</b-alert>
+                <b-alert v-for="resultMessage in resultMessages" :variant="resultMessage[1]" show>{{
+                    resultMessage[0]
+                }}</b-alert>
+                <FormElement v-if="!user.email" id="email" v-model="email" title="Please provide your email:" />
+                <FormElement
+                    id="message"
+                    v-model="message"
+                    :area="true"
+                    title="Please provide detailed information on the activities leading to this issue:"
+                />
+                <b-button variant="primary" @click="submit(dataset, user.email)" class="mt-2">
+                    <font-awesome-icon icon="bug" class="mr-1" />Report
+                </b-button>
+            </div>
+        </DatasetProvider>
+    </CurrentUser>
 </template>
 
 <script>
+import CurrentUser from "components/providers/CurrentUser";
+import FormElement from "components/Form/FormElement";
 import { DatasetProvider } from "components/WorkflowInvocationState/providers";
 import { JobDetailsProvider, JobProblemProvider } from "components/providers/JobProvider";
-import FormDisplay from "components/Form/FormDisplay";
-import FormCard from "components/Form/FormCard";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faBug } from "@fortawesome/free-solid-svg-icons";
+import { sendErrorReport } from "./services";
+
+library.add(faBug);
 
 export default {
     components: {
+        CurrentUser,
         DatasetProvider,
-        FormDisplay,
-        FormCard,
+        FontAwesomeIcon,
+        FormElement,
         JobDetailsProvider,
         JobProblemProvider,
     },
@@ -80,15 +103,26 @@ export default {
         },
     },
     data() {
-        return {};
-    },
-    computed: {
-        inputs() {
-            return [];
-        },
+        return {
+            message: null,
+            email: null,
+            errorMessage: null,
+            resultMessages: [],
+        };
     },
     methods: {
-        onChange(data) {},
+        submit(dataset, userEmail) {
+            const email = this.email || userEmail;
+            const message = this.message;
+            sendErrorReport(dataset, message, email).then(
+                (resultMessages) => {
+                    this.resultMessages = resultMessages;
+                },
+                (errorMessage) => {
+                    this.errorMessage = errorMessage;
+                }
+            );
+        },
     },
 };
 </script>
diff --git a/client/src/mvc/dataset/dataset-error.js b/client/src/mvc/dataset/dataset-error.js
deleted file mode 100644
index 2312a55e1b9..00000000000
--- a/client/src/mvc/dataset/dataset-error.js
+++ /dev/null
@@ -1,244 +0,0 @@
-import _ from "underscore";
-import $ from "jquery";
-import Backbone from "backbone";
-import { getAppRoot } from "onload/loadConfig";
-import { getGalaxyInstance } from "app";
-import _l from "utils/localization";
-import Utils from "utils/utils";
-import Ui from "mvc/ui/ui-misc";
-import Form from "mvc/form/form-view";
-
-/** Dataset edit attributes view */
-var View = Backbone.View.extend({
-    initialize: function () {
-        const Galaxy = getGalaxyInstance();
-        this.setElement("<div/>");
-        this.model = new Backbone.Model({
-            dataset_id: Galaxy.params.dataset_id,
-        });
-        this.active_tab = "user";
-        this.render();
-    },
-
-    // Fetch data for the selected dataset and
-    render: function () {
-        var data_url = `${getAppRoot()}api/datasets/${this.model.get("dataset_id")}`;
-        Utils.get({
-            url: data_url,
-            success: (dataset) => {
-                var job_url = `${getAppRoot()}api/jobs/${dataset.creating_job}?full=True`;
-                Utils.get({
-                    url: job_url,
-                    success: (job) => {
-                        this.render_error_page(dataset, job);
-                        this.find_common_problems(job);
-                    },
-                    error: () => {
-                        var error_response = {
-                            status: "error",
-                            message: "Error occurred while loading the job.",
-                            persistent: true,
-                            cls: "errormessage",
-                        };
-                        this.display_message(error_response, this.$(".response-message"));
-                    },
-                });
-            },
-            error: () => {
-                var error_response = {
-                    status: "error",
-                    message: "Error occurred while loading the dataset.",
-                    persistent: true,
-                    cls: "errormessage",
-                };
-                this.display_message(error_response, this.$(".response-message"));
-            },
-        });
-    },
-
-    find_common_problems: function (job) {
-        var job_url = `${getAppRoot()}api/jobs/${job.id}/common_problems`;
-        Utils.get({
-            url: job_url,
-            success: (common_problems) => {
-                this.render_common_problems(common_problems);
-            },
-            error: (response) => {
-                console.log("error");
-                console.log(response);
-            },
-        });
-        return;
-    },
-
-    render_common_problems: function (common_problems) {
-        const has_duplicate_inputs = common_problems.has_duplicate_inputs;
-        const has_empty_inputs = common_problems.has_empty_inputs;
-        if (has_duplicate_inputs || has_empty_inputs) {
-            const reportEl = this.$el.find(".common_problems");
-            reportEl.text("Detected Common Potential Problems");
-            if (has_empty_inputs) {
-                reportEl.after(`
-                    <p>
-                        The tool was executed with one or more empty input datasets. This frequently
-                        results in tool errors due to problematic input choices.
-                    <p>`);
-            }
-            if (has_duplicate_inputs) {
-                reportEl.after(`
-                    <p>
-                        The tool was executed with one or more duplicate input datasets. This frequently
-                        results in tool errors due to problematic input choices.
-                    <p>`);
-            }
-        }
-    },
-
-    /** Render the view */
-    render_error_page: function (dataset, job) {
-        this.$el.empty().append(`
-            ${this._templateHeader()}
-            <h2>Dataset Error Report</h2>
-            <p>An error occurred while running the tool <b>${job.tool_id}</b>.</p>
-            ${this.job_summary(job)}
-            <h3>Troubleshooting</h3>
-            <p>
-                There are a number of helpful resources to self diagnose and
-                correct problems.
-                <br>
-                Start here:
-                <b>
-                    <a href="https://galaxyproject.org/support/tool-error/" target="_blank">
-                        My job ended with an error. What can I do?
-                    </a>
-                </b>
-            </p>`);
-        this.$el.append("<h3>Issue Report</h3>").append(this._getBugFormTemplate(dataset, job));
-    },
-
-    job_summary: function (job) {
-        const tool_stderr = job.tool_stderr;
-        const job_stderr = job.job_stderr;
-        const job_messages = job.job_messages;
-        if (!tool_stderr && !job_stderr && !job_messages) {
-            return '<h3 class="common_problems"></h3>';
-        }
-        var message = "<h3>Details</h3>";
-        if (job_messages) {
-            message += "<p>Execution resulted in the following messages:</p>";
-            for (const job_message of job_messages) {
-                message += `<p><pre class="rounded code">${_.escape(job_message["desc"])}</pre></p>`;
-            }
-        }
-        if (tool_stderr) {
-            message += "<p>Tool generated the following standard error:</p>";
-            message += `<pre class="rounded code">${_.escape(tool_stderr)}</pre>`;
-        }
-        if (job_stderr) {
-            message += "<p>Galaxy job runner generated the following standard error:</p>";
-            message += `<pre class="code">${_.escape(job_stderr)}</pre>`;
-        }
-        message += `<h3 class="common_problems"></h3>`;
-        return message;
-    },
-
-    /** Display actions messages */
-    display_message: function (response, $el, doNotClear, safe) {
-        if (!safe) {
-            if (doNotClear) {
-                $el.append(new Ui.Message(response).$el);
-            } else {
-                $el.empty().html(new Ui.Message(response).$el);
-            }
-        } else {
-            if (doNotClear) {
-                $el.append(new Ui.UnescapedMessage(response).$el);
-            } else {
-                $el.empty().html(new Ui.UnescapedMessage(response).$el);
-            }
-        }
-    },
-
-    /** Main template */
-    _templateHeader: function () {
-        return `<div class="page-container edit-attr"><div class="response-message"></div></div>`;
-    },
-
-    /** Convert tab template */
-    _getBugFormTemplate: function (dataset, job) {
-        const Galaxy = getGalaxyInstance();
-        const userEmail = Galaxy.user.get("email");
-        const form = new Form({
-            inputs: [
-                {
-                    type: "text",
-                    hidden: !!userEmail,
-                    name: "email",
-                    value: userEmail,
-                    label: "Please provide your email:",
-                },
-                {
-                    type: "text",
-                    area: true,
-                    name: "message",
-                    label: "Please provide detailed information on the activities leading to this issue:",
-                },
-            ],
-            buttons: {
-                save: new Ui.Button({
-                    icon: "fa-bug",
-                    title: _l("Report"),
-                    cls: "btn btn-primary",
-                    floating: "clear",
-                    onclick: () => {
-                        var form_data = form.data.create();
-                        var url = `${getAppRoot()}api/jobs/${job.id}/error`;
-                        form_data.dataset_id = dataset.id;
-                        this.submit(form_data, url);
-                    },
-                }),
-            },
-        });
-        return form.$el;
-    },
-
-    /** Make ajax request */
-    submit: function (form_data, url) {
-        // Some required metadata
-        $.ajax({
-            type: "POST",
-            url: url,
-            data: form_data,
-            success: (response) => {
-                // Clear out the div
-                this.$el.empty().append(this._templateHeader());
-                // And display the messages.
-                response.messages.forEach((message) => {
-                    this.display_message(
-                        {
-                            status: message[1],
-                            message: message[0],
-                            persistent: true,
-                        },
-                        this.$(".response-message"),
-                        true,
-                        true
-                    );
-                });
-            },
-            error: () => {
-                var error_response = {
-                    status: "error",
-                    message: "Error occurred while saving. Please fill all the required fields and try again.",
-                    persistent: true,
-                    cls: "errormessage",
-                };
-                this.display_message(error_response, this.$(".response-message"));
-            },
-        });
-    },
-});
-
-export default {
-    View: View,
-};

From 982464d8efee908f8b7b492cbcf597362379f442 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 27 Jul 2021 18:06:09 -0400
Subject: [PATCH 100/218] Align styling to previous dataset error reporting
 page

---
 client/src/components/DatasetInformation/DatasetError.vue | 4 ++--
 client/src/components/Form/Elements/FormInput.vue         | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetError.vue b/client/src/components/DatasetInformation/DatasetError.vue
index 56109288092..e46e5910cc0 100644
--- a/client/src/components/DatasetInformation/DatasetError.vue
+++ b/client/src/components/DatasetInformation/DatasetError.vue
@@ -55,7 +55,7 @@
                         </a>
                     </b>
                 </p>
-                <h3 class="mb-2">Issue Report</h3>
+                <h3 class="mb-3">Issue Report</h3>
                 <b-alert v-if="errorMessage" variant="danger" show>{{ errorMessage }}</b-alert>
                 <b-alert v-for="resultMessage in resultMessages" :variant="resultMessage[1]" show>{{
                     resultMessage[0]
@@ -67,7 +67,7 @@
                     :area="true"
                     title="Please provide detailed information on the activities leading to this issue:"
                 />
-                <b-button variant="primary" @click="submit(dataset, user.email)" class="mt-2">
+                <b-button variant="primary" @click="submit(dataset, user.email)" class="mt-3">
                     <font-awesome-icon icon="bug" class="mr-1" />Report
                 </b-button>
             </div>
diff --git a/client/src/components/Form/Elements/FormInput.vue b/client/src/components/Form/Elements/FormInput.vue
index 05758a19b28..4bf6c1d70e9 100644
--- a/client/src/components/Form/Elements/FormInput.vue
+++ b/client/src/components/Form/Elements/FormInput.vue
@@ -1,5 +1,5 @@
 <template>
-    <textarea v-if="area" class="ui-input" v-model="currentValue" />
+    <textarea v-if="area" class="ui-textarea" v-model="currentValue"/>
     <input v-else class="ui-input" v-model="currentValue" />
 </template>
 <script>

From f6cf42d58cc632957a3cc8f6fcc2aad2b36a1773 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 27 Jul 2021 23:52:03 -0400
Subject: [PATCH 101/218] Use email returned from job details instead using the
 user provider, fix linting issues

---
 .../DatasetInformation/DatasetError.vue       | 76 +++++++++----------
 .../components/Form/Elements/FormInput.vue    |  2 +-
 2 files changed, 39 insertions(+), 39 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetError.vue b/client/src/components/DatasetInformation/DatasetError.vue
index e46e5910cc0..e4196333f3f 100644
--- a/client/src/components/DatasetInformation/DatasetError.vue
+++ b/client/src/components/DatasetInformation/DatasetError.vue
@@ -1,37 +1,33 @@
 <template>
-    <CurrentUser v-slot="{ user }">
-        <DatasetProvider :id="datasetId" v-slot="{ item: dataset, loading }">
+    <DatasetProvider :id="datasetId" v-slot="{ item: dataset }">
+        <JobDetailsProvider :jobid="dataset.creating_job" v-slot="{ result, loading }">
             <div v-if="!loading">
-                <JobDetailsProvider :jobid="dataset.creating_job" v-slot="{ result, loading }">
-                    <div v-if="!loading">
-                        <div class="page-container edit-attr">
-                            <div class="response-message"></div>
-                        </div>
-                        <h2>Dataset Error Report</h2>
-                        <p>
-                            An error occurred while running the tool <b>{{ result.tool_id }}</b
-                            >.
-                        </p>
-                        <div v-if="result.tool_stderr || result.job_stderr || result.job_messages">
-                            <h3>Details</h3>
-                        </div>
-                        <div v-if="result.job_messages">
-                            <p>Execution resulted in the following messages:</p>
-                            <div v-for="job_message in result.job_messages">
-                                <pre class="rounded code">{{ job_message["desc"] }}</pre>
-                            </div>
-                        </div>
-                        <div v-if="result.tool_stderr">
-                            <p>Tool generated the following standard error:</p>
-                            <pre class="rounded code">{{ result.tool_stderr }}</pre>
-                        </div>
-                        <div v-if="result.job_stderr">
-                            <p>Galaxy job runner generated the following standard error:</p>
-                            <pre class="rounded code">{{ result.job_stderr }}</pre>
-                        </div>
+                <div class="page-container edit-attr">
+                    <div class="response-message"></div>
+                </div>
+                <h2>Dataset Error Report</h2>
+                <p>
+                    An error occurred while running the tool <b>{{ result.tool_id }}</b
+                    >.
+                </p>
+                <div v-if="result.tool_stderr || result.job_stderr || result.job_messages">
+                    <h3>Details</h3>
+                </div>
+                <div v-if="result.job_messages">
+                    <p>Execution resulted in the following messages:</p>
+                    <div v-for="(job_message, index) in result.job_messages" :key="index">
+                        <pre class="rounded code">{{ job_message["desc"] }}</pre>
                     </div>
-                </JobDetailsProvider>
-                <JobProblemProvider :jobid="dataset.creating_job" v-slot="{ result, loading }">
+                </div>
+                <div v-if="result.tool_stderr">
+                    <p>Tool generated the following standard error:</p>
+                    <pre class="rounded code">{{ result.tool_stderr }}</pre>
+                </div>
+                <div v-if="result.job_stderr">
+                    <p>Galaxy job runner generated the following standard error:</p>
+                    <pre class="rounded code">{{ result.job_stderr }}</pre>
+                </div>
+                <JobProblemProvider :jobid="dataset.creating_job" v-slot="{ result }">
                     <div v-if="result && (result.has_duplicate_inputs || result.has_empty_inputs)">
                         <h3 class="common_problems">Detected Common Potential Problems</h3>
                         <p v-if="result.has_empty_inputs">
@@ -57,22 +53,26 @@
                 </p>
                 <h3 class="mb-3">Issue Report</h3>
                 <b-alert v-if="errorMessage" variant="danger" show>{{ errorMessage }}</b-alert>
-                <b-alert v-for="resultMessage in resultMessages" :variant="resultMessage[1]" show>{{
-                    resultMessage[0]
-                }}</b-alert>
-                <FormElement v-if="!user.email" id="email" v-model="email" title="Please provide your email:" />
+                <b-alert
+                    v-for="(resultMessage, index) in resultMessages"
+                    :key="index"
+                    :variant="resultMessage[1]"
+                    show
+                    >{{ resultMessage[0] }}</b-alert
+                >
+                <FormElement v-if="!result.user_email" id="email" v-model="email" title="Please provide your email:" />
                 <FormElement
                     id="message"
                     v-model="message"
                     :area="true"
                     title="Please provide detailed information on the activities leading to this issue:"
                 />
-                <b-button variant="primary" @click="submit(dataset, user.email)" class="mt-3">
+                <b-button variant="primary" @click="submit(dataset, result.user_email)" class="mt-3">
                     <font-awesome-icon icon="bug" class="mr-1" />Report
                 </b-button>
             </div>
-        </DatasetProvider>
-    </CurrentUser>
+        </JobDetailsProvider>
+    </DatasetProvider>
 </template>
 
 <script>
diff --git a/client/src/components/Form/Elements/FormInput.vue b/client/src/components/Form/Elements/FormInput.vue
index 4bf6c1d70e9..c667572e13c 100644
--- a/client/src/components/Form/Elements/FormInput.vue
+++ b/client/src/components/Form/Elements/FormInput.vue
@@ -1,5 +1,5 @@
 <template>
-    <textarea v-if="area" class="ui-textarea" v-model="currentValue"/>
+    <textarea v-if="area" class="ui-textarea" v-model="currentValue" />
     <input v-else class="ui-input" v-model="currentValue" />
 </template>
 <script>

From 629aae1008717ad1dc4eb82b29522d977b8e6c86 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 28 Jul 2021 10:20:11 -0400
Subject: [PATCH 102/218] Use proper provider key names in error display
 component, add services to submit error report

---
 .../DatasetInformation/DatasetError.vue       | 41 +++++++++++--------
 .../components/DatasetInformation/services.js | 18 ++++++++
 2 files changed, 43 insertions(+), 16 deletions(-)
 create mode 100644 client/src/components/DatasetInformation/services.js

diff --git a/client/src/components/DatasetInformation/DatasetError.vue b/client/src/components/DatasetInformation/DatasetError.vue
index e4196333f3f..aa8b346ea36 100644
--- a/client/src/components/DatasetInformation/DatasetError.vue
+++ b/client/src/components/DatasetInformation/DatasetError.vue
@@ -1,40 +1,44 @@
 <template>
-    <DatasetProvider :id="datasetId" v-slot="{ item: dataset }">
-        <JobDetailsProvider :jobid="dataset.creating_job" v-slot="{ result, loading }">
+    <DatasetProvider :id="datasetId" v-slot="{ item: dataset, loading: datasetLoading }">
+        <JobDetailsProvider
+            v-if="!datasetLoading"
+            :jobid="dataset.creating_job"
+            v-slot="{ result: jobDetails, loading }"
+        >
             <div v-if="!loading">
                 <div class="page-container edit-attr">
                     <div class="response-message"></div>
                 </div>
                 <h2>Dataset Error Report</h2>
                 <p>
-                    An error occurred while running the tool <b>{{ result.tool_id }}</b
+                    An error occurred while running the tool <b>{{ jobDetails.tool_id }}</b
                     >.
                 </p>
-                <div v-if="result.tool_stderr || result.job_stderr || result.job_messages">
+                <div v-if="jobDetails.tool_stderr || jobDetails.job_stderr || jobDetails.job_messages">
                     <h3>Details</h3>
                 </div>
-                <div v-if="result.job_messages">
+                <div v-if="jobDetails.job_messages">
                     <p>Execution resulted in the following messages:</p>
-                    <div v-for="(job_message, index) in result.job_messages" :key="index">
+                    <div v-for="(job_message, index) in jobDetails.job_messages" :key="index">
                         <pre class="rounded code">{{ job_message["desc"] }}</pre>
                     </div>
                 </div>
-                <div v-if="result.tool_stderr">
+                <div v-if="jobDetails.tool_stderr">
                     <p>Tool generated the following standard error:</p>
-                    <pre class="rounded code">{{ result.tool_stderr }}</pre>
+                    <pre class="rounded code">{{ jobDetails.tool_stderr }}</pre>
                 </div>
-                <div v-if="result.job_stderr">
+                <div v-if="jobDetails.job_stderr">
                     <p>Galaxy job runner generated the following standard error:</p>
-                    <pre class="rounded code">{{ result.job_stderr }}</pre>
+                    <pre class="rounded code">{{ jobDetails.job_stderr }}</pre>
                 </div>
-                <JobProblemProvider :jobid="dataset.creating_job" v-slot="{ result }">
-                    <div v-if="result && (result.has_duplicate_inputs || result.has_empty_inputs)">
+                <JobProblemProvider :jobid="dataset.creating_job" v-slot="{ result: jobProblems }">
+                    <div v-if="jobProblems && (jobProblems.has_duplicate_inputs || jobProblems.has_empty_inputs)">
                         <h3 class="common_problems">Detected Common Potential Problems</h3>
-                        <p v-if="result.has_empty_inputs">
+                        <p v-if="jobProblems.has_empty_inputs">
                             The tool was executed with one or more empty input datasets. This frequently results in tool
                             errors due to problematic input choices.
                         </p>
-                        <p v-if="result && result.has_duplicate_inputs">
+                        <p v-if="jobProblems.has_duplicate_inputs">
                             The tool was executed with one or more duplicate input datasets. This frequently results in
                             tool errors due to problematic input choices.
                         </p>
@@ -60,14 +64,19 @@
                     show
                     >{{ resultMessage[0] }}</b-alert
                 >
-                <FormElement v-if="!result.user_email" id="email" v-model="email" title="Please provide your email:" />
+                <FormElement
+                    v-if="!jobDetails.user_email"
+                    id="email"
+                    v-model="email"
+                    title="Please provide your email:"
+                />
                 <FormElement
                     id="message"
                     v-model="message"
                     :area="true"
                     title="Please provide detailed information on the activities leading to this issue:"
                 />
-                <b-button variant="primary" @click="submit(dataset, result.user_email)" class="mt-3">
+                <b-button variant="primary" @click="submit(dataset, jobDetails.user_email)" class="mt-3">
                     <font-awesome-icon icon="bug" class="mr-1" />Report
                 </b-button>
             </div>
diff --git a/client/src/components/DatasetInformation/services.js b/client/src/components/DatasetInformation/services.js
new file mode 100644
index 00000000000..7739f7fed83
--- /dev/null
+++ b/client/src/components/DatasetInformation/services.js
@@ -0,0 +1,18 @@
+import axios from "axios";
+import { rethrowSimple } from "utils/simple-error";
+import { getAppRoot } from "onload/loadConfig";
+
+export async function sendErrorReport(dataset, message, email) {
+    const payload = {
+        dataset_id: dataset.id,
+        message,
+        email,
+    };
+    const url = `${getAppRoot()}api/jobs/${dataset.creating_job}/error`;
+    try {
+        const { data } = await axios.post(url, payload);
+        return data.messages;
+    } catch (e) {
+        rethrowSimple(e);
+    }
+}

From 7e09bf7d85810f1bdb81a8c95594a747768c5853 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 28 Jul 2021 11:01:06 -0400
Subject: [PATCH 103/218] Remove unused import from dataset error component

---
 client/src/components/DatasetInformation/DatasetError.vue | 2 --
 1 file changed, 2 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetError.vue b/client/src/components/DatasetInformation/DatasetError.vue
index aa8b346ea36..6c09f3856c9 100644
--- a/client/src/components/DatasetInformation/DatasetError.vue
+++ b/client/src/components/DatasetInformation/DatasetError.vue
@@ -85,7 +85,6 @@
 </template>
 
 <script>
-import CurrentUser from "components/providers/CurrentUser";
 import FormElement from "components/Form/FormElement";
 import { DatasetProvider } from "components/WorkflowInvocationState/providers";
 import { JobDetailsProvider, JobProblemProvider } from "components/providers/JobProvider";
@@ -98,7 +97,6 @@ library.add(faBug);
 
 export default {
     components: {
-        CurrentUser,
         DatasetProvider,
         FontAwesomeIcon,
         FormElement,

From 00644733374e71e496a7120d5e98c109c22a303d Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 2 Aug 2021 11:19:57 -0400
Subject: [PATCH 104/218] Slightly increase margins in error page sections

---
 client/src/components/DatasetInformation/DatasetError.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetError.vue b/client/src/components/DatasetInformation/DatasetError.vue
index 6c09f3856c9..8802b74f70d 100644
--- a/client/src/components/DatasetInformation/DatasetError.vue
+++ b/client/src/components/DatasetInformation/DatasetError.vue
@@ -33,7 +33,7 @@
                 </div>
                 <JobProblemProvider :jobid="dataset.creating_job" v-slot="{ result: jobProblems }">
                     <div v-if="jobProblems && (jobProblems.has_duplicate_inputs || jobProblems.has_empty_inputs)">
-                        <h3 class="common_problems">Detected Common Potential Problems</h3>
+                        <h3 class="common_problems mt-3">Detected Common Potential Problems</h3>
                         <p v-if="jobProblems.has_empty_inputs">
                             The tool was executed with one or more empty input datasets. This frequently results in tool
                             errors due to problematic input choices.
@@ -44,7 +44,7 @@
                         </p>
                     </div>
                 </JobProblemProvider>
-                <h3>Troubleshooting</h3>
+                <h3 class="mt-3">Troubleshooting</h3>
                 <p>
                     There are a number of helpful resources to self diagnose and correct problems.
                     <br />

From 6451f7ff89817f82f8d6e6daf19a25d5f2fa6f67 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 2 Aug 2021 12:05:30 -0400
Subject: [PATCH 105/218] Add error handling to single query provider

---
 .../DatasetInformation/DatasetError.vue       | 171 +++++++++---------
 .../src/components/providers/JobProvider.js   |  17 +-
 .../providers/SingleQueryProvider.js          |   4 +-
 3 files changed, 106 insertions(+), 86 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetError.vue b/client/src/components/DatasetInformation/DatasetError.vue
index 8802b74f70d..b3be71720b2 100644
--- a/client/src/components/DatasetInformation/DatasetError.vue
+++ b/client/src/components/DatasetInformation/DatasetError.vue
@@ -1,87 +1,93 @@
 <template>
-    <DatasetProvider :id="datasetId" v-slot="{ item: dataset, loading: datasetLoading }">
-        <JobDetailsProvider
-            v-if="!datasetLoading"
-            :jobid="dataset.creating_job"
-            v-slot="{ result: jobDetails, loading }"
-        >
-            <div v-if="!loading">
-                <div class="page-container edit-attr">
-                    <div class="response-message"></div>
-                </div>
-                <h2>Dataset Error Report</h2>
-                <p>
-                    An error occurred while running the tool <b>{{ jobDetails.tool_id }}</b
-                    >.
-                </p>
-                <div v-if="jobDetails.tool_stderr || jobDetails.job_stderr || jobDetails.job_messages">
-                    <h3>Details</h3>
-                </div>
-                <div v-if="jobDetails.job_messages">
-                    <p>Execution resulted in the following messages:</p>
-                    <div v-for="(job_message, index) in jobDetails.job_messages" :key="index">
-                        <pre class="rounded code">{{ job_message["desc"] }}</pre>
+    <div>
+        <b-alert v-if="errorMessage" variant="danger" show>
+            <h4 class="alert-heading">Failed to access Dataset details.</h4>
+            {{ errorMessage }}
+        </b-alert>
+        <DatasetProvider :id="datasetId" v-slot="{ item: dataset, loading: datasetLoading }">
+            <JobDetailsProvider
+                v-if="!datasetLoading"
+                :jobid="dataset.creating_job"
+                v-slot="{ result: jobDetails, loading }"
+                @error="onError"
+            >
+                <div v-if="!loading">
+                    <div class="page-container edit-attr">
+                        <div class="response-message"></div>
                     </div>
-                </div>
-                <div v-if="jobDetails.tool_stderr">
-                    <p>Tool generated the following standard error:</p>
-                    <pre class="rounded code">{{ jobDetails.tool_stderr }}</pre>
-                </div>
-                <div v-if="jobDetails.job_stderr">
-                    <p>Galaxy job runner generated the following standard error:</p>
-                    <pre class="rounded code">{{ jobDetails.job_stderr }}</pre>
-                </div>
-                <JobProblemProvider :jobid="dataset.creating_job" v-slot="{ result: jobProblems }">
-                    <div v-if="jobProblems && (jobProblems.has_duplicate_inputs || jobProblems.has_empty_inputs)">
-                        <h3 class="common_problems mt-3">Detected Common Potential Problems</h3>
-                        <p v-if="jobProblems.has_empty_inputs">
-                            The tool was executed with one or more empty input datasets. This frequently results in tool
-                            errors due to problematic input choices.
-                        </p>
-                        <p v-if="jobProblems.has_duplicate_inputs">
-                            The tool was executed with one or more duplicate input datasets. This frequently results in
-                            tool errors due to problematic input choices.
-                        </p>
+                    <h2>Dataset Error Report</h2>
+                    <p>
+                        An error occurred while running the tool <b>{{ jobDetails.tool_id }}</b
+                        >.
+                    </p>
+                    <div v-if="jobDetails.tool_stderr || jobDetails.job_stderr || jobDetails.job_messages">
+                        <h3>Details</h3>
                     </div>
-                </JobProblemProvider>
-                <h3 class="mt-3">Troubleshooting</h3>
-                <p>
-                    There are a number of helpful resources to self diagnose and correct problems.
-                    <br />
-                    Start here:
-                    <b>
-                        <a href="https://galaxyproject.org/support/tool-error/" target="_blank">
-                            My job ended with an error. What can I do?
-                        </a>
-                    </b>
-                </p>
-                <h3 class="mb-3">Issue Report</h3>
-                <b-alert v-if="errorMessage" variant="danger" show>{{ errorMessage }}</b-alert>
-                <b-alert
-                    v-for="(resultMessage, index) in resultMessages"
-                    :key="index"
-                    :variant="resultMessage[1]"
-                    show
-                    >{{ resultMessage[0] }}</b-alert
-                >
-                <FormElement
-                    v-if="!jobDetails.user_email"
-                    id="email"
-                    v-model="email"
-                    title="Please provide your email:"
-                />
-                <FormElement
-                    id="message"
-                    v-model="message"
-                    :area="true"
-                    title="Please provide detailed information on the activities leading to this issue:"
-                />
-                <b-button variant="primary" @click="submit(dataset, jobDetails.user_email)" class="mt-3">
-                    <font-awesome-icon icon="bug" class="mr-1" />Report
-                </b-button>
-            </div>
-        </JobDetailsProvider>
-    </DatasetProvider>
+                    <div v-if="jobDetails.job_messages">
+                        <p>Execution resulted in the following messages:</p>
+                        <div v-for="(job_message, index) in jobDetails.job_messages" :key="index">
+                            <pre class="rounded code">{{ job_message["desc"] }}</pre>
+                        </div>
+                    </div>
+                    <div v-if="jobDetails.tool_stderr">
+                        <p>Tool generated the following standard error:</p>
+                        <pre class="rounded code">{{ jobDetails.tool_stderr }}</pre>
+                    </div>
+                    <div v-if="jobDetails.job_stderr">
+                        <p>Galaxy job runner generated the following standard error:</p>
+                        <pre class="rounded code">{{ jobDetails.job_stderr }}</pre>
+                    </div>
+                    <JobProblemProvider :jobid="dataset.creating_job" v-slot="{ result: jobProblems }" @error="onError">
+                        <div v-if="jobProblems && (jobProblems.has_duplicate_inputs || jobProblems.has_empty_inputs)">
+                            <h3 class="common_problems mt-3">Detected Common Potential Problems</h3>
+                            <p v-if="jobProblems.has_empty_inputs">
+                                The tool was executed with one or more empty input datasets. This frequently results in
+                                tool errors due to problematic input choices.
+                            </p>
+                            <p v-if="jobProblems.has_duplicate_inputs">
+                                The tool was executed with one or more duplicate input datasets. This frequently results
+                                in tool errors due to problematic input choices.
+                            </p>
+                        </div>
+                    </JobProblemProvider>
+                    <h3 class="mt-3">Troubleshooting</h3>
+                    <p>
+                        There are a number of helpful resources to self diagnose and correct problems.
+                        <br />
+                        Start here:
+                        <b>
+                            <a href="https://galaxyproject.org/support/tool-error/" target="_blank">
+                                My job ended with an error. What can I do?
+                            </a>
+                        </b>
+                    </p>
+                    <h3 class="mb-3">Issue Report</h3>
+                    <b-alert
+                        v-for="(resultMessage, index) in resultMessages"
+                        :key="index"
+                        :variant="resultMessage[1]"
+                        show
+                        >{{ resultMessage[0] }}</b-alert
+                    >
+                    <FormElement
+                        v-if="!jobDetails.user_email"
+                        id="email"
+                        v-model="email"
+                        title="Please provide your email:"
+                    />
+                    <FormElement
+                        id="message"
+                        v-model="message"
+                        :area="true"
+                        title="Please provide detailed information on the activities leading to this issue:"
+                    />
+                    <b-button variant="primary" @click="submit(dataset, jobDetails.user_email)" class="mt-3">
+                        <font-awesome-icon icon="bug" class="mr-1" />Report
+                    </b-button>
+                </div>
+            </JobDetailsProvider>
+        </DatasetProvider>
+    </div>
 </template>
 
 <script>
@@ -118,6 +124,9 @@ export default {
         };
     },
     methods: {
+        onError(err) {
+            this.errorMessage = err;
+        },
         submit(dataset, userEmail) {
             const email = this.email || userEmail;
             const message = this.message;
diff --git a/client/src/components/providers/JobProvider.js b/client/src/components/providers/JobProvider.js
index 913af215cc4..484432e3415 100644
--- a/client/src/components/providers/JobProvider.js
+++ b/client/src/components/providers/JobProvider.js
@@ -1,17 +1,26 @@
 import axios from "axios";
 import { getAppRoot } from "onload/loadConfig";
 import { SingleQueryProvider } from "components/providers/SingleQueryProvider";
+import { rethrowSimple } from "utils/simple-error";
 
 async function jobDetails({ jobid }) {
     const url = `${getAppRoot()}api/jobs/${jobid}?full=True`;
-    const { data } = await axios.get(url);
-    return data;
+    try {
+        const { data } = await axios.get(url);
+        return data;
+    } catch (e) {
+        rethrowSimple(e);
+    }
 }
 
 async function jobProblems({ jobid }) {
     const url = `${getAppRoot()}api/jobs/${jobid}/common_problems`;
-    const { data } = await axios.get(url);
-    return data;
+    try {
+        const { data } = await axios.get(url);
+        return data;
+    } catch (e) {
+        rethrowSimple(e);
+    }
 }
 
 export const JobDetailsProvider = SingleQueryProvider(jobDetails);
diff --git a/client/src/components/providers/SingleQueryProvider.js b/client/src/components/providers/SingleQueryProvider.js
index 5327ac4e506..dff317ba5d4 100644
--- a/client/src/components/providers/SingleQueryProvider.js
+++ b/client/src/components/providers/SingleQueryProvider.js
@@ -35,7 +35,9 @@ export const SingleQueryProvider = (lookup) => {
 
             let lookupPromise = promiseCache.get(this.cacheKey);
             if (!lookupPromise) {
-                lookupPromise = lookup(this.$attrs);
+                lookupPromise = lookup(this.$attrs).catch((err) => {
+                    this.$emit("error", err);
+                });
                 promiseCache.set(this.cacheKey, lookupPromise);
             }
 

From 421427af2650ebdca9c7b70312b05ddb260b4664 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Aug 2021 16:48:32 -0400
Subject: [PATCH 106/218] Add DatasetError test case

---
 .../DatasetInformation/DatasetError.test.js   | 40 +++++++++++++++++++
 .../DatasetInformation/DatasetError.vue       |  5 ++-
 .../src/components/providers/MockProvider.js  | 11 +++++
 3 files changed, 54 insertions(+), 2 deletions(-)
 create mode 100644 client/src/components/DatasetInformation/DatasetError.test.js
 create mode 100644 client/src/components/providers/MockProvider.js

diff --git a/client/src/components/DatasetInformation/DatasetError.test.js b/client/src/components/DatasetInformation/DatasetError.test.js
new file mode 100644
index 00000000000..b1af6fb2da9
--- /dev/null
+++ b/client/src/components/DatasetInformation/DatasetError.test.js
@@ -0,0 +1,40 @@
+import { mount } from "@vue/test-utils";
+import { getLocalVue } from "jest/helpers";
+import DatasetError from "./DatasetError";
+import MockProvider from "../providers/MockProvider";
+
+jest.mock("components/WorkflowInvocationState/providers", () => {
+    return {}; // stubbed below
+});
+
+const localVue = getLocalVue();
+
+describe("DatasetError", () => {
+    let wrapper;
+    
+    beforeEach(() => {
+        wrapper = mount(DatasetError, {
+            propsData: {
+                datasetId: "dataset_id",
+            },
+            localVue,
+            stubs: {
+                JobDetailsProvider: MockProvider({
+                    result: { tool_id: "tool_id", tool_stderr: "tool_stderr", job_stderr: "job_stderr" },
+                }),
+                JobProblemProvider: MockProvider({ result: { has_duplicate_inputs: true, has_empty_inputs: true } }),
+                DatasetProvider: MockProvider({
+                    resultLabel: "item",
+                    result: { id: "dataset_id", creating_job: "creating_job" },
+                }),
+                FontAwesomeIcon: false,
+                FormElement: false,
+            },
+        });
+    });
+
+    it("check props", async () => {
+        expect(wrapper.find("#dataset-error-tool-id").text()).toBe("tool_id");
+        expect(wrapper.find("#dataset-error-tool-stderr").text()).toBe("tool_stderr");
+    });
+});
diff --git a/client/src/components/DatasetInformation/DatasetError.vue b/client/src/components/DatasetInformation/DatasetError.vue
index b3be71720b2..616ede5624f 100644
--- a/client/src/components/DatasetInformation/DatasetError.vue
+++ b/client/src/components/DatasetInformation/DatasetError.vue
@@ -17,7 +17,8 @@
                     </div>
                     <h2>Dataset Error Report</h2>
                     <p>
-                        An error occurred while running the tool <b>{{ jobDetails.tool_id }}</b
+                        An error occurred while running the tool
+                        <b id="dataset-error-tool-id">{{ jobDetails.tool_id }}</b
                         >.
                     </p>
                     <div v-if="jobDetails.tool_stderr || jobDetails.job_stderr || jobDetails.job_messages">
@@ -31,7 +32,7 @@
                     </div>
                     <div v-if="jobDetails.tool_stderr">
                         <p>Tool generated the following standard error:</p>
-                        <pre class="rounded code">{{ jobDetails.tool_stderr }}</pre>
+                        <pre id="dataset-error-tool-stderr" class="rounded code">{{ jobDetails.tool_stderr }}</pre>
                     </div>
                     <div v-if="jobDetails.job_stderr">
                         <p>Galaxy job runner generated the following standard error:</p>
diff --git a/client/src/components/providers/MockProvider.js b/client/src/components/providers/MockProvider.js
new file mode 100644
index 00000000000..c35e49d92e5
--- /dev/null
+++ b/client/src/components/providers/MockProvider.js
@@ -0,0 +1,11 @@
+const MockProvider = (fakeData) => ({
+    render() {
+        const resultLabel = fakeData.resultLabel || "result";
+        return this.$scopedSlots.default({
+            [resultLabel]: fakeData.result,
+            loaded: true,
+        });
+    },
+});
+
+export default MockProvider;

From eb1439cae3547833deda536f9a2bfc956830c9bf Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Aug 2021 17:18:17 -0400
Subject: [PATCH 107/218] Expand dataset error rendering test case

---
 .../DatasetInformation/DatasetError.test.js   | 67 ++++++++++++-------
 .../DatasetInformation/DatasetError.vue       |  8 +--
 2 files changed, 48 insertions(+), 27 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetError.test.js b/client/src/components/DatasetInformation/DatasetError.test.js
index b1af6fb2da9..c50488aac85 100644
--- a/client/src/components/DatasetInformation/DatasetError.test.js
+++ b/client/src/components/DatasetInformation/DatasetError.test.js
@@ -9,32 +9,53 @@ jest.mock("components/WorkflowInvocationState/providers", () => {
 
 const localVue = getLocalVue();
 
-describe("DatasetError", () => {
-    let wrapper;
-    
-    beforeEach(() => {
-        wrapper = mount(DatasetError, {
-            propsData: {
-                datasetId: "dataset_id",
-            },
-            localVue,
-            stubs: {
-                JobDetailsProvider: MockProvider({
-                    result: { tool_id: "tool_id", tool_stderr: "tool_stderr", job_stderr: "job_stderr" },
-                }),
-                JobProblemProvider: MockProvider({ result: { has_duplicate_inputs: true, has_empty_inputs: true } }),
-                DatasetProvider: MockProvider({
-                    resultLabel: "item",
-                    result: { id: "dataset_id", creating_job: "creating_job" },
-                }),
-                FontAwesomeIcon: false,
-                FormElement: false,
-            },
-        });
+function buildWrapper(has_duplicate_inputs = true, has_empty_inputs = true) {
+    return mount(DatasetError, {
+        propsData: {
+            datasetId: "dataset_id",
+        },
+        localVue,
+        stubs: {
+            JobDetailsProvider: MockProvider({
+                result: {
+                    tool_id: "tool_id",
+                    tool_stderr: "tool_stderr",
+                    job_stderr: "job_stderr",
+                    job_messages: [{ desc: "message_1" }, { desc: "message_2" }],
+                },
+            }),
+            JobProblemProvider: MockProvider({
+                result: { has_duplicate_inputs: has_duplicate_inputs, has_empty_inputs: has_empty_inputs },
+            }),
+            DatasetProvider: MockProvider({
+                resultLabel: "item",
+                result: { id: "dataset_id", creating_job: "creating_job" },
+            }),
+            FontAwesomeIcon: false,
+            FormElement: false,
+        },
     });
+}
 
-    it("check props", async () => {
+describe("DatasetError", () => {
+    it("check props with common problems", async () => {
+        const wrapper = buildWrapper();
         expect(wrapper.find("#dataset-error-tool-id").text()).toBe("tool_id");
         expect(wrapper.find("#dataset-error-tool-stderr").text()).toBe("tool_stderr");
+        expect(wrapper.find("#dataset-error-job-stderr").text()).toBe("job_stderr");
+        const messages = wrapper.findAll("#dataset-error-job-messages .code");
+        expect(messages.at(0).text()).toBe("message_1");
+        expect(messages.at(1).text()).toBe("message_2");
+        expect(wrapper.find("#dataset-error-has-empty-inputs")).toBeDefined();
+        expect(wrapper.find("#dataset-error-has-duplicate-inputs")).toBeDefined();
+    });
+
+    it("check props without common problems", async () => {
+        const wrapper = buildWrapper(false, false);
+        expect(wrapper.find("#dataset-error-tool-id").text()).toBe("tool_id");
+        expect(wrapper.find("#dataset-error-tool-stderr").text()).toBe("tool_stderr");
+        expect(wrapper.find("#dataset-error-job-stderr").text()).toBe("job_stderr");
+        expect(wrapper.findAll("#dataset-error-has-empty-inputs").length).toBe(0);
+        expect(wrapper.findAll("#dataset-error-has-duplicate-inputs").length).toBe(0);
     });
 });
diff --git a/client/src/components/DatasetInformation/DatasetError.vue b/client/src/components/DatasetInformation/DatasetError.vue
index 616ede5624f..5f5d27957b0 100644
--- a/client/src/components/DatasetInformation/DatasetError.vue
+++ b/client/src/components/DatasetInformation/DatasetError.vue
@@ -24,7 +24,7 @@
                     <div v-if="jobDetails.tool_stderr || jobDetails.job_stderr || jobDetails.job_messages">
                         <h3>Details</h3>
                     </div>
-                    <div v-if="jobDetails.job_messages">
+                    <div v-if="jobDetails.job_messages" id="dataset-error-job-messages">
                         <p>Execution resulted in the following messages:</p>
                         <div v-for="(job_message, index) in jobDetails.job_messages" :key="index">
                             <pre class="rounded code">{{ job_message["desc"] }}</pre>
@@ -36,16 +36,16 @@
                     </div>
                     <div v-if="jobDetails.job_stderr">
                         <p>Galaxy job runner generated the following standard error:</p>
-                        <pre class="rounded code">{{ jobDetails.job_stderr }}</pre>
+                        <pre id="dataset-error-job-stderr" class="rounded code">{{ jobDetails.job_stderr }}</pre>
                     </div>
                     <JobProblemProvider :jobid="dataset.creating_job" v-slot="{ result: jobProblems }" @error="onError">
                         <div v-if="jobProblems && (jobProblems.has_duplicate_inputs || jobProblems.has_empty_inputs)">
                             <h3 class="common_problems mt-3">Detected Common Potential Problems</h3>
-                            <p v-if="jobProblems.has_empty_inputs">
+                            <p v-if="jobProblems.has_empty_inputs" id="dataset-error-has-empty-inputs">
                                 The tool was executed with one or more empty input datasets. This frequently results in
                                 tool errors due to problematic input choices.
                             </p>
-                            <p v-if="jobProblems.has_duplicate_inputs">
+                            <p v-if="jobProblems.has_duplicate_inputs" id="dataset-error-has-duplicate-inputs">
                                 The tool was executed with one or more duplicate input datasets. This frequently results
                                 in tool errors due to problematic input choices.
                             </p>

From 3398d1e617ef1965a893a55655fef48cf9c38095 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Aug 2021 17:28:04 -0400
Subject: [PATCH 108/218] Add email input element rendering test to dataset
 error

---
 .../DatasetInformation/DatasetError.test.js           |  7 +++++--
 .../components/DatasetInformation/DatasetError.vue    | 11 ++++++++---
 client/src/components/Form/Elements/FormInput.vue     |  4 ++--
 3 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetError.test.js b/client/src/components/DatasetInformation/DatasetError.test.js
index c50488aac85..9fd95ad9310 100644
--- a/client/src/components/DatasetInformation/DatasetError.test.js
+++ b/client/src/components/DatasetInformation/DatasetError.test.js
@@ -9,7 +9,7 @@ jest.mock("components/WorkflowInvocationState/providers", () => {
 
 const localVue = getLocalVue();
 
-function buildWrapper(has_duplicate_inputs = true, has_empty_inputs = true) {
+function buildWrapper(has_duplicate_inputs = true, has_empty_inputs = true, user_email = "") {
     return mount(DatasetError, {
         propsData: {
             datasetId: "dataset_id",
@@ -22,6 +22,7 @@ function buildWrapper(has_duplicate_inputs = true, has_empty_inputs = true) {
                     tool_stderr: "tool_stderr",
                     job_stderr: "job_stderr",
                     job_messages: [{ desc: "message_1" }, { desc: "message_2" }],
+                    user_email: user_email,
                 },
             }),
             JobProblemProvider: MockProvider({
@@ -48,14 +49,16 @@ describe("DatasetError", () => {
         expect(messages.at(1).text()).toBe("message_2");
         expect(wrapper.find("#dataset-error-has-empty-inputs")).toBeDefined();
         expect(wrapper.find("#dataset-error-has-duplicate-inputs")).toBeDefined();
+        expect(wrapper.findAll("#dataset-error-email").length).toBe(1);
     });
 
     it("check props without common problems", async () => {
-        const wrapper = buildWrapper(false, false);
+        const wrapper = buildWrapper(false, false, "user_email");
         expect(wrapper.find("#dataset-error-tool-id").text()).toBe("tool_id");
         expect(wrapper.find("#dataset-error-tool-stderr").text()).toBe("tool_stderr");
         expect(wrapper.find("#dataset-error-job-stderr").text()).toBe("job_stderr");
         expect(wrapper.findAll("#dataset-error-has-empty-inputs").length).toBe(0);
         expect(wrapper.findAll("#dataset-error-has-duplicate-inputs").length).toBe(0);
+        expect(wrapper.findAll("#dataset-error-email").length).toBe(0);
     });
 });
diff --git a/client/src/components/DatasetInformation/DatasetError.vue b/client/src/components/DatasetInformation/DatasetError.vue
index 5f5d27957b0..2e3c2c14ec7 100644
--- a/client/src/components/DatasetInformation/DatasetError.vue
+++ b/client/src/components/DatasetInformation/DatasetError.vue
@@ -72,17 +72,22 @@
                     >
                     <FormElement
                         v-if="!jobDetails.user_email"
-                        id="email"
+                        id="dataset-error-email"
                         v-model="email"
                         title="Please provide your email:"
                     />
                     <FormElement
-                        id="message"
+                        id="dataset-error-message"
                         v-model="message"
                         :area="true"
                         title="Please provide detailed information on the activities leading to this issue:"
                     />
-                    <b-button variant="primary" @click="submit(dataset, jobDetails.user_email)" class="mt-3">
+                    <b-button
+                        id="dataset-error-submit"
+                        variant="primary"
+                        @click="submit(dataset, jobDetails.user_email)"
+                        class="mt-3"
+                    >
                         <font-awesome-icon icon="bug" class="mr-1" />Report
                     </b-button>
                 </div>
diff --git a/client/src/components/Form/Elements/FormInput.vue b/client/src/components/Form/Elements/FormInput.vue
index c667572e13c..d2cc0264769 100644
--- a/client/src/components/Form/Elements/FormInput.vue
+++ b/client/src/components/Form/Elements/FormInput.vue
@@ -1,6 +1,6 @@
 <template>
-    <textarea v-if="area" class="ui-textarea" v-model="currentValue" />
-    <input v-else class="ui-input" v-model="currentValue" />
+    <textarea v-if="area" :id="id" class="ui-textarea" v-model="currentValue" />
+    <input v-else :id="id" class="ui-input" v-model="currentValue" />
 </template>
 <script>
 export default {

From 20e7c8f534d717e5976ec9bdce2630de6b5bba49 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Aug 2021 23:16:54 -0400
Subject: [PATCH 109/218] Fix tool id style in dataset error report to avoid
 overflow

---
 client/src/components/DatasetInformation/DatasetError.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/DatasetInformation/DatasetError.vue b/client/src/components/DatasetInformation/DatasetError.vue
index 2e3c2c14ec7..5618117ab4d 100644
--- a/client/src/components/DatasetInformation/DatasetError.vue
+++ b/client/src/components/DatasetInformation/DatasetError.vue
@@ -18,7 +18,7 @@
                     <h2>Dataset Error Report</h2>
                     <p>
                         An error occurred while running the tool
-                        <b id="dataset-error-tool-id">{{ jobDetails.tool_id }}</b
+                        <b id="dataset-error-tool-id" class="text-break">{{ jobDetails.tool_id }}</b
                         >.
                     </p>
                     <div v-if="jobDetails.tool_stderr || jobDetails.job_stderr || jobDetails.job_messages">

From 2907c284abcb323c4964801c46830f2df8c4bc00 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 4 Aug 2021 07:54:41 -0400
Subject: [PATCH 110/218] Use workflow step title as defined in the workflow
 model

---
 client/src/components/Workflow/Run/WorkflowRunToolStep.vue | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
index c1f616f070d..5d28ea26698 100644
--- a/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunToolStep.vue
@@ -1,6 +1,6 @@
 <template>
     <div :step-label="model.step_label">
-        <FormCard :title="title" icon="fa-wrench" :collapsible="true" :collapsed.sync="collapsed">
+        <FormCard :title="model.fixed_title" icon="fa-wrench" :collapsible="true" :collapsed.sync="collapsed">
             <template v-slot:body>
                 <FormMessage :message="errorText" variant="danger" :persistent="true" />
                 <FormDisplay
@@ -77,11 +77,6 @@ export default {
             }
         },
     },
-    computed: {
-        title() {
-            return `${this.model.name} ${this.model.description} (Galaxy Version ${this.model.version})`;
-        },
-    },
     methods: {
         onReplaceParams() {
             const params = {};

From aebdfe9bba8fbcec5fdba36e3d61d55810f325ed Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 4 Aug 2021 15:27:08 -0400
Subject: [PATCH 111/218] Redirect analysis route from dataset edit attribute
 module to vue component

---
 client/src/entry/analysis/AnalysisRouter.js | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/client/src/entry/analysis/AnalysisRouter.js b/client/src/entry/analysis/AnalysisRouter.js
index 1e34faef65a..09b69422919 100644
--- a/client/src/entry/analysis/AnalysisRouter.js
+++ b/client/src/entry/analysis/AnalysisRouter.js
@@ -42,7 +42,7 @@ import HistoryList from "mvc/history/history-list";
 import PluginList from "components/PluginList.vue";
 import QueryStringParsing from "utils/query-string-parsing";
 import DatasetError from "components/DatasetInformation/DatasetError";
-import DatasetEditAttributes from "mvc/dataset/dataset-edit-attributes";
+import DatasetAttributes from "components/DatasetInformation/DatasetAttributes";
 import Citations from "components/Citation/Citations.vue";
 import DisplayStructure from "components/DisplayStructured.vue";
 import { CloudAuth } from "components/User/CloudAuth";
@@ -385,8 +385,9 @@ export const getAnalysisRouter = (Galaxy) => {
             this._display_vue_helper(CustomBuilds);
         },
 
-        show_dataset_edit_attributes: function () {
-            this.page.display(new DatasetEditAttributes.View());
+        show_dataset_edit_attributes: function (params) {
+            const datasetId = params.dataset_id;
+            this._display_vue_helper(DatasetAttributes, { datasetId: datasetId });
         },
 
         show_dataset_error: function (params) {

From 39cdadd5d444d52efc28e82a77305c10fdead2b1 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 4 Aug 2021 15:43:18 -0400
Subject: [PATCH 112/218] Add preliminary dataset attributes vue component
 shell

---
 .../DatasetInformation/DatasetAttributes.vue  | 92 +++++++++++++++++++
 1 file changed, 92 insertions(+)
 create mode 100644 client/src/components/DatasetInformation/DatasetAttributes.vue

diff --git a/client/src/components/DatasetInformation/DatasetAttributes.vue b/client/src/components/DatasetInformation/DatasetAttributes.vue
new file mode 100644
index 00000000000..1a44606107d
--- /dev/null
+++ b/client/src/components/DatasetInformation/DatasetAttributes.vue
@@ -0,0 +1,92 @@
+<template>
+    <div>
+        <h4>Edit dataset attributes</h4>
+        <b-alert v-if="messageText" :variant="messageVariant" show>
+            <h4 class="alert-heading">Failed to access Dataset details.</h4>
+            {{ messageText }}
+        </b-alert>
+        <DatasetProvider :id="datasetId" v-slot="{ item: dataset, loading: datasetLoading }">
+            <div class="mt-3">
+                <b-tabs>
+                    <b-tab>
+                        <template #title>
+                            <font-awesome-icon icon="bars" class="mr-1"/>Attributes
+                        </template>
+                        <p>I'm the first tab</p>
+                    </b-tab>
+                    <b-tab>
+                        <template #title>
+                            <font-awesome-icon icon="fas-gear" class="mr-1"/>Convert
+                        </template>
+                        <p>I'm the second tab</p>
+                    </b-tab>
+                    <b-tab>
+                        <template #title>
+                            <font-awesome-icon icon="database" class="mr-1"/>Datatypes
+                        </template>
+                        <p>I'm the second tab</p>
+                    </b-tab>
+                    <b-tab>
+                        <template #title>
+                            <font-awesome-icon icon="user" class="mr-1"/>Permissions
+                        </template>
+                        <p>I'm the second tab</p>
+                    </b-tab>
+                </b-tabs>
+            </div>
+        </DatasetProvider>
+    </div>
+</template>
+
+<script>
+import FormElement from "components/Form/FormElement";
+import { DatasetProvider } from "components/WorkflowInvocationState/providers";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faBars, faDatabase, faGear, faUser } from "@fortawesome/free-solid-svg-icons";
+import { sendErrorReport } from "./services";
+
+library.add(faBars);
+library.add(faDatabase);
+library.add(faGear);
+library.add(faUser);
+
+export default {
+    components: {
+        DatasetProvider,
+        FontAwesomeIcon,
+    },
+    props: {
+        datasetId: {
+            type: String,
+            required: true,
+        },
+    },
+    data() {
+        return {
+            message: null,
+            email: null,
+            messageText: null,
+            messageVariant: null,
+            resultMessages: [],
+        };
+    },
+    methods: {
+        onError(err) {
+            this.messageText = err;
+        },
+        submit(dataset, userEmail) {
+            const email = this.email || userEmail;
+            const message = this.message;
+            sendErrorReport(dataset, message, email).then(
+                (resultMessages) => {
+                    this.resultMessages = resultMessages;
+                },
+                (messageText) => {
+                    this.messageText = messageText;
+                }
+            );
+        },
+    },
+};
+</script>

From 1d0a7c6a1e672322458a26057892da4cb5fd7c94 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 4 Aug 2021 15:51:59 -0400
Subject: [PATCH 113/218] Add tabs, icons and titles to dataset attributes
 component

---
 .../DatasetInformation/DatasetAttributes.vue  | 29 +++++++------------
 1 file changed, 10 insertions(+), 19 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetAttributes.vue b/client/src/components/DatasetInformation/DatasetAttributes.vue
index 1a44606107d..b469840b7b7 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.vue
+++ b/client/src/components/DatasetInformation/DatasetAttributes.vue
@@ -1,36 +1,28 @@
 <template>
     <div>
-        <h4>Edit dataset attributes</h4>
+        <h4>Edit Dataset Attributes</h4>
         <b-alert v-if="messageText" :variant="messageVariant" show>
-            <h4 class="alert-heading">Failed to access Dataset details.</h4>
+            <h4 class="alert-heading">Failed to access dataset details.</h4>
             {{ messageText }}
         </b-alert>
         <DatasetProvider :id="datasetId" v-slot="{ item: dataset, loading: datasetLoading }">
             <div class="mt-3">
                 <b-tabs>
                     <b-tab>
-                        <template #title>
-                            <font-awesome-icon icon="bars" class="mr-1"/>Attributes
-                        </template>
+                        <template #title><font-awesome-icon icon="bars" class="mr-1" />Attributes</template>
                         <p>I'm the first tab</p>
                     </b-tab>
                     <b-tab>
-                        <template #title>
-                            <font-awesome-icon icon="fas-gear" class="mr-1"/>Convert
-                        </template>
+                        <template #title><font-awesome-icon icon="cog" class="mr-1" />Convert</template>
                         <p>I'm the second tab</p>
                     </b-tab>
                     <b-tab>
-                        <template #title>
-                            <font-awesome-icon icon="database" class="mr-1"/>Datatypes
-                        </template>
-                        <p>I'm the second tab</p>
+                        <template #title><font-awesome-icon icon="database" class="mr-1" />Datatypes</template>
+                        <p>I'm the third tab</p>
                     </b-tab>
                     <b-tab>
-                        <template #title>
-                            <font-awesome-icon icon="user" class="mr-1"/>Permissions
-                        </template>
-                        <p>I'm the second tab</p>
+                        <template #title><font-awesome-icon icon="user" class="mr-1" />Permissions</template>
+                        <p>I'm the fourth tab</p>
                     </b-tab>
                 </b-tabs>
             </div>
@@ -43,12 +35,12 @@ import FormElement from "components/Form/FormElement";
 import { DatasetProvider } from "components/WorkflowInvocationState/providers";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { library } from "@fortawesome/fontawesome-svg-core";
-import { faBars, faDatabase, faGear, faUser } from "@fortawesome/free-solid-svg-icons";
+import { faBars, faDatabase, faCog, faUser } from "@fortawesome/free-solid-svg-icons";
 import { sendErrorReport } from "./services";
 
 library.add(faBars);
 library.add(faDatabase);
-library.add(faGear);
+library.add(faCog);
 library.add(faUser);
 
 export default {
@@ -68,7 +60,6 @@ export default {
             email: null,
             messageText: null,
             messageVariant: null,
-            resultMessages: [],
         };
     },
     methods: {

From fc62f82a2e534f20cb60a5bcb8f5eb66c70a6ed0 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 4 Aug 2021 16:05:35 -0400
Subject: [PATCH 114/218] Add dataset attributes provider and embed in
 component

---
 .../DatasetInformation/DatasetAttributes.vue     | 10 +++++-----
 .../src/components/providers/DatasetProvider.js  | 16 ++++++++++++++++
 2 files changed, 21 insertions(+), 5 deletions(-)
 create mode 100644 client/src/components/providers/DatasetProvider.js

diff --git a/client/src/components/DatasetInformation/DatasetAttributes.vue b/client/src/components/DatasetInformation/DatasetAttributes.vue
index b469840b7b7..e9f33aa7e31 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.vue
+++ b/client/src/components/DatasetInformation/DatasetAttributes.vue
@@ -5,8 +5,8 @@
             <h4 class="alert-heading">Failed to access dataset details.</h4>
             {{ messageText }}
         </b-alert>
-        <DatasetProvider :id="datasetId" v-slot="{ item: dataset, loading: datasetLoading }">
-            <div class="mt-3">
+        <DatasetAttributesProvider :id="datasetId" v-slot="{ result: dataset, loading }">
+            <div v-if="!loading" class="mt-3">
                 <b-tabs>
                     <b-tab>
                         <template #title><font-awesome-icon icon="bars" class="mr-1" />Attributes</template>
@@ -26,13 +26,13 @@
                     </b-tab>
                 </b-tabs>
             </div>
-        </DatasetProvider>
+        </DatasetAttributesProvider>
     </div>
 </template>
 
 <script>
 import FormElement from "components/Form/FormElement";
-import { DatasetProvider } from "components/WorkflowInvocationState/providers";
+import { DatasetAttributesProvider } from "components/providers/DatasetProvider";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { library } from "@fortawesome/fontawesome-svg-core";
 import { faBars, faDatabase, faCog, faUser } from "@fortawesome/free-solid-svg-icons";
@@ -45,7 +45,7 @@ library.add(faUser);
 
 export default {
     components: {
-        DatasetProvider,
+        DatasetAttributesProvider,
         FontAwesomeIcon,
     },
     props: {
diff --git a/client/src/components/providers/DatasetProvider.js b/client/src/components/providers/DatasetProvider.js
new file mode 100644
index 00000000000..0ab3e5e2c0a
--- /dev/null
+++ b/client/src/components/providers/DatasetProvider.js
@@ -0,0 +1,16 @@
+import axios from "axios";
+import { getAppRoot } from "onload/loadConfig";
+import { SingleQueryProvider } from "components/providers/SingleQueryProvider";
+import { rethrowSimple } from "utils/simple-error";
+
+async function datasetAttributes({ id }) {
+    const url = `${getAppRoot()}dataset/get_edit?dataset_id=${id}`;
+    try {
+        const { data } = await axios.get(url);
+        return data;
+    } catch (e) {
+        rethrowSimple(e);
+    }
+}
+
+export const DatasetAttributesProvider = SingleQueryProvider(datasetAttributes);

From ea530cec514d3c9d48b409be8bbb77db13a4d359 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 4 Aug 2021 16:17:38 -0400
Subject: [PATCH 115/218] Add edit forms to dataset attributes component

---
 .../DatasetInformation/DatasetAttributes.vue  | 21 ++++++++++---------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetAttributes.vue b/client/src/components/DatasetInformation/DatasetAttributes.vue
index e9f33aa7e31..2f4dcebe89c 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.vue
+++ b/client/src/components/DatasetInformation/DatasetAttributes.vue
@@ -5,24 +5,24 @@
             <h4 class="alert-heading">Failed to access dataset details.</h4>
             {{ messageText }}
         </b-alert>
-        <DatasetAttributesProvider :id="datasetId" v-slot="{ result: dataset, loading }">
+        <DatasetAttributesProvider :id="datasetId" v-slot="{ result, loading }">
             <div v-if="!loading" class="mt-3">
                 <b-tabs>
-                    <b-tab>
+                    <b-tab v-if="!result['attribute_disable']">
                         <template #title><font-awesome-icon icon="bars" class="mr-1" />Attributes</template>
-                        <p>I'm the first tab</p>
+                        <FormDisplay :inputs="result['attribute_inputs']" />
                     </b-tab>
-                    <b-tab>
+                    <b-tab v-if="!result['conversion_disable']">
                         <template #title><font-awesome-icon icon="cog" class="mr-1" />Convert</template>
-                        <p>I'm the second tab</p>
+                        <FormDisplay :inputs="result['conversion_inputs']" />
                     </b-tab>
-                    <b-tab>
+                    <b-tab v-if="!result['datatype_disable']">
                         <template #title><font-awesome-icon icon="database" class="mr-1" />Datatypes</template>
-                        <p>I'm the third tab</p>
+                        <FormDisplay :inputs="result['datatype_inputs']" />
                     </b-tab>
-                    <b-tab>
+                    <b-tab v-if="!result['permission_disable']">
                         <template #title><font-awesome-icon icon="user" class="mr-1" />Permissions</template>
-                        <p>I'm the fourth tab</p>
+                        <FormDisplay :inputs="result['permission_inputs']" />
                     </b-tab>
                 </b-tabs>
             </div>
@@ -31,7 +31,7 @@
 </template>
 
 <script>
-import FormElement from "components/Form/FormElement";
+import FormDisplay from "components/Form/FormDisplay";
 import { DatasetAttributesProvider } from "components/providers/DatasetProvider";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { library } from "@fortawesome/fontawesome-svg-core";
@@ -47,6 +47,7 @@ export default {
     components: {
         DatasetAttributesProvider,
         FontAwesomeIcon,
+        FormDisplay,
     },
     props: {
         datasetId: {

From 55e3812e97ad0047323aff33c926012c00162437 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 4 Aug 2021 16:53:28 -0400
Subject: [PATCH 116/218] Add operation buttons to dataset attribute editing
 component

---
 .../DatasetInformation/DatasetAttributes.vue  | 27 +++++++++++++++++--
 1 file changed, 25 insertions(+), 2 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetAttributes.vue b/client/src/components/DatasetInformation/DatasetAttributes.vue
index 2f4dcebe89c..e5adf62c881 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.vue
+++ b/client/src/components/DatasetInformation/DatasetAttributes.vue
@@ -11,18 +11,38 @@
                     <b-tab v-if="!result['attribute_disable']">
                         <template #title><font-awesome-icon icon="bars" class="mr-1" />Attributes</template>
                         <FormDisplay :inputs="result['attribute_inputs']" />
+                        <div class="mt-2">
+                            <b-button variant="primary" class="mr-1">
+                                <font-awesome-icon icon="save" class="mr-1" />Save
+                            </b-button>
+                            <b-button> <font-awesome-icon icon="redo" class="mr-1" />Auto-detect </b-button>
+                        </div>
                     </b-tab>
                     <b-tab v-if="!result['conversion_disable']">
                         <template #title><font-awesome-icon icon="cog" class="mr-1" />Convert</template>
                         <FormDisplay :inputs="result['conversion_inputs']" />
+                        <div class="mt-2">
+                            <b-button variant="primary">
+                                <font-awesome-icon icon="exchange-alt" class="mr-1" />Create Dataset
+                            </b-button>
+                        </div>
                     </b-tab>
                     <b-tab v-if="!result['datatype_disable']">
                         <template #title><font-awesome-icon icon="database" class="mr-1" />Datatypes</template>
                         <FormDisplay :inputs="result['datatype_inputs']" />
+                        <div class="mt-2">
+                            <b-button variant="primary" class="mr-1">
+                                <font-awesome-icon icon="save" class="mr-1" />Save
+                            </b-button>
+                            <b-button> <font-awesome-icon icon="redo" class="mr-1" />Auto-detect </b-button>
+                        </div>
                     </b-tab>
                     <b-tab v-if="!result['permission_disable']">
                         <template #title><font-awesome-icon icon="user" class="mr-1" />Permissions</template>
                         <FormDisplay :inputs="result['permission_inputs']" />
+                        <div class="mt-2">
+                            <b-button variant="primary"> <font-awesome-icon icon="save" class="mr-1" />Save </b-button>
+                        </div>
                     </b-tab>
                 </b-tabs>
             </div>
@@ -35,12 +55,15 @@ import FormDisplay from "components/Form/FormDisplay";
 import { DatasetAttributesProvider } from "components/providers/DatasetProvider";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { library } from "@fortawesome/fontawesome-svg-core";
-import { faBars, faDatabase, faCog, faUser } from "@fortawesome/free-solid-svg-icons";
+import { faBars, faCog, faDatabase, faExchangeAlt, faRedo, faSave, faUser } from "@fortawesome/free-solid-svg-icons";
 import { sendErrorReport } from "./services";
 
 library.add(faBars);
-library.add(faDatabase);
 library.add(faCog);
+library.add(faDatabase);
+library.add(faExchangeAlt);
+library.add(faRedo);
+library.add(faSave);
 library.add(faUser);
 
 export default {

From d3b3d6e54999ec37fd4ce92a7a08f4cc0bcfa323 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 4 Aug 2021 17:33:57 -0400
Subject: [PATCH 117/218] Add operation handling to dataset attributes
 component

---
 .../DatasetInformation/DatasetAttributes.vue  | 87 ++++++++++++-------
 .../components/DatasetInformation/services.js | 15 ++++
 2 files changed, 72 insertions(+), 30 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetAttributes.vue b/client/src/components/DatasetInformation/DatasetAttributes.vue
index e5adf62c881..602ec36e225 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.vue
+++ b/client/src/components/DatasetInformation/DatasetAttributes.vue
@@ -2,46 +2,55 @@
     <div>
         <h4>Edit Dataset Attributes</h4>
         <b-alert v-if="messageText" :variant="messageVariant" show>
-            <h4 class="alert-heading">Failed to access dataset details.</h4>
-            {{ messageText }}
+            {{ messageText | l }}
         </b-alert>
         <DatasetAttributesProvider :id="datasetId" v-slot="{ result, loading }">
             <div v-if="!loading" class="mt-3">
                 <b-tabs>
                     <b-tab v-if="!result['attribute_disable']">
-                        <template #title><font-awesome-icon icon="bars" class="mr-1" />Attributes</template>
-                        <FormDisplay :inputs="result['attribute_inputs']" />
+                        <template #title><font-awesome-icon icon="bars" class="mr-1" />{{ "Attributes" | l }}</template>
+                        <FormDisplay :inputs="result['attribute_inputs']" @onChange="onAttribute" />
                         <div class="mt-2">
-                            <b-button variant="primary" class="mr-1">
-                                <font-awesome-icon icon="save" class="mr-1" />Save
+                            <b-button @click="submit('attribute', 'attributes')" variant="primary" class="mr-1">
+                                <font-awesome-icon icon="save" class="mr-1" />{{ "Save" | l }}
+                            </b-button>
+                            <b-button @click="submit('attribute', 'autodetect')">
+                                <font-awesome-icon icon="redo" class="mr-1" />{{ "Auto-detect" | l }}
                             </b-button>
-                            <b-button> <font-awesome-icon icon="redo" class="mr-1" />Auto-detect </b-button>
                         </div>
                     </b-tab>
                     <b-tab v-if="!result['conversion_disable']">
-                        <template #title><font-awesome-icon icon="cog" class="mr-1" />Convert</template>
-                        <FormDisplay :inputs="result['conversion_inputs']" />
+                        <template #title><font-awesome-icon icon="cog" class="mr-1" />{{ "Convert" | l }}</template>
+                        <FormDisplay :inputs="result['conversion_inputs']" @onChange="onConversion" />
                         <div class="mt-2">
-                            <b-button variant="primary">
-                                <font-awesome-icon icon="exchange-alt" class="mr-1" />Create Dataset
+                            <b-button @click="submit('conversion', 'conversion')" variant="primary">
+                                <font-awesome-icon icon="exchange-alt" class="mr-1" />{{ "Create Dataset" | l }}
                             </b-button>
                         </div>
                     </b-tab>
                     <b-tab v-if="!result['datatype_disable']">
-                        <template #title><font-awesome-icon icon="database" class="mr-1" />Datatypes</template>
-                        <FormDisplay :inputs="result['datatype_inputs']" />
+                        <template #title
+                            ><font-awesome-icon icon="database" class="mr-1" />{{ "Datatypes" | l }}</template
+                        >
+                        <FormDisplay :inputs="result['datatype_inputs']" @onChange="onDatatype" />
                         <div class="mt-2">
-                            <b-button variant="primary" class="mr-1">
-                                <font-awesome-icon icon="save" class="mr-1" />Save
+                            <b-button @click="submit('datatype', 'datatype')" variant="primary" class="mr-1">
+                                <font-awesome-icon icon="save" class="mr-1" />{{ "Save" | l }}
+                            </b-button>
+                            <b-button @click="submit('datatype', 'datatype_detect')">
+                                <font-awesome-icon icon="redo" class="mr-1" />{{ "Auto-detect" | l }}
                             </b-button>
-                            <b-button> <font-awesome-icon icon="redo" class="mr-1" />Auto-detect </b-button>
                         </div>
                     </b-tab>
                     <b-tab v-if="!result['permission_disable']">
-                        <template #title><font-awesome-icon icon="user" class="mr-1" />Permissions</template>
-                        <FormDisplay :inputs="result['permission_inputs']" />
+                        <template #title
+                            ><font-awesome-icon icon="user" class="mr-1" />{{ "Permissions" | l }}</template
+                        >
+                        <FormDisplay :inputs="result['permission_inputs']" @onChange="onPermission" />
                         <div class="mt-2">
-                            <b-button variant="primary"> <font-awesome-icon icon="save" class="mr-1" />Save </b-button>
+                            <b-button @click="submit('permission', 'permission')" variant="primary">
+                                <font-awesome-icon icon="save" class="mr-1" />{{ "Save" | l }}
+                            </b-button>
                         </div>
                     </b-tab>
                 </b-tabs>
@@ -51,12 +60,13 @@
 </template>
 
 <script>
+import { getGalaxyInstance } from "app";
 import FormDisplay from "components/Form/FormDisplay";
 import { DatasetAttributesProvider } from "components/providers/DatasetProvider";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { library } from "@fortawesome/fontawesome-svg-core";
 import { faBars, faCog, faDatabase, faExchangeAlt, faRedo, faSave, faUser } from "@fortawesome/free-solid-svg-icons";
-import { sendErrorReport } from "./services";
+import { setAttributes } from "./services";
 
 library.add(faBars);
 library.add(faCog);
@@ -80,28 +90,45 @@ export default {
     },
     data() {
         return {
-            message: null,
-            email: null,
             messageText: null,
             messageVariant: null,
+            formData: {},
         };
     },
     methods: {
-        onError(err) {
-            this.messageText = err;
+        onAttribute(data) {
+            this.formData["attribute"] = data;
         },
-        submit(dataset, userEmail) {
-            const email = this.email || userEmail;
-            const message = this.message;
-            sendErrorReport(dataset, message, email).then(
-                (resultMessages) => {
-                    this.resultMessages = resultMessages;
+        onConversion(data) {
+            this.formData["conversion"] = data;
+        },
+        onDatatype(data) {
+            this.formData["datatype"] = data;
+        },
+        onPermission(data) {
+            this.formData["permission"] = data;
+        },
+        submit(key, operation) {
+            setAttributes(this.datasetId, this.formData[key], operation).then(
+                (response) => {
+                    this.messageText = response.message;
+                    this.messageVariant = response.status;
+                    this._reloadHistory();
                 },
                 (messageText) => {
                     this.messageText = messageText;
+                    this.messageVariant = "danger";
                 }
             );
         },
+
+        /** reload Galaxy's history after updating dataset's attributes */
+        _reloadHistory: function () {
+            const Galaxy = getGalaxyInstance();
+            if (Galaxy) {
+                Galaxy.currHistoryPanel.loadCurrentHistory();
+            }
+        },
     },
 };
 </script>
diff --git a/client/src/components/DatasetInformation/services.js b/client/src/components/DatasetInformation/services.js
index 7739f7fed83..310c5b51ca0 100644
--- a/client/src/components/DatasetInformation/services.js
+++ b/client/src/components/DatasetInformation/services.js
@@ -16,3 +16,18 @@ export async function sendErrorReport(dataset, message, email) {
         rethrowSimple(e);
     }
 }
+
+export async function setAttributes(datasetId, settings, operation) {
+    const payload = {
+        dataset_id: datasetId,
+        operation: operation,
+        ...settings,
+    };
+    const url = `${getAppRoot()}dataset/set_edit`;
+    try {
+        const { data } = await axios.put(url, payload);
+        return data;
+    } catch (e) {
+        rethrowSimple(e);
+    }
+}

From 9f3fe3ab7827882ed7ff647fcefdb0e4d5a88887 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 4 Aug 2021 17:34:33 -0400
Subject: [PATCH 118/218] Remove legacy backbone based dataset attribute edit
 view

---
 .../mvc/dataset/dataset-edit-attributes.js    | 225 ------------------
 1 file changed, 225 deletions(-)
 delete mode 100644 client/src/mvc/dataset/dataset-edit-attributes.js

diff --git a/client/src/mvc/dataset/dataset-edit-attributes.js b/client/src/mvc/dataset/dataset-edit-attributes.js
deleted file mode 100644
index f14bfaad0ee..00000000000
--- a/client/src/mvc/dataset/dataset-edit-attributes.js
+++ /dev/null
@@ -1,225 +0,0 @@
-/** Dataset edit attributes view */
-import _ from "underscore";
-import $ from "jquery";
-import Backbone from "backbone";
-import { getAppRoot } from "onload/loadConfig";
-import { getGalaxyInstance } from "app";
-import _l from "utils/localization";
-import Tabs from "mvc/ui/ui-tabs";
-import Ui from "mvc/ui/ui-misc";
-import Form from "mvc/form/form-view";
-
-var View = Backbone.View.extend({
-    initialize: function () {
-        const Galaxy = getGalaxyInstance();
-        this.setElement("<div/>");
-        this.model = new Backbone.Model({
-            dataset_id: Galaxy.params.dataset_id,
-        });
-        this.message = new Ui.Message({ persistent: true });
-        this.tabs = this._createTabs();
-        this.active_tab = "user";
-        this.$el
-            .append($("<h4/>").append("Edit dataset attributes"))
-            .append(this.message.$el)
-            .append("<p/>")
-            .append(this.tabs.$el)
-            .hide();
-        this.render();
-    },
-
-    /** fetch data for the selected dataset and build forms */
-    render: function () {
-        var self = this;
-        $.ajax({
-            url: `${getAppRoot()}dataset/get_edit?dataset_id=${self.model.get("dataset_id")}`,
-            success: function (response) {
-                !self.initial_message && self.message.update(response);
-                self.initial_message = true;
-                _.each(self.forms, (form, key) => {
-                    form.model.set("inputs", response[`${key}_inputs`]);
-                    form.model.set("hide_operations", response[`${key}_disable`]);
-                    form.render();
-                });
-                self.$el.show();
-            },
-            error: function (response) {
-                var err_msg = response.responseJSON && response.responseJSON.err_msg;
-                self.message.update({
-                    status: "danger",
-                    message: err_msg || "Error occurred while loading the dataset.",
-                });
-            },
-        });
-    },
-
-    /** submit data to backend to update attributes */
-    _submit: function (operation, form) {
-        var self = this;
-        var data = form.data.create();
-        data.dataset_id = this.model.get("dataset_id");
-        data.operation = operation;
-        $.ajax({
-            type: "PUT",
-            url: `${getAppRoot()}dataset/set_edit`,
-            data: data,
-            success: function (response) {
-                self.message.update(response);
-                self.render();
-                self._reloadHistory();
-            },
-            error: function (response) {
-                var err_msg = response.responseJSON && response.responseJSON.err_msg;
-                self.message.update({
-                    status: "danger",
-                    message: err_msg || "Error occurred while editing the dataset attributes.",
-                });
-            },
-        });
-    },
-
-    /** create tabs for different dataset attribute categories*/
-    _createTabs: function () {
-        this.forms = {
-            attribute: this._getAttribute(),
-            conversion: this._getConversion(),
-            datatype: this._getDatatype(),
-            permission: this._getPermission(),
-        };
-        var tabs = new Tabs.View();
-        tabs.add({
-            id: "attribute",
-            title: _l("Attributes"),
-            icon: "fa fa-bars",
-            tooltip: _l("Edit dataset attributes"),
-            $el: this.forms.attribute.$el,
-        });
-        tabs.add({
-            id: "convert",
-            title: _l("Convert"),
-            icon: "fa-gear",
-            tooltip: _l("Convert to new format"),
-            $el: this.forms.conversion.$el,
-        });
-        tabs.add({
-            id: "datatype",
-            title: _l("Datatypes"),
-            icon: "fa-database",
-            tooltip: _l("Change data type"),
-            $el: this.forms.datatype.$el,
-        });
-        tabs.add({
-            id: "permissions",
-            title: _l("Permissions"),
-            icon: "fa-user",
-            tooltip: _l("Permissions"),
-            $el: this.forms.permission.$el,
-        });
-        return tabs;
-    },
-
-    /** edit main attributes form */
-    _getAttribute: function () {
-        var self = this;
-        var form = new Form({
-            title: _l("Edit attributes"),
-            operations: {
-                submit_attributes: new Ui.Button({
-                    tooltip: _l("Save attributes of the dataset."),
-                    icon: "fa-floppy-o",
-                    title: _l("Save"),
-                    onclick: function () {
-                        self._submit("attributes", form);
-                    },
-                }),
-                submit_autodetect: new Ui.Button({
-                    tooltip:
-                        "This will inspect the dataset and attempt to correct the values of fields if they are not accurate.",
-                    icon: "fa-redo",
-                    title: "Auto-detect",
-                    onclick: function () {
-                        self._submit("autodetect", form);
-                    },
-                }),
-            },
-        });
-        return form;
-    },
-
-    /** datatype conversion form */
-    _getConversion: function () {
-        var self = this;
-        var form = new Form({
-            title: _l("Convert to new format"),
-            operations: {
-                submit_conversion: new Ui.Button({
-                    tooltip: _l("Convert the datatype to a new format."),
-                    title: _l("Convert datatype"),
-                    icon: "fa-exchange",
-                    onclick: function () {
-                        self._submit("conversion", form);
-                    },
-                }),
-            },
-        });
-        return form;
-    },
-
-    /** change datatype form */
-    _getDatatype: function () {
-        var self = this;
-        var form = new Form({
-            title: _l("Change datatype"),
-            operations: {
-                submit_datatype: new Ui.Button({
-                    tooltip: _l("Change the datatype to a new type."),
-                    title: _l("Change datatype"),
-                    icon: "fa-exchange",
-                    onclick: function () {
-                        self._submit("datatype", form);
-                    },
-                }),
-                submit_datatype_detect: new Ui.Button({
-                    tooltip: _l("Detect the datatype and change it."),
-                    title: _l("Detect datatype"),
-                    icon: "fa-redo",
-                    onclick: function () {
-                        self._submit("datatype_detect", form);
-                    },
-                }),
-            },
-        });
-        return form;
-    },
-
-    /** dataset permissions form */
-    _getPermission: function () {
-        var self = this;
-        var form = new Form({
-            title: _l("Manage dataset permissions"),
-            operations: {
-                submit_permission: new Ui.Button({
-                    tooltip: _l("Save permissions."),
-                    title: _l("Save permissions"),
-                    icon: "fa-floppy-o ",
-                    onclick: function () {
-                        self._submit("permission", form);
-                    },
-                }),
-            },
-        });
-        return form;
-    },
-
-    /** reload Galaxy's history after updating dataset's attributes */
-    _reloadHistory: function () {
-        const Galaxy = getGalaxyInstance();
-        if (Galaxy) {
-            Galaxy.currHistoryPanel.loadCurrentHistory();
-        }
-    },
-});
-
-export default {
-    View: View,
-};

From 0c14ef3ae47ac9b39a7c58da1dc9e6d2e6f123d9 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 4 Aug 2021 17:57:25 -0400
Subject: [PATCH 119/218] Add error handling to dataset attributes, fix v-slot
 tag

---
 .../DatasetInformation/DatasetAttributes.vue  | 32 +++++++++++--------
 1 file changed, 18 insertions(+), 14 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetAttributes.vue b/client/src/components/DatasetInformation/DatasetAttributes.vue
index 602ec36e225..cb1dbe70f64 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.vue
+++ b/client/src/components/DatasetInformation/DatasetAttributes.vue
@@ -4,11 +4,13 @@
         <b-alert v-if="messageText" :variant="messageVariant" show>
             {{ messageText | l }}
         </b-alert>
-        <DatasetAttributesProvider :id="datasetId" v-slot="{ result, loading }">
+        <DatasetAttributesProvider :id="datasetId" v-slot="{ result, loading }" @error="onError">
             <div v-if="!loading" class="mt-3">
                 <b-tabs>
                     <b-tab v-if="!result['attribute_disable']">
-                        <template #title><font-awesome-icon icon="bars" class="mr-1" />{{ "Attributes" | l }}</template>
+                        <template v-slot:title>
+                            <font-awesome-icon icon="bars" class="mr-1" />{{ "Attributes" | l }}
+                        </template>
                         <FormDisplay :inputs="result['attribute_inputs']" @onChange="onAttribute" />
                         <div class="mt-2">
                             <b-button @click="submit('attribute', 'attributes')" variant="primary" class="mr-1">
@@ -20,7 +22,9 @@
                         </div>
                     </b-tab>
                     <b-tab v-if="!result['conversion_disable']">
-                        <template #title><font-awesome-icon icon="cog" class="mr-1" />{{ "Convert" | l }}</template>
+                        <template v-slot:title>
+                            <font-awesome-icon icon="cog" class="mr-1" />{{ "Convert" | l }}
+                        </template>
                         <FormDisplay :inputs="result['conversion_inputs']" @onChange="onConversion" />
                         <div class="mt-2">
                             <b-button @click="submit('conversion', 'conversion')" variant="primary">
@@ -29,9 +33,9 @@
                         </div>
                     </b-tab>
                     <b-tab v-if="!result['datatype_disable']">
-                        <template #title
-                            ><font-awesome-icon icon="database" class="mr-1" />{{ "Datatypes" | l }}</template
-                        >
+                        <template v-slot:title>
+                            <font-awesome-icon icon="database" class="mr-1" />{{ "Datatypes" | l }}
+                        </template>
                         <FormDisplay :inputs="result['datatype_inputs']" @onChange="onDatatype" />
                         <div class="mt-2">
                             <b-button @click="submit('datatype', 'datatype')" variant="primary" class="mr-1">
@@ -43,9 +47,9 @@
                         </div>
                     </b-tab>
                     <b-tab v-if="!result['permission_disable']">
-                        <template #title
-                            ><font-awesome-icon icon="user" class="mr-1" />{{ "Permissions" | l }}</template
-                        >
+                        <template v-slot:title>
+                            <font-awesome-icon icon="user" class="mr-1" />{{ "Permissions" | l }}
+                        </template>
                         <FormDisplay :inputs="result['permission_inputs']" @onChange="onPermission" />
                         <div class="mt-2">
                             <b-button @click="submit('permission', 'permission')" variant="primary">
@@ -108,6 +112,10 @@ export default {
         onPermission(data) {
             this.formData["permission"] = data;
         },
+        onError(messageText) {
+            this.messageText = messageText;
+            this.messageVariant = "danger";
+        },
         submit(key, operation) {
             setAttributes(this.datasetId, this.formData[key], operation).then(
                 (response) => {
@@ -115,13 +123,9 @@ export default {
                     this.messageVariant = response.status;
                     this._reloadHistory();
                 },
-                (messageText) => {
-                    this.messageText = messageText;
-                    this.messageVariant = "danger";
-                }
+                this.onError
             );
         },
-
         /** reload Galaxy's history after updating dataset's attributes */
         _reloadHistory: function () {
             const Galaxy = getGalaxyInstance();

From 0b5688a600ee74279d803233f36e4fa2dbd7413e Mon Sep 17 00:00:00 2001
From: Dannon <dannon.baker@gmail.com>
Date: Thu, 5 Aug 2021 08:02:40 -0700
Subject: [PATCH 120/218] Update
 client/src/components/DatasetInformation/DatasetAttributes.vue

---
 .../components/DatasetInformation/DatasetAttributes.vue   | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetAttributes.vue b/client/src/components/DatasetInformation/DatasetAttributes.vue
index cb1dbe70f64..90ba8a46333 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.vue
+++ b/client/src/components/DatasetInformation/DatasetAttributes.vue
@@ -72,13 +72,7 @@ import { library } from "@fortawesome/fontawesome-svg-core";
 import { faBars, faCog, faDatabase, faExchangeAlt, faRedo, faSave, faUser } from "@fortawesome/free-solid-svg-icons";
 import { setAttributes } from "./services";
 
-library.add(faBars);
-library.add(faCog);
-library.add(faDatabase);
-library.add(faExchangeAlt);
-library.add(faRedo);
-library.add(faSave);
-library.add(faUser);
+library.add(faBars, faCog, faDatabase, faExchangeAlt, faRedo, faSave, faUser);
 
 export default {
     components: {

From 2af3ef5ca6ca836843cc59b5833e5cd81cf683dc Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 5 Aug 2021 19:04:03 -0400
Subject: [PATCH 121/218] Format client

---
 .../DatasetInformation/DatasetAttributes.vue        | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetAttributes.vue b/client/src/components/DatasetInformation/DatasetAttributes.vue
index 90ba8a46333..ac267d191df 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.vue
+++ b/client/src/components/DatasetInformation/DatasetAttributes.vue
@@ -111,14 +111,11 @@ export default {
             this.messageVariant = "danger";
         },
         submit(key, operation) {
-            setAttributes(this.datasetId, this.formData[key], operation).then(
-                (response) => {
-                    this.messageText = response.message;
-                    this.messageVariant = response.status;
-                    this._reloadHistory();
-                },
-                this.onError
-            );
+            setAttributes(this.datasetId, this.formData[key], operation).then((response) => {
+                this.messageText = response.message;
+                this.messageVariant = response.status;
+                this._reloadHistory();
+            }, this.onError);
         },
         /** reload Galaxy's history after updating dataset's attributes */
         _reloadHistory: function () {

From a7cea39d5ea3bf072092220118c26cc2a8a8a342 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 5 Aug 2021 21:35:15 -0400
Subject: [PATCH 122/218] Fix button identifier used in selenium test

---
 .../components/DatasetInformation/DatasetAttributes.vue    | 7 ++++++-
 lib/galaxy/selenium/navigation.yml                         | 2 +-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetAttributes.vue b/client/src/components/DatasetInformation/DatasetAttributes.vue
index ac267d191df..f740347dcbe 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.vue
+++ b/client/src/components/DatasetInformation/DatasetAttributes.vue
@@ -13,7 +13,12 @@
                         </template>
                         <FormDisplay :inputs="result['attribute_inputs']" @onChange="onAttribute" />
                         <div class="mt-2">
-                            <b-button @click="submit('attribute', 'attributes')" variant="primary" class="mr-1">
+                            <b-button
+                                id="dataset-attributes-default-save"
+                                @click="submit('attribute', 'attributes')"
+                                variant="primary"
+                                class="mr-1"
+                            >
                                 <font-awesome-icon icon="save" class="mr-1" />{{ "Save" | l }}
                             </b-button>
                             <b-button @click="submit('attribute', 'autodetect')">
diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index 11fc8a5c98c..8e69f39e21c 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -234,7 +234,7 @@ history_structure:
 edit_dataset_attributes:
   selectors:
     database_build_dropdown: '[data-label="Database/Build"]'
-    save_btn: '#submit_attributes'
+    save_btn: '#dataset-attributes-default-save'
 
   dbkey_dropdown_results:
     selectors:

From 7fb5e5c9c42f8dd0baae094873a555012cf493be Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 5 Aug 2021 22:25:38 -0400
Subject: [PATCH 123/218] Fix hash-key generation in single query provider

---
 client/src/components/providers/SingleQueryProvider.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/providers/SingleQueryProvider.js b/client/src/components/providers/SingleQueryProvider.js
index dff317ba5d4..ba5c3677467 100644
--- a/client/src/components/providers/SingleQueryProvider.js
+++ b/client/src/components/providers/SingleQueryProvider.js
@@ -23,7 +23,7 @@ export const SingleQueryProvider = (lookup) => {
                 return this.result === undefined;
             },
             cacheKey() {
-                hash(this.$attrs || {});
+                return hash(this.$attrs || {});
             },
         },
         mounted() {

From b020fdb9cd7a47e3f8ba622382da8e6d7069eafb Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 6 Aug 2021 17:49:32 -0400
Subject: [PATCH 124/218] Add vue test cases for dataset attributes component

---
 .../DatasetAttributes.test.js                 | 62 +++++++++++++++++++
 .../DatasetInformation/DatasetAttributes.vue  |  1 +
 2 files changed, 63 insertions(+)
 create mode 100644 client/src/components/DatasetInformation/DatasetAttributes.test.js

diff --git a/client/src/components/DatasetInformation/DatasetAttributes.test.js b/client/src/components/DatasetInformation/DatasetAttributes.test.js
new file mode 100644
index 00000000000..a5533ecbe4e
--- /dev/null
+++ b/client/src/components/DatasetInformation/DatasetAttributes.test.js
@@ -0,0 +1,62 @@
+import { mount } from "@vue/test-utils";
+import { getLocalVue } from "jest/helpers";
+import DatasetAttributes from "./DatasetAttributes";
+import MockProvider from "../providers/MockProvider";
+import axios from "axios";
+import MockAdapter from "axios-mock-adapter";
+import Vue from "vue";
+
+const localVue = getLocalVue();
+const flushPromises = () => new Promise((resolve) => setTimeout(resolve));
+
+function buildWrapper(conversion_disable = false) {
+    return mount(DatasetAttributes, {
+        propsData: {
+            datasetId: "dataset_id",
+        },
+        localVue,
+        stubs: {
+            DatasetAttributesProvider: MockProvider({
+                result: {
+                    attribute_inputs: [{ name: "attribute_text", type: "text" }],
+                    conversion_inputs: [{ name: "conversion_text", type: "text" }],
+                    conversion_disable: conversion_disable,
+                    datatype_inputs: [{ name: "datatype_text", type: "text" }],
+                    permission_inputs: [{ name: "permission_text", type: "text" }],
+                },
+            }),
+            FontAwesomeIcon: false,
+            FormElement: false,
+        },
+    });
+}
+
+describe("DatasetAttributes", () => {
+    it("check rendering", async () => {
+        const axiosMock = new MockAdapter(axios);
+        axiosMock.onPut(`/dataset/set_edit`).reply(200, { message: "success", status: "success" });
+        const wrapper = buildWrapper();
+        await Vue.nextTick();
+        expect(wrapper.findAll("button").length).toBe(6);
+        expect(wrapper.findAll("[tour_id=attribute_text]").length).toBe(1);
+        expect(wrapper.findAll("[tour_id=conversion_text]").length).toBe(1);
+        expect(wrapper.findAll("[tour_id=datatype_text]").length).toBe(1);
+        expect(wrapper.findAll("[tour_id=permission_text]").length).toBe(1);
+        expect(wrapper.findAll(".tab-pane").length).toBe(4);
+        const $button = wrapper.find("#dataset-attributes-default-save");
+        await $button.trigger("click");
+        await flushPromises();
+        expect(wrapper.find("[role=alert]").text()).toBe("success");
+    });
+
+    it("check rendering without conversion option", async () => {
+        const wrapper = buildWrapper(true);
+        await Vue.nextTick();
+        expect(wrapper.findAll("button").length).toBe(5);
+        expect(wrapper.findAll("[tour_id=attribute_text]").length).toBe(1);
+        expect(wrapper.findAll("[tour_id=conversion_text]").length).toBe(0);
+        expect(wrapper.findAll("[tour_id=datatype_text]").length).toBe(1);
+        expect(wrapper.findAll("[tour_id=permission_text]").length).toBe(1);
+        expect(wrapper.findAll(".tab-pane").length).toBe(3);
+    });
+});
diff --git a/client/src/components/DatasetInformation/DatasetAttributes.vue b/client/src/components/DatasetInformation/DatasetAttributes.vue
index f740347dcbe..824d0cc67bf 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.vue
+++ b/client/src/components/DatasetInformation/DatasetAttributes.vue
@@ -120,6 +120,7 @@ export default {
                 this.messageText = response.message;
                 this.messageVariant = response.status;
                 this._reloadHistory();
+                this.$emit("onSubmit", this.messageText);
             }, this.onError);
         },
         /** reload Galaxy's history after updating dataset's attributes */

From 36114459af01c8e17a114dbd0819d7b03f7f078c Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 6 Aug 2021 17:51:23 -0400
Subject: [PATCH 125/218] Remove unused submission event emission

---
 .../components/DatasetInformation/DatasetAttributes.test.js   | 4 ++--
 .../src/components/DatasetInformation/DatasetAttributes.vue   | 1 -
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetAttributes.test.js b/client/src/components/DatasetInformation/DatasetAttributes.test.js
index a5533ecbe4e..7f9d5de41a6 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.test.js
+++ b/client/src/components/DatasetInformation/DatasetAttributes.test.js
@@ -1,10 +1,10 @@
+import Vue from "vue";
+import axios from "axios";
 import { mount } from "@vue/test-utils";
 import { getLocalVue } from "jest/helpers";
 import DatasetAttributes from "./DatasetAttributes";
 import MockProvider from "../providers/MockProvider";
-import axios from "axios";
 import MockAdapter from "axios-mock-adapter";
-import Vue from "vue";
 
 const localVue = getLocalVue();
 const flushPromises = () => new Promise((resolve) => setTimeout(resolve));
diff --git a/client/src/components/DatasetInformation/DatasetAttributes.vue b/client/src/components/DatasetInformation/DatasetAttributes.vue
index 824d0cc67bf..f740347dcbe 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.vue
+++ b/client/src/components/DatasetInformation/DatasetAttributes.vue
@@ -120,7 +120,6 @@ export default {
                 this.messageText = response.message;
                 this.messageVariant = response.status;
                 this._reloadHistory();
-                this.$emit("onSubmit", this.messageText);
             }, this.onError);
         },
         /** reload Galaxy's history after updating dataset's attributes */

From 861ebf182b7337494577c28d4fd9751c72c967c9 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 6 Aug 2021 18:31:24 -0400
Subject: [PATCH 126/218] Augment SingleQueryProvider, remove unnecessary
 result cache, add non-caching option

---
 .../DatasetInformation/DatasetAttributes.vue  |  2 +-
 .../providers/SingleQueryProvider.js          | 39 +++++++++++--------
 2 files changed, 23 insertions(+), 18 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetAttributes.vue b/client/src/components/DatasetInformation/DatasetAttributes.vue
index f740347dcbe..a63485f4223 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.vue
+++ b/client/src/components/DatasetInformation/DatasetAttributes.vue
@@ -4,7 +4,7 @@
         <b-alert v-if="messageText" :variant="messageVariant" show>
             {{ messageText | l }}
         </b-alert>
-        <DatasetAttributesProvider :id="datasetId" v-slot="{ result, loading }" @error="onError">
+        <DatasetAttributesProvider :id="datasetId" :useCache="false" v-slot="{ result, loading }" @error="onError">
             <div v-if="!loading" class="mt-3">
                 <b-tabs>
                     <b-tab v-if="!result['attribute_disable']">
diff --git a/client/src/components/providers/SingleQueryProvider.js b/client/src/components/providers/SingleQueryProvider.js
index ba5c3677467..bee613787e0 100644
--- a/client/src/components/providers/SingleQueryProvider.js
+++ b/client/src/components/providers/SingleQueryProvider.js
@@ -10,9 +10,14 @@ import hash from "object-hash";
  */
 export const SingleQueryProvider = (lookup) => {
     const promiseCache = new Map();
-    const resultCache = new Map();
 
     return {
+        props: {
+            useCache: {
+                type: Boolean,
+                default: true,
+            },
+        },
         data() {
             return {
                 result: undefined,
@@ -27,24 +32,24 @@ export const SingleQueryProvider = (lookup) => {
             },
         },
         mounted() {
-            const cachedResult = resultCache.get(this.cacheKey);
-            if (cachedResult) {
-                this.result = cachedResult;
-                return;
+            let lookupPromise;
+            if (this.useCache) {
+                lookupPromise = promiseCache.get(this.cacheKey);
+                if (!lookupPromise) {
+                    lookupPromise = lookup(this.$attrs);
+                    promiseCache.set(this.cacheKey, lookupPromise);
+                }
+            } else {
+                lookupPromise = lookup(this.$attrs);
             }
-
-            let lookupPromise = promiseCache.get(this.cacheKey);
-            if (!lookupPromise) {
-                lookupPromise = lookup(this.$attrs).catch((err) => {
+            lookupPromise.then(
+                (result) => {
+                    this.result = result;
+                },
+                (err) => {
                     this.$emit("error", err);
-                });
-                promiseCache.set(this.cacheKey, lookupPromise);
-            }
-
-            lookupPromise.then((result) => {
-                resultCache.set(this.cacheKey, result);
-                this.result = result;
-            });
+                }
+            );
         },
         render() {
             return this.$scopedSlots.default({

From 62ee25091479f1c2044e853420f3ee21843ed5c8 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 6 Aug 2021 18:44:42 -0400
Subject: [PATCH 127/218] Fix lint issue, hyphenate use cache prop

---
 client/src/components/DatasetInformation/DatasetAttributes.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/DatasetInformation/DatasetAttributes.vue b/client/src/components/DatasetInformation/DatasetAttributes.vue
index a63485f4223..4685833941a 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.vue
+++ b/client/src/components/DatasetInformation/DatasetAttributes.vue
@@ -4,7 +4,7 @@
         <b-alert v-if="messageText" :variant="messageVariant" show>
             {{ messageText | l }}
         </b-alert>
-        <DatasetAttributesProvider :id="datasetId" :useCache="false" v-slot="{ result, loading }" @error="onError">
+        <DatasetAttributesProvider :id="datasetId" :use-cache="false" v-slot="{ result, loading }" @error="onError">
             <div v-if="!loading" class="mt-3">
                 <b-tabs>
                     <b-tab v-if="!result['attribute_disable']">

From d8e95aede7b3f1f741ff029e98e4fc4a325d647a Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 10 Aug 2021 09:50:23 +0200
Subject: [PATCH 128/218] Including column to order in distinct breaks tests

---
 lib/galaxy/model/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 66013884c7a..ae3d3fcbdee 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -4299,7 +4299,7 @@ class DatasetCollection(Dictifiable, UsesAnnotations, RepresentById):
             q = q.add_entity(entity)
             if entity == DatasetCollectionElement:
                 q = q.filter(entity.id == dce.c.id)
-        return q.distinct(*order_by_columns).order_by(*order_by_columns)
+        return q.distinct().order_by(*order_by_columns)
 
     @property
     def dataset_states_and_extensions_summary(self):

From 760461a1c722990fbf9bc8f81c08eb272a57c5f6 Mon Sep 17 00:00:00 2001
From: selten <selten@users.noreply.github.com>
Date: Tue, 10 Aug 2021 15:21:03 +0200
Subject: [PATCH 129/218] Gitlab Error report - Remove previously required
 urllib

## Why these changes
The library has been updated whereby it no longer accepts urlencoded data that used to be required.

## Description on changes
Removal of previously required urllib for URL encoding. Combined with enforced minimum version of python-gitlab to fix the issue.
---
 .../tools/error_reports/plugins/gitlab.py     | 22 +++++--------------
 1 file changed, 6 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy/tools/error_reports/plugins/gitlab.py b/lib/galaxy/tools/error_reports/plugins/gitlab.py
index ada1ff7462a..f3615060581 100644
--- a/lib/galaxy/tools/error_reports/plugins/gitlab.py
+++ b/lib/galaxy/tools/error_reports/plugins/gitlab.py
@@ -5,12 +5,6 @@ import os
 import sys
 
 import requests
-if sys.version_info[0] < 3:
-    import urllib as urllib
-    import urlparse as urlparse
-else:
-    import urllib.parse as urllib
-    urlparse = urllib
 
 try:
     import gitlab
@@ -115,21 +109,18 @@ class GitLabPlugin(BaseGitPlugin):
                     else "/".join((self.git_default_repo_owner, self.git_default_repo_name))
                 issue_cache_key = self._get_issue_cache_key(job, ts_repourl)
 
-                gitlab_urlencodedpath = urllib.quote_plus(gitlab_projecturl)
-
                 # Make sure we are always logged in, then retrieve the GitLab project if it isn't cached.
                 self.gitlab.auth()
                 try:
                     if gitlab_projecturl not in self.git_project_cache:
-                        self.git_project_cache[gitlab_projecturl] = self.gitlab.projects.get(gitlab_urlencodedpath)
+                        self.git_project_cache[gitlab_projecturl] = self.gitlab.projects.get(gitlab_projecturl)
                 except gitlab.GitlabGetError:
                     # Handle scenario where the repository doesn't exist so we can still continue
-                    log.warning(f"GitLab error reporting - Repository '{gitlab_urlencodedpath}' doesn't exist, using default repository.")
+                    log.warning(f"GitLab error reporting - Repository '{gitlab_projecturl}' doesn't exist, using default repository.")
                     # Redo some of the previous steps to recover from such an issue but continue issue creation
                     gitlab_projecturl = "/".join((self.git_default_repo_owner, self.git_default_repo_name))
-                    gitlab_urlencodedpath = urllib.quote_plus(gitlab_projecturl)
                     if gitlab_projecturl not in self.git_project_cache:
-                        self.git_project_cache[gitlab_projecturl] = self.gitlab.projects.get(gitlab_urlencodedpath)
+                        self.git_project_cache[gitlab_projecturl] = self.gitlab.projects.get(gitlab_projecturl)
                 gl_project = self.git_project_cache[gitlab_projecturl]
 
                 # Make sure we keep a cache of the issues, per tool in this case
@@ -175,7 +166,7 @@ class GitLabPlugin(BaseGitPlugin):
 
                         # Add a comment to an issue...
                         self._append_issue(issue_cache_key, error_title, error_message,
-                                           gitlab_urlencodedpath=gitlab_urlencodedpath)
+                                           gitlab_projecturl=gitlab_projecturl)
                     else:
                         self._open_issue(error_message, error_title, gitlab_projecturl, gl_project, gl_userid,
                                          issue_cache_key)
@@ -222,11 +213,10 @@ class GitLabPlugin(BaseGitPlugin):
         except (gitlab.GitlabOwnershipError, gitlab.GitlabGetError):
             # Create an issue in the default location
             gitlab_projecturl = "/".join((self.git_default_repo_owner, self.git_default_repo_name))
-            gitlab_urlencodedpath = urllib.quote_plus(gitlab_projecturl)
             # Make sure we are always logged in, then retrieve the GitLab project if it isn't cached.
             self.gitlab = self.gitlab_connect()
             if gitlab_projecturl not in self.git_project_cache:
-                self.git_project_cache[gitlab_projecturl] = self.gitlab.projects.get(gitlab_urlencodedpath)
+                self.git_project_cache[gitlab_projecturl] = self.gitlab.projects.get(gitlab_projecturl)
             gl_project = self.git_project_cache[gitlab_projecturl]
 
             # Submit issue to default project
@@ -262,7 +252,7 @@ class GitLabPlugin(BaseGitPlugin):
             "api",
             "v4",
             "projects",
-            kwargs.get('gitlab_urlencodedpath'),
+            kwargs.get('gitlab_projecturl'),
             "issues",
             str(self.issue_cache[issue_cache_key][error_title]),
             "notes"

From 0a686a46b43278746755c0d1a431967bdb4afc15 Mon Sep 17 00:00:00 2001
From: selten <selten@users.noreply.github.com>
Date: Tue, 10 Aug 2021 15:28:31 +0200
Subject: [PATCH 130/218] Update python-gitlab dependency

Update the dependency so it works with the updated GitLab error reporting system
---
 lib/galaxy/dependencies/conditional-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt
index e8076d51508..758b8607d14 100644
--- a/lib/galaxy/dependencies/conditional-requirements.txt
+++ b/lib/galaxy/dependencies/conditional-requirements.txt
@@ -33,7 +33,7 @@ kamaki
 watchdog
 
 # Error reporters optional modules
-python-gitlab
+python-gitlab>=2.10.0
 pygithub
 influxdb
 

From ece39129d2662c4924d4555be57263ebfe6630ba Mon Sep 17 00:00:00 2001
From: Aysam Guerler <aysam.guerler@gmail.com>
Date: Tue, 10 Aug 2021 10:47:39 -0400
Subject: [PATCH 131/218] Update
 client/src/components/DatasetInformation/DatasetAttributes.test.js

Co-authored-by: Dannon <dannon.baker@gmail.com>
---
 .../src/components/DatasetInformation/DatasetAttributes.test.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/DatasetInformation/DatasetAttributes.test.js b/client/src/components/DatasetInformation/DatasetAttributes.test.js
index 7f9d5de41a6..524d2de08d3 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.test.js
+++ b/client/src/components/DatasetInformation/DatasetAttributes.test.js
@@ -5,9 +5,9 @@ import { getLocalVue } from "jest/helpers";
 import DatasetAttributes from "./DatasetAttributes";
 import MockProvider from "../providers/MockProvider";
 import MockAdapter from "axios-mock-adapter";
+import flushPromises from "flush-promises";
 
 const localVue = getLocalVue();
-const flushPromises = () => new Promise((resolve) => setTimeout(resolve));
 
 function buildWrapper(conversion_disable = false) {
     return mount(DatasetAttributes, {

From 48df4b910dff66578a00fa40aeb5aececdf99dcc Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 19 Jul 2021 15:17:59 -0400
Subject: [PATCH 132/218] Systematic handling of remotely required tool files.

- Allow tools to define "pulsar file action"-like paths for files to include and exclude during remote job setup.
- Package up a list of defaults for older tools.
---
 doc/schema_template.md                        |   3 +
 lib/galaxy/jobs/runners/pulsar.py             |   3 +-
 lib/galaxy/tool_util/parser/__init__.py       |   3 +-
 lib/galaxy/tool_util/parser/interface.py      |  58 ++++++
 lib/galaxy/tool_util/parser/xml.py            |  22 +++
 lib/galaxy/tool_util/xsd/galaxy.xsd           |  72 ++++++++
 lib/galaxy/tools/__init__.py                  |  21 +++
 packages/app/requirements.txt                 |   2 +-
 test/unit/tool_util/test_required_files.py    | 170 ++++++++++++++++++
 .../tool_directories/r-tool-dir/my_script.R   |   1 +
 .../r-tool-dir/other_script.R                 |   1 +
 11 files changed, 353 insertions(+), 3 deletions(-)
 create mode 100644 test/unit/tool_util/test_required_files.py
 create mode 100644 test/unit/tool_util/tool_directories/r-tool-dir/my_script.R
 create mode 100644 test/unit/tool_util/tool_directories/r-tool-dir/other_script.R

diff --git a/doc/schema_template.md b/doc/schema_template.md
index 2f98d31a22d..a78b21180bf 100644
--- a/doc/schema_template.md
+++ b/doc/schema_template.md
@@ -26,6 +26,9 @@ $tag:tool|creator|organization://complexType[@name='Organization']
 $tag:tool|requirements://complexType[@name='Requirements']
 $tag:tool|requirements|requirement://complexType[@name='Requirement']
 $tag:tool|requirements|container://complexType[@name='Container']
+$tag:tool|required_files://complexType[@name='RequiredFiles']
+$tag:tool|required_files|include://complexType[@name='RequiredFileInclude']
+$tag:tool|required_files|exclude://complexType[@name='RequiredFileExclude']
 $tag:tool|code://complexType[@name='Code']
 $tag:tool|stdio://complexType[@name='Stdio']
 $tag:tool|stdio|exit_code://complexType[@name='ExitCode'] hide_attributes
diff --git a/lib/galaxy/jobs/runners/pulsar.py b/lib/galaxy/jobs/runners/pulsar.py
index 5d7dfa19830..d84e3af48ee 100644
--- a/lib/galaxy/jobs/runners/pulsar.py
+++ b/lib/galaxy/jobs/runners/pulsar.py
@@ -395,7 +395,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
                 job_directory_path = tool_env.get("job_directory_path")
                 if job_directory_path:
                     config_files.append(job_directory_path)
-
+            tool_directory_required_files = job_wrapper.tool.required_files
             client_job_description = ClientJobDescription(
                 command_line=command_line,
                 input_files=input_files,
@@ -414,6 +414,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
                 job_directory_files=job_directory_files,
                 container=None if not remote_container else remote_container.container_id,
                 guest_ports=job_wrapper.guest_ports,
+                tool_directory_required_files=tool_directory_required_files,
             )
             job_id = pulsar_submit_job(client, client_job_description, remote_job_config)
             log.info(f"Pulsar job submitted with job_id {job_id}")
diff --git a/lib/galaxy/tool_util/parser/__init__.py b/lib/galaxy/tool_util/parser/__init__.py
index 771fbaf3202..2a215042946 100644
--- a/lib/galaxy/tool_util/parser/__init__.py
+++ b/lib/galaxy/tool_util/parser/__init__.py
@@ -1,7 +1,7 @@
 """ Package responsible for parsing tools from files/abstract tool sources.
 """
 from .factory import get_input_source, get_tool_source, get_tool_source_from_representation
-from .interface import ToolSource
+from .interface import RequiredFiles, ToolSource
 from .output_objects import (
     ToolOutputCollectionPart,
 )
@@ -10,6 +10,7 @@ __all__ = (
     "get_input_source",
     "get_tool_source",
     "get_tool_source_from_representation",
+    "RequiredFiles",
     "ToolOutputCollectionPart",
     "ToolSource",
 )
diff --git a/lib/galaxy/tool_util/parser/interface.py b/lib/galaxy/tool_util/parser/interface.py
index a30040a19b2..8cfead61887 100644
--- a/lib/galaxy/tool_util/parser/interface.py
+++ b/lib/galaxy/tool_util/parser/interface.py
@@ -1,9 +1,14 @@
+import fnmatch
 import os
+import re
 from abc import (
     ABCMeta,
     abstractmethod
 )
+from os.path import join
+from typing import Dict, List, Optional
 
+from galaxy.util.path import safe_walk
 from .util import _parse_name
 
 NOT_IMPLEMENTED_MESSAGE = "Galaxy tool format does not yet support this tool feature."
@@ -167,6 +172,10 @@ class ToolSource(metaclass=ABCMeta):
         """
         return False
 
+    def parse_required_files(self) -> Optional['RequiredFiles']:
+        """ Parse explicit RequiredFiles object or return None to let Galaxy decide implicit logic."""
+        return None
+
     @abstractmethod
     def parse_requirements_and_containers(self):
         """ Return pair of ToolRequirement and ContainerDescription lists. """
@@ -452,6 +461,55 @@ class TestCollectionDef:
         return inputs
 
 
+class RequiredFiles:
+
+    def __init__(self, includes: List[Dict], excludes: List[Dict], extend_default_excludes: bool):
+        self.includes = includes
+        self.excludes = excludes
+        self.extend_default_excludes = extend_default_excludes
+
+    @staticmethod
+    def from_dict(as_dict):
+        extend_default_excludes: bool = as_dict.get("extend_default_excludes", True)
+        includes: List = as_dict.get("includes", [])
+        excludes: List = as_dict.get("excludes", [])
+        return RequiredFiles(includes, excludes, extend_default_excludes)
+
+    def find_required_files(self, tool_directory: str) -> List[str]:
+
+        def matches(ie_list: List, rel_path: str):
+            for ie_item in ie_list:
+                ie_item_path = ie_item["path"]
+                ie_item_type = ie_item.get("path_type", "literal")
+                if ie_item_type == "literal":
+                    if rel_path == ie_item_path:
+                        return True
+                elif ie_item_type == "prefix":
+                    if rel_path.startswith(ie_item_path):
+                        return True
+                elif ie_item_type == "glob":
+                    if fnmatch.fnmatch(rel_path, ie_item_path):
+                        return True
+                else:
+                    if re.match(ie_item_path, rel_path) is not None:
+                        return True
+            return False
+
+        excludes = self.excludes
+        if self.extend_default_excludes:
+            excludes.append({"path": "tool-data", "path_type": "prefix"})
+            excludes.append({"path": "test-data", "path_type": "prefix"})
+            excludes.append({"path": ".hg", "path_type": "prefix"})
+
+        files: List[str] = []
+        for (dirpath, _, filenames) in safe_walk(tool_directory):
+            for filename in filenames:
+                rel_path = join(dirpath, filename).replace(tool_directory + os.path.sep, '')
+                if matches(self.includes, rel_path) and not matches(self.excludes, rel_path):
+                    files.append(rel_path)
+        return files
+
+
 class TestCollectionOutputDef:
     __test__ = False  # Prevent pytest from discovering this class (issue #12071)
 
diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index 3af561ca65c..a3bde5e3f2d 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -3,6 +3,7 @@ import logging
 import re
 import uuid
 from math import isinf
+from typing import Optional
 
 import packaging.version
 
@@ -20,6 +21,7 @@ from .interface import (
     InputSource,
     PageSource,
     PagesSource,
+    RequiredFiles,
     TestCollectionDef,
     TestCollectionOutputDef,
     ToolSource,
@@ -261,6 +263,26 @@ class XmlToolSource(ToolSource):
             elem = self.root
         return string_as_bool(elem.get(attribute, default))
 
+    def parse_required_files(self) -> Optional[RequiredFiles]:
+        required_files = self.root.find("required_files")
+        if required_files is None:
+            return None
+
+        def parse_include_exclude_list(tag_name):
+            as_list = []
+            for ref in required_files.findall(tag_name):
+                path = ref.get("path")
+                assert path is not None, f'"path" must be specified in {tag_name}'
+                path_type = ref.get("type", "literal")
+                as_list.append({"path": path, "path_type": path_type})
+            return as_list
+
+        as_dict = {}
+        as_dict["extend_default_excludes"] = self._get_attribute_as_bool("extend_default_excludes", True, elem=required_files)
+        as_dict["includes"] = parse_include_exclude_list("include")
+        as_dict["excludes"] = parse_include_exclude_list("exclude")
+        return RequiredFiles.from_dict(as_dict)
+
     def parse_requirements_and_containers(self):
         return requirements.parse_requirements_from_xml(self.root)
 
diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
index 719962630b6..2ecbbf6eec5 100644
--- a/lib/galaxy/tool_util/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -89,6 +89,7 @@ A ``data_source`` tool contains a few more relevant attributes.
         <xs:element name="xrefs" type="xrefs" minOccurs="0" />
         <xs:element name="creator" type="Creator" minOccurs="0" />
         <xs:element name="requirements" type="Requirements" minOccurs="0"/>
+        <xs:element name="required_files" type="RequiredFiles" minOccurs="0"/>
         <xs:element name="entry_points" type="EntryPoints" minOccurs="0" maxOccurs="1" />
         <xs:element name="description" type="xs:string" minOccurs="0">
           <xs:annotation gxdocs:best_practices="tool-descriptions">
@@ -522,6 +523,77 @@ Describes an organization. Tries to stay close to [schema.org/Organization](http
     </xs:sequence>
   </xs:complexType>
 
+  <xs:complexType name="RequiredFiles">
+    <xs:annotation>
+      <xs:documentation xml:lang="en"><![CDATA[
+This declaration is used to define files that must be shipped from the tool directory
+for the tool to function properly in remote environments where the tool directory
+is not available to the job.
+
+All includes should be list before excludes. By default, the exclude list includes
+the tool-data/**, test-data/**, and .hg/** glob patterns.
+
+Pulsar hacks to implicitly find referenced files from the tool directory will be disabled
+when this block is used. A future Galaxy tool profile version may disable these hacks
+altogether and specifying this block for all referenced files should be considered a best
+practice.
+]]></xs:documentation>
+    </xs:annotation>
+    <xs:sequence>
+      <xs:element name="include" type="RequiredFileInclude" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element name="exclude" type="RequiredFileExclude" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
+    <xs:attribute name="extend_default_excludes" type="xs:boolean" default="true">
+      <xs:annotation>
+        <xs:documentation xml:lang="en">Set this to `false` to override the default excludes for mercurial, reference, and test data.</xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+  </xs:complexType>
+
+  <xs:simpleType name="RequiredFileReferenceType">
+    <xs:annotation>
+      <xs:documentation xml:lang="en">How are files referenced in RequiredFileIncludes and RequiredFileExcludes. Paths are matched relative to the tool directory. `literal` must match the filename exactly. `prefix` will match paths based on their start. `glob` and `regex` use patterns to match files.</xs:documentation>
+    </xs:annotation>
+    <xs:restriction base="xs:string">
+      <xs:enumeration value="literal"/>
+      <xs:enumeration value="prefix"/>
+      <xs:enumeration value="glob"/>
+      <xs:enumeration value="regex"/>
+    </xs:restriction>
+  </xs:simpleType>
+
+  <xs:complexType name="RequiredFileInclude">
+    <xs:annotation>
+      <xs:documentation xml:lang="en">Describe files to include when relocating tool directory for remote execution.</xs:documentation>
+    </xs:annotation>
+    <xs:attribute name="type" type="RequiredFileReferenceType">
+      <xs:annotation>
+        <xs:documentation xml:lang="en">Type of file reference `path` is.</xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+    <xs:attribute name="path" type="xs:string">
+      <xs:annotation>
+        <xs:documentation xml:lang="en">Path to referenced files - this should be relative to the tool's directory (this is the file the tool is located in not the repository directory if these conflict).</xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+  </xs:complexType>
+
+  <xs:complexType name="RequiredFileExclude">
+    <xs:annotation>
+      <xs:documentation xml:lang="en">Describe files to exclude when relocating tool directory for remote execution.</xs:documentation>
+    </xs:annotation>
+    <xs:attribute name="type" type="RequiredFileReferenceType">
+      <xs:annotation>
+        <xs:documentation xml:lang="en">Type of file reference `path` is.</xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+    <xs:attribute name="path" type="xs:string">
+      <xs:annotation>
+        <xs:documentation xml:lang="en">Path to referenced files - this should be relative to the tool's directory (this is the file the tool is located in not the repository directory if these conflict).</xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+  </xs:complexType>
+
   <xs:complexType name="Requirements">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index e4dcc7b6669..a1681fcb135 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -43,6 +43,7 @@ from galaxy.tool_util.output_checker import DETECTED_JOB_STATE
 from galaxy.tool_util.parser import (
     get_tool_source,
     get_tool_source_from_representation,
+    RequiredFiles,
     ToolOutputCollectionPart
 )
 from galaxy.tool_util.parser.xml import XmlPageSource
@@ -195,6 +196,16 @@ GALAXY_LIB_TOOLS_VERSIONED = {
 BIOTOOLS_MAPPING_CONTENT = resource_string(__name__, 'biotools_mappings.tsv').decode("UTF-8")
 BIOTOOLS_MAPPING: Dict[str, str] = dict([cast(Tuple[str, str], tuple(x.split("\t"))) for x in BIOTOOLS_MAPPING_CONTENT.splitlines() if not x.startswith("#")])
 
+REQUIRE_FULL_DIRECTORY = {
+    "includes": [{"path": "**", "path_type": "glob"}],
+}
+IMPLICITLY_REQUIRED_TOOL_FILES: Dict[str, Dict] = {
+    "deseq2": {"version": packaging.version.parse("2.11.40.6"), "required": {"includes": [{"path": "*.R", "path_type": "glob"}]}},
+    # minimum example:
+    # "foobar": {"required": REQUIRE_FULL_DIRECTORY}
+    # if no version is specified, all versions without explicit RequiredFiles will be selected
+}
+
 
 class safe_update(NamedTuple):
     min_version: Union[packaging.version.LegacyVersion, packaging.version.Version]
@@ -963,6 +974,16 @@ class Tool(Dictifiable):
         self.requirements = requirements
         self.containers = containers
 
+        required_files = tool_source.parse_required_files()
+        if required_files is None:
+            old_id = self.old_id
+            if old_id in IMPLICITLY_REQUIRED_TOOL_FILES:
+                lineage_requirement = IMPLICITLY_REQUIRED_TOOL_FILES[old_id]
+                lineage_requirement_until = lineage_requirement.get("version")
+                if lineage_requirement_until is None or self.version_object < lineage_requirement_until:
+                    required_files = RequiredFiles.from_dict(lineage_requirement["required"])
+        self.required_files = required_files
+
         self.citations = self._parse_citations(tool_source)
         xrefs = tool_source.parse_xrefs()
         has_biotools_reference = any(x["reftype"] == "bio.tools" for x in xrefs)
diff --git a/packages/app/requirements.txt b/packages/app/requirements.txt
index 4faa725a7df..d5572846ea2 100644
--- a/packages/app/requirements.txt
+++ b/packages/app/requirements.txt
@@ -9,7 +9,7 @@ celery
 kombu
 Beaker
 pykwalify
-pulsar-galaxy-lib
+pulsar-galaxy-lib>=0.14.7
 gxformat2
 Mako
 sqlitedict
diff --git a/test/unit/tool_util/test_required_files.py b/test/unit/tool_util/test_required_files.py
new file mode 100644
index 00000000000..f65ceca32e1
--- /dev/null
+++ b/test/unit/tool_util/test_required_files.py
@@ -0,0 +1,170 @@
+import os
+from pathlib import Path
+
+from .test_parsing import BaseLoaderTestCase
+
+SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
+TEST_TOOL_DIRECTORIES = os.path.join(SCRIPT_DIRECTORY, "tool_directories")
+
+
+TOOL_REQUIRED_FILES_XML_1 = """
+<tool name="required_files_1" id="required_files_1" version="0.1.0">
+    <command>foo</command>
+    <required_files>
+        <include path="my_script.R" />
+    </required_files>
+    <inputs>
+        <input type="text" label="Text to parse." name="input1" />
+    </inputs>
+    <outputs>
+        <output type="integer" name="out1" from="output" />
+    </outputs>
+</tool>
+"""
+
+
+TOOL_REQUIRED_FILES_XML_2 = """
+<tool name="required_files_1" id="required_files_1" version="0.1.0">
+    <command>foo</command>
+    <required_files>
+        <include path="*.R" type="glob" />
+        <exclude path="other_script.R" />
+    </required_files>
+    <inputs>
+        <input type="text" label="Text to parse." name="input1" />
+    </inputs>
+    <outputs>
+        <output type="integer" name="out1" from="output" />
+    </outputs>
+</tool>
+"""
+
+
+TOOL_REQUIRED_FILES_XML_3 = """
+<tool name="required_files_1" id="required_files_1" version="0.1.0">
+    <command>foo</command>
+    <required_files>
+        <include path="*.R" type="glob" />
+    </required_files>
+    <inputs>
+        <input type="text" label="Text to parse." name="input1" />
+    </inputs>
+    <outputs>
+        <output type="integer" name="out1" from="output" />
+    </outputs>
+</tool>
+"""
+
+
+TOOL_REQUIRED_FILES_XML_4 = """
+<tool name="required_files_1" id="required_files_1" version="0.1.0">
+    <command>foo</command>
+    <required_files>
+        <include path=".*R" type="regex" />
+        <exclude path="other_script*" type="glob" />
+    </required_files>
+    <inputs>
+        <input type="text" label="Text to parse." name="input1" />
+    </inputs>
+    <outputs>
+        <output type="integer" name="out1" from="output" />
+    </outputs>
+</tool>
+"""
+
+
+TOOL_REQUIRED_FILES_XML_DISABLED_DEFAULT_EXCLUSIONS = """
+<tool name="required_files_1" id="required_files_1" version="0.1.0">
+    <command>foo</command>
+    <required_files extend_default_excludes="false">
+        <include path="*.R" type="glob" />
+    </required_files>
+    <inputs>
+        <input type="text" label="Text to parse." name="input1" />
+    </inputs>
+    <outputs>
+        <output type="integer" name="out1" from="output" />
+    </outputs>
+</tool>
+"""
+
+
+class BaseRequiredFilesTestCase(BaseLoaderTestCase):
+    source_file_name = "required_files.xml"
+
+    def _required_files(self, tool_directory: str):
+        tool_source = self._tool_source
+        required_files = tool_source.parse_required_files()
+        return required_files.find_required_files(tool_directory)
+
+
+# directly include just one file that is there
+class RequiredFiles1TestCase(BaseRequiredFilesTestCase):
+    source_contents = TOOL_REQUIRED_FILES_XML_1
+
+    def test_expected_files(self):
+        files = self._required_files(os.path.join(TEST_TOOL_DIRECTORIES, "r-tool-dir"))
+        assert len(files) == 1
+        assert "my_script.R" in files
+
+
+# include a glob and exclude a file in the glob
+class RequiredFiles2TestCase(BaseRequiredFilesTestCase):
+    source_contents = TOOL_REQUIRED_FILES_XML_2
+
+    def test_expected_files(self):
+        files = self._required_files(os.path.join(TEST_TOOL_DIRECTORIES, "r-tool-dir"))
+        assert len(files) == 1
+        assert "my_script.R" in files
+
+
+# include a glob with multiple matches
+class RequiredFiles3TestCase(BaseRequiredFilesTestCase):
+    source_contents = TOOL_REQUIRED_FILES_XML_3
+
+    def test_expected_files(self):
+        files = self._required_files(os.path.join(TEST_TOOL_DIRECTORIES, "r-tool-dir"))
+        assert len(files) == 2
+        assert "my_script.R" in files
+        assert "other_script.R" in files
+
+
+# include a file with regex and exclude with glob
+class RequiredFiles4TestCase(BaseRequiredFilesTestCase):
+    source_contents = TOOL_REQUIRED_FILES_XML_4
+
+    def test_expected_files(self):
+        files = self._required_files(os.path.join(TEST_TOOL_DIRECTORIES, "r-tool-dir"))
+        assert len(files) == 1
+        assert "my_script.R" in files
+
+
+class HgExcludedByDefaultTestCase(BaseRequiredFilesTestCase):
+    source_contents = TOOL_REQUIRED_FILES_XML_3
+
+    def test_expected_files(self):
+        repo_dir = setup_dir_with_repo(self.temp_directory)
+        files = self._required_files(repo_dir)
+        assert len(files) == 1
+        assert "my_script.R" in files
+
+
+class HgExclusionDisabledTestCase(BaseRequiredFilesTestCase):
+    source_contents = TOOL_REQUIRED_FILES_XML_DISABLED_DEFAULT_EXCLUSIONS
+
+    def test_expected_files(self):
+        repo_dir = setup_dir_with_repo(self.temp_directory)
+        files = self._required_files(repo_dir)
+        assert len(files) == 2
+        assert "my_script.R" in files
+        assert ".hg/index.R" in files
+
+
+def setup_dir_with_repo(tmp_dir):
+    repo = os.path.join(tmp_dir, "repo")
+    os.makedirs(repo)
+    hg = os.path.join(repo, ".hg")
+    os.makedirs(hg)
+    Path(hg, "index.R").touch()
+    Path(repo, "my_script.R").touch()
+    return repo
diff --git a/test/unit/tool_util/tool_directories/r-tool-dir/my_script.R b/test/unit/tool_util/tool_directories/r-tool-dir/my_script.R
new file mode 100644
index 00000000000..fee7cb0d403
--- /dev/null
+++ b/test/unit/tool_util/tool_directories/r-tool-dir/my_script.R
@@ -0,0 +1 @@
+my cool R script
diff --git a/test/unit/tool_util/tool_directories/r-tool-dir/other_script.R b/test/unit/tool_util/tool_directories/r-tool-dir/other_script.R
new file mode 100644
index 00000000000..6e7a2cc1241
--- /dev/null
+++ b/test/unit/tool_util/tool_directories/r-tool-dir/other_script.R
@@ -0,0 +1 @@
+another R script

From b6f75b7ea64c324cbe94767bfdcb7ca904c29ec5 Mon Sep 17 00:00:00 2001
From: setlen <peter.selten98@gmail.com>
Date: Tue, 10 Aug 2021 20:15:22 +0200
Subject: [PATCH 133/218] Fix unused dependencies

---
 lib/galaxy/tools/error_reports/plugins/gitlab.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/tools/error_reports/plugins/gitlab.py b/lib/galaxy/tools/error_reports/plugins/gitlab.py
index f3615060581..12bf02b2207 100644
--- a/lib/galaxy/tools/error_reports/plugins/gitlab.py
+++ b/lib/galaxy/tools/error_reports/plugins/gitlab.py
@@ -2,9 +2,9 @@
 
 import logging
 import os
-import sys
 
 import requests
+import urllib.parse
 
 try:
     import gitlab
@@ -39,7 +39,8 @@ class GitLabPlugin(BaseGitPlugin):
 
         try:
             if gitlab is None:
-                raise Exception("GitLab error reporting plugin is configured, but gitlab is not installed. Please install python-gitlab.")
+                raise Exception("GitLab error reporting plugin is configured, but gitlab is not installed. "
+                                "Please install python-gitlab v2.10.0 or higher.")
             self.gitlab = self.gitlab_connect()
             self.gitlab.auth()
 
@@ -93,7 +94,7 @@ class GitLabPlugin(BaseGitPlugin):
                 # this will be detected by requests and used further down the line. Also cache this so everything is
                 # as fast as possible
                 ts_url = self._determine_ts_url(tool)
-                log.info("GitLab error reporting - Determined ToolShed is %s", ts_url)
+                log.info("GitLab error reporting - Determined ToolShed is {ts_url}")
 
                 # Find the repo inside the ToolShed
                 ts_repourl = self._get_gitrepo_from_ts(job, ts_url)
@@ -102,10 +103,10 @@ class GitLabPlugin(BaseGitPlugin):
                 if ts_repourl is not None and ts_repourl.endswith(".git"):
                     ts_repourl = ts_repourl[:-4]
 
-                log.info("GitLab error reporting - Determine ToolShed Repository URL: %s", ts_repourl)
+                log.info(f"GitLab error reporting - Determine ToolShed Repository URL: {ts_repourl}")
 
                 # Determine the GitLab project URL and the issue cache key
-                gitlab_projecturl = urlparse.urlparse(ts_repourl).path[1:] if (ts_repourl and not self.git_default_repo_only)\
+                gitlab_projecturl = urllib.parse.urlparse(ts_repourl).path[1:] if (ts_repourl and not self.git_default_repo_only)\
                     else "/".join((self.git_default_repo_owner, self.git_default_repo_name))
                 issue_cache_key = self._get_issue_cache_key(job, ts_repourl)
 
@@ -143,8 +144,7 @@ class GitLabPlugin(BaseGitPlugin):
                         gl_emailquery = self.gitlab.users.list(search=gl_useremail)
                         log.debug(f"GitLab error reporting - User list: {gl_emailquery}")
                         if len(gl_emailquery) > 0:
-                            log.debug("GitLab error reporting - Last Committer user ID: %d" %
-                                      gl_emailquery[0].get_id())
+                            log.debug("GitLab error reporting - Last Committer user ID: " % gl_emailquery[0].get_id())
                             self.git_username_id_cache[gl_useremail] = gl_emailquery[0].get_id()
                     gl_userid = self.git_username_id_cache.get(gl_useremail, None)
 

From c98cf15fd5885d94c4c4d9065b25be667a430290 Mon Sep 17 00:00:00 2001
From: Mason Houtz <nerdinacan@gmail.com>
Date: Tue, 10 Aug 2021 11:20:37 -0700
Subject: [PATCH 134/218] restore ability to bulk-update history visibility

---
 lib/galaxy/schema/schema.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index 8c31eb11ada..98eb6b47436 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -632,6 +632,13 @@ class UpdateHistoryContentsBatchPayload(Model):
             "otherwise cannot delete uploading files, so it will raise an error."
         ),
     )
+    visible: Optional[bool] = Field(
+        default=False,
+        title="Visible",
+        description=(
+            "Show or hide history contents"
+        ),
+    )
 
 
 class HistoryBase(BaseModel):

From c1f39f6e9fb62b8b881b9bf393b5b8c168eaf948 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sat, 7 Aug 2021 17:20:46 -0400
Subject: [PATCH 135/218] Add generic form component, and redirect permissions
 route

---
 client/src/components/Form/FormGeneric.vue    | 140 ++++++++++++++++++
 .../components/providers/UrlDataProvider.js   |  17 +++
 client/src/entry/analysis/AnalysisRouter.js   |  11 +-
 3 files changed, 162 insertions(+), 6 deletions(-)
 create mode 100644 client/src/components/Form/FormGeneric.vue
 create mode 100644 client/src/components/providers/UrlDataProvider.js

diff --git a/client/src/components/Form/FormGeneric.vue b/client/src/components/Form/FormGeneric.vue
new file mode 100644
index 00000000000..4a269dd173c
--- /dev/null
+++ b/client/src/components/Form/FormGeneric.vue
@@ -0,0 +1,140 @@
+<template>
+    <UrlDataProvider :url="url" v-slot="{ result, loading }" @error="onError">
+        <div v-if="!loading">
+            <b-alert v-if="result.message" :variant="resultMessageVariant" show>
+                {{ result.message }}
+            </b-alert>
+            <b-alert v-if="messageText" :variant="messageVariant" show>
+                {{ messageText }}
+            </b-alert>
+            <FormCard :title="result.title" :icon="result.icon">
+                <template v-slot:body>
+                    <FormDisplay :inputs="result.inputs" @onChange="onChange" />
+                </template>
+            </FormCard>
+            <div class="mt-2">
+                <b-button
+                    variant="primary"
+                    class="mr-1"
+                    v-b-tooltip.hover
+                    :title="result.submit_tooltip"
+                    @click="onSubmit(result)"
+                >
+                    <span :class="submitIcon(result)" />{{ submitTitle(result) | l }}
+                </b-button>
+                <b-button
+                    v-if="result.cancel_redirect"
+                    v-b-tooltip.hover
+                    :title="result.cancel_tooltip"
+                    @click="onCancel(result)"
+                >
+                    <span :class="cancelIcon(result)" />{{ cancelTitle(result) | l }}
+                </b-button>
+            </div>
+        </div>
+    </UrlDataProvider>
+</template>
+
+<script>
+import { getAppRoot } from "onload/loadConfig";
+import { UrlDataProvider } from "components/providers/UrlDataProvider";
+import FormCard from "components/Form/FormCard";
+import FormDisplay from "components/Form/FormDisplay";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faSave, faTimes } from "@fortawesome/free-solid-svg-icons";
+
+library.add(faSave, faTimes);
+
+export default {
+    props: {
+        url: {
+            type: String,
+            required: true,
+        },
+        redirect: {
+            type: String,
+            required: false,
+        },
+    },
+    components: {
+        FontAwesomeIcon,
+        FormCard,
+        FormDisplay,
+        UrlDataProvider,
+    },
+    data() {
+        return {
+            messageText: null,
+            messageVariant: null,
+            formData: {},
+        };
+    },
+    methods: {
+        resultMessageVariant(options) {
+            return result.status || "warning";
+        },
+        cancelTitle(options) {
+            return options.cancel_title || "Cancel";
+        },
+        cancelIcon(options) {
+            const icon = options.cancel_icon || "fa-times";
+            return `mr-1 fa ${icon}`;
+        },
+        submitTitle(options) {
+            return options.submit_title || "Save";
+        },
+        submitIcon(options) {
+            const icon = options.submit_icon || "fa-save";
+            return `mr-1 fa ${icon}`;
+        },
+        onChange(formData) {
+            this.formData = formData;
+        },
+        onCancel(options) {
+            window.location = `${getAppRoot()}${options.cancel_redirect}`;
+        },
+        onSubmit(options) {
+            /*
+            var self = this;
+        $.ajax({
+            url: getAppRoot() + self.url,
+            data: JSON.stringify(form.data.create()),
+            type: "PUT",
+            contentType: "application/json",
+        })
+            .done((response) => {
+                var params = {};
+                if (response.id) {
+                    params.id = response.id;
+                } else {
+                    params = {
+                        message: response.message,
+                        status: "success",
+                        persistent: false,
+                    };
+                }
+                if (self.redirect) {
+                    window.location = `${getAppRoot()}${self.redirect}?${$.param(params)}`;
+                } else {
+                    form.data.matchModel(response, (input, input_id) => {
+                        form.field_list[input_id].value(input.value);
+                    });
+                    self._showMessage(form, response.message);
+                }
+            })
+            .fail((response) => {
+                self._showMessage(form, {
+                    message: response.responseJSON.err_msg,
+                    status: "danger",
+                    persistent: false,
+                });
+            });*/
+        },
+        onError(error) {
+            this.messageText = `Failed to load resource ${this.url}.`;
+            this.messageVariant = "danger";
+        },
+    },
+};
+</script>
diff --git a/client/src/components/providers/UrlDataProvider.js b/client/src/components/providers/UrlDataProvider.js
new file mode 100644
index 00000000000..00d96d0c51b
--- /dev/null
+++ b/client/src/components/providers/UrlDataProvider.js
@@ -0,0 +1,17 @@
+import axios from "axios";
+import { getAppRoot } from "onload/loadConfig";
+import { SingleQueryProvider } from "components/providers/SingleQueryProvider";
+import { rethrowSimple } from "utils/simple-error";
+
+async function urlData({ url }) {
+    console.log(url);
+    try {
+        const { data } = await axios.get(`${getAppRoot()}${url}`);
+        console.log(data);
+        return data;
+    } catch (e) {
+        rethrowSimple(e);
+    }
+}
+
+export const UrlDataProvider = SingleQueryProvider(urlData);
diff --git a/client/src/entry/analysis/AnalysisRouter.js b/client/src/entry/analysis/AnalysisRouter.js
index 9c67d51ce28..987afcf71ef 100644
--- a/client/src/entry/analysis/AnalysisRouter.js
+++ b/client/src/entry/analysis/AnalysisRouter.js
@@ -16,6 +16,7 @@ import { getAppRoot } from "onload";
 import decodeUriComponent from "decode-uri-component";
 import Router from "layout/router";
 import ToolForm from "components/Tool/ToolForm";
+import FormGeneric from "components/Form/FormGeneric";
 import FormWrapper from "mvc/form/form-wrapper";
 import Sharing from "components/Sharing.vue";
 import UserPreferences from "components/User/UserPreferences.vue";
@@ -268,12 +269,10 @@ export const getAnalysisRouter = (Galaxy) => {
         },
 
         show_histories_permissions: function () {
-            this.page.display(
-                new FormWrapper.View({
-                    url: `history/permissions?id=${QueryStringParsing.get("id")}`,
-                    redirect: "histories/list",
-                })
-            );
+            this._display_vue_helper(FormGeneric, {
+                url: `history/permissions?id=${QueryStringParsing.get("id")}`,
+                redirect: "histories/list",
+            });
         },
 
         show_datasets: function () {

From daad9ff94490177c7361fb9b7f08abc58960665f Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sat, 7 Aug 2021 17:22:03 -0400
Subject: [PATCH 136/218] Remove font awesome important, icons are dynamic

---
 client/src/components/Form/FormGeneric.vue | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/client/src/components/Form/FormGeneric.vue b/client/src/components/Form/FormGeneric.vue
index 4a269dd173c..08788291ed0 100644
--- a/client/src/components/Form/FormGeneric.vue
+++ b/client/src/components/Form/FormGeneric.vue
@@ -40,11 +40,6 @@ import { getAppRoot } from "onload/loadConfig";
 import { UrlDataProvider } from "components/providers/UrlDataProvider";
 import FormCard from "components/Form/FormCard";
 import FormDisplay from "components/Form/FormDisplay";
-import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { library } from "@fortawesome/fontawesome-svg-core";
-import { faSave, faTimes } from "@fortawesome/free-solid-svg-icons";
-
-library.add(faSave, faTimes);
 
 export default {
     props: {

From 7aedfc91bf339afcfce1c30ae1ecae513dbf4c6e Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sat, 7 Aug 2021 17:42:53 -0400
Subject: [PATCH 137/218] Add event handler to generic forms submit operation

---
 client/src/components/Form/FormGeneric.vue    | 39 ++++++-------------
 .../components/providers/UrlDataProvider.js   |  2 -
 2 files changed, 12 insertions(+), 29 deletions(-)

diff --git a/client/src/components/Form/FormGeneric.vue b/client/src/components/Form/FormGeneric.vue
index 08788291ed0..80ba47a3441 100644
--- a/client/src/components/Form/FormGeneric.vue
+++ b/client/src/components/Form/FormGeneric.vue
@@ -18,7 +18,7 @@
                     class="mr-1"
                     v-b-tooltip.hover
                     :title="result.submit_tooltip"
-                    @click="onSubmit(result)"
+                    @click="onSubmit()"
                 >
                     <span :class="submitIcon(result)" />{{ submitTitle(result) | l }}
                 </b-button>
@@ -37,6 +37,7 @@
 
 <script>
 import { getAppRoot } from "onload/loadConfig";
+import { submitData } from "./services";
 import { UrlDataProvider } from "components/providers/UrlDataProvider";
 import FormCard from "components/Form/FormCard";
 import FormDisplay from "components/Form/FormDisplay";
@@ -53,7 +54,6 @@ export default {
         },
     },
     components: {
-        FontAwesomeIcon,
         FormCard,
         FormDisplay,
         UrlDataProvider,
@@ -89,17 +89,9 @@ export default {
         onCancel(options) {
             window.location = `${getAppRoot()}${options.cancel_redirect}`;
         },
-        onSubmit(options) {
-            /*
-            var self = this;
-        $.ajax({
-            url: getAppRoot() + self.url,
-            data: JSON.stringify(form.data.create()),
-            type: "PUT",
-            contentType: "application/json",
-        })
-            .done((response) => {
-                var params = {};
+        onSubmit() {
+            submitData(this.url, this.formData).then((response) => {
+                let params = {};
                 if (response.id) {
                     params.id = response.id;
                 } else {
@@ -109,22 +101,15 @@ export default {
                         persistent: false,
                     };
                 }
-                if (self.redirect) {
-                    window.location = `${getAppRoot()}${self.redirect}?${$.param(params)}`;
+                if (this.redirect) {
+                    window.location = `${getAppRoot()}${this.redirect}?${$.param(params)}`;
                 } else {
-                    form.data.matchModel(response, (input, input_id) => {
-                        form.field_list[input_id].value(input.value);
-                    });
-                    self._showMessage(form, response.message);
+                    /*form.data.matchModel(response, (input, input_id) => {
+                            form.field_list[input_id].value(input.value);
+                        });
+                        self._showMessage(form, response.message);*/
                 }
-            })
-            .fail((response) => {
-                self._showMessage(form, {
-                    message: response.responseJSON.err_msg,
-                    status: "danger",
-                    persistent: false,
-                });
-            });*/
+            }, this.onError);
         },
         onError(error) {
             this.messageText = `Failed to load resource ${this.url}.`;
diff --git a/client/src/components/providers/UrlDataProvider.js b/client/src/components/providers/UrlDataProvider.js
index 00d96d0c51b..a7051ceef71 100644
--- a/client/src/components/providers/UrlDataProvider.js
+++ b/client/src/components/providers/UrlDataProvider.js
@@ -4,10 +4,8 @@ import { SingleQueryProvider } from "components/providers/SingleQueryProvider";
 import { rethrowSimple } from "utils/simple-error";
 
 async function urlData({ url }) {
-    console.log(url);
     try {
         const { data } = await axios.get(`${getAppRoot()}${url}`);
-        console.log(data);
         return data;
     } catch (e) {
         rethrowSimple(e);

From 6884674d3171ae1434ee2895ce13ef6e315acea0 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sat, 7 Aug 2021 17:52:21 -0400
Subject: [PATCH 138/218] Replace all form-wrapper instances with form generic
 vue component, remove legacy module

---
 client/src/components/Form/FormGeneric.vue  |   2 +-
 client/src/entry/admin/AdminRouter.js       |   4 +-
 client/src/entry/analysis/AnalysisRouter.js |  58 ++++-----
 client/src/mvc/form/form-wrapper.js         | 123 --------------------
 4 files changed, 27 insertions(+), 160 deletions(-)
 delete mode 100644 client/src/mvc/form/form-wrapper.js

diff --git a/client/src/components/Form/FormGeneric.vue b/client/src/components/Form/FormGeneric.vue
index 80ba47a3441..21ad8aec281 100644
--- a/client/src/components/Form/FormGeneric.vue
+++ b/client/src/components/Form/FormGeneric.vue
@@ -112,7 +112,7 @@ export default {
             }, this.onError);
         },
         onError(error) {
-            this.messageText = `Failed to load resource ${this.url}.`;
+            this.messageText = error || `Failed to load resource ${this.url}.`;
             this.messageVariant = "danger";
         },
     },
diff --git a/client/src/entry/admin/AdminRouter.js b/client/src/entry/admin/AdminRouter.js
index 62a8147de41..2b55152cb84 100644
--- a/client/src/entry/admin/AdminRouter.js
+++ b/client/src/entry/admin/AdminRouter.js
@@ -1,7 +1,7 @@
 import { getGalaxyInstance } from "app";
 import { getAppRoot } from "onload";
 import _l from "utils/localization";
-import FormWrapper from "mvc/form/form-wrapper";
+import FormGeneric from "components/Form/FormGeneric";
 import GridView from "mvc/grid/grid-view";
 import QueryStringParsing from "utils/query-string-parsing";
 import Router from "layout/router";
@@ -225,7 +225,7 @@ export const getAdminRouter = (Galaxy, options) => {
                     redirect: "admin/forms",
                 },
             };
-            this.page.display(new FormWrapper.View(form_defs[form_id]));
+            this._display_vue_helper(FormGeneric, form_defs[form_id]);
         },
     });
 };
diff --git a/client/src/entry/analysis/AnalysisRouter.js b/client/src/entry/analysis/AnalysisRouter.js
index 987afcf71ef..cf27c1a4124 100644
--- a/client/src/entry/analysis/AnalysisRouter.js
+++ b/client/src/entry/analysis/AnalysisRouter.js
@@ -17,7 +17,6 @@ import decodeUriComponent from "decode-uri-component";
 import Router from "layout/router";
 import ToolForm from "components/Tool/ToolForm";
 import FormGeneric from "components/Form/FormGeneric";
-import FormWrapper from "mvc/form/form-wrapper";
 import Sharing from "components/Sharing.vue";
 import UserPreferences from "components/User/UserPreferences.vue";
 import DatasetList from "components/Dataset/DatasetList.vue";
@@ -114,7 +113,6 @@ export const getAnalysisRouter = (Galaxy) => {
                 container.active_tab = active_tab;
             }
             this.page.display(container, noPadding);
-
             const mountFn = mountVueComponent(component);
             return mountFn(propsData, container);
         },
@@ -141,7 +139,7 @@ export const getAnalysisRouter = (Galaxy) => {
 
         show_user_form: function (form_id, params) {
             const model = getUserPreferencesModel(params.id);
-            this.page.display(new FormWrapper.View(_.extend(model[form_id], { active_tab: "user" })));
+            this._display_vue_helper(FormGeneric, _.extend(model[form_id], { active_tab: "user" }));
         },
 
         show_interactivetool_list: function () {
@@ -175,13 +173,11 @@ export const getAnalysisRouter = (Galaxy) => {
         },
 
         show_visualizations_edit: function () {
-            this.page.display(
-                new FormWrapper.View({
-                    url: `visualization/edit?id=${QueryStringParsing.get("id")}`,
-                    redirect: "visualizations/list",
-                    active_tab: "visualization",
-                })
-            );
+            this._display_vue_helper(FormGeneric, {
+                url: `visualization/edit?id=${QueryStringParsing.get("id")}`,
+                redirect: "visualizations/list",
+                active_tab: "visualization",
+            });
         },
 
         show_visualizations_sharing: function () {
@@ -297,23 +293,19 @@ export const getAnalysisRouter = (Galaxy) => {
             if (invocation_id) {
                 url += `?invocation_id=${invocation_id}`;
             }
-            this.page.display(
-                new FormWrapper.View({
-                    url: url,
-                    redirect: "pages/list",
-                    active_tab: "user",
-                })
-            );
+            this._display_vue_helper(FormGeneric, {
+                url: url,
+                redirect: "pages/list",
+                active_tab: "user",
+            });
         },
 
         show_pages_edit: function () {
-            this.page.display(
-                new FormWrapper.View({
-                    url: `page/edit?id=${QueryStringParsing.get("id")}`,
-                    redirect: "pages/list",
-                    active_tab: "user",
-                })
-            );
+            this._display_vue_helper(FormGeneric, {
+                url: `page/edit?id=${QueryStringParsing.get("id")}`,
+                redirect: "pages/list",
+                active_tab: "user",
+            });
         },
 
         show_pages_sharing: function () {
@@ -333,16 +325,14 @@ export const getAnalysisRouter = (Galaxy) => {
         },
 
         show_workflows_create: function () {
-            this.page.display(
-                new FormWrapper.View({
-                    url: "workflow/create",
-                    redirect: "workflow/editor",
-                    active_tab: "workflow",
-                    submit_title: "Create",
-                    submit_icon: "fa-check",
-                    cancel_redirect: "workflows/list",
-                })
-            );
+            this._display_vue_helper(FormGeneric, {
+                url: "workflow/create",
+                redirect: "workflow/editor",
+                active_tab: "workflow",
+                submit_title: "Create",
+                submit_icon: "fa-check",
+                cancel_redirect: "workflows/list",
+            });
         },
 
         show_workflows_run: function () {
diff --git a/client/src/mvc/form/form-wrapper.js b/client/src/mvc/form/form-wrapper.js
deleted file mode 100644
index 79612b2c54a..00000000000
--- a/client/src/mvc/form/form-wrapper.js
+++ /dev/null
@@ -1,123 +0,0 @@
-/** Generic form view */
-import $ from "jquery";
-import Backbone from "backbone";
-import { getAppRoot } from "onload/loadConfig";
-import Form from "mvc/form/form-view";
-import Ui from "mvc/ui/ui-misc";
-
-var View = Backbone.View.extend({
-    initialize: function (options) {
-        this.model = new Backbone.Model(options);
-        this.url = this.model.get("url");
-        this.redirect = this.model.get("redirect");
-        if (options && options.active_tab) {
-            this.active_tab = options.active_tab;
-        }
-        this.setElement("<div/>");
-        this.render();
-    },
-
-    render: function () {
-        var self = this;
-        $.ajax({
-            url: getAppRoot() + this.url,
-            type: "GET",
-        })
-            .done((response) => {
-                var options = $.extend({}, self.model.attributes, response);
-                var form = new Form({
-                    title: options.title,
-                    title_id: options.title_id,
-                    message: options.message,
-                    status: options.status || "warning",
-                    icon: options.icon,
-                    initial_errors: true,
-                    errors: options.errors,
-                    inputs: options.inputs,
-                    buttons: {
-                        cancel:
-                            options.cancel_redirect &&
-                            new Ui.Button({
-                                tooltip: options.cancel_tooltip,
-                                title: options.cancel_title || "Cancel",
-                                icon: options.cancel_icon || "fa-times",
-                                onclick: function () {
-                                    window.location = `${getAppRoot()}${options.cancel_redirect}`;
-                                },
-                            }),
-                        submit: new Ui.Button({
-                            tooltip: options.submit_tooltip,
-                            title: options.submit_title || "Save",
-                            icon: options.submit_icon || "fa-save",
-                            cls: "btn btn-primary",
-                            onclick: function () {
-                                self._submit(form);
-                            },
-                        }),
-                    },
-                });
-                self.$el.empty().append(form.$el);
-            })
-            .fail((response) => {
-                self.$el.empty().append(
-                    new Ui.Message({
-                        message: `Failed to load resource ${self.url}.`,
-                        status: "danger",
-                        persistent: true,
-                    }).$el
-                );
-            });
-    },
-
-    _submit: function (form) {
-        var self = this;
-        $.ajax({
-            url: getAppRoot() + self.url,
-            data: JSON.stringify(form.data.create()),
-            type: "PUT",
-            contentType: "application/json",
-        })
-            .done((response) => {
-                var params = {};
-                if (response.id) {
-                    params.id = response.id;
-                } else {
-                    params = {
-                        message: response.message,
-                        status: "success",
-                        persistent: false,
-                    };
-                }
-                if (self.redirect) {
-                    window.location = `${getAppRoot()}${self.redirect}?${$.param(params)}`;
-                } else {
-                    form.data.matchModel(response, (input, input_id) => {
-                        form.field_list[input_id].value(input.value);
-                    });
-                    self._showMessage(form, response.message);
-                }
-            })
-            .fail((response) => {
-                self._showMessage(form, {
-                    message: response.responseJSON.err_msg,
-                    status: "danger",
-                    persistent: false,
-                });
-            });
-    },
-
-    _showMessage: function (form, options) {
-        var $panel = form.$el
-            .parents()
-            .filter(function () {
-                return ["auto", "scroll"].indexOf($(this).css("overflow")) != -1;
-            })
-            .first();
-        $panel.animate({ scrollTop: 0 }, 500);
-        form.message.update(options);
-    },
-});
-
-export default {
-    View: View,
-};

From 520eca9228580ec8fd786bdb833e851c497c5aac Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sat, 7 Aug 2021 18:02:54 -0400
Subject: [PATCH 139/218] Remove unused legacy condition for specific error
 highlighting in generic wrapper

---
 client/src/components/Form/FormGeneric.vue | 15 ++++-----------
 1 file changed, 4 insertions(+), 11 deletions(-)

diff --git a/client/src/components/Form/FormGeneric.vue b/client/src/components/Form/FormGeneric.vue
index 21ad8aec281..0ce95fd3f6c 100644
--- a/client/src/components/Form/FormGeneric.vue
+++ b/client/src/components/Form/FormGeneric.vue
@@ -1,7 +1,7 @@
 <template>
     <UrlDataProvider :url="url" v-slot="{ result, loading }" @error="onError">
         <div v-if="!loading">
-            <b-alert v-if="result.message" :variant="resultMessageVariant" show>
+            <b-alert v-if="result.message" :variant="resultMessageVariant(result)" show>
                 {{ result.message }}
             </b-alert>
             <b-alert v-if="messageText" :variant="messageVariant" show>
@@ -50,7 +50,7 @@ export default {
         },
         redirect: {
             type: String,
-            required: false,
+            required: true,
         },
     },
     components: {
@@ -67,7 +67,7 @@ export default {
     },
     methods: {
         resultMessageVariant(options) {
-            return result.status || "warning";
+            return options.status || "warning";
         },
         cancelTitle(options) {
             return options.cancel_title || "Cancel";
@@ -101,14 +101,7 @@ export default {
                         persistent: false,
                     };
                 }
-                if (this.redirect) {
-                    window.location = `${getAppRoot()}${this.redirect}?${$.param(params)}`;
-                } else {
-                    /*form.data.matchModel(response, (input, input_id) => {
-                            form.field_list[input_id].value(input.value);
-                        });
-                        self._showMessage(form, response.message);*/
-                }
+                window.location = `${getAppRoot()}${this.redirect}?${$.param(params)}`;
             }, this.onError);
         },
         onError(error) {

From 1c278327b626f1210e0372de9c94fde066382b53 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sat, 7 Aug 2021 18:16:50 -0400
Subject: [PATCH 140/218] Handle title and icon parsing from client in generic
 form component

---
 client/src/components/Form/FormGeneric.vue | 42 +++++++++++++++-------
 1 file changed, 30 insertions(+), 12 deletions(-)

diff --git a/client/src/components/Form/FormGeneric.vue b/client/src/components/Form/FormGeneric.vue
index 0ce95fd3f6c..c5cee06886f 100644
--- a/client/src/components/Form/FormGeneric.vue
+++ b/client/src/components/Form/FormGeneric.vue
@@ -1,15 +1,15 @@
 <template>
-    <UrlDataProvider :url="url" v-slot="{ result, loading }" @error="onError">
+    <UrlDataProvider :url="url" v-slot="{ result: config, loading }" @error="onError">
         <div v-if="!loading">
-            <b-alert v-if="result.message" :variant="resultMessageVariant(result)" show>
-                {{ result.message }}
+            <b-alert v-if="config.message" :variant="configMessageVariant(config)" show>
+                {{ config.message }}
             </b-alert>
             <b-alert v-if="messageText" :variant="messageVariant" show>
                 {{ messageText }}
             </b-alert>
-            <FormCard :title="result.title" :icon="result.icon">
+            <FormCard :title="configTitle(config)" :icon="configIcon(config)">
                 <template v-slot:body>
-                    <FormDisplay :inputs="result.inputs" @onChange="onChange" />
+                    <FormDisplay :inputs="config.inputs" @onChange="onChange" />
                 </template>
             </FormCard>
             <div class="mt-2">
@@ -17,18 +17,18 @@
                     variant="primary"
                     class="mr-1"
                     v-b-tooltip.hover
-                    :title="result.submit_tooltip"
+                    :title="config.submit_tooltip"
                     @click="onSubmit()"
                 >
-                    <span :class="submitIcon(result)" />{{ submitTitle(result) | l }}
+                    <span :class="submitIcon(config)" />{{ submitTitle(config) | l }}
                 </b-button>
                 <b-button
-                    v-if="result.cancel_redirect"
+                    v-if="config.cancel_redirect"
                     v-b-tooltip.hover
-                    :title="result.cancel_tooltip"
-                    @click="onCancel(result)"
+                    :title="config.cancel_tooltip"
+                    @click="onCancel(config)"
                 >
-                    <span :class="cancelIcon(result)" />{{ cancelTitle(result) | l }}
+                    <span :class="cancelIcon(config)" />{{ cancelTitle(config) | l }}
                 </b-button>
             </div>
         </div>
@@ -44,6 +44,18 @@ import FormDisplay from "components/Form/FormDisplay";
 
 export default {
     props: {
+        id: {
+            type: String,
+            required: false,
+        },
+        title: {
+            type: String,
+            required: false,
+        },
+        icon: {
+            type: String,
+            required: false,
+        },
         url: {
             type: String,
             required: true,
@@ -66,7 +78,13 @@ export default {
         };
     },
     methods: {
-        resultMessageVariant(options) {
+        configTitle(options) {
+            return this.title || options.title;
+        },
+        configIcon(options) {
+            return this.icon || options.icon;
+        },
+        configMessageVariant(options) {
             return options.status || "warning";
         },
         cancelTitle(options) {

From 89bef05915a51caf36a1e8bee2867267bb58df84 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sat, 7 Aug 2021 18:19:13 -0400
Subject: [PATCH 141/218] Remove unsued custom tooltip option from generic form
 component

---
 client/src/components/Form/FormGeneric.vue | 15 ++-------------
 1 file changed, 2 insertions(+), 13 deletions(-)

diff --git a/client/src/components/Form/FormGeneric.vue b/client/src/components/Form/FormGeneric.vue
index c5cee06886f..2f121ae7fe5 100644
--- a/client/src/components/Form/FormGeneric.vue
+++ b/client/src/components/Form/FormGeneric.vue
@@ -13,21 +13,10 @@
                 </template>
             </FormCard>
             <div class="mt-2">
-                <b-button
-                    variant="primary"
-                    class="mr-1"
-                    v-b-tooltip.hover
-                    :title="config.submit_tooltip"
-                    @click="onSubmit()"
-                >
+                <b-button variant="primary" class="mr-1" @click="onSubmit()">
                     <span :class="submitIcon(config)" />{{ submitTitle(config) | l }}
                 </b-button>
-                <b-button
-                    v-if="config.cancel_redirect"
-                    v-b-tooltip.hover
-                    :title="config.cancel_tooltip"
-                    @click="onCancel(config)"
-                >
+                <b-button v-if="config.cancel_redirect" @click="onCancel(config)">
                     <span :class="cancelIcon(config)" />{{ cancelTitle(config) | l }}
                 </b-button>
             </div>

From d1d6c166445c0885b705233d842eb3e5460ac0cc Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sat, 7 Aug 2021 18:32:00 -0400
Subject: [PATCH 142/218] Remove unused portlet and message dependencies from
 form-view

---
 client/src/mvc/form/form-view.js | 30 +-----------------------------
 1 file changed, 1 insertion(+), 29 deletions(-)

diff --git a/client/src/mvc/form/form-view.js b/client/src/mvc/form/form-view.js
index 93ac9c7956d..a6cd52efbca 100644
--- a/client/src/mvc/form/form-view.js
+++ b/client/src/mvc/form/form-view.js
@@ -4,7 +4,6 @@
 import $ from "jquery";
 import _ from "underscore";
 import Backbone from "backbone";
-import Portlet from "mvc/ui/ui-portlet";
 import Ui from "mvc/ui/ui-misc";
 import FormSection from "mvc/form/form-section";
 import FormData from "mvc/form/form-data";
@@ -13,11 +12,7 @@ export default Backbone.View.extend({
     initialize: function (options) {
         this.model = new Backbone.Model({
             initial_errors: false,
-            cls: "ui-portlet",
-            icon: null,
             always_refresh: true,
-            status: "warning",
-            hide_operations: false,
             onchange: function () {},
         }).set(options);
         this.setElement(options.el || "<div/>");
@@ -52,8 +47,6 @@ export default Backbone.View.extend({
         var input_element = this.element_list[input_id];
         if (input_element) {
             input_element.error(message || "Please verify this option.");
-            this.portlet.expand();
-            this.trigger("expand", input_id);
             if (!silent) {
                 var $panel = this.$el
                     .parents()
@@ -126,33 +119,12 @@ export default Backbone.View.extend({
     _renderForm: function () {
         $(".tooltip").remove();
         var options = this.model.attributes;
-        this.message = new Ui.UnescapedMessage();
         this.section = new FormSection.View(this, {
             inputs: options.inputs,
         });
-        this.portlet = new Portlet.View({
-            icon: options.icon,
-            title: options.title,
-            title_id: options.title_id,
-            operations: !options.hide_operations && options.operations,
-            cls: options.cls,
-            buttons: options.buttons,
-            collapsible: options.collapsible,
-            collapsed: options.collapsed,
-            onchange_title: options.onchange_title,
-        });
-        this.portlet.append(this.message.$el);
-        this.portlet.append(this.section.$el);
         this.$el.empty();
         if (options.inputs) {
-            this.$el.append(this.portlet.$el);
-        }
-        if (options.message) {
-            this.message.update({
-                persistent: true,
-                status: options.status,
-                message: options.message,
-            });
+            this.$el.append(this.section.$el);
         }
         console.debug("form-view::initialize()", "Completed");
     },

From 3bec81d3d1238c7219c8afc42364a1b4b9d38b4a Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sat, 7 Aug 2021 19:41:51 -0400
Subject: [PATCH 143/218] Fix missing history rename form mounting

---
 client/src/entry/analysis/AnalysisRouter.js | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/client/src/entry/analysis/AnalysisRouter.js b/client/src/entry/analysis/AnalysisRouter.js
index cf27c1a4124..8e78eabc312 100644
--- a/client/src/entry/analysis/AnalysisRouter.js
+++ b/client/src/entry/analysis/AnalysisRouter.js
@@ -228,12 +228,10 @@ export const getAnalysisRouter = (Galaxy) => {
         },
 
         show_histories_rename: function () {
-            this.page.display(
-                new FormWrapper.View({
-                    url: `history/rename?id=${QueryStringParsing.get("id")}`,
-                    redirect: "histories/list",
-                })
-            );
+            this._display_vue_helper(FormGeneric, {
+                url: `history/rename?id=${QueryStringParsing.get("id")}`,
+                redirect: "histories/list",
+            });
         },
 
         show_histories_sharing: function () {

From bd74606468db66f692b28fb7ee7e597ea80ad000 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 8 Aug 2021 00:18:57 -0400
Subject: [PATCH 144/218] Remove unused ui module import in form-view

---
 client/src/mvc/form/form-view.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/client/src/mvc/form/form-view.js b/client/src/mvc/form/form-view.js
index a6cd52efbca..6954afc9e6f 100644
--- a/client/src/mvc/form/form-view.js
+++ b/client/src/mvc/form/form-view.js
@@ -4,7 +4,6 @@
 import $ from "jquery";
 import _ from "underscore";
 import Backbone from "backbone";
-import Ui from "mvc/ui/ui-misc";
 import FormSection from "mvc/form/form-section";
 import FormData from "mvc/form/form-data";
 

From 28524c73f61f335b07d43586411a9b1dd0d3c732 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 8 Aug 2021 00:21:03 -0400
Subject: [PATCH 145/218] Add service module to generic form component

---
 client/src/components/Form/services.js | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 client/src/components/Form/services.js

diff --git a/client/src/components/Form/services.js b/client/src/components/Form/services.js
new file mode 100644
index 00000000000..ca3a1fd24f7
--- /dev/null
+++ b/client/src/components/Form/services.js
@@ -0,0 +1,12 @@
+import axios from "axios";
+import { rethrowSimple } from "utils/simple-error";
+import { getAppRoot } from "onload/loadConfig";
+
+export async function submitData(url, payload) {
+    try {
+        const { data } = await axios.put(`${getAppRoot()}${url}`, payload);
+        return data;
+    } catch (e) {
+        rethrowSimple(e);
+    }
+}

From e95a106143f47cd06f7b2e35aa9f299d8b86a1a7 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 8 Aug 2021 00:55:27 -0400
Subject: [PATCH 146/218] Add scrolling, replace vue scroll with js-native
 instant scrolling

---
 client/package.json                        |  1 -
 client/src/components/Form/FormGeneric.vue |  1 +
 client/src/components/Tool/ToolForm.vue    |  3 +--
 client/src/mvc/form/form-view.js           |  1 -
 client/yarn.lock                           | 12 ------------
 5 files changed, 2 insertions(+), 16 deletions(-)

diff --git a/client/package.json b/client/package.json
index 2c70f9711bf..0011ab19a15 100644
--- a/client/package.json
+++ b/client/package.json
@@ -82,7 +82,6 @@
     "vue-observe-visibility": "^1.0.0",
     "vue-router": "^3.3.1",
     "vue-rx": "^6.2.0",
-    "vue-scrollto": "^2.20.0",
     "vuedraggable": "2.24.1",
     "vueisotope": "^3.1.2",
     "vuex": "^3.4.0",
diff --git a/client/src/components/Form/FormGeneric.vue b/client/src/components/Form/FormGeneric.vue
index 2f121ae7fe5..bbc7e5a8b50 100644
--- a/client/src/components/Form/FormGeneric.vue
+++ b/client/src/components/Form/FormGeneric.vue
@@ -114,6 +114,7 @@ export default {
         onError(error) {
             this.messageText = error || `Failed to load resource ${this.url}.`;
             this.messageVariant = "danger";
+            document.querySelector(".center-panel").scrollTop = 0;
         },
     },
 };
diff --git a/client/src/components/Tool/ToolForm.vue b/client/src/components/Tool/ToolForm.vue
index 33aadafb650..60ecf918f8e 100644
--- a/client/src/components/Tool/ToolForm.vue
+++ b/client/src/components/Tool/ToolForm.vue
@@ -89,7 +89,6 @@
 </template>
 
 <script>
-import Scroller from "vue-scrollto";
 import { getGalaxyInstance } from "app";
 import { getToolFormData, updateToolFormData, submitJob } from "./services";
 import { allowCachedJobs } from "./utilities";
@@ -287,7 +286,7 @@ export default {
                     if ([true, "true"].includes(config.enable_tool_recommendations)) {
                         this.showRecommendation = true;
                     }
-                    Scroller.scrollTo("body");
+                    document.querySelector(".center-panel").scrollTop = 0;
                 },
                 (e) => {
                     this.showExecuting = false;
diff --git a/client/src/mvc/form/form-view.js b/client/src/mvc/form/form-view.js
index 6954afc9e6f..a7590991442 100644
--- a/client/src/mvc/form/form-view.js
+++ b/client/src/mvc/form/form-view.js
@@ -125,6 +125,5 @@ export default Backbone.View.extend({
         if (options.inputs) {
             this.$el.append(this.section.$el);
         }
-        console.debug("form-view::initialize()", "Completed");
     },
 });
diff --git a/client/yarn.lock b/client/yarn.lock
index 829749ec72d..52d83e861ff 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -3248,11 +3248,6 @@ better-assert@~1.0.0:
   dependencies:
     callsite "1.0.0"
 
-bezier-easing@2.1.0:
-  version "2.1.0"
-  resolved "https://registry.yarnpkg.com/bezier-easing/-/bezier-easing-2.1.0.tgz#c04dfe8b926d6ecaca1813d69ff179b7c2025d86"
-  integrity sha1-wE3+i5JtbsrKGBPWn/F5t8ICXYY=
-
 big.js@^3.1.3:
   version "3.2.0"
   resolved "https://registry.yarnpkg.com/big.js/-/big.js-3.2.0.tgz#a5fc298b81b9e0dca2e458824784b65c52ba588e"
@@ -15179,13 +15174,6 @@ vue-rx@^6.2.0:
   resolved "https://registry.yarnpkg.com/vue-rx/-/vue-rx-6.2.0.tgz#c3b86462b252626edd16417385bb9054a3a23acb"
   integrity sha512-tpKUcqS5IUYS+HsdbR5TlE5LL9PK4zwlplEtmMeydnbqaUTa9ciLMplJXAtFSiQw1vuURoyEJmCXqMxaVEIloQ==
 
-vue-scrollto@^2.20.0:
-  version "2.20.0"
-  resolved "https://registry.yarnpkg.com/vue-scrollto/-/vue-scrollto-2.20.0.tgz#3ba52239a62710c97003d12d4393f1f3393cd5cc"
-  integrity sha512-7i+AGKJTThZnMEkhIPgrZjyAX+fXV7/rGdg+CV283uZZwCxwiMXaBLTmIc5RTA4uwGnT+E6eJle3mXQfM2OD3A==
-  dependencies:
-    bezier-easing "2.1.0"
-
 vue-style-loader@^4.1.0:
   version "4.1.2"
   resolved "https://registry.yarnpkg.com/vue-style-loader/-/vue-style-loader-4.1.2.tgz#dedf349806f25ceb4e64f3ad7c0a44fba735fcf8"

From 48ee8b699356288af53447242326d4a423531825 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 8 Aug 2021 01:11:21 -0400
Subject: [PATCH 147/218] Scroll to top of right panel when active node in
 workflow editor changes

---
 client/src/components/Workflow/Editor/Index.vue | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/client/src/components/Workflow/Editor/Index.vue b/client/src/components/Workflow/Editor/Index.vue
index 5093697d162..102fbe755ba 100644
--- a/client/src/components/Workflow/Editor/Index.vue
+++ b/client/src/components/Workflow/Editor/Index.vue
@@ -113,7 +113,7 @@
                                 />
                             </div>
                         </div>
-                        <div class="unified-panel-body workflow-right">
+                        <div class="unified-panel-body workflow-right" ref="right-panel">
                             <div class="m-1">
                                 <FormTool
                                     v-if="hasActiveNodeTool"
@@ -335,6 +335,7 @@ export default {
                 node.makeActive();
                 this.activeNode = node;
                 this.canvasManager.drawOverview();
+                this.$refs["right-panel"].scrollTop = 0;
             }
         },
         onDeactivate() {

From b279170bab33174d829cede767a7cb608e86ea5a Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 8 Aug 2021 04:40:44 -0400
Subject: [PATCH 148/218] Assemble search string without jquery, add id to
 generic form

---
 client/src/components/Form/FormGeneric.vue | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/client/src/components/Form/FormGeneric.vue b/client/src/components/Form/FormGeneric.vue
index bbc7e5a8b50..f9c2f64ed3d 100644
--- a/client/src/components/Form/FormGeneric.vue
+++ b/client/src/components/Form/FormGeneric.vue
@@ -1,6 +1,6 @@
 <template>
     <UrlDataProvider :url="url" v-slot="{ result: config, loading }" @error="onError">
-        <div v-if="!loading">
+        <div :id="id" v-if="!loading">
             <b-alert v-if="config.message" :variant="configMessageVariant(config)" show>
                 {{ config.message }}
             </b-alert>
@@ -13,7 +13,7 @@
                 </template>
             </FormCard>
             <div class="mt-2">
-                <b-button variant="primary" class="mr-1" @click="onSubmit()">
+                <b-button id="submit" variant="primary" class="mr-1" @click="onSubmit()">
                     <span :class="submitIcon(config)" />{{ submitTitle(config) | l }}
                 </b-button>
                 <b-button v-if="config.cancel_redirect" @click="onCancel(config)">
@@ -108,7 +108,8 @@ export default {
                         persistent: false,
                     };
                 }
-                window.location = `${getAppRoot()}${this.redirect}?${$.param(params)}`;
+                const urlParams = new URLSearchParams(params);
+                window.location = `${getAppRoot()}${this.redirect}?${urlParams.toString()}`;
             }, this.onError);
         },
         onError(error) {

From 25725bf4642b3e1488fd8bba6cd56c2cccbea373 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 8 Aug 2021 13:26:48 -0400
Subject: [PATCH 149/218] Fix selenium test cases, allow parameter replacement
 in generic forms

---
 client/src/components/Form/FormGeneric.vue    | 24 +++++++++++++++----
 .../mvc/visualization/chart/views/groups.js   |  4 ++--
 .../mvc/visualization/chart/views/settings.js |  4 ++--
 lib/galaxy/selenium/navigation.yml            |  2 +-
 .../webapps/galaxy/controllers/admin.py       |  6 +++--
 5 files changed, 28 insertions(+), 12 deletions(-)

diff --git a/client/src/components/Form/FormGeneric.vue b/client/src/components/Form/FormGeneric.vue
index f9c2f64ed3d..80dc77f113e 100644
--- a/client/src/components/Form/FormGeneric.vue
+++ b/client/src/components/Form/FormGeneric.vue
@@ -9,7 +9,7 @@
             </b-alert>
             <FormCard :title="configTitle(config)" :icon="configIcon(config)">
                 <template v-slot:body>
-                    <FormDisplay :inputs="config.inputs" @onChange="onChange" />
+                    <FormDisplay :inputs="config.inputs" :replace-params="replaceParams" @onChange="onChange" />
                 </template>
             </FormCard>
             <div class="mt-2">
@@ -28,6 +28,7 @@
 import { getAppRoot } from "onload/loadConfig";
 import { submitData } from "./services";
 import { UrlDataProvider } from "components/providers/UrlDataProvider";
+import { visitInputs } from "components/Form/utilities";
 import FormCard from "components/Form/FormCard";
 import FormDisplay from "components/Form/FormDisplay";
 
@@ -64,6 +65,7 @@ export default {
             messageText: null,
             messageVariant: null,
             formData: {},
+            replaceParams: null,
         };
     },
     methods: {
@@ -108,13 +110,25 @@ export default {
                         persistent: false,
                     };
                 }
-                const urlParams = new URLSearchParams(params);
-                window.location = `${getAppRoot()}${this.redirect}?${urlParams.toString()}`;
+                if (this.redirect) {
+                    const urlParams = new URLSearchParams(params);
+                    window.location = `${getAppRoot()}${this.redirect}?${urlParams.toString()}`;
+                } else {
+                    const replaceParams = {};
+                    visitInputs(response.inputs, (input, name) => {
+                        replaceParams[name] = input.value;
+                    });
+                    this.replaceParams = replaceParams;
+                    this.showMessage(response.message);
+                }
             }, this.onError);
         },
         onError(error) {
-            this.messageText = error || `Failed to load resource ${this.url}.`;
-            this.messageVariant = "danger";
+            this.showMessage(error || `Failed to load resource ${this.url}.`, "danger");
+        },
+        showMessage(message, variant = "success") {
+            this.messageText = message;
+            this.messageVariant = variant;
             document.querySelector(".center-panel").scrollTop = 0;
         },
     },
diff --git a/client/src/mvc/visualization/chart/views/groups.js b/client/src/mvc/visualization/chart/views/groups.js
index d26259fcba8..9d9a543e5da 100644
--- a/client/src/mvc/visualization/chart/views/groups.js
+++ b/client/src/mvc/visualization/chart/views/groups.js
@@ -6,7 +6,7 @@ import Backbone from "backbone";
 import { getAppRoot } from "onload/loadConfig";
 import Utils from "utils/utils";
 import Repeat from "mvc/form/form-repeat";
-import FormData from "mvc/form/form-data";
+import { visitInputs } from "components/Form/utilities";
 import FormDisplay from "components/Form/FormDisplay";
 import { appendVueComponent } from "utils/mountVueComponent";
 
@@ -34,7 +34,7 @@ var GroupView = Backbone.View.extend({
                     cache: true,
                     success: function (dataset) {
                         var data_columns = {};
-                        FormData.visitInputs(inputs, function (input, prefixed) {
+                        visitInputs(inputs, function (input, prefixed) {
                             if (input.type == "data_column") {
                                 data_columns[prefixed] = Utils.clone(input);
                                 var columns = [];
diff --git a/client/src/mvc/visualization/chart/views/settings.js b/client/src/mvc/visualization/chart/views/settings.js
index e78404b223d..5bcc63ef044 100644
--- a/client/src/mvc/visualization/chart/views/settings.js
+++ b/client/src/mvc/visualization/chart/views/settings.js
@@ -2,7 +2,7 @@
 import _ from "underscore";
 import Backbone from "backbone";
 import Utils from "utils/utils";
-import FormData from "mvc/form/form-data";
+import { visitInputs } from "components/Form/utilities";
 import FormDisplay from "components/Form/FormDisplay";
 import { appendVueComponent } from "utils/mountVueComponent";
 
@@ -32,7 +32,7 @@ export default Backbone.View.extend({
         }
         this.$el.empty();
         if (_.size(inputs) > 0) {
-            FormData.visitInputs(inputs, function (input, name) {
+            visitInputs(inputs, function (input, name) {
                 var model_value = self.chart.settings.get(name);
                 if (model_value !== undefined && !input.hidden) {
                     input.value = model_value;
diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index 8e69f39e21c..ef60882e9b0 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -619,7 +619,7 @@ admin:
     registration_form: 'form#registration'
     groups_grid: '#groups-grid'
     roles_grid: '#roles-grid'
-    groups_create_view: '#create-group'
+    groups_create_view: '#submit'
 
 libraries:
 
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index 53545bd9446..1f429bd5c5e 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -957,7 +957,8 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
                     build_select_input('in_users', 'Users', all_users, []), {
                     'name': 'auto_create',
                     'label': 'Create a new group of the same name for this role:',
-                    'type': 'boolean'
+                    'type': 'boolean',
+                    'optional': True,
                 }]}
         else:
             name = util.restore_text(payload.get('name', ''))
@@ -1270,7 +1271,8 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
                     build_select_input('in_users', 'Users', all_users, []), {
                     'name': 'auto_create',
                     'label': 'Create a new role of the same name for this group:',
-                    'type': 'boolean'
+                    'type': 'boolean',
+                    'optional': True,
                 }]
             }
         else:

From 15f6082944ce738e3b2795b8944a7ccb0b7647b8 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 8 Aug 2021 14:47:04 -0400
Subject: [PATCH 150/218] Align option parsing to generic form, remove unused
 props

---
 client/src/components/Form/FormGeneric.vue    | 34 ++++++++++---------
 .../components/User/UserPreferencesModel.js   | 16 ++++-----
 client/src/entry/admin/AdminRouter.js         |  2 +-
 client/src/entry/analysis/AnalysisRouter.js   |  6 ++--
 .../webapps/galaxy/controllers/forms.py       |  2 +-
 5 files changed, 31 insertions(+), 29 deletions(-)

diff --git a/client/src/components/Form/FormGeneric.vue b/client/src/components/Form/FormGeneric.vue
index 80dc77f113e..05fd226e14c 100644
--- a/client/src/components/Form/FormGeneric.vue
+++ b/client/src/components/Form/FormGeneric.vue
@@ -14,10 +14,10 @@
             </FormCard>
             <div class="mt-2">
                 <b-button id="submit" variant="primary" class="mr-1" @click="onSubmit()">
-                    <span :class="submitIcon(config)" />{{ submitTitle(config) | l }}
+                    <span :class="getSubmitIcon()" />{{ submitTitle | l }}
                 </b-button>
-                <b-button v-if="config.cancel_redirect" @click="onCancel(config)">
-                    <span :class="cancelIcon(config)" />{{ cancelTitle(config) | l }}
+                <b-button v-if="cancelRedirect" @click="onCancel(config)">
+                    <span class="mr-1 fa fa-times" />{{ "Cancel" | l }}
                 </b-button>
             </div>
         </div>
@@ -46,6 +46,18 @@ export default {
             type: String,
             required: false,
         },
+        submitIcon: {
+            type: String,
+            required: false,
+        },
+        submitTitle: {
+            type: String,
+            default: "Save",
+        },
+        cancelRedirect: {
+            type: String,
+            required: false,
+        },
         url: {
             type: String,
             required: true,
@@ -78,25 +90,15 @@ export default {
         configMessageVariant(options) {
             return options.status || "warning";
         },
-        cancelTitle(options) {
-            return options.cancel_title || "Cancel";
-        },
-        cancelIcon(options) {
-            const icon = options.cancel_icon || "fa-times";
-            return `mr-1 fa ${icon}`;
-        },
-        submitTitle(options) {
-            return options.submit_title || "Save";
-        },
-        submitIcon(options) {
-            const icon = options.submit_icon || "fa-save";
+        getSubmitIcon() {
+            const icon = this.submitIcon || "fa-save";
             return `mr-1 fa ${icon}`;
         },
         onChange(formData) {
             this.formData = formData;
         },
         onCancel(options) {
-            window.location = `${getAppRoot()}${options.cancel_redirect}`;
+            window.location = `${getAppRoot()}${this.cancelRedirect}`;
         },
         onSubmit() {
             submitData(this.url, this.formData).then((response) => {
diff --git a/client/src/components/User/UserPreferencesModel.js b/client/src/components/User/UserPreferencesModel.js
index ad33b25be74..9082a4f1a77 100644
--- a/client/src/components/User/UserPreferencesModel.js
+++ b/client/src/components/User/UserPreferencesModel.js
@@ -30,8 +30,8 @@ export const getUserPreferencesModel = (user_id) => {
             id: "manage-third-party-identities",
             description: _l("Connect or disconnect access to your third-party identities."),
             icon: "fa-id-card-o",
-            submit_title: "Disconnect identity",
-            submit_icon: "fa-trash",
+            submitTitle: "Disconnect identity",
+            submitIcon: "fa-trash",
             shouldRender: config.enable_oidc,
         },
         permissions: {
@@ -41,7 +41,7 @@ export const getUserPreferencesModel = (user_id) => {
                 "Grant others default access to newly created histories. Changes made here will only affect histories created after these settings have been stored.",
             url: `api/users/${user_id}/permissions/inputs`,
             icon: "fa-users",
-            submit_title: "Save Permissions",
+            submitTitle: "Save Permissions",
             redirect: "user",
             shouldRender: !config.single_user,
         },
@@ -58,16 +58,16 @@ export const getUserPreferencesModel = (user_id) => {
             description: _l("Access your current API key or create a new one."),
             url: `api/users/${user_id}/api_key/inputs`,
             icon: "fa-key",
-            submit_title: "Create a new Key",
-            submit_icon: "fa-check",
+            submitTitle: "Create a new Key",
+            submitIcon: "fa-check",
         },
         cloud_auth: {
             id: "edit-preferences-cloud-auth",
             title: _l("Manage Cloud Authorization"),
             description: _l("Add or modify the configuration that grants Galaxy to access your cloud-based resources."),
             icon: "fa-cloud",
-            submit_title: "Create a new Key",
-            submit_icon: "fa-check",
+            submitTitle: "Create a new Key",
+            submitIcon: "fa-check",
             shouldRender: config.enable_account_interface,
         },
         toolbox_filters: {
@@ -76,7 +76,7 @@ export const getUserPreferencesModel = (user_id) => {
             description: _l("Customize your Toolbox by displaying or omitting sets of Tools."),
             url: `api/users/${user_id}/toolbox_filters/inputs`,
             icon: "fa-filter",
-            submit_title: "Save Filters",
+            submitTitle: "Save Filters",
             redirect: "user",
             shouldRender: !!config.has_user_tool_filters,
         },
diff --git a/client/src/entry/admin/AdminRouter.js b/client/src/entry/admin/AdminRouter.js
index 2b55152cb84..fc45d4e3ecf 100644
--- a/client/src/entry/admin/AdminRouter.js
+++ b/client/src/entry/admin/AdminRouter.js
@@ -164,7 +164,7 @@ export const getAdminRouter = (Galaxy, options) => {
                     title: _l("Reset passwords"),
                     url: `admin/reset_user_password${id}`,
                     icon: "fa-user",
-                    submit_title: "Save new password",
+                    submitTitle: "Save new password",
                     redirect: "admin/users",
                 },
                 manage_roles_and_groups_for_user: {
diff --git a/client/src/entry/analysis/AnalysisRouter.js b/client/src/entry/analysis/AnalysisRouter.js
index 8e78eabc312..e17bdcdd4f1 100644
--- a/client/src/entry/analysis/AnalysisRouter.js
+++ b/client/src/entry/analysis/AnalysisRouter.js
@@ -327,9 +327,9 @@ export const getAnalysisRouter = (Galaxy) => {
                 url: "workflow/create",
                 redirect: "workflow/editor",
                 active_tab: "workflow",
-                submit_title: "Create",
-                submit_icon: "fa-check",
-                cancel_redirect: "workflows/list",
+                submitTitle: "Create",
+                submitIcon: "fa-check",
+                cancelRedirect: "workflows/list",
             });
         },
 
diff --git a/lib/galaxy/webapps/galaxy/controllers/forms.py b/lib/galaxy/webapps/galaxy/controllers/forms.py
index 79364892f5b..df6d867f192 100644
--- a/lib/galaxy/webapps/galaxy/controllers/forms.py
+++ b/lib/galaxy/webapps/galaxy/controllers/forms.py
@@ -106,7 +106,7 @@ class Forms(BaseUIController):
             fd_types = sorted(trans.app.model.FormDefinition.types.__members__.items())
             return {
                 'title': 'Create new form',
-                'submit_title': 'Create',
+                'submitTitle': 'Create',
                 'inputs': [{
                     'name': 'name',
                     'label': 'Name'

From d54474d79633579297ef32cb15939a9552708771 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 8 Aug 2021 14:50:22 -0400
Subject: [PATCH 151/218] Remove custom button title for form creator from
 backend

---
 lib/galaxy/webapps/galaxy/controllers/forms.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/forms.py b/lib/galaxy/webapps/galaxy/controllers/forms.py
index df6d867f192..fe9bda6d77c 100644
--- a/lib/galaxy/webapps/galaxy/controllers/forms.py
+++ b/lib/galaxy/webapps/galaxy/controllers/forms.py
@@ -106,7 +106,6 @@ class Forms(BaseUIController):
             fd_types = sorted(trans.app.model.FormDefinition.types.__members__.items())
             return {
                 'title': 'Create new form',
-                'submitTitle': 'Create',
                 'inputs': [{
                     'name': 'name',
                     'label': 'Name'

From 18926add1ed46a4ec96016e07c2517a0dd4c37f7 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 8 Aug 2021 14:53:20 -0400
Subject: [PATCH 152/218] Remove unused config parsing to redirect option in
 generic form component

---
 client/src/components/Form/FormGeneric.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Form/FormGeneric.vue b/client/src/components/Form/FormGeneric.vue
index 05fd226e14c..ff1ba265a5f 100644
--- a/client/src/components/Form/FormGeneric.vue
+++ b/client/src/components/Form/FormGeneric.vue
@@ -16,7 +16,7 @@
                 <b-button id="submit" variant="primary" class="mr-1" @click="onSubmit()">
                     <span :class="getSubmitIcon()" />{{ submitTitle | l }}
                 </b-button>
-                <b-button v-if="cancelRedirect" @click="onCancel(config)">
+                <b-button v-if="cancelRedirect" @click="onCancel()">
                     <span class="mr-1 fa fa-times" />{{ "Cancel" | l }}
                 </b-button>
             </div>
@@ -97,7 +97,7 @@ export default {
         onChange(formData) {
             this.formData = formData;
         },
-        onCancel(options) {
+        onCancel() {
             window.location = `${getAppRoot()}${this.cancelRedirect}`;
         },
         onSubmit() {

From 3a2bf1bf70c220ea3cc08074e7fc58558ae59928 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 8 Aug 2021 14:55:53 -0400
Subject: [PATCH 153/218] Increase spacing between generic form and buttons
 below

---
 client/src/components/Form/FormGeneric.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Form/FormGeneric.vue b/client/src/components/Form/FormGeneric.vue
index ff1ba265a5f..71909de7246 100644
--- a/client/src/components/Form/FormGeneric.vue
+++ b/client/src/components/Form/FormGeneric.vue
@@ -12,7 +12,7 @@
                     <FormDisplay :inputs="config.inputs" :replace-params="replaceParams" @onChange="onChange" />
                 </template>
             </FormCard>
-            <div class="mt-2">
+            <div class="mt-3">
                 <b-button id="submit" variant="primary" class="mr-1" @click="onSubmit()">
                     <span :class="getSubmitIcon()" />{{ submitTitle | l }}
                 </b-button>

From fb0b4af71fe0b7eaa2a785cb38a2a6aa1f99c79e Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 8 Aug 2021 15:00:40 -0400
Subject: [PATCH 154/218] Move icon determination to computed values in generic
 form component

---
 client/src/components/Form/FormGeneric.vue | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/client/src/components/Form/FormGeneric.vue b/client/src/components/Form/FormGeneric.vue
index 71909de7246..30914db59c9 100644
--- a/client/src/components/Form/FormGeneric.vue
+++ b/client/src/components/Form/FormGeneric.vue
@@ -14,7 +14,7 @@
             </FormCard>
             <div class="mt-3">
                 <b-button id="submit" variant="primary" class="mr-1" @click="onSubmit()">
-                    <span :class="getSubmitIcon()" />{{ submitTitle | l }}
+                    <span :class="submitIconClass" />{{ submitTitle | l }}
                 </b-button>
                 <b-button v-if="cancelRedirect" @click="onCancel()">
                     <span class="mr-1 fa fa-times" />{{ "Cancel" | l }}
@@ -48,7 +48,7 @@ export default {
         },
         submitIcon: {
             type: String,
-            required: false,
+            default: "fa-save",
         },
         submitTitle: {
             type: String,
@@ -80,6 +80,11 @@ export default {
             replaceParams: null,
         };
     },
+    computed: {
+        submitIconClass() {
+            return `mr-1 fa ${this.submitIcon}`;
+        },
+    },
     methods: {
         configTitle(options) {
             return this.title || options.title;
@@ -90,10 +95,6 @@ export default {
         configMessageVariant(options) {
             return options.status || "warning";
         },
-        getSubmitIcon() {
-            const icon = this.submitIcon || "fa-save";
-            return `mr-1 fa ${icon}`;
-        },
         onChange(formData) {
             this.formData = formData;
         },

From b8c5c56d07041abf48277afdb5df463f495aa1bc Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 8 Aug 2021 21:21:32 -0400
Subject: [PATCH 155/218] Fix tour based selenium test for core galaxy ui

---
 config/plugins/tours/core.galaxy_ui.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/plugins/tours/core.galaxy_ui.yaml b/config/plugins/tours/core.galaxy_ui.yaml
index 45f0d9956d2..5a06f770b21 100644
--- a/config/plugins/tours/core.galaxy_ui.yaml
+++ b/config/plugins/tours/core.galaxy_ui.yaml
@@ -95,7 +95,7 @@ steps:
       #backdrop: true
 
     - title: "Tool parameters"
-      element: '.center-panel .ui-portlet'
+      element: '.center-panel .portlet-content'
       intro: "Here you can choose your tool parameters. Select your input dataset from your history and specify parameters for your analysis."
       position: "right"
 

From 0bd338a334c657067560a9473af6f24305cd70f8 Mon Sep 17 00:00:00 2001
From: setlen <peter.selten98@gmail.com>
Date: Tue, 10 Aug 2021 20:51:46 +0200
Subject: [PATCH 156/218] Fix flake8 errors for gitlab error reporting

---
 lib/galaxy/tools/error_reports/plugins/gitlab.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/error_reports/plugins/gitlab.py b/lib/galaxy/tools/error_reports/plugins/gitlab.py
index 12bf02b2207..62c4a2b5bbe 100644
--- a/lib/galaxy/tools/error_reports/plugins/gitlab.py
+++ b/lib/galaxy/tools/error_reports/plugins/gitlab.py
@@ -2,9 +2,9 @@
 
 import logging
 import os
+import urllib.parse
 
 import requests
-import urllib.parse
 
 try:
     import gitlab

From 1ac10c292248e8ca71066bec40c222612193566d Mon Sep 17 00:00:00 2001
From: Mason Houtz <nerdinacan@gmail.com>
Date: Thu, 29 Jul 2021 07:33:30 -0700
Subject: [PATCH 157/218] updated history contents api to return changed
 collection tags

---
 lib/galaxy/managers/collections.py           | 11 ++++++++++-
 test/unit/managers/test_CollectionManager.py |  6 ++++--
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/managers/collections.py b/lib/galaxy/managers/collections.py
index acd4fea2d8c..ebfe09185f9 100644
--- a/lib/galaxy/managers/collections.py
+++ b/lib/galaxy/managers/collections.py
@@ -309,17 +309,26 @@ class DatasetCollectionManager:
     def _set_from_dict(self, trans, dataset_collection_instance, new_data):
         # send what we can down into the model
         changed = dataset_collection_instance.set_from_dict(new_data)
+
         # the rest (often involving the trans) - do here
         if 'annotation' in new_data.keys() and trans.get_user():
             dataset_collection_instance.add_item_annotation(trans.sa_session, trans.get_user(), dataset_collection_instance, new_data['annotation'])
             changed['annotation'] = new_data['annotation']
+
+        # the api promises a list of changed fields, but tags are not marked as changed to avoid the
+        # flush, so we must handle changed tag responses manually
+        new_tags = None
         if 'tags' in new_data.keys() and trans.get_user():
             # set_tags_from_list will flush on its own, no need to add to 'changed' here and incur a second flush.
-            self.tag_handler.set_tags_from_list(trans.get_user(), dataset_collection_instance, new_data['tags'])
+            new_tags = self.tag_handler.set_tags_from_list(trans.get_user(), dataset_collection_instance, new_data['tags'])
 
         if changed.keys():
             trans.sa_session.flush()
 
+        # set client tag field response after the flush
+        if new_tags is not None:
+            changed['tags'] = dataset_collection_instance.make_tag_string_list()
+
         return changed
 
     def _validate_and_parse_update_payload(self, payload):
diff --git a/test/unit/managers/test_CollectionManager.py b/test/unit/managers/test_CollectionManager.py
index 410ea1c99cb..a6f6a7d47e0 100644
--- a/test/unit/managers/test_CollectionManager.py
+++ b/test/unit/managers/test_CollectionManager.py
@@ -100,14 +100,16 @@ class DatasetCollectionManagerTestCase(BaseTestCase, CreatesCollectionsMixin):
             'deleted': True,
             'visible': False,
             'name': 'New Name',
+            'tags': ['name:one', 'group:two', 'three']
             # TODO: doesn't work
-            # 'tags'      : [ 'one', 'two', 'three' ]
             # 'annotations'      : [?]
         })
         self.assertEqual(hdca.name, 'New Name')
         self.assertTrue(hdca.deleted)
         self.assertFalse(hdca.visible)
-        # self.assertEqual( hdca.tags, [ 'one', 'two', 'three' ] )
+
+        tag_names = hdca.make_tag_string_list()
+        self.assertEqual(tag_names, ['name:one', 'group:two', 'three'])
         # self.assertEqual( hdca.annotations, [ 'one', 'two', 'three' ] )
 
     # def test_validation( self ):

From 9d2cdb8fa97bd0287177306e08e40d6abfe2fc66 Mon Sep 17 00:00:00 2001
From: setlen <peter.selten98@gmail.com>
Date: Wed, 11 Aug 2021 00:02:47 +0200
Subject: [PATCH 158/218] Fix incorrect formatting of string

---
 lib/galaxy/tools/error_reports/plugins/gitlab.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/error_reports/plugins/gitlab.py b/lib/galaxy/tools/error_reports/plugins/gitlab.py
index 62c4a2b5bbe..ae40c51c520 100644
--- a/lib/galaxy/tools/error_reports/plugins/gitlab.py
+++ b/lib/galaxy/tools/error_reports/plugins/gitlab.py
@@ -94,7 +94,7 @@ class GitLabPlugin(BaseGitPlugin):
                 # this will be detected by requests and used further down the line. Also cache this so everything is
                 # as fast as possible
                 ts_url = self._determine_ts_url(tool)
-                log.info("GitLab error reporting - Determined ToolShed is {ts_url}")
+                log.info(f"GitLab error reporting - Determined ToolShed is {ts_url}")
 
                 # Find the repo inside the ToolShed
                 ts_repourl = self._get_gitrepo_from_ts(job, ts_url)
@@ -144,7 +144,7 @@ class GitLabPlugin(BaseGitPlugin):
                         gl_emailquery = self.gitlab.users.list(search=gl_useremail)
                         log.debug(f"GitLab error reporting - User list: {gl_emailquery}")
                         if len(gl_emailquery) > 0:
-                            log.debug("GitLab error reporting - Last Committer user ID: " % gl_emailquery[0].get_id())
+                            log.debug("GitLab error reporting - Last Committer user ID: %s" % gl_emailquery[0].get_id())
                             self.git_username_id_cache[gl_useremail] = gl_emailquery[0].get_id()
                     gl_userid = self.git_username_id_cache.get(gl_useremail, None)
 

From f1e122c0ba63874f73131bb0f97d687120e7cf4b Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Wed, 11 Aug 2021 03:13:58 +0200
Subject: [PATCH 159/218] Migrate group_roles endpoints

---
 lib/galaxy/managers/group_roles.py           |  6 ++-
 lib/galaxy/schema/schema.py                  | 10 ++++
 lib/galaxy/webapps/galaxy/api/group_roles.py | 55 +++++++++++++++++++-
 lib/galaxy/webapps/galaxy/fast_app.py        |  4 ++
 4 files changed, 73 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/managers/group_roles.py b/lib/galaxy/managers/group_roles.py
index a6e488272d0..1991863f072 100644
--- a/lib/galaxy/managers/group_roles.py
+++ b/lib/galaxy/managers/group_roles.py
@@ -106,8 +106,12 @@ class GroupRolesManager:
 
     def _serialize_group_role(self, encoded_group_id: EncodedDatabaseIdField, role: model.Role):
         encoded_role_id = self._app.security.encode_id(role.id)
+        try:
+            url  = url_for('role', group_id=encoded_group_id, id=encoded_role_id)
+        except AttributeError:
+            url  = "*deprecated attribute not filled in by FastAPI server*"
         return {
             "id": encoded_role_id,
             "name": role.name,
-            "url": url_for('group_role', group_id=encoded_group_id, id=encoded_role_id)
+            "url": url
         }
diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index 8c31eb11ada..c1b2edfa187 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -1902,6 +1902,16 @@ class RoleListModel(BaseModel):
 # Keeping it as a Tuple for now for backward compatibility
 RoleNameIdTuple = Tuple[str, EncodedDatabaseIdField]
 
+# Group_Roles -----------------------------------------------------------------
+
+
+class GroupRoleModel(BaseModel):
+    id: EncodedDatabaseIdField = RoleIdField
+    name: str = RoleNameField
+    url: str = Field(title="URL", description="URL for the group role")
+    
+class GroupRoleListModel(BaseModel):
+    __root__: List[GroupRoleModel]
 
 # Libraries -----------------------------------------------------------------
 
diff --git a/lib/galaxy/webapps/galaxy/api/group_roles.py b/lib/galaxy/webapps/galaxy/api/group_roles.py
index 2e2410bf3ae..d7e0ed51e2b 100644
--- a/lib/galaxy/webapps/galaxy/api/group_roles.py
+++ b/lib/galaxy/webapps/galaxy/api/group_roles.py
@@ -1,8 +1,12 @@
 """
 API operations on Group objects.
 """
+
+from lib.galaxy.schema.schema import GroupRoleListModel, GroupRoleModel
 import logging
 
+from fastapi import Path
+
 from galaxy.managers.context import ProvidesAppContext
 from galaxy.managers.group_roles import GroupRolesManager
 from galaxy.schema.fields import EncodedDatabaseIdField
@@ -10,10 +14,59 @@ from galaxy.web import (
     expose_api,
     require_admin,
 )
-from . import BaseGalaxyAPIController, depends
+from . import (
+    BaseGalaxyAPIController, 
+    depends, 
+    Router, 
+    DependsOnTrans
+)
+
 
 log = logging.getLogger(__name__)
 
+router = Router(tags=['group_roles'])
+
+GroupIDParam: EncodedDatabaseIdField = Path(
+    ...,
+    title='GroupID',
+    description='The ID of the group'
+)
+
+RoleIDParam: EncodedDatabaseIdField = Path(
+    ...,
+    title='RoleID',
+    description='The ID of the role'
+)
+
+
+@router.cbv
+class FastAPIGroupRoles:
+    manager: GroupRolesManager = depends(GroupRolesManager)
+
+    @router.get('/api/groups/{group_id}/roles',
+                require_admin=True,
+                summary='Displays a collection (list) of groups.')
+    def index(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam) -> GroupRoleListModel:
+        return self.manager.index(trans, group_id)
+
+    @router.get('/api/groups/{group_id}/roles/{role_id}',
+                require_admin=True,
+                summary='Displays information about a group role.')
+    def show(self,  trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam, role_id: EncodedDatabaseIdField = RoleIDParam) -> GroupRoleModel:
+        return self.manager.show(trans, role_id, group_id)
+
+    @router.put('/api/groups/{group_id}/roles/{role_id}',
+                require_admin=True,
+                summary='Adds a role to a group')
+    def update(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam, role_id: EncodedDatabaseIdField = RoleIDParam):
+        return self.manager.update(trans, role_id, group_id)
+
+    @router.delete('/api/groups/{group_id}/roles/{role_id}',
+                    require_admin=True,
+                    summary='Removes a role from a group')
+    def delete(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam, role_id: EncodedDatabaseIdField = RoleIDParam):
+        return self.manager.delete(trans, role_id, group_id)
+
 
 class GroupRolesAPIController(BaseGalaxyAPIController):
     manager = depends(GroupRolesManager)
diff --git a/lib/galaxy/webapps/galaxy/fast_app.py b/lib/galaxy/webapps/galaxy/fast_app.py
index 518a9dc2129..11bb6b16c55 100644
--- a/lib/galaxy/webapps/galaxy/fast_app.py
+++ b/lib/galaxy/webapps/galaxy/fast_app.py
@@ -25,6 +25,10 @@ api_tags_metadata = [
         "name": "genomes",
         "description": "Operations with genome data.",
     },
+    {
+        "name": "group_roles",
+        "description": "Operations with group roles.",
+    },
     {
         "name": "licenses",
         "description": "Operations with [SPDX licenses](https://spdx.org/licenses/).",

From 7692e6203663bd3c3a711194a5d53c0526660cdc Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 3 Aug 2021 10:01:19 -0400
Subject: [PATCH 160/218] Load EDAM from PyPI if not configured instead of
 unexpected download.

---
 lib/galaxy/dependencies/dev-requirements.txt  |  1 +
 .../dependencies/pinned-requirements.txt      |  1 +
 lib/galaxy/tool_util/edam_util.py             | 62 +++++++++++++++++++
 lib/galaxy/tool_util/toolbox/base.py          | 49 ++-------------
 lib/galaxy/webapps/galaxy/config_schema.yml   |  2 +-
 packages/test.sh                              |  2 +-
 packages/tool_util/setup.py                   |  3 +
 pyproject.toml                                |  1 +
 test/unit/tool_util/test_edam_util.py         | 28 +++++++++
 9 files changed, 102 insertions(+), 47 deletions(-)
 create mode 100644 lib/galaxy/tool_util/edam_util.py
 create mode 100644 test/unit/tool_util/test_edam_util.py

diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index fa0c98b11c3..85b8fdd2ce9 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -60,6 +60,7 @@ docopt==0.6.2
 docutils==0.16; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
 dogpile.cache==1.1.2; python_version >= "3.6"
 ecdsa==0.14.1; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
+edam-ontology==1.25.2
 fabric3==1.14.post1
 fastapi-utils==0.2.1; python_version >= "3.6" and python_version < "4.0"
 fastapi==0.65.2; python_version >= "3.6"
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index bd4d0587550..d88ba36986c 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -55,6 +55,7 @@ docopt==0.6.2
 docutils==0.16; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
 dogpile.cache==1.1.2; python_version >= "3.6"
 ecdsa==0.14.1; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
+edam-ontology==1.25.2
 fabric3==1.14.post1
 fastapi-utils==0.2.1; python_version >= "3.6" and python_version < "4.0"
 fastapi==0.65.2; python_version >= "3.6"
diff --git a/lib/galaxy/tool_util/edam_util.py b/lib/galaxy/tool_util/edam_util.py
new file mode 100644
index 00000000000..fb8917e64b0
--- /dev/null
+++ b/lib/galaxy/tool_util/edam_util.py
@@ -0,0 +1,62 @@
+import io
+import os
+from typing import Dict, Optional, TextIO
+
+try:
+    from edam_ontology.streams import tabular_stream
+except ImportError:
+    tabular_stream = None
+
+EDAM_PREFIX = 'http://edamontology.org/'
+COLUMN_TERM = 0
+COLUMN_LABEL = 1
+COLUMN_PARENTS = 7
+
+
+def load_edam_tree(path: Optional[str] = None):
+    if path is not None:
+        assert os.path.exists(path), f"Failed to load EDAM tabular data at [{path}] path does not exist."
+        handle = io.open(path, "r")
+    else:
+        assert tabular_stream is not None, "Failed to load optional import from edam-onotology package, install using [pip install edam-ontology]."
+        handle = tabular_stream()
+    return load_edam_tree_from_tsv_stream(handle)
+
+
+def load_edam_tree_from_tsv_stream(tsv_stream: TextIO):
+    edam: Dict[str, Dict] = {}
+
+    def _recurse_edam_parents(term, path=None):
+        if edam[term]['parents'] and len(edam[term]['parents']) > 0:
+            for parent in edam[term]['parents']:
+                yield from _recurse_edam_parents(parent, path + [parent])
+        else:
+            yield path
+
+    for line in tsv_stream.readlines():
+        fields = line.split('\t')
+
+        term = fields[COLUMN_TERM]
+        if not term.startswith(EDAM_PREFIX):
+            continue
+
+        term_id = term[len(EDAM_PREFIX):]
+
+        # Only care about formats and operations
+        if not (term_id.startswith('operation_') or term_id.startswith('topic_')):
+            continue
+
+        parents = fields[COLUMN_PARENTS].split('|')
+        edam[term_id] = {
+            'label': fields[COLUMN_LABEL],  # preferred label
+            'parents': [x[len(EDAM_PREFIX):] for x in parents if x.startswith(EDAM_PREFIX)],
+        }
+
+    for term in sorted(edam.keys()):
+        tails = []
+        for x in _recurse_edam_parents(term, path=[]):
+            if x[-2:] not in tails:
+                tails.append(x[-2:])
+        edam[term]['path'] = tails
+
+    return edam
diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index 4728139c2ff..a42b4208aee 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -3,7 +3,6 @@ import logging
 import os
 import string
 import time
-import urllib.request
 from collections import namedtuple
 from errno import ENOENT
 from urllib.parse import urlparse
@@ -19,14 +18,13 @@ from galaxy.tool_util.deps import (
     build_dependency_manager,
     NullDependencyManager
 )
+from galaxy.tool_util.edam_util import load_edam_tree
 from galaxy.tool_util.loader_directory import looks_like_a_tool
 from galaxy.util import (
     etree,
     ExecutionTimer,
-    get_charset_from_http_headers,
     listify,
     parse_xml,
-    stream_to_open_named_file,
     string_as_bool,
     unicodify,
 )
@@ -124,52 +122,13 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         if save_integrated_tool_panel:
             self._save_integrated_tool_panel()
 
-    def _recurse_edam_parents(self, term, path=None):
-        log.debug(f"term:{term} path:{path} parents:{self.edam[term]['parents']}")
-        if self.edam[term]['parents'] and len(self.edam[term]['parents']) > 0:
-            for parent in self.edam[term]['parents']:
-                yield from self._recurse_edam_parents(parent, path + [parent])
-        else:
-            yield path
-
     def _load_edam(self):
         if not self.app.config.enable_beta_edam_toolbox:
             return
         log.debug('Loading EDAM Terms')
-
-        if not os.path.exists(self.app.config.beta_edam_toolbox_ontology_path):
-            log.debug('EDAM ontology file not present, downloading')
-
-            page = urllib.request.urlopen('https://edamontology.org/EDAM.tsv')
-            stream_to_open_named_file(page, os.open(self.app.config.beta_edam_toolbox_ontology_path, os.O_WRONLY | os.O_CREAT), None, source_encoding=get_charset_from_http_headers(page.headers))
-
-        log.debug('Processing EDAM Terms')
-        with open(self.app.config.beta_edam_toolbox_ontology_path, 'r') as handle:
-            log.debug(f'Processing {handle}')
-            self.edam = {}
-            for line in handle.readlines():
-                fields = line.split('\t')
-                if not fields[0].startswith('http://edamontology.org/'):
-                    continue
-                term_id = fields[0][len('http://edamontology.org/'):]
-
-                # Only care about formats and operations
-                if not (term_id.startswith('operation_') or term_id.startswith('topic_')):
-                    continue
-
-                parents = fields[7].split('|')
-                self.edam[term_id] = {
-                    'label': fields[1],  # preferred label
-                    'parents': [x[len('http://edamontology.org/'):] for x in parents if x.startswith('http://edamontology.org/')],
-                }
-                log.debug(f'Loaded term {term_id} => {fields[1]}')
-
-        for term in sorted(self.edam.keys()):
-            tails = []
-            for x in self._recurse_edam_parents(term, path=[]):
-                if x[-2:] not in tails:
-                    tails.append(x[-2:])
-            self.edam[term]['path'] = tails
+        edam_path = self.app.config.beta_edam_toolbox_ontology_path
+        edam = load_edam_tree(None if not os.path.exists(edam_path) else edam_path)
+        self.edam = edam
 
     def create_tool(self, config_file, tool_shed_repository=None, guid=None, **kwds):
         raise NotImplementedError()
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index be85ddc24ef..4d2739e3351 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -2454,7 +2454,7 @@ mapping:
         path_resolves_to: data_dir
         required: false
         desc: |
-          Sets the path to EDAM ontology file.
+          Sets the path to EDAM ontology file - if the path doesn't exist PyPI package data will be loaded.
 
       default_workflow_export_format:
         type: str
diff --git a/packages/test.sh b/packages/test.sh
index 033e1d8d202..0c9ddfe5f2f 100755
--- a/packages/test.sh
+++ b/packages/test.sh
@@ -50,7 +50,7 @@ for ((i=0; i<${#PACKAGE_DIRS[@]}; i++)); do
         pip install -e '.[template,jstree]'
     fi
     if [ "$package_dir" = "tool_util" ]; then
-        pip install -e '.[mulled]'
+        pip install -e '.[mulled,edam]'
     fi
 
     if [[ "$run_tests" == "1" ]]; then
diff --git a/packages/tool_util/setup.py b/packages/tool_util/setup.py
index 2d3a6a349ad..d7863021cd3 100644
--- a/packages/tool_util/setup.py
+++ b/packages/tool_util/setup.py
@@ -104,6 +104,9 @@ setup(
             'jinja2',
             'Whoosh',
         ],
+        'edam': [
+            'edam-ontology',
+        ],
     },
     license="AFL",
     zip_safe=False,
diff --git a/pyproject.toml b/pyproject.toml
index e85ffdbee53..985e6947c69 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,6 +34,7 @@ circus = "*"
 cwltool = "==3.0.20201109103151"
 dictobj = "*"
 docutils = "!=0.17, !=0.17.1"
+edam-ontology = "*"
 Fabric3 = "*"
 fastapi = ">=0.65.2"
 fastapi-utils = "*"
diff --git a/test/unit/tool_util/test_edam_util.py b/test/unit/tool_util/test_edam_util.py
new file mode 100644
index 00000000000..7697f547728
--- /dev/null
+++ b/test/unit/tool_util/test_edam_util.py
@@ -0,0 +1,28 @@
+import tempfile
+from typing import Any, Dict
+
+from edam_ontology.streams import tabular_stream
+
+from galaxy.tool_util.edam_util import load_edam_tree
+
+
+def test_load_edam_tree():
+    tree = load_edam_tree()
+    _verify_tree(tree)
+
+
+def test_load_edam_tree_from_path():
+    tf = tempfile.NamedTemporaryFile("w")
+    tf.write(tabular_stream().read())
+    tf.flush()
+    tree = load_edam_tree(tf.name)
+    _verify_tree(tree)
+
+
+def _verify_tree(tree: Dict[str, Any]):
+    assert tree is not None
+    assert "operation_0004" in tree
+    assert "topic_3974" in tree
+    assert tree["topic_3974"]["label"] == "Epistasis"
+    assert tree["topic_3974"]["parents"] == ['topic_0622', 'topic_3295']
+    assert tree["topic_3974"]["path"] == [['topic_3391', 'topic_0003'], ['topic_3070', 'topic_0003']]

From 7b665d81679b033c471817a01c60aa33847f875a Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 3 Aug 2021 10:50:16 -0400
Subject: [PATCH 161/218] test case for get_integrated_section_for_tool method

---
 test/unit/tools/test_toolbox.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/test/unit/tools/test_toolbox.py b/test/unit/tools/test_toolbox.py
index 13ef949bd0f..ab06eac419b 100644
--- a/test/unit/tools/test_toolbox.py
+++ b/test/unit/tools/test_toolbox.py
@@ -371,6 +371,10 @@ class ToolBoxTestCase(BaseToolBoxTestCase):
         assert len(section.elems) == 1
         assert next(iter(section.elems.values())).id == "github.com/galaxyproject/example/test_tool/0.2"
 
+        test_tool = self.toolbox.get_tool("test_tool", tool_version="0.1")
+        section_pair = self.toolbox.get_integrated_section_for_tool(test_tool)
+        assert section_pair == ("tid", "TID")
+
     def test_group_tools_out_of_section(self):
         self._init_tool()
         self._setup_two_versions_in_config(section=False)

From 7aba4216f910c314c002a77bf5ee5bc5cf107afa Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 3 Aug 2021 10:53:30 -0400
Subject: [PATCH 162/218] Some initial typing for toolbox lineage stuff.

---
 lib/galaxy/tool_util/toolbox/lineages/factory.py  | 15 +++++++++------
 .../tool_util/toolbox/lineages/interface.py       | 12 ++++++------
 2 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/lib/galaxy/tool_util/toolbox/lineages/factory.py b/lib/galaxy/tool_util/toolbox/lineages/factory.py
index a9f4f98563c..e7053e5c6b3 100644
--- a/lib/galaxy/tool_util/toolbox/lineages/factory.py
+++ b/lib/galaxy/tool_util/toolbox/lineages/factory.py
@@ -1,3 +1,5 @@
+from typing import Dict, Optional
+
 from galaxy.util.tool_version import remove_version_from_guid
 from .interface import ToolLineage
 
@@ -7,16 +9,17 @@ class LineageMap:
     """
 
     def __init__(self, app):
-        self.lineage_map = {}
+        self.lineage_map: Dict[str, ToolLineage] = {}
         self.app = app
 
-    def register(self, tool):
+    def register(self, tool) -> ToolLineage:
         tool_id = tool.id
         versionless_tool_id = remove_version_from_guid(tool_id)
-        lineage = self.lineage_map.get(versionless_tool_id)
-        if not lineage:
+        lineage: ToolLineage
+        if versionless_tool_id not in self.lineage_map:
             lineage = ToolLineage.from_tool(tool)
         else:
+            lineage = self.lineage_map[versionless_tool_id]
             # A lineage for a tool with the same versionless_tool_id exists,
             # but this lineage may not have the current tools' version,
             # so we add tool.version to the lineage
@@ -27,7 +30,7 @@ class LineageMap:
             self.lineage_map[tool_id] = lineage
         return self.lineage_map[tool_id]
 
-    def get(self, tool_id):
+    def get(self, tool_id) -> Optional[ToolLineage]:
         """
         Get lineage for `tool_id`.
 
@@ -46,7 +49,7 @@ class LineageMap:
                 self.lineage_map[tool_id] = lineage
         return self.lineage_map.get(tool_id)
 
-    def _get_versionless(self, tool_id):
+    def _get_versionless(self, tool_id) -> Optional[ToolLineage]:
         versionless_tool_id = remove_version_from_guid(tool_id)
         return self.lineage_map.get(versionless_tool_id, None)
 
diff --git a/lib/galaxy/tool_util/toolbox/lineages/interface.py b/lib/galaxy/tool_util/toolbox/lineages/interface.py
index eb305a25d76..b8f48657bac 100644
--- a/lib/galaxy/tool_util/toolbox/lineages/interface.py
+++ b/lib/galaxy/tool_util/toolbox/lineages/interface.py
@@ -1,5 +1,5 @@
 import threading
-from typing import Dict
+from typing import Any, Dict, List
 
 import packaging.version
 from sortedcontainers import SortedSet
@@ -44,13 +44,13 @@ class ToolLineage:
         self.tool_versions = SortedSet(key=packaging.version.parse)
 
     @property
-    def tool_ids(self):
+    def tool_ids(self) -> List[str]:
         versionless_tool_id = remove_version_from_guid(self.tool_id)
         tool_id = versionless_tool_id or self.tool_id
         return [f"{tool_id}/{version}" for version in self.tool_versions]
 
     @staticmethod
-    def from_tool(tool):
+    def from_tool(tool) -> 'ToolLineage':
         tool_id = tool.id
         lineages_by_id = ToolLineage.lineages_by_id
         with ToolLineage.lock:
@@ -60,7 +60,7 @@ class ToolLineage:
         lineage.register_version(tool.version)
         return lineage
 
-    def register_version(self, tool_version):
+    def register_version(self, tool_version) -> None:
         assert tool_version is not None
         self.tool_versions.add(str(tool_version))
 
@@ -71,12 +71,12 @@ class ToolLineage:
         """
         return [ToolLineageVersion(tool_id, tool_version) for tool_id, tool_version in zip(self.tool_ids, self.tool_versions)]
 
-    def get_version_ids(self, reverse=False):
+    def get_version_ids(self, reverse=False) -> List[str]:
         if reverse:
             return list(reversed(self.tool_ids))
         return self.tool_ids
 
-    def to_dict(self):
+    def to_dict(self) -> Dict[str, Any]:
         return dict(
             tool_id=self.tool_id,
             tool_versions=list(self.tool_versions),

From 45f7dcb10c9767ab76bb13ae3fbe90591d1f9ef8 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 3 Aug 2021 10:57:50 -0400
Subject: [PATCH 163/218] Rename method for clarify it is a general view
 concern not a merged toolbox concern.

---
 lib/galaxy/tool_util/toolbox/base.py | 2 +-
 lib/galaxy/tools/__init__.py         | 2 +-
 test/unit/tools/test_toolbox.py      | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index a42b4208aee..91381d84e45 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -329,7 +329,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         log.debug(f"Loading new tool panel section: {str(tool_section.name)}")
         return tool_section
 
-    def get_integrated_section_for_tool(self, tool):
+    def get_section_for_tool(self, tool):
         tool_id = tool.id
 
         if tool_id in self._integrated_section_by_tool:
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index e4dcc7b6669..efbb7950443 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -760,7 +760,7 @@ class Tool(Dictifiable):
         return self.app.job_config.get_destination(self.__get_job_tool_configuration(job_params=job_params).destination)
 
     def get_panel_section(self):
-        return self.app.toolbox.get_integrated_section_for_tool(self)
+        return self.app.toolbox.get_section_for_tool(self)
 
     def allow_user_access(self, user, attempting_access=True):
         """
diff --git a/test/unit/tools/test_toolbox.py b/test/unit/tools/test_toolbox.py
index ab06eac419b..5728f20d99a 100644
--- a/test/unit/tools/test_toolbox.py
+++ b/test/unit/tools/test_toolbox.py
@@ -372,7 +372,7 @@ class ToolBoxTestCase(BaseToolBoxTestCase):
         assert next(iter(section.elems.values())).id == "github.com/galaxyproject/example/test_tool/0.2"
 
         test_tool = self.toolbox.get_tool("test_tool", tool_version="0.1")
-        section_pair = self.toolbox.get_integrated_section_for_tool(test_tool)
+        section_pair = self.toolbox.get_section_for_tool(test_tool)
         assert section_pair == ("tid", "TID")
 
     def test_group_tools_out_of_section(self):

From 7f07987175e83021e8ea80e1692b60531b4bd8f8 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 3 Aug 2021 11:10:07 -0400
Subject: [PATCH 164/218] Refactor toolbox._integrated_section_by_tool to make
 it clear tool_panel is responsible for section info.

---
 lib/galaxy/tool_util/toolbox/base.py  | 19 +++++++------------
 lib/galaxy/tool_util/toolbox/panel.py | 11 ++++++++++-
 2 files changed, 17 insertions(+), 13 deletions(-)

diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index 91381d84e45..5a67a94ab82 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -86,7 +86,6 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         self._dynamic_tool_confs = []
         self._tools_by_id = {}
         self._tools_by_uuid = {}
-        self._integrated_section_by_tool = {}
         # Tool lineages can contain chains of related tools with different ids
         # so each will be present once in the above dictionary. The following
         # dictionary can instead hold multiple tools with different versions.
@@ -331,11 +330,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
 
     def get_section_for_tool(self, tool):
         tool_id = tool.id
-
-        if tool_id in self._integrated_section_by_tool:
-            return self._integrated_section_by_tool[tool_id]
-
-        return None, None
+        return self._tool_panel.get_section_for_tool_id(tool_id)
 
     def __resolve_tool_path(self, tool_path, config_filename):
         if not tool_path:
@@ -522,7 +517,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             for (term, tool_id, key, val, val_name) in operations[term].values():
                 section = self._get_section(term, self.edam[term]['label'])
                 self.__add_tool_to_tool_panel(val, section, section=True)
-                self._integrated_section_by_tool[tool_id] = key, val_name
+                self._tool_panel.record_section_for_tool_id(tool_id, key, val_name)
 
         for term in sorted(topics.keys(), key=lambda x: self._sort_edam_key(x)):
             if len(topics[term].keys()) == 0:
@@ -536,13 +531,13 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             for (term, tool_id, key, val, val_name) in topics[term].values():
                 section = self._get_section(term, self.edam[term]['label'])
                 self.__add_tool_to_tool_panel(val, section, section=True)
-                self._integrated_section_by_tool[tool_id] = key, val_name
+                self._tool_panel.record_section_for_tool_id(tool_id, key, val_name)
 
         section = self._get_section('uncategorized', 'Uncategorized')
         for (tool_id, key, val, val_name) in uncategorized:
             print(tool_id, key, val, val_name)
             self.__add_tool_to_tool_panel(val, section, section=True)
-            self._integrated_section_by_tool[tool_id] = key, val_name
+            self._tool_panel.record_section_for_tool_id(tool_id, key, val_name)
 
     def _sort_edam_key(self, x):
         if x in ('operation_0004', 'topic_0003'):
@@ -557,7 +552,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                 tool_id = key.replace('tool_', '', 1)
                 if tool_id in self._tools_by_id:
                     self.__add_tool_to_tool_panel(val, self._tool_panel, section=False)
-                    self._integrated_section_by_tool[tool_id] = '', ''
+                    self._tool_panel.record_section_for_tool_id(tool_id, '', '')
             elif item_type == panel_item_types.WORKFLOW:
                 workflow_id = key.replace('workflow_', '', 1)
                 if workflow_id in self._workflows_by_id:
@@ -579,7 +574,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                         tool_id = section_key.replace('tool_', '', 1)
                         if tool_id in self._tools_by_id:
                             self.__add_tool_to_tool_panel(section_val, section, section=True)
-                            self._integrated_section_by_tool[tool_id] = key, val.name
+                            self._tool_panel.record_section_for_tool_id(tool_id, key, val.name)
                     elif section_item_type == panel_item_types.WORKFLOW:
                         workflow_id = section_key.replace('workflow_', '', 1)
                         if workflow_id in self._workflows_by_id:
@@ -943,7 +938,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             if section_item_type == panel_item_types.TOOL:
                 if section_item:
                     tool_id = section_key.replace('tool_', '', 1)
-                    self._integrated_section_by_tool[tool_id] = integrated_section.id, integrated_section.name
+                    self._tool_panel.record_section_for_tool_id(tool_id, integrated_section.id, integrated_section.name)
 
         if load_panel_dict:
             self._tool_panel[key] = section
diff --git a/lib/galaxy/tool_util/toolbox/panel.py b/lib/galaxy/tool_util/toolbox/panel.py
index 71d67a78c5e..a33e164a8a2 100644
--- a/lib/galaxy/tool_util/toolbox/panel.py
+++ b/lib/galaxy/tool_util/toolbox/panel.py
@@ -1,5 +1,5 @@
 from abc import abstractmethod
-
+from typing import Dict, Optional, Tuple
 
 from galaxy.util import bunch
 from galaxy.util.dictifiable import Dictifiable
@@ -115,6 +115,15 @@ class ToolPanelElements(odict, HasPanelItems):
     """ Represents an ordered dictionary of tool entries - abstraction
     used both by tool panel itself (normal and integrated) and its sections.
     """
+    _section_by_tool: Dict[str, Tuple[str, str]] = {}
+
+    def record_section_for_tool_id(self, tool_id: str, key: str, val: str):
+        self._section_by_tool[tool_id] = (key, val)
+
+    def get_section_for_tool_id(self, tool_id: str) -> Tuple[Optional[str], Optional[str]]:
+        if tool_id in self._section_by_tool:
+            return self._section_by_tool[tool_id]
+        return (None, None)
 
     def update_or_append(self, index, key, value):
         if key in self or index is None:

From e5747b294ae5265da24680289b0734845b0973b5 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 3 Aug 2021 11:39:16 -0400
Subject: [PATCH 165/218] Abstraction for replacing tools in tool panel.

---
 lib/galaxy/tool_util/toolbox/base.py  | 10 +---------
 lib/galaxy/tool_util/toolbox/panel.py | 11 +++++++++++
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index 5a67a94ab82..5ce50f50636 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -1095,15 +1095,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             new_tool.installed_changeset_revision = old_tool.installed_changeset_revision
             new_tool.old_id = old_tool.old_id
             # Replace old_tool with new_tool in self._tool_panel
-            tool_key = f"tool_{tool_id}"
-            for key, val in self._tool_panel.items():
-                if key == tool_key:
-                    self._tool_panel[key] = new_tool
-                    break
-                elif key.startswith('section'):
-                    if tool_key in val.elems:
-                        self._tool_panel[key].elems[tool_key] = new_tool
-                        break
+            self._tool_panel.replace_tool_for_id(tool_id, new_tool)
             # (Re-)Register the reloaded tool, this will handle
             #  _tools_by_id and _tool_versions_by_id
             self.register_tool(new_tool)
diff --git a/lib/galaxy/tool_util/toolbox/panel.py b/lib/galaxy/tool_util/toolbox/panel.py
index a33e164a8a2..89075ad287a 100644
--- a/lib/galaxy/tool_util/toolbox/panel.py
+++ b/lib/galaxy/tool_util/toolbox/panel.py
@@ -125,6 +125,17 @@ class ToolPanelElements(odict, HasPanelItems):
             return self._section_by_tool[tool_id]
         return (None, None)
 
+    def replace_tool_for_id(self, tool_id: str, new_tool) -> None:
+        tool_key = f"tool_{tool_id}"
+        for key, val in self.items():
+            if key == tool_key:
+                self[key] = new_tool
+                break
+            elif key.startswith('section'):
+                if tool_key in val.elems:
+                    self[key].elems[tool_key] = new_tool
+                    break
+
     def update_or_append(self, index, key, value):
         if key in self or index is None:
             self[key] = value

From 2314058fe0c590d2724b12ceae3d6a606efdc2fd Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 3 Aug 2021 12:41:09 -0400
Subject: [PATCH 166/218] Reduce duplication around loading EDAM panel, fix log
 message.

---
 lib/galaxy/tool_util/toolbox/base.py | 78 ++++++++++------------------
 1 file changed, 28 insertions(+), 50 deletions(-)

diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index 5ce50f50636..e30bf81eb16 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -431,6 +431,19 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             if parentTerm in self.edam[term]['parents']:
                 yield term
 
+    def _walk_integrated_tools(self):
+        for key, item_type, val in self._integrated_tool_panel.panel_items_iter():
+            if item_type == panel_item_types.TOOL:
+                tool_id = key.replace('tool_', '', 1)
+                if tool_id in self._tools_by_id:
+                    yield (tool_id, key, val, val.name)
+            elif item_type == panel_item_types.SECTION:
+                for section_key, section_item_type, section_val in val.panel_items_iter():
+                    if section_item_type == panel_item_types.TOOL:
+                        tool_id = section_key.replace('tool_', '', 1)
+                        if tool_id in self._tools_by_id:
+                            yield (tool_id, key, section_val, val.name)
+
     def _load_tool_panel_edam(self):
         execution_timer = ExecutionTimer()
 
@@ -453,57 +466,21 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         }
         uncategorized = []
 
-        for key, item_type, val in self._integrated_tool_panel.panel_items_iter():
-            if item_type == panel_item_types.TOOL:
-                tool_id = key.replace('tool_', '', 1)
-                if tool_id in self._tools_by_id:
-                    if tool_id in self._tools_by_id:
-                        for term in self._get_edam_sec(val):
-                            if term == 'uncategorized':
-                                uncategorized.append((tool_id, key, val, val.name))
-                            else:
-                                for path in self.edam[term]['path']:
-                                    if len(path) == 1:
-                                        t = term
-                                    else:
-                                        t = path[0]
+        for tool_id, key, val, val_name in self._walk_integrated_tools():
+            for term in self._get_edam_sec(val):
+                if term == 'uncategorized':
+                    uncategorized.append((tool_id, key, val, val_name))
+                else:
+                    for path in self.edam[term]['path']:
+                        if len(path) == 1:
+                            t = term
+                        else:
+                            t = path[0]
 
-                                    if path[0].startswith('operation_'):
-                                        operations[t][tool_id] = (term, tool_id, key, val, val.name)
-                                    elif path[0].startswith('topic_'):
-                                        topics[t][tool_id] = (term, tool_id, key, val, val.name)
-            # elif item_type == panel_item_types.WORKFLOW:
-                # workflow_id = key.replace('workflow_', '', 1)
-                # if workflow_id in self._workflows_by_id:
-                    # workflow = self._workflows_by_id[workflow_id]
-                    # self._tool_panel[key] = workflow
-                    # log.debug(f"Loaded workflow: {workflow_id} {workflow.name}")
-            elif item_type == panel_item_types.SECTION:
-                for section_key, section_item_type, section_val in val.panel_items_iter():
-                    if section_item_type == panel_item_types.TOOL:
-                        tool_id = section_key.replace('tool_', '', 1)
-                        if tool_id in self._tools_by_id:
-                            for term in self._get_edam_sec(section_val):
-                                if term == 'uncategorized':
-                                    uncategorized.append((tool_id, key, section_val, val.name))
-                                else:
-                                    for path in self.edam[term]['path']:
-                                        if len(path) == 1:
-                                            t = term
-                                        else:
-                                            t = path[0]
-
-                                        if path[0].startswith('operation_'):
-                                            operations[t][tool_id] = (term, tool_id, key, section_val, val.name)
-                                        if path[0].startswith('topic_'):
-                                            topics[t][tool_id] = (term, tool_id, key, section_val, val.name)
-                    # elif section_item_type == panel_item_types.WORKFLOW:
-                        # workflow_id = section_key.replace('workflow_', '', 1)
-                        # if workflow_id in self._workflows_by_id:
-                            # workflow = self._workflows_by_id[workflow_id]
-                            # section.elems[section_key] = workflow
-                            # log.debug(f"Loaded workflow: {workflow_id} {workflow.name}")
-        log.debug("Loading tool panel finished %s", execution_timer)
+                        if path[0].startswith('operation_'):
+                            operations[t][tool_id] = (term, tool_id, key, val, val_name)
+                        elif path[0].startswith('topic_'):
+                            topics[t][tool_id] = (term, tool_id, key, val, val_name)
 
         for term in sorted(operations.keys(), key=lambda x: self._sort_edam_key(x)):
             if len(operations[term].keys()) == 0:
@@ -538,6 +515,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             print(tool_id, key, val, val_name)
             self.__add_tool_to_tool_panel(val, section, section=True)
             self._tool_panel.record_section_for_tool_id(tool_id, key, val_name)
+        log.debug("Loading EDAM tool panel finished %s", execution_timer)
 
     def _sort_edam_key(self, x):
         if x in ('operation_0004', 'topic_0003'):

From cc187a38f334defe155eeb4f314e02aa73622983 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 3 Aug 2021 12:41:37 -0400
Subject: [PATCH 167/218] Abstraction for removing tool from tool panel.

---
 lib/galaxy/tool_util/toolbox/base.py  | 10 +---------
 lib/galaxy/tool_util/toolbox/panel.py | 11 +++++++++++
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index e30bf81eb16..09ca91e8f6d 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -1099,15 +1099,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             if tool_cache:
                 tool_cache.expire_tool(tool_id)
             if remove_from_panel:
-                tool_key = f"tool_{tool_id}"
-                for key, val in self._tool_panel.items():
-                    if key == tool_key:
-                        del self._tool_panel[key]
-                        break
-                    elif key.startswith('section'):
-                        if tool_key in val.elems:
-                            del self._tool_panel[key].elems[tool_key]
-                            break
+                self._tool_panel.remove_tool(tool_id)
                 if tool_id in self.data_manager_tools:
                     del self.data_manager_tools[tool_id]
             # TODO: do we need to manually remove from the integrated panel here?
diff --git a/lib/galaxy/tool_util/toolbox/panel.py b/lib/galaxy/tool_util/toolbox/panel.py
index 89075ad287a..5f01e6e5478 100644
--- a/lib/galaxy/tool_util/toolbox/panel.py
+++ b/lib/galaxy/tool_util/toolbox/panel.py
@@ -136,6 +136,17 @@ class ToolPanelElements(odict, HasPanelItems):
                     self[key].elems[tool_key] = new_tool
                     break
 
+    def remove_tool(self, tool_id: str) -> None:
+        tool_key = f"tool_{tool_id}"
+        for key, val in self.items():
+            if key == tool_key:
+                del self[key]
+                break
+            elif key.startswith('section'):
+                if tool_key in val.elems:
+                    del self[key].elems[tool_key]
+                    break
+
     def update_or_append(self, index, key, value):
         if key in self or index is None:
             self[key] = value

From 5b87813620d51b1539440f82ed7abc14f302141b Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 3 Aug 2021 12:44:00 -0400
Subject: [PATCH 168/218] Abstractions for root topic and operation in edam.

---
 lib/galaxy/tool_util/edam_util.py    |  6 ++++++
 lib/galaxy/tool_util/toolbox/base.py | 12 ++++++++----
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/tool_util/edam_util.py b/lib/galaxy/tool_util/edam_util.py
index fb8917e64b0..6f6f26059ec 100644
--- a/lib/galaxy/tool_util/edam_util.py
+++ b/lib/galaxy/tool_util/edam_util.py
@@ -12,6 +12,9 @@ COLUMN_TERM = 0
 COLUMN_LABEL = 1
 COLUMN_PARENTS = 7
 
+ROOT_OPERATION = 'operation_0004'
+ROOT_TOPIC = 'topic_0003'
+
 
 def load_edam_tree(path: Optional[str] = None):
     if path is not None:
@@ -60,3 +63,6 @@ def load_edam_tree_from_tsv_stream(tsv_stream: TextIO):
         edam[term]['path'] = tails
 
     return edam
+
+
+__all__ = ('load_edam_tree', 'ROOT_OPERATION', 'ROOT_TOPIC')
diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index 09ca91e8f6d..2c589ce0cd2 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -18,7 +18,11 @@ from galaxy.tool_util.deps import (
     build_dependency_manager,
     NullDependencyManager
 )
-from galaxy.tool_util.edam_util import load_edam_tree
+from galaxy.tool_util.edam_util import (
+    load_edam_tree,
+    ROOT_OPERATION,
+    ROOT_TOPIC,
+)
 from galaxy.tool_util.loader_directory import looks_like_a_tool
 from galaxy.util import (
     etree,
@@ -448,8 +452,8 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         execution_timer = ExecutionTimer()
 
         # Find the children of the top level topics
-        operations = ['operation_0004'] + list(self._edam_children_of('operation_0004'))
-        topics = ['topic_0003'] + list(self._edam_children_of('topic_0003'))
+        operations = [ROOT_OPERATION] + list(self._edam_children_of(ROOT_OPERATION))
+        topics = [ROOT_TOPIC] + list(self._edam_children_of(ROOT_TOPIC))
 
         # Sort them (by english label)
         # operations = sorted(operations, key=lambda x: self.edam[x]['label'])
@@ -518,7 +522,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         log.debug("Loading EDAM tool panel finished %s", execution_timer)
 
     def _sort_edam_key(self, x):
-        if x in ('operation_0004', 'topic_0003'):
+        if x in (ROOT_OPERATION, ROOT_TOPIC):
             return f"!{x}"
         else:
             return self.edam[x]['label']

From a554fdd4b6d2b006184cd8148249a94d2c48d5f9 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 3 Aug 2021 13:10:37 -0400
Subject: [PATCH 169/218] Toolbox docstring.

---
 lib/galaxy/tool_util/toolbox/base.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index 2c589ce0cd2..50a75ff820d 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -1115,6 +1115,10 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         return message, status
 
     def get_sections(self):
+        """Return section id and name pairs.
+
+        Only used by build_tool_panel_section_select_field in tool shed client code.
+        """
         for v in self._tool_panel.values():
             if isinstance(v, ToolSection):
                 yield (v.id, v.name)

From e4d7cb520820b2d88abb42dc9934dec25d1d59ce Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 3 Aug 2021 13:10:51 -0400
Subject: [PATCH 170/218] EDAM info on test tools.

---
 test/functional/tools/for_workflows/mapper.xml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/test/functional/tools/for_workflows/mapper.xml b/test/functional/tools/for_workflows/mapper.xml
index 3a6f325d475..8160dd89300 100644
--- a/test/functional/tools/for_workflows/mapper.xml
+++ b/test/functional/tools/for_workflows/mapper.xml
@@ -1,4 +1,10 @@
 <tool id="mapper" name="Mapper" version="0.1.0">
+    <edam_topics>
+        <edam_topic>topic_0102</edam_topic><!-- CompBio -> SeqAnalysis -> Mapping  -->
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_3198</edam_operation> <!-- Analysis -> SeqAnalysis -> Nucleic acid sequence analysis -> Sequence read processing -> Read Mapping -->
+    </edam_operations>
     <command><![CDATA[
 cp '$__tool_directory__/1.bam' '$out_file1'
     ]]></command>

From 618fa7713be510440fd7332d31fb45489c2ff678 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 3 Aug 2021 13:55:35 -0400
Subject: [PATCH 171/218] Integration tests for EDAM toolbox.

---
 lib/galaxy/tool_util/toolbox/base.py  |  3 +++
 test/integration/test_edam_toolbox.py | 24 ++++++++++++++++++++++++
 2 files changed, 27 insertions(+)
 create mode 100644 test/integration/test_edam_toolbox.py

diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index 50a75ff820d..59aea84b652 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -122,6 +122,9 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                 self._load_tool_panel_edam()
             else:
                 self._load_tool_panel()
+        elif self.app.name == 'galaxy' and self.app.config.enable_beta_edam_toolbox:
+            # This would have been ignored in the integrated tool panel loading right?
+            self._load_tool_panel_edam()
         if save_integrated_tool_panel:
             self._save_integrated_tool_panel()
 
diff --git a/test/integration/test_edam_toolbox.py b/test/integration/test_edam_toolbox.py
new file mode 100644
index 00000000000..66b0ab7503c
--- /dev/null
+++ b/test/integration/test_edam_toolbox.py
@@ -0,0 +1,24 @@
+from galaxy_test.driver import integration_util
+
+
+class EdamToolboxIntegrationTestCase(integration_util.IntegrationTestCase):
+
+    framework_tool_and_types = True
+
+    def setUp(self):
+        super().setUp()
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["enable_beta_edam_toolbox"] = True
+
+    def test_edam_toolbox(self):
+        index = self.galaxy_interactor.get("tools", data=dict(in_panel=True))
+        index_as_list = index.json()
+        sections = [x for x in index_as_list if x["model_class"] == "ToolSection"]
+        section_names = [s["name"] for s in sections]
+        assert "Mapping" in section_names
+        mapping_section = [s for s in sections if s["name"] == "Mapping"][0]
+        mapping_section_elems = mapping_section["elems"]
+        # make sure our mapper tool was mapped using Edam correctly...
+        assert [x for x in mapping_section_elems if x["id"] == "mapper"]

From 45df5c6c36b9c3be5cd468fcc58d216c83b3cf92 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 4 Aug 2021 15:57:09 -0400
Subject: [PATCH 172/218] Typing for toolbox panel.

---
 lib/galaxy/tool_util/toolbox/panel.py | 40 +++++++++++++--------------
 1 file changed, 20 insertions(+), 20 deletions(-)

diff --git a/lib/galaxy/tool_util/toolbox/panel.py b/lib/galaxy/tool_util/toolbox/panel.py
index 5f01e6e5478..e8cdbf6e733 100644
--- a/lib/galaxy/tool_util/toolbox/panel.py
+++ b/lib/galaxy/tool_util/toolbox/panel.py
@@ -1,18 +1,17 @@
 from abc import abstractmethod
+from enum import Enum
 from typing import Dict, Optional, Tuple
 
-from galaxy.util import bunch
 from galaxy.util.dictifiable import Dictifiable
 from galaxy.util.odict import odict
 from .parser import ensure_tool_conf_item
 
 
-panel_item_types = bunch.Bunch(
-    TOOL="TOOL",
-    WORKFLOW="WORKFLOW",
-    SECTION="SECTION",
-    LABEL="LABEL",
-)
+class panel_item_types(str, Enum):
+    TOOL = "TOOL"
+    WORKFLOW = "WORKFLOW"
+    SECTION = "SECTION"
+    LABEL = "LABEL"
 
 
 class HasPanelItems:
@@ -147,61 +146,62 @@ class ToolPanelElements(odict, HasPanelItems):
                     del self[key].elems[tool_key]
                     break
 
-    def update_or_append(self, index, key, value):
+    def update_or_append(self, index: int, key: str, value) -> None:
         if key in self or index is None:
             self[key] = value
         else:
             self.insert(index, key, value)
 
-    def get_label(self, label):
+    def get_label(self, label: str) -> Optional[ToolSection]:
         for element in self.values():
             if isinstance(element, ToolSection) and element.name == label:
                 return element
+        return None
 
-    def has_tool_with_id(self, tool_id):
+    def has_tool_with_id(self, tool_id: str) -> bool:
         key = f'tool_{tool_id}'
         return key in self
 
-    def replace_tool(self, previous_tool_id, new_tool_id, tool):
+    def replace_tool(self, previous_tool_id: str, new_tool_id: str, tool) -> None:
         previous_key = f'tool_{previous_tool_id}'
         new_key = f'tool_{new_tool_id}'
         index = self.keys().index(previous_key)
         del self[previous_key]
         self.insert(index, new_key, tool)
 
-    def index_of_tool_id(self, tool_id):
+    def index_of_tool_id(self, tool_id: str) -> Optional[int]:
         query_key = f'tool_{tool_id}'
         for index, target_key in enumerate(self.keys()):
             if query_key == target_key:
                 return index
         return None
 
-    def insert_tool(self, index, tool):
+    def insert_tool(self, index: int, tool) -> None:
         key = f"tool_{tool.id}"
         self.insert(index, key, tool)
 
-    def get_tool_with_id(self, tool_id):
+    def get_tool_with_id(self, tool_id: str):
         key = f"tool_{tool_id}"
         return self[key]
 
-    def append_tool(self, tool):
+    def append_tool(self, tool) -> None:
         key = f"tool_{tool.id}"
         self[key] = tool
 
-    def stub_tool(self, key):
+    def stub_tool(self, key: str) -> None:
         key = f"tool_{key}"
         self[key] = None
 
-    def stub_workflow(self, key):
+    def stub_workflow(self, key: str) -> None:
         key = f'workflow_{key}'
         self[key] = None
 
-    def stub_label(self, key):
+    def stub_label(self, key: str) -> None:
         key = f'label_{key}'
         self[key] = None
 
-    def append_section(self, key, section_elems):
-        self[key] = section_elems
+    def append_section(self, key: str, section: ToolSection) -> None:
+        self[key] = section
 
     def panel_items(self):
         return self

From b036d3a81c0950d7f1cb529d3d12704df29de8da Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 5 Aug 2021 13:12:28 -0400
Subject: [PATCH 173/218] typing for galaxy.tools.search

---
 lib/galaxy/tools/search/__init__.py | 40 +++++++++++++++++++----------
 1 file changed, 27 insertions(+), 13 deletions(-)

diff --git a/lib/galaxy/tools/search/__init__.py b/lib/galaxy/tools/search/__init__.py
index 3aeb835b984..849139b6d31 100644
--- a/lib/galaxy/tools/search/__init__.py
+++ b/lib/galaxy/tools/search/__init__.py
@@ -7,6 +7,7 @@ through the library docs at https://whoosh.readthedocs.io.
 import logging
 import os
 import re
+from typing import Dict, List, Tuple, Union
 
 from whoosh import (
     analysis,
@@ -34,8 +35,11 @@ from galaxy.web.framework.helpers import to_unicode
 
 log = logging.getLogger(__name__)
 
+CanConvertToFloat = Union[str, int, float]
+CanConvertToInt = Union[str, int, float]
 
-def get_or_create_index(index_dir, schema):
+
+def get_or_create_index(index_dir: str, schema: Schema) -> index.Index:
     if not os.path.exists(index_dir):
         os.makedirs(index_dir)
     if index.exists_in(index_dir):
@@ -54,7 +58,7 @@ class ToolBoxSearch:
     the Whoosh search library.
     """
 
-    def __init__(self, toolbox, index_dir=None, index_help=True):
+    def __init__(self, toolbox, index_dir: str, index_help: bool = True):
         self.schema = Schema(id=ID(stored=True, unique=True),
                              old_id=ID,
                              stub=KEYWORD,
@@ -73,10 +77,10 @@ class ToolBoxSearch:
         # reindexing if the index count is equal to the toolbox reload count.
         self.index_count = -1
 
-    def _index_setup(self):
+    def _index_setup(self) -> index.Index:
         return get_or_create_index(index_dir=self.index_dir, schema=self.schema)
 
-    def build_index(self, tool_cache, index_help=True):
+    def build_index(self, tool_cache, index_help: bool = True) -> None:
         """
         Prepare search index for tools loaded in toolbox.
         Use `tool_cache` to determine which tools need indexing and which tools should be expired.
@@ -119,7 +123,7 @@ class ToolBoxSearch:
                     writer.update_document(**add_doc_kwds)
         log.debug("Toolbox index finished %s", execution_timer)
 
-    def _create_doc(self, tool_id, tool, index_help=True):
+    def _create_doc(self, tool_id: str, tool, index_help: bool = True) -> Dict[str, str]:
         #  Do not add data managers to the public index
         if tool.tool_type == 'manage_data':
             return {}
@@ -153,10 +157,20 @@ class ToolBoxSearch:
                     pass
         return add_doc_kwds
 
-    def search(self, q, tool_name_boost, tool_id_boost, tool_section_boost,
-            tool_description_boost, tool_label_boost, tool_stub_boost,
-            tool_help_boost, tool_search_limit, tool_enable_ngram_search,
-            tool_ngram_minsize, tool_ngram_maxsize):
+    def search(
+        self, q: str,
+        tool_name_boost: CanConvertToFloat,
+        tool_id_boost: CanConvertToFloat,
+        tool_section_boost: CanConvertToFloat,
+        tool_description_boost: CanConvertToFloat,
+        tool_label_boost: CanConvertToFloat,
+        tool_stub_boost: CanConvertToFloat,
+        tool_help_boost: CanConvertToFloat,
+        tool_search_limit: CanConvertToFloat,
+        tool_enable_ngram_search: bool,
+        tool_ngram_minsize: CanConvertToInt,
+        tool_ngram_maxsize: CanConvertToInt
+    ) -> List[str]:
         """
         Perform search on the in-memory index. Weight in the given boosts.
         """
@@ -194,13 +208,13 @@ class ToolBoxSearch:
             hits = self.searcher.search(parsed_query, limit=float(tool_search_limit), sortedby='')
             return [hit['id'] for hit in hits]
 
-    def _search_ngrams(self, cleaned_query, tool_ngram_minsize, tool_ngram_maxsize, tool_search_limit):
+    def _search_ngrams(self, cleaned_query: str, tool_ngram_minsize: CanConvertToInt, tool_ngram_maxsize: CanConvertToInt, tool_search_limit: CanConvertToFloat) -> List[str]:
         """
         Break tokens into ngrams and search on those instead.
         This should make searching more resistant to typos and unfinished words.
         See docs at https://whoosh.readthedocs.io/en/latest/ngrams.html
         """
-        hits_with_score = {}
+        hits_with_score: Dict[str, float] = {}
         token_analyzer = StandardAnalyzer() | analysis.NgramFilter(minsize=int(tool_ngram_minsize), maxsize=int(tool_ngram_maxsize))
         ngrams = [token.text for token in token_analyzer(cleaned_query)]
         for query in ngrams:
@@ -219,6 +233,6 @@ class ToolBoxSearch:
                 if not is_present:
                     hits_with_score[curr_hit['id']] = curr_hits.score(i)
         # Sort the results based on aggregated BM25 score in decreasing order of scores
-        hits_with_score = sorted(hits_with_score.items(), key=lambda x: x[1], reverse=True)
+        hits_with_score_list: List[Tuple[str, float]] = sorted(hits_with_score.items(), key=lambda x: x[1], reverse=True)
         # Return the tool ids
-        return [item[0] for item in hits_with_score[0:int(tool_search_limit)]]
+        return [item[0] for item in hits_with_score_list[0:int(tool_search_limit)]]

From 8f05a055f26aafba9d7e5bb5ad63c056c2d4caba Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 3 Aug 2021 15:16:43 -0400
Subject: [PATCH 174/218] get_or_create_section abstraction in toolbox panel.

---
 lib/galaxy/tool_util/toolbox/base.py  | 9 ++-------
 lib/galaxy/tool_util/toolbox/panel.py | 8 ++++++++
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index 59aea84b652..82fac6d8518 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -425,13 +425,8 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         else:
             yield 'uncategorized'
 
-    def _get_section(self, sec_id, sec_nm):
-        if sec_id not in self._tool_panel:
-            section = ToolSection({'id': sec_id, 'name': sec_nm, 'version': ''})
-            self._tool_panel[sec_id] = section
-        else:
-            section = self._tool_panel[sec_id]
-        return section
+    def _get_section(self, sec_id: str, sec_nm: str) -> ToolSection:
+        return self._tool_panel.get_or_create_section(sec_id, sec_nm)
 
     def _edam_children_of(self, parentTerm):
         for term in self.edam.keys():
diff --git a/lib/galaxy/tool_util/toolbox/panel.py b/lib/galaxy/tool_util/toolbox/panel.py
index e8cdbf6e733..044ab8aea10 100644
--- a/lib/galaxy/tool_util/toolbox/panel.py
+++ b/lib/galaxy/tool_util/toolbox/panel.py
@@ -135,6 +135,14 @@ class ToolPanelElements(odict, HasPanelItems):
                     self[key].elems[tool_key] = new_tool
                     break
 
+    def get_or_create_section(self, sec_id: str, sec_nm: str) -> ToolSection:
+        if sec_id not in self:
+            section = ToolSection({'id': sec_id, 'name': sec_nm, 'version': ''})
+            self[sec_id] = section
+        else:
+            section = self[sec_id]
+        return section
+
     def remove_tool(self, tool_id: str) -> None:
         tool_key = f"tool_{tool_id}"
         for key, val in self.items():

From 2dddcac8c86043e451939453154aa760745b77d6 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 3 Aug 2021 15:15:03 -0400
Subject: [PATCH 175/218] Implement tool panel views - config, toolbox, search,
 client.

---
 .../Panels/Buttons/PanelViewButton.vue        | 103 ++++++++
 .../Panels/Buttons/PanelViewMenuItem.vue      |  52 ++++
 .../components/Panels/Common/ToolSearch.vue   |   6 +-
 .../Panels/ProviderAwareToolBox.vue           |  52 ++++
 .../Panels/ProviderAwareToolBoxWorkflow.vue   |  72 +++++
 client/src/components/Panels/ToolBox.vue      |  26 +-
 .../src/components/Panels/ToolBoxWorkflow.vue |  26 +-
 .../src/components/Workflow/Editor/Index.vue  |  11 +-
 .../providers/ToolPanelViewProvider.js        |  25 ++
 client/src/entry/panels/tool-panel.js         |   6 +-
 client/src/store/index.js                     |   2 +
 client/src/store/panelStore.js                |  55 ++++
 lib/galaxy/managers/configuration.py          |   2 +
 lib/galaxy/tool_util/toolbox/base.py          | 250 ++++++++----------
 lib/galaxy/tool_util/toolbox/panel.py         |  43 ++-
 lib/galaxy/tool_util/toolbox/parser.py        |   6 +
 .../tool_util/toolbox/views/__init__.py       |   0
 .../tool_util/toolbox/views/definitions.py    | 155 +++++++++++
 lib/galaxy/tool_util/toolbox/views/edam.py    | 168 ++++++++++++
 .../tool_util/toolbox/views/interface.py      |  75 ++++++
 lib/galaxy/tool_util/toolbox/views/sources.py |  52 ++++
 lib/galaxy/tool_util/toolbox/views/static.py  | 168 ++++++++++++
 lib/galaxy/tools/__init__.py                  |   8 +
 lib/galaxy/tools/search/__init__.py           |  47 +++-
 lib/galaxy/webapps/galaxy/api/tools.py        |  10 +-
 lib/galaxy/webapps/galaxy/config_schema.yml   |  41 ++-
 lib/galaxy_test/driver/driver_util.py         |  14 +-
 packages/tool_util/requirements.txt           |   2 +
 packages/tool_util/setup.py                   |   1 +
 test/integration/panel_views_1/custom_1.yml   |  14 +
 test/integration/panel_views_1/custom_10.yml  |   4 +
 test/integration/panel_views_1/custom_2.yml   |   7 +
 test/integration/panel_views_1/custom_3.yml   |   8 +
 test/integration/panel_views_1/custom_4.yml   |  15 ++
 test/integration/panel_views_1/custom_5.yml   |   9 +
 test/integration/panel_views_1/custom_6.yml   |  13 +
 test/integration/panel_views_1/custom_7.yml   |  13 +
 test/integration/panel_views_1/custom_8.yml   |   9 +
 test/integration/panel_views_1/custom_9.yml   |   7 +
 test/integration/panel_views_1/filter.yml     |   5 +
 test/integration/test_edam_toolbox.py         |  46 +++-
 test/integration/test_panel_views.py          | 178 +++++++++++++
 test/unit/config/test_config_values.py        |   2 +-
 .../tool_util/test_toolbox_view_parsing.py    | 101 +++++++
 .../tool_util/test_toolbox_view_sources.py    |  45 ++++
 test/unit/unittest_utils/galaxy_mock.py       |   5 +
 46 files changed, 1774 insertions(+), 185 deletions(-)
 create mode 100644 client/src/components/Panels/Buttons/PanelViewButton.vue
 create mode 100644 client/src/components/Panels/Buttons/PanelViewMenuItem.vue
 create mode 100644 client/src/components/Panels/ProviderAwareToolBox.vue
 create mode 100644 client/src/components/Panels/ProviderAwareToolBoxWorkflow.vue
 create mode 100644 client/src/components/providers/ToolPanelViewProvider.js
 create mode 100644 client/src/store/panelStore.js
 create mode 100644 lib/galaxy/tool_util/toolbox/views/__init__.py
 create mode 100644 lib/galaxy/tool_util/toolbox/views/definitions.py
 create mode 100644 lib/galaxy/tool_util/toolbox/views/edam.py
 create mode 100644 lib/galaxy/tool_util/toolbox/views/interface.py
 create mode 100644 lib/galaxy/tool_util/toolbox/views/sources.py
 create mode 100644 lib/galaxy/tool_util/toolbox/views/static.py
 create mode 100644 test/integration/panel_views_1/custom_1.yml
 create mode 100644 test/integration/panel_views_1/custom_10.yml
 create mode 100644 test/integration/panel_views_1/custom_2.yml
 create mode 100644 test/integration/panel_views_1/custom_3.yml
 create mode 100644 test/integration/panel_views_1/custom_4.yml
 create mode 100644 test/integration/panel_views_1/custom_5.yml
 create mode 100644 test/integration/panel_views_1/custom_6.yml
 create mode 100644 test/integration/panel_views_1/custom_7.yml
 create mode 100644 test/integration/panel_views_1/custom_8.yml
 create mode 100644 test/integration/panel_views_1/custom_9.yml
 create mode 100644 test/integration/panel_views_1/filter.yml
 create mode 100644 test/integration/test_panel_views.py
 create mode 100644 test/unit/tool_util/test_toolbox_view_parsing.py
 create mode 100644 test/unit/tool_util/test_toolbox_view_sources.py

diff --git a/client/src/components/Panels/Buttons/PanelViewButton.vue b/client/src/components/Panels/Buttons/PanelViewButton.vue
new file mode 100644
index 00000000000..84fc12ddc2e
--- /dev/null
+++ b/client/src/components/Panels/Buttons/PanelViewButton.vue
@@ -0,0 +1,103 @@
+<template>
+    <b-dropdown
+        no-caret
+        right
+        role="button"
+        title="Panel Views"
+        variant="link"
+        aria-label="View all tool panel configurations"
+        class="tool-panel-dropdown float-right"
+        size="sm"
+        v-b-tooltip.hover
+    >
+        <template v-slot:button-content>
+            <span class="fa fa-list" />
+            <!-- Maybe cog? -->
+        </template>
+        <PanelViewMenuItem
+            :current-panel-view="currentPanelView"
+            :panel-view="defaultPanelView"
+            @onSelect="updatePanelView"
+        />
+        <b-dropdown-divider></b-dropdown-divider>
+        <b-dropdown-group v-for="group in groupedPanelViews" :key="group.type" :id="group.type" :header="group.title">
+            <PanelViewMenuItem
+                v-for="(panelView, key) in group.panelViews"
+                :key="key"
+                :current-panel-view="currentPanelView"
+                :panel-view="panelView"
+                @onSelect="updatePanelView"
+            />
+        </b-dropdown-group>
+        <b-dropdown-divider v-if="groupedPanelViews.length > 0"></b-dropdown-divider>
+        <PanelViewMenuItem
+            v-if="ungroupedPanelViews.length > 0"
+            v-for="(panelView, key) in ungroupedPanelViews"
+            :key="key"
+            :current-panel-view="currentPanelView"
+            :panel-view="panelView"
+            @onSelect="updatePanelView"
+        />
+    </b-dropdown>
+</template>
+
+<script>
+import PanelViewMenuItem from "./PanelViewMenuItem";
+
+const groupsDefinitions = [
+    { type: "ontology", title: "... by Ontology" },
+    { type: "activity", title: "... for Activity" },
+    { type: "publication", title: "... from Publication" },
+    { type: "training", title: "... for Training" },
+];
+
+export default {
+    components: { PanelViewMenuItem },
+    props: {
+        panelViews: {
+            type: Object,
+        },
+        currentPanelView: {
+            type: String,
+        },
+    },
+    computed: {
+        defaultPanelView() {
+            return this.panelViewsOfType("default")[0];
+        },
+        groupedPanelViews() {
+            const groups = [];
+            for (const group of groupsDefinitions) {
+                const viewType = group.type;
+                const panelViews = this.panelViewsOfType(viewType);
+                if (panelViews.length > 0) {
+                    groups.push({
+                        type: viewType,
+                        title: group.title,
+                        panelViews: panelViews,
+                    });
+                }
+            }
+            return groups;
+        },
+        ungroupedPanelViews() {
+            return this.panelViewsOfType("generic");
+        },
+    },
+    methods: {
+        updatePanelView(panelView) {
+            this.$emit("updatePanelView", panelView.id);
+        },
+        panelViewsOfType(panelViewType) {
+            const panelViews = [];
+            for (const panelViewId in this.panelViews) {
+                const panelView = this.panelViews[panelViewId];
+                if (panelView.view_type == panelViewType) {
+                    panelViews.push(panelView);
+                }
+            }
+            return panelViews;
+        },
+    },
+};
+</script>
diff --git a/client/src/components/Panels/Buttons/PanelViewMenuItem.vue b/client/src/components/Panels/Buttons/PanelViewMenuItem.vue
new file mode 100644
index 00000000000..7e03eb20efc
--- /dev/null
+++ b/client/src/components/Panels/Buttons/PanelViewMenuItem.vue
@@ -0,0 +1,52 @@
+<template>
+    <b-dropdown-item
+        :active="currentPanelView == panelView.id"
+        :disabled="currentPanelView == panelView.id"
+        @click="onClick"
+    >
+        <span :class="icon" />
+        <span :title="title" v-localize>{{ name }}</span>
+    </b-dropdown-item>
+</template>
+
+<script>
+const types_to_icons = {
+    default: "fa-backspace",
+    generic: "fa-filter",
+    ontology: "fa-sitemap",
+    activity: "fa-project-diagram",
+    publication: "fa-newspaper",
+    training: "fa-graduation-cap",
+};
+
+export default {
+    props: {
+        currentPanelView: {
+            type: String,
+            required: true,
+        },
+        panelView: {
+            type: Object,
+            required: true,
+        },
+    },
+    computed: {
+        title() {
+            return this.panelView.description;
+        },
+        icon() {
+            const viewType = this.panelView.view_type;
+            const faIcon = types_to_icons[viewType];
+            return ["fa", faIcon];
+        },
+        name() {
+            return this.panelView.name;
+        },
+    },
+    methods: {
+        onClick() {
+            this.$emit("onSelect", this.panelView);
+        },
+    },
+};
+</script>
diff --git a/client/src/components/Panels/Common/ToolSearch.vue b/client/src/components/Panels/Common/ToolSearch.vue
index 11fe95f8f77..67c12215669 100644
--- a/client/src/components/Panels/Common/ToolSearch.vue
+++ b/client/src/components/Panels/Common/ToolSearch.vue
@@ -14,6 +14,10 @@ export default {
         DelayedInput,
     },
     props: {
+        currentPanelView: {
+            type: String,
+            required: true,
+        },
         query: {
             type: String,
             default: "",
@@ -46,7 +50,7 @@ export default {
                     this.loading = true;
                     axios
                         .get(`${getAppRoot()}api/tools`, {
-                            params: { q },
+                            params: { q, view: this.currentPanelView },
                         })
                         .then((response) => {
                             this.loading = false;
diff --git a/client/src/components/Panels/ProviderAwareToolBox.vue b/client/src/components/Panels/ProviderAwareToolBox.vue
new file mode 100644
index 00000000000..ad61547a267
--- /dev/null
+++ b/client/src/components/Panels/ProviderAwareToolBox.vue
@@ -0,0 +1,52 @@
+<template>
+    <ConfigProvider class="d-flex flex-column" v-slot="{ config }">
+        <ToolPanelViewProvider
+            v-slot="{ currentPanel, currentPanelView }"
+            :site-default-panel-view="config.default_panel_view"
+            v-if="config.default_panel_view"
+        >
+            <ToolBox
+                :toolbox="currentPanel"
+                :panel-views="config.panel_views"
+                :current-panel-view="currentPanelView"
+                :stored-workflow-menu-entries="storedWorkflowMenuEntries"
+                :workflow-title="workflowTitle"
+                @updatePanelView="updatePanelView"
+                v-if="currentPanelView"
+            >
+            </ToolBox>
+        </ToolPanelViewProvider>
+    </ConfigProvider>
+</template>
+
+<script>
+import ToolBox from "./ToolBox";
+import ConfigProvider from "components/providers/ConfigProvider";
+import ToolPanelViewProvider from "components/providers/ToolPanelViewProvider";
+import _l from "utils/localization";
+import { mapActions } from "vuex";
+
+export default {
+    components: {
+        ConfigProvider,
+        ToolBox,
+        ToolPanelViewProvider,
+    },
+    props: {
+        storedWorkflowMenuEntries: {
+            type: Array,
+            required: true,
+        },
+        workflowTitle: {
+            type: String,
+            default: _l("Workflows"),
+        },
+    },
+    methods: {
+        updatePanelView(panelView) {
+            this.setCurrentPanelView(panelView);
+        },
+        ...mapActions("panels", ["setCurrentPanelView"]),
+    },
+};
+</script>
diff --git a/client/src/components/Panels/ProviderAwareToolBoxWorkflow.vue b/client/src/components/Panels/ProviderAwareToolBoxWorkflow.vue
new file mode 100644
index 00000000000..2ab248a6097
--- /dev/null
+++ b/client/src/components/Panels/ProviderAwareToolBoxWorkflow.vue
@@ -0,0 +1,72 @@
+<template>
+    <ConfigProvider class="d-flex flex-column" v-slot="{ config }">
+        <ToolPanelViewProvider
+            v-slot="{ currentPanel, currentPanelView }"
+            :site-default-panel-view="config.default_panel_view"
+            v-if="config.default_panel_view"
+        >
+            <ToolBoxWorkflow
+                :toolbox="currentPanel"
+                :panel-views="config.panel_views"
+                :current-panel-view="currentPanelView"
+                :workflows="workflows"
+                :data-managers="dataManagers"
+                :module-sections="moduleSections"
+                @updatePanelView="updatePanelView"
+                @onInsertTool="onInsertTool"
+                @onInsertModule="onInsertModule"
+                @onInsertWorkflow="onInsertWorkflow"
+                @onInsertWorkflowSteps="onInsertWorkflowSteps"
+                v-if="currentPanelView"
+            >
+            </ToolBoxWorkflow>
+        </ToolPanelViewProvider>
+    </ConfigProvider>
+</template>
+
+<script>
+import ToolBoxWorkflow from "./ToolBoxWorkflow";
+import ConfigProvider from "components/providers/ConfigProvider";
+import ToolPanelViewProvider from "components/providers/ToolPanelViewProvider";
+import { mapActions } from "vuex";
+
+export default {
+    components: {
+        ConfigProvider,
+        ToolBoxWorkflow,
+        ToolPanelViewProvider,
+    },
+    props: {
+        workflows: {
+            type: Array,
+            required: true,
+        },
+        dataManagers: {
+            type: Array,
+            required: true,
+        },
+        moduleSections: {
+            type: Array,
+            required: true,
+        },
+    },
+    methods: {
+        updatePanelView(panelView) {
+            this.setCurrentPanelView(panelView);
+        },
+        ...mapActions("panels", ["setCurrentPanelView"]),
+        onInsertTool(toolId, toolName) {
+            this.$emit("onInsertTool", toolId, toolName);
+        },
+        onInsertModule(moduleName, moduleTitle) {
+            this.$emit("onInsertModule", moduleName, moduleTitle);
+        },
+        onInsertWorkflow(workflowId, workflowName) {
+            this.$emit("onInsertWorkflow", workflowId, workflowName);
+        },
+        onInsertWorkflowSteps(workflowId, workflowStepCount) {
+            this.$emit("onInsertWorkflowSteps", workflowId, workflowStepCount);
+        },
+    },
+};
+</script>
diff --git a/client/src/components/Panels/ToolBox.vue b/client/src/components/Panels/ToolBox.vue
index fca9bd812ce..d57a03c7b64 100644
--- a/client/src/components/Panels/ToolBox.vue
+++ b/client/src/components/Panels/ToolBox.vue
@@ -4,12 +4,24 @@
             <div class="unified-panel-header-inner">
                 <div class="panel-header-buttons">
                     <favorites-button :query="query" @onFavorites="onFavorites" v-if="isUser" />
+                    <panel-view-button
+                        :panel-views="panelViews"
+                        :current-panel-view="currentPanelView"
+                        @updatePanelView="updatePanelView"
+                        v-if="panelViews && Object.keys(panelViews).length > 1"
+                    />
                 </div>
                 <div class="panel-header-text">Tools</div>
             </div>
         </div>
         <div class="unified-panel-controls">
-            <tool-search :query="query" placeholder="search tools" @onQuery="onQuery" @onResults="onResults" />
+            <tool-search
+                :current-panel-view="currentPanelView"
+                :query="query"
+                placeholder="search tools"
+                @onQuery="onQuery"
+                @onResults="onResults"
+            />
             <upload-button />
             <div class="py-2" v-if="hasResults">
                 <b-button @click="onToggle" size="sm" class="w-100">
@@ -52,16 +64,17 @@ import ToolSection from "./Common/ToolSection";
 import ToolSearch from "./Common/ToolSearch";
 import { UploadButton, openGlobalUploadModal } from "components/Upload";
 import FavoritesButton from "./Buttons/FavoritesButton";
+import PanelViewButton from "./Buttons/PanelViewButton";
 import { filterToolSections, filterTools } from "./utilities";
 import { getGalaxyInstance } from "app";
 import { getAppRoot } from "onload";
 import _l from "utils/localization";
 
 export default {
-    name: "ToolBox",
     components: {
         UploadButton,
         FavoritesButton,
+        PanelViewButton,
         ToolSection,
         ToolSearch,
     },
@@ -81,6 +94,12 @@ export default {
             type: Array,
             required: true,
         },
+        panelViews: {
+            type: Object,
+        },
+        currentPanelView: {
+            type: String,
+        },
         storedWorkflowMenuEntries: {
             type: Array,
             required: true,
@@ -163,6 +182,9 @@ export default {
             this.buttonText = this.showSections ? "Hide Sections" : "Show Sections";
             this.buttonIcon = this.showSections ? "fa fa-eye-slash" : "fa fa-eye";
         },
+        updatePanelView(panelView) {
+            this.$emit("updatePanelView", panelView);
+        },
     },
 };
 </script>
diff --git a/client/src/components/Panels/ToolBoxWorkflow.vue b/client/src/components/Panels/ToolBoxWorkflow.vue
index 64e98721273..8847b9d1958 100644
--- a/client/src/components/Panels/ToolBoxWorkflow.vue
+++ b/client/src/components/Panels/ToolBoxWorkflow.vue
@@ -2,11 +2,24 @@
     <div class="unified-panel">
         <div class="unified-panel-header" unselectable="on">
             <div class="unified-panel-header-inner">
+                <div class="panel-header-buttons">
+                    <panel-view-button
+                        :panel-views="panelViews"
+                        :current-panel-view="currentPanelView"
+                        @updatePanelView="updatePanelView"
+                        v-if="panelViews && Object.keys(panelViews).length > 1"
+                    />
+                </div>
                 <div class="panel-header-text">Tools</div>
             </div>
         </div>
         <div class="unified-panel-controls">
-            <tool-search placeholder="search tools" @onQuery="onQuery" @onResults="onResults" />
+            <tool-search
+                :current-panel-view="currentPanelView"
+                placeholder="search tools"
+                @onQuery="onQuery"
+                @onResults="onResults"
+            />
         </div>
         <div class="unified-panel-body">
             <div class="toolMenuContainer">
@@ -58,12 +71,14 @@ import _l from "utils/localization";
 import ToolSection from "./Common/ToolSection";
 import ToolSearch from "./Common/ToolSearch";
 import { filterToolSections } from "./utilities";
+import PanelViewButton from "./Buttons/PanelViewButton";
 
 export default {
     name: "ToolBox",
     components: {
         ToolSection,
         ToolSearch,
+        PanelViewButton,
     },
     data() {
         return {
@@ -76,6 +91,12 @@ export default {
             type: Array,
             required: true,
         },
+        panelViews: {
+            type: Object,
+        },
+        currentPanelView: {
+            type: String,
+        },
         workflows: {
             type: Array,
             required: true,
@@ -147,6 +168,9 @@ export default {
         onInsertWorkflowSteps(workflow) {
             this.$emit("onInsertWorkflowSteps", workflow.id, workflow.step_count);
         },
+        updatePanelView(panelView) {
+            this.$emit("updatePanelView", panelView);
+        },
     },
 };
 </script>
diff --git a/client/src/components/Workflow/Editor/Index.vue b/client/src/components/Workflow/Editor/Index.vue
index 5093697d162..3789b594661 100644
--- a/client/src/components/Workflow/Editor/Index.vue
+++ b/client/src/components/Workflow/Editor/Index.vue
@@ -39,8 +39,7 @@
         <div v-show="isCanvas">
             <SidePanel id="left" side="left">
                 <template v-slot:panel>
-                    <ToolBoxWorkflow
-                        :toolbox="toolbox"
+                    <ProviderAwareToolBoxWorkflow
                         :module-sections="moduleSections"
                         :data-managers="dataManagers"
                         :workflows="workflows"
@@ -186,7 +185,7 @@ import WorkflowOptions from "./Options";
 import FormDefault from "./Forms/FormDefault";
 import FormTool from "./Forms/FormTool";
 import MarkdownEditor from "components/Markdown/MarkdownEditor";
-import ToolBoxWorkflow from "components/Panels/ToolBoxWorkflow";
+import ProviderAwareToolBoxWorkflow from "components/Panels/ProviderAwareToolBoxWorkflow";
 import SidePanel from "components/Panels/SidePanel";
 import { getAppRoot } from "onload/loadConfig";
 import reportDefault from "./reportDefault";
@@ -205,7 +204,7 @@ export default {
         MarkdownEditor,
         SidePanel,
         StateUpgradeModal,
-        ToolBoxWorkflow,
+        ProviderAwareToolBoxWorkflow,
         FormDefault,
         FormTool,
         WorkflowOptions,
@@ -241,10 +240,6 @@ export default {
             type: Array,
             required: true,
         },
-        toolbox: {
-            type: Array,
-            required: true,
-        },
     },
     data() {
         return {
diff --git a/client/src/components/providers/ToolPanelViewProvider.js b/client/src/components/providers/ToolPanelViewProvider.js
new file mode 100644
index 00000000000..11c09cdcc50
--- /dev/null
+++ b/client/src/components/providers/ToolPanelViewProvider.js
@@ -0,0 +1,25 @@
+import { mapGetters, mapActions } from "vuex";
+
+export default {
+    props: {
+        siteDefaultPanelView: {
+            type: String,
+            required: true,
+        },
+    },
+    computed: {
+        ...mapGetters("panels", ["currentPanel", "currentPanelView"]),
+    },
+    methods: {
+        ...mapActions("panels", ["initCurrentPanelView"]),
+    },
+    created() {
+        this.initCurrentPanelView(this.siteDefaultPanelView);
+    },
+    render() {
+        return this.$scopedSlots.default({
+            currentPanel: this.currentPanel,
+            currentPanelView: this.currentPanelView,
+        });
+    },
+};
diff --git a/client/src/entry/panels/tool-panel.js b/client/src/entry/panels/tool-panel.js
index c37f8f6dfa7..ee71792ef67 100644
--- a/client/src/entry/panels/tool-panel.js
+++ b/client/src/entry/panels/tool-panel.js
@@ -1,7 +1,7 @@
 import Backbone from "backbone";
 import _l from "utils/localization";
 import { getGalaxyInstance } from "app";
-import ToolBox from "../../components/Panels/ToolBox";
+import ToolBox from "../../components/Panels/ProviderAwareToolBox";
 import SidePanel from "../../components/Panels/SidePanel";
 import { mountVueComponent } from "../../utils/mountVueComponent";
 
@@ -23,7 +23,9 @@ const ToolPanel = Backbone.View.extend({
                 currentPanel: ToolBox,
                 currentPanelProperties: {
                     storedWorkflowMenuEntries: Galaxy.config.stored_workflow_menu_entries,
-                    toolbox: Galaxy.config.toolbox,
+                    // TODO: find a way to seed to Vuex store's default panel view with data
+                    // or just stop including it in the response.
+                    // toolbox: Galaxy.config.toolbox,
                 },
             },
             el
diff --git a/client/src/store/index.js b/client/src/store/index.js
index a85b06a82be..4dcb0320444 100644
--- a/client/src/store/index.js
+++ b/client/src/store/index.js
@@ -20,6 +20,7 @@ import { toolStore } from "./toolStore";
 import { datasetPathDestinationStore } from "./datasetPathDestinationStore";
 import { datasetExtFilesStore } from "./datasetExtFilesStore";
 import { jobStore } from "./jobStore";
+import { panelStore } from "./panelStore";
 
 // beta features
 import { historyStore as betaHistoryStore } from "components/History/model/historyStore";
@@ -36,6 +37,7 @@ export function createStore() {
             user: userStore,
             config: configStore,
             betaHistory: betaHistoryStore,
+            panels: panelStore,
 
             // TODO: please namespace all store modules
             gridSearch: gridSearchStore,
diff --git a/client/src/store/panelStore.js b/client/src/store/panelStore.js
new file mode 100644
index 00000000000..d34cfd58f88
--- /dev/null
+++ b/client/src/store/panelStore.js
@@ -0,0 +1,55 @@
+export const state = {
+    panel: {},
+    currentPanelView: null,
+};
+
+import Vue from "vue";
+import { getAppRoot } from "onload/loadConfig";
+import axios from "axios";
+
+const getters = {
+    panel: (state) => (panelView) => {
+        return state.panel[panelView] || [];
+    },
+    currentPanel: (state) => {
+        const effectiveView = state.currentPanelView || "default";
+        const val = state.panel[effectiveView] || [];
+        return val;
+    },
+    currentPanelView: (state) => {
+        return state.currentPanelView;
+    },
+};
+
+const actions = {
+    initCurrentPanelView: async ({ commit, state }, siteDefaultPanelView) => {
+        const panelView = state.currentPanelView || siteDefaultPanelView;
+        if (state.currentPanelView == null) {
+            commit("setCurrentPanelView", { panelView });
+        }
+        const { data } = await axios.get(`${getAppRoot()}api/tools?in_panel=true&view=${panelView}`);
+        commit("savePanelView", { panelView, panel: data });
+    },
+    setCurrentPanelView: async ({ commit }, panelView) => {
+        commit("setCurrentPanelView", { panelView });
+        const { data } = await axios.get(`${getAppRoot()}api/tools?in_panel=true&view=${panelView}`);
+        commit("savePanelView", { panelView, panel: data });
+    },
+};
+
+const mutations = {
+    savePanelView: (state, { panelView, panel }) => {
+        Vue.set(state.panel, panelView, panel);
+    },
+    setCurrentPanelView: (state, { panelView }) => {
+        state.currentPanelView = panelView;
+    },
+};
+
+export const panelStore = {
+    namespaced: true,
+    state,
+    getters,
+    actions,
+    mutations,
+};
diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py
index 3e43f4320c4..9f9385d6880 100644
--- a/lib/galaxy/managers/configuration.py
+++ b/lib/galaxy/managers/configuration.py
@@ -200,6 +200,8 @@ class ConfigSerializer(base.ModelSerializer):
             'python': _defaults_to((sys.version_info.major, sys.version_info.minor)),
             'select_type_workflow_threshold': _use_config,
             'file_sources_configured': lambda config, key, **context: self.app.file_sources.custom_sources_configured,
+            'panel_views': lambda config, key, **content: self.app.toolbox.panel_view_dicts(),
+            'default_panel_view': _use_config,
             'upload_from_form_button': _use_config,
             'release_doc_base_url': _use_config,
             'user_library_import_dir_available': lambda config, key, **context: bool(config.get('user_library_import_dir')),
diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index 82fac6d8518..ed58ec431e3 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -5,6 +5,7 @@ import string
 import time
 from collections import namedtuple
 from errno import ENOENT
+from typing import Dict, List
 from urllib.parse import urlparse
 
 from markupsafe import escape
@@ -13,16 +14,12 @@ from galaxy.exceptions import (
     ConfigurationError,
     MessageException,
     ObjectNotFound,
+    RequestParameterInvalidException,
 )
 from galaxy.tool_util.deps import (
     build_dependency_manager,
     NullDependencyManager
 )
-from galaxy.tool_util.edam_util import (
-    load_edam_tree,
-    ROOT_OPERATION,
-    ROOT_TOPIC,
-)
 from galaxy.tool_util.loader_directory import looks_like_a_tool
 from galaxy.util import (
     etree,
@@ -48,6 +45,14 @@ from .parser import (
     get_toolbox_parser
 )
 from .tags import tool_tag_manager
+from .views.edam import EdamPanelMode, EdamToolPanelView
+from .views.interface import (
+    ToolBoxRegistry,
+    ToolPanelView,
+    ToolPanelViewModel,
+    ToolPanelViewModelType,
+)
+from .views.static import StaticToolPanelView
 
 log = logging.getLogger(__name__)
 
@@ -73,17 +78,37 @@ class ToolConfRepository(_ToolConfRepository):
         return self.tool_path, self.repository_path
 
 
+class ToolBoxRegistryImpl(ToolBoxRegistry):
+    """View of ToolBox provided to ToolPanelView to reason about tools loaded."""
+
+    def __init__(self, toolbox: 'AbstractToolBox'):
+        self.__toolbox = toolbox
+
+    def has_tool(self, tool_id: str) -> bool:
+        return tool_id in self.__toolbox._tools_by_id
+
+    def get_tool(self, tool_id: str):
+        return self.__toolbox.get_tool(tool_id)
+
+    def get_workflow(self, id: str):
+        return self.__toolbox._workflows_by_id[id]
+
+    def add_tool_to_tool_panel_view(self, tool, tool_panel_component) -> None:
+        self.__toolbox.add_tool_to_tool_panel_view(tool, tool_panel_component)
+
+
 class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
     """
     Abstract container for managing a ToolPanel - containing tools and
     workflows optionally in labelled sections.
     """
 
-    def __init__(self, config_filenames, tool_root_dir, app, save_integrated_tool_panel=True):
+    def __init__(self, config_filenames, tool_root_dir, app, view_sources=None, default_panel_view="default", save_integrated_tool_panel=True):
         """
         Create a toolbox from the config files named by `config_filenames`, using
         `tool_root_dir` as the base directory for finding individual tool config files.
         """
+        self._default_panel_view = default_panel_view
         # The _dynamic_tool_confs list contains dictionaries storing
         # information about the tools defined in each shed-related
         # shed_tool_conf.xml file.
@@ -114,28 +139,53 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         self._filter_factory = FilterFactory(self)
         self._tool_tag_manager = tool_tag_manager(app)
         self._init_tools_from_configs(config_filenames)
-        self._load_edam()
 
         if self.app.name == 'galaxy' and self._integrated_tool_panel_config_has_contents:
-            # Load self._tool_panel based on the order in self._integrated_tool_panel.
-            if self.app.config.enable_beta_edam_toolbox:
-                self._load_tool_panel_edam()
-            else:
-                self._load_tool_panel()
-        elif self.app.name == 'galaxy' and self.app.config.enable_beta_edam_toolbox:
-            # This would have been ignored in the integrated tool panel loading right?
-            self._load_tool_panel_edam()
+            self._load_tool_panel()
+
+        toolbox = self
+
+        class DefaultToolPanelView(ToolPanelView):
+
+            def apply_view(self, base_tool_panel: ToolPanelElements, toolbox_registry: ToolBoxRegistry) -> ToolPanelElements:
+                return toolbox._tool_panel
+
+            def to_model(self) -> ToolPanelViewModel:
+                model_id = "default"
+                name = "Full Tool Panel"
+                description = "Galaxy's fully configured toolbox panel with all sections, tools, and configured workflows loaded."
+                view_type = ToolPanelViewModelType.default_type
+                model_class = DefaultToolPanelView.__class__.__name__
+                return ToolPanelViewModel(
+                    id=model_id,
+                    name=name,
+                    description=description,
+                    model_class=model_class,
+                    view_type=view_type,
+                    searchable=True,
+                )
+
+        tool_panel_views_list = [
+            DefaultToolPanelView(),
+        ]
+
+        for edam_view in listify(self.app.config.edam_panel_views):
+            mode = EdamPanelMode[edam_view]
+            tool_panel_views_list.append(EdamToolPanelView(self.app.config.edam_toolbox_ontology_path, mode=mode))
+
+        if view_sources is not None:
+            for definition in view_sources.get_definitions():
+                tool_panel_views_list.append(StaticToolPanelView(definition))
+
+        self._tool_panel_views = {}
+        for tool_panel_view in tool_panel_views_list:
+            self._tool_panel_views[tool_panel_view.to_model().id] = tool_panel_view
+
+        if self.app.name == 'galaxy':
+            self._load_tool_panel_views()
         if save_integrated_tool_panel:
             self._save_integrated_tool_panel()
 
-    def _load_edam(self):
-        if not self.app.config.enable_beta_edam_toolbox:
-            return
-        log.debug('Loading EDAM Terms')
-        edam_path = self.app.config.beta_edam_toolbox_ontology_path
-        edam = load_edam_tree(None if not os.path.exists(edam_path) else edam_path)
-        self.edam = edam
-
     def create_tool(self, config_file, tool_shed_repository=None, guid=None, **kwds):
         raise NotImplementedError()
 
@@ -254,6 +304,16 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
 
         return None
 
+    def panel_views(self) -> List[ToolPanelViewModel]:
+        return [v.to_model() for v in self._tool_panel_views.values()]
+
+    def panel_view_dicts(self) -> Dict[str, Dict]:
+        return {m.id: m.dict() for m in self.panel_views()}
+
+    def panel_has_tool(self, tool, panel_view_id):
+        panel_view_rendered = self._tool_panel_view_rendered[panel_view_id]
+        return panel_view_rendered.has_item_recursive(tool)
+
     def load_dynamic_tool(self, dynamic_tool):
         if not dynamic_tool.active:
             return None
@@ -350,7 +410,12 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             tool_path = string.Template(tool_path).safe_substitute(tool_path_vars)
         return tool_path
 
-    def __add_tool_to_tool_panel(self, tool, panel_component, section=False):
+    def add_tool_to_tool_panel_view(self, tool, view_panel_component):
+        self.__add_tool_to_tool_panel(tool, view_panel_component)
+
+    def __add_tool_to_tool_panel(self, tool, panel_component, section=None):
+        if section is None:
+            section = isinstance(panel_component, ToolSection)
         # See if a version of this tool is already loaded into the tool panel.
         # The value of panel_component will be a ToolSection (if the value of
         # section=True) or self._tool_panel (if section=False).
@@ -417,113 +482,11 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         if log_msg and (not hasattr(self.app, 'tool_cache') or tool_id in self.app.tool_cache._new_tool_ids):
             log.debug(log_msg)
 
-    def _get_edam_sec(self, tool):
-        edam = tool.edam_operations + tool.edam_topics
-        if len(edam) > 0:
-            for term in edam:
-                yield term
-        else:
-            yield 'uncategorized'
-
-    def _get_section(self, sec_id: str, sec_nm: str) -> ToolSection:
-        return self._tool_panel.get_or_create_section(sec_id, sec_nm)
-
-    def _edam_children_of(self, parentTerm):
-        for term in self.edam.keys():
-            if parentTerm in self.edam[term]['parents']:
-                yield term
-
-    def _walk_integrated_tools(self):
-        for key, item_type, val in self._integrated_tool_panel.panel_items_iter():
-            if item_type == panel_item_types.TOOL:
-                tool_id = key.replace('tool_', '', 1)
-                if tool_id in self._tools_by_id:
-                    yield (tool_id, key, val, val.name)
-            elif item_type == panel_item_types.SECTION:
-                for section_key, section_item_type, section_val in val.panel_items_iter():
-                    if section_item_type == panel_item_types.TOOL:
-                        tool_id = section_key.replace('tool_', '', 1)
-                        if tool_id in self._tools_by_id:
-                            yield (tool_id, key, section_val, val.name)
-
-    def _load_tool_panel_edam(self):
-        execution_timer = ExecutionTimer()
-
-        # Find the children of the top level topics
-        operations = [ROOT_OPERATION] + list(self._edam_children_of(ROOT_OPERATION))
-        topics = [ROOT_TOPIC] + list(self._edam_children_of(ROOT_TOPIC))
-
-        # Sort them (by english label)
-        # operations = sorted(operations, key=lambda x: self.edam[x]['label'])
-        # topics = sorted(topics, key=lambda x: self.edam[x]['label'])
-
-        # Convert these to list of dicts, wherein we'll add our tools/etc.
-        operations = {
-            x: {}
-            for x in operations
-        }
-        topics = {
-            x: {}
-            for x in topics
-        }
-        uncategorized = []
-
-        for tool_id, key, val, val_name in self._walk_integrated_tools():
-            for term in self._get_edam_sec(val):
-                if term == 'uncategorized':
-                    uncategorized.append((tool_id, key, val, val_name))
-                else:
-                    for path in self.edam[term]['path']:
-                        if len(path) == 1:
-                            t = term
-                        else:
-                            t = path[0]
-
-                        if path[0].startswith('operation_'):
-                            operations[t][tool_id] = (term, tool_id, key, val, val_name)
-                        elif path[0].startswith('topic_'):
-                            topics[t][tool_id] = (term, tool_id, key, val, val_name)
-
-        for term in sorted(operations.keys(), key=lambda x: self._sort_edam_key(x)):
-            if len(operations[term].keys()) == 0:
-                continue
-
-            elem = etree.Element('label')
-            elem.attrib['text'] = self.edam[term]['label']
-            elem.attrib['id'] = term
-            self._tool_panel[f"label_{term}"] = ToolSectionLabel(elem)
-
-            for (term, tool_id, key, val, val_name) in operations[term].values():
-                section = self._get_section(term, self.edam[term]['label'])
-                self.__add_tool_to_tool_panel(val, section, section=True)
-                self._tool_panel.record_section_for_tool_id(tool_id, key, val_name)
-
-        for term in sorted(topics.keys(), key=lambda x: self._sort_edam_key(x)):
-            if len(topics[term].keys()) == 0:
-                continue
-
-            elem = etree.Element('label')
-            elem.attrib['text'] = self.edam[term]['label']
-            elem.attrib['id'] = term
-            self._tool_panel[f"label_{term}"] = ToolSectionLabel(elem)
-
-            for (term, tool_id, key, val, val_name) in topics[term].values():
-                section = self._get_section(term, self.edam[term]['label'])
-                self.__add_tool_to_tool_panel(val, section, section=True)
-                self._tool_panel.record_section_for_tool_id(tool_id, key, val_name)
-
-        section = self._get_section('uncategorized', 'Uncategorized')
-        for (tool_id, key, val, val_name) in uncategorized:
-            print(tool_id, key, val, val_name)
-            self.__add_tool_to_tool_panel(val, section, section=True)
-            self._tool_panel.record_section_for_tool_id(tool_id, key, val_name)
-        log.debug("Loading EDAM tool panel finished %s", execution_timer)
-
-    def _sort_edam_key(self, x):
-        if x in (ROOT_OPERATION, ROOT_TOPIC):
-            return f"!{x}"
-        else:
-            return self.edam[x]['label']
+    def _load_tool_panel_views(self):
+        self._tool_panel_view_rendered = {}
+        registry = ToolBoxRegistryImpl(self)
+        for key, view in self._tool_panel_views.items():
+            self._tool_panel_view_rendered[key] = view.apply_view(self._integrated_tool_panel, registry)
 
     def _load_tool_panel(self):
         execution_timer = ExecutionTimer()
@@ -864,7 +827,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         tool._lineage = self._lineage_map.register(tool)
         self.register_tool(tool)
         if load_panel_dict:
-            self.__add_tool_to_tool_panel(tool, panel_dict, section=isinstance(panel_dict, ToolSection))
+            self.__add_tool_to_tool_panel(tool, panel_dict)
 
     def _load_workflow_tag_set(self, item, panel_dict, integrated_panel_dict, load_panel_dict, index=None):
         try:
@@ -941,10 +904,8 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                 integrated_elems[key] = tool
 
                 if async_load:
-                    if self.app.config.enable_beta_edam_toolbox:
-                        self._load_tool_panel_edam()
-                    else:
-                        self._load_tool_panel()
+                    self._load_tool_panel()
+                    self._load_tool_panel_views()
                     self._save_integrated_tool_panel()
                 return tool.id
             except Exception:
@@ -1148,11 +1109,16 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         stored = self.app.model.context.query(self.app.model.StoredWorkflow).get(id)
         return stored.latest_workflow
 
-    def tool_panel_contents(self, trans, **kwds):
+    def tool_panel_contents(self, trans, view=None, **kwds):
         """ Filter tool_panel contents for displaying for user.
         """
+        if view is None:
+            view = self._default_panel_view
+        if view not in self._tool_panel_view_rendered:
+            raise RequestParameterInvalidException(f"No panel view {view} found.")
         filter_method = self._build_filter_method(trans)
-        for _, item_type, elt in self._tool_panel.panel_items_iter():
+        tool_panel_view = self._tool_panel_view_rendered[view]
+        for _, item_type, elt in tool_panel_view.panel_items_iter():
             elt = filter_method(elt, item_type)
             if elt:
                 yield elt
@@ -1179,14 +1145,14 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                     self._tool_to_dict_cache_admin[tool.id] = to_dict
         return to_dict
 
-    def to_dict(self, trans, in_panel=True, tool_help=False, **kwds):
+    def to_dict(self, trans, in_panel=True, tool_help=False, view=None, **kwds):
         """
         Create a dictionary representation of the toolbox.
         Uses primitive cache for toolbox-specific tool 'to_dict's.
         """
         rval = []
         if in_panel:
-            panel_elts = list(self.tool_panel_contents(trans, **kwds))
+            panel_elts = list(self.tool_panel_contents(trans, view=view, **kwds))
             for elt in panel_elts:
                 # Only use cache for objects that are Tools.
                 if hasattr(elt, "tool_type"):
@@ -1304,8 +1270,8 @@ class BaseGalaxyToolBox(AbstractToolBox):
     shouldn't really depend on.
     """
 
-    def __init__(self, config_filenames, tool_root_dir, app, save_integrated_tool_panel=True):
-        super().__init__(config_filenames, tool_root_dir, app, save_integrated_tool_panel)
+    def __init__(self, config_filenames, tool_root_dir, app, view_sources=None, default_panel_view=None, save_integrated_tool_panel=True):
+        super().__init__(config_filenames, tool_root_dir, app, view_sources, default_panel_view, save_integrated_tool_panel)
         old_toolbox = getattr(app, 'toolbox', None)
         if old_toolbox:
             self.dependency_manager = old_toolbox.dependency_manager
diff --git a/lib/galaxy/tool_util/toolbox/panel.py b/lib/galaxy/tool_util/toolbox/panel.py
index 044ab8aea10..1846e18ce9f 100644
--- a/lib/galaxy/tool_util/toolbox/panel.py
+++ b/lib/galaxy/tool_util/toolbox/panel.py
@@ -64,7 +64,7 @@ class ToolSection(Dictifiable, HasPanelItems):
         copy.name = self.name
         copy.id = self.id
         copy.version = self.version
-        copy.elems = self.elems.copy()
+        copy.elems.update(self.elems)
         return copy
 
     def to_dict(self, trans, link_details=False, tool_help=False, toolbox=None):
@@ -213,3 +213,44 @@ class ToolPanelElements(odict, HasPanelItems):
 
     def panel_items(self):
         return self
+
+    def walk_sections(self):
+        for key, item in self.items():
+            if isinstance(item, ToolSection):
+                yield (key, item)
+
+    def closest_section(self, target_section_id: Optional[str], target_section_name: Optional[str]):
+        for (section_id, section) in self.walk_sections():
+            if section_id == target_section_id:
+                return section
+
+        for (_, section) in self.walk_sections():
+            if section.name == target_section_name:
+                return section
+
+        return None
+
+    def apply_filter(self, f):
+        to_remove = []
+
+        for key, item in self.items():
+            if not f(key, item):
+                to_remove.append(key)
+
+        for key in to_remove:
+            del self[key]
+
+    def copy(self) -> 'ToolPanelElements':
+        the_copy = ToolPanelElements()
+        the_copy.update(self)
+        return the_copy
+
+    def has_item_recursive(self, item):
+        """Check panel and section elements for supplied item."""
+        for value in self.values():
+            if value == item:
+                return True
+            if isinstance(value, ToolSection):
+                if item in value.elems.values():
+                    return True
+        return False
diff --git a/lib/galaxy/tool_util/toolbox/parser.py b/lib/galaxy/tool_util/toolbox/parser.py
index 787ac9fc876..e4df9ff5492 100644
--- a/lib/galaxy/tool_util/toolbox/parser.py
+++ b/lib/galaxy/tool_util/toolbox/parser.py
@@ -137,6 +137,12 @@ def ensure_tool_conf_item(xml_or_item):
         return None
     elif isinstance(xml_or_item, ToolConfItem):
         return xml_or_item
+    elif isinstance(xml_or_item, dict):
+        # TODO: handle sections...
+        as_dict = xml_or_item.copy()
+        type = as_dict.pop("type")
+        attributes = as_dict
+        return ToolConfItem(type, attributes, None)
     else:
         elem = xml_or_item
         type = elem.tag
diff --git a/lib/galaxy/tool_util/toolbox/views/__init__.py b/lib/galaxy/tool_util/toolbox/views/__init__.py
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/lib/galaxy/tool_util/toolbox/views/definitions.py b/lib/galaxy/tool_util/toolbox/views/definitions.py
new file mode 100644
index 00000000000..8f10c548550
--- /dev/null
+++ b/lib/galaxy/tool_util/toolbox/views/definitions.py
@@ -0,0 +1,155 @@
+from enum import Enum
+from typing import List, Optional, Union
+
+from pydantic import BaseModel, Field
+from typing_extensions import Literal
+
+
+class StaticToolBoxViewTypeEnum(str, Enum):
+    generic = 'generic'
+    activity = 'activity'
+    publication = 'publication'
+    training = 'training'
+
+
+class ExcludeTool(BaseModel):
+    tool_id: str
+
+
+class ExcludeToolRegex(BaseModel):
+    tool_id_regex: str
+
+
+class ExcludeTypes(BaseModel):
+    types: List[str]
+
+
+Exclusions = Union[
+    ExcludeTool,
+    ExcludeToolRegex,
+    ExcludeTypes,
+]
+OptionalExclusionList = Optional[List[Exclusions]]
+
+
+class Tool(BaseModel):
+    content_type: Literal['tool'] = Field(alias="type")
+    id: str
+
+    class Config:
+        allow_population_by_field_name = True
+
+
+class Label(BaseModel):
+    content_type: Literal['label'] = Field(alias="type")
+    id: Optional[str]
+    text: str
+
+    class Config:
+        allow_population_by_field_name = True
+
+
+class LabelShortcut(BaseModel):
+    content_type = "simple_label"
+    label: str
+
+
+class Workflow(BaseModel):
+    content_type: Literal['workflow'] = Field(alias="type")
+    id: str
+
+    class Config:
+        allow_population_by_field_name = True
+
+
+class ItemsFrom(BaseModel):
+    content_type = "items_from"
+    items_from: str
+    excludes: OptionalExclusionList
+
+
+SectionContent = Union[
+    Tool,
+    Label,
+    LabelShortcut,
+    Workflow,
+    ItemsFrom,
+]
+
+
+class HasItems:
+
+    @property
+    def items_expanded(self):
+        # replace SectionAliases with individual SectionAlias objects
+        # replace LabelShortcuts with Labels
+        items = []
+        for item in self.items:
+            if isinstance(item, SectionAliases):
+                for section in item.sections:
+                    section_alias = SectionAlias(
+                        section=section,
+                        excludes=item.excludes,
+                    )
+                    items.append(section_alias)
+            elif isinstance(item, LabelShortcut):
+                new_item = Label(
+                    id=None,
+                    text=item.label,
+                    content_type="label",
+                )
+                items.append(new_item)
+            else:
+                items.append(item)
+        return items
+
+
+class Section(BaseModel, HasItems):
+    content_type: Literal['section'] = Field(alias="type")
+    id: Optional[str]
+    name: Optional[str]
+    items: Optional[List[SectionContent]]
+    excludes: OptionalExclusionList
+
+    class Config:
+        allow_population_by_field_name = True
+
+
+class SectionAlias(BaseModel):
+    content_type = "section_alias"
+    section: str
+    excludes: OptionalExclusionList
+
+
+class SectionAliases(BaseModel):
+    content_type = "section_aliases"
+    sections: List[str]
+    excludes: OptionalExclusionList
+
+
+RootContent = Union[
+    Section,
+    SectionAlias,
+    SectionAliases,
+    Tool,
+    Label,
+    LabelShortcut,
+    Workflow,
+    ItemsFrom,
+]
+
+
+class StaticToolBoxView(BaseModel, HasItems):
+    id: str
+    name: str
+    description: Optional[str]
+    view_type: StaticToolBoxViewTypeEnum = Field(alias="type")
+    items: List[RootContent]
+    excludes: Optional[List[Exclusions]]
+
+    @staticmethod
+    def from_dict(as_dict):
+        return StaticToolBoxView(**as_dict)
+
+    class Config:
+        allow_population_by_field_name = True
diff --git a/lib/galaxy/tool_util/toolbox/views/edam.py b/lib/galaxy/tool_util/toolbox/views/edam.py
new file mode 100644
index 00000000000..a5088711bd5
--- /dev/null
+++ b/lib/galaxy/tool_util/toolbox/views/edam.py
@@ -0,0 +1,168 @@
+import logging
+import os
+from enum import Enum
+from typing import Dict, List, Optional, Tuple
+
+from galaxy.tool_util.edam_util import (
+    load_edam_tree,
+    ROOT_OPERATION,
+    ROOT_TOPIC,
+)
+from galaxy.util import (
+    etree,
+    ExecutionTimer,
+)
+from .interface import (
+    ToolBoxRegistry,
+    ToolPanelView,
+    ToolPanelViewModel,
+    ToolPanelViewModelType,
+    walk_loaded_tools,
+)
+from ..panel import (
+    ToolPanelElements,
+    ToolSectionLabel,
+)
+
+log = logging.getLogger(__name__)
+
+
+class EdamPanelMode(str, Enum):
+    merged = "merged"
+    topics = "topics"
+    operations = "operations"
+
+
+class EdamToolPanelView(ToolPanelView):
+
+    def __init__(self, edam_ontology_path: Optional[str], mode: EdamPanelMode = EdamPanelMode.merged):
+        edam = load_edam_tree(None if not edam_ontology_path or not os.path.exists(edam_ontology_path) else edam_ontology_path)
+        self.edam = edam
+        self.mode = mode
+        self.include_topics = mode in [EdamPanelMode.merged, EdamPanelMode.topics]
+        self.include_operations = mode in [EdamPanelMode.merged, EdamPanelMode.operations]
+
+    def apply_view(self, base_tool_panel: ToolPanelElements, toolbox_registry: ToolBoxRegistry) -> ToolPanelElements:
+        execution_timer = ExecutionTimer()
+
+        # Find the children of the top level topics
+        operations_list = [ROOT_OPERATION] + list(self._edam_children_of(ROOT_OPERATION))
+        topics_list = [ROOT_TOPIC] + list(self._edam_children_of(ROOT_TOPIC))
+
+        # Sort them (by english label)
+        # operations = sorted(operations, key=lambda x: self.edam[x]['label'])
+        # topics = sorted(topics, key=lambda x: self.edam[x]['label'])
+
+        # Convert these to list of dicts, wherein we'll add our tools/etc.
+        operations: Dict[str, Dict] = {
+            x: {}
+            for x in operations_list
+        }
+        topics: Dict[str, Dict] = {
+            x: {}
+            for x in topics_list
+        }
+        uncategorized: List[Tuple] = []
+
+        for tool_id, key, val, val_name in walk_loaded_tools(base_tool_panel, toolbox_registry):
+            for term in self._get_edam_sec(val):
+                if term == 'uncategorized':
+                    uncategorized.append((tool_id, key, val, val_name))
+                else:
+                    for path in self.edam[term]['path']:
+                        if len(path) == 1:
+                            t = term
+                        else:
+                            t = path[0]
+
+                        if path[0].startswith('operation_'):
+                            operations[t][tool_id] = (term, tool_id, key, val, val_name)
+                        elif path[0].startswith('topic_'):
+                            topics[t][tool_id] = (term, tool_id, key, val, val_name)
+
+        new_panel = ToolPanelElements()
+        for term in sorted(operations.keys(), key=lambda x: self._sort_edam_key(x)):
+            if len(operations[term].keys()) == 0:
+                continue
+
+            elem = etree.Element('label')
+            elem.attrib['text'] = self.edam[term]['label']
+            elem.attrib['id'] = term
+            new_panel[f"label_{term}"] = ToolSectionLabel(elem)
+
+            for (term, tool_id, key, val, val_name) in operations[term].values():
+                section = new_panel.get_or_create_section(term, self.edam[term]['label'])
+
+                toolbox_registry.add_tool_to_tool_panel_view(val, section)
+                new_panel.record_section_for_tool_id(tool_id, key, val_name)
+
+        for term in sorted(topics.keys(), key=lambda x: self._sort_edam_key(x)):
+            if len(topics[term].keys()) == 0:
+                continue
+
+            elem = etree.Element('label')
+            elem.attrib['text'] = self.edam[term]['label']
+            elem.attrib['id'] = term
+            new_panel[f"label_{term}"] = ToolSectionLabel(elem)
+
+            for (term, tool_id, key, val, val_name) in topics[term].values():
+                section = new_panel.get_or_create_section(term, self.edam[term]['label'])
+                toolbox_registry.add_tool_to_tool_panel_view(val, section)
+                new_panel.record_section_for_tool_id(tool_id, key, val_name)
+
+        section = new_panel.get_or_create_section('uncategorized', 'Uncategorized')
+        for (tool_id, key, val, val_name) in uncategorized:
+            toolbox_registry.add_tool_to_tool_panel_view(val, section)
+            new_panel.record_section_for_tool_id(tool_id, key, val_name)
+        log.debug("Loading EDAM tool panel finished %s", execution_timer)
+        return new_panel
+
+    def _get_edam_sec(self, tool):
+        edam = []
+        if self.include_operations:
+            edam.extend(tool.edam_operations)
+        if self.include_topics:
+            edam.extend(tool.edam_topics)
+        if len(edam) > 0:
+            for term in edam:
+                yield term
+        else:
+            yield 'uncategorized'
+
+    def _sort_edam_key(self, x):
+        if x in (ROOT_OPERATION, ROOT_TOPIC):
+            return f"!{x}"
+        else:
+            return self.edam[x]['label']
+
+    def _edam_children_of(self, parentTerm):
+        for term in self.edam.keys():
+            if parentTerm in self.edam[term]['parents']:
+                yield term
+
+    def to_model(self) -> ToolPanelViewModel:
+        mode = self.mode
+        if mode == EdamPanelMode.merged:
+            model_id = "ontology:edam_merged"
+            name = "EDAM Operations and Topics"
+            description = "Tools are grouped using both annotated operation and topic information (if availabled)."
+        elif mode == EdamPanelMode.operations:
+            model_id = "ontology:edam_operations"
+            name = "EDAM Operations"
+            description = "Tools are grouped using annotated EDAM operation information (if availabled)."
+        elif mode == EdamPanelMode.topics:
+            model_id = "ontology:edam_topics"
+            name = "EDAM Topics"
+            description = "Tools are grouped using annotated EDAM topic information (if availabled)."
+        else:
+            raise AssertionError(f"Invalid EDAM mode encountered {mode}")
+        model_class = self.__class__.__name__
+        view_type = ToolPanelViewModelType.ontology
+        return ToolPanelViewModel(
+            id=model_id,
+            name=name,
+            description=description,
+            model_class=model_class,
+            view_type=view_type,
+            searchable=True,
+        )
diff --git a/lib/galaxy/tool_util/toolbox/views/interface.py b/lib/galaxy/tool_util/toolbox/views/interface.py
new file mode 100644
index 00000000000..e7bea38174e
--- /dev/null
+++ b/lib/galaxy/tool_util/toolbox/views/interface.py
@@ -0,0 +1,75 @@
+from abc import abstractmethod
+from enum import Enum
+from typing import Optional
+
+from pydantic import BaseModel
+
+from ..panel import (
+    HasPanelItems,
+    panel_item_types,
+    ToolPanelElements,
+)
+
+
+class ToolPanelViewModelType(str, Enum):
+    default_type = 'default'
+    generic = 'generic'
+    activity = 'activity'
+    ontology = 'ontology'
+    publication = 'publication'
+    training = 'training'
+
+
+class ToolPanelViewModel(BaseModel):
+    """A view of ToolPanelView objects serialized for the API."""
+    id: str
+    model_class: str
+    name: str
+    description: Optional[str]
+    view_type: ToolPanelViewModelType
+    searchable: bool  # Allow for more dynamic views that don't plug into fixed search indicies in the future...
+
+
+class ToolBoxRegistry:
+    """View of ToolBox provided to ToolPanelView to reason about tools loaded."""
+
+    @abstractmethod
+    def has_tool(self, tool_id: str) -> bool:
+        """Return bool indicating if tool with specified id is loaded."""
+
+    @abstractmethod
+    def get_tool(self, tool_id: str):
+        """Return tool with supplied tool id."""
+
+    @abstractmethod
+    def get_workflow(self, id: str):
+        """Return workflow from panel with supplied id."""
+
+    @abstractmethod
+    def add_tool_to_tool_panel_view(self, tool, tool_panel_component: HasPanelItems) -> None:
+        """Add tool to the tool panel view component (root or section)."""
+
+
+class ToolPanelView:
+
+    @abstractmethod
+    def apply_view(self, base_tool_panel: ToolPanelElements, toolbox_registry: ToolBoxRegistry) -> ToolPanelElements:
+        """Consume tool panel state and return custom tool panel view."""
+
+    @abstractmethod
+    def to_model(self) -> ToolPanelViewModel:
+        """Convert abstract description to dictionary description to emit via the API."""
+
+
+def walk_loaded_tools(tool_panel: ToolPanelElements, toolbox_registry: ToolBoxRegistry):
+    for key, item_type, val in tool_panel.panel_items_iter():
+        if item_type == panel_item_types.TOOL:
+            tool_id = key.replace('tool_', '', 1)
+            if toolbox_registry.has_tool(tool_id):
+                yield (tool_id, key, val, val.name)
+        elif item_type == panel_item_types.SECTION:
+            for section_key, section_item_type, section_val in val.panel_items_iter():
+                if section_item_type == panel_item_types.TOOL:
+                    tool_id = section_key.replace('tool_', '', 1)
+                    if toolbox_registry.has_tool(tool_id):
+                        yield (tool_id, key, section_val, val.name)
diff --git a/lib/galaxy/tool_util/toolbox/views/sources.py b/lib/galaxy/tool_util/toolbox/views/sources.py
new file mode 100644
index 00000000000..286a46a07ee
--- /dev/null
+++ b/lib/galaxy/tool_util/toolbox/views/sources.py
@@ -0,0 +1,52 @@
+import logging
+import os
+from typing import Dict, List
+
+import yaml
+
+from galaxy.util import config_directories_from_setting
+from .definitions import StaticToolBoxView
+
+log = logging.getLogger(__name__)
+
+EXTENSIONS = [".yml", ".yaml", ".json"]
+
+
+class StaticToolBoxViewSources:
+    view_directories: List[str]
+    view_dicts: List[Dict]
+
+    def __init__(self, view_directories=None, view_dicts=None):
+        self.view_directories = config_directories_from_setting(view_directories) or []
+        self.view_dicts = view_dicts or []
+
+    def get_definitions(self) -> List[StaticToolBoxView]:
+        view_definitions = []
+
+        for view_dict in self.view_dicts:
+            view_definitions.append(StaticToolBoxView.from_dict(view_dict))
+
+        for view_directory in self.view_directories:
+            if not os.path.exists(view_directory):
+                log.warning(f"Failed to find toolbox view directory {view_directory}")
+
+            for filename in os.listdir(view_directory):
+                if not looks_like_view_source_filename(filename):
+                    continue
+
+                view_path = os.path.join(view_directory, filename)
+                with open(view_path) as f:
+                    view_dict = yaml.safe_load(f)
+                if "id" not in view_dict:
+                    file_id = os.path.splitext(filename)[0]
+                    view_dict["id"] = file_id
+                view_definitions.append(StaticToolBoxView.from_dict(view_dict))
+
+        return view_definitions
+
+
+def looks_like_view_source_filename(filename: str) -> bool:
+    for ext in EXTENSIONS:
+        if filename.endswith(ext):
+            return True
+    return False
diff --git a/lib/galaxy/tool_util/toolbox/views/static.py b/lib/galaxy/tool_util/toolbox/views/static.py
new file mode 100644
index 00000000000..60c094d3ee8
--- /dev/null
+++ b/lib/galaxy/tool_util/toolbox/views/static.py
@@ -0,0 +1,168 @@
+import logging
+import re
+
+from .definitions import (
+    ExcludeTool,
+    ExcludeToolRegex,
+    ExcludeTypes,
+    Section,
+    StaticToolBoxView,
+    Workflow,
+)
+from .interface import (
+    ToolBoxRegistry,
+    ToolPanelView,
+    ToolPanelViewModel,
+    ToolPanelViewModelType,
+)
+from ..panel import (
+    ToolPanelElements,
+    ToolSection,
+    ToolSectionLabel,
+)
+
+
+log = logging.getLogger(__name__)
+
+
+def build_filter(excludes_):
+    excludes = excludes_ or []
+
+    def filter_function(panel_key, panel_value):
+        for exclude in excludes:
+            if panel_key.startswith("tool_"):
+                if isinstance(exclude, ExcludeTool):
+                    if panel_value.id == exclude.tool_id:
+                        return False
+                    if panel_value.old_id == exclude.tool_id:
+                        return False
+
+                if isinstance(exclude, ExcludeToolRegex):
+                    if re.match(exclude.tool_id_regex, panel_value.id):
+                        return False
+                    if re.match(exclude.tool_id_regex, panel_value.old_id):
+                        return False
+
+            if isinstance(exclude, ExcludeTypes):
+                if panel_key.startswith("label_") and "label" in exclude.types:
+                    return False
+                if panel_key.startswith("tool_") and "tool" in exclude.types:
+                    return False
+                if panel_key.startswith("workflow_") and "workflow" in exclude.types:
+                    return False
+
+        return True
+
+    return filter_function
+
+
+class StaticToolPanelView(ToolPanelView):
+    _definition: StaticToolBoxView
+
+    def __init__(self, definition: StaticToolBoxView):
+        self._definition = definition
+
+    def apply_view(self, base_tool_panel: ToolPanelElements, toolbox_registry: ToolBoxRegistry) -> ToolPanelElements:
+
+        def apply_filter(definition, elems):
+            if definition.excludes:
+                elems.apply_filter(build_filter(definition.excludes))
+
+        def definition_with_items_to_panel(definition, allow_sections: bool = True):
+            new_panel = ToolPanelElements()
+            for element in definition.items_expanded:
+                if element.content_type == "section":
+                    assert allow_sections
+                    section_def: Section = element
+                    section: ToolSection
+                    assert section_def.id is not None or section_def.name is not None
+                    if element.items:
+                        panel = definition_with_items_to_panel(section_def, allow_sections=False)
+                        section = ToolSection()
+                        if section_def.name is not None:
+                            name = section_def.name
+                        else:
+                            assert section_def.id is not None
+                            name = section_def.id
+                        section.name = name
+                        if section_def.id is not None:
+                            section.id = section_def.id
+                        else:
+                            # TODO: there has to be tool shed code to do this in a consistent way... where is it?
+                            section.id = name.replace(" ", "-").lower()
+                        section.elems = panel
+                    else:
+                        closest_section = base_tool_panel.closest_section(section_def.id, section_def.name)
+                        if closest_section is None:
+                            log.warning(f"Failed to find matching section for (id, name) = ({section_def.id}, {section_def.name})")
+                            continue
+                        section = closest_section.copy()
+                        if section_def.id is not None:
+                            section.id = section_def.id
+                        if section_def.name is not None:
+                            section.name = section_def.name
+                        apply_filter(section_def, section.elems)
+                    new_panel.append_section(section.id, section)
+                elif element.content_type == "section_alias":
+                    assert allow_sections
+                    closest_section = base_tool_panel.closest_section(element.section, element.section)
+                    if closest_section is None:
+                        log.warning(f"Failed to find matching section for (id, name) = ({element.section}, {element.section})")
+                        continue
+                    section = closest_section.copy()
+                    apply_filter(element, section.elems)
+                    new_panel.append_section(section.id, section)
+                elif element.content_type == "label":
+                    as_dict = {
+                        "id": element.id or element.text.lower().replace(" ", "-"),
+                        "text": element.text,
+                        "type": "label",
+                    }
+                    label = ToolSectionLabel(as_dict)
+                    key = f"label_{label.id}"
+                    new_panel[key] = label
+                elif element.content_type == "tool":
+                    tool_id = element.id
+                    if not toolbox_registry.has_tool(tool_id):
+                        log.warning(f"Failed to find tool_id {tool_id} from parent toolbox, cannot load into panel view")
+                        continue
+                    tool = toolbox_registry.get_tool(tool_id)
+                    toolbox_registry.add_tool_to_tool_panel_view(tool, new_panel)
+                elif element.content_type == "workflow":
+                    workflow_def: Workflow = element
+                    workflow = toolbox_registry.get_workflow(element.id)
+                    panel_id = f"workflow_{workflow_def.id}"
+                    new_panel[panel_id] = workflow
+                elif element.content_type == "items_from":
+                    closest_section = base_tool_panel.closest_section(element.items_from, element.items_from)
+                    if closest_section is None:
+                        log.warning(f"Failed to find matching section for (id, name) = ({element.items_from}, None)")
+                        continue
+                    elems = closest_section.elems.copy()
+                    apply_filter(element, elems)
+                    for key, item in elems.items():
+                        new_panel[key] = item
+                else:
+                    raise AssertionError("Unknown static toolbox configuration element encountered.")
+
+            if definition.excludes:
+                new_panel.apply_filter(build_filter(definition.excludes))
+
+            return new_panel
+
+        return definition_with_items_to_panel(self._definition)
+
+    def to_model(self) -> ToolPanelViewModel:
+        model_id = self._definition.id
+        name = self._definition.name
+        description = self._definition.description
+        view_type = ToolPanelViewModelType[self._definition.view_type.value]
+        model_class = self.__class__.__name__
+        return ToolPanelViewModel(
+            id=model_id,
+            name=name,
+            description=description,
+            model_class=model_class,
+            view_type=view_type,
+            searchable=True,
+        )
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index efbb7950443..fd3fa256697 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -48,6 +48,7 @@ from galaxy.tool_util.parser import (
 from galaxy.tool_util.parser.xml import XmlPageSource
 from galaxy.tool_util.provided_metadata import parse_tool_provided_metadata
 from galaxy.tool_util.toolbox import BaseGalaxyToolBox
+from galaxy.tool_util.toolbox.views.sources import StaticToolBoxViewSources
 from galaxy.tools import expressions
 from galaxy.tools.actions import DefaultToolAction
 from galaxy.tools.actions.data_manager import DataManagerToolAction
@@ -268,10 +269,17 @@ class ToolBox(BaseGalaxyToolBox):
         # FIXME: ./
         if tool_root_dir == './tools':
             tool_root_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), 'bundled'))
+        view_sources = StaticToolBoxViewSources(
+            view_directories=app.config.panel_views_dir,
+            view_dicts=app.config.panel_views,
+        )
+        default_panel_view = app.config.default_panel_view
         super().__init__(
             config_filenames=config_filenames,
             tool_root_dir=tool_root_dir,
             app=app,
+            view_sources=view_sources,
+            default_panel_view=default_panel_view,
             save_integrated_tool_panel=save_integrated_tool_panel,
         )
 
diff --git a/lib/galaxy/tools/search/__init__.py b/lib/galaxy/tools/search/__init__.py
index 849139b6d31..a324321e9e9 100644
--- a/lib/galaxy/tools/search/__init__.py
+++ b/lib/galaxy/tools/search/__init__.py
@@ -53,12 +53,44 @@ def get_or_create_index(index_dir: str, schema: Schema) -> index.Index:
 
 
 class ToolBoxSearch:
+    """Support searching across all fixed panel views in a toolbox.
+
+    Search is delegated off to ToolPanelViewSearch for each panel object.
+    """
+
+    def __init__(self, toolbox, index_dir: str, index_help: bool = True):
+        panel_searches = {}
+        for panel_view in toolbox.panel_views():
+            panel_view_id = panel_view.id
+            panel_index_dir = os.path.join(index_dir, panel_view_id)
+            panel_searches[panel_view_id] = ToolPanelViewSearch(toolbox, panel_view_id, panel_index_dir, index_help=index_help)
+        self.panel_searches = panel_searches
+        # We keep track of how many times the tool index has been rebuilt.
+        # We start at -1, so that after the first index the count is at 0,
+        # which is the same as the toolbox reload count. This way we can skip
+        # reindexing if the index count is equal to the toolbox reload count.
+        self.index_count = -1
+
+    def build_index(self, tool_cache, index_help: bool = True) -> None:
+        self.index_count += 1
+        for panel_search in self.panel_searches.values():
+            panel_search.build_index(tool_cache, index_help=index_help)
+
+    def search(self, *args, **kwd) -> List[str]:
+        panel_view = kwd.pop("panel_view")
+        if panel_view not in self.panel_searches:
+            raise KeyError(f"Unknown panel_view specified {panel_view}")
+        panel_search = self.panel_searches[panel_view]
+        return panel_search.search(*args, **kwd)
+
+
+class ToolPanelViewSearch:
     """
     Support searching tools in a toolbox. This implementation uses
     the Whoosh search library.
     """
 
-    def __init__(self, toolbox, index_dir: str, index_help: bool = True):
+    def __init__(self, toolbox, panel_view_id: str, index_dir: str, index_help: bool = True):
         self.schema = Schema(id=ID(stored=True, unique=True),
                              old_id=ID,
                              stub=KEYWORD,
@@ -70,12 +102,8 @@ class ToolBoxSearch:
         self.rex = analysis.RegexTokenizer()
         self.index_dir = index_dir
         self.toolbox = toolbox
+        self.panel_view_id = panel_view_id
         self.index = self._index_setup()
-        # We keep track of how many times the tool index has been rebuilt.
-        # We start at -1, so that after the first index the count is at 0,
-        # which is the same as the toolbox reload count. This way we can skip
-        # reindexing if the index count is equal to the toolbox reload count.
-        self.index_count = -1
 
     def _index_setup(self) -> index.Index:
         return get_or_create_index(index_dir=self.index_dir, schema=self.schema)
@@ -85,8 +113,7 @@ class ToolBoxSearch:
         Prepare search index for tools loaded in toolbox.
         Use `tool_cache` to determine which tools need indexing and which tools should be expired.
         """
-        log.debug('Starting to build toolbox index.')
-        self.index_count += 1
+        log.debug(f"Starting to build toolbox index of panel {self.panel_view_id}.")
         execution_timer = ExecutionTimer()
         with self.index.reader() as reader:
             # Index ocasionally contains empty stored fields
@@ -106,7 +133,7 @@ class ToolBoxSearch:
                 writer.delete_by_term('id', tool_id)
             for tool_id in tool_cache._new_tool_ids - indexed_tool_ids:
                 tool = self.toolbox.get_tool(tool_id)
-                if tool and tool.is_latest_version:
+                if tool and tool.is_latest_version and self.toolbox.panel_has_tool(tool, self.panel_view_id):
                     if tool.hidden:
                         # we check if there is an older tool we can return
                         if tool.lineage:
@@ -121,7 +148,7 @@ class ToolBoxSearch:
                             continue
                     add_doc_kwds = self._create_doc(tool_id=tool_id, tool=tool, index_help=index_help)
                     writer.update_document(**add_doc_kwds)
-        log.debug("Toolbox index finished %s", execution_timer)
+        log.debug(f"Toolbox index of panel {self.panel_view_id} finished {execution_timer}")
 
     def _create_doc(self, tool_id: str, tool, index_help: bool = True) -> Dict[str, str]:
         #  Do not add data managers to the public index
diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index 5b65f247666..0d7eebb9e73 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -46,6 +46,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
 
         :param in_panel: if true, tools are returned in panel structure,
                          including sections and labels
+        :param view: ToolBox view to apply (default is 'default')
         :param trackster: if true, only tools that are compatible with
                           Trackster are returned
         :param q: if present search on the given query will be performed
@@ -59,6 +60,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         q = kwds.get('q', '')
         tool_id = kwds.get('tool_id', '')
         tool_help = util.string_as_bool(kwds.get('tool_help', 'False'))
+        view = kwds.get("view", None)
 
         # Find whether to search.
         if q:
@@ -69,7 +71,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
                 else:
                     hits = None
             else:
-                hits = self._search(q)
+                hits = self._search(q, view)
             results = []
             if hits:
                 for hit in hits:
@@ -90,7 +92,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
 
         # Return everything.
         try:
-            return self.app.toolbox.to_dict(trans, in_panel=in_panel, trackster=trackster, tool_help=tool_help)
+            return self.app.toolbox.to_dict(trans, in_panel=in_panel, trackster=trackster, tool_help=tool_help, view=view)
         except Exception:
             raise exceptions.InternalServerError("Error: Could not convert toolbox to dictionary")
 
@@ -377,7 +379,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
                     detected_versions.append(tool.version)
         return detected_versions
 
-    def _search(self, q):
+    def _search(self, q, view):
         """
         Perform the search on the given query.
         Boosts and numer of results are configurable in galaxy.ini file.
@@ -388,6 +390,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         :return:      Dictionary containing the tools' ids of the best hits.
         :return type: dict
         """
+        panel_view = view or self.app.config.default_panel_view
         tool_name_boost = self.app.config.get('tool_name_boost', 9)
         tool_id_boost = self.app.config.get('tool_id_boost', 9)
         tool_section_boost = self.app.config.get('tool_section_boost', 3)
@@ -401,6 +404,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         tool_ngram_maxsize = self.app.config.get('tool_ngram_maxsize', 4)
 
         results = self.app.toolbox_search.search(q=q,
+                                                 panel_view=panel_view,
                                                  tool_name_boost=tool_name_boost,
                                                  tool_id_boost=tool_id_boost,
                                                  tool_section_boost=tool_section_boost,
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 4d2739e3351..f758026b3f2 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -2440,15 +2440,16 @@ mapping:
           stable API. (The module state definitions may change and workflows built using
           these modules may not function in the future.)
 
-      enable_beta_edam_toolbox:
-        type: bool
-        default: false
+      edam_panel_views:
+        type: str
+        default: 'operations,topics'
         required: false
         desc: |
-          Enable beta EDAM organised toolbox which ignores admin managed
-          sections in lieu of EDAM topics only.
+          Comma-separated list of the EDAM panel views to load - choose from merged, operations, topics.
+          Set to empty string to disable EDAM all together. Set default_panel_view to 'ontology:edam_topics'
+          to override default tool panel to use an EDAM view.
 
-      beta_edam_toolbox_ontology_path:
+      edam_toolbox_ontology_path:
         type: str
         default: EDAM.tsv
         path_resolves_to: data_dir
@@ -2456,6 +2457,34 @@ mapping:
         desc: |
           Sets the path to EDAM ontology file - if the path doesn't exist PyPI package data will be loaded.
 
+      panel_views_dir:
+        type: str
+        default: config/plugins/activities
+        required: false
+        desc: |
+          Directory to check out for toolbox tool panel views. The path is relative to the
+          Galaxy root dir.  To use an absolute path begin the path with '/'.  This is a
+          comma-separated list.
+
+      panel_views:
+        type: seq
+        sequence:
+          - type: any
+        required: false
+        desc: |
+          Definitions of static toolbox panel views embedded directly in the config instead of reading
+          YAML from directory with panel_views_dir.
+
+      default_panel_view:
+        type: str
+        default: default
+        required: false
+        desc: |
+          Default tool panel view for the current Galaxy configuration. This should refer to an id of
+          a panel view defined using the panel_views or panel_views_dir configuration options or an
+          EDAM panel view. The default panel view is simply called `default` and refers to the tool
+          panel state defined by the integrated tool panel.
+
       default_workflow_export_format:
         type: str
         default: ga
diff --git a/lib/galaxy_test/driver/driver_util.py b/lib/galaxy_test/driver/driver_util.py
index 5b4882b7040..e0868ba2115 100644
--- a/lib/galaxy_test/driver/driver_util.py
+++ b/lib/galaxy_test/driver/driver_util.py
@@ -15,6 +15,7 @@ import sys
 import tempfile
 import threading
 import time
+from typing import Optional
 from urllib.parse import urlparse
 
 import nose.config
@@ -155,6 +156,7 @@ def setup_galaxy_config(
     conda_auto_init=False,
     conda_auto_install=False,
     use_shared_connection_for_amqp=False,
+    allow_tool_conf_override: bool = True,
 ):
     """Setup environment and build config for test Galaxy instance."""
     # For certain docker operations this needs to be evaluated out - e.g. for cwltool.
@@ -165,6 +167,7 @@ def setup_galaxy_config(
     new_file_path = tempfile.mkdtemp(prefix='new_files_path_', dir=tmpdir)
     job_working_directory = tempfile.mkdtemp(prefix='job_working_directory_', dir=tmpdir)
 
+    user_library_import_dir: Optional[str]
     if use_test_file_dir:
         first_test_file_dir = ensure_test_file_dir_set()
         if not os.path.isabs(first_test_file_dir):
@@ -196,7 +199,10 @@ def setup_galaxy_config(
     # For storing Data Manager outputs and .loc files so that real ones don't get clobbered
     galaxy_data_manager_data_path = tempfile.mkdtemp(prefix='data_manager_tool-data', dir=tmpdir)
 
-    tool_conf = os.environ.get('GALAXY_TEST_TOOL_CONF', default_tool_conf)
+    if allow_tool_conf_override:
+        tool_conf = os.environ.get('GALAXY_TEST_TOOL_CONF', default_tool_conf)
+    else:
+        tool_conf = default_tool_conf
     conda_auto_install = os.environ.get('GALAXY_TEST_CONDA_AUTO_INSTALL', conda_auto_install)
     conda_auto_init = os.environ.get('GALAXY_TEST_CONDA_AUTO_INIT', conda_auto_init)
     conda_prefix = os.environ.get('GALAXY_TEST_CONDA_PREFIX')
@@ -1002,7 +1008,8 @@ class GalaxyTestDriver(TestDriver):
         else:
             default_tool_conf = getattr(config_object, "default_tool_conf", None)
             datatypes_conf_override = getattr(config_object, "datatypes_conf_override", None)
-
+        allow_tool_conf_override = getattr(config_object, "allow_tool_conf_override", True)
+        self.allow_tool_conf_override = allow_tool_conf_override
         self.default_tool_conf = default_tool_conf
         self.datatypes_conf_override = datatypes_conf_override
 
@@ -1047,7 +1054,8 @@ class GalaxyTestDriver(TestDriver):
                         log_format=self.log_format,
                         conda_auto_init=getattr(config_object, "conda_auto_init", False),
                         conda_auto_install=getattr(config_object, "conda_auto_install", False),
-                        use_shared_connection_for_amqp=getattr(config_object, "use_shared_connection_for_amqp", False)
+                        use_shared_connection_for_amqp=getattr(config_object, "use_shared_connection_for_amqp", False),
+                        allow_tool_conf_override=self.allow_tool_conf_override,
                     )
                     galaxy_config = setup_galaxy_config(
                         galaxy_db_path,
diff --git a/packages/tool_util/requirements.txt b/packages/tool_util/requirements.txt
index f0ac0b2b776..85b88243440 100644
--- a/packages/tool_util/requirements.txt
+++ b/packages/tool_util/requirements.txt
@@ -2,3 +2,5 @@ galaxy-util>=20.1.0.dev0
 galaxy-containers
 lxml
 sortedcontainers
+pydantic
+typing-extensions
diff --git a/packages/tool_util/setup.py b/packages/tool_util/setup.py
index d7863021cd3..2f4d88de6f6 100644
--- a/packages/tool_util/setup.py
+++ b/packages/tool_util/setup.py
@@ -43,6 +43,7 @@ PACKAGES = [
     'galaxy.tool_util.toolbox',
     'galaxy.tool_util.toolbox.filters',
     'galaxy.tool_util.toolbox.lineages',
+    'galaxy.tool_util.toolbox.views',
     'galaxy.tool_util.verify',
     'galaxy.tool_util.verify.asserts',
 ]
diff --git a/test/integration/panel_views_1/custom_1.yml b/test/integration/panel_views_1/custom_1.yml
new file mode 100644
index 00000000000..b3bafb71850
--- /dev/null
+++ b/test/integration/panel_views_1/custom_1.yml
@@ -0,0 +1,14 @@
+id: my-custom
+name: Custom Panel Filter
+type: generic
+items:
+- type: label
+  text: The Start
+- type: tool
+  id: empty_list
+- type: label
+  text: The Middle
+- type: tool
+  id: count_list
+- type: label
+  text: The End
diff --git a/test/integration/panel_views_1/custom_10.yml b/test/integration/panel_views_1/custom_10.yml
new file mode 100644
index 00000000000..2141fdfecb4
--- /dev/null
+++ b/test/integration/panel_views_1/custom_10.yml
@@ -0,0 +1,4 @@
+name: Filtered Test Section
+type: generic
+items:
+- sections: [test,filter]
diff --git a/test/integration/panel_views_1/custom_2.yml b/test/integration/panel_views_1/custom_2.yml
new file mode 100644
index 00000000000..b9c6dc229ff
--- /dev/null
+++ b/test/integration/panel_views_1/custom_2.yml
@@ -0,0 +1,7 @@
+name: Filtered Test Section
+type: activity
+items:
+- type: section
+  id: test
+  excludes:
+  - tool_id: multi_data_optional
diff --git a/test/integration/panel_views_1/custom_3.yml b/test/integration/panel_views_1/custom_3.yml
new file mode 100644
index 00000000000..80a5e07c028
--- /dev/null
+++ b/test/integration/panel_views_1/custom_3.yml
@@ -0,0 +1,8 @@
+name: Filtered Test Section
+type: activity
+items:
+- type: section
+  id: test
+  excludes:
+  - tool_id_regex: 'multi_data_.*'
+  - tool_id_regex: '.*_text_option'
diff --git a/test/integration/panel_views_1/custom_4.yml b/test/integration/panel_views_1/custom_4.yml
new file mode 100644
index 00000000000..e6e21e5376a
--- /dev/null
+++ b/test/integration/panel_views_1/custom_4.yml
@@ -0,0 +1,15 @@
+name: Custom Panel 4
+type: generic
+items:
+- type: label
+  text: The Start
+- type: tool
+  id: empty_list
+- type: label
+  text: The Middle
+- type: tool
+  id: count_list
+- type: label
+  text: The End
+excludes:
+- types: [label]
diff --git a/test/integration/panel_views_1/custom_5.yml b/test/integration/panel_views_1/custom_5.yml
new file mode 100644
index 00000000000..e7477aa923f
--- /dev/null
+++ b/test/integration/panel_views_1/custom_5.yml
@@ -0,0 +1,9 @@
+name: Merged Section Example
+type: generic
+items:
+- type: section
+  id: my-new-section
+  name: My New Section
+  items:
+  - items_from: test
+  - items_from: filter
diff --git a/test/integration/panel_views_1/custom_6.yml b/test/integration/panel_views_1/custom_6.yml
new file mode 100644
index 00000000000..9567ba32413
--- /dev/null
+++ b/test/integration/panel_views_1/custom_6.yml
@@ -0,0 +1,13 @@
+name: Custom Panel in a New Section
+type: generic
+items:
+- type: section
+  name: My Completely New Sectin
+  items:
+  - type: label
+    text: The Start
+  - type: tool
+    id: empty_list
+  - label: The Middle
+  - type: tool
+    id: count_list
diff --git a/test/integration/panel_views_1/custom_7.yml b/test/integration/panel_views_1/custom_7.yml
new file mode 100644
index 00000000000..299246b9939
--- /dev/null
+++ b/test/integration/panel_views_1/custom_7.yml
@@ -0,0 +1,13 @@
+name: Merged Section Example
+type: generic
+items:
+- type: section
+  id: my-new-section
+  name: My New Section
+  items:
+  - items_from: test
+    excludes:
+    -  tool_id_regex: '.*column.*'
+  - type: label
+    text: A cool label is here
+  - items_from: filter
diff --git a/test/integration/panel_views_1/custom_8.yml b/test/integration/panel_views_1/custom_8.yml
new file mode 100644
index 00000000000..ab913f8164a
--- /dev/null
+++ b/test/integration/panel_views_1/custom_8.yml
@@ -0,0 +1,9 @@
+name: Merged Section Example
+type: generic
+items:
+- type: section
+  id: my-new-section
+  name: My New Section
+  items:
+  - items_from: Test Section
+  - items_from: filter
diff --git a/test/integration/panel_views_1/custom_9.yml b/test/integration/panel_views_1/custom_9.yml
new file mode 100644
index 00000000000..17ca47e6417
--- /dev/null
+++ b/test/integration/panel_views_1/custom_9.yml
@@ -0,0 +1,7 @@
+name: Filtered Test Section
+type: activity
+items:
+- section: test
+  excludes:
+  - tool_id_regex: 'multi_data_.*'
+  - tool_id_regex: '.*_text_option'
diff --git a/test/integration/panel_views_1/filter.yml b/test/integration/panel_views_1/filter.yml
new file mode 100644
index 00000000000..0afa0d6b211
--- /dev/null
+++ b/test/integration/panel_views_1/filter.yml
@@ -0,0 +1,5 @@
+name: Filtering Tools
+type: activity
+items:
+- type: section
+  id: filter
diff --git a/test/integration/test_edam_toolbox.py b/test/integration/test_edam_toolbox.py
index 66b0ab7503c..6509ab750ac 100644
--- a/test/integration/test_edam_toolbox.py
+++ b/test/integration/test_edam_toolbox.py
@@ -5,15 +5,13 @@ class EdamToolboxIntegrationTestCase(integration_util.IntegrationTestCase):
 
     framework_tool_and_types = True
 
-    def setUp(self):
-        super().setUp()
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
-        config["enable_beta_edam_toolbox"] = True
+        config["edam_panel_views"] = "merged"
 
     def test_edam_toolbox(self):
-        index = self.galaxy_interactor.get("tools", data=dict(in_panel=True))
+        index = self.galaxy_interactor.get("tools", data=dict(in_panel=True, view="ontology:edam_merged"))
+        index.raise_for_status()
         index_as_list = index.json()
         sections = [x for x in index_as_list if x["model_class"] == "ToolSection"]
         section_names = [s["name"] for s in sections]
@@ -22,3 +20,41 @@ class EdamToolboxIntegrationTestCase(integration_util.IntegrationTestCase):
         mapping_section_elems = mapping_section["elems"]
         # make sure our mapper tool was mapped using Edam correctly...
         assert [x for x in mapping_section_elems if x["id"] == "mapper"]
+
+        config_index = self.galaxy_interactor.get("configuration")
+        config_index.raise_for_status()
+        panel_views = config_index.json()["panel_views"]
+        assert len(panel_views) > 1
+        assert isinstance(panel_views, dict)
+        edam_panel_view = panel_views["ontology:edam_merged"]
+        assert edam_panel_view["view_type"] == "ontology"
+
+
+class EdamToolboxDefaultIntegrationTestCase(integration_util.IntegrationTestCase):
+
+    framework_tool_and_types = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["edam_panel_views"] = "topics"
+        config["default_panel_view"] = "ontology:edam_topics"
+
+    def test_edam_toolbox(self):
+        index = self.galaxy_interactor.get("tools", data=dict(in_panel=True))
+        index.raise_for_status()
+        index_as_list = index.json()
+        sections = [x for x in index_as_list if x["model_class"] == "ToolSection"]
+        section_names = [s["name"] for s in sections]
+        assert "Mapping" in section_names
+        mapping_section = [s for s in sections if s["name"] == "Mapping"][0]
+        mapping_section_elems = mapping_section["elems"]
+        # make sure our mapper tool was mapped using Edam correctly...
+        assert [x for x in mapping_section_elems if x["id"] == "mapper"]
+
+        config_index = self.galaxy_interactor.get("configuration")
+        config_index.raise_for_status()
+        panel_views = config_index.json()["panel_views"]
+        assert len(panel_views) > 1
+        assert isinstance(panel_views, dict)
+        edam_panel_view = panel_views["ontology:edam_topics"]
+        assert edam_panel_view["view_type"] == "ontology"
diff --git a/test/integration/test_panel_views.py b/test/integration/test_panel_views.py
new file mode 100644
index 00000000000..38fcb413ef2
--- /dev/null
+++ b/test/integration/test_panel_views.py
@@ -0,0 +1,178 @@
+import os
+
+from galaxy_test.driver import integration_util
+
+THIS_DIR = os.path.dirname(__file__)
+PANEL_VIEWS_DIR_1 = os.path.join(THIS_DIR, "panel_views_1")
+
+
+class PanelViewsFromDirectoryIntegrationTestCase(integration_util.IntegrationTestCase):
+
+    framework_tool_and_types = True
+    allow_tool_conf_override = False
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["panel_views_dir"] = PANEL_VIEWS_DIR_1
+
+    def test_section_copy(self):
+        index = self.galaxy_interactor.get("tools", data=dict(in_panel=True, view="filter"))
+        index_as_list = index.json()
+        sections = [x for x in index_as_list if x["model_class"] == "ToolSection"]
+        section_names = [s["name"] for s in sections]
+        assert len(section_names) == 1
+        assert "For Tours" in section_names
+
+    def test_custom_label_order(self):
+        index = self.galaxy_interactor.get("tools", data=dict(in_panel=True, view="my-custom"))
+        verify_my_custom(index)
+
+    def test_filtering_sections_by_tool_id(self):
+        index = self.galaxy_interactor.get("tools", data=dict(in_panel=True, view="custom_2"))
+        index.raise_for_status()
+        index_as_list = index.json()
+        sections = [x for x in index_as_list if x["model_class"] == "ToolSection"]
+        assert len(sections) == 1
+        section = sections[0]
+        tools = section["elems"]
+        assert len(tools) == 3, len(tools)
+
+    def test_filtering_sections_by_tool_id_regex(self):
+        index = self.galaxy_interactor.get("tools", data=dict(in_panel=True, view="custom_3"))
+        verify_custom_regex_filtered(index)
+
+    def test_filtering_root_by_type(self):
+        index = self.galaxy_interactor.get("tools", data=dict(in_panel=True, view="custom_4"))
+        index.raise_for_status()
+        index_as_list = index.json()
+        assert len(index_as_list) == 2
+        # Labels are filtered out...
+        assert model_classes(index_as_list) == ["Tool", "Tool"]
+        assert element_ids(index_as_list) == ["empty_list", "count_list"]
+
+    def test_custom_section_def(self):
+        index = self.galaxy_interactor.get("tools", data=dict(in_panel=True, view="custom_6"))
+        index.raise_for_status()
+        index_as_list = index.json()
+        assert len(index_as_list) == 1
+        assert model_classes(index_as_list) == ["ToolSection"]
+        section = index_as_list[0]
+        section_elems = section["elems"]
+        assert len(section_elems) == 4, model_classes(section_elems)
+        assert model_classes(section_elems) == ["ToolSectionLabel", "Tool", "ToolSectionLabel", "Tool"]
+        assert element_ids(section_elems) == ["the-start", "empty_list", "the-middle", "count_list"]
+
+    def test_section_embed(self):
+        index = self.galaxy_interactor.get("tools", data=dict(in_panel=True, view="custom_5"))
+        verify_custom_embed(index)
+
+    def test_section_embed_filtering(self):
+        index = self.galaxy_interactor.get("tools", data=dict(in_panel=True, view="custom_7"))
+        index.raise_for_status()
+        index_as_list = index.json()
+        assert len(index_as_list) == 1
+        assert model_classes(index_as_list) == ["ToolSection"]
+        section = index_as_list[0]
+        section_elems = section["elems"]
+        assert len(section_elems) == 5, model_classes(section_elems)
+        assert model_classes(section_elems) == ["Tool", "Tool", "Tool", "ToolSectionLabel", "Tool"]
+        elem_ids = element_ids(section_elems)
+        assert elem_ids[0:3] == ["multi_data_optional", "paths_as_file", "param_text_option"]
+        assert elem_ids[4] == "Filter1"
+
+    def test_section_reference_by_name(self):
+        index = self.galaxy_interactor.get("tools", data=dict(in_panel=True, view="custom_8"))
+        verify_custom_embed(index)
+
+    def test_section_alias(self):
+        index = self.galaxy_interactor.get("tools", data=dict(in_panel=True, view="custom_9"))
+        verify_custom_regex_filtered(index)
+
+    def test_expand_section_aliases(self):
+        index = self.galaxy_interactor.get("tools", data=dict(in_panel=True, view="custom_10"))
+        index.raise_for_status()
+        index_as_list = index.json()
+        assert len(index_as_list) == 2
+        assert model_classes(index_as_list) == ["ToolSection", "ToolSection"]
+
+
+class PanelViewsFromConfigIntegrationTestCase(integration_util.IntegrationTestCase):
+
+    framework_tool_and_types = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["panel_views"] = [
+            {
+                "id": "my-custom",
+                "name": "My Custom",
+                "type": "generic",
+                "items": [
+                    {
+                        "type": "label",
+                        "text": "The Start",
+                    }, {
+                        "type": "tool",
+                        "id": "empty_list",
+                    }, {
+                        "type": "label",
+                        "text": "The Middle",
+                    }, {
+                        "type": "tool",
+                        "id": "count_list",
+                    }, {
+                        "type": "label",
+                        "text": "The End",
+                    }
+                ],
+            }
+        ]
+        config["default_panel_view"] = "my-custom"
+
+    def test_custom_label_order(self):
+        index = self.galaxy_interactor.get("tools", data=dict(in_panel=True))
+        verify_my_custom(index)
+
+
+def verify_my_custom(index):
+    index.raise_for_status()
+    index_as_list = index.json()
+    sections = [x for x in index_as_list if x["model_class"] == "ToolSection"]
+    assert len(sections) == 0
+
+    assert len(index_as_list) == 5
+    assert model_classes(index_as_list) == ["ToolSectionLabel", "Tool", "ToolSectionLabel", "Tool", "ToolSectionLabel"]
+
+
+def verify_custom_embed(index):
+    # custom_5 / custom_8
+    index.raise_for_status()
+    index_as_list = index.json()
+    assert len(index_as_list) == 1
+    assert model_classes(index_as_list) == ["ToolSection"]
+    section = index_as_list[0]
+    assert section["name"] == "My New Section"
+    assert section["id"] == "my-new-section"
+    section_elems = section["elems"]
+    assert len(section_elems) == 5, model_classes(section_elems)
+    assert model_classes(section_elems) == ["Tool", "Tool", "Tool", "Tool", "Tool"]
+    assert element_ids(section_elems) == ["multi_data_optional", "paths_as_file", "param_text_option", "column_param", "Filter1"]
+
+
+def verify_custom_regex_filtered(index):
+    # custom_3 / custom_9
+    index.raise_for_status()
+    index_as_list = index.json()
+    sections = [x for x in index_as_list if x["model_class"] == "ToolSection"]
+    assert len(sections) == 1
+    section = sections[0]
+    tools = section["elems"]
+    assert len(tools) == 2, len(tools)
+
+
+def element_ids(elements):
+    return [x["id"] for x in elements]
+
+
+def model_classes(elements):
+    return [x["model_class"] for x in elements]
diff --git a/test/unit/config/test_config_values.py b/test/unit/config/test_config_values.py
index b0cfa1856d9..a7e7a13317f 100644
--- a/test/unit/config/test_config_values.py
+++ b/test/unit/config/test_config_values.py
@@ -99,7 +99,6 @@ class ExpectedValues:
         self._expected_paths = {
             'admin_tool_recommendations_path': self._in_config_dir('tool_recommendations_overwrite.yml'),
             'auth_config_file': self._in_config_dir('auth_conf.xml'),
-            'beta_edam_toolbox_ontology_path': self._in_data_dir('EDAM.tsv'),
             'build_sites_config_file': self._in_sample_dir('build_sites.yml.sample'),
             'builds_file_path': self._in_root_dir('tool-data/shared/ucsc/builds.txt'),
             'cache_dir': self._in_data_dir('cache'),
@@ -113,6 +112,7 @@ class ExpectedValues:
             'datatypes_config_file': self._in_sample_dir('datatypes_conf.xml.sample'),
             'dependency_resolvers_config_file': self._in_config_dir('dependency_resolvers_conf.xml'),
             'dynamic_proxy_session_map': self._in_data_dir('session_map.sqlite'),
+            'edam_toolbox_ontology_path': self._in_data_dir('EDAM.tsv'),
             'error_report_file': self._in_config_dir('error_report.yml'),
             'file_path': self._in_data_dir('objects'),
             'file_sources_config_file': self._in_config_dir('file_sources_conf.yml'),
diff --git a/test/unit/tool_util/test_toolbox_view_parsing.py b/test/unit/tool_util/test_toolbox_view_parsing.py
new file mode 100644
index 00000000000..7c8ffd9468b
--- /dev/null
+++ b/test/unit/tool_util/test_toolbox_view_parsing.py
@@ -0,0 +1,101 @@
+import pydantic
+
+from galaxy.tool_util.toolbox.views.definitions import StaticToolBoxView, StaticToolBoxViewTypeEnum
+
+EXAMPLE_1 = {
+    "id": "rna",
+    "name": "RNA Seq",
+    "type": "activity",
+    "items": [
+        {
+            "type": "workflow",
+            "id": "12345abcd",
+        },
+        {
+            "type": "section",
+            "name": "My Cool Section",
+        },
+        {
+            "type": "label",
+            "text": "My Cool Label",
+            "id": "my-cool-label-id",
+        },
+        {
+            "type": "tool",
+            "id": "cat1",
+        },
+    ],
+}
+
+
+def test_root_parsing():
+    view = StaticToolBoxView.from_dict(EXAMPLE_1)
+    assert view.id == "rna"
+    assert view.name == "RNA Seq"
+    assert view.view_type == StaticToolBoxViewTypeEnum.activity
+    assert len(view.items) == 4
+    workflow_item = view.items[0]
+    assert workflow_item.content_type == "workflow"
+    assert workflow_item.id == "12345abcd"
+
+    section_item = view.items[1]
+    assert section_item.content_type == "section"
+    assert section_item.id is None
+    assert section_item.name == "My Cool Section"
+
+    outer_label_item = view.items[2]
+    assert outer_label_item.content_type == "label"
+    assert outer_label_item.id == "my-cool-label-id"
+    assert outer_label_item.text == "My Cool Label"
+
+    output_tool_item = view.items[3]
+    assert output_tool_item.content_type == "tool"
+    assert output_tool_item.id == "cat1"
+
+
+def test_section_parsing():
+    view = StaticToolBoxView.from_dict({
+        "id": "rna",
+        "name": "RNA Seq",
+        "type": "activity",
+        "items": [
+            {
+                "type": "section",
+                "name": "My Cool Section",
+                "items": [
+                    {
+                        "type": "workflow",
+                        "id": "123456",
+                    }
+                ],
+            },
+        ],
+    })
+    section_item = view.items[0]
+    assert len(section_item.items) == 1
+    assert section_item.items[0].content_type == "workflow"
+
+
+def test_no_nested_sections():
+    exception_raised = False
+    try:
+        StaticToolBoxView.from_dict({
+            "id": "rna",
+            "name": "RNA Seq",
+            "type": "activity",
+            "items": [
+                {
+                    "type": "section",
+                    "name": "My Cool Section",
+                    "items": [
+                        {
+                            "type": "section",
+                            "name": "My Cool Inner Section",
+                        },
+                    ],
+                },
+            ],
+        })
+    except pydantic.ValidationError:
+        exception_raised = True
+    assert exception_raised
diff --git a/test/unit/tool_util/test_toolbox_view_sources.py b/test/unit/tool_util/test_toolbox_view_sources.py
new file mode 100644
index 00000000000..9b608f7a7aa
--- /dev/null
+++ b/test/unit/tool_util/test_toolbox_view_sources.py
@@ -0,0 +1,45 @@
+import json
+import os
+import shutil
+import tempfile
+
+from galaxy.tool_util.toolbox.views.sources import StaticToolBoxViewSources
+from galaxy.util import safe_makedirs
+from .test_toolbox_view_parsing import EXAMPLE_1
+
+
+def test_from_dicts():
+    sources = StaticToolBoxViewSources(
+        view_dicts=[EXAMPLE_1]
+    )
+    defs = sources.get_definitions()
+    assert len(defs) == 1
+    assert defs[0].id == "rna"
+
+
+def test_from_directory():
+    target_dir = tempfile.mkdtemp()
+    dir_1 = os.path.join(target_dir, "dir1")
+    dir_2 = os.path.join(target_dir, "dir2")
+    safe_makedirs(dir_1)
+    safe_makedirs(dir_2)
+    with open(os.path.join(dir_1, "foo.json"), "w") as f:
+        json.dump(EXAMPLE_1, f)
+    with open(os.path.join(dir_2, "seqanalysis.yml"), "w") as f:
+        f.write("""
+name: Sequence Analysis
+type: generic
+items:
+- type: workflow
+  id: 12345abcd
+""")
+
+    config_param = f"{os.path.abspath(dir_1)},{os.path.abspath(dir_2)}"
+    try:
+        sources = StaticToolBoxViewSources(view_directories=config_param)
+        defs = sources.get_definitions()
+        assert len(defs) == 2
+        assert defs[0].id == "rna"
+        assert defs[1].id == "seqanalysis"
+    finally:
+        shutil.rmtree(target_dir)
diff --git a/test/unit/unittest_utils/galaxy_mock.py b/test/unit/unittest_utils/galaxy_mock.py
index 62782beea85..f8b3b973a0a 100644
--- a/test/unit/unittest_utils/galaxy_mock.py
+++ b/test/unit/unittest_utils/galaxy_mock.py
@@ -197,6 +197,11 @@ class MockAppConfig(Bunch):
         self.delay_tool_initialization = True
         self.external_chown_script = None
 
+        self.default_panel_view = "default"
+        self.panel_views_dir = ''
+        self.panel_views = {}
+        self.edam_panel_views = ''
+
         self.config_file = None
 
     @property

From 5473bdd6b2c07e0e6d35f85c8e3411d300f9a63c Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 5 Aug 2021 19:52:02 -0400
Subject: [PATCH 176/218] Persist selected tool panel.

---
 client/package.json       |  3 ++-
 client/src/store/index.js |  8 +++++++-
 client/yarn.lock          | 13 +++++++++++++
 3 files changed, 22 insertions(+), 2 deletions(-)

diff --git a/client/package.json b/client/package.json
index 2c70f9711bf..c9e77080628 100644
--- a/client/package.json
+++ b/client/package.json
@@ -87,7 +87,8 @@
     "vueisotope": "^3.1.2",
     "vuex": "^3.4.0",
     "vuex-cache": "^3.2.0",
-    "vuex-persist": "^3.1.3"
+    "vuex-persist": "^3.1.3",
+    "vuex-persistedstate": "^4.0.0"
   },
   "scripts": {
     "watch": "gulp && yarn run save-build-hash && yarn run webpack-watch",
diff --git a/client/src/store/index.js b/client/src/store/index.js
index 4dcb0320444..30685be19cd 100644
--- a/client/src/store/index.js
+++ b/client/src/store/index.js
@@ -5,6 +5,8 @@
 import Vue from "vue";
 import Vuex from "vuex";
 import createCache from "vuex-cache";
+import createPersistedState from "vuex-persistedstate";
+
 import config from "config";
 
 import { gridSearchStore } from "./gridSearchStore";
@@ -30,9 +32,13 @@ import { syncVuextoGalaxy } from "./syncVuextoGalaxy";
 
 Vue.use(Vuex);
 
+const panelsState = createPersistedState({
+    paths: ["panels"],
+});
+
 export function createStore() {
     const storeConfig = {
-        plugins: [createCache()],
+        plugins: [createCache(), panelsState],
         modules: {
             user: userStore,
             config: configStore,
diff --git a/client/yarn.lock b/client/yarn.lock
index 829749ec72d..4e05539e974 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -13338,6 +13338,11 @@ shellwords@^0.1.1:
   resolved "https://registry.yarnpkg.com/shellwords/-/shellwords-0.1.1.tgz#d6b9181c1a48d397324c84871efbcfc73fc0654b"
   integrity sha512-vFwSUfQvqybiICwZY5+DAWIPLKsWO31Q91JSKl3UYv+K5c2QRPzn0qzec6QPu1Qc9eHYItiP3NdJqNVqetYAww==
 
+shvl@^2.0.3:
+  version "2.0.3"
+  resolved "https://registry.yarnpkg.com/shvl/-/shvl-2.0.3.tgz#eb4bd37644f5684bba1fc52c3010c96fb5e6afd1"
+  integrity sha512-V7C6S9Hlol6SzOJPnQ7qzOVEWUQImt3BNmmzh40wObhla3XOYMe4gGiYzLrJd5TFa+cI2f9LKIRJTTKZSTbWgw==
+
 side-channel@^1.0.3:
   version "1.0.3"
   resolved "https://registry.yarnpkg.com/side-channel/-/side-channel-1.0.3.tgz#cdc46b057550bbab63706210838df5d4c19519c3"
@@ -15304,6 +15309,14 @@ vuex-persist@^3.1.3:
     deepmerge "^4.2.2"
     flatted "^3.0.5"
 
+vuex-persistedstate@^4.0.0:
+  version "4.0.0"
+  resolved "https://registry.yarnpkg.com/vuex-persistedstate/-/vuex-persistedstate-4.0.0.tgz#ed82f266ca98c869a2aad9cb9880c2f608c05f3a"
+  integrity sha512-jDs+awbV9YD2A2F6S5zgtYq1Bjd8v0YldOK6HPv1EJZzGMse0FtZTREfXvA7zlVfq9MpmSZJNmYQVylfpZ5znQ==
+  dependencies:
+    deepmerge "^4.2.2"
+    shvl "^2.0.3"
+
 vuex@^3.4.0:
   version "3.4.0"
   resolved "https://registry.yarnpkg.com/vuex/-/vuex-3.4.0.tgz#20cc086062d750769fce1febb34e7fceeaebde45"

From 9bf22b4e693ab049b2bca8ebf2c92c9ba5431d06 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 6 Aug 2021 11:07:01 -0400
Subject: [PATCH 177/218] Don't serialize the toolbox in requests, pulling it
 from persistedstate and doesn't respect default panel view.

---
 lib/galaxy/webapps/base/controller.py             | 1 -
 lib/galaxy/webapps/galaxy/controllers/workflow.py | 1 -
 2 files changed, 2 deletions(-)

diff --git a/lib/galaxy/webapps/base/controller.py b/lib/galaxy/webapps/base/controller.py
index e7780e5d424..fb1f8c82f17 100644
--- a/lib/galaxy/webapps/base/controller.py
+++ b/lib/galaxy/webapps/base/controller.py
@@ -307,7 +307,6 @@ class JSAppLauncher(BaseUIController):
         config = {
             'active_view': 'analysis',
             'enable_webhooks': True if trans.app.webhooks_registry.webhooks else False,
-            'toolbox': trans.app.toolbox.to_dict(trans),
             'message_box_visible': trans.app.config.message_box_visible,
             'show_inactivity_warning': trans.app.config.user_activation_on and trans.user and not trans.user.active,
             'tool_shed_urls': list(trans.app.tool_shed_registry.tool_sheds.values()) if trans.app.tool_shed_registry else [],
diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py
index 80870f8d1c0..c9f456047f6 100644
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -724,7 +724,6 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
             'tags': item_tag_names,
             'initialVersion': version,
             'annotation': self.get_item_annotation_str(trans.sa_session, trans.user, stored),
-            'toolbox': trans.app.toolbox.to_dict(trans),
             'moduleSections': module_sections,
             'dataManagers': data_managers,
             'workflows': workflows

From 0f2235e9c306ca76895f242640ceee9b71847fac Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 10 Aug 2021 16:20:46 -0400
Subject: [PATCH 178/218] Fix linting.

---
 client/src/components/Panels/Buttons/PanelViewButton.vue | 1 -
 1 file changed, 1 deletion(-)

diff --git a/client/src/components/Panels/Buttons/PanelViewButton.vue b/client/src/components/Panels/Buttons/PanelViewButton.vue
index 84fc12ddc2e..4bb5e22a01a 100644
--- a/client/src/components/Panels/Buttons/PanelViewButton.vue
+++ b/client/src/components/Panels/Buttons/PanelViewButton.vue
@@ -31,7 +31,6 @@
         </b-dropdown-group>
         <b-dropdown-divider v-if="groupedPanelViews.length > 0"></b-dropdown-divider>
         <PanelViewMenuItem
-            v-if="ungroupedPanelViews.length > 0"
             v-for="(panelView, key) in ungroupedPanelViews"
             :key="key"
             :current-panel-view="currentPanelView"

From 7846d47d6d14707cb43cdbc4a1fcf20ef6009b7f Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Wed, 11 Aug 2021 18:19:24 +0200
Subject: [PATCH 179/218] Style fixes

---
 lib/galaxy/managers/group_roles.py           |  4 ++--
 lib/galaxy/schema/schema.py                  |  3 ++-
 lib/galaxy/webapps/galaxy/api/group_roles.py | 14 +++++++-------
 3 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/managers/group_roles.py b/lib/galaxy/managers/group_roles.py
index 1991863f072..0fd5ba8ea3b 100644
--- a/lib/galaxy/managers/group_roles.py
+++ b/lib/galaxy/managers/group_roles.py
@@ -107,9 +107,9 @@ class GroupRolesManager:
     def _serialize_group_role(self, encoded_group_id: EncodedDatabaseIdField, role: model.Role):
         encoded_role_id = self._app.security.encode_id(role.id)
         try:
-            url  = url_for('role', group_id=encoded_group_id, id=encoded_role_id)
+            url = url_for('role', group_id=encoded_group_id, id=encoded_role_id)
         except AttributeError:
-            url  = "*deprecated attribute not filled in by FastAPI server*"
+            url = "*deprecated attribute not filled in by FastAPI server*"
         return {
             "id": encoded_role_id,
             "name": role.name,
diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index c1b2edfa187..cc6df51681d 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -1909,7 +1909,8 @@ class GroupRoleModel(BaseModel):
     id: EncodedDatabaseIdField = RoleIdField
     name: str = RoleNameField
     url: str = Field(title="URL", description="URL for the group role")
-    
+
+
 class GroupRoleListModel(BaseModel):
     __root__: List[GroupRoleModel]
 
diff --git a/lib/galaxy/webapps/galaxy/api/group_roles.py b/lib/galaxy/webapps/galaxy/api/group_roles.py
index d7e0ed51e2b..8494fc15a7a 100644
--- a/lib/galaxy/webapps/galaxy/api/group_roles.py
+++ b/lib/galaxy/webapps/galaxy/api/group_roles.py
@@ -15,9 +15,9 @@ from galaxy.web import (
     require_admin,
 )
 from . import (
-    BaseGalaxyAPIController, 
-    depends, 
-    Router, 
+    BaseGalaxyAPIController,
+    depends,
+    Router,
     DependsOnTrans
 )
 
@@ -46,13 +46,13 @@ class FastAPIGroupRoles:
     @router.get('/api/groups/{group_id}/roles',
                 require_admin=True,
                 summary='Displays a collection (list) of groups.')
-    def index(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam) -> GroupRoleListModel:
+    def indexAfe(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam) -> GroupRoleListModel:
         return self.manager.index(trans, group_id)
 
     @router.get('/api/groups/{group_id}/roles/{role_id}',
                 require_admin=True,
                 summary='Displays information about a group role.')
-    def show(self,  trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam, role_id: EncodedDatabaseIdField = RoleIDParam) -> GroupRoleModel:
+    def show(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam, role_id: EncodedDatabaseIdField = RoleIDParam) -> GroupRoleModel:
         return self.manager.show(trans, role_id, group_id)
 
     @router.put('/api/groups/{group_id}/roles/{role_id}',
@@ -62,8 +62,8 @@ class FastAPIGroupRoles:
         return self.manager.update(trans, role_id, group_id)
 
     @router.delete('/api/groups/{group_id}/roles/{role_id}',
-                    require_admin=True,
-                    summary='Removes a role from a group')
+                   require_admin=True,
+                   summary='Removes a role from a group')
     def delete(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam, role_id: EncodedDatabaseIdField = RoleIDParam):
         return self.manager.delete(trans, role_id, group_id)
 

From 384697d5bae786eb3987dffcbd7d9dc55e96f25d Mon Sep 17 00:00:00 2001
From: Mason Houtz <nerdinacan@gmail.com>
Date: Wed, 11 Aug 2021 10:16:23 -0700
Subject: [PATCH 180/218] added visibility flag test

---
 lib/galaxy_test/api/test_history_contents.py | 20 +++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy_test/api/test_history_contents.py b/lib/galaxy_test/api/test_history_contents.py
index 831c2122585..3919a6906d4 100644
--- a/lib/galaxy_test/api/test_history_contents.py
+++ b/lib/galaxy_test/api/test_history_contents.py
@@ -225,10 +225,28 @@ class HistoryContentsApiTestCase(ApiTestCase):
     def test_update_batch(self):
         hda1 = self._wait_for_new_hda()
         assert str(hda1["deleted"]).lower() == "false"
+        assert str(hda1["visible"]).lower() == "true"
+
+        # update deleted flag => true
         payload = dict(items=[{"history_content_type": "dataset", "id": hda1["id"]}], deleted=True)
         update_response = self._raw_update_batch(payload)
         objects = update_response.json()
-        assert objects[0]["deleted"]
+        assert objects[0]["deleted"] is True
+        assert objects[0]["visible"] is True
+
+        # update visibility flag => false
+        payload = dict(items=[{"history_content_type": "dataset", "id": hda1["id"]}], visible=False)
+        update_response = self._raw_update_batch(payload)
+        objects = update_response.json()
+        assert objects[0]["deleted"] is True
+        assert objects[0]["visible"] is False
+
+        # update both flags
+        payload = dict(items=[{"history_content_type": "dataset", "id": hda1["id"]}], deleted=False, visible=True)
+        update_response = self._raw_update_batch(payload)
+        objects = update_response.json()
+        assert objects[0]["deleted"] is False
+        assert objects[0]["visible"] is True
 
     def test_update_type_failures(self):
         hda1 = self._wait_for_new_hda()

From 501efc47e0eb7f49c027231bc9a5d568b136ef51 Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Wed, 11 Aug 2021 19:20:49 +0200
Subject: [PATCH 181/218] Fix imports

---
 lib/galaxy/webapps/galaxy/api/group_roles.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/group_roles.py b/lib/galaxy/webapps/galaxy/api/group_roles.py
index 8494fc15a7a..7a7f8a3e445 100644
--- a/lib/galaxy/webapps/galaxy/api/group_roles.py
+++ b/lib/galaxy/webapps/galaxy/api/group_roles.py
@@ -1,11 +1,10 @@
 """
 API operations on Group objects.
 """
-
-from lib.galaxy.schema.schema import GroupRoleListModel, GroupRoleModel
 import logging
 
 from fastapi import Path
+from lib.galaxy.schema.schema import GroupRoleListModel, GroupRoleModel
 
 from galaxy.managers.context import ProvidesAppContext
 from galaxy.managers.group_roles import GroupRolesManager
@@ -17,8 +16,8 @@ from galaxy.web import (
 from . import (
     BaseGalaxyAPIController,
     depends,
-    Router,
-    DependsOnTrans
+    DependsOnTrans,
+    Router
 )
 
 

From 8833d7763d03d49be034bf86481671118e741646 Mon Sep 17 00:00:00 2001
From: Peter van Heusden <pvh@sanbi.ac.za>
Date: Wed, 11 Aug 2021 19:27:58 +0200
Subject: [PATCH 182/218] Identify tool by name, owner, toolshed

---
 .../Toolshed/InstalledList/Index.test.js      |  2 +
 .../Toolshed/InstalledList/Index.vue          | 44 +++++++++++++------
 client/src/components/Toolshed/services.js    |  3 +-
 3 files changed, 35 insertions(+), 14 deletions(-)

diff --git a/client/src/components/Toolshed/InstalledList/Index.test.js b/client/src/components/Toolshed/InstalledList/Index.test.js
index 6342ea7e7c0..eff7c3e8741 100644
--- a/client/src/components/Toolshed/InstalledList/Index.test.js
+++ b/client/src/components/Toolshed/InstalledList/Index.test.js
@@ -20,6 +20,7 @@ Services.mockImplementation(() => {
                 {
                     name: "name_0",
                     description: "description_0",
+                    tool_shed: "toolshed_1",
                     tool_shed_status: {
                         latest_installable_revision: false,
                     },
@@ -27,6 +28,7 @@ Services.mockImplementation(() => {
                 {
                     name: "name_1",
                     description: "description_1",
+                    tool_shed: "toolshed_1",
                     tool_shed_status: {
                         latest_installable_revision: true,
                     },
diff --git a/client/src/components/Toolshed/InstalledList/Index.vue b/client/src/components/Toolshed/InstalledList/Index.vue
index 5f61b916b61..583142ddbf9 100644
--- a/client/src/components/Toolshed/InstalledList/Index.vue
+++ b/client/src/components/Toolshed/InstalledList/Index.vue
@@ -60,6 +60,7 @@ import { Services } from "../services";
 import LoadingSpan from "components/LoadingSpan";
 import Monitor from "./Monitor";
 import RepositoryDetails from "./Details";
+import {getGalaxyInstance} from "../../../app";
 
 Vue.use(BootstrapVue);
 
@@ -71,21 +72,9 @@ export default {
     },
     props: ["filter"],
     data() {
+
         return {
             error: null,
-            fields: [
-                {
-                    key: "name",
-                    sortable: true,
-                    sortByFormatted: (value, key, item) => {
-                        return `${this.isLatest(item)}_${value}`;
-                    },
-                },
-                {
-                    key: "owner",
-                    sortable: true,
-                },
-            ],
             loading: true,
             message: null,
             messageVariant: null,
@@ -105,6 +94,35 @@ export default {
         showMessage() {
             return !!this.message;
         },
+        numToolsheds() {
+            const toolsheds = new Set();
+            this.repositories.forEach((x) => {
+              toolsheds.add(x.tool_shed)
+            });
+            return toolsheds.size
+        },
+        fields() {
+            const fields = [
+                  {
+                    key: "name",
+                    sortable: true,
+                    sortByFormatted: (value, key, item) => {
+                      return `${this.isLatest(item)}_${value}`;
+                    },
+                  },
+                  {
+                    key: "owner",
+                    sortable: true,
+                  },
+                ];
+            if (this.numToolsheds > 1) {
+                fields.push({
+                  key: "tool_shed",
+                  sortable: true,
+                });
+            }
+            return fields;
+        }
     },
     created() {
         this.root = getAppRoot();
diff --git a/client/src/components/Toolshed/services.js b/client/src/components/Toolshed/services.js
index 2fb162ced2a..f67d9805ce0 100644
--- a/client/src/components/Toolshed/services.js
+++ b/client/src/components/Toolshed/services.js
@@ -134,6 +134,7 @@ export class Services {
                 return (
                     getSortValue(a.name, b.name) ||
                     getSortValue(a.owner, b.owner) ||
+                    getSortValue(a.tool_shed, b.tool_shed) ||
                     getSortValue(parseInt(b.ctx_rev), parseInt(a.ctx_rev))
                 );
             });
@@ -141,7 +142,7 @@ export class Services {
         const hash = {};
         const repositories = [];
         incoming.forEach((x) => {
-            const hashCode = `${x.name}_${x.owner}`;
+            const hashCode = `${x.name}_${x.owner}_${x.tool_shed}`;
             if (!filter || filter(x)) {
                 if (!hash[hashCode]) {
                     hash[hashCode] = true;

From 91c5bbbdb983cf2615e900fc3b3dbc2edce63db0 Mon Sep 17 00:00:00 2001
From: Peter van Heusden <pvh@sanbi.ac.za>
Date: Wed, 11 Aug 2021 19:41:51 +0200
Subject: [PATCH 183/218] Add explicit test for Tool Shed header

---
 client/src/components/Toolshed/InstalledList/Index.test.js | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/client/src/components/Toolshed/InstalledList/Index.test.js b/client/src/components/Toolshed/InstalledList/Index.test.js
index eff7c3e8741..38c5016b382 100644
--- a/client/src/components/Toolshed/InstalledList/Index.test.js
+++ b/client/src/components/Toolshed/InstalledList/Index.test.js
@@ -28,7 +28,7 @@ Services.mockImplementation(() => {
                 {
                     name: "name_1",
                     description: "description_1",
-                    tool_shed: "toolshed_1",
+                    tool_shed: "toolshed_2",
                     tool_shed_status: {
                         latest_installable_revision: true,
                     },
@@ -60,5 +60,6 @@ describe("InstalledList", () => {
         expect(links.length).toBe(3);
         const badge = links.at(1).find(".badge");
         expect(badge.text()).toBe("Newer version available!");
+        expect(wrapper.find('th[role="columnheader"][aria-colindex="3"] > div').text()).toBe("Tool Shed");
     });
 });

From 39787cea89bfb03be6e59165c254d155ef68033a Mon Sep 17 00:00:00 2001
From: Peter van Heusden <pvh@sanbi.ac.za>
Date: Wed, 11 Aug 2021 20:44:28 +0200
Subject: [PATCH 184/218] Fix eslint / vue linting errors

---
 .../Toolshed/InstalledList/Details.vue        |  7 +++++-
 .../Toolshed/InstalledList/Index.vue          |  8 +++++--
 .../Toolshed/RepositoryDetails/Index.vue      | 11 ++++++++-
 .../RepositoryDetails/InstallationButton.vue  | 11 ++++++++-
 .../InstallationSettings.vue                  | 23 ++++++++++++++++++-
 .../RepositoryDetails/RepositoryTools.vue     |  7 +++++-
 .../Toolshed/SearchList/Categories.vue        | 11 ++++++++-
 .../components/Toolshed/SearchList/Index.vue  | 11 ++++++++-
 .../Toolshed/SearchList/Repositories.test.js  |  2 +-
 .../Toolshed/SearchList/Repositories.vue      | 15 +++++++++++-
 .../SearchList/ServerSelection.test.js        |  4 ++--
 .../Toolshed/SearchList/ServerSelection.vue   | 19 ++++++++++++++-
 client/src/components/Toolshed/services.js    |  4 ++--
 .../src/components/Toolshed/services.test.js  |  2 +-
 14 files changed, 118 insertions(+), 17 deletions(-)

diff --git a/client/src/components/Toolshed/InstalledList/Details.vue b/client/src/components/Toolshed/InstalledList/Details.vue
index 10b167cacda..933f749d0b6 100644
--- a/client/src/components/Toolshed/InstalledList/Details.vue
+++ b/client/src/components/Toolshed/InstalledList/Details.vue
@@ -20,7 +20,12 @@ import RepositoryDetails from "../RepositoryDetails/Index.vue";
 import LoadingSpan from "components/LoadingSpan";
 
 export default {
-    props: ["repo"],
+    props: {
+      repo: {
+        type: Object,
+        required: true
+      }
+    },
     components: {
         LoadingSpan,
         RepositoryDetails,
diff --git a/client/src/components/Toolshed/InstalledList/Index.vue b/client/src/components/Toolshed/InstalledList/Index.vue
index 583142ddbf9..2fcc8916c17 100644
--- a/client/src/components/Toolshed/InstalledList/Index.vue
+++ b/client/src/components/Toolshed/InstalledList/Index.vue
@@ -60,7 +60,6 @@ import { Services } from "../services";
 import LoadingSpan from "components/LoadingSpan";
 import Monitor from "./Monitor";
 import RepositoryDetails from "./Details";
-import {getGalaxyInstance} from "../../../app";
 
 Vue.use(BootstrapVue);
 
@@ -70,7 +69,12 @@ export default {
         Monitor,
         RepositoryDetails,
     },
-    props: ["filter"],
+    props: {
+      filter: {
+        type: String,
+        required: true
+      }
+    },
     data() {
 
         return {
diff --git a/client/src/components/Toolshed/RepositoryDetails/Index.vue b/client/src/components/Toolshed/RepositoryDetails/Index.vue
index 17d6d998d76..4fa3b84d898 100644
--- a/client/src/components/Toolshed/RepositoryDetails/Index.vue
+++ b/client/src/components/Toolshed/RepositoryDetails/Index.vue
@@ -67,7 +67,16 @@ export default {
         InstallationButton,
         RepositoryTools,
     },
-    props: ["repo", "toolshedUrl"],
+    props: {
+      repo: {
+        type: Object,
+        required: true
+      },
+      toolshedUrl: {
+        type: String,
+        required: true
+      },
+    },
     data() {
         return {
             repoChecked: "fa fa-check text-success",
diff --git a/client/src/components/Toolshed/RepositoryDetails/InstallationButton.vue b/client/src/components/Toolshed/RepositoryDetails/InstallationButton.vue
index 6a0b84d1dd0..0f09f22fc87 100644
--- a/client/src/components/Toolshed/RepositoryDetails/InstallationButton.vue
+++ b/client/src/components/Toolshed/RepositoryDetails/InstallationButton.vue
@@ -19,7 +19,16 @@ import BootstrapVue from "bootstrap-vue";
 Vue.use(BootstrapVue);
 
 export default {
-    props: ["installed", "status"],
+    props: {
+      installed: {
+        type: Boolean,
+        required: false
+      },
+      status: {
+        type: String,
+        required: true
+      }
+    },
     data() {
         return {
             buttonClass: "btn-sm text-nowrap",
diff --git a/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.vue b/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.vue
index a4c6cf163dd..28fe26845e1 100644
--- a/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.vue
+++ b/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.vue
@@ -55,7 +55,28 @@ import { getGalaxyInstance } from "app";
 Vue.use(BootstrapVue);
 
 export default {
-    props: ["repo", "changesetRevision", "requiresPanel", "toolshedUrl", "modalStatic"],
+    props: {
+      repo: {
+        type: Object,
+        required: true,
+      },
+      changesetRevision: {
+        type: String,
+        required: true,
+      },
+      requiresPanel: {
+        type: Boolean,
+        required: true,
+      },
+      toolshedUrl: {
+        type: String,
+        required: true,
+      },
+      modalStatic: {
+        type: Boolean,
+        required: true,
+      },
+    },
     data() {
         return {
             modalShow: true,
diff --git a/client/src/components/Toolshed/RepositoryDetails/RepositoryTools.vue b/client/src/components/Toolshed/RepositoryDetails/RepositoryTools.vue
index c7b2b6e5565..32b6e313de0 100644
--- a/client/src/components/Toolshed/RepositoryDetails/RepositoryTools.vue
+++ b/client/src/components/Toolshed/RepositoryDetails/RepositoryTools.vue
@@ -33,7 +33,12 @@
 </template>
 <script>
 export default {
-    props: ["tools"],
+    props: {
+      tools: {
+        type: Array,
+        required: true
+      },
+    },
     data() {
         return {
             clsExpanded: "bg-transparent border-bottom",
diff --git a/client/src/components/Toolshed/SearchList/Categories.vue b/client/src/components/Toolshed/SearchList/Categories.vue
index 88e999cbf19..8ee6ab15bf9 100644
--- a/client/src/components/Toolshed/SearchList/Categories.vue
+++ b/client/src/components/Toolshed/SearchList/Categories.vue
@@ -24,7 +24,16 @@ import LoadingSpan from "components/LoadingSpan";
 Vue.use(BootstrapVue);
 
 export default {
-    props: ["toolshedUrl", "loading"],
+    props: {
+      toolshedUrl: {
+        type: String,
+        required: true
+      },
+      loading: {
+        type: Boolean,
+        required: true
+      },
+    },
     components: { LoadingSpan },
     data() {
         return {
diff --git a/client/src/components/Toolshed/SearchList/Index.vue b/client/src/components/Toolshed/SearchList/Index.vue
index 63dba70f2c1..742d16acd4f 100644
--- a/client/src/components/Toolshed/SearchList/Index.vue
+++ b/client/src/components/Toolshed/SearchList/Index.vue
@@ -34,7 +34,16 @@ import Categories from "./Categories.vue";
 import Repositories from "./Repositories.vue";
 import ServerSelection from "./ServerSelection.vue";
 export default {
-    props: ["query", "scrolled"],
+    props: {
+      query: {
+        type: String,
+        required: true
+      },
+      scrolled: {
+        type: Boolean,
+        required: true
+      },
+    },
     components: {
         Categories,
         Repositories,
diff --git a/client/src/components/Toolshed/SearchList/Repositories.test.js b/client/src/components/Toolshed/SearchList/Repositories.test.js
index ea3c1fb7d08..90e660a3216 100644
--- a/client/src/components/Toolshed/SearchList/Repositories.test.js
+++ b/client/src/components/Toolshed/SearchList/Repositories.test.js
@@ -33,7 +33,7 @@ describe("Repositories", () => {
     it("test repository details loading", async () => {
         const wrapper = mount(Repositories, {
             propsData: {
-                query: true,
+                query: "toolname",
                 scrolled: false,
                 toolshedUrl: "toolshedUrl",
             },
diff --git a/client/src/components/Toolshed/SearchList/Repositories.vue b/client/src/components/Toolshed/SearchList/Repositories.vue
index 4f9bdfa5140..f7ad240e86e 100644
--- a/client/src/components/Toolshed/SearchList/Repositories.vue
+++ b/client/src/components/Toolshed/SearchList/Repositories.vue
@@ -32,7 +32,20 @@ export default {
         LoadingSpan,
         RepositoryDetails,
     },
-    props: ["query", "scrolled", "toolshedUrl"],
+    props: {
+      query: {
+        type: String,
+        required: true
+      },
+      scrolled: {
+        type: Boolean,
+        required: true,
+      },
+      toolshedUrl: {
+        type: String,
+        required: true
+      },
+    },
     data() {
         return {
             repositories: [],
diff --git a/client/src/components/Toolshed/SearchList/ServerSelection.test.js b/client/src/components/Toolshed/SearchList/ServerSelection.test.js
index d3e138113fc..80524750123 100644
--- a/client/src/components/Toolshed/SearchList/ServerSelection.test.js
+++ b/client/src/components/Toolshed/SearchList/ServerSelection.test.js
@@ -11,11 +11,11 @@ describe("ServerSelection", () => {
                 toolshedUrl: "url_0",
                 toolshedUrls: ["url_0", "url_1"],
                 loading: false,
-                total: "total",
+                total: 10,
             },
             localVue,
         });
-        expect(wrapper.find(".description").text()).toBe("total repositories available at");
+        expect(wrapper.find(".description").text()).toBe("10 repositories available at");
         const $options = wrapper.findAll("a");
         expect($options.at(0).text()).toBe("url_0");
         expect($options.at(1).text()).toBe("url_0");
diff --git a/client/src/components/Toolshed/SearchList/ServerSelection.vue b/client/src/components/Toolshed/SearchList/ServerSelection.vue
index 8a7701feb3f..1a394cfdcce 100644
--- a/client/src/components/Toolshed/SearchList/ServerSelection.vue
+++ b/client/src/components/Toolshed/SearchList/ServerSelection.vue
@@ -38,7 +38,24 @@ import BootstrapVue from "bootstrap-vue";
 Vue.use(BootstrapVue);
 
 export default {
-    props: ["toolshedUrl", "toolshedUrls", "loading", "total"],
+    props: {
+      toolshedUrl: {
+        type: String,
+        required: true,
+      },
+      toolshedUrls: {
+        type: Array,
+        required: true,
+      },
+      loading: {
+        type: Boolean,
+        required: true,
+      },
+      total: {
+        type: Number,
+        required: true
+      },
+    },
     computed: {
         showDropdown() {
             return this.toolshedUrls.length > 1;
diff --git a/client/src/components/Toolshed/services.js b/client/src/components/Toolshed/services.js
index f67d9805ce0..eb00273238b 100644
--- a/client/src/components/Toolshed/services.js
+++ b/client/src/components/Toolshed/services.js
@@ -78,7 +78,7 @@ export class Services {
         const url = `${getAppRoot()}api/tool_shed_repositories/?uninstalled=False`;
         try {
             const response = await axios.get(url);
-            const repositories = this._groupByNameOwner(response.data, options.filter, options.selectLatest);
+            const repositories = this._groupByNameOwnerToolshed(response.data, options.filter, options.selectLatest);
             this._fixToolshedUrls(repositories, Galaxy.config.tool_shed_urls);
             return repositories;
         } catch (e) {
@@ -125,7 +125,7 @@ export class Services {
             rethrowSimple(e);
         }
     }
-    _groupByNameOwner(incoming, filter, selectLatest) {
+    _groupByNameOwnerToolshed(incoming, filter, selectLatest) {
         if (selectLatest) {
             const getSortValue = (x, y) => {
                 return x == y ? 0 : x < y ? -1 : 1;
diff --git a/client/src/components/Toolshed/services.test.js b/client/src/components/Toolshed/services.test.js
index ed3d573bffd..e8602826335 100644
--- a/client/src/components/Toolshed/services.test.js
+++ b/client/src/components/Toolshed/services.test.js
@@ -40,7 +40,7 @@ describe("Toolshed service helpers", () => {
     it("test fix toolshed helper", () => {
         const services = new Services();
         const filter = (x) => x.status !== "Installed";
-        const grouped = services._groupByNameOwner(incoming, filter, true);
+        const grouped = services._groupByNameOwnerToolshed(incoming, filter, true);
         services._fixToolshedUrls(grouped, urls);
         expect(grouped.length).toBe(2);
         expect(grouped[0].name).toBe("name_0");

From f520c6a70c3f92e746c8fecd5c698bc5a94f7171 Mon Sep 17 00:00:00 2001
From: Peter van Heusden <pvh@sanbi.ac.za>
Date: Wed, 11 Aug 2021 21:11:07 +0200
Subject: [PATCH 185/218] Reformat code with prettier

---
 .../Toolshed/InstalledList/Details.vue        | 10 ++---
 .../Toolshed/InstalledList/Index.vue          | 33 ++++++++-------
 .../Toolshed/InstalledList/Monitor.vue        |  2 +-
 .../Toolshed/RepositoryDetails/Index.vue      | 16 ++++----
 .../RepositoryDetails/InstallationButton.vue  | 16 ++++----
 .../InstallationSettings.vue                  | 40 +++++++++----------
 .../RepositoryDetails/RepositoryTools.vue     |  8 ++--
 .../Toolshed/SearchList/Categories.vue        | 16 ++++----
 .../components/Toolshed/SearchList/Index.vue  | 16 ++++----
 .../Toolshed/SearchList/Repositories.vue      | 24 +++++------
 .../Toolshed/SearchList/ServerSelection.vue   | 32 +++++++--------
 client/src/components/Toolshed/services.js    |  2 +-
 12 files changed, 107 insertions(+), 108 deletions(-)

diff --git a/client/src/components/Toolshed/InstalledList/Details.vue b/client/src/components/Toolshed/InstalledList/Details.vue
index 933f749d0b6..18b75966f22 100644
--- a/client/src/components/Toolshed/InstalledList/Details.vue
+++ b/client/src/components/Toolshed/InstalledList/Details.vue
@@ -21,10 +21,10 @@ import LoadingSpan from "components/LoadingSpan";
 
 export default {
     props: {
-      repo: {
-        type: Object,
-        required: true
-      }
+        repo: {
+            type: Object,
+            required: true,
+        },
     },
     components: {
         LoadingSpan,
@@ -39,7 +39,7 @@ export default {
     },
     created() {
         this.root = getAppRoot();
-        this.services = new Services({ root: this.root });
+        this.services = new Services();
         this.load();
     },
     methods: {
diff --git a/client/src/components/Toolshed/InstalledList/Index.vue b/client/src/components/Toolshed/InstalledList/Index.vue
index 2fcc8916c17..39e7d767655 100644
--- a/client/src/components/Toolshed/InstalledList/Index.vue
+++ b/client/src/components/Toolshed/InstalledList/Index.vue
@@ -70,13 +70,12 @@ export default {
         RepositoryDetails,
     },
     props: {
-      filter: {
-        type: String,
-        required: true
-      }
+        filter: {
+            type: String,
+            required: true,
+        },
     },
     data() {
-
         return {
             error: null,
             loading: true,
@@ -101,36 +100,36 @@ export default {
         numToolsheds() {
             const toolsheds = new Set();
             this.repositories.forEach((x) => {
-              toolsheds.add(x.tool_shed)
+                toolsheds.add(x.tool_shed);
             });
-            return toolsheds.size
+            return toolsheds.size;
         },
         fields() {
             const fields = [
-                  {
+                {
                     key: "name",
                     sortable: true,
                     sortByFormatted: (value, key, item) => {
-                      return `${this.isLatest(item)}_${value}`;
+                        return `${this.isLatest(item)}_${value}`;
                     },
-                  },
-                  {
+                },
+                {
                     key: "owner",
                     sortable: true,
-                  },
-                ];
+                },
+            ];
             if (this.numToolsheds > 1) {
                 fields.push({
-                  key: "tool_shed",
-                  sortable: true,
+                    key: "tool_shed",
+                    sortable: true,
                 });
             }
             return fields;
-        }
+        },
     },
     created() {
         this.root = getAppRoot();
-        this.services = new Services({ root: this.root });
+        this.services = new Services();
         this.load();
     },
     methods: {
diff --git a/client/src/components/Toolshed/InstalledList/Monitor.vue b/client/src/components/Toolshed/InstalledList/Monitor.vue
index 7c7a97349ce..0f22d2775ef 100644
--- a/client/src/components/Toolshed/InstalledList/Monitor.vue
+++ b/client/src/components/Toolshed/InstalledList/Monitor.vue
@@ -59,7 +59,7 @@ export default {
     },
     created() {
         this.root = getAppRoot();
-        this.services = new Services({ root: this.root });
+        this.services = new Services();
         this.load();
     },
     destroyed() {
diff --git a/client/src/components/Toolshed/RepositoryDetails/Index.vue b/client/src/components/Toolshed/RepositoryDetails/Index.vue
index 4fa3b84d898..503dbb0d08f 100644
--- a/client/src/components/Toolshed/RepositoryDetails/Index.vue
+++ b/client/src/components/Toolshed/RepositoryDetails/Index.vue
@@ -68,14 +68,14 @@ export default {
         RepositoryTools,
     },
     props: {
-      repo: {
-        type: Object,
-        required: true
-      },
-      toolshedUrl: {
-        type: String,
-        required: true
-      },
+        repo: {
+            type: Object,
+            required: true,
+        },
+        toolshedUrl: {
+            type: String,
+            required: true,
+        },
     },
     data() {
         return {
diff --git a/client/src/components/Toolshed/RepositoryDetails/InstallationButton.vue b/client/src/components/Toolshed/RepositoryDetails/InstallationButton.vue
index 0f09f22fc87..7a4f7b134b7 100644
--- a/client/src/components/Toolshed/RepositoryDetails/InstallationButton.vue
+++ b/client/src/components/Toolshed/RepositoryDetails/InstallationButton.vue
@@ -20,14 +20,14 @@ Vue.use(BootstrapVue);
 
 export default {
     props: {
-      installed: {
-        type: Boolean,
-        required: false
-      },
-      status: {
-        type: String,
-        required: true
-      }
+        installed: {
+            type: Boolean,
+            required: false,
+        },
+        status: {
+            type: String,
+            required: true,
+        },
     },
     data() {
         return {
diff --git a/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.vue b/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.vue
index 28fe26845e1..9fae81a8d6b 100644
--- a/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.vue
+++ b/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.vue
@@ -56,26 +56,26 @@ Vue.use(BootstrapVue);
 
 export default {
     props: {
-      repo: {
-        type: Object,
-        required: true,
-      },
-      changesetRevision: {
-        type: String,
-        required: true,
-      },
-      requiresPanel: {
-        type: Boolean,
-        required: true,
-      },
-      toolshedUrl: {
-        type: String,
-        required: true,
-      },
-      modalStatic: {
-        type: Boolean,
-        required: true,
-      },
+        repo: {
+            type: Object,
+            required: true,
+        },
+        changesetRevision: {
+            type: String,
+            required: true,
+        },
+        requiresPanel: {
+            type: Boolean,
+            required: true,
+        },
+        toolshedUrl: {
+            type: String,
+            required: true,
+        },
+        modalStatic: {
+            type: Boolean,
+            required: true,
+        },
     },
     data() {
         return {
diff --git a/client/src/components/Toolshed/RepositoryDetails/RepositoryTools.vue b/client/src/components/Toolshed/RepositoryDetails/RepositoryTools.vue
index 32b6e313de0..1963f13da11 100644
--- a/client/src/components/Toolshed/RepositoryDetails/RepositoryTools.vue
+++ b/client/src/components/Toolshed/RepositoryDetails/RepositoryTools.vue
@@ -34,10 +34,10 @@
 <script>
 export default {
     props: {
-      tools: {
-        type: Array,
-        required: true
-      },
+        tools: {
+            type: Array,
+            required: true,
+        },
     },
     data() {
         return {
diff --git a/client/src/components/Toolshed/SearchList/Categories.vue b/client/src/components/Toolshed/SearchList/Categories.vue
index 8ee6ab15bf9..dba32473dc3 100644
--- a/client/src/components/Toolshed/SearchList/Categories.vue
+++ b/client/src/components/Toolshed/SearchList/Categories.vue
@@ -25,14 +25,14 @@ Vue.use(BootstrapVue);
 
 export default {
     props: {
-      toolshedUrl: {
-        type: String,
-        required: true
-      },
-      loading: {
-        type: Boolean,
-        required: true
-      },
+        toolshedUrl: {
+            type: String,
+            required: true,
+        },
+        loading: {
+            type: Boolean,
+            required: true,
+        },
     },
     components: { LoadingSpan },
     data() {
diff --git a/client/src/components/Toolshed/SearchList/Index.vue b/client/src/components/Toolshed/SearchList/Index.vue
index 742d16acd4f..54c58f2a0c0 100644
--- a/client/src/components/Toolshed/SearchList/Index.vue
+++ b/client/src/components/Toolshed/SearchList/Index.vue
@@ -35,14 +35,14 @@ import Repositories from "./Repositories.vue";
 import ServerSelection from "./ServerSelection.vue";
 export default {
     props: {
-      query: {
-        type: String,
-        required: true
-      },
-      scrolled: {
-        type: Boolean,
-        required: true
-      },
+        query: {
+            type: String,
+            required: true,
+        },
+        scrolled: {
+            type: Boolean,
+            required: true,
+        },
     },
     components: {
         Categories,
diff --git a/client/src/components/Toolshed/SearchList/Repositories.vue b/client/src/components/Toolshed/SearchList/Repositories.vue
index f7ad240e86e..3e8c73f721b 100644
--- a/client/src/components/Toolshed/SearchList/Repositories.vue
+++ b/client/src/components/Toolshed/SearchList/Repositories.vue
@@ -33,18 +33,18 @@ export default {
         RepositoryDetails,
     },
     props: {
-      query: {
-        type: String,
-        required: true
-      },
-      scrolled: {
-        type: Boolean,
-        required: true,
-      },
-      toolshedUrl: {
-        type: String,
-        required: true
-      },
+        query: {
+            type: String,
+            required: true,
+        },
+        scrolled: {
+            type: Boolean,
+            required: true,
+        },
+        toolshedUrl: {
+            type: String,
+            required: true,
+        },
     },
     data() {
         return {
diff --git a/client/src/components/Toolshed/SearchList/ServerSelection.vue b/client/src/components/Toolshed/SearchList/ServerSelection.vue
index 1a394cfdcce..27bb3b51aa1 100644
--- a/client/src/components/Toolshed/SearchList/ServerSelection.vue
+++ b/client/src/components/Toolshed/SearchList/ServerSelection.vue
@@ -39,22 +39,22 @@ Vue.use(BootstrapVue);
 
 export default {
     props: {
-      toolshedUrl: {
-        type: String,
-        required: true,
-      },
-      toolshedUrls: {
-        type: Array,
-        required: true,
-      },
-      loading: {
-        type: Boolean,
-        required: true,
-      },
-      total: {
-        type: Number,
-        required: true
-      },
+        toolshedUrl: {
+            type: String,
+            required: true,
+        },
+        toolshedUrls: {
+            type: Array,
+            required: true,
+        },
+        loading: {
+            type: Boolean,
+            required: true,
+        },
+        total: {
+            type: Number,
+            required: true,
+        },
     },
     computed: {
         showDropdown() {
diff --git a/client/src/components/Toolshed/services.js b/client/src/components/Toolshed/services.js
index eb00273238b..9fe192a15bf 100644
--- a/client/src/components/Toolshed/services.js
+++ b/client/src/components/Toolshed/services.js
@@ -128,7 +128,7 @@ export class Services {
     _groupByNameOwnerToolshed(incoming, filter, selectLatest) {
         if (selectLatest) {
             const getSortValue = (x, y) => {
-                return x == y ? 0 : x < y ? -1 : 1;
+                return x === y ? 0 : x < y ? -1 : 1;
             };
             incoming = incoming.sort((a, b) => {
                 return (

From 574d520540f0e5e6a9079a6814684b04a2194b67 Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Thu, 12 Aug 2021 14:27:37 +0200
Subject: [PATCH 186/218] Fix typo
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: David López <46503462+davelopez@users.noreply.github.com>
---
 lib/galaxy/webapps/galaxy/api/group_roles.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/api/group_roles.py b/lib/galaxy/webapps/galaxy/api/group_roles.py
index 7a7f8a3e445..9af8282aebf 100644
--- a/lib/galaxy/webapps/galaxy/api/group_roles.py
+++ b/lib/galaxy/webapps/galaxy/api/group_roles.py
@@ -45,7 +45,7 @@ class FastAPIGroupRoles:
     @router.get('/api/groups/{group_id}/roles',
                 require_admin=True,
                 summary='Displays a collection (list) of groups.')
-    def indexAfe(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam) -> GroupRoleListModel:
+    def index(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam) -> GroupRoleListModel:
         return self.manager.index(trans, group_id)
 
     @router.get('/api/groups/{group_id}/roles/{role_id}',

From 35d31d6081b47ce8dda0384ceb2e122fb7a31048 Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Thu, 12 Aug 2021 14:28:19 +0200
Subject: [PATCH 187/218] Replace str url type with RelativeUrl
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: David López <46503462+davelopez@users.noreply.github.com>
---
 lib/galaxy/schema/schema.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index cc6df51681d..8702fc86504 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -1908,7 +1908,7 @@ RoleNameIdTuple = Tuple[str, EncodedDatabaseIdField]
 class GroupRoleModel(BaseModel):
     id: EncodedDatabaseIdField = RoleIdField
     name: str = RoleNameField
-    url: str = Field(title="URL", description="URL for the group role")
+    url: RelativeUrl = RelativeUrlField
 
 
 class GroupRoleListModel(BaseModel):

From b0bc577b0f0e78abd67c2613f6d7c62958337e80 Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Thu, 12 Aug 2021 15:14:46 +0200
Subject: [PATCH 188/218] Replace dict types with Pydantic models

---
 lib/galaxy/managers/group_roles.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/managers/group_roles.py b/lib/galaxy/managers/group_roles.py
index 0fd5ba8ea3b..758c01a60c0 100644
--- a/lib/galaxy/managers/group_roles.py
+++ b/lib/galaxy/managers/group_roles.py
@@ -2,10 +2,11 @@ import logging
 from typing import (
     Any,
     Dict,
-    List,
     Optional,
 )
 
+from lib.galaxy.schema.schema import GroupRoleListModel, GroupRoleModel
+
 from galaxy import model
 from galaxy.app import MinimalManagerApp
 from galaxy.exceptions import (
@@ -25,7 +26,7 @@ class GroupRolesManager:
     def __init__(self, app: MinimalManagerApp) -> None:
         self._app = app
 
-    def index(self, trans: ProvidesAppContext, group_id: EncodedDatabaseIdField) -> List[Dict[str, Any]]:
+    def index(self, trans: ProvidesAppContext, group_id: EncodedDatabaseIdField):
         """
         Returns a collection roles associated with the given group.
         """
@@ -34,7 +35,7 @@ class GroupRolesManager:
         for gra in group.roles:
             group_role = self._serialize_group_role(group_id, gra.role)
             rval.append(group_role)
-        return rval
+        return GroupRoleListModel(__root__=rval)
 
     def show(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, group_id: EncodedDatabaseIdField) -> Dict[str, Any]:
         """
@@ -110,8 +111,9 @@ class GroupRolesManager:
             url = url_for('role', group_id=encoded_group_id, id=encoded_role_id)
         except AttributeError:
             url = "*deprecated attribute not filled in by FastAPI server*"
-        return {
+
+        return GroupRoleModel(**{
             "id": encoded_role_id,
             "name": role.name,
             "url": url
-        }
+        })

From 3515a219733453ed42b207028075dbce3b5b1c1c Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Thu, 12 Aug 2021 15:15:31 +0200
Subject: [PATCH 189/218] Consider url field deprecation in group_roles test

---
 lib/galaxy_test/api/test_group_roles.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy_test/api/test_group_roles.py b/lib/galaxy_test/api/test_group_roles.py
index 67b00527ec3..d445a900f79 100644
--- a/lib/galaxy_test/api/test_group_roles.py
+++ b/lib/galaxy_test/api/test_group_roles.py
@@ -67,7 +67,7 @@ class GroupRolesApiTestCase(ApiTestCase):
         self._assert_status_code_is_ok(update_response)
         group_role = update_response.json()
         self._assert_valid_group_role(group_role, assert_id=encoded_role_id)
-        assert group_role["url"] == f"/api/groups/{encoded_group_id}/roles/{encoded_role_id}"
+        assert (group_role["url"] == f"/api/groups/{encoded_group_id}/roles/{encoded_role_id}" or group_role["url"] == "*deprecated attribute not filled in by FastAPI server*")
 
     def test_update_only_admin(self):
         encoded_group_id = "any-group-id"

From cf2ccb02a50f4ef0bf16b5a8981a1f973ec135c6 Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Thu, 12 Aug 2021 16:18:49 +0200
Subject: [PATCH 190/218] Fix imports

---
 lib/galaxy/managers/group_roles.py           | 6 ++----
 lib/galaxy/webapps/galaxy/api/group_roles.py | 2 +-
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/managers/group_roles.py b/lib/galaxy/managers/group_roles.py
index 758c01a60c0..d0456987c0c 100644
--- a/lib/galaxy/managers/group_roles.py
+++ b/lib/galaxy/managers/group_roles.py
@@ -1,12 +1,9 @@
 import logging
 from typing import (
     Any,
-    Dict,
     Optional,
 )
 
-from lib.galaxy.schema.schema import GroupRoleListModel, GroupRoleModel
-
 from galaxy import model
 from galaxy.app import MinimalManagerApp
 from galaxy.exceptions import (
@@ -15,6 +12,7 @@ from galaxy.exceptions import (
 from galaxy.managers.base import decode_id
 from galaxy.managers.context import ProvidesAppContext
 from galaxy.schema.fields import EncodedDatabaseIdField
+from galaxy.schema.schema import GroupRoleListModel, GroupRoleModel
 from galaxy.web import url_for
 
 log = logging.getLogger(__name__)
@@ -37,7 +35,7 @@ class GroupRolesManager:
             rval.append(group_role)
         return GroupRoleListModel(__root__=rval)
 
-    def show(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, group_id: EncodedDatabaseIdField) -> Dict[str, Any]:
+    def show(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, group_id: EncodedDatabaseIdField):
         """
         Returns information about a group role.
         """
diff --git a/lib/galaxy/webapps/galaxy/api/group_roles.py b/lib/galaxy/webapps/galaxy/api/group_roles.py
index 9af8282aebf..a0ce3592113 100644
--- a/lib/galaxy/webapps/galaxy/api/group_roles.py
+++ b/lib/galaxy/webapps/galaxy/api/group_roles.py
@@ -4,11 +4,11 @@ API operations on Group objects.
 import logging
 
 from fastapi import Path
-from lib.galaxy.schema.schema import GroupRoleListModel, GroupRoleModel
 
 from galaxy.managers.context import ProvidesAppContext
 from galaxy.managers.group_roles import GroupRolesManager
 from galaxy.schema.fields import EncodedDatabaseIdField
+from galaxy.schema.schema import GroupRoleListModel, GroupRoleModel
 from galaxy.web import (
     expose_api,
     require_admin,

From 8e384e554adfc2193fa1ac416fb31df7b396ff18 Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Thu, 12 Aug 2021 16:27:55 +0200
Subject: [PATCH 191/218] Fix group_role url typo

---
 lib/galaxy/managers/group_roles.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/managers/group_roles.py b/lib/galaxy/managers/group_roles.py
index d0456987c0c..19bb2c8285a 100644
--- a/lib/galaxy/managers/group_roles.py
+++ b/lib/galaxy/managers/group_roles.py
@@ -106,7 +106,7 @@ class GroupRolesManager:
     def _serialize_group_role(self, encoded_group_id: EncodedDatabaseIdField, role: model.Role):
         encoded_role_id = self._app.security.encode_id(role.id)
         try:
-            url = url_for('role', group_id=encoded_group_id, id=encoded_role_id)
+            url = url_for('group_role', group_id=encoded_group_id, id=encoded_role_id)
         except AttributeError:
             url = "*deprecated attribute not filled in by FastAPI server*"
 

From e0ca1a932c238be6d31e4b60ab2dcdc778c8fed9 Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Thu, 12 Aug 2021 18:45:25 +0200
Subject: [PATCH 192/218] Refactor

---
 lib/galaxy/managers/group_roles.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/managers/group_roles.py b/lib/galaxy/managers/group_roles.py
index 19bb2c8285a..0ec67583641 100644
--- a/lib/galaxy/managers/group_roles.py
+++ b/lib/galaxy/managers/group_roles.py
@@ -24,7 +24,7 @@ class GroupRolesManager:
     def __init__(self, app: MinimalManagerApp) -> None:
         self._app = app
 
-    def index(self, trans: ProvidesAppContext, group_id: EncodedDatabaseIdField):
+    def index(self, trans: ProvidesAppContext, group_id: EncodedDatabaseIdField) -> GroupRoleListModel:
         """
         Returns a collection roles associated with the given group.
         """
@@ -110,8 +110,8 @@ class GroupRolesManager:
         except AttributeError:
             url = "*deprecated attribute not filled in by FastAPI server*"
 
-        return GroupRoleModel(**{
-            "id": encoded_role_id,
-            "name": role.name,
-            "url": url
-        })
+        return GroupRoleModel(
+            id=encoded_role_id,
+            name=role.name,
+            url=url
+        )

From f204483b76e051dbf9eb0a82fc2424bef1be3ff4 Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Thu, 12 Aug 2021 18:45:42 +0200
Subject: [PATCH 193/218] Remove url assertion from group_roles test

---
 lib/galaxy_test/api/test_group_roles.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy_test/api/test_group_roles.py b/lib/galaxy_test/api/test_group_roles.py
index d445a900f79..bec1c7e08a4 100644
--- a/lib/galaxy_test/api/test_group_roles.py
+++ b/lib/galaxy_test/api/test_group_roles.py
@@ -67,7 +67,6 @@ class GroupRolesApiTestCase(ApiTestCase):
         self._assert_status_code_is_ok(update_response)
         group_role = update_response.json()
         self._assert_valid_group_role(group_role, assert_id=encoded_role_id)
-        assert (group_role["url"] == f"/api/groups/{encoded_group_id}/roles/{encoded_role_id}" or group_role["url"] == "*deprecated attribute not filled in by FastAPI server*")
 
     def test_update_only_admin(self):
         encoded_group_id = "any-group-id"

From e05aaa99f32df3c92da11f5110ef803c614852f2 Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Thu, 12 Aug 2021 18:53:44 +0200
Subject: [PATCH 194/218] Add type hints to other functions for consistency

---
 lib/galaxy/managers/group_roles.py           | 6 +++---
 lib/galaxy/webapps/galaxy/api/group_roles.py | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/managers/group_roles.py b/lib/galaxy/managers/group_roles.py
index 0ec67583641..6ac4c2163b0 100644
--- a/lib/galaxy/managers/group_roles.py
+++ b/lib/galaxy/managers/group_roles.py
@@ -35,7 +35,7 @@ class GroupRolesManager:
             rval.append(group_role)
         return GroupRoleListModel(__root__=rval)
 
-    def show(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, group_id: EncodedDatabaseIdField):
+    def show(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, group_id: EncodedDatabaseIdField) -> GroupRoleModel:
         """
         Returns information about a group role.
         """
@@ -48,7 +48,7 @@ class GroupRolesManager:
 
         return self._serialize_group_role(group_id, role)
 
-    def update(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, group_id: EncodedDatabaseIdField):
+    def update(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, group_id: EncodedDatabaseIdField) -> GroupRoleModel:
         """
         Adds a role to a group if it is not already associated.
         """
@@ -61,7 +61,7 @@ class GroupRolesManager:
 
         return self._serialize_group_role(group_id, role)
 
-    def delete(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, group_id: EncodedDatabaseIdField):
+    def delete(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, group_id: EncodedDatabaseIdField) -> GroupRoleModel:
         """
         Removes a role from a group.
         """
diff --git a/lib/galaxy/webapps/galaxy/api/group_roles.py b/lib/galaxy/webapps/galaxy/api/group_roles.py
index a0ce3592113..291a09ebbc0 100644
--- a/lib/galaxy/webapps/galaxy/api/group_roles.py
+++ b/lib/galaxy/webapps/galaxy/api/group_roles.py
@@ -57,13 +57,13 @@ class FastAPIGroupRoles:
     @router.put('/api/groups/{group_id}/roles/{role_id}',
                 require_admin=True,
                 summary='Adds a role to a group')
-    def update(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam, role_id: EncodedDatabaseIdField = RoleIDParam):
+    def update(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam, role_id: EncodedDatabaseIdField = RoleIDParam) -> GroupRoleModel:
         return self.manager.update(trans, role_id, group_id)
 
     @router.delete('/api/groups/{group_id}/roles/{role_id}',
                    require_admin=True,
                    summary='Removes a role from a group')
-    def delete(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam, role_id: EncodedDatabaseIdField = RoleIDParam):
+    def delete(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam, role_id: EncodedDatabaseIdField = RoleIDParam) -> GroupRoleModel:
         return self.manager.delete(trans, role_id, group_id)
 
 

From 749e280a4520eab223333be98d7d5af47b5e5196 Mon Sep 17 00:00:00 2001
From: Peter van Heusden <pvh@sanbi.ac.za>
Date: Thu, 12 Aug 2021 21:04:42 +0200
Subject: [PATCH 195/218] Remove unused variables

---
 client/src/components/Toolshed/InstalledList/Monitor.vue      | 2 --
 client/src/components/Toolshed/RepositoryDetails/Index.vue    | 1 -
 .../Toolshed/RepositoryDetails/InstallationButton.vue         | 4 ----
 3 files changed, 7 deletions(-)

diff --git a/client/src/components/Toolshed/InstalledList/Monitor.vue b/client/src/components/Toolshed/InstalledList/Monitor.vue
index 0f22d2775ef..8b851ae64bb 100644
--- a/client/src/components/Toolshed/InstalledList/Monitor.vue
+++ b/client/src/components/Toolshed/InstalledList/Monitor.vue
@@ -30,7 +30,6 @@
 <script>
 import Vue from "vue";
 import BootstrapVue from "bootstrap-vue";
-import { getAppRoot } from "onload/loadConfig";
 import { Services } from "../services";
 import InstallationButton from "../RepositoryDetails/InstallationButton";
 
@@ -58,7 +57,6 @@ export default {
         },
     },
     created() {
-        this.root = getAppRoot();
         this.services = new Services();
         this.load();
     },
diff --git a/client/src/components/Toolshed/RepositoryDetails/Index.vue b/client/src/components/Toolshed/RepositoryDetails/Index.vue
index 503dbb0d08f..df38971c330 100644
--- a/client/src/components/Toolshed/RepositoryDetails/Index.vue
+++ b/client/src/components/Toolshed/RepositoryDetails/Index.vue
@@ -30,7 +30,6 @@
                         </template>
                         <template v-slot:cell(actions)="row">
                             <InstallationButton
-                                :installed="row.item.installed"
                                 :status="row.item.status"
                                 @onInstall="setupRepository(row.item)"
                                 @onUninstall="uninstallRepository(row.item)"
diff --git a/client/src/components/Toolshed/RepositoryDetails/InstallationButton.vue b/client/src/components/Toolshed/RepositoryDetails/InstallationButton.vue
index 7a4f7b134b7..ad8de843837 100644
--- a/client/src/components/Toolshed/RepositoryDetails/InstallationButton.vue
+++ b/client/src/components/Toolshed/RepositoryDetails/InstallationButton.vue
@@ -20,10 +20,6 @@ Vue.use(BootstrapVue);
 
 export default {
     props: {
-        installed: {
-            type: Boolean,
-            required: false,
-        },
         status: {
             type: String,
             required: true,

From ed53b05f61aee216c1bf1aea933c9281d6050f8a Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 12 Aug 2021 16:50:18 -0400
Subject: [PATCH 196/218] Fix for empty docker_volumes/singularity_volumes in
 job config

---
 lib/galaxy/tool_util/deps/container_classes.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/lib/galaxy/tool_util/deps/container_classes.py b/lib/galaxy/tool_util/deps/container_classes.py
index e9cc48803ec..29ec8bb7148 100644
--- a/lib/galaxy/tool_util/deps/container_classes.py
+++ b/lib/galaxy/tool_util/deps/container_classes.py
@@ -117,6 +117,10 @@ def preprocess_volumes(volumes_raw_str, container_type):
     ro for Singularity iff no subdirectories are rw (Singularity does not allow ro
     parent directories with rw subdirectories).
 
+    >>> preprocess_volumes(None, DOCKER_CONTAINER_TYPE)
+    []
+    >>> preprocess_volumes("", DOCKER_CONTAINER_TYPE)
+    []
     >>> preprocess_volumes("/a/b", DOCKER_CONTAINER_TYPE)
     ['/a/b:rw']
     >>> preprocess_volumes("/a/b:ro,/a/b/c:rw", DOCKER_CONTAINER_TYPE)
@@ -131,6 +135,9 @@ def preprocess_volumes(volumes_raw_str, container_type):
     ['/a/b', '/a/b/c']
     """
 
+    if not volumes_raw_str:
+        return []
+
     volumes_raw_strs = [v.strip() for v in volumes_raw_str.split(",")]
     volumes = []
     rw_paths = []

From 7f54f9da0cd7b04348830339f4e30af279849634 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 12 Aug 2021 14:03:47 -0400
Subject: [PATCH 197/218] Move page export button to title

---
 client/src/components/Markdown/Markdown.vue | 21 ++++++++++++++++-----
 1 file changed, 16 insertions(+), 5 deletions(-)

diff --git a/client/src/components/Markdown/Markdown.vue b/client/src/components/Markdown/Markdown.vue
index a1e7727f9e8..24b081b19c0 100644
--- a/client/src/components/Markdown/Markdown.vue
+++ b/client/src/components/Markdown/Markdown.vue
@@ -2,10 +2,18 @@
     <div class="markdown-wrapper">
         <LoadingSpan v-if="loading" />
         <div v-else>
-            <a v-if="effectiveExportLink" :href="exportLink" class="markdown-export position-absolute p-3">
-                <i class="fa fa-3x fa-download" />
-            </a>
             <div>
+                <b-button
+                    v-if="effectiveExportLink"
+                    class="float-right"
+                    title="Download PDF"
+                    variant="link"
+                    role="button"
+                    v-b-tooltip.hover.bottom
+                    @click="onDownload"
+                >
+                    <font-awesome-icon icon="download" />
+                </b-button>
                 <b-button
                     v-if="!readOnly"
                     class="float-right"
@@ -97,7 +105,7 @@ import MarkdownIt from "markdown-it";
 import markdownItRegexp from "markdown-it-regexp";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { library } from "@fortawesome/fontawesome-svg-core";
-import { faEdit } from "@fortawesome/free-solid-svg-icons";
+import { faDownload, faEdit } from "@fortawesome/free-solid-svg-icons";
 
 import LoadingSpan from "components/LoadingSpan";
 import HistoryDatasetAsImage from "./Elements/HistoryDatasetAsImage";
@@ -128,7 +136,7 @@ md.use(mdNewline);
 
 Vue.use(BootstrapVue);
 
-library.add(faEdit);
+library.add(faDownload, faEdit);
 
 export default {
     store: store,
@@ -279,6 +287,9 @@ export default {
                 content: content,
             };
         },
+        onDownload() {
+            window.location.href = this.exportLink;
+        },
     },
 };
 </script>

From 9ac8ad07f1f937c60d1878eae8fd818f3d137e04 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 5 Aug 2021 12:00:25 -0400
Subject: [PATCH 198/218] Add collection import button to collection element in
 pages

Add collection import handling to dataset collection display compoenent in pages

Add service handler for markdown elements

Remove debug statement in collection display

Add link hash to import button in collection display

Add dataset type to payload
---
 .../CollectionDisplay.vue                     | 43 ++++++++++++++++++-
 client/src/components/Markdown/services.js    | 19 ++++++++
 2 files changed, 61 insertions(+), 1 deletion(-)
 create mode 100644 client/src/components/Markdown/services.js

diff --git a/client/src/components/Markdown/Elements/HistoryDatasetCollection/CollectionDisplay.vue b/client/src/components/Markdown/Elements/HistoryDatasetCollection/CollectionDisplay.vue
index 1d3b81dff4d..6b69dc66870 100644
--- a/client/src/components/Markdown/Elements/HistoryDatasetCollection/CollectionDisplay.vue
+++ b/client/src/components/Markdown/Elements/HistoryDatasetCollection/CollectionDisplay.vue
@@ -15,6 +15,23 @@
                     >
                         <span class="fa fa-download" />
                     </b-button>
+                    <CurrentUser v-slot="{ user }">
+                        <UserHistories v-if="user" :user="user" v-slot="{ currentHistoryId }">
+                            <b-button
+                                v-if="currentHistoryId"
+                                @click="onCopyCollection(currentHistoryId)"
+                                href="#"
+                                role="button"
+                                variant="link"
+                                title="Import Collection"
+                                type="button"
+                                class="py-0 px-1"
+                                v-b-tooltip.hover
+                            >
+                                <span class="fa fa-file-import" />
+                            </b-button>
+                        </UserHistories>
+                    </CurrentUser>
                 </span>
                 <span>
                     <span>Dataset Collection:</span>
@@ -24,6 +41,9 @@
             <b-card-body>
                 <LoadingSpan v-if="loading" message="Loading Collection" />
                 <div v-else class="content-height">
+                    <b-alert v-if="!!messageText" :variant="messageVariant" show>
+                        {{ messageText }}
+                    </b-alert>
                     <CollectionTree :node="itemContent" :skip-head="true" />
                 </div>
             </b-card-body>
@@ -32,14 +52,20 @@
 </template>
 
 <script>
-import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
+import { getAppRoot } from "onload/loadConfig";
 import CollectionTree from "./CollectionTree";
 import LoadingSpan from "components/LoadingSpan";
+import CurrentUser from "components/providers/CurrentUser";
+import UserHistories from "components/History/providers/UserHistories";
+import { copyCollection } from "components/Markdown/services";
+
 export default {
     components: {
         CollectionTree,
+        CurrentUser,
         LoadingSpan,
+        UserHistories,
     },
     props: {
         args: {
@@ -55,6 +81,8 @@ export default {
         return {
             itemContent: null,
             loading: true,
+            messageText: null,
+            messageVariant: null,
         };
     },
     created() {
@@ -78,6 +106,19 @@ export default {
         },
     },
     methods: {
+        onCopyCollection(currentHistoryId) {
+            const hdcaId = this.args.history_dataset_collection_id;
+            copyCollection(hdcaId, currentHistoryId).then(
+                (response) => {
+                    this.messageVariant = "success";
+                    this.messageText = "Successfully copied to current history.";
+                },
+                (error) => {
+                    this.messageVariant = "danger";
+                    this.messageText = error;
+                }
+            );
+        },
         async getContent() {
             try {
                 const response = await axios.get(this.itemUrl);
diff --git a/client/src/components/Markdown/services.js b/client/src/components/Markdown/services.js
new file mode 100644
index 00000000000..f7c6f36a315
--- /dev/null
+++ b/client/src/components/Markdown/services.js
@@ -0,0 +1,19 @@
+import axios from "axios";
+import { rethrowSimple } from "utils/simple-error";
+import { getAppRoot } from "onload/loadConfig";
+
+export async function copyCollection(hdcaId, historyId) {
+    const url = `${getAppRoot()}api/histories/${historyId}/contents/dataset_collections`;
+    const payload = {
+        source: "hdca",
+        type: "dataset_collection",
+        content: hdcaId,
+        copy_elements: true,
+    };
+    try {
+        const { data } = await axios.post(url, payload);
+        return data;
+    } catch (e) {
+        rethrowSimple(e);
+    }
+}

From 7742e76972e547a7f3cec4940dbb4b01c0bbf774 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 12 Aug 2021 12:49:25 -0400
Subject: [PATCH 199/218] Add upload dialog to global Galaxy object

---
 client/src/app/galaxy.js | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/client/src/app/galaxy.js b/client/src/app/galaxy.js
index 86dd4f59728..4eb46506d29 100644
--- a/client/src/app/galaxy.js
+++ b/client/src/app/galaxy.js
@@ -8,6 +8,7 @@ import addLogging from "utils/add-logging";
 import localize from "utils/localization";
 import { getGalaxyInstance } from "app";
 import { create, dialog } from "utils/data";
+import { openGlobalUploadModal } from "components/upload/mount";
 
 // ============================================================================
 /** Base galaxy client-side application.
@@ -293,6 +294,11 @@ GalaxyApp.prototype.debuggingNamespaces = function _debuggingNamespaces(namespac
     }
 };
 
+/** Open Upload Dialog */
+GalaxyApp.prototype.uploadDialog = function uploadDialog() {
+    openGlobalUploadModal();
+};
+
 /** string rep */
 GalaxyApp.prototype.toString = function toString() {
     const userEmail = this.user ? this.user.get("email") || "(anonymous)" : "uninitialized";

From c8b5c12884eb42cee19ff3dee21e8383ab1418c7 Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Thu, 12 Aug 2021 23:30:23 +0200
Subject: [PATCH 200/218] Add fastapi deprecation message function

---
 lib/galaxy/managers/group_roles.py      | 3 ++-
 lib/galaxy/webapps/galaxy/api/common.py | 4 ++++
 lib/galaxy/webapps/galaxy/api/roles.py  | 3 ++-
 lib/galaxy_test/api/test_group_roles.py | 2 ++
 4 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/managers/group_roles.py b/lib/galaxy/managers/group_roles.py
index 6ac4c2163b0..bef283c9f64 100644
--- a/lib/galaxy/managers/group_roles.py
+++ b/lib/galaxy/managers/group_roles.py
@@ -14,6 +14,7 @@ from galaxy.managers.context import ProvidesAppContext
 from galaxy.schema.fields import EncodedDatabaseIdField
 from galaxy.schema.schema import GroupRoleListModel, GroupRoleModel
 from galaxy.web import url_for
+from galaxy.webapps.galaxy.api.common import fastapi_deprecation_message
 
 log = logging.getLogger(__name__)
 
@@ -108,7 +109,7 @@ class GroupRolesManager:
         try:
             url = url_for('group_role', group_id=encoded_group_id, id=encoded_role_id)
         except AttributeError:
-            url = "*deprecated attribute not filled in by FastAPI server*"
+            url = fastapi_deprecation_message()
 
         return GroupRoleModel(
             id=encoded_role_id,
diff --git a/lib/galaxy/webapps/galaxy/api/common.py b/lib/galaxy/webapps/galaxy/api/common.py
index f8bc267c2c6..dbd889c1f60 100644
--- a/lib/galaxy/webapps/galaxy/api/common.py
+++ b/lib/galaxy/webapps/galaxy/api/common.py
@@ -28,3 +28,7 @@ def parse_serialization_params(
     if keys:
         key_list = keys.split(',')
     return dict(view=view, keys=key_list, default_view=default_view)
+
+
+def fastapi_deprecation_message():
+    return "*deprecated attribute not filled in by FastAPI server*"
diff --git a/lib/galaxy/webapps/galaxy/api/roles.py b/lib/galaxy/webapps/galaxy/api/roles.py
index 210d96a0ae7..d427cc5f5f8 100644
--- a/lib/galaxy/webapps/galaxy/api/roles.py
+++ b/lib/galaxy/webapps/galaxy/api/roles.py
@@ -19,6 +19,7 @@ from galaxy.schema.schema import (
     RoleModel,
 )
 from galaxy.webapps.base.controller import url_for
+from galaxy.webapps.galaxy.api.common import fastapi_deprecation_message
 from . import (
     BaseGalaxyAPIController,
     depends,
@@ -40,7 +41,7 @@ def role_to_model(trans, role):
     try:
         item['url'] = url_for('role', id=role_id)
     except AttributeError:
-        item['url'] = "*deprecated attribute not filled in by FastAPI server*"
+        item['url'] = fastapi_deprecation_message()
     return RoleModel(**item)
 
 
diff --git a/lib/galaxy_test/api/test_group_roles.py b/lib/galaxy_test/api/test_group_roles.py
index bec1c7e08a4..aa56df78ddd 100644
--- a/lib/galaxy_test/api/test_group_roles.py
+++ b/lib/galaxy_test/api/test_group_roles.py
@@ -1,5 +1,6 @@
 from typing import List
 
+from galaxy.webapps.galaxy.api.common import fastapi_deprecation_message
 from galaxy_test.base.populators import DatasetPopulator
 from ._framework import ApiTestCase
 
@@ -67,6 +68,7 @@ class GroupRolesApiTestCase(ApiTestCase):
         self._assert_status_code_is_ok(update_response)
         group_role = update_response.json()
         self._assert_valid_group_role(group_role, assert_id=encoded_role_id)
+        assert (group_role["url"] == f"/api/groups/{encoded_group_id}/roles/{encoded_role_id}" or group_role["url"] == fastapi_deprecation_message())
 
     def test_update_only_admin(self):
         encoded_group_id = "any-group-id"

From fe8366e6cbf36083b86556e6342effdf76bf9d39 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 13 Aug 2021 11:05:33 -0400
Subject: [PATCH 201/218] Fix component case-sensitivity; import from primary
 interface instead of mount

---
 client/src/app/galaxy.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/app/galaxy.js b/client/src/app/galaxy.js
index 4eb46506d29..e8cc2c67ce7 100644
--- a/client/src/app/galaxy.js
+++ b/client/src/app/galaxy.js
@@ -8,7 +8,7 @@ import addLogging from "utils/add-logging";
 import localize from "utils/localization";
 import { getGalaxyInstance } from "app";
 import { create, dialog } from "utils/data";
-import { openGlobalUploadModal } from "components/upload/mount";
+import { openGlobalUploadModal } from "components/Upload";
 
 // ============================================================================
 /** Base galaxy client-side application.

From 7c9c7f830536a0d15e5c8036618379d461743fa0 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Fri, 13 Aug 2021 14:24:16 -0400
Subject: [PATCH 202/218] Rename containers_resolvers_config_file to
 container_resolvers_config_file

---
 doc/source/admin/galaxy_options.rst                    | 10 +++++-----
 lib/galaxy/config/__init__.py                          | 10 ++++++----
 .../config/sample/container_resolvers_conf.xml.sample  |  4 ++--
 lib/galaxy/config/sample/galaxy.yml.sample             |  8 ++++----
 lib/galaxy/tool_util/deps/containers.py                |  8 ++++----
 lib/galaxy/tool_util/deps/dependencies.py              |  4 ++--
 lib/galaxy/webapps/galaxy/config_schema.yml            |  6 +++---
 7 files changed, 26 insertions(+), 24 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index ba2ba87389a..55c452e3e78 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -679,14 +679,14 @@
 :Type: bool
 
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``containers_resolvers_config_file``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``container_resolvers_config_file``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 :Description:
     Container resolvers configuration (beta). Set up a file describing
     container resolvers to use when discovering containers for Galaxy.
-    If this is set to None, the default containers loaded is
+    If this is set to None, the default container resolvers loaded is
     determined by enable_mulled_containers.
 :Default: ``None``
 :Type: str
@@ -4449,7 +4449,7 @@
     filtering
     (https://galaxyproject.org/user-defined-toolbox-filters/)
     functions.
-:Default: ``galaxy.tools.filters,galaxy.tools.toolbox.filters``
+:Default: ``galaxy.tools.filters,galaxy.tools.toolbox.filters,galaxy.tool_util.toolbox.filters``
 :Type: str
 
 
diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 0eb7403b1ae..a49c3e32f9a 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -491,13 +491,15 @@ class CommonConfigurationMixin:
 
 class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
     deprecated_options = ('database_file', 'track_jobs_in_database', 'blacklist_file', 'whitelist_file',
-                          'sanitize_whitelist_file', 'user_library_import_symlink_whitelist', 'fetch_url_whitelist')
+                          'sanitize_whitelist_file', 'user_library_import_symlink_whitelist', 'fetch_url_whitelist',
+                          'containers_resolvers_config_file')
     renamed_options = {
         'blacklist_file': 'email_domain_blocklist_file',
         'whitelist_file': 'email_domain_allowlist_file',
         'sanitize_whitelist_file': 'sanitize_allowlist_file',
         'user_library_import_symlink_whitelist': 'user_library_import_symlink_allowlist',
         'fetch_url_whitelist': 'fetch_url_allowlist',
+        'containers_resolvers_config_file': 'container_resolvers_config_file',
     }
     default_config_file_name = 'galaxy.yml'
     deprecated_dirs = {'config_dir': 'config', 'data_dir': 'database'}
@@ -728,8 +730,8 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
             # self, populate config_dict
             self.config_dict["conda_mapping_files"] = [self.local_conda_mapping_file, _default_mapping]
 
-        if self.containers_resolvers_config_file:
-            self.containers_resolvers_config_file = self._in_config_dir(self.containers_resolvers_config_file)
+        if self.container_resolvers_config_file:
+            self.container_resolvers_config_file = self._in_config_dir(self.container_resolvers_config_file)
 
         # tool_dependency_dir can be "none" (in old configs). If so, set it to None
         if self.tool_dependency_dir and self.tool_dependency_dir.lower() == 'none':
@@ -1175,7 +1177,7 @@ class ConfiguresGalaxyMixin:
             container_image_cache_path=self.config.container_image_cache_path,
             library_import_dir=self.config.library_import_dir,
             enable_mulled_containers=self.config.enable_mulled_containers,
-            containers_resolvers_config_file=self.config.containers_resolvers_config_file,
+            container_resolvers_config_file=self.config.container_resolvers_config_file,
             involucro_path=self.config.involucro_path,
             involucro_auto_init=self.config.involucro_auto_init,
             mulled_channels=self.config.mulled_channels,
diff --git a/lib/galaxy/config/sample/container_resolvers_conf.xml.sample b/lib/galaxy/config/sample/container_resolvers_conf.xml.sample
index 78051d5cb64..ce59312b097 100644
--- a/lib/galaxy/config/sample/container_resolvers_conf.xml.sample
+++ b/lib/galaxy/config/sample/container_resolvers_conf.xml.sample
@@ -1,4 +1,4 @@
-<containers_resolvers>
+<container_resolvers>
   <explicit />
   <!-- explicit: resolves container URI for a job through explict container
        tags in the tool XML wrapper. -->
@@ -63,4 +63,4 @@
   <!-- Specify a fallback container for tools/jobs that don't match the above
        resolvers. -->
 
-</containers_resolvers>
+</container_resolvers>
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 1184e78bfa4..89924ec739b 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -438,9 +438,9 @@ galaxy:
 
   # Container resolvers configuration (beta). Set up a file describing
   # container resolvers to use when discovering containers for Galaxy.
-  # If this is set to None, the default containers loaded is determined
-  # by enable_mulled_containers.
-  #containers_resolvers_config_file: null
+  # If this is set to None, the default container resolvers loaded is
+  # determined by enable_mulled_containers.
+  #container_resolvers_config_file: null
 
   # involucro is a tool used to build Docker or Singularity containers
   # for tools from Conda dependencies referenced in tools as
@@ -2188,7 +2188,7 @@ galaxy:
   # The base module(s) that are searched for modules for toolbox
   # filtering (https://galaxyproject.org/user-defined-toolbox-filters/)
   # functions.
-  #toolbox_filter_base_modules: galaxy.tools.filters,galaxy.tools.toolbox.filters
+  #toolbox_filter_base_modules: galaxy.tools.filters,galaxy.tools.toolbox.filters,galaxy.tool_util.toolbox.filters
 
   # Galaxy uses AMQP internally for communicating between processes.
   # For example, when reloading the toolbox or locking job execution,
diff --git a/lib/galaxy/tool_util/deps/containers.py b/lib/galaxy/tool_util/deps/containers.py
index af49c501556..5bd43e4b453 100644
--- a/lib/galaxy/tool_util/deps/containers.py
+++ b/lib/galaxy/tool_util/deps/containers.py
@@ -194,12 +194,12 @@ class ContainerRegistry:
         self.mulled_resolution_cache = mulled_resolution_cache
 
     def __build_container_resolvers(self, app_info):
-        conf_file = getattr(app_info, 'containers_resolvers_config_file', None)
+        conf_file = getattr(app_info, 'container_resolvers_config_file', None)
         if not conf_file:
-            return self.__default_containers_resolvers()
+            return self.__default_container_resolvers()
         if not os.path.exists(conf_file):
             log.debug("Unable to find config file '%s'", conf_file)
-            return self.__default_containers_resolvers()
+            return self.__default_container_resolvers()
         plugin_source = plugin_config.plugin_source_from_path(conf_file)
         return self._parse_resolver_conf(plugin_source)
 
@@ -209,7 +209,7 @@ class ContainerRegistry:
         }
         return plugin_config.load_plugins(self.resolver_classes, plugin_source, extra_kwds)
 
-    def __default_containers_resolvers(self):
+    def __default_container_resolvers(self):
         default_resolvers = [
             ExplicitContainerResolver(self.app_info),
             ExplicitSingularityContainerResolver(self.app_info),
diff --git a/lib/galaxy/tool_util/deps/dependencies.py b/lib/galaxy/tool_util/deps/dependencies.py
index 760eac66239..8d513d01cf1 100644
--- a/lib/galaxy/tool_util/deps/dependencies.py
+++ b/lib/galaxy/tool_util/deps/dependencies.py
@@ -15,7 +15,7 @@ class AppInfo:
         container_image_cache_path=None,
         library_import_dir=None,
         enable_mulled_containers=False,
-        containers_resolvers_config_file=None,
+        container_resolvers_config_file=None,
         involucro_path=None,
         involucro_auto_init=True,
         mulled_channels=DEFAULT_CHANNELS,
@@ -29,7 +29,7 @@ class AppInfo:
         self.container_image_cache_path = container_image_cache_path
         self.library_import_dir = library_import_dir
         self.enable_mulled_containers = enable_mulled_containers
-        self.containers_resolvers_config_file = containers_resolvers_config_file
+        self.container_resolvers_config_file = container_resolvers_config_file
         self.involucro_path = involucro_path
         self.involucro_auto_init = involucro_auto_init
         self.mulled_channels = mulled_channels
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index be85ddc24ef..ec6f109fa19 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -504,14 +504,14 @@ mapping:
           Container availability will vary by tool, this option will only be used
           for job destinations with Docker or Singularity enabled.
 
-      containers_resolvers_config_file:
+      container_resolvers_config_file:
         type: str
         required: false
         desc: |
           Container resolvers configuration (beta). Set up a file describing
           container resolvers to use when discovering containers for Galaxy. If
-          this is set to None, the default containers loaded is determined by
-          enable_mulled_containers.
+          this is set to None, the default container resolvers loaded is
+          determined by enable_mulled_containers.
 
       involucro_path:
         type: str

From 0d3ef9d060e86f38db85675c9502662fe8f45460 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Fri, 13 Aug 2021 14:55:23 -0400
Subject: [PATCH 203/218] Update tests for config option rename

---
 test/integration/test_config_defaults.py    | 2 +-
 test/integration/test_containerized_jobs.py | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/test/integration/test_config_defaults.py b/test/integration/test_config_defaults.py
index 343029b941a..bf91badb288 100644
--- a/test/integration/test_config_defaults.py
+++ b/test/integration/test_config_defaults.py
@@ -54,7 +54,7 @@ PATH_CONFIG_PROPERTIES = [
     'citation_cache_data_dir',
     'citation_cache_lock_dir',
     'cluster_files_directory',
-    'containers_resolvers_config_file',
+    'container_resolvers_config_file',
     'data_manager_config_file',
     'datatypes_config_file',
     'dependency_resolvers_config_file',
diff --git a/test/integration/test_containerized_jobs.py b/test/integration/test_containerized_jobs.py
index 3ee0a3dbcd6..d7abc533f56 100644
--- a/test/integration/test_containerized_jobs.py
+++ b/test/integration/test_containerized_jobs.py
@@ -155,8 +155,8 @@ class MappingContainerResolverTestCase(integration_util.IntegrationTestCase):
         config["jobs_directory"] = cls.jobs_directory
         config["job_config_file"] = cls.job_config_file
         disable_dependency_resolution(config)
-        containers_resolvers_config_path = os.path.join(cls.jobs_directory, "container_resolvers.yml")
-        with open(containers_resolvers_config_path, "w") as f:
+        container_resolvers_config_path = os.path.join(cls.jobs_directory, "container_resolvers.yml")
+        with open(container_resolvers_config_path, "w") as f:
             f.write("""
 - type: mapping
   mappings:
@@ -164,7 +164,7 @@ class MappingContainerResolverTestCase(integration_util.IntegrationTestCase):
       tool_id: mulled_example_broken_no_requirements
       identifier: 'quay.io/biocontainers/bwa:0.7.15--0'
 """)
-        config["containers_resolvers_config_file"] = containers_resolvers_config_path
+        config["container_resolvers_config_file"] = container_resolvers_config_path
 
     @classmethod
     def setUpClass(cls):

From db6944523f4cbdb6e28b2567c37959741d82020b Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Fri, 13 Aug 2021 15:23:30 -0400
Subject: [PATCH 204/218] Support setting container resolvers directly in the
 app config

---
 doc/source/admin/galaxy_options.rst         | 16 ++++++++++++++++
 lib/galaxy/config/__init__.py               |  1 +
 lib/galaxy/config/sample/galaxy.yml.sample  |  9 +++++++++
 lib/galaxy/tool_util/deps/containers.py     | 20 +++++++++++++-------
 lib/galaxy/tool_util/deps/dependencies.py   |  2 ++
 lib/galaxy/webapps/galaxy/config_schema.yml | 14 ++++++++++++++
 test/integration/test_containerized_jobs.py | 19 +++++++++++++++++++
 7 files changed, 74 insertions(+), 7 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 55c452e3e78..70c10644e8a 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -692,6 +692,22 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~~
+``container_resolvers``
+~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Rather than specifying a container_resolvers_config_file, the
+    definition of the resolvers to enable can be embedded into
+    Galaxy's config with this option. This has no effect if a
+    container_resolvers_config_file is used.
+    The syntax, available resolvers, and documentation of their
+    options is explained in detail in the documentation:
+    https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html
+:Default: ``None``
+:Type: seq
+
+
 ~~~~~~~~~~~~~~~~~~
 ``involucro_path``
 ~~~~~~~~~~~~~~~~~~
diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index a49c3e32f9a..216379255e1 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -1178,6 +1178,7 @@ class ConfiguresGalaxyMixin:
             library_import_dir=self.config.library_import_dir,
             enable_mulled_containers=self.config.enable_mulled_containers,
             container_resolvers_config_file=self.config.container_resolvers_config_file,
+            container_resolvers_config_dict=self.config.container_resolvers,
             involucro_path=self.config.involucro_path,
             involucro_auto_init=self.config.involucro_auto_init,
             mulled_channels=self.config.mulled_channels,
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 89924ec739b..59df1a5a4ae 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -442,6 +442,15 @@ galaxy:
   # determined by enable_mulled_containers.
   #container_resolvers_config_file: null
 
+  # Rather than specifying a container_resolvers_config_file, the
+  # definition of the resolvers to enable can be embedded into Galaxy's
+  # config with this option. This has no effect if a
+  # container_resolvers_config_file is used.
+  # The syntax, available resolvers, and documentation of their options
+  # is explained in detail in the documentation:
+  # https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html
+  #container_resolvers: null
+
   # involucro is a tool used to build Docker or Singularity containers
   # for tools from Conda dependencies referenced in tools as
   # `requirement` s. The following path is the location of involucro on
diff --git a/lib/galaxy/tool_util/deps/containers.py b/lib/galaxy/tool_util/deps/containers.py
index 5bd43e4b453..30dc9456607 100644
--- a/lib/galaxy/tool_util/deps/containers.py
+++ b/lib/galaxy/tool_util/deps/containers.py
@@ -195,13 +195,19 @@ class ContainerRegistry:
 
     def __build_container_resolvers(self, app_info):
         conf_file = getattr(app_info, 'container_resolvers_config_file', None)
-        if not conf_file:
-            return self.__default_container_resolvers()
-        if not os.path.exists(conf_file):
-            log.debug("Unable to find config file '%s'", conf_file)
-            return self.__default_container_resolvers()
-        plugin_source = plugin_config.plugin_source_from_path(conf_file)
-        return self._parse_resolver_conf(plugin_source)
+        conf_dict = getattr(app_info, 'container_resolvers_config_dict', None)
+        plugin_source = None
+        if conf_file and not os.path.exists(conf_file):
+            log.warning(f"Unable to find config file '{conf_file}'")
+        elif conf_file:
+            log.debug("Loading container resolution config from file '{conf_file}'")
+            plugin_source = plugin_config.plugin_source_from_path(conf_file)
+        elif conf_dict:
+            log.debug("Loading container resolution config inline from Galaxy configuration file")
+            plugin_source = plugin_config.plugin_source_from_dict(conf_dict)
+        if plugin_source:
+            return self._parse_resolver_conf(plugin_source)
+        return self.__default_container_resolvers()
 
     def _parse_resolver_conf(self, plugin_source):
         extra_kwds = {
diff --git a/lib/galaxy/tool_util/deps/dependencies.py b/lib/galaxy/tool_util/deps/dependencies.py
index 8d513d01cf1..ec22c43afe1 100644
--- a/lib/galaxy/tool_util/deps/dependencies.py
+++ b/lib/galaxy/tool_util/deps/dependencies.py
@@ -16,6 +16,7 @@ class AppInfo:
         library_import_dir=None,
         enable_mulled_containers=False,
         container_resolvers_config_file=None,
+        container_resolvers_config_dict=None,
         involucro_path=None,
         involucro_auto_init=True,
         mulled_channels=DEFAULT_CHANNELS,
@@ -30,6 +31,7 @@ class AppInfo:
         self.library_import_dir = library_import_dir
         self.enable_mulled_containers = enable_mulled_containers
         self.container_resolvers_config_file = container_resolvers_config_file
+        self.container_resolvers_config_dict = container_resolvers_config_dict
         self.involucro_path = involucro_path
         self.involucro_auto_init = involucro_auto_init
         self.mulled_channels = mulled_channels
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index ec6f109fa19..a26c08487eb 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -513,6 +513,20 @@ mapping:
           this is set to None, the default container resolvers loaded is
           determined by enable_mulled_containers.
 
+      container_resolvers:
+        type: seq
+        sequence:
+          - type: any
+        desc: |
+          Rather than specifying a container_resolvers_config_file, the definition of the
+          resolvers to enable can be embedded into Galaxy's config with this option.
+          This has no effect if a container_resolvers_config_file is used.
+
+          The syntax, available resolvers, and documentation of their options is explained in detail in the
+          documentation:
+
+          https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html
+
       involucro_path:
         type: str
         default: involucro
diff --git a/test/integration/test_containerized_jobs.py b/test/integration/test_containerized_jobs.py
index d7abc533f56..3887650cf55 100644
--- a/test/integration/test_containerized_jobs.py
+++ b/test/integration/test_containerized_jobs.py
@@ -183,6 +183,25 @@ class MappingContainerResolverTestCase(integration_util.IntegrationTestCase):
         assert "0.7.15-r1140" in output
 
 
+class InlineContainerConfigurationTestCase(MappingContainerResolverTestCase):
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        cls.jobs_directory = cls._test_driver.mkdtemp()
+        config["jobs_directory"] = cls.jobs_directory
+        config["job_config_file"] = cls.job_config_file
+        disable_dependency_resolution(config)
+        container_resolvers_config = [{
+            'type': 'mapping',
+            'mappings': [{
+                'container_type': 'docker',
+                'tool_id': 'mulled_example_broken_no_requirements',
+                'identifier': 'quay.io/biocontainers/bwa:0.7.15--0',
+            }],
+        }]
+        config["container_resolvers"] = container_resolvers_config
+
+
 # Singularity 2.4 in the official Vagrant issue has some problems running this test
 # case by default because subdirectories of /tmp don't bind correctly. Overridding
 # TMPDIR can fix this.

From 509e61998ec184b0e7f45826ebbe260fd671b1c9 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 16 Aug 2021 15:17:33 -0400
Subject: [PATCH 205/218] Swap globalUpload function to bundleEntries, as is
 more appropriate for externally exposed functionality

---
 client/src/app/galaxy.js    | 6 ------
 client/src/bundleEntries.js | 1 +
 2 files changed, 1 insertion(+), 6 deletions(-)

diff --git a/client/src/app/galaxy.js b/client/src/app/galaxy.js
index e8cc2c67ce7..86dd4f59728 100644
--- a/client/src/app/galaxy.js
+++ b/client/src/app/galaxy.js
@@ -8,7 +8,6 @@ import addLogging from "utils/add-logging";
 import localize from "utils/localization";
 import { getGalaxyInstance } from "app";
 import { create, dialog } from "utils/data";
-import { openGlobalUploadModal } from "components/Upload";
 
 // ============================================================================
 /** Base galaxy client-side application.
@@ -294,11 +293,6 @@ GalaxyApp.prototype.debuggingNamespaces = function _debuggingNamespaces(namespac
     }
 };
 
-/** Open Upload Dialog */
-GalaxyApp.prototype.uploadDialog = function uploadDialog() {
-    openGlobalUploadModal();
-};
-
 /** string rep */
 GalaxyApp.prototype.toString = function toString() {
     const userEmail = this.user ? this.user.get("email") || "(anonymous)" : "uninitialized";
diff --git a/client/src/bundleEntries.js b/client/src/bundleEntries.js
index a4bfdcd9dcd..824504c7b43 100644
--- a/client/src/bundleEntries.js
+++ b/client/src/bundleEntries.js
@@ -32,6 +32,7 @@ export { default as LegacyGridView } from "legacy/grid/grid-view";
 export { create_chart, create_histogram } from "reports/run_stats";
 export { default as ToolshedGroups } from "toolshed/toolshed.groups";
 export { default as IES } from "galaxy.interactive_environments";
+export { openGlobalUploadModal } from "components/Upload";
 
 export { Toast } from "ui/toast"; // TODO: remove when external consumers are updated/gone (IES right now)
 

From e3a0fe543b91177593165ec44d3e1a3cbe8fa9a7 Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Mon, 16 Aug 2021 22:46:57 +0200
Subject: [PATCH 206/218] Move API related code to api/group_roles.py

---
 lib/galaxy/managers/group_roles.py           | 39 +++++---------------
 lib/galaxy/webapps/galaxy/api/group_roles.py | 29 +++++++++++++--
 lib/galaxy_test/api/test_group_roles.py      |  3 +-
 3 files changed, 35 insertions(+), 36 deletions(-)

diff --git a/lib/galaxy/managers/group_roles.py b/lib/galaxy/managers/group_roles.py
index bef283c9f64..e6a484c26e9 100644
--- a/lib/galaxy/managers/group_roles.py
+++ b/lib/galaxy/managers/group_roles.py
@@ -12,9 +12,6 @@ from galaxy.exceptions import (
 from galaxy.managers.base import decode_id
 from galaxy.managers.context import ProvidesAppContext
 from galaxy.schema.fields import EncodedDatabaseIdField
-from galaxy.schema.schema import GroupRoleListModel, GroupRoleModel
-from galaxy.web import url_for
-from galaxy.webapps.galaxy.api.common import fastapi_deprecation_message
 
 log = logging.getLogger(__name__)
 
@@ -25,18 +22,14 @@ class GroupRolesManager:
     def __init__(self, app: MinimalManagerApp) -> None:
         self._app = app
 
-    def index(self, trans: ProvidesAppContext, group_id: EncodedDatabaseIdField) -> GroupRoleListModel:
+    def index(self, trans: ProvidesAppContext, group_id: EncodedDatabaseIdField):
         """
         Returns a collection roles associated with the given group.
         """
         group = self._get_group(trans, group_id)
-        rval = []
-        for gra in group.roles:
-            group_role = self._serialize_group_role(group_id, gra.role)
-            rval.append(group_role)
-        return GroupRoleListModel(__root__=rval)
+        return group.roles
 
-    def show(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, group_id: EncodedDatabaseIdField) -> GroupRoleModel:
+    def show(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, group_id: EncodedDatabaseIdField):
         """
         Returns information about a group role.
         """
@@ -46,10 +39,10 @@ class GroupRolesManager:
         group_role = self._get_group_role(trans, group, role)
         if group_role is None:
             raise ObjectNotFound(f"Role {role.name} not in group {group.name}")
+        return role
+        # return self._serialize_group_role(group_id, role)
 
-        return self._serialize_group_role(group_id, role)
-
-    def update(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, group_id: EncodedDatabaseIdField) -> GroupRoleModel:
+    def update(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, group_id: EncodedDatabaseIdField):
         """
         Adds a role to a group if it is not already associated.
         """
@@ -59,10 +52,9 @@ class GroupRolesManager:
         group_role = self._get_group_role(trans, group, role)
         if group_role is None:
             self._add_role_to_group(trans, group, role)
+        return role
 
-        return self._serialize_group_role(group_id, role)
-
-    def delete(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, group_id: EncodedDatabaseIdField) -> GroupRoleModel:
+    def delete(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, group_id: EncodedDatabaseIdField):
         """
         Removes a role from a group.
         """
@@ -73,7 +65,7 @@ class GroupRolesManager:
         if group_role is None:
             raise ObjectNotFound(f"Role {role.name} not in group {group.name}")
         self._remove_role_from_group(trans, group_role)
-        return self._serialize_group_role(group_id, role)
+        return role
 
     def _get_group(self, trans: ProvidesAppContext, encoded_group_id: EncodedDatabaseIdField) -> Any:
         decoded_group_id = decode_id(self._app, encoded_group_id)
@@ -103,16 +95,3 @@ class GroupRolesManager:
     def _remove_role_from_group(self, trans: ProvidesAppContext, group_role: model.GroupRoleAssociation):
         trans.sa_session.delete(group_role)
         trans.sa_session.flush()
-
-    def _serialize_group_role(self, encoded_group_id: EncodedDatabaseIdField, role: model.Role):
-        encoded_role_id = self._app.security.encode_id(role.id)
-        try:
-            url = url_for('group_role', group_id=encoded_group_id, id=encoded_role_id)
-        except AttributeError:
-            url = fastapi_deprecation_message()
-
-        return GroupRoleModel(
-            id=encoded_role_id,
-            name=role.name,
-            url=url
-        )
diff --git a/lib/galaxy/webapps/galaxy/api/group_roles.py b/lib/galaxy/webapps/galaxy/api/group_roles.py
index 291a09ebbc0..ad5bfe086f3 100644
--- a/lib/galaxy/webapps/galaxy/api/group_roles.py
+++ b/lib/galaxy/webapps/galaxy/api/group_roles.py
@@ -1,9 +1,11 @@
 """
 API operations on Group objects.
 """
+
 import logging
 
 from fastapi import Path
+from routes.util import url_for
 
 from galaxy.managers.context import ProvidesAppContext
 from galaxy.managers.group_roles import GroupRolesManager
@@ -13,6 +15,7 @@ from galaxy.web import (
     expose_api,
     require_admin,
 )
+from galaxy.webapps.galaxy.api.common import fastapi_deprecation_message
 from . import (
     BaseGalaxyAPIController,
     depends,
@@ -38,6 +41,20 @@ RoleIDParam: EncodedDatabaseIdField = Path(
 )
 
 
+def group_role_to_model(trans, encoded_group_id, role):
+    encoded_role_id = trans.security.encode_id(role.id)
+    try:
+        url = url_for('group_role', group_id=encoded_group_id, id=encoded_role_id)
+    except AttributeError:
+        url = fastapi_deprecation_message()
+
+    return GroupRoleModel(
+        id=encoded_role_id,
+        name=role.name,
+        url=url
+    )
+
+
 @router.cbv
 class FastAPIGroupRoles:
     manager: GroupRolesManager = depends(GroupRolesManager)
@@ -46,25 +63,29 @@ class FastAPIGroupRoles:
                 require_admin=True,
                 summary='Displays a collection (list) of groups.')
     def index(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam) -> GroupRoleListModel:
-        return self.manager.index(trans, group_id)
+        group_roles = self.manager.index(trans, group_id)
+        return GroupRoleListModel(__root__=[group_role_to_model(trans, group_id, gr.role) for gr in group_roles])
 
     @router.get('/api/groups/{group_id}/roles/{role_id}',
                 require_admin=True,
                 summary='Displays information about a group role.')
     def show(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam, role_id: EncodedDatabaseIdField = RoleIDParam) -> GroupRoleModel:
-        return self.manager.show(trans, role_id, group_id)
+        role = self.manager.show(trans, role_id, group_id)
+        return group_role_to_model(trans, group_id, role)
 
     @router.put('/api/groups/{group_id}/roles/{role_id}',
                 require_admin=True,
                 summary='Adds a role to a group')
     def update(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam, role_id: EncodedDatabaseIdField = RoleIDParam) -> GroupRoleModel:
-        return self.manager.update(trans, role_id, group_id)
+        role = self.manager.update(trans, role_id, group_id)
+        return group_role_to_model(trans, group_id, role)
 
     @router.delete('/api/groups/{group_id}/roles/{role_id}',
                    require_admin=True,
                    summary='Removes a role from a group')
     def delete(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam, role_id: EncodedDatabaseIdField = RoleIDParam) -> GroupRoleModel:
-        return self.manager.delete(trans, role_id, group_id)
+        role = self.manager.delete(trans, role_id, group_id)
+        return group_role_to_model(trans, group_id, role)
 
 
 class GroupRolesAPIController(BaseGalaxyAPIController):
diff --git a/lib/galaxy_test/api/test_group_roles.py b/lib/galaxy_test/api/test_group_roles.py
index aa56df78ddd..d445a900f79 100644
--- a/lib/galaxy_test/api/test_group_roles.py
+++ b/lib/galaxy_test/api/test_group_roles.py
@@ -1,6 +1,5 @@
 from typing import List
 
-from galaxy.webapps.galaxy.api.common import fastapi_deprecation_message
 from galaxy_test.base.populators import DatasetPopulator
 from ._framework import ApiTestCase
 
@@ -68,7 +67,7 @@ class GroupRolesApiTestCase(ApiTestCase):
         self._assert_status_code_is_ok(update_response)
         group_role = update_response.json()
         self._assert_valid_group_role(group_role, assert_id=encoded_role_id)
-        assert (group_role["url"] == f"/api/groups/{encoded_group_id}/roles/{encoded_role_id}" or group_role["url"] == fastapi_deprecation_message())
+        assert (group_role["url"] == f"/api/groups/{encoded_group_id}/roles/{encoded_role_id}" or group_role["url"] == "*deprecated attribute not filled in by FastAPI server*")
 
     def test_update_only_admin(self):
         encoded_group_id = "any-group-id"

From ae38fb79572d591ee0db06d7e764f0502393f50c Mon Sep 17 00:00:00 2001
From: Mason Houtz <nerdinacan@gmail.com>
Date: Mon, 16 Aug 2021 17:55:43 -0700
Subject: [PATCH 207/218] persist expanded items in session between page loads

---
 .../History/providers/ExpandedItems.js        | 19 ++++++++++++++
 .../components/History/providers/setCache.js  | 25 +++++++++++++++++++
 2 files changed, 44 insertions(+)
 create mode 100644 client/src/components/History/providers/setCache.js

diff --git a/client/src/components/History/providers/ExpandedItems.js b/client/src/components/History/providers/ExpandedItems.js
index a281794ef35..05c4fdc3452 100644
--- a/client/src/components/History/providers/ExpandedItems.js
+++ b/client/src/components/History/providers/ExpandedItems.js
@@ -1,3 +1,5 @@
+import { saveSet, loadSet } from "./setCache";
+
 export default {
     props: {
         scopeKey: { type: String, required: true },
@@ -8,6 +10,11 @@ export default {
             items: new Set(),
         };
     },
+    computed: {
+        expandedCount() {
+            return this.items.size;
+        },
+    },
     methods: {
         isExpanded(item) {
             const key = this.getItemKey(item);
@@ -29,11 +36,23 @@ export default {
                 this.reset();
             }
         },
+        items(newSet) {
+            saveSet(this.key, newSet);
+        },
+    },
+    created() {
+        this.key = "expanded-history-items";
+        const cachedSet = loadSet(this.key);
+        if (cachedSet) {
+            this.items = cachedSet;
+        }
     },
     render() {
         return this.$scopedSlots.default({
             isExpanded: this.isExpanded,
             setExpanded: this.setExpanded,
+            collapseAll: this.reset,
+            expandedCount: this.expandedCount,
         });
     },
 };
diff --git a/client/src/components/History/providers/setCache.js b/client/src/components/History/providers/setCache.js
new file mode 100644
index 00000000000..90d9bbe5b40
--- /dev/null
+++ b/client/src/components/History/providers/setCache.js
@@ -0,0 +1,25 @@
+// Caches expanded/selected Sets in sessionStorage
+// Putting this in separate file for ease of mocking
+
+export function saveSet(key, setObject) {
+    try {
+        const setToArray = Array.from(setObject);
+        const json = JSON.stringify(setToArray);
+        sessionStorage.setItem(key, json);
+    } catch (err) {
+        console.log("error saving stuff to cache", err);
+        sessionStorage.removeItem(key);
+    }
+}
+
+export function loadSet(key) {
+    try {
+        const arrJson = sessionStorage.getItem(key) || [];
+        const cachedArray = JSON.parse(arrJson);
+        return Array.isArray(cachedArray) ? new Set(cachedArray) : new Set();
+    } catch (err) {
+        console.log("erorr loading cached list", err);
+        sessionStorage.removeItem(key);
+        return null;
+    }
+}

From e37e8842e45f431bd2cb9857923842bc6b8868d4 Mon Sep 17 00:00:00 2001
From: Mason Houtz <nerdinacan@gmail.com>
Date: Mon, 16 Aug 2021 18:03:24 -0700
Subject: [PATCH 208/218] lint, cleanup

---
 client/src/components/History/providers/setCache.js | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/client/src/components/History/providers/setCache.js b/client/src/components/History/providers/setCache.js
index 90d9bbe5b40..94c3225f40b 100644
--- a/client/src/components/History/providers/setCache.js
+++ b/client/src/components/History/providers/setCache.js
@@ -1,5 +1,4 @@
 // Caches expanded/selected Sets in sessionStorage
-// Putting this in separate file for ease of mocking
 
 export function saveSet(key, setObject) {
     try {
@@ -7,7 +6,7 @@ export function saveSet(key, setObject) {
         const json = JSON.stringify(setToArray);
         sessionStorage.setItem(key, json);
     } catch (err) {
-        console.log("error saving stuff to cache", err);
+        console.warn("Error saving set to cache", key, err);
         sessionStorage.removeItem(key);
     }
 }
@@ -18,7 +17,7 @@ export function loadSet(key) {
         const cachedArray = JSON.parse(arrJson);
         return Array.isArray(cachedArray) ? new Set(cachedArray) : new Set();
     } catch (err) {
-        console.log("erorr loading cached list", err);
+        console.warn("Error loading cached list", key, err);
         sessionStorage.removeItem(key);
         return null;
     }

From d3a4e9d22a66dbd8faa978188c6df54ee60c0bd9 Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Tue, 17 Aug 2021 14:15:55 +0200
Subject: [PATCH 209/218] Fix legacy endpoints

---
 lib/galaxy/webapps/galaxy/api/group_roles.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/group_roles.py b/lib/galaxy/webapps/galaxy/api/group_roles.py
index ad5bfe086f3..4d73f0f511a 100644
--- a/lib/galaxy/webapps/galaxy/api/group_roles.py
+++ b/lib/galaxy/webapps/galaxy/api/group_roles.py
@@ -98,7 +98,8 @@ class GroupRolesAPIController(BaseGalaxyAPIController):
         GET /api/groups/{encoded_group_id}/roles
         Displays a collection (list) of groups.
         """
-        return self.manager.index(trans, group_id)
+        group_roles = self.manager.index(trans, group_id)
+        return GroupRoleListModel(__root__=[group_role_to_model(trans, group_id, gr.role) for gr in group_roles])
 
     @require_admin
     @expose_api
@@ -107,7 +108,8 @@ class GroupRolesAPIController(BaseGalaxyAPIController):
         GET /api/groups/{encoded_group_id}/roles/{encoded_role_id}
         Displays information about a group role.
         """
-        return self.manager.show(trans, id, group_id)
+        role = self.manager.show(trans, id, group_id)
+        return group_role_to_model(trans, group_id, role)
 
     @require_admin
     @expose_api
@@ -116,7 +118,8 @@ class GroupRolesAPIController(BaseGalaxyAPIController):
         PUT /api/groups/{encoded_group_id}/roles/{encoded_role_id}
         Adds a role to a group
         """
-        return self.manager.update(trans, id, group_id)
+        role = self.manager.update(trans, id, group_id)
+        return group_role_to_model(trans, group_id, role)
 
     @require_admin
     @expose_api
@@ -125,4 +128,5 @@ class GroupRolesAPIController(BaseGalaxyAPIController):
         DELETE /api/groups/{encoded_group_id}/roles/{encoded_role_id}
         Removes a role from a group
         """
-        return self.manager.delete(trans, id, group_id)
+        role = self.manager.delete(trans, id, group_id)
+        return group_role_to_model(trans, group_id, role)

From a6ac841f85f36a2d73fa5398a0fb022ec3d3486e Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Mon, 16 Aug 2021 14:38:53 -0400
Subject: [PATCH 210/218] Support setting per-job-environment container
 resolvers using the `container_resolvers` key in the environment config.

---
 lib/galaxy/config/__init__.py                 |  4 +-
 lib/galaxy/tool_util/deps/containers.py       | 54 ++++++++++++++-----
 ...xample_broken_no_requirements_fallback.xml | 25 +++++++++
 test/functional/tools/samples_tool_conf.xml   |  1 +
 test/integration/dockerized_job_conf.xml      | 22 --------
 test/integration/dockerized_job_conf.yml      | 26 +++++++++
 test/integration/singularity_job_conf.xml     | 21 --------
 test/integration/singularity_job_conf.yml     | 18 +++++++
 test/integration/test_containerized_jobs.py   | 34 +++++++++++-
 9 files changed, 144 insertions(+), 61 deletions(-)
 create mode 100644 test/functional/tools/mulled_example_broken_no_requirements_fallback.xml
 delete mode 100644 test/integration/dockerized_job_conf.xml
 create mode 100644 test/integration/dockerized_job_conf.yml
 delete mode 100644 test/integration/singularity_job_conf.xml
 create mode 100644 test/integration/singularity_job_conf.yml

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 216379255e1..83231bbb541 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -1208,8 +1208,8 @@ class ConfiguresGalaxyMixin:
                 for enabled_container_type in self.container_finder._enabled_container_types(destination.params):
                     container_types_to_destinations[enabled_container_type].append(destination)
         self.toolbox.dependency_manager.set_enabled_container_types(container_types_to_destinations)
-        self.toolbox.dependency_manager.resolver_classes.update(self.container_finder.container_registry.resolver_classes)
-        self.toolbox.dependency_manager.dependency_resolvers.extend(self.container_finder.container_registry.container_resolvers)
+        self.toolbox.dependency_manager.resolver_classes.update(self.container_finder.default_container_registry.resolver_classes)
+        self.toolbox.dependency_manager.dependency_resolvers.extend(self.container_finder.default_container_registry.container_resolvers)
 
     def _configure_tool_data_tables(self, from_shed_config):
         from galaxy.tools.data import ToolDataTableManager
diff --git a/lib/galaxy/tool_util/deps/containers.py b/lib/galaxy/tool_util/deps/containers.py
index 30dc9456607..2d0d74ff409 100644
--- a/lib/galaxy/tool_util/deps/containers.py
+++ b/lib/galaxy/tool_util/deps/containers.py
@@ -42,7 +42,9 @@ class ContainerFinder:
 
     def __init__(self, app_info, mulled_resolution_cache=None):
         self.app_info = app_info
-        self.container_registry = ContainerRegistry(app_info, mulled_resolution_cache=mulled_resolution_cache)
+        self.mulled_resolution_cache = mulled_resolution_cache
+        self.default_container_registry = ContainerRegistry(app_info, mulled_resolution_cache=mulled_resolution_cache)
+        self.destination_container_registeries = {}
 
     def _enabled_container_types(self, destination_info):
         return [t for t in ALL_CONTAINER_TYPES if self.__container_type_enabled(t, destination_info)]
@@ -51,11 +53,26 @@ class ContainerFinder:
         """Regardless of destination properties - find best container for tool.
 
         Given container types and container.ToolInfo description of the tool."""
-        return self.container_registry.find_best_container_description(enabled_container_types, tool_info, **kwds)
+        return self.default_container_registry.find_best_container_description(enabled_container_types, tool_info, **kwds)
 
     def resolve(self, enabled_container_types, tool_info, **kwds):
         """Regardless of destination properties - find ResolvedContainerDescription for tool."""
-        return self.container_registry.resolve(enabled_container_types, tool_info, **kwds)
+        return self.default_container_registry.resolve(enabled_container_types, tool_info, **kwds)
+
+    def _container_registry_for_destination(self, destination_info):
+        destination_id = destination_info.get("id")  # Probably not the way to get the ID?
+        destination_container_registry = None
+        if destination_id and destination_id not in self.destination_container_registeries:
+            if 'container_resolvers' in destination_info:
+                destination_container_registry = ContainerRegistry(self.app_info, destination_info=destination_info, mulled_resolution_cache=self.mulled_resolution_cache)
+                self.destination_container_registeries[destination_id] = destination_container_registry
+        elif not destination_id and 'container_resolvers' in destination_info:
+            destination_container_registry = ContainerRegistry(self.app_info, destination_info=destination_info, mulled_resolution_cache=self.mulled_resolution_cache)
+
+        if destination_container_registry is None and destination_id and destination_id in self.destination_container_registeries:
+            destination_container_registry = self.destination_container_registeries[destination_id]
+
+        return destination_container_registry or self.default_container_registry
 
     def find_container(self, tool_info, destination_info, job_info):
         enabled_container_types = self._enabled_container_types(destination_info)
@@ -102,7 +119,8 @@ class ContainerFinder:
                     return container
 
         # Otherwise lets see if we can find container for the tool.
-        container_description = self.find_best_container_description(enabled_container_types, tool_info)
+        container_registry = self._container_registry_for_destination(destination_info)
+        container_description = container_registry.find_best_container_description(enabled_container_types, tool_info)
         container = __destination_container(container_description)
         if container:
             return container
@@ -124,7 +142,7 @@ class ContainerFinder:
         return NULL_CONTAINER
 
     def resolution_cache(self):
-        return self.container_registry.get_resolution_cache()
+        return self.default_container_registry.get_resolution_cache()
 
     def __overridden_container_id(self, container_type, destination_info):
         if not self.__container_type_enabled(container_type, destination_info):
@@ -186,25 +204,33 @@ class NullContainerFinder:
 class ContainerRegistry:
     """Loop through enabled ContainerResolver plugins and find first match."""
 
-    def __init__(self, app_info, mulled_resolution_cache=None):
+    def __init__(self, app_info, destination_info=None, mulled_resolution_cache=None):
         self.resolver_classes = self.__resolvers_dict()
         self.enable_mulled_containers = app_info.enable_mulled_containers
         self.app_info = app_info
-        self.container_resolvers = self.__build_container_resolvers(app_info)
+        self.container_resolvers = self.__build_container_resolvers(app_info, destination_info)
         self.mulled_resolution_cache = mulled_resolution_cache
 
-    def __build_container_resolvers(self, app_info):
-        conf_file = getattr(app_info, 'container_resolvers_config_file', None)
-        conf_dict = getattr(app_info, 'container_resolvers_config_dict', None)
+    def __build_container_resolvers(self, app_info, destination_info):
+        app_conf_file = getattr(app_info, 'container_resolvers_config_file', None)
+        app_conf_dict = getattr(app_info, 'container_resolvers_config_dict', None)
+
+        if destination_info is not None:
+            conf_file = destination_info.get('container_resolvers_config_file', app_conf_file)
+            conf_dict = destination_info.get('container_resolvers', app_conf_dict)
+        else:
+            conf_file = app_conf_file
+            conf_dict = app_conf_dict
+
         plugin_source = None
-        if conf_file and not os.path.exists(conf_file):
+        if conf_dict:
+            log.debug("Loading container resolution config inline from Galaxy or job configuration file")
+            plugin_source = plugin_config.plugin_source_from_dict(conf_dict)
+        elif conf_file and not os.path.exists(conf_file):
             log.warning(f"Unable to find config file '{conf_file}'")
         elif conf_file:
             log.debug("Loading container resolution config from file '{conf_file}'")
             plugin_source = plugin_config.plugin_source_from_path(conf_file)
-        elif conf_dict:
-            log.debug("Loading container resolution config inline from Galaxy configuration file")
-            plugin_source = plugin_config.plugin_source_from_dict(conf_dict)
         if plugin_source:
             return self._parse_resolver_conf(plugin_source)
         return self.__default_container_resolvers()
diff --git a/test/functional/tools/mulled_example_broken_no_requirements_fallback.xml b/test/functional/tools/mulled_example_broken_no_requirements_fallback.xml
new file mode 100644
index 00000000000..f22d820c2c0
--- /dev/null
+++ b/test/functional/tools/mulled_example_broken_no_requirements_fallback.xml
@@ -0,0 +1,25 @@
+<tool id="mulled_example_broken_no_requirements_fallback" name="mulled_example_broken_no_requirements_fallback" version="0.1.0">
+    <!-- mulled_example_explicit without requirements... to test mapping with job conf inline container resolvers config -->
+    <!--
+    <requirements>
+        <requirement type="package" version="0.7.15">bwa</requirement>
+        <container type="docker">quay.io/biocontainers/bwa:0.7.15-\-0</container>
+    </requirements>
+    -->
+    <stdio>
+        <exit_code range="2:" />
+    </stdio>
+    <command><![CDATA[
+bwa > $output_1 2>&1
+    ]]></command>
+    <inputs>
+    </inputs>
+    <outputs>
+        <data name="output_1" />
+    </outputs>
+    <tests>
+    </tests>
+    <help><![CDATA[
+TODO: Fill in help.
+    ]]></help>
+</tool>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 4c27f1a0c8c..7c82aca504e 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -243,6 +243,7 @@
   <tool file="mulled_example_explicit.xml" />
   <tool file="mulled_example_invalid_case.xml" />
   <tool file="mulled_example_broken_no_requirements.xml" />
+  <tool file="mulled_example_broken_no_requirements_fallback.xml" />
 
   <tool file="simple_constructs.yml" />
 
diff --git a/test/integration/dockerized_job_conf.xml b/test/integration/dockerized_job_conf.xml
deleted file mode 100644
index d4cdce9f651..00000000000
--- a/test/integration/dockerized_job_conf.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0"?>
-<job_conf>
-    <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
-    </plugins>
-
-    <destinations default="local_docker">
-        <destination id="local_docker" runner="local">
-            <param id="docker_enabled">true</param>
-            <param id="docker_sudo">false</param>
-        </destination>
-
-        <destination id="local_upload" runner="local">
-        </destination>
-
-    </destinations>
-
-    <tools>
-        <tool id="upload1" destination="local_upload" />
-    </tools>
-
-</job_conf>
diff --git a/test/integration/dockerized_job_conf.yml b/test/integration/dockerized_job_conf.yml
new file mode 100644
index 00000000000..dda06d8ae65
--- /dev/null
+++ b/test/integration/dockerized_job_conf.yml
@@ -0,0 +1,26 @@
+---
+runners:
+  local:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+    workers: 1
+
+execution:
+  default: local_docker
+  environments:
+    local_docker:
+      runner: local
+      docker_enabled: true
+    local_docker_inline_container_resolvers:
+      runner: local
+      docker_enabled: true
+      container_resolvers:
+        - type: fallback
+          identifier: 'quay.io/biocontainers/bwa:0.7.15--0'
+    local_upload:
+      runner: local
+
+tools:
+  - id: upload1
+    environment: local_upload
+  - id: mulled_example_broken_no_requirements_fallback
+    environment: local_docker_inline_container_resolvers
diff --git a/test/integration/singularity_job_conf.xml b/test/integration/singularity_job_conf.xml
deleted file mode 100644
index 1a500dcab3f..00000000000
--- a/test/integration/singularity_job_conf.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0"?>
-<job_conf>
-    <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
-    </plugins>
-
-    <destinations default="local_singularity">
-        <destination id="local_singularity" runner="local">
-            <param id="singularity_enabled">true</param>
-        </destination>
-
-        <destination id="local_upload" runner="local">
-        </destination>
-
-    </destinations>
-
-    <tools>
-        <tool class="local" destination="local_upload" />
-    </tools>
-
-</job_conf>
diff --git a/test/integration/singularity_job_conf.yml b/test/integration/singularity_job_conf.yml
new file mode 100644
index 00000000000..470a4a9685d
--- /dev/null
+++ b/test/integration/singularity_job_conf.yml
@@ -0,0 +1,18 @@
+---
+runners:
+  local:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+    workers: 1
+
+execution:
+  default: local_singularity
+  environments:
+    local_singularity:
+      runner: local
+      singularity_enabled: true
+    local_upload:
+      runner: local
+
+tools:
+  - id: upload1
+    environment: local_upload
diff --git a/test/integration/test_containerized_jobs.py b/test/integration/test_containerized_jobs.py
index 3887650cf55..2981e0d1e3f 100644
--- a/test/integration/test_containerized_jobs.py
+++ b/test/integration/test_containerized_jobs.py
@@ -12,8 +12,8 @@ from galaxy_test.driver import integration_util
 from .test_job_environments import RunsEnvironmentJobs
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-DOCKERIZED_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "dockerized_job_conf.xml")
-SINGULARITY_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "singularity_job_conf.xml")
+DOCKERIZED_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "dockerized_job_conf.yml")
+SINGULARITY_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "singularity_job_conf.yml")
 EXTENDED_TIMEOUT = 120
 
 
@@ -202,6 +202,36 @@ class InlineContainerConfigurationTestCase(MappingContainerResolverTestCase):
         config["container_resolvers"] = container_resolvers_config
 
 
+class InlineJobEnvironmentContainerResolverTestCase(integration_util.IntegrationTestCase):
+
+    framework_tool_and_types = True
+    container_type = 'docker'
+    job_config_file = DOCKERIZED_JOB_CONFIG_FILE
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        cls.jobs_directory = cls._test_driver.mkdtemp()
+        config["jobs_directory"] = cls.jobs_directory
+        config["job_config_file"] = cls.job_config_file
+        disable_dependency_resolution(config)
+
+    @classmethod
+    def setUpClass(cls):
+        skip_if_container_type_unavailable(cls)
+        super().setUpClass()
+
+    def setUp(self):
+        super().setUp()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        self.history_id = self.dataset_populator.new_history()
+
+    def test_inline_environment_container_resolver_configuration(self):
+        self.dataset_populator.run_tool("mulled_example_broken_no_requirements_fallback", {}, self.history_id)
+        self.dataset_populator.wait_for_history(self.history_id, assert_ok=True)
+        output = self.dataset_populator.get_history_dataset_content(self.history_id, timeout=EXTENDED_TIMEOUT)
+        assert "0.7.15-r1140" in output
+
+
 # Singularity 2.4 in the official Vagrant issue has some problems running this test
 # case by default because subdirectories of /tmp don't bind correctly. Overridding
 # TMPDIR can fix this.

From 19c469c9cda847b6b924d90c645a90edc4735ff8 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 17 Aug 2021 15:30:08 -0400
Subject: [PATCH 211/218] Fix up plugin_config module modifying configuration
 dictionaries.

---
 lib/galaxy/util/plugin_config.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/util/plugin_config.py b/lib/galaxy/util/plugin_config.py
index 66deafe4bcb..aec2a2a1856 100644
--- a/lib/galaxy/util/plugin_config.py
+++ b/lib/galaxy/util/plugin_config.py
@@ -89,7 +89,9 @@ def __load_plugins_from_dicts(plugins_dict, configs, extra_kwds, plugin_type_key
                 break
         assert plugin_type is not None, f"Could not determine plugin type for [{config}]"
         plugin_kwds = config
-        plugin_kwds.update(extra_kwds)
+        if extra_kwds:
+            plugin_kwds = plugin_kwds.copy()
+            plugin_kwds.update(extra_kwds)
         plugin = plugins_dict[plugin_type](**plugin_kwds)
         plugins.append(plugin)
 

From c4951e86abbe689d8bb2fe7b516e24e666a1ae47 Mon Sep 17 00:00:00 2001
From: Mason Houtz <nerdinacan@gmail.com>
Date: Tue, 17 Aug 2021 13:37:54 -0700
Subject: [PATCH 212/218] beta history, editing ui fixes

---
 client/package.json                           |   3 +-
 .../src/components/History/ContentFilters.vue |   2 +-
 .../ContentItem/CollectionContentItem.js      |   2 +-
 .../History/ContentItem/ContentItem.js        |  28 +-
 .../History/ContentItem/Dataset/Dataset.vue   |   2 +
 .../ContentItem/Dataset/DatasetMenu.vue       | 299 +++++++++---------
 .../History/ContentItem/Dataset/DatasetUI.vue | 186 +++++++----
 .../ContentItem/DatasetCollection/DscMenu.vue |  12 +-
 .../ContentItem/DatasetCollection/DscUI.vue   |  62 ++--
 .../History/ContentItem/Subcollection.vue     |   1 -
 .../History/ContentItem/Subdataset.vue        |  62 ++++
 .../components/History/ContentItem/index.js   |   3 -
 .../History/ContentItem/styles.scss           |  51 +--
 .../components/History/ContentOperations.vue  | 291 ++++++++++-------
 client/src/components/History/CopyModal.vue   |  13 +-
 .../History/CurrentCollection/Details.vue     | 105 ++++--
 .../History/CurrentCollection/Panel.vue       |  32 +-
 .../History/CurrentCollection/TopNav.vue      |  54 +---
 .../History/CurrentHistoryPanel.vue           |  36 +--
 client/src/components/History/EditorMenu.vue  |  73 +++++
 .../src/components/History/HistoriesMenu.vue  | 117 ++++---
 client/src/components/History/History.vue     |  21 +-
 .../src/components/History/HistoryDetails.vue | 272 ++++++----------
 client/src/components/History/HistoryMenu.vue | 119 +++++++
 .../History/HistorySelectorModal.vue          | 106 +++++++
 client/src/components/History/HistoryTags.vue |   3 +-
 client/src/components/History/Layout.vue      |  59 ++--
 client/src/components/History/Scroller.vue    |  78 +++--
 client/src/components/History/StatusIcon.vue  |  91 ++----
 .../History/caching/loadDscContent.js         |   4 +-
 .../History/caching/operators/chunk.js        |  42 ---
 .../src/components/History/model/Dataset.js   |  25 ++
 .../History/model/DatasetCollection.js        |  22 +-
 .../src/components/History/model/History.js   |  25 ++
 .../components/History/model/History.test.js  | 101 ++++++
 client/src/components/History/model/crud.js   |   4 +-
 .../src/components/History/model/queries.js   |  21 +-
 .../CollectionContentProvider.js              |   6 +-
 .../collectionPayload.js                      |   7 +-
 .../ContentProvider/aggregateCacheUpdates.js  |  14 +-
 .../ContentProvider/processContentStreams.js  |  10 +-
 .../History/providers/DatasetProvider.js      |   0
 .../History/providers/ExpandedItems.js        |  19 ++
 .../HistoryContentProvider/contentPayload.js  |  20 +-
 .../providers/UserHistories/UserHistories.js  |  10 +-
 .../components/History/providers/setCache.js  |  25 ++
 client/src/components/IconButton.vue          |  51 +++
 .../src/components/Workflow/WorkflowList.vue  |  10 +-
 client/src/components/plugins/icons.js        |  93 ++++++
 client/src/components/plugins/index.js        |   1 +
 client/src/utils/mountVueComponent.js         |   5 +-
 client/src/utils/observable/chunk.js          |  18 +-
 client/src/utils/safeAssign.js                |  19 ++
 client/tests/jest/helpers.js                  |   4 +-
 client/yarn.lock                              |  56 ++--
 55 files changed, 1814 insertions(+), 981 deletions(-)
 create mode 100644 client/src/components/History/ContentItem/Subdataset.vue
 create mode 100644 client/src/components/History/EditorMenu.vue
 create mode 100644 client/src/components/History/HistoryMenu.vue
 create mode 100644 client/src/components/History/HistorySelectorModal.vue
 delete mode 100644 client/src/components/History/caching/operators/chunk.js
 create mode 100644 client/src/components/History/model/History.test.js
 create mode 100644 client/src/components/History/providers/DatasetProvider.js
 create mode 100644 client/src/components/History/providers/setCache.js
 create mode 100644 client/src/components/IconButton.vue
 create mode 100644 client/src/components/plugins/icons.js

diff --git a/client/package.json b/client/package.json
index 0011ab19a15..2bc381f9237 100644
--- a/client/package.json
+++ b/client/package.json
@@ -29,7 +29,7 @@
     "axios": "^0.21.1",
     "backbone": "1.4.0",
     "bootstrap": "4.5.0",
-    "bootstrap-vue": "^2.15.0",
+    "bootstrap-vue": "^2.21.2",
     "citation-js": "^0.5.0-alpha.5",
     "d3": "3",
     "date-fns": "^2.21.1",
@@ -63,6 +63,7 @@
     "pouchdb-erase": "^1.0.2",
     "pouchdb-find": "^7.2.2",
     "pouchdb-upsert": "^2.2.0",
+    "pretty-bytes": "^5.6.0",
     "proper-skip-list": "^4.0.2",
     "pyre-to-regexp": "^0.0.5",
     "regression": "^2.0.1",
diff --git a/client/src/components/History/ContentFilters.vue b/client/src/components/History/ContentFilters.vue
index da1663d41b8..03c9536728f 100644
--- a/client/src/components/History/ContentFilters.vue
+++ b/client/src/components/History/ContentFilters.vue
@@ -1,7 +1,7 @@
 <template>
     <b-input-group v-if="params">
         <DebouncedInput v-model.trim="filterText" v-slot="{ value, input }">
-            <b-form-input size="sm" :value="value" @input="input" :placeholder="'Search Filter' | localize" />
+            <b-form-input size="sm" :value="value" @input="input" :placeholder="'Content Filter' | localize" />
         </DebouncedInput>
 
         <b-input-group-append>
diff --git a/client/src/components/History/ContentItem/CollectionContentItem.js b/client/src/components/History/ContentItem/CollectionContentItem.js
index efa92a9083a..eb785ff8d8e 100644
--- a/client/src/components/History/ContentItem/CollectionContentItem.js
+++ b/client/src/components/History/ContentItem/CollectionContentItem.js
@@ -8,7 +8,7 @@ export default {
             const { history_content_type } = this.item;
             switch (history_content_type) {
                 case "dataset":
-                    return "Dataset";
+                    return "Subdataset";
                 case "dataset_collection":
                     return "Subcollection";
                 default:
diff --git a/client/src/components/History/ContentItem/ContentItem.js b/client/src/components/History/ContentItem/ContentItem.js
index f17e129a5f3..b39fd514d4e 100644
--- a/client/src/components/History/ContentItem/ContentItem.js
+++ b/client/src/components/History/ContentItem/ContentItem.js
@@ -11,18 +11,25 @@
 import Placeholder from "./Placeholder";
 import Dataset from "./Dataset";
 import DatasetCollection from "./DatasetCollection";
-// import SubDataset from "./SubDataset";
+import Subdataset from "./Subdataset";
 import Subcollection from "./Subcollection";
+import "./styles.scss";
 
 export default {
     template: `
         <component :is="contentItemComponent"
-            class="content-item p-1"
+            :data-ci-type="contentItemComponent"
+            class="content-item"
             :class="{ loading }"
             :tabindex="index"
+            :writable="writable"
             v-on="$listeners"
-            v-bind="bindProps"
-            @mouseover.native.self.stop="setFocus(index)"
+            v-bind="$attrs"
+            :item="item"
+            :index="index"
+            :row-key="rowKey"
+            :writable="writable"
+            @mouseover.native.stop="setFocus(index)"
             @keydown.native.arrow-up.self.stop="setFocus(index - 1)"
             @keydown.native.arrow-down.self.stop="setFocus(index + 1)"
         />
@@ -32,13 +39,15 @@ export default {
         Placeholder,
         Dataset,
         DatasetCollection,
-        // SubDataset,
+        Subdataset,
         Subcollection,
     },
 
     props: {
         item: { type: Object, required: true },
-        index: { type: Number, required: true },
+        index: { type: Number, required: false, default: null },
+        rowKey: { type: [Number, String], required: false, default: "" },
+        writable: { type: Boolean, required: false, default: true },
     },
 
     data: () => ({
@@ -50,8 +59,8 @@ export default {
             if (this.suppressFocus) {
                 return;
             }
-            const ul = this.$el.closest(".scroller");
-            const el = ul.querySelector(`[tabindex="${index}"]`);
+            const scrollContainer = this.$el.closest(".scroller");
+            const el = scrollContainer.querySelector(`[tabindex="${index}"]`);
             if (el) {
                 el.focus();
             }
@@ -66,9 +75,6 @@ export default {
             // override me
             return "Placeholder";
         },
-        bindProps() {
-            return { ...this.$props, ...this.$attrs };
-        },
     },
 
     created() {
diff --git a/client/src/components/History/ContentItem/Dataset/Dataset.vue b/client/src/components/History/ContentItem/Dataset/Dataset.vue
index cc00d07b0d4..14b3c358276 100644
--- a/client/src/components/History/ContentItem/Dataset/Dataset.vue
+++ b/client/src/components/History/ContentItem/Dataset/Dataset.vue
@@ -4,6 +4,7 @@
         v-bind="$attrs"
         v-on="$listeners"
         :dataset="dataset"
+        :row-key="rowKey"
         @update:dataset="onUpdate"
         @delete="onDelete"
         @undelete="onUndelete"
@@ -26,6 +27,7 @@ export default {
     },
     props: {
         item: { type: Object, required: true },
+        rowKey: { type: [Number, String], required: false, default: "" },
     },
     computed: {
         dataset() {
diff --git a/client/src/components/History/ContentItem/Dataset/DatasetMenu.vue b/client/src/components/History/ContentItem/Dataset/DatasetMenu.vue
index 42225f34e82..c037ddbc56a 100644
--- a/client/src/components/History/ContentItem/Dataset/DatasetMenu.vue
+++ b/client/src/components/History/ContentItem/Dataset/DatasetMenu.vue
@@ -1,159 +1,170 @@
 <template>
-    <PriorityMenu :starting-height="27">
-        <PriorityMenuItem
-            v-if="notIn(STATES.NOT_VIEWABLE, STATES.DISCARDED)"
-            key="view-dataset"
-            :title="displayButtonTitle"
-            :disabled="dataset.purged || isIn(STATES.UPLOAD, STATES.NEW)"
-            @click.stop="viewData"
-            icon="fas fa-eye"
-        />
-
-        <PriorityMenuItem
-            v-if="notIn(STATES.DISCARDED)"
-            key="edit-dataset"
-            :title="editButtonTitle"
-            :disabled="dataset.deleted || isIn(STATES.UPLOAD, STATES.NEW)"
-            @click.stop="
-                backboneRoute('datasets/edit', {
-                    dataset_id: dataset.id,
-                })
-            "
-            icon="fa fa-pencil"
-        />
-
-        <PriorityMenuItem
-            v-if="dataset.accessible"
-            key="delete-dataset"
-            :title="deleteButtonTitle"
-            :disabled="dataset.purged"
-            @click.stop="onDeleteClick"
-            :icon="dataset.deleted ? 'fas fa-trash-restore' : 'fas fa-trash'"
-        />
-
-        <PriorityMenuItem
-            v-if="expanded"
-            key="edit-tags"
-            title="Edit Dataset Tags"
-            :pressed="showTags"
-            @click.stop="$emit('update:showTags', !showTags)"
-            icon="fas fa-tags"
-        />
-
-        <PriorityMenuItem
-            v-if="isIn(STATES.ERROR)"
-            key="show-error"
-            title="Error"
-            @click.stop="
-                backboneRoute('datasets/error', {
-                    dataset_id: dataset.id,
-                })
-            "
-            icon="fa fa-bug"
-        />
-
-        <PriorityMenuItem
-            v-if="!(showDownloads && dataset.hasMetaData)"
-            key="download"
-            title="Download"
-            :href="prependPath(dataset.getUrl('download'))"
-            target="_blank"
-            download
-            icon="fas fa-file-download"
-        />
-
-        <PriorityMenuItem
-            v-if="showDownloads && dataset.hasMetaData"
-            key="download-metadata"
-            title="Download"
-            :href="prependPath(dataset.getUrl('download'))"
-            target="_blank"
-            download
-            icon="fas fa-file-download"
-        />
-
-        <PriorityMenuItem
-            v-if="!dataset.purged && dataset.getUrl('download')"
-            key="copy-link"
-            title="Copy Link"
-            icon="fa fa-chain"
-            @click.stop="$emit('copy-link')"
-        />
-
-        <div v-if="showDownloads && dataset.hasMetaData">
-            <PriorityMenuItem
-                v-for="mf in dataset.meta_files"
-                :key="'download-' + mf.download_url"
-                :title="'Download ' + mf.file_type"
-                :href="prependPath(dataset.getUrl('meta_download') + mf.file_type)"
-                target="_blank"
-                download
-                icon="fas fa-file-download"
+    <div>
+        <b-button-group>
+            <IconButton
+                v-if="notIn(STATES.NOT_VIEWABLE, STATES.DISCARDED)"
+                icon="eye"
+                :title="displayButtonTitle"
+                :disabled="dataset.purged || isIn(STATES.UPLOAD, STATES.NEW)"
+                @click.stop="viewData"
+                variant="link"
+                class="px-1"
+            />
+            <IconButton
+                v-if="notIn(STATES.DISCARDED)"
+                icon="pen"
+                :title="editButtonTitle"
+                :disabled="dataset.deleted || isIn(STATES.UPLOAD, STATES.NEW)"
+                @click.stop="backboneRoute('datasets/edit', { dataset_id: dataset.id })"
+                variant="link"
+                class="px-1"
+            />
+            <IconButton
+                v-if="dataset.accessible"
+                :icon="dataset.deleted ? 'trash-restore' : 'trash'"
+                :title="deleteButtonTitle"
+                :disabled="dataset.purged"
+                v-b-modal="bsId('delete-modal')"
+                variant="link"
+                class="px-1"
+                @click.stop
             />
-        </div>
 
-        <PriorityMenuItem
-            v-if="dataset.rerunnable && dataset.creating_job && notIn(STATES.UPLOAD, STATES.NOT_VIEWABLE)"
-            key="run-job"
-            title="Run job again"
-            :href="prependPath(dataset.getUrl('rerun'))"
-            @click.stop="
-                backboneRoute('/', {
-                    job_id: dataset.creating_job,
-                })
-            "
-            icon="fa fa-redo"
-        />
+            <b-dropdown
+                size="sm"
+                variant="link"
+                :text="'Dataset Operations' | l"
+                toggle-class="p-1 pl-2"
+                class="flex-grow-0"
+                v-if="expanded"
+                boundary="window"
+            >
+                <template v-slot:button-content>
+                    <Icon icon="ellipsis-v" variant="link" />
+                    <span class="sr-only">Dataset Operations</span>
+                </template>
 
-        <PriorityMenuItem
-            v-if="showViz && hasViz && isIn(STATES.OK, STATES.FAILED_METADATA)"
-            key="visualize"
-            title="Visualize Data"
-            @click.stop.prevent="visualize"
-            icon="fa-bar-chart"
-        />
+                <b-dropdown-item
+                    v-if="isIn(STATES.ERROR)"
+                    key="show-error"
+                    title="Error"
+                    @click.stop="
+                        backboneRoute('datasets/error', {
+                            dataset_id: dataset.id,
+                        })
+                    "
+                >
+                    <Icon icon="exclamation-triangle" class="mr-1" />
+                    <span v-localize>Show Error</span>
+                </b-dropdown-item>
 
-        <PriorityMenuItem
-            v-if="currentUser && currentUser.id && dataset.creating_job"
-            key="tool-tip"
-            title="Tool Help"
-            @click.stop="showToolHelp(dataset.creating_job)"
-            icon="fa fa-question"
-        />
+                <b-dropdown-item
+                    v-if="!dataset.purged && dataset.getUrl('download')"
+                    title="Copy Link"
+                    @click.stop="$emit('copy-link')"
+                >
+                    <Icon icon="link" class="mr-1" />
+                    <span v-localize>Copy Link</span>
+                </b-dropdown-item>
 
-        <PriorityMenuItem
-            v-if="notIn(STATES.NOT_VIEWABLE)"
-            key="dataset-details"
-            title="View Details"
-            @click.stop.prevent="
-                iframeAdd({
-                    path: dataset.getUrl('show_params'),
-                    title: 'Dataset details',
-                })
-            "
-            icon="fa fa-info-circle"
-        />
-    </PriorityMenu>
+                <b-dropdown-item
+                    v-if="!(showDownloads && dataset.hasMetaData)"
+                    title="Download"
+                    :href="prependPath(dataset.getUrl('download'))"
+                    target="_blank"
+                    download
+                >
+                    <Icon icon="download" class="mr-1" />
+                    <span v-localize>Download</span>
+                </b-dropdown-item>
+
+                <b-dropdown-group v-if="showDownloads && dataset.hasMetaData">
+                    <b-dropdown-item
+                        v-for="mf in dataset.meta_files"
+                        :key="'download-' + mf.download_url"
+                        :title="'Download ' + mf.file_type"
+                        :href="prependPath(dataset.getUrl('meta_download') + mf.file_type)"
+                        target="_blank"
+                        download
+                    >
+                        <Icon icon="download" class="mr-1" />
+                        <span v-localize>{{ "Download " + mf.file_type }}</span>
+                    </b-dropdown-item>
+                </b-dropdown-group>
+
+                <b-dropdown-item
+                    v-if="dataset.rerunnable && dataset.creating_job && notIn(STATES.UPLOAD, STATES.NOT_VIEWABLE)"
+                    title="Run job again"
+                    :href="prependPath(dataset.getUrl('rerun'))"
+                    @click.stop="
+                        backboneRoute('/', {
+                            job_id: dataset.creating_job,
+                        })
+                    "
+                >
+                    <Icon icon="play" class="mr-1" />
+                    <span v-localize>Run job again</span>
+                </b-dropdown-item>
+
+                <b-dropdown-item
+                    v-if="showViz && hasViz && isIn(STATES.OK, STATES.FAILED_METADATA)"
+                    title="Visualize Data"
+                    @click.stop.prevent="visualize"
+                >
+                    <Icon icon="chart-area" class="mr-1" />
+                    <span v-localize>Visualize Data</span>
+                </b-dropdown-item>
+
+                <b-dropdown-item
+                    v-if="currentUser && currentUser.id && dataset.creating_job"
+                    title="Tool Help"
+                    @click.stop="showToolHelp(dataset.creating_job)"
+                >
+                    <Icon icon="question" class="mr-1" />
+                    <span v-localize>Tool Help</span>
+                </b-dropdown-item>
+
+                <b-dropdown-item
+                    v-if="notIn(STATES.NOT_VIEWABLE)"
+                    key="dataset-details"
+                    title="View Dataset Details"
+                    @click.stop.prevent="
+                        iframeAdd({
+                            path: dataset.getUrl('show_params'),
+                            title: 'View Dataset Details',
+                        })
+                    "
+                >
+                    <Icon icon="info-circle" class="mr-1" />
+                    <span v-localize>View Dataset Details</span>
+                </b-dropdown-item>
+            </b-dropdown>
+        </b-button-group>
+
+        <!-- modals -->
+        <b-modal :id="bsId('delete-modal')" title="Delete Dataset?" title-tag="h2" @ok="onDeleteClick">
+            <p v-localize>Really delete this dataset?</p>
+        </b-modal>
+    </div>
 </template>
 
 <script>
 import { mapGetters } from "vuex";
-import { Dataset, STATES } from "../../model";
-import { PriorityMenu, PriorityMenuItem } from "components/PriorityMenu";
+import { Dataset } from "../../model";
 import { legacyNavigationMixin } from "components/plugins/legacyNavigation";
+import IconButton from "components/IconButton";
 
 export default {
     mixins: [legacyNavigationMixin],
+    inject: ["STATES"],
 
     components: {
-        PriorityMenu,
-        PriorityMenuItem,
+        IconButton,
     },
 
     props: {
         dataset: { type: Dataset, required: true },
         expanded: { type: Boolean, required: true },
-        showTags: { type: Boolean, required: false, default: false },
     },
 
     data() {
@@ -163,11 +174,6 @@ export default {
         };
     },
 
-    created() {
-        // make available to template
-        this.STATES = STATES;
-    },
-
     computed: {
         ...mapGetters("user", ["currentUser"]),
         ...mapGetters("config", ["config"]),
@@ -180,10 +186,10 @@ export default {
             if (this.dataset.purged) {
                 return "Cannot display datasets removed from disk";
             }
-            if (this.dataset.state == STATES.UPLOAD) {
+            if (this.dataset.state == this.STATES.UPLOAD) {
                 return "This dataset must finish uploading before it can be viewed";
             }
-            if (this.dataset.state == STATES.NEW) {
+            if (this.dataset.state == this.STATES.NEW) {
                 return "This dataset is not yet viewable";
             }
             return "View data";
@@ -196,7 +202,7 @@ export default {
             if (this.dataset.purged) {
                 return "Cannot edit attributes of datasets removed from disk";
             }
-            const unreadyStates = new Set([STATES.UPLOAD, STATES.NEW]);
+            const unreadyStates = new Set([this.STATES.UPLOAD, this.STATES.NEW]);
             if (unreadyStates.has(this.dataset.state)) {
                 return "This dataset is not yet editable";
             }
@@ -218,7 +224,7 @@ export default {
             if (!this.dataset.hasData) {
                 return false;
             }
-            const okStates = new Set([STATES.OK, STATES.FAILED_METADATA, STATES.ERROR]);
+            const okStates = new Set([this.STATES.OK, this.STATES.FAILED_METADATA, this.STATES.ERROR]);
             return okStates.has(this.dataset.state);
         },
 
@@ -278,6 +284,11 @@ export default {
             const eventName = this.dataset.deleted ? "undelete" : "delete";
             this.$emit(eventName);
         },
+
+        // bootstrap demands ids instead of simply using a ref so I guess we're doing this
+        bsId(suffix) {
+            return `dataset-${this.dataset.id}-${suffix}`;
+        },
     },
 };
 </script>
diff --git a/client/src/components/History/ContentItem/Dataset/DatasetUI.vue b/client/src/components/History/ContentItem/Dataset/DatasetUI.vue
index 59fe2466f95..2b15be928e9 100644
--- a/client/src/components/History/ContentItem/Dataset/DatasetUI.vue
+++ b/client/src/components/History/ContentItem/Dataset/DatasetUI.vue
@@ -8,7 +8,7 @@ either through the props, and make updates through the events -->
 <template>
     <div
         class="dataset history-content"
-        :id="typedId"
+        :data-content-type-id="typeId"
         :class="{ expanded, collapsed, selected }"
         :data-state="dataset.state"
         @keydown.arrow-left.self.stop="$emit('update:expanded', false)"
@@ -16,73 +16,101 @@ either through the props, and make updates through the events -->
         @keydown.space.self.stop.prevent="$emit('update:selected', !selected)"
     >
         <!-- name, state buttons, menus -->
-        <nav class="content-top-menu" @click.stop="$emit('update:expanded', !expanded)">
-            <div class="content-status-indicators" @click.stop>
-                <b-check
-                    class="selector"
-                    v-if="showSelection"
-                    :checked="selected"
-                    @change="$emit('update:selected', $event)"
+        <nav class="p-1 d-flex align-items-center cursor-pointer" @click.stop="$emit('update:expanded', !expanded)">
+            <div class="d-flex align-items-center flex-grow-1 overflow-hidden">
+                <div class="pl-1" v-if="showSelectionBox">
+                    <b-check class="selector" :checked="selected" @change="$emit('update:selected', $event)"></b-check>
+                </div>
+
+                <StatusIcon
+                    v-if="!collapsed"
+                    class="status-icon px-1"
+                    :state="dataset.state"
+                    @click.stop="onStatusClick"
                 />
-                <StatusIcon v-if="!ok" class="status-icon px-1" :state="dataset.state" @click.stop="onStatusClick" />
-                <StateBtn
-                    v-if="!dataset.visible"
+
+                <IconButton
+                    v-if="!collapsed && !dataset.visible"
                     class="px-1"
                     state="hidden"
                     title="Unhide"
-                    icon="fa fa-eye-slash"
+                    icon="eye-slash"
                     @click.stop="$emit('unhide')"
                 />
-                <StateBtn
-                    v-if="dataset.isDeleted && !dataset.purged"
+
+                <IconButton
+                    v-if="!collapsed && dataset.isDeleted && !dataset.purged"
                     class="px-1"
                     state="deleted"
                     title="Undelete"
-                    icon="fas fa-trash-restore"
+                    icon="trash-restore"
                     @click.stop="$emit('undelete')"
                 />
+
+                <div class="content-title p-1 overflow-hidden">
+                    <h5 class="text-truncate" v-if="collapsed">
+                        <!-- <span class="hid">{{ dataset.hid }}</span> -->
+                        <span class="name">{{ dataset.title }}</span>
+                    </h5>
+                </div>
             </div>
 
-            <div class="content-title">
-                <h5 class="text-truncate">
-                    <span class="hid">{{ dataset.hid }}</span>
-                    <span v-if="collapsed || !dataset.canEditName" class="name">{{ dataset.title }}</span>
-                </h5>
-            </div>
-
-            <div class="content-item-menu">
+            <div class="d-flex">
                 <slot name="menu">
-                    <DatasetMenu :dataset="dataset" :expanded="expanded" v-on="$listeners" :show-tags.sync="showTags" />
+                    <DatasetMenu :dataset="dataset" :expanded="expanded" v-on="$listeners" />
                 </slot>
             </div>
         </nav>
 
-        <!--- read-only tags with name: prefix -->
-        <div v-if="collapsed && dataset.nameTags.length" class="nametags p-1">
+        <!--- read-only tags with name: prefix
+        <div v-if="collapsed && dataset.nameTags.length" class="nametags p-2">
             <Nametag v-for="tag in dataset.nameTags" :key="tag" :tag="tag" />
-        </div>
+        </div> -->
 
-        <!-- expanded view with editors -->
-        <header v-if="expanded" class="p-2 details">
-            <ClickToEdit
-                v-if="dataset.canEditName"
-                tag-name="h4"
-                :value="dataset.name"
-                @input="$emit('update:dataset', { name: $event })"
-                :display-label="dataset.title"
-                :tooltip-title="'Edit dataset name...' | localize"
-                tooltip-placement="left"
-            />
+        <div v-if="expanded" class="p-3 details">
+            <div class="d-flex">
+                <div class="flex-grow-1">
+                    <h4>{{ name || "(Dataset Name)" }}</h4>
 
-            <Annotation
-                class="mt-1"
-                :value="dataset.annotation"
-                @input="$emit('update:dataset', { annotation: $event })"
-            />
+                    <template v-if="!editing">
+                        <p v-if="annotation">{{ annotation }}</p>
+                        <div v-if="dataset.nameTags.length" class="nametags mt-2">
+                            <Nametag v-for="tag in dataset.nameTags" :key="tag" :tag="tag" />
+                        </div>
+                    </template>
 
-            <ContentTags v-if="showTags" class="mt-2" :content="dataset" />
-            <div v-else-if="dataset.nameTags.length" class="nametags mt-2">
-                <Nametag v-for="tag in dataset.nameTags" :key="tag" :tag="tag" />
+                    <div v-else class="my-3">
+                        <b-textarea
+                            class="mb-3"
+                            v-model="name"
+                            placeholder="Dataset Name"
+                            trim
+                            max-rows="4"
+                        ></b-textarea>
+
+                        <b-textarea
+                            class="mb-3"
+                            v-model="annotation"
+                            placeholder="Annotation (optional)"
+                            trim
+                            max-rows="4"
+                        ></b-textarea>
+
+                        <ContentTags class="mt-2" :content="dataset" />
+                    </div>
+                </div>
+
+                <EditorMenu
+                    class="ml-3 flex-grow-0 d-flex flex-column"
+                    v-if="writable"
+                    model-name="Collection"
+                    :editing.sync="editing"
+                    :writable="writable"
+                    :valid="valid"
+                    :dirty="dirty"
+                    @save="save"
+                    @revert="revert"
+                />
             </div>
 
             <div class="details">
@@ -102,41 +130,44 @@ either through the props, and make updates through the events -->
                 </div>
                 <pre v-if="dataset.peek" class="dataset-peek p-1" v-html="dataset.peek"></pre>
             </div>
-        </header>
+        </div>
     </div>
 </template>
 
 <script>
 import { Dataset, STATES } from "../../model";
-import ClickToEdit from "components/ClickToEdit";
-import Annotation from "components/Annotation";
 import { Nametag } from "components/Nametags";
-import { StatusIcon, StateBtn } from "../../StatusIcon";
+import StatusIcon from "../../StatusIcon";
 import DatasetMenu from "./DatasetMenu";
 import DatasetSummary from "./Summary";
 import ContentTags from "../../ContentTags";
 import { legacyNavigationMixin } from "components/plugins/legacyNavigation";
+import IconButton from "components/IconButton";
+import EditorMenu from "../../EditorMenu";
+
 export default {
     mixins: [legacyNavigationMixin],
     components: {
-        ClickToEdit,
-        Annotation,
         StatusIcon,
-        StateBtn,
         DatasetMenu,
         DatasetSummary,
         ContentTags,
         Nametag,
+        IconButton,
+        EditorMenu,
     },
     props: {
         dataset: { type: Dataset, required: true },
         expanded: { type: Boolean, required: true },
         selected: { type: Boolean, required: false, default: false },
         showSelection: { type: Boolean, required: false, default: false },
+        writable: { type: Boolean, required: false, default: true },
+        selectable: { type: Boolean, required: false, default: true },
     },
     data() {
         return {
-            showTags: false,
+            editing: false,
+            tempContent: this.dataset.clone(),
         };
     },
     computed: {
@@ -146,11 +177,33 @@ export default {
         typeId() {
             return this.dataset.type_id;
         },
-        ok() {
-            return this.dataset.state == "ok";
+        isEditing() {
+            return this.writable && this.editing;
         },
-        typedId() {
-            return `dataset-${this.dataset.id}`;
+        valid() {
+            return true;
+        },
+        dirty() {
+            return !this.tempContent.equals(this.dataset);
+        },
+        name: {
+            get() {
+                return this.tempContent?.name || "";
+            },
+            set(newVal) {
+                this.patchTempContent({ name: newVal });
+            },
+        },
+        annotation: {
+            get() {
+                return this.tempContent?.annotation || "";
+            },
+            set(newVal) {
+                this.patchTempContent({ annotation: newVal });
+            },
+        },
+        showSelectionBox() {
+            return this.selectable && this.showSelection;
         },
     },
     methods: {
@@ -163,6 +216,23 @@ export default {
                     console.log("unhandled status icon click", this.dataset.state);
             }
         },
+        patchTempContent(props = {}) {
+            this.tempContent = this.tempContent.patch(props);
+        },
+        save() {
+            if (this.valid) {
+                this.$emit("update:dataset", this.tempContent);
+                this.editing = false;
+            }
+        },
+        reset() {
+            this.tempContent = this.dataset.clone();
+        },
+        revert() {
+            if (this.dirty) {
+                this.reset();
+            }
+        },
     },
 };
 </script>
diff --git a/client/src/components/History/ContentItem/DatasetCollection/DscMenu.vue b/client/src/components/History/ContentItem/DatasetCollection/DscMenu.vue
index fbe90484749..1f64d1e503c 100644
--- a/client/src/components/History/ContentItem/DatasetCollection/DscMenu.vue
+++ b/client/src/components/History/ContentItem/DatasetCollection/DscMenu.vue
@@ -1,18 +1,20 @@
 <template>
-    <b-dropdown no-caret right variant="link" size="sm" boundary="window" toggle-class="p-1">
+    <b-dropdown no-caret right variant="link" size="sm" boundary="window" toggle-class="p-1 pl-3">
         <template v-slot:button-content>
-            <i class="fas fa-trash" />
+            <Icon icon="trash" variant="link" />
             <span class="sr-only">Delete Collection</span>
         </template>
 
-        <b-dropdown-item @click.stop="$emit('delete')"> Delete Collection Only </b-dropdown-item>
+        <b-dropdown-item @click.stop="$emit('delete')">
+            <span v-localize>Delete Collection Only </span>
+        </b-dropdown-item>
 
         <b-dropdown-item @click.stop="$emit('delete', { recursive: true })">
-            Delete Contained Datasets
+            <span v-localize>Delete Contained Datasets</span>
         </b-dropdown-item>
 
         <b-dropdown-item @click.stop="$emit('delete', { recursive: true, purge: true })">
-            Purge Contained Datasets
+            <span v-localize>Purge Contained Datasets</span>
         </b-dropdown-item>
     </b-dropdown>
 </template>
diff --git a/client/src/components/History/ContentItem/DatasetCollection/DscUI.vue b/client/src/components/History/ContentItem/DatasetCollection/DscUI.vue
index 1795656350f..8c712e6176a 100644
--- a/client/src/components/History/ContentItem/DatasetCollection/DscUI.vue
+++ b/client/src/components/History/ContentItem/DatasetCollection/DscUI.vue
@@ -9,16 +9,17 @@
         :data-state="dsc.state"
         @keydown.arrow-right.self.stop="$emit('viewCollection')"
         @keydown.space.self.stop.prevent="$emit('update:selected', !selected)"
-        @click.stop="$emit('viewCollection')"
     >
-        <nav class="content-top-menu">
-            <div class="content-status-indicators mr-1" @click.stop>
-                <b-check
-                    class="selector"
-                    v-if="showSelection"
-                    :checked="selected"
-                    @change="$emit('update:selected', $event)"
-                />
+        <nav class="p-1 d-flex align-items-center cursor-pointer">
+            <div class="d-flex align-items-center flex-grow-1 overflow-hidden">
+                <div class="pl-1" v-if="showSelection">
+                    <b-check
+                        class="selector"
+                        :checked="selected"
+                        @click.stop
+                        @change="$emit('update:selected', $event)"
+                    />
+                </div>
 
                 <StatusIcon
                     v-if="dsc.state != 'ok'"
@@ -27,44 +28,45 @@
                     @click.stop="onStatusClick"
                 />
 
-                <StateBtn
+                <IconButton
                     v-if="!dsc.visible"
                     class="px-1"
                     state="hidden"
                     title="Unhide"
-                    icon="fa fa-eye-slash"
+                    icon="eye-slash"
                     @click.stop="$emit('unhide')"
                 />
 
-                <StateBtn
+                <IconButton
                     v-if="dsc.deleted"
                     class="px-1"
                     state="deleted"
                     title="Undelete"
-                    icon="fas fa-trash-restore"
+                    icon="trash-restore"
                     @click.stop="$emit('undelete')"
                 />
 
-                <StateBtn
+                <IconButton
                     class="px-1"
                     state="ok"
                     title="Collection"
-                    icon="fas fa-folder"
+                    icon="folder"
                     @click.stop="$emit('viewCollection')"
+                    variant="link"
                 />
+
+                <div class="content-title flex-grow-1 overflow-hidden" @click.stop="$emit('viewCollection')">
+                    <h5 class="text-truncate">
+                        <!-- <span class="hid">{{ dsc.hid }}</span> -->
+                        <span class="name">{{ dsc.name }}</span>
+                        <span class="description">
+                            ({{ dsc.collectionType | localize }} {{ dsc.collectionCountDescription | localize }})
+                        </span>
+                    </h5>
+                </div>
             </div>
 
-            <div class="content-title mr-1">
-                <h5 class="text-truncate">
-                    <span class="hid">{{ dsc.hid }}</span>
-                    <span class="name">{{ dsc.name }}</span>
-                    <span class="description">
-                        ({{ dsc.collectionType | localize }} {{ dsc.collectionCountDescription | localize }})
-                    </span>
-                </h5>
-            </div>
-
-            <div class="content-item-menu">
+            <div class="d-flex" v-if="writable">
                 <slot name="menu">
                     <DscMenu v-if="!dsc.deleted" v-on="$listeners" />
                 </slot>
@@ -72,7 +74,7 @@
         </nav>
 
         <!--- read-only tags with name: prefix -->
-        <div v-if="dsc.nameTags.length" class="nametags p-1">
+        <div v-if="dsc.nameTags.length" class="nametags p-2">
             <Nametag v-for="tag in dsc.nameTags" :key="tag" :tag="tag" />
         </div>
 
@@ -82,23 +84,25 @@
 
 <script>
 import { DatasetCollection } from "../../model/DatasetCollection";
-import { StatusIcon, StateBtn } from "../../StatusIcon";
+import StatusIcon from "../../StatusIcon";
 import JobStateProgress from "./JobStateProgress";
 import DscMenu from "./DscMenu";
 import { Nametag } from "components/Nametags";
+import IconButton from "components/IconButton";
 
 export default {
     components: {
         StatusIcon,
-        StateBtn,
         JobStateProgress,
         DscMenu,
         Nametag,
+        IconButton,
     },
     props: {
         dsc: { type: DatasetCollection, required: true },
         selected: { type: Boolean, required: false, default: false },
         showSelection: { type: Boolean, required: false, default: false },
+        writable: { type: Boolean, required: false, default: true },
     },
     methods: {
         onStatusClick() {
diff --git a/client/src/components/History/ContentItem/Subcollection.vue b/client/src/components/History/ContentItem/Subcollection.vue
index d17a8f6b5a0..45b4a7e8f78 100644
--- a/client/src/components/History/ContentItem/Subcollection.vue
+++ b/client/src/components/History/ContentItem/Subcollection.vue
@@ -28,7 +28,6 @@ import { STATES } from "../model";
 export default {
     props: {
         item: { type: Object, required: true },
-        index: { type: Number, required: true },
     },
     computed: {
         dsc() {
diff --git a/client/src/components/History/ContentItem/Subdataset.vue b/client/src/components/History/ContentItem/Subdataset.vue
new file mode 100644
index 00000000000..010dfa38315
--- /dev/null
+++ b/client/src/components/History/ContentItem/Subdataset.vue
@@ -0,0 +1,62 @@
+<!-- a read-only dataset inside a collection. The collection query does not return enough
+information to properly render the dataset, so what we do is look it up on expand, checking the
+cache first to see if we already have the data -->
+
+<template>
+    <DatasetUI
+        v-if="dataset"
+        v-bind="$attrs"
+        v-on="$listeners"
+        :dataset="dataset"
+        :writable="false"
+        :selectable="false"
+        :row-key="rowKey"
+        @update:expanded="onExpand"
+    />
+</template>
+
+<script>
+import { Dataset } from "../model";
+import { getContentByTypeId, cacheContent } from "../caching";
+import { getContentDetails } from "../model/queries";
+import DatasetUI from "./Dataset/DatasetUI";
+
+export default {
+    components: {
+        DatasetUI,
+    },
+    props: {
+        item: { type: Object, required: true },
+    },
+    data() {
+        return {
+            localItem: { ...this.item },
+            loading: false,
+        };
+    },
+    computed: {
+        dataset() {
+            return new Dataset(this.localItem);
+        },
+    },
+    methods: {
+        onExpand(val) {
+            if (val) {
+                this.loadDetails();
+            }
+            this.$emit("update:expand", val);
+        },
+        async loadDetails() {
+            const { type_id, history_id } = this.item;
+            const existingDataset = await getContentByTypeId(history_id, type_id);
+            if (existingDataset) {
+                this.localItem = existingDataset;
+            } else {
+                const loadedDataset = await getContentDetails(this.item);
+                await cacheContent(loadedDataset);
+                this.localItem = loadedDataset;
+            }
+        },
+    },
+};
+</script>
diff --git a/client/src/components/History/ContentItem/index.js b/client/src/components/History/ContentItem/index.js
index 32d866ab9d0..5543ce9497a 100644
--- a/client/src/components/History/ContentItem/index.js
+++ b/client/src/components/History/ContentItem/index.js
@@ -1,9 +1,6 @@
 /**
  * Scrolling components for history contents and collection contents.
  */
-
-import "./styles.scss";
-
 export { default as ContentItem } from "./ContentItem";
 export { default as CollectionContentItem } from "./CollectionContentItem";
 export { default as HistoryContentItem } from "./HistoryContentItem";
diff --git a/client/src/components/History/ContentItem/styles.scss b/client/src/components/History/ContentItem/styles.scss
index f5384b3e8f8..03fcc5f41dd 100644
--- a/client/src/components/History/ContentItem/styles.scss
+++ b/client/src/components/History/ContentItem/styles.scss
@@ -3,7 +3,7 @@
 
 .content-item {
     outline: none;
-    border-bottom: 1px solid white;
+    border-bottom: 2px solid white;
     &:focus-within {
         box-shadow: inset 0 0 1em 0.25em rgba(255, 255, 255, 0.25);
     }
@@ -11,36 +11,9 @@
 
 // Nav across the top of the content item
 .content-item .content-top-menu {
-    /* a fixed-height is important for proper
-    functioning of the PriorityMenuItem dropdown since
-    it relies on flexbox and overflow */
     min-height: 2em;
 
-    cursor: pointer;
-
-    // flex parent
-    display: flex;
-    align-items: center;
-    justify-content: space-between;
-
-    // error, clock, etc.
-    .content-status-indicators {
-        // d-flex mr-1 align-items-center
-        display: flex;
-        align-items: center;
-    
-        &:blank {
-            display: none;
-        }
-    }
-
-    // name & labelling
     .content-title {
-
-        // flex child
-        flex-grow: 1;
-        overflow: hidden;
-
         .hid {
             color: adjust-color($text-color, $alpha: -0.6);
             font-size: 80%;
@@ -56,24 +29,4 @@
             font-weight: 700;
         }
     }
-
-    // priority menu on right side
-    .content-item-menu {
-        display: flex;
-        justify-content: flex-end;
-    }
-
-}
-
-// Setting a max-width here limits the number of icons that
-// will show. The priority menu is css awayre
-
-.content-item.collapsed .content-item-menu {
-    max-width: 90px;
-}
-
-// .content-menu button:hover,
-// .content-menu .show > button.dropdown-toggle {
-//     background-color: transparent;
-//     border-color: transparent;
-// }
+}
\ No newline at end of file
diff --git a/client/src/components/History/ContentOperations.vue b/client/src/components/History/ContentOperations.vue
index 3b3bd01cff4..33abb59142f 100644
--- a/client/src/components/History/ContentOperations.vue
+++ b/client/src/components/History/ContentOperations.vue
@@ -1,136 +1,168 @@
 <template>
     <section>
-        <header class="d-flex align-items-center justify-content-between">
-            <h6 class="text-nowrap mr-3">
-                <span v-localize>Matches</span>
-                <a href="#" @click="showFilter = !showFilter">
-                    <span>{{ totalMatches }}</span>
-                </a>
-            </h6>
-
-            <PriorityMenu style="max-width: 50%" :starting-height="27">
-                <PriorityMenuItem
-                    key="filter"
+        <nav class="content-operations-menu d-flex justify-content-between bg-secondary">
+            <b-button-group>
+                <IconButton
+                    :title="hasSelection ? 'Select All Contents' : 'Unselect All Contents'"
+                    icon="check-square"
+                    :disabled="!totalMatches"
+                    :pressed="hasSelection"
+                    @click="toggleSelectAll"
+                />
+                <IconButton
                     title="Filter History Content"
-                    icon="fa fa-filter"
-                    @click="showFilter = !showFilter"
+                    icon="filter"
+                    :disabled="!totalMatches"
                     :pressed="showFilter"
+                    @click="showFilter = !showFilter"
                 />
-
-                <PriorityMenuItem
-                    key="selection"
-                    title="Operations on multiple datasets"
-                    class="show-history-content-selectors-btn"
-                    icon="fas fa-check-square"
-                    @click="$emit('update:show-selection', !showSelection)"
-                    :pressed="showSelection"
+                <IconButton
+                    title="Collapse Expanded Items"
+                    icon="compress"
+                    :disabled="!expandedCount"
+                    @click="$emit('collapseAllContent')"
                 />
+            </b-button-group>
 
-                <PriorityMenuItem
-                    key="copy-datasets"
-                    class="copy-datasets-menu-item"
-                    title="Copy Datasets"
-                    icon="fas fa-copy"
-                    @click="iframeRedirect('/dataset/copy_datasets')"
-                />
-
-                <PriorityMenuItem
-                    key="collapse-expanded"
-                    title="Collapse Expanded Datasets"
-                    icon="fas fa-compress-alt"
-                    @click="emit('collapseAllContent')"
-                />
-
-                <PriorityMenuItem
-                    key="show-hidden-datasets"
-                    title="Unhide All Hidden Datasets"
-                    icon="fas fa-eye"
-                    @click="$bvModal.show('show-hidden-content')"
-                />
-
-                <PriorityMenuItem
-                    key="delete-hidden"
-                    title="Delete Hidden Datasets"
-                    icon="fas fa-trash"
-                    @click="$bvModal.show('delete-hidden-content')"
-                />
-
-                <PriorityMenuItem
-                    key="purge-hidden"
-                    title="Purge Hidden Datasets"
-                    icon="fas fa-burn"
-                    @click="$bvModal.show('purge-deleted-content')"
-                />
-            </PriorityMenu>
-        </header>
-
-        <transition name="shutterfade">
-            <content-filters v-if="showContentFilters" class="content-filters mt-1" :params.sync="localParams" />
-        </transition>
-
-        <transition name="shutterfade">
-            <b-button-toolbar
-                v-if="showSelection"
-                class="content-selection justify-content-between mt-1 list-action-menu"
-            >
-                <b-button-group>
-                    <b-button size="sm" @click="$emit('selectAllContent')">
-                        {{ "Select All" | localize }}
-                    </b-button>
-                    <b-button size="sm" @click="$emit('resetSelection')">
-                        {{ "Unselect All" | localize }}
-                    </b-button>
-                </b-button-group>
-
+            <b-button-group>
                 <b-dropdown
-                    class="ml-auto history-contents-list-action-menu-btn"
+                    class="history-contents-list-action-menu-btn"
                     size="sm"
-                    text="With Selected"
+                    text="Selection"
                     :disabled="!hasSelection"
                 >
-                    <b-dropdown-item @click="hideSelected">
-                        {{ "Hide Datasets" | localize }}
+                    <b-dropdown-text id="history-op-selected-content">
+                        <span v-localize v-if="hasSelection">With {{ numSelected }} selected items...</span>
+                        <span v-localize v-else>You don't have any selected content.</span>
+                    </b-dropdown-text>
+
+                    <b-dropdown-item aria-describedby="history-op-selected-content" v-b-modal:hide-selected-content>
+                        <span v-localize>Hide</span>
                     </b-dropdown-item>
-                    <b-dropdown-item @click="unhideSelected">
-                        {{ "Unhide Datasets" | localize }}
+
+                    <b-dropdown-item aria-describedby="history-op-selected-content" v-b-modal:show-selected-content>
+                        <span v-localize>Unhide</span>
                     </b-dropdown-item>
-                    <b-dropdown-item @click="deleteSelected">
-                        {{ "Delete Datasets" | localize }}
+
+                    <b-dropdown-item aria-describedby="history-op-selected-content" v-b-modal:delete-selected-content>
+                        <span v-localize>Delete</span>
                     </b-dropdown-item>
-                    <b-dropdown-item @click="undeleteSelected">
-                        {{ "Undelete Datasets" | localize }}
+
+                    <b-dropdown-item aria-describedby="history-op-selected-content" v-b-modal:restore-selected-content>
+                        <span v-localize>Undelete</span>
                     </b-dropdown-item>
-                    <b-dropdown-item @click="purgeSelected">
-                        {{ "Permanently Delete Datasets" | localize }}
-                    </b-dropdown-item>
-                    <b-dropdown-item @click="buildDatasetList">
-                        {{ "Build Dataset List" | localize }}
-                    </b-dropdown-item>
-                    <b-dropdown-item @click="buildDatasetPair">
-                        {{ "Build Dataset Pair" | localize }}
-                    </b-dropdown-item>
-                    <b-dropdown-item @click="buildListOfPairs">
-                        {{ "Build List of Dataset Pairs" | localize }}
-                    </b-dropdown-item>
-                    <b-dropdown-item @click="buildCollectionFromRules">
-                        {{ "Build Collection from Rules" | localize }}
+
+                    <b-dropdown-item
+                        aria-describedby="history-op-selected-content"
+                        v-b-modal:purge-selected-content
+                        :disabled="!hasSelection"
+                    >
+                        <span v-localize>Permanently Delete</span>
+                        <span v-if="numSelected">{{ numSelected }} items</span>
+                        <span v-else>(Disabled)</span>
                     </b-dropdown-item>
                 </b-dropdown>
-            </b-button-toolbar>
+
+                <b-dropdown
+                    class="history-contents-list-action-menu-btn"
+                    size="sm"
+                    text="History"
+                    :disabled="!totalMatches"
+                >
+                    <b-dropdown-text id="history-op-all-content">
+                        <span v-localize>With entire history...</span>
+                    </b-dropdown-text>
+
+                    <b-dropdown-item v-b-modal:show-all-hidden-content aria-describedby="history-op-all-content">
+                        <span v-localize>Unhide All Hidden Content</span>
+                    </b-dropdown-item>
+
+                    <b-dropdown-item v-b-modal:delete-all-hidden-content aria-describedby="history-op-all-content">
+                        <span v-localize>Delete All Hidden Content</span>
+                    </b-dropdown-item>
+
+                    <b-dropdown-item v-b-modal:purge-all-deleted-content aria-describedby="history-op-all-content">
+                        <span v-localize>Purge All Hidden Content</span>
+                    </b-dropdown-item>
+                </b-dropdown>
+
+                <b-dropdown
+                    class="history-contents-list-action-menu-btn"
+                    size="sm"
+                    text="Create New Content"
+                    :disabled="!totalMatches"
+                >
+                    <template v-slot:button-content>
+                        <Icon icon="plus" />
+                        <span class="sr-only" v-localize>Create New Content</span>
+                    </template>
+
+                    <b-dropdown-text id="history-op-new-content">
+                        <span>Create new content</span>
+                    </b-dropdown-text>
+
+                    <b-dropdown-item
+                        aria-describedby="history-op-new-content"
+                        @click="iframeRedirect('/dataset/copy_datasets')"
+                    >
+                        <span v-localize>Copy Datasets</span>
+                    </b-dropdown-item>
+
+                    <b-dropdown-item aria-describedby="history-op-new-content" @click="buildDatasetList">
+                        <span v-localize>Build Dataset List</span>
+                    </b-dropdown-item>
+
+                    <b-dropdown-item aria-describedby="history-op-new-content" @click="buildDatasetPair">
+                        <span v-localize>Build Dataset Pair</span>
+                    </b-dropdown-item>
+
+                    <b-dropdown-item aria-describedby="history-op-new-content" @click="buildListOfPairs">
+                        <span v-localize>Build List of Dataset Pairs</span>
+                    </b-dropdown-item>
+
+                    <b-dropdown-item aria-describedby="history-op-new-content" @click="buildCollectionFromRules">
+                        <span v-localize>Build Collection from Rules</span>
+                    </b-dropdown-item>
+                </b-dropdown>
+            </b-button-group>
+        </nav>
+
+        <transition name="shutterfade">
+            <content-filters v-if="showContentFilters" class="content-filters p-2" :params.sync="localParams" />
         </transition>
 
         <!-- #region Menus and popovers -->
 
-        <b-modal id="show-hidden-content" title="Show Hidden Datasets" title-tag="h2" @ok="unhideAll">
-            <p>{{ "Really unhide all hidden datasets?" | localize }}</p>
+        <b-modal id="hide-selected-content" title="Hide Selected Content?" title-tag="h2" @ok="hideSelected">
+            <p v-localize>Really hide {{ numSelected }} content items?</p>
         </b-modal>
 
-        <b-modal id="delete-hidden-content" title="Delete Hidden Datasets" title-tag="h2" @ok="deleteAllHidden">
-            <p>{{ "Really delete all hidden datasets?" | localize }}</p>
+        <b-modal id="show-selected-content" title="Show Selected Content?" title-tag="h2" @ok="unhideSelected">
+            <p v-localize>Really show {{ numSelected }} content items?</p>
         </b-modal>
 
-        <b-modal id="purge-deleted-content" title="Purge Deleted Datasets" title-tag="h2" @ok="purgeAllDeleted">
-            <p>{{ "Really delete all deleted datasets permanently? This cannot be undone." | localize }}</p>
+        <b-modal id="delete-selected-content" title="Delete Selected Content?" title-tag="h2" @ok="deleteSelected">
+            <p v-localize>Really delete {{ numSelected }} content items?</p>
+        </b-modal>
+
+        <b-modal id="restore-selected-content" title="Restore Selected Content?" title-tag="h2" @ok="undeleteSelected">
+            <p v-localize>Really restore {{ numSelected }} content items?</p>
+        </b-modal>
+
+        <b-modal id="purge-selected-content" title="Purge Selected Content?" title-tag="h2" @ok="purgeSelected">
+            <p v-localize>Permanently delete {{ numSelected }} content items? This cannot be undone.</p>
+        </b-modal>
+
+        <b-modal id="show-all-hidden-content" title="Show Hidden Datasets" title-tag="h2" @ok="unhideAll">
+            <p v-localize>Really unhide all hidden datasets?</p>
+        </b-modal>
+
+        <b-modal id="delete-all-hidden-content" title="Delete Hidden Datasets" title-tag="h2" @ok="deleteAllHidden">
+            <p v-localize>Really delete all hidden datasets?</p>
+        </b-modal>
+
+        <b-modal id="purge-all-deleted-content" title="Purge Deleted Datasets" title-tag="h2" @ok="purgeAllDeleted">
+            <p v-localize>"Really delete all deleted datasets permanently? This cannot be undone.</p>
         </b-modal>
 
         <!-- #endregion -->
@@ -152,18 +184,16 @@ import {
 } from "./model";
 import { createDatasetCollection } from "./model/queries";
 import { cacheContent } from "./caching";
-
 import { legacyNavigationMixin } from "components/plugins/legacyNavigation";
-import ContentFilters from "./ContentFilters";
-import { PriorityMenu, PriorityMenuItem } from "components/PriorityMenu";
 import { buildCollectionModal } from "./adapters/buildCollectionModal";
+import ContentFilters from "./ContentFilters";
+import IconButton from "components/IconButton";
 
 export default {
     mixins: [legacyNavigationMixin],
     components: {
         ContentFilters,
-        PriorityMenu,
-        PriorityMenuItem,
+        IconButton,
     },
     props: {
         history: { type: History, required: true },
@@ -171,6 +201,8 @@ export default {
         contentSelection: { type: Map, required: true },
         showSelection: { type: Boolean, required: true },
         totalMatches: { type: Number, required: true },
+        expandedCount: { type: Number, required: false, default: 0 },
+        debug: { type: Boolean, default: false },
     },
     data() {
         return {
@@ -178,13 +210,11 @@ export default {
         };
     },
     computed: {
-        // pop it open if anything is selected
         showContentFilters() {
             const { showHidden, showDeleted, filterText } = this.params;
             return this.showFilter || showHidden || showDeleted || filterText;
         },
 
-        // pass-through
         localParams: {
             get() {
                 return this.params;
@@ -194,8 +224,12 @@ export default {
             },
         },
 
+        numSelected() {
+            return this.contentSelection.size || 0;
+        },
+
         hasSelection() {
-            return this.contentSelection.size > 0;
+            return this.numSelected > 0;
         },
 
         countHidden() {
@@ -203,22 +237,29 @@ export default {
         },
     },
     methods: {
+        toggleSelectAll() {
+            if (this.hasSelection) {
+                this.$emit("resetSelection");
+                this.$emit("update:show-selection", false);
+            } else {
+                this.$emit("selectAllContent");
+                this.$emit("update:show-selection", true);
+            }
+        },
+
         // #region history-wide bulk updates, does server query first to determine "selection"
 
         async unhideAll(evt) {
             await unhideAllHiddenContent(this.history);
             this.$emit("manualReload");
-            evt.vueTarget.hide();
         },
         async deleteAllHidden(evt) {
             await deleteAllHiddenContent(this.history);
             this.$emit("manualReload");
-            evt.vueTarget.hide();
         },
         async purgeAllDeleted(evt) {
             await purgeAllDeletedContent(this.history);
             this.$emit("manualReload");
-            evt.vueTarget.hide();
         },
 
         // #endregion
@@ -243,7 +284,10 @@ export default {
         async runOnSelection(fn) {
             const items = Array.from(this.contentSelection.values());
             const type_ids = items.map((o) => o.type_id);
-            await fn(this.history, type_ids);
+            const results = await fn(this.history, type_ids);
+            if (this.debug) {
+                console.log("operation results", results);
+            }
             this.$emit("resetSelection");
             this.$emit("manualReload");
         },
@@ -282,3 +326,10 @@ export default {
     },
 };
 </script>
+
+<style lang="scss">
+// remove borders around buttons in menu
+.content-operations-menu .btn-group .btn {
+    border-color: transparent !important;
+}
+</style>
diff --git a/client/src/components/History/CopyModal.vue b/client/src/components/History/CopyModal.vue
index 92314604b28..5d93707c302 100644
--- a/client/src/components/History/CopyModal.vue
+++ b/client/src/components/History/CopyModal.vue
@@ -1,5 +1,5 @@
 <template>
-    <b-modal ref="copyModal" v-model="showModal" :title="title" title-tag="h2">
+    <b-modal v-bind="$attrs" v-on="$listeners" :title="title" title-tag="h2">
         <transition name="fade">
             <b-alert :show="currentUser.isAnonymous" variant="warning" v-localize>
                 As an anonymous user, unless you login or register, you will lose your current history after copying
@@ -51,7 +51,6 @@ import { mapActions, mapGetters } from "vuex";
 export default {
     props: {
         history: { type: History, required: true },
-        value: { type: Boolean, required: false, default: false },
     },
     data() {
         return {
@@ -81,16 +80,6 @@ export default {
         formValid() {
             return this.newNameValid;
         },
-        showModal: {
-            get() {
-                return this.value;
-            },
-            set(newVal, oldVal) {
-                if (newVal !== oldVal) {
-                    this.$emit("input", newVal);
-                }
-            },
-        },
     },
     methods: {
         ...mapActions("betaHistory", ["copyHistory"]),
diff --git a/client/src/components/History/CurrentCollection/Details.vue b/client/src/components/History/CurrentCollection/Details.vue
index 32b4fbb2ec5..855d1567c20 100644
--- a/client/src/components/History/CurrentCollection/Details.vue
+++ b/client/src/components/History/CurrentCollection/Details.vue
@@ -1,45 +1,108 @@
+<!-- Edits a collection, if that collection is editable. -->
+
 <template>
-    <section class="history-details controls">
-        <ClickToEdit
-            :value="dsc.name"
-            v-if="writable"
-            @input="(name) => $emit('update:dsc', { name })"
-            tag-name="h3"
-            class="history-title mt-3"
-            :tooltip-title="'Rename collection...' | localize"
-        />
-        <h3 v-else class="history-title mt-3">{{ dsc.name }}</h3>
+    <section class="history-details d-flex">
+        <div class="flex-grow-1">
+            <h3 class="history-title">{{ dscName || "(Collection Name)" }}</h3>
+            <p class="mt-1">
+                <i class="fas fa-folder"></i>
+                a {{ dsc.collectionType | localize }}
+                {{ dsc.collectionCount | localize }}
+            </p>
 
-        <p class="mt-1">
-            <i class="fas fa-folder"></i>
-            a {{ dsc.collectionType | localize }}
-            {{ dsc.collectionCount | localize }}
-        </p>
+            <div v-if="isEditing" class="mt-3">
+                <b-textarea v-model="dscName" placeholder="Collection Name" trim max-rows="4"></b-textarea>
+                <ContentTags :content="dsc" class="mt-3" />
+            </div>
 
-        <transition name="shutterfade">
-            <ContentTags v-if="writable" :content="dsc" />
-            <div v-else-if="dsc.tags && dsc.tags.length" class="nametags p-1">
+            <div v-else-if="dsc.tags && dsc.tags.length">
                 <Nametag v-for="tag in dsc.tags" :key="tag" :tag="tag" />
             </div>
-        </transition>
+        </div>
+
+        <EditorMenu
+            class="ml-3 flex-grow-0 d-flex flex-column"
+            v-if="writable"
+            model-name="Collection"
+            :editing.sync="editing"
+            :writable="writable"
+            :valid="valid"
+            :dirty="dirty"
+            @save="save"
+            @revert="revert"
+        />
     </section>
 </template>
 
 <script>
 import { DatasetCollection } from "../model";
-import ClickToEdit from "components/ClickToEdit";
 import { Nametag } from "components/Nametags";
 import ContentTags from "../ContentTags";
+import EditorMenu from "../EditorMenu";
 
 export default {
     components: {
-        ClickToEdit,
         ContentTags,
         Nametag,
+        EditorMenu,
     },
     props: {
         dsc: { type: DatasetCollection, required: true },
         writable: { type: Boolean, required: true },
     },
+    data() {
+        return {
+            editing: false,
+            tempContent: this.dsc.clone(),
+        };
+    },
+    computed: {
+        dscId() {
+            return this.dsc.id;
+        },
+        isEditing() {
+            return this.writable && this.editing;
+        },
+        valid() {
+            return this.tempContent.name.length > 0;
+        },
+        dirty() {
+            return !this.tempContent.equals(this.dsc);
+        },
+        dscName: {
+            get() {
+                return this.tempContent.name;
+            },
+            set(newName) {
+                this.patchTempDsc({ name: newName });
+            },
+        },
+    },
+    watch: {
+        dscId(newId, oldId) {
+            if (newId != oldId) {
+                this.reset();
+            }
+        },
+    },
+    methods: {
+        reset() {
+            this.tempContent = this.dsc.clone();
+        },
+        patchTempDsc(props = {}) {
+            this.tempContent = this.tempContent.patch(props);
+        },
+        save() {
+            if (this.valid) {
+                this.$emit("update:dsc", this.tempContent);
+                this.editing = false;
+            }
+        },
+        revert() {
+            if (this.dirty) {
+                this.reset();
+            }
+        },
+    },
 };
 </script>
diff --git a/client/src/components/History/CurrentCollection/Panel.vue b/client/src/components/History/CurrentCollection/Panel.vue
index 298ba97e2be..9a259d92e05 100644
--- a/client/src/components/History/CurrentCollection/Panel.vue
+++ b/client/src/components/History/CurrentCollection/Panel.vue
@@ -9,10 +9,19 @@
                 v-slot="{ isExpanded, setExpanded }"
             >
                 <Layout class="dataset-collection-panel">
-                    <template v-slot:nav>
+                    <template v-slot:globalNav>
                         <TopNav :history="history" :selected-collections="selectedCollections" v-on="$listeners" />
                     </template>
 
+                    <template v-slot:localNav>
+                        <IconButton
+                            icon="download"
+                            title="Download Collection"
+                            :href="downloadCollectionUrl"
+                            download
+                        />
+                    </template>
+
                     <template v-slot:details>
                         <Details :dsc="dsc" :writable="writable" @update:dsc="updateDsc(dsc, $event)" />
                     </template>
@@ -23,13 +32,16 @@
                             :class="{ loadingBackground: loading }"
                             v-bind="payload"
                             @scroll="setScrollPos"
+                            :debug="false"
                         >
-                            <template v-slot="{ item, index }">
+                            <template v-slot="{ item, index, rowKey }">
                                 <CollectionContentItem
                                     :item="item"
                                     :index="index"
+                                    :row-key="rowKey"
                                     :expanded="isExpanded(item)"
-                                    :writable="writable"
+                                    :writable="false"
+                                    :selectable="false"
                                     @update:expanded="setExpanded(item, $event)"
                                     @viewCollection="$emit('viewCollection', item)"
                                 />
@@ -55,6 +67,7 @@ import Scroller from "../Scroller";
 import { CollectionContentItem } from "../ContentItem";
 
 import { reportPayload } from "../providers/ContentProvider/helpers";
+import IconButton from "components/IconButton";
 
 export default {
     filters: {
@@ -69,6 +82,7 @@ export default {
         Scroller,
         CollectionContentItem,
         ExpandedItems,
+        IconButton,
     },
     props: {
         history: { type: History, required: true },
@@ -86,14 +100,22 @@ export default {
         writable() {
             return this.isRoot;
         },
+        rootCollection() {
+            return this.selectedCollections[0];
+        },
+        downloadCollectionUrl() {
+            let url = "";
+            if (this.rootCollection) {
+                url = `${this.rootCollection.url}/download`;
+            }
+            return url;
+        },
     },
     methods: {
         // change the data of the root collection, anything past the root
         // collection is part of the dataset collection, which i believe is supposed to
         // be immutable, so only edit name, tags, blah of top-level selected collection,
-
         async updateDsc(collection, fields) {
-            // console.log("updateDsc", this.writable, collection, fields);
             if (this.writable) {
                 const ajaxResult = await updateContentFields(collection, fields);
                 await cacheContent({ ...collection, ...ajaxResult });
diff --git a/client/src/components/History/CurrentCollection/TopNav.vue b/client/src/components/History/CurrentCollection/TopNav.vue
index 85f324d930b..cea439b63df 100644
--- a/client/src/components/History/CurrentCollection/TopNav.vue
+++ b/client/src/components/History/CurrentCollection/TopNav.vue
@@ -1,46 +1,34 @@
 <template>
-    <div class="navigation">
-        <b-dropdown v-if="breadCrumbOptions.length" class="mr-auto" size="sm" text="Go to..." boundary="viewport">
-            <b-dropdown-item @click="close"> History: {{ history.name }} </b-dropdown-item>
-            <b-dropdown-item v-for="option in breadCrumbOptions" :key="option.key" @click="reselect(option.value)">
-                {{ option.text }}
-            </b-dropdown-item>
-        </b-dropdown>
+    <b-dropdown v-if="breadCrumbOptions.length" size="sm" text="Return to..." boundary="viewport" no-caret>
+        <template v-slot:button-content>
+            <Icon icon="arrow-up" class="mr-1" />
+            <b class="text-nowrap" v-localize>Return to...</b>
+        </template>
 
-        <b-button v-else size="sm" class="mr-auto back" @click="close"> Back to: {{ history.name }} </b-button>
+        <b-dropdown-item @click="close">
+            <span>History: {{ history.name }}</span>
+        </b-dropdown-item>
 
-        <PriorityMenu :starting-height="27">
-            <PriorityMenuItem
-                key="download-collection"
-                title="Download Collection"
-                icon="fas fa-file-download"
-                tag="a"
-                download
-                :href="downloadCollectionUrl"
-            />
-            <PriorityMenuItem key="back-up" title="Back One" icon="fas fa-level-up-alt" @click="back" />
-        </PriorityMenu>
-    </div>
+        <b-dropdown-item v-for="option in breadCrumbOptions" :key="option.key" @click="reselect(option.value)">
+            <span>{{ option.text }}</span>
+        </b-dropdown-item>
+    </b-dropdown>
+
+    <b-button v-else size="sm" title="`Return to: ${history.name}`" @click="close">
+        <Icon icon="arrow-up" class="mr-1" />
+        <b class="text-nowrap">Return to: {{ history.name }}</b>
+    </b-button>
 </template>
 
 <script>
 import { History } from "../model";
-import { PriorityMenuItem, PriorityMenu } from "components/PriorityMenu";
 
 export default {
-    components: {
-        PriorityMenuItem,
-        PriorityMenu,
-    },
     props: {
         history: { type: History, required: true },
         selectedCollections: { type: Array, required: true, validate: (val) => val.length > 0 },
     },
     computed: {
-        rootCollection() {
-            return this.selectedCollections[0];
-        },
-
         // List for the dropdown. Should be the history and every parent
         // collection excepting the current one.
         breadCrumbOptions() {
@@ -54,14 +42,6 @@ export default {
             });
             return options;
         },
-
-        downloadCollectionUrl() {
-            let url = "";
-            if (this.rootCollection) {
-                url = `${this.rootCollection.url}/download`;
-            }
-            return url;
-        },
     },
     methods: {
         reselect(newList) {
diff --git a/client/src/components/History/CurrentHistoryPanel.vue b/client/src/components/History/CurrentHistoryPanel.vue
index 6b58fe67d01..b54c8619a55 100644
--- a/client/src/components/History/CurrentHistoryPanel.vue
+++ b/client/src/components/History/CurrentHistoryPanel.vue
@@ -2,20 +2,17 @@
     <CurrentUser class="d-flex flex-column" v-slot="{ user }">
         <UserHistories v-if="user" :user="user" v-slot="{ currentHistory, histories, handlers }">
             <HistoryPanel v-if="currentHistory" :history="currentHistory" v-on="handlers" id="current-history-panel">
-                <template v-slot:nav>
-                    <div>
-                        <HistorySelector
-                            :histories="histories"
-                            :current-history="currentHistory"
-                            :show-modal="showModal"
-                            @update:currentHistory="handlers.setCurrentHistory"
-                            @hideModal="showModalHandler"
-                        />
-                        <HistoriesMenu v-on="handlers" @selectHistoryModal="showModalHandler" />
-                    </div>
+                <template v-slot:globalNav>
+                    <HistoriesMenu
+                        v-on="handlers"
+                        :histories="histories"
+                        :current-history="currentHistory"
+                        title="Current History"
+                    />
                 </template>
             </HistoryPanel>
 
+            <!-- still loading -->
             <div v-else class="flex-grow-1 loadingBackground h-100">
                 <span class="sr-only" v-localize>Loading History...</span>
             </div>
@@ -27,7 +24,6 @@
 import CurrentUser from "components/providers/CurrentUser";
 import UserHistories from "./providers/UserHistories";
 import HistoryPanel from "./HistoryPanel";
-import HistorySelector from "./HistorySelector";
 import HistoriesMenu from "./HistoriesMenu";
 
 export default {
@@ -35,18 +31,12 @@ export default {
         CurrentUser,
         UserHistories,
         HistoryPanel,
-        HistorySelector,
         HistoriesMenu,
     },
-    data() {
-        return {
-            showModal: false,
-        };
-    },
-    methods: {
-        showModalHandler(event) {
-            this.showModal = !this.showModal;
-        },
-    },
+    // data() {
+    //     return {
+    //         showModal: false,
+    //     };
+    // },
 };
 </script>
diff --git a/client/src/components/History/EditorMenu.vue b/client/src/components/History/EditorMenu.vue
new file mode 100644
index 00000000000..a3c84878860
--- /dev/null
+++ b/client/src/components/History/EditorMenu.vue
@@ -0,0 +1,73 @@
+<template>
+    <nav class="edit-controls">
+        <IconButton
+            :title="label('Edit') | l"
+            class="edit-button mb-1"
+            :pressed="editing"
+            icon="pen"
+            @click="$emit('update:editing', !editing)"
+        />
+
+        <template v-if="editing">
+            <!-- save -->
+            <IconButton
+                :title="label('Save') | l"
+                class="save-button mb-1"
+                :class="{ disabled: !valid }"
+                icon="save"
+                @click="$emit('save')"
+            />
+
+            <!-- revert -->
+            <IconButton
+                :title="label('Revert') | l"
+                class="revert-changes-button mb-1"
+                :class="{ disabled: !dirty }"
+                icon="undo"
+                @click="$emit('revert')"
+            />
+
+            <!-- form status -->
+            <IconButton
+                :title="statusLabel | l"
+                class="status-button mb-1"
+                :class="{ valid: valid, disabled: !valid }"
+                :icon="valid ? 'check' : 'exclamation-triangle'"
+                variant="link"
+            />
+        </template>
+    </nav>
+</template>
+
+<script>
+import IconButton from "components/IconButton";
+
+export default {
+    components: {
+        IconButton,
+    },
+    props: {
+        modelName: { type: String, required: true },
+        editing: { type: Boolean, required: true },
+        dirty: { type: Boolean, required: false, default: false },
+        valid: { type: Boolean, required: false, default: false },
+    },
+    computed: {
+        statusLabel() {
+            const status = this.valid ? "Valid" : "Invalid";
+            return `${status} ${this.modelName}`;
+        },
+    },
+    methods: {
+        label(verb) {
+            return `${verb} ${this.modelName}`;
+        },
+    },
+};
+</script>
+
+<style lang="scss">
+.edit-controls .disabled {
+    opacity: 0.25;
+}
+</style>
diff --git a/client/src/components/History/HistoriesMenu.vue b/client/src/components/History/HistoriesMenu.vue
index ceb38a7df17..8e88a20cf3a 100644
--- a/client/src/components/History/HistoriesMenu.vue
+++ b/client/src/components/History/HistoriesMenu.vue
@@ -1,66 +1,83 @@
+<!-- menu allowing user to change the current history, make a new one, basically anything that's
+"above" editing the current history -->
+
 <template>
-    <PriorityMenu :starting-height="27">
-        <PriorityMenuItem
-            key="select-new-history"
-            title="Select History"
-            icon="fa fa-folder-open"
-            @click="$emit('selectHistoryModal')"
+    <div>
+        <b-dropdown
+            size="sm"
+            variant="link"
+            :text="title | l"
+            toggle-class="text-decoration-none"
+            no-caret
+            class="histories-operation-menu"
+            data-description="histories operation menu"
+        >
+            <template v-slot:button-content>
+                <Icon class="mr-1" icon="folder" />
+                <span id="click-me-fool" class="text-nowrap">{{ title | l }}</span>
+            </template>
+
+            <b-dropdown-text>
+                <span>You have {{ histories.length }} histories.</span>
+            </b-dropdown-text>
+
+            <b-dropdown-divider></b-dropdown-divider>
+
+            <b-dropdown-item v-b-modal.history-selector-modal>
+                <Icon class="mr-1" icon="exchange-alt" />
+                <span v-localize>Change the Current History</span>
+            </b-dropdown-item>
+
+            <b-dropdown-item @click="$emit('createNewHistory')">
+                <Icon class="mr-1" icon="plus" />
+                <span v-localize>Create a New History</span>
+            </b-dropdown-item>
+
+            <b-dropdown-item @click="backboneRoute('/histories/list')">
+                <Icon class="mr-1" icon="list" />
+                <span v-localize>View Saved Histories</span>
+            </b-dropdown-item>
+
+            <b-dropdown-item @click="redirect('/history/view_multiple')">
+                <Icon class="mr-1" icon="columns" />
+                <span v-localize>Show Histories Side-by-Side</span>
+            </b-dropdown-item>
+
+            <b-dropdown-divider></b-dropdown-divider>
+
+            <b-dropdown-item @click="switchToLegacyHistoryPanel">
+                <Icon class="mr-1" icon="arrow-up" />
+                <span v-localize>Return to legacy panel</span>
+            </b-dropdown-item>
+        </b-dropdown>
+
+        <!-- modals -->
+        <HistorySelectorModal
+            id="history-selector-modal"
+            :histories="histories"
+            :current-history="currentHistory"
+            @selectHistory="$emit('setCurrentHistory', $event)"
         />
-        <PriorityMenuItem
-            key="create-new-history"
-            title="Create New History"
-            class="history-new-button"
-            icon="fa fa-plus"
-            @click="$emit('createNewHistory')"
-        />
-        <PriorityMenuItem
-            key="view-all-histories"
-            title="View All Histories"
-            icon="fa fa-columns"
-            class="history-view-multi-button"
-            @click="redirect('/history/view_multiple')"
-        />
-        <PriorityMenuItem
-            key="saved-histories"
-            title="Saved Histories"
-            icon="fas fa-save"
-            @click="backboneRoute('/histories/list')"
-        />
-        <PriorityMenuItem
-            key="clear-history-cache"
-            title="Refresh History"
-            icon="fa fa-refresh"
-            class="history-refresh-button"
-            @click.stop="clearCache"
-        />
-        <PriorityMenuItem
-            key="use-legacy-history"
-            title="Return to legacy history panel"
-            icon="fas fa-exchange-alt"
-            @click="switchToLegacyHistoryPanel"
-        />
-    </PriorityMenu>
+    </div>
 </template>
 
 <script>
-import { PriorityMenuItem, PriorityMenu } from "components/PriorityMenu";
-import { wipeDatabase, clearHistoryDateStore } from "./caching";
+import { History } from "./model";
 import { legacyNavigationMixin } from "components/plugins/legacyNavigation";
 import { switchToLegacyHistoryPanel } from "./adapters/betaToggle";
-import { reloadPage } from "utils/redirect";
+import HistorySelectorModal from "./HistorySelectorModal";
 
 export default {
     mixins: [legacyNavigationMixin],
     components: {
-        PriorityMenu,
-        PriorityMenuItem,
+        HistorySelectorModal,
+    },
+    props: {
+        histories: { type: Array, required: true },
+        currentHistory: { type: History, required: true },
+        title: { type: String, required: false, default: "Histories" },
     },
     methods: {
-        async clearCache() {
-            await wipeDatabase();
-            await clearHistoryDateStore();
-            reloadPage();
-        },
         switchToLegacyHistoryPanel,
     },
 };
diff --git a/client/src/components/History/History.vue b/client/src/components/History/History.vue
index 5a6d3a2514b..48b1013848c 100644
--- a/client/src/components/History/History.vue
+++ b/client/src/components/History/History.vue
@@ -10,7 +10,7 @@
         <ExpandedItems
             :scope-key="history.id"
             :get-item-key="(item) => item.type_id"
-            v-slot="{ isExpanded, setExpanded }"
+            v-slot="{ expandedCount, isExpanded, setExpanded, collapseAll }"
         >
             <SelectedItems
                 :scope-key="history.id"
@@ -26,16 +26,20 @@
                 }"
             >
                 <Layout>
-                    <template v-slot:nav>
-                        <slot name="nav"></slot>
+                    <template v-slot:globalNav>
+                        <slot name="globalNav" :history="history"></slot>
+                    </template>
+
+                    <template v-slot:localNav>
+                        <HistoryMenu :history="history" v-on="$listeners" />
                     </template>
 
                     <template v-slot:details>
-                        <HistoryDetails class="history-details" :history="history" v-on="$listeners" />
+                        <HistoryDetails :history="history" v-on="$listeners" />
                     </template>
 
                     <template v-slot:messages>
-                        <HistoryMessages class="history-messages m-2" :history="history" />
+                        <HistoryMessages class="m-2" :history="history" />
                     </template>
 
                     <template v-slot:listcontrols>
@@ -51,6 +55,8 @@
                             @resetSelection="resetSelection"
                             @selectAllContent="selectItems(payload.contents)"
                             @manualReload="manualReload"
+                            :expanded-count="expandedCount"
+                            @collapseAllContent="collapseAll"
                         />
                     </template>
 
@@ -65,10 +71,11 @@
                             :debug="false"
                             @scroll="setScrollPos"
                         >
-                            <template v-slot="{ item, index }">
+                            <template v-slot="{ item, index, rowKey }">
                                 <HistoryContentItem
                                     :item="item"
                                     :index="index"
+                                    :row-key="rowKey"
                                     :show-selection="showSelection"
                                     :expanded="isExpanded(item)"
                                     @update:expanded="setExpanded(item, $event)"
@@ -101,6 +108,7 @@ import ToolHelpModal from "./ToolHelpModal";
 import Scroller from "./Scroller";
 import { HistoryContentItem } from "./ContentItem";
 import { reportPayload } from "./providers/ContentProvider/helpers";
+import HistoryMenu from "./HistoryMenu";
 
 export default {
     filters: {
@@ -118,6 +126,7 @@ export default {
         HistoryContentItem,
         ExpandedItems,
         SelectedItems,
+        HistoryMenu,
     },
     props: {
         history: { type: History, required: true },
diff --git a/client/src/components/History/HistoryDetails.vue b/client/src/components/History/HistoryDetails.vue
index a271f0e6006..a9bc27bf1e7 100644
--- a/client/src/components/History/HistoryDetails.vue
+++ b/client/src/components/History/HistoryDetails.vue
@@ -1,215 +1,145 @@
-<template>
-    <header>
-        <div class="d-flex justify-content-between align-items-center actions">
-            <h6 class="text-nowrap text-truncate mr-auto">
-                <span class="size history-size">{{ history.niceSize | localize }}</span>
-            </h6>
+<!--
+History object editor. Change name, edit tags, description.
+Emit new History model object when done via .sync syntax
+-->
 
-            <PriorityMenu style="max-width: 50%" :starting-height="28">
-                <PriorityMenuItem
-                    key="edit-history-tags"
-                    title="Edit History Tags"
-                    class="history-tag-btn"
-                    icon="fas fa-tags"
-                    :pressed="showTags"
-                    @click="showTags = !showTags"
-                />
-                <PriorityMenuItem
-                    key="edit-history-annotation"
-                    title="Edit Annotation"
-                    class="history-annotate-btn"
-                    icon="fas fa-comment"
-                    :pressed="showAnnotation"
-                    @click="showAnnotation = !showAnnotation"
-                />
-                <PriorityMenuItem
-                    key="copy-history"
-                    title="Copy History"
-                    icon="fas fa-copy"
-                    @click="showCopyModal = !showCopyModal"
-                />
-                <PriorityMenuItem
-                    key="share"
-                    title="Share or Publish"
-                    icon="fas fa-share-alt"
-                    @click="backboneRoute('/histories/sharing', { id: history.id })"
-                />
-                <PriorityMenuItem
-                    key="delete-this-history"
-                    title="Delete this History"
-                    icon="fas fa-trash"
-                    @click="showDeleteModal = !showDeleteModal"
-                />
-                <PriorityMenuItem
-                    key="purge-this-history"
-                    title="Purge this History"
-                    icon="fas fa-burn"
-                    @click="showPurgeModal = !showPurgeModal"
-                />
-                <PriorityMenuItem
-                    key="structure"
-                    title="Show Structure"
-                    icon="fas fa-code-branch"
-                    @click="backboneRoute('/histories/show_structure')"
-                />
-                <PriorityMenuItem
-                    key="extract-workflow"
-                    title="Extract Workflow"
-                    icon="fas fa-file-export"
-                    @click="iframeRedirect('/workflow/build_from_current_history')"
-                />
-                <PriorityMenuItem
-                    key="set-permissions"
-                    title="Set Permissions"
-                    icon="fas fa-user-lock"
-                    @click="backboneRoute('/histories/permissions', { id: history.id })"
-                />
-                <PriorityMenuItem
-                    key="make-private"
-                    title="Make Private"
-                    icon="fas fa-lock"
-                    @click="showPrivacyModal = !showPrivacyModal"
-                />
-                <PriorityMenuItem
-                    key="resume-paused-jobs"
-                    title="Resume Paused Jobs"
-                    icon="fas fa-play"
-                    @click="iframeRedirect('/history/resume_paused_jobs?current=True')"
-                />
-                <PriorityMenuItem
-                    key="export-citations"
-                    title="Export Tool Citations"
-                    icon="fas fa-stream"
-                    @click="backboneRoute('/histories/citations', { id: history.id })"
-                />
-                <PriorityMenuItem
-                    key="export-history-to-file"
-                    title="Export History to File"
-                    icon="fas fa-file-archive"
-                    @click="backboneRoute(exportLink)"
-                />
-            </PriorityMenu>
+<template>
+    <section class="history-details d-flex">
+        <div class="flex-grow-1">
+            <h3>{{ historyName || "(History Name)" }}</h3>
+            <h5 class="history-size">{{ history.size | niceFileSize }}</h5>
+
+            <!-- display title, annotation, tags -->
+            <div v-if="!editing">
+                <p v-if="annotation" class="mt-1">{{ annotation }}</p>
+                <HistoryTags class="mt-2" :history="history" :disabled="true" />
+            </div>
+
+            <!-- edit form, change title, annotation, or tags -->
+            <div v-else class="mt-3">
+                <b-textarea
+                    class="mb-2"
+                    v-model="historyName"
+                    placeholder="History Name"
+                    trim
+                    max-rows="4"
+                ></b-textarea>
+
+                <b-textarea
+                    class="mb-2"
+                    v-model="annotation"
+                    placeholder="Annotation (optional)"
+                    trim
+                    max-rows="4"
+                ></b-textarea>
+
+                <HistoryTags class="mt-3" :history="history" />
+            </div>
         </div>
 
-        <!-- click to edit the name of the history -->
-        <ClickToEdit
-            class="history-title mt-2"
-            tag-name="h3"
-            v-model="historyName"
-            :title="'Rename history...' | localize"
-            v-b-tooltip.hover="{ boundary: 'viewport', placement: 'left' }"
+        <EditorMenu
+            class="ml-3 flex-grow-0 d-flex flex-column"
+            v-if="writable"
+            model-name="History"
+            :editing.sync="editing"
+            :writable="writable"
+            :valid="valid"
+            :dirty="dirty"
+            @save="save"
+            @revert="revert"
         />
-
-        <transition name="shutterfade">
-            <Annotation v-if="showAnnotation" class="history-annotation mt-2" v-model="annotation" />
-        </transition>
-
-        <transition name="shutterfade">
-            <HistoryTags v-if="showTags" class="mt-2" :history="history" />
-        </transition>
-
-        <!-- #region modals -->
-
-        <CopyHistoryModal v-model="showCopyModal" :history="history" />
-
-        <b-modal v-model="showPrivacyModal" title="Make History Private" title-tag="h2" @ok="makePrivate">
-            <p v-localize>
-                This will make all the data in this history private (excluding library datasets), and will set
-                permissions such that all new data is created as private. Any datasets within that are currently shared
-                will need to be re-shared or published. Are you sure you want to do this?
-            </p>
-        </b-modal>
-
-        <b-modal v-model="showDeleteModal" title="Delete History?" title-tag="h2" @ok="deleteHistory">
-            <p v-localize>Really delete the current history?</p>
-        </b-modal>
-
-        <b-modal v-model="showPurgeModal" title="Permanently Delete History?" title-tag="h2" @ok="purgeHistory">
-            <p v-localize>Really delete the current history permanently? This cannot be undone.</p>
-        </b-modal>
-
-        <!-- #endregion -->
-    </header>
+    </section>
 </template>
 
 <script>
+import prettyBytes from "pretty-bytes";
 import { History } from "./model";
-import { PriorityMenuItem, PriorityMenu } from "components/PriorityMenu";
-import { legacyNavigationMixin } from "components/plugins/legacyNavigation";
-import ClickToEdit from "components/ClickToEdit";
-import Annotation from "components/Annotation";
 import HistoryTags from "./HistoryTags";
-import CopyHistoryModal from "./CopyModal";
+import EditorMenu from "./EditorMenu";
 
 export default {
-    mixins: [legacyNavigationMixin],
     components: {
-        PriorityMenu,
-        PriorityMenuItem,
         HistoryTags,
-        Annotation,
-        ClickToEdit,
-        CopyHistoryModal,
+        EditorMenu,
+    },
+    filters: {
+        niceFileSize(rawSize = 0) {
+            return prettyBytes(rawSize);
+        },
     },
     props: {
         history: { type: History, required: true },
+        writable: { type: Boolean, required: false, default: true },
     },
     data() {
         return {
-            showTags: false,
-            showAnnotation: false,
-            showCopyModal: false,
-            showPrivacyModal: false,
-            showDeleteModal: false,
-            showPurgeModal: false,
+            editing: false,
+            tempHistory: this.history.clone(),
         };
     },
     computed: {
+        historyId() {
+            return this.history.id;
+        },
+        isEditing() {
+            return this.writable && this.editing;
+        },
+        valid() {
+            return this.tempHistory.name.length > 0;
+        },
+        dirty() {
+            return !this.tempHistory.equals(this.history);
+        },
         annotation: {
             get() {
-                return this.history.annotation || "";
+                return this.tempHistory.annotation;
             },
             set(annotation) {
-                if (annotation.length && annotation !== this.history.annotation) {
-                    this.updateFields({ annotation });
-                }
+                this.patchTempHistory({ annotation });
             },
         },
-
         historyName: {
             get() {
-                return this.history?.name || "";
+                return this.tempHistory.name;
             },
             set(name) {
-                if (name.length && name !== this.history.name) {
-                    this.updateFields({ name });
-                }
+                this.patchTempHistory({ name });
             },
         },
-        exportLink() {
-            return `histories/${this.history.id}/export`;
+        tags: {
+            get() {
+                return this.tempHistory.tags || [];
+            },
+            set(newTags) {
+                this.patchTempHistory({ tags: newTags });
+            },
+        },
+    },
+    watch: {
+        historyId(newId, oldId) {
+            if (newId != oldId) {
+                this.reset();
+            }
         },
     },
     methods: {
-        async updateFields(fields = {}) {
-            this.$emit("updateHistory", { id: this.history.id, ...fields });
+        reset() {
+            this.tempHistory = this.history.clone();
         },
-        async deleteHistory(evt) {
-            this.$emit("deleteHistory", this.history);
-            evt.vueTarget.hide();
+        patchTempHistory(props = {}) {
+            this.tempHistory = this.tempHistory.patch(props);
         },
-        async purgeHistory(evt) {
-            this.$emit("purgeHistory", this.history);
-            evt.vueTarget.hide();
+        save() {
+            if (this.valid) {
+                this.$emit("update:history", this.tempHistory);
+                this.editing = false;
+            }
         },
-        async makePrivate(evt) {
-            this.$emit("secureHistory", this.history);
-            evt.vueTarget.hide();
+        revert() {
+            if (this.dirty) {
+                this.reset();
+            }
         },
     },
 };
 </script>
-
-<style lang="scss">
-@import "scss/transitions.scss";
-</style>
diff --git a/client/src/components/History/HistoryMenu.vue b/client/src/components/History/HistoryMenu.vue
new file mode 100644
index 00000000000..a80bf9a9925
--- /dev/null
+++ b/client/src/components/History/HistoryMenu.vue
@@ -0,0 +1,119 @@
+<template>
+    <div>
+        <b-dropdown size="sm" variant="link" text="Histories" toggle-class="text-decoration-none">
+            <template v-slot:button-content>
+                <Icon icon="wrench" />
+                <span class="sr-only">Operations on the current history</span>
+            </template>
+
+            <b-dropdown-item v-b-modal:copy-history-modal>
+                <Icon icon="copy" class="mr-1" />
+                <span v-localize>Copy this History</span>
+            </b-dropdown-item>
+
+            <b-dropdown-item v-b-modal:delete-history-modal>
+                <Icon icon="trash" class="mr-1" />
+                <span v-localize>Delete this History</span>
+            </b-dropdown-item>
+
+            <b-dropdown-item v-b-modal:purge-history-modal>
+                <Icon icon="burn" class="mr-1" />
+                <span v-localize>Purge this History</span>
+            </b-dropdown-item>
+
+            <b-dropdown-divider></b-dropdown-divider>
+
+            <b-dropdown-item @click="iframeRedirect('/history/resume_paused_jobs?current=True')">
+                <Icon icon="play" class="mr-1" />
+                <span v-localize>Resume Paused Jobs</span>
+            </b-dropdown-item>
+
+            <b-dropdown-item @click="iframeRedirect('/workflow/build_from_current_history')">
+                <Icon icon="file-export" class="mr-1" />
+                <span v-localize>Extract Workflow</span>
+            </b-dropdown-item>
+
+            <b-dropdown-item @click="backboneRoute('/histories/show_structure')">
+                <Icon icon="code-branch" class="mr-1" />
+                <span v-localize>Show Structure</span>
+            </b-dropdown-item>
+
+            <b-dropdown-divider></b-dropdown-divider>
+
+            <b-dropdown-item @click="backboneRoute('/histories/sharing', { id: history.id })">
+                <Icon icon="share-alt" class="mr-1" />
+                <span v-localize>Share or Publish</span>
+            </b-dropdown-item>
+
+            <b-dropdown-item @click="backboneRoute('/histories/permissions', { id: history.id })">
+                <Icon icon="user-lock" class="mr-1" />
+                <span v-localize>Set Permissions</span>
+            </b-dropdown-item>
+
+            <b-dropdown-item v-b-modal:history-privacy-modal>
+                <Icon icon="lock" class="mr-1" />
+                <span v-localize>Make Private</span>
+            </b-dropdown-item>
+
+            <b-dropdown-divider></b-dropdown-divider>
+
+            <b-dropdown-item @click="backboneRoute('/histories/citations', { id: history.id })">
+                <Icon icon="stream" class="mr-1" />
+                <span v-localize>Export Tool Citations</span>
+            </b-dropdown-item>
+
+            <b-dropdown-item @click="backboneRoute(history.exportLink)">
+                <Icon icon="file-archive" class="mr-1" />
+                <span v-localize>Export History to File</span>
+            </b-dropdown-item>
+        </b-dropdown>
+
+        <!-- #region modals -->
+
+        <CopyHistoryModal id="copy-history-modal" :history="history" />
+
+        <b-modal
+            id="history-privacy-modal"
+            title="Make History Private"
+            title-tag="h2"
+            @ok="$emit('secureHistory', history)"
+        >
+            <p v-localize>
+                This will make all the data in this history private (excluding library datasets), and will set
+                permissions such that all new data is created as private. Any datasets within that are currently shared
+                will need to be re-shared or published. Are you sure you want to do this?
+            </p>
+        </b-modal>
+
+        <b-modal id="delete-history-modal" title="Delete History?" title-tag="h2" @ok="$emit('deleteHistory', history)">
+            <p v-localize>Really delete the current history?</p>
+        </b-modal>
+
+        <b-modal
+            id="purge-history-modal"
+            title="Permanently Delete History?"
+            title-tag="h2"
+            @ok="$emit('purgeHistory', history)"
+        >
+            <p v-localize>Really delete the current history permanently? This cannot be undone.</p>
+        </b-modal>
+
+        <!-- #endregion -->
+    </div>
+</template>
+
+<script>
+import { History } from "./model";
+import CopyHistoryModal from "./CopyModal";
+import { legacyNavigationMixin } from "components/plugins/legacyNavigation";
+
+export default {
+    mixins: [legacyNavigationMixin],
+    components: {
+        CopyHistoryModal,
+    },
+    props: {
+        history: { type: History, required: true },
+    },
+};
+</script>
diff --git a/client/src/components/History/HistorySelectorModal.vue b/client/src/components/History/HistorySelectorModal.vue
new file mode 100644
index 00000000000..58e2ffeea45
--- /dev/null
+++ b/client/src/components/History/HistorySelectorModal.vue
@@ -0,0 +1,106 @@
+<template>
+    <b-modal ref="modal" v-on="$listeners" v-bind="$attrs" :title="'Switch to History' | l">
+        <b-form-group :description="'Filter histories' | l">
+            <b-input v-model="filter" :placeholder="'Search Filter' | l" />
+        </b-form-group>
+
+        <b-table
+            ref="history-list"
+            striped
+            hover
+            sticky-header="50vh"
+            v-model="currentRows"
+            primary-key="id"
+            :fields="fields"
+            :filter="filter"
+            :items="histories"
+            :per-page="perPage"
+            :current-page="currentPage"
+            :selectable="true"
+            select-mode="single"
+            selected-variant="success"
+            @row-selected="switchToHistory"
+        >
+            <template v-slot:cell(tags)="row">
+                <stateless-tags :value="row.item.tags" :disabled="true" />
+            </template>
+            <template v-slot:cell(update_time)="data">
+                <UtcDate :date="data.value" mode="elapsed" />
+            </template>
+        </b-table>
+
+        <template v-slot:modal-footer>
+            <b-pagination v-model="currentPage" :total-rows="filteredRowCount" :per-page="perPage"></b-pagination>
+        </template>
+    </b-modal>
+</template>
+
+<script>
+import { StatelessTags } from "components/Tags";
+import UtcDate from "components/UtcDate";
+import { debounce } from "underscore";
+
+export default {
+    components: {
+        StatelessTags,
+        UtcDate,
+    },
+    props: {
+        currentHistory: { type: Object, required: true },
+        histories: { type: Array, default: () => [] },
+        perPage: { type: Number, required: false, default: 50 },
+    },
+    data() {
+        return {
+            filter: null,
+            currentPage: 1,
+            currentRows: [],
+        };
+    },
+    computed: {
+        filteredRowCount() {
+            return this.currentRows.length;
+        },
+        selectedIndex() {
+            return this.currentRows.findIndex((h) => h.id == this.currentHistory.id);
+        },
+    },
+    created() {
+        this.fields = [
+            { key: "name", sortable: true },
+            { key: "tags", sortable: true },
+            { key: "update_time", label: "Updated", sortable: true },
+        ];
+        this.debounceSelectCurrentRow = debounce(this.selectCurrentRow, 100);
+    },
+    watch: {
+        currentRows() {
+            this.selectCurrentRow();
+        },
+        filteredRowCount(newVal, oldVal) {
+            if (newVal != oldVal) {
+                this.currentPage = 1;
+            }
+        },
+        selectedIndex(idx, oldIdx) {
+            if (idx != oldIdx) {
+                this.debounceSelectCurrentRow();
+            }
+        },
+    },
+    methods: {
+        switchToHistory(selected) {
+            if (selected.length == 1) {
+                this.$emit("selectHistory", selected[0]);
+            }
+        },
+        selectCurrentRow() {
+            const idx = this.selectedIndex;
+            const list = this.$refs["history-list"];
+            if (list && idx > -1) {
+                list.selectRow(idx);
+            }
+        },
+    },
+};
+</script>
diff --git a/client/src/components/History/HistoryTags.vue b/client/src/components/History/HistoryTags.vue
index c8388e1380f..3623963e158 100644
--- a/client/src/components/History/HistoryTags.vue
+++ b/client/src/components/History/HistoryTags.vue
@@ -1,5 +1,5 @@
 <template>
-    <Tags :tags="history.tags" :store-key="storeKey" :tag-service="historyTagService" />
+    <Tags :tags="history.tags" :store-key="storeKey" :tag-service="historyTagService" :disabled="disabled" />
 </template>
 
 <script>
@@ -48,6 +48,7 @@ export default {
     components: { Tags },
     props: {
         history: { type: History, required: true },
+        disabled: { type: Boolean, required: false, default: false },
     },
     computed: {
         storeKey() {
diff --git a/client/src/components/History/Layout.vue b/client/src/components/History/Layout.vue
index b36f8bd1772..cbcf3e1ee3f 100644
--- a/client/src/components/History/Layout.vue
+++ b/client/src/components/History/Layout.vue
@@ -4,14 +4,17 @@ amateur-hour baby-tool like Bootstrap instead of taking the afternoon
 to learn how CSS is supposed to work. -->
 
 <template>
-    <section class="history d-flex flex-column">
-        <header class="p-2">
-            <!-- optional slot for injecting global navigation -->
-            <nav v-if="$slots.nav" class="top-nav pb-2">
-                <slot name="nav"></slot>
+    <section class="history beta d-flex flex-column">
+        <header>
+            <nav class="d-flex justify-content-between bg-secondary">
+                <slot name="globalNav">Global Nav Default</slot>
+                <slot name="localNav">Local nav Default</slot>
             </nav>
+
             <!-- details about the thing you're looking at -->
-            <slot name="details"></slot>
+            <div class="px-3 py-4 details">
+                <slot name="details"></slot>
+            </div>
         </header>
 
         <!-- warnings, messages, dirty limericks -->
@@ -20,12 +23,12 @@ to learn how CSS is supposed to work. -->
         </section>
 
         <!-- controls atop the list -->
-        <section v-if="$slots.listcontrols" class="p-2">
+        <section v-if="$slots.listcontrols" class="list-controls">
             <slot name="listcontrols"></slot>
         </section>
 
         <!-- scrolling list -->
-        <section class="scroller flex-grow-1">
+        <section class="position-relative flex-grow-1 scroller">
             <slot name="listing"></slot>
         </section>
 
@@ -37,13 +40,8 @@ to learn how CSS is supposed to work. -->
 </template>
 
 <style lang="scss">
-@import "scss/mixins.scss";
-@import "scss/transitions.scss";
-@import "scss/loadingBackground.scss";
-
-/* TODO: css reset? */
-
-.history {
+.history.beta {
+    /* TODO: css reset? */
     h1,
     h2,
     h3,
@@ -52,31 +50,14 @@ to learn how CSS is supposed to work. -->
     h6 {
         margin: 0;
     }
-}
 
-/*
-container css for first child of top-nav,
-flex horizontally
+    .list-controls {
+        margin-bottom: 2px;
+    }
 
-Vue can't put in multi-root slot contents so we have to do some kung-fu to get
-the layout right on the top-nav. There will have to be an extra div container
-around the contents of the nav slot, so we'll style that right here so the user
-doesn't need to do it manually every time. */
-
-.history > header > .top-nav > * {
-    display: flex;
-    flex-direction: row;
-    align-items: center;
-    justify-content: space-between;
-}
-
-.history .messages:empty {
-    display: none;
-}
-
-/* make sure scroller actually scrolls */
-
-.history .scroller {
-    position: relative;
+    .list-controls:empty,
+    .messages:empty {
+        display: none;
+    }
 }
 </style>
diff --git a/client/src/components/History/Scroller.vue b/client/src/components/History/Scroller.vue
index 1ca1c7ed8b0..a9ba80d71ab 100644
--- a/client/src/components/History/Scroller.vue
+++ b/client/src/components/History/Scroller.vue
@@ -3,9 +3,14 @@
         <!-- mousewheel moves up and down linearly, allows for fine-tuning of view by moving just a
         few rows at a time -->
         <div ref="listing" class="listing">
-            <ul>
-                <li v-for="(item, index) in itemWindow" :key="getItemKey(item, index)">
-                    <slot :item="item" :index="index" :row-key="getItemKey(item, index)">
+            <ul class="list-unstyled m-0">
+                <li
+                    v-for="(item, index) in itemWindow"
+                    :key="getItemKey(item)"
+                    :data-row-index="index"
+                    :data-row-key="getItemKey(item)"
+                >
+                    <slot :item="item" :index="index" :row-key="getItemKey(item)">
                         <pre>{{ item }}</pre>
                     </slot>
                 </li>
@@ -15,6 +20,7 @@
         <!-- big blank scroll region uses scroll bar to drag view to entirely new region, calculated
         by visual height of the scroller knob --->
         <div
+            v-if="overlayActive"
             v-show="showScroller"
             ref="scrollSliderContainer"
             class="scrollSliderContainer"
@@ -23,6 +29,12 @@
         >
             <div ref="scrollSlider"></div>
         </div>
+
+        <!-- debugging overlay -->
+        <div v-if="debug" class="debugOverlay">
+            <pre>{{ $attrs }}</pre>
+            <pre>{{ debugProps }}</pre>
+        </div>
     </div>
 </template>
 
@@ -75,10 +87,26 @@ export default {
 
             // width of scroll bar container
             sbWidth: 30,
+
+            // whether to activate the 2nd scrollbar which does a fast-seek on large histories
+            overlayActive: true,
         };
     },
 
     computed: {
+        debugProps() {
+            return {
+                manualStartIndex: this.manualStartIndex,
+                keyField: this.keyField,
+                contentsLength: this.contents.length,
+                startKeyIndex: this.startKeyIndex,
+                totalMatches: this.totalMatches,
+                topRows: this.topRows,
+                bottomRows: this.bottomRows,
+                pageSize: this.pageSize,
+            };
+        },
+
         // The index to start rendering content at, can be manually adjusted with
         // the mouse wheel, and must be updated when new contents come in
         itemStartIndex() {
@@ -144,7 +172,7 @@ export default {
         // non-reactive data
         this.suppressEvents = false;
         this.suppressionTimeout = null;
-        this.debouncedUpdateCursor = debounce(this.updateCursor, 100);
+        // this.debouncedUpdateCursor = debounce(this.updateCursor, 100);
         this.debouncedAdjustScrollTop = debounce(this.adjustScrollTop, 100);
     },
 
@@ -193,7 +221,8 @@ export default {
         // value which we send out on scrollPos
 
         onScroll() {
-            this.debouncedUpdateCursor();
+            // this.debouncedUpdateCursor();
+            this.updateCursor();
         },
 
         // determines cursor from scrollTop, need to wait until after render to calculate
@@ -290,22 +319,15 @@ export default {
 </script>
 
 <style lang="scss">
+@import "scss/mixins.scss";
+
+.scrollContainer,
+.listing,
+.scrollSliderContainer {
+    @include absfill();
+}
+
 .scrollContainer {
-    position: absolute;
-    top: 0;
-    left: 0;
-    right: 0;
-    bottom: 0;
-
-    .listing,
-    .scrollSliderContainer {
-        position: absolute;
-        top: 0;
-        left: 0;
-        right: 0;
-        bottom: 0;
-    }
-
     .listing {
         overflow-y: scroll;
         z-index: 0;
@@ -326,14 +348,14 @@ export default {
         }
     }
 
-    ul {
-        list-style: none;
-    }
-
-    ul,
-    li {
-        padding: 0;
-        margin: 0;
+    .debugOverlay {
+        background: rgba(255, 255, 255, 0.75);
+        z-index: 2;
+        position: absolute;
+        bottom: 0;
+        left: 0;
+        right: 0;
+        height: auto;
     }
 }
 </style>
diff --git a/client/src/components/History/StatusIcon.vue b/client/src/components/History/StatusIcon.vue
index b626cf7fccf..033e6fc2739 100644
--- a/client/src/components/History/StatusIcon.vue
+++ b/client/src/components/History/StatusIcon.vue
@@ -1,82 +1,55 @@
 <template>
-    <StateBtn
-        v-if="inState(STATES.RUNNING)"
-        :state="state"
-        icon="upload-symbol upload-icon fa fa-spinner fa-spin"
+    <IconButton
+        v-if="stateIcon"
+        v-b-tooltip
+        :title="theTitle"
+        :icon="stateIcon"
+        :variant="variant"
         v-on="$listeners"
+        v-bind="$attrs"
     />
-
-    <StateBtn v-else-if="inState(STATES.QUEUED, STATES.NEW)" :state="state" icon="fas fa-clock" v-on="$listeners" />
-
-    <StateBtn v-else-if="inState(STATES.PAUSED)" :state="state" icon="fas fa-pause" v-on="$listeners" />
-
-    <StateBtn v-else-if="inState(STATES.ERROR)" :state="state" icon="fas fa-exclamation-triangle" v-on="$listeners" />
-
-    <StateBtn v-else-if="inState(STATES.MIXED)" :state="state" icon="fas fa-exclamation-circle" v-on="$listeners" />
-
-    <span v-else class="sr-only">
-        {{ state | localize }}
-    </span>
 </template>
 
 <script>
 import capitalize from "underscore.string/capitalize";
+import IconButton from "components/IconButton";
 
-export const StateBtn = {
-    template: `
-        <b-button class="state-button"
-            v-b-tooltip
-            :title="theTitle | localize"
-            size="sm"
-            variant="link"
-            v-on="$listeners"
-            v-bind="$attrs">
-            <i :class="icon" />
-            <span class="sr-only">{{ theTitle | localize }}</span>
-        </b-button>
-    `,
+export default {
+    inject: ["STATES"],
+    components: {
+        IconButton,
+    },
     props: {
         state: { type: String, required: true },
-        icon: { type: String, required: true },
-        title: { type: String, required: false, default: "" },
+        variant: { type: String, required: false, default: "link" },
     },
-    inject: ["STATES"],
     computed: {
+        stateIcon() {
+            if (this.inState(this.STATES.QUEUED, this.STATES.NEW)) {
+                return "clock";
+            }
+            if (this.inState(this.STATES.PAUSED)) {
+                return "pause";
+            }
+            if (this.inState(this.STATES.ERROR)) {
+                return "exclamation-triangle";
+            }
+            if (this.inState(this.STATES.MIXED)) {
+                return "exclamation-circle";
+            }
+            if (this.inState(this.STATES.OK)) {
+                return "check";
+            }
+            return null;
+        },
         theTitle() {
             return this.title || capitalize(this.state);
         },
     },
-};
-
-export const StatusIcon = {
-    components: {
-        StateBtn,
-    },
-    props: {
-        state: { type: String, required: true },
-    },
-    inject: ["STATES"],
     methods: {
         inState(...states) {
             return states.includes(this.state);
         },
     },
 };
-
-export default StatusIcon;
 </script>
-
-<style lang="css">
-/* Override ham-fisted base css rules */
-
-button.state-button,
-button.state-button.disabled,
-button.state-button:disabled,
-button.state-button:focus,
-button.state-button:hover,
-button.state-button:not(:disabled):active {
-    background-color: transparent !important;
-    border-style: none !important;
-    box-shadow: none !important;
-}
-</style>
diff --git a/client/src/components/History/caching/loadDscContent.js b/client/src/components/History/caching/loadDscContent.js
index 9ed786007f9..aa65fd96092 100644
--- a/client/src/components/History/caching/loadDscContent.js
+++ b/client/src/components/History/caching/loadDscContent.js
@@ -10,13 +10,14 @@ import { bulkCacheDscContent } from "./db";
 import { SearchParams } from "../model/SearchParams";
 import { prependPath } from "./workerConfig";
 import { summarizeCacheOperation, dateStore } from "./loadHistoryContents";
+import { show } from "utils/observable";
 
 /**
  * Load collection content (drill down)
  * Params: contents_url + search params + element_index
  */
 export const loadDscContent = (cfg = {}) => {
-    // const { onceEvery = 10 * 1000 } = cfg;
+    const { debug = false } = cfg;
 
     return publish((inputs$) => {
         const url$ = inputs$.pipe(nth(0));
@@ -24,6 +25,7 @@ export const loadDscContent = (cfg = {}) => {
         return inputs$.pipe(
             map(buildDscContentUrl),
             map(prependPath),
+            show(debug, (url) => console.log("Sending collection request:", url)),
             requestWithUpdateTime({ dateStore }),
             pluck("response"),
             withLatestFrom(url$),
diff --git a/client/src/components/History/caching/operators/chunk.js b/client/src/components/History/caching/operators/chunk.js
deleted file mode 100644
index 74a1a7f9cc2..00000000000
--- a/client/src/components/History/caching/operators/chunk.js
+++ /dev/null
@@ -1,42 +0,0 @@
-import { pipe } from "rxjs";
-import { map } from "rxjs/operators";
-
-/**
- * Bust incoming numeric source values into blocks of designated size.
- *
- * @param {*} chunkSize
- * @param {*} ceil
- */
-// prettier-ignore
-export const chunk = (chunkSize, ceil = false) => pipe(
-    map((chunkMe) => {
-        const rawVal = chunkMe / chunkSize;
-        return chunkSize * (ceil ? Math.ceil(rawVal) : Math.floor(rawVal));
-    })
-);
-
-/**
- * Change one parameter to be an multiple of indicated block size. Used to
- * regulate the URLs we send to the server so that some will be cached. Pos is
- * the position in the combined inputs array, and the chunkSize is the size of
- * the block to break the value into.
- *
- * Ex: Source Inputs [ x, y, z, 750 ],
- *     chunkParam(3, 200)
- *     Results in [ x, y, z, 600]
- *
- * @param {integer} pos Input array parameter number to chunk
- * @param {integer} chunkSize Size of chunks
- * @param {Boolean} ceil Math.ceil or Math.floor chunk value
- */
-// prettier-ignore
-export const chunkParam = (pos, chunkSize, ceil = false) => pipe(
-    map((inputs) => {
-        const chunkMe = inputs[pos];
-        const rawVal = 1.0 * chunkMe / chunkSize;
-        const chunkedVal = chunkSize * (ceil ? Math.ceil(rawVal) : Math.floor(rawVal));
-        const newInputs = inputs.slice();
-        newInputs[pos] = chunkedVal;
-        return newInputs;
-    })
-);
diff --git a/client/src/components/History/model/Dataset.js b/client/src/components/History/model/Dataset.js
index 68ca88bdcea..f5c3b6eae64 100644
--- a/client/src/components/History/model/Dataset.js
+++ b/client/src/components/History/model/Dataset.js
@@ -5,6 +5,7 @@
  */
 
 import { Content } from "./Content";
+import { scrubModelProps } from "utils/safeAssign";
 
 export class Dataset extends Content {
     getUrl(urlType) {
@@ -40,4 +41,28 @@ export class Dataset extends Content {
         const { display_apps = [], display_types = [] } = this;
         return [...display_apps, ...display_types];
     }
+
+    clone() {
+        const newProps = cleanDatasetProps(this);
+        return new Dataset(newProps);
+    }
+
+    patch(newProps) {
+        const cleanProps = cleanDatasetProps({ ...this, ...newProps });
+        return new Dataset(cleanProps);
+    }
+
+    equals(other) {
+        return Dataset.equals(this, other);
+    }
 }
+
+Dataset.equals = function (a, b) {
+    return JSON.stringify(a) == JSON.stringify(b);
+};
+
+const scrubber = scrubModelProps(Dataset);
+export const cleanDatasetProps = (props = {}) => {
+    const cleanProps = JSON.parse(JSON.stringify(props));
+    return scrubber(cleanProps);
+};
diff --git a/client/src/components/History/model/DatasetCollection.js b/client/src/components/History/model/DatasetCollection.js
index 2dc5f3f60fc..196bd186c31 100644
--- a/client/src/components/History/model/DatasetCollection.js
+++ b/client/src/components/History/model/DatasetCollection.js
@@ -7,11 +7,11 @@
 
 import { Content } from "./Content";
 import { JobStateSummary } from "./JobStateSummary";
+import { scrubModelProps } from "utils/safeAssign";
 
 export class DatasetCollection extends Content {
     loadProps(raw = {}) {
         if (!raw.contents_url) {
-            // console.log("ouch", raw);
             throw new Error("missing contents_url", raw);
         }
         super.loadProps(raw);
@@ -64,8 +64,28 @@ export class DatasetCollection extends Content {
     get jobSummary() {
         return new JobStateSummary(this);
     }
+
+    clone() {
+        const newProps = cleanDscProps(this);
+        return new DatasetCollection(newProps);
+    }
+
+    patch(newProps) {
+        const cleanProps = cleanDscProps({ ...this, ...newProps });
+        return new DatasetCollection(cleanProps);
+    }
+
+    equals(other) {
+        return DatasetCollection.equals(this, other);
+    }
 }
 
 DatasetCollection.equals = function (a, b) {
     return JSON.stringify(a) == JSON.stringify(b);
 };
+
+const scrubber = scrubModelProps(DatasetCollection);
+export const cleanDscProps = (props = {}) => {
+    const cleanProps = JSON.parse(JSON.stringify(props));
+    return scrubber(cleanProps);
+};
diff --git a/client/src/components/History/model/History.js b/client/src/components/History/model/History.js
index 5285eecbd19..388db974538 100644
--- a/client/src/components/History/model/History.js
+++ b/client/src/components/History/model/History.js
@@ -1,4 +1,5 @@
 import { dateMixin, ModelBase } from "./ModelBase";
+import { scrubModelProps } from "utils/safeAssign";
 
 export class History extends dateMixin(ModelBase) {
     // not deleted
@@ -36,8 +37,32 @@ export class History extends dateMixin(ModelBase) {
         }
         return status.join(", ");
     }
+
+    get exportLink() {
+        return `histories/${this.id}/export`;
+    }
+
+    clone() {
+        const newProps = cleanHistoryProps(this);
+        return new History(newProps);
+    }
+
+    patch(newProps) {
+        const cleanProps = cleanHistoryProps({ ...this, ...newProps });
+        return new History(cleanProps);
+    }
+
+    equals(other) {
+        return History.equals(this, other);
+    }
 }
 
 History.equals = function (a, b) {
     return JSON.stringify(a) == JSON.stringify(b);
 };
+
+const scrubber = scrubModelProps(History);
+export const cleanHistoryProps = (props = {}) => {
+    const cleanProps = JSON.parse(JSON.stringify(props));
+    return scrubber(cleanProps);
+};
diff --git a/client/src/components/History/model/History.test.js b/client/src/components/History/model/History.test.js
new file mode 100644
index 00000000000..2571b24120e
--- /dev/null
+++ b/client/src/components/History/model/History.test.js
@@ -0,0 +1,101 @@
+import { History, cleanHistoryProps } from "./History";
+
+describe("History model", () => {
+    const initialProps = {
+        id: "abc123",
+        name: "Foo",
+        tags: ["a", "b", "c"],
+        annotation: "I am a test history",
+    };
+
+    const h = new History(initialProps);
+
+    describe("clone", () => {
+        const c = h.clone();
+
+        it("must be able to clone itself for use in editors", () => {
+            // should be == but not ===
+            expect(h).not.toBe(c);
+            expect(c).toBeInstanceOf(History);
+            expect(History.equals(h, c)).toBeTruthy();
+        });
+
+        it("should have the same props before and after cloning", () => {
+            expect(h.id).toEqual(c.id);
+            expect(h.name).toEqual(c.name);
+            expect(h.tags).toEqual(c.tags);
+            expect(h.annotation).toEqual(c.annotation);
+        });
+    });
+
+    describe("cleanHistoryProps", () => {
+        it("should ignore computed prop names during cloning", () => {
+            const sloppyProps = {
+                ...initialProps,
+                // these are all computed values in the history class which are defined by getters,
+                // if we feed thsm into the constructor they should be ignored
+                statusDescription: "123",
+                totalItems: Number.POSITIVE_INFINITY,
+                hidItems: "four",
+                active: "The Fonz",
+            };
+
+            const cleanProps = cleanHistoryProps(sloppyProps);
+            expect(cleanProps).toEqual(initialProps);
+            expect(cleanProps).not.toBe(initialProps);
+
+            expect(cleanProps).not.toHaveProperty("statusDescription");
+            expect(cleanProps).not.toHaveProperty("totalItems");
+            expect(cleanProps).not.toHaveProperty("hidItems");
+            expect(cleanProps).not.toHaveProperty("active");
+
+            const h = new History(cleanProps);
+            expect(h.statusDescription).not.toEqual(sloppyProps.statusDescription);
+        });
+    });
+
+    describe("patch", () => {
+        const patchVals = {
+            name: "i was patched",
+            annotation: "patched annotation",
+            tags: ["foo", "bar", "blech"],
+        };
+
+        const clone = h.patch(patchVals);
+
+        it("should return a new instance of History", () => {
+            expect(h).not.toBe(clone);
+            expect(clone).toBeInstanceOf(History);
+            expect(History.equals(h, clone)).toBeFalsy();
+        });
+
+        it("should patch in passed properties", () => {
+            expect(clone.name).toEqual(patchVals.name);
+            expect(clone.annotation).toEqual(patchVals.annotation);
+            expect(clone.tags).toEqual(patchVals.tags);
+        });
+    });
+
+    describe("equivalence comparison", () => {
+        it("should recognize different props", () => {
+            const hDifferent = new History({ id: "def345" });
+            expect(History.equals(h, hDifferent)).toBeFalsy();
+        });
+
+        it("equivalence should work fine with cloned histories", () => {
+            const clone = h.clone();
+            // different object
+            expect(h).not.toBe(clone);
+            // but equivalent because props the same
+            expect(History.equals(h, clone)).toBeTruthy();
+        });
+
+        it("should work with patch", () => {
+            const clone = h.patch({ id: "floobar" });
+            // different object
+            expect(h).not.toBe(clone);
+            // not equivalent because different val
+            expect(History.equals(h, clone)).toBeFalsy();
+        });
+    });
+});
diff --git a/client/src/components/History/model/crud.js b/client/src/components/History/model/crud.js
index efab5d41316..b74a5ca9178 100644
--- a/client/src/components/History/model/crud.js
+++ b/client/src/components/History/model/crud.js
@@ -8,7 +8,9 @@ import { bulkContentUpdate, getAllContentByFilter } from "./queries";
 export const updateSelectedContent = (updates) => async (history, type_ids) => {
     // single ajax call with wierd syntax because.... reasons
     const changes = await bulkContentUpdate(history, type_ids, updates);
-    await bulkCacheContent(changes);
+    const cacheResult = await bulkCacheContent(changes, true);
+    console.log("cacheResult", changes, cacheResult);
+    return cacheResult;
 };
 
 export const hideSelectedContent = updateSelectedContent({
diff --git a/client/src/components/History/model/queries.js b/client/src/components/History/model/queries.js
index d497434cf3b..3b96eab7918 100644
--- a/client/src/components/History/model/queries.js
+++ b/client/src/components/History/model/queries.js
@@ -8,6 +8,7 @@
 import axios from "axios";
 import moment from "moment";
 import { prependPath } from "utils/redirect";
+import { History } from "./History";
 
 // #region setup & utils
 
@@ -87,9 +88,10 @@ const stdHistoryParams = {
  * Return list of available histories
  */
 export async function getHistoryList() {
-    const params = { view: "summary" };
+    const params = { view: "summary", keys: "size" };
     const response = await api.get("/histories", { params });
-    return doResponse(response);
+    const rawList = doResponse(response);
+    return rawList.map((props) => new History(props));
 }
 
 /**
@@ -101,7 +103,8 @@ export async function getHistoryById(id, since) {
     const sinceParam = since !== undefined ? moment.utc(since).toISOString() : null;
     const url = sinceParam ? `${path}?q=update_time-gt&qv=${sinceParam}` : path;
     const response = await api.get(url, { params: stdHistoryParams });
-    return doResponse(response);
+    const props = doResponse(response);
+    return new History(props);
 }
 
 /**
@@ -121,7 +124,8 @@ export async function createNewHistory(props = {}) {
     if (!id) {
         throw new Error("failed to create and select new history");
     }
-    return doResponse(createResponse);
+    const newHistoryProps = doResponse(createResponse);
+    return new History(newHistoryProps);
 }
 
 /**
@@ -139,7 +143,8 @@ export async function cloneHistory(history, name, copyAll) {
         current: true,
     };
     const response = await api.post(url, payload, { params: stdHistoryParams });
-    return doResponse(response);
+    const clonedProps = doResponse(response);
+    return new History(clonedProps);
 }
 
 /**
@@ -171,7 +176,8 @@ export async function undeleteHistoryById(id) {
 export async function updateHistoryFields(id, payload) {
     const url = `/histories/${id}`;
     const response = await api.put(url, payload, { params: stdHistoryParams });
-    return doResponse(response);
+    const props = doResponse(response);
+    return new History(props);
 }
 
 /**
@@ -202,7 +208,8 @@ export async function getCurrentHistoryFromServer() {
     const response = await api.get(url, {
         baseURL: prependPath("/"), // old api doesn't use api path
     });
-    return doResponse(response);
+    const props = doResponse(response);
+    return new History(props);
 }
 
 export async function setCurrentHistoryOnServer(history_id) {
diff --git a/client/src/components/History/providers/CollectionContentProvider/CollectionContentProvider.js b/client/src/components/History/providers/CollectionContentProvider/CollectionContentProvider.js
index d1c13228b19..5c4c07315fe 100644
--- a/client/src/components/History/providers/CollectionContentProvider/CollectionContentProvider.js
+++ b/client/src/components/History/providers/CollectionContentProvider/CollectionContentProvider.js
@@ -1,10 +1,14 @@
-import { DatasetCollection } from "../../model";
+import { SearchParams, DatasetCollection } from "../../model";
 import { ContentProvider, processContentStreams } from "../ContentProvider";
 import { collectionPayload } from "./collectionPayload";
 
 export default {
     mixins: [ContentProvider],
 
+    props: {
+        params: { type: SearchParams, default: () => new SearchParams({ showHidden: false }) },
+    },
+
     computed: {
         dsc() {
             if (this.parent instanceof DatasetCollection) {
diff --git a/client/src/components/History/providers/CollectionContentProvider/collectionPayload.js b/client/src/components/History/providers/CollectionContentProvider/collectionPayload.js
index 7ba1df9c3de..c0e92bc4501 100644
--- a/client/src/components/History/providers/CollectionContentProvider/collectionPayload.js
+++ b/client/src/components/History/providers/CollectionContentProvider/collectionPayload.js
@@ -1,5 +1,5 @@
 import { of, Observable, Subject, partition, merge } from "rxjs";
-import { tap, map, pluck, switchMap, publish, distinctUntilChanged, share } from "rxjs/operators";
+import { tap, map, pluck, switchMap, publish, distinctUntilChanged, share, throttleTime } from "rxjs/operators";
 import { chunk } from "utils/observable";
 import { SearchParams } from "../../model/SearchParams";
 import { loadDscContent } from "../../caching";
@@ -13,6 +13,8 @@ export const collectionPayload = (cfg = {}) => {
         pageSize = SearchParams.pageSize,
         debug = false,
         loadingEvents$ = new Subject(),
+        debouncePeriod = 100,
+        chunkSize = pageSize
     } = cfg;
 
     const { totalElements: totalMatches, contents_url } = dsc;
@@ -34,7 +36,7 @@ export const collectionPayload = (cfg = {}) => {
 
         // chunk the input to the server request so we don't request for every single mouse move
         const chunked$ = elementIndex$.pipe(
-            chunk(pageSize, false),
+            chunk(chunkSize),
             distinctUntilChanged(),
         );
 
@@ -48,6 +50,7 @@ export const collectionPayload = (cfg = {}) => {
         );
 
         const serverLoad$ = pagination$.pipe(
+            throttleTime(debouncePeriod, undefined, { trailing: true }),
             switchMap(pagination => of([contents_url, filters, pagination]).pipe(
                 tap(() => loadingEvents$.next(true)),
                 loadDscContent({ debug }),
diff --git a/client/src/components/History/providers/ContentProvider/aggregateCacheUpdates.js b/client/src/components/History/providers/ContentProvider/aggregateCacheUpdates.js
index 4875fd52970..41bcad3d798 100644
--- a/client/src/components/History/providers/ContentProvider/aggregateCacheUpdates.js
+++ b/client/src/components/History/providers/ContentProvider/aggregateCacheUpdates.js
@@ -14,7 +14,7 @@ import {
     timeoutWith,
     ignoreElements,
 } from "rxjs/operators";
-import { chunk, show, debounceBurst, shareButDie } from "utils/observable";
+import { show, debounceBurst, shareButDie } from "utils/observable";
 import { SearchParams } from "../../model/SearchParams";
 import { processContentUpdate, newUpdateMap, buildContentResult, getKeyForUpdateMap } from "./aggregation";
 import { SEEK } from "../../caching/enums";
@@ -41,7 +41,7 @@ export const aggregateCacheUpdates = (monitor, cfg = {}) => (src$) => {
         // interval in which we create new monitors
         // if we chunk the inputs then we won't make as many
         // might be easier on memory
-        inputChunk = Math.floor(pageSize / 2),
+        // inputChunk = Math.floor(pageSize / 2),
 
         // reduces duplicate updates to the skiplist
         // which can be expensive
@@ -59,7 +59,7 @@ export const aggregateCacheUpdates = (monitor, cfg = {}) => (src$) => {
     // avoids creating a new monitor for every single key emission
     // chunk to ceiling if descending, floor if ascending
     const monitorInputKey$ = targetKey$.pipe(
-        chunk(inputChunk, keyDirection == SEEK.DESC), 
+        // chunk(inputChunk, keyDirection == SEEK.DESC, "monitorInputKey"),
         distinctUntilChanged(),
         show(debug, (key) => console.log("monitorInputKey", key)),
     );
@@ -76,10 +76,10 @@ export const aggregateCacheUpdates = (monitor, cfg = {}) => (src$) => {
     // when we're just going to change it again shortly
     const groupedUpdates$ = cacheUpdates$.pipe(
         groupBy(
-            update => update.key, 
-            update => update, 
+            update => update.key,
+            update => update,
             updateByKey$ => updateByKey$.pipe(
-                timeoutWith(updateGroupLifetime, EMPTY), 
+                timeoutWith(updateGroupLifetime, EMPTY),
                 ignoreElements()
             )
         ),
@@ -104,7 +104,7 @@ export const aggregateCacheUpdates = (monitor, cfg = {}) => (src$) => {
         withLatestFrom(targetKey$),
     );
 
-    // query skiplist with scroll position (transformed into a key from the skiplist) 
+    // query skiplist with scroll position (transformed into a key from the skiplist)
     // to produce list of nearby content
     const contentList$ = contentListInputs$.pipe(
         map(buildContentResult({ pageSize, keyDirection, getKey })),
diff --git a/client/src/components/History/providers/ContentProvider/processContentStreams.js b/client/src/components/History/providers/ContentProvider/processContentStreams.js
index a589fdb2acb..6b28650ee2b 100644
--- a/client/src/components/History/providers/ContentProvider/processContentStreams.js
+++ b/client/src/components/History/providers/ContentProvider/processContentStreams.js
@@ -1,9 +1,9 @@
 /**
- * General plumbing for the 2 types of content providers. This funcction emits 3 observables:
+ * General plumbing for the 2 types of content providers. This function returns 3 observables:
  * loading, scrolling, and payload. Payload's the most important and the operator that genrates the
  * payload from the inputs is passed in as a parameter to this factory.
  */
-import { debounceTime, distinctUntilChanged, share, startWith, switchMap } from "rxjs/operators";
+import { distinctUntilChanged, share, startWith, switchMap } from "rxjs/operators";
 import { activity, whenAny, show } from "utils/observable";
 import { propMatch } from "./helpers";
 import { SearchParams, ScrollPos } from "../../model";
@@ -23,7 +23,7 @@ import { Subject } from "rxjs";
  */
 // prettier-ignore
 export function processContentStreams(payloadOperator, sources = {}, settings = {}) {
-    const { debouncePeriod, debug = false } = settings;
+    const { debouncePeriod, debug = true } = settings;
 
     // clean incoming source streams
     const parent$ = sources.parent$.pipe(
@@ -35,7 +35,7 @@ export function processContentStreams(payloadOperator, sources = {}, settings =
         show(debug, (params) => console.log('processContentStreams: params changed', params)),
     );
     const pos$ = sources.scrollPos$.pipe(
-        debounceTime(debouncePeriod),
+        // debounceTime(debouncePeriod),
         show(debug, (pos) => console.log('processContentStreams: pos changed', pos)),
         distinctUntilChanged(ScrollPos.equals),
     );
@@ -48,7 +48,7 @@ export function processContentStreams(payloadOperator, sources = {}, settings =
         activity(debouncePeriod),
         startWith(true)
     );
-    
+
     const resetPos$ = new Subject();
 
     // The actual loader, when history or params change we poll against the api and
diff --git a/client/src/components/History/providers/DatasetProvider.js b/client/src/components/History/providers/DatasetProvider.js
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/client/src/components/History/providers/ExpandedItems.js b/client/src/components/History/providers/ExpandedItems.js
index a281794ef35..05c4fdc3452 100644
--- a/client/src/components/History/providers/ExpandedItems.js
+++ b/client/src/components/History/providers/ExpandedItems.js
@@ -1,3 +1,5 @@
+import { saveSet, loadSet } from "./setCache";
+
 export default {
     props: {
         scopeKey: { type: String, required: true },
@@ -8,6 +10,11 @@ export default {
             items: new Set(),
         };
     },
+    computed: {
+        expandedCount() {
+            return this.items.size;
+        },
+    },
     methods: {
         isExpanded(item) {
             const key = this.getItemKey(item);
@@ -29,11 +36,23 @@ export default {
                 this.reset();
             }
         },
+        items(newSet) {
+            saveSet(this.key, newSet);
+        },
+    },
+    created() {
+        this.key = "expanded-history-items";
+        const cachedSet = loadSet(this.key);
+        if (cachedSet) {
+            this.items = cachedSet;
+        }
     },
     render() {
         return this.$scopedSlots.default({
             isExpanded: this.isExpanded,
             setExpanded: this.setExpanded,
+            collapseAll: this.reset,
+            expandedCount: this.expandedCount,
         });
     },
 };
diff --git a/client/src/components/History/providers/HistoryContentProvider/contentPayload.js b/client/src/components/History/providers/HistoryContentProvider/contentPayload.js
index 9da5846b91f..881d9b033eb 100644
--- a/client/src/components/History/providers/HistoryContentProvider/contentPayload.js
+++ b/client/src/components/History/providers/HistoryContentProvider/contentPayload.js
@@ -34,10 +34,10 @@ import { defaultPayload } from "../ContentProvider";
  */
 // prettier-ignore
 export const contentPayload = (cfg = {}) => {
-    const { 
-        parent: history, 
+    const {
+        parent: history,
         filters = new SearchParams(),
-        pageSize = SearchParams.pageSize, 
+        pageSize = SearchParams.pageSize,
         debouncePeriod = 250,
         loadingTimeout = 2000,
         disablePoll = false,
@@ -45,6 +45,7 @@ export const contentPayload = (cfg = {}) => {
         // optional feedback indicators
         loadingEvents$ = new Subject(),
         resetPos$ = new Subject(),
+        chunkSize = pageSize
     } = cfg;
 
     // These running totals are shared between instances of content payload because a lot of the
@@ -78,14 +79,15 @@ export const contentPayload = (cfg = {}) => {
             filter(hid => !isNaN(hid)),
             share(),
         );
-        
+
         // #endregion
 
         // #region server loading
 
         const serverHid$ = hid$.pipe(
-            chunk(pageSize, true),
+            chunk({ chunkSize, debug, label: "serverHid" }),
             distinctUntilChanged(),
+            debounceTime(debouncePeriod),
             show(debug, hid => console.log("serverHid", hid)),
             share(),
         );
@@ -109,7 +111,7 @@ export const contentPayload = (cfg = {}) => {
             mergeAll(),
             debounceTime(100),
         );
-        
+
         const cacheMonitor$ = cacheHid$.pipe(
             watchHistoryContents({ history, filters, pageSize, debouncePeriod, debug }),
             show(debug, (result) => console.log("cacheMonitor.contents (hid)", result.contents.map(o => o.hid))),
@@ -133,7 +135,7 @@ export const contentPayload = (cfg = {}) => {
         // #endregion
 
         // #region Reposition View to accomodate recent updates
-        
+
         // When new updates to the history come in, we should shift the scrollPos so that we can see
         // them. Without some kind of explicit move, the system will think they're just random
         // updates that are happening outside the region of interest, and there would be no
@@ -151,7 +153,7 @@ export const contentPayload = (cfg = {}) => {
                 const fudge = 2;
                 const scrollNearLastTop = Math.abs(hid - lastResponse.maxContentHid) < fudge;
                 const scrollerAtTop = scrollerInDefault || scrollNearLastTop;
-                
+
                 // console.group("should i reposition?");
                 // console.log("updatesAtTop", updatesAtTop);
                 // console.log("scrollerAtTop", scrollerAtTop);
@@ -190,7 +192,7 @@ export const contentPayload = (cfg = {}) => {
             const sub = payload$.subscribe(obs);
 
             // Tie stat feedback subscriptions to main payload sub
-            // Make sure not to combineLatest these subject accumulators or we'll 
+            // Make sure not to combineLatest these subject accumulators or we'll
             // end up with an infinite loop
             sub.add(newCursorToHid$.subscribe(cursorToHid$));
             sub.add(newHidToTopRows$.subscribe(hidToTopRows$));
diff --git a/client/src/components/History/providers/UserHistories/UserHistories.js b/client/src/components/History/providers/UserHistories/UserHistories.js
index e9547e7db02..22ac28a3b7e 100644
--- a/client/src/components/History/providers/UserHistories/UserHistories.js
+++ b/client/src/components/History/providers/UserHistories/UserHistories.js
@@ -43,6 +43,10 @@ export default {
             "loadUserHistories",
             "secureHistory",
         ]),
+
+        updateCurrentHistory(updates) {
+            this.updateHistory({ ...updates, id: this.currentHistory.id });
+        },
     },
     watch: {
         // when user changes reload histories
@@ -81,7 +85,11 @@ export default {
                 // save new history params should be an object with an id property and any additional
                 // properties that are to be updated on the server. A full history object is not required
                 updateHistory: this.updateHistory,
-                updateCurrentHistory: () => this.updateHistory(this.currentHistory),
+                updateCurrentHistory: this.updateCurrentHistory,
+
+                // also conform to .sync event name format
+                "update:history": this.updateHistory,
+                "update:currentHistory": this.updateCurrentHistory,
 
                 // delete history then clear currentHistoryId
                 deleteHistory: (history) => this.deleteHistory({ history }),
diff --git a/client/src/components/History/providers/setCache.js b/client/src/components/History/providers/setCache.js
new file mode 100644
index 00000000000..90d9bbe5b40
--- /dev/null
+++ b/client/src/components/History/providers/setCache.js
@@ -0,0 +1,25 @@
+// Caches expanded/selected Sets in sessionStorage
+// Putting this in separate file for ease of mocking
+
+export function saveSet(key, setObject) {
+    try {
+        const setToArray = Array.from(setObject);
+        const json = JSON.stringify(setToArray);
+        sessionStorage.setItem(key, json);
+    } catch (err) {
+        console.log("error saving stuff to cache", err);
+        sessionStorage.removeItem(key);
+    }
+}
+
+export function loadSet(key) {
+    try {
+        const arrJson = sessionStorage.getItem(key) || [];
+        const cachedArray = JSON.parse(arrJson);
+        return Array.isArray(cachedArray) ? new Set(cachedArray) : new Set();
+    } catch (err) {
+        console.log("erorr loading cached list", err);
+        sessionStorage.removeItem(key);
+        return null;
+    }
+}
diff --git a/client/src/components/IconButton.vue b/client/src/components/IconButton.vue
new file mode 100644
index 00000000000..713e34f9e2e
--- /dev/null
+++ b/client/src/components/IconButton.vue
@@ -0,0 +1,51 @@
+<template>
+    <b-button
+        class="galaxy-icon-button"
+        v-bind="$attrs"
+        v-on="$listeners"
+        :title="title"
+        :size="size"
+        :pressed="pressed"
+        :disabled="disabled"
+        :variant="localVariant"
+    >
+        <Icon :icon="icon" />
+        <span class="sr-only">{{ title | l }}</span>
+    </b-button>
+</template>
+
+<script>
+export default {
+    props: {
+        icon: { type: [String, Array, Object], required: true },
+        title: { type: String, required: true },
+        size: { type: String, required: false, default: "sm" },
+        pressed: { type: Boolean, required: false, default: false },
+        disabled: { type: Boolean, required: false, default: false },
+        // overrides variant set by pressed/disabled
+        variant: { type: String, required: false, default: null },
+    },
+    computed: {
+        localVariant() {
+            if (this.variant) {
+                // override with prop
+                return this.variant;
+            }
+            if (this.disabled) {
+                return "secondary";
+            }
+            return this.pressed ? "info" : "secondary";
+        },
+    },
+};
+</script>
+
+<style lang="scss">
+// removes irritating bootstrap outline
+.galaxy-icon-button.btn {
+    box-shadow: none !important;
+    &.disabled > svg {
+        opacity: 0.5;
+    }
+}
+</style>
diff --git a/client/src/components/Workflow/WorkflowList.vue b/client/src/components/Workflow/WorkflowList.vue
index c6985bbf017..e7a507d3c1c 100644
--- a/client/src/components/Workflow/WorkflowList.vue
+++ b/client/src/components/Workflow/WorkflowList.vue
@@ -59,7 +59,10 @@
                         <font-awesome-icon v-if="row.item.shared" v-b-tooltip.hover title="Shared" icon="share-alt" />
                     </template>
                     <template v-slot:cell(show_in_tool_panel)="row">
-                        <b-form-checkbox v-model="row.item.show_in_tool_panel" @change="bookmarkWorkflow(row.item)" />
+                        <b-form-checkbox
+                            :checked="row.item.show_in_tool_panel"
+                            @change="(checked) => bookmarkWorkflow(row.item, checked)"
+                        />
                     </template>
                     <template v-slot:cell(update_time)="data">
                         <UtcDate :date="data.value" mode="elapsed" />
@@ -192,14 +195,13 @@ export default {
         executeWorkflow: function (workflow) {
             window.location = `${this.root}workflows/run?id=${workflow.id}`;
         },
-        bookmarkWorkflow: function (workflow) {
+        bookmarkWorkflow: function (workflow, checked) {
             // This reloads the whole page, so that the workflow appears in the tool panel.
             // Ideally we would notify only the tool panel of a change
             const id = workflow.id;
-            const show_in_tool_panel = workflow.show_in_tool_panel;
             const tags = workflow.tags;
             const data = {
-                show_in_tool_panel: !show_in_tool_panel,
+                show_in_tool_panel: checked,
                 tags: tags,
             };
             this.services
diff --git a/client/src/components/plugins/icons.js b/client/src/components/plugins/icons.js
new file mode 100644
index 00000000000..348fb5965a9
--- /dev/null
+++ b/client/src/components/plugins/icons.js
@@ -0,0 +1,93 @@
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import {
+    faArrowUp,
+    faBolt,
+    faBurn,
+    faChartArea,
+    faCheckSquare,
+    faClock,
+    faCodeBranch,
+    faColumns,
+    faCompress,
+    faCopy,
+    faDownload,
+    faEllipsisH,
+    faEllipsisV,
+    faExchangeAlt,
+    faEye,
+    faFileArchive,
+    faFileExport,
+    faFilter,
+    faFolder,
+    faInfoCircle,
+    faList,
+    faLink,
+    faLock,
+    faPause,
+    faPen,
+    faPlay,
+    faPlus,
+    faQuestion,
+    faShareAlt,
+    faStream,
+    faTags,
+    faTrash,
+    faTrashRestore,
+    faExclamationTriangle,
+    faUndo,
+    faUserLock,
+    faWrench,
+} from "@fortawesome/free-solid-svg-icons";
+
+library.add(
+    faArrowUp,
+    faBolt,
+    faBurn,
+    faChartArea,
+    faCheckSquare,
+    faClock,
+    faCodeBranch,
+    faColumns,
+    faCompress,
+    faCopy,
+    faDownload,
+    faEllipsisH,
+    faEllipsisV,
+    faExchangeAlt,
+    faEye,
+    faFileArchive,
+    faFileExport,
+    faFilter,
+    faFolder,
+    faInfoCircle,
+    faLink,
+    faList,
+    faLock,
+    faPause,
+    faPen,
+    faPlay,
+    faPlus,
+    faQuestion,
+    faShareAlt,
+    faStream,
+    faTags,
+    faTrash,
+    faTrashRestore,
+    faExclamationTriangle,
+    faUndo,
+    faUserLock,
+    faWrench
+);
+
+export const iconMixin = {
+    components: {
+        Icon: FontAwesomeIcon,
+    },
+};
+
+export const iconPlugin = {
+    install(Vue) {
+        Vue.mixin(iconMixin);
+    },
+};
diff --git a/client/src/components/plugins/index.js b/client/src/components/plugins/index.js
index 5dd87fa1e5f..fa6ee155b98 100644
--- a/client/src/components/plugins/index.js
+++ b/client/src/components/plugins/index.js
@@ -1,6 +1,7 @@
 export { eventHubMixin, eventHubPlugin } from "./eventHub";
 export { vueRxShortcutPlugin, vueRxShortcuts } from "./vueRxShortcuts";
 export { localizationPlugin } from "./localization";
+export { iconPlugin, iconMixin } from "./icons";
 
 // I'm explicitly ommitting this because of its ugly dependencies, I want us to have to import the
 // legacy nav features manually (when required) rather than it coming in every time somebody accesses
diff --git a/client/src/utils/mountVueComponent.js b/client/src/utils/mountVueComponent.js
index 8f685614822..8ef37f8e9dc 100644
--- a/client/src/utils/mountVueComponent.js
+++ b/client/src/utils/mountVueComponent.js
@@ -6,7 +6,7 @@ import Vue from "vue";
 import Vuex from "vuex";
 import BootstrapVue from "bootstrap-vue";
 import store from "../store";
-import { eventHubPlugin, localizationPlugin, vueRxShortcutPlugin } from "components/plugins";
+import { eventHubPlugin, localizationPlugin, vueRxShortcutPlugin, iconPlugin } from "components/plugins";
 
 Vue.use(Vuex);
 
@@ -24,6 +24,9 @@ Vue.use(localizationPlugin);
 // rxjs utilities
 Vue.use(vueRxShortcutPlugin);
 
+// font-awesome svg icon registration/loading
+Vue.use(iconPlugin);
+
 export const mountVueComponent = (ComponentDefinition) => {
     const component = Vue.extend(ComponentDefinition);
     return (propsData, el) => new component({ store, propsData, el });
diff --git a/client/src/utils/observable/chunk.js b/client/src/utils/observable/chunk.js
index 2994b3f0570..850d6358705 100644
--- a/client/src/utils/observable/chunk.js
+++ b/client/src/utils/observable/chunk.js
@@ -3,14 +3,24 @@ import { map } from "rxjs/operators";
 /**
  * Bust incoming numeric source values into blocks of designated size.
  *
- * @param {*} chunkSize
+ * @param {Number|Object} cfg object or numeric chunksize
  * @param {*} ceil
  */
 // prettier-ignore
-export const chunk = (chunkSize, ceil = false) => {
+export const chunk = (cfg) => {
+    const settings = Number.isInteger(cfg) ? { chunkSize: Math.round(cfg) } : cfg;
+    const { chunkSize = 0, ceil = false, debug = false, label } = settings;
+    if (chunkSize == 0) {
+        throw new Error("Please provide a chunk size");
+    }
+
     return map((chunkMe) => {
-        const rawVal = chunkMe / chunkSize;
-        return chunkSize * (ceil ? Math.ceil(rawVal) : Math.floor(rawVal));
+        const rawVal = 1.0 * chunkMe / chunkSize;
+        const result = chunkSize * (ceil ? Math.ceil(rawVal) : Math.floor(rawVal));
+        if (debug) {
+            console.log(`chunk: ${label}`, chunkMe, result, settings);
+        }
+        return result;
     })
 };
 
diff --git a/client/src/utils/safeAssign.js b/client/src/utils/safeAssign.js
index 52d4cff9d0b..bef98ecefdd 100644
--- a/client/src/utils/safeAssign.js
+++ b/client/src/utils/safeAssign.js
@@ -9,3 +9,22 @@ export function safeAssign(target, source = {}) {
         .filter((prop) => Object.prototype.hasOwnProperty.call(target, prop))
         .forEach((prop) => (target[prop] = source[prop]));
 }
+
+/**
+ * Creates a reusable utility scrubber function that removes reserved initialization props from raw
+ * which are already defined by Klass. This lets us just stick one model instance into.
+ *
+ * Ex: const scrubber = scrubModelProps(History); *
+ *     const newHistory = new History(scrubber(oldHistory));
+ */
+
+export function scrubModelProps(Klass) {
+    const restrictedKeys = new Set(Object.getOwnPropertyNames(Klass.prototype));
+
+    return (raw = {}) => {
+        const pairs = Object.entries(raw || {});
+        return pairs.reduce((clean, [propName, val]) => {
+            return restrictedKeys.has(propName) ? clean : { ...clean, [propName]: val };
+        }, {});
+    };
+}
diff --git a/client/tests/jest/helpers.js b/client/tests/jest/helpers.js
index 369dcaf51a8..6da42993a13 100644
--- a/client/tests/jest/helpers.js
+++ b/client/tests/jest/helpers.js
@@ -7,6 +7,7 @@ import { createLocalVue, shallowMount } from "@vue/test-utils";
 import { localizationPlugin } from "components/plugins/localization";
 import { vueRxShortcutPlugin } from "components/plugins/vueRxShortcuts";
 import { eventHubPlugin } from "components/plugins/eventHub";
+import { iconPlugin } from "components/plugins/icons";
 import BootstrapVue from "bootstrap-vue";
 import Vuex from "vuex";
 
@@ -95,6 +96,7 @@ export function getLocalVue() {
     localVue.use(localizationPlugin);
     localVue.use(vueRxShortcutPlugin);
     localVue.use(eventHubPlugin);
+    localVue.use(iconPlugin);
     localVue.directive("b-tooltip", mockedDirective);
     localVue.directive("b-popover", mockedDirective);
     return localVue;
@@ -137,7 +139,7 @@ export const untilNthEmission = (src$, n = 1, safetyTimeout = 2000) => {
         let result;
         // prettier-ignore
         src$.pipe(
-            take(n), 
+            take(n),
             takeUntil(timer(safetyTimeout))
         ).subscribe({
             next: (val) => (result = val),
diff --git a/client/yarn.lock b/client/yarn.lock
index 52d83e861ff..6b9ca8eda87 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -1719,14 +1719,14 @@
     "@nodelib/fs.scandir" "2.1.3"
     fastq "^1.6.0"
 
-"@nuxt/opencollective@^0.3.0":
-  version "0.3.0"
-  resolved "https://registry.yarnpkg.com/@nuxt/opencollective/-/opencollective-0.3.0.tgz#11d8944dcf2d526e31660bb69570be03f8fb72b7"
-  integrity sha512-Vf09BxCdj1iT2IRqVwX5snaY2WCTkvM0O4cWWSO1ThCFuc4if0Q/nNwAgCxRU0FeYHJ7DdyMUNSdswCLKlVqeg==
+"@nuxt/opencollective@^0.3.2":
+  version "0.3.2"
+  resolved "https://registry.yarnpkg.com/@nuxt/opencollective/-/opencollective-0.3.2.tgz#83cb70cdb2bac5fad6f8c93529e7b11187d49c02"
+  integrity sha512-XG7rUdXG9fcafu9KTDIYjJSkRO38EwjlKYIb5TQ/0WDbiTUTtUtgncMscKOYzfsY86kGs05pAuMOR+3Fi0aN3A==
   dependencies:
-    chalk "^2.4.2"
-    consola "^2.10.1"
-    node-fetch "^2.6.0"
+    chalk "^4.1.0"
+    consola "^2.15.0"
+    node-fetch "^2.6.1"
 
 "@sentry/browser@^5.20.1":
   version "5.20.1"
@@ -3323,18 +3323,18 @@ boolbase@^1.0.0, boolbase@~1.0.0:
   resolved "https://registry.yarnpkg.com/boolbase/-/boolbase-1.0.0.tgz#68dff5fbe60c51eb37725ea9e3ed310dcc1e776e"
   integrity sha1-aN/1++YMUes3cl6p4+0xDcwed24=
 
-bootstrap-vue@^2.15.0:
-  version "2.15.0"
-  resolved "https://registry.yarnpkg.com/bootstrap-vue/-/bootstrap-vue-2.15.0.tgz#0dfc12c054496c0f10efed510da1def41697cf3c"
-  integrity sha512-ncxWkDG0mKFVot314wWKJELi+ESO7k6ngV//qvJFs9iVzlFI8Hx3rBVbpcPW2vrJ+0vitH8N2SOwn4fdQ3frMQ==
+bootstrap-vue@^2.21.2:
+  version "2.21.2"
+  resolved "https://registry.yarnpkg.com/bootstrap-vue/-/bootstrap-vue-2.21.2.tgz#ec38f66c3a2205becccddb6158a991d96509ed0b"
+  integrity sha512-0Exe+4MZysqhZNXIKf4TzkvXaupxh9EHsoCRez0o5Dc0J7rlafayOEwql63qXv74CgZO8E4U8ugRNJko1vMvNw==
   dependencies:
-    "@nuxt/opencollective" "^0.3.0"
-    bootstrap ">=4.5.0 <5.0.0"
+    "@nuxt/opencollective" "^0.3.2"
+    bootstrap ">=4.5.3 <5.0.0"
     popper.js "^1.16.1"
     portal-vue "^2.1.7"
     vue-functional-data-merge "^3.1.0"
 
-bootstrap@4.5.0, "bootstrap@>=4.5.0 <5.0.0":
+bootstrap@4.5.0:
   version "4.5.0"
   resolved "https://registry.yarnpkg.com/bootstrap/-/bootstrap-4.5.0.tgz#97d9dbcb5a8972f8722c9962483543b907d9b9ec"
   integrity sha512-Z93QoXvodoVslA+PWNdk23Hze4RBYIkpb5h8I2HY2Tu2h7A0LpAgLcyrhrSUyo2/Oxm2l1fRZPs1e5hnxnliXA==
@@ -3344,6 +3344,11 @@ bootstrap@>=4.0.0-beta:
   resolved "https://registry.yarnpkg.com/bootstrap/-/bootstrap-5.0.2.tgz#aff23d5e0e03c31255ad437530ee6556e78e728e"
   integrity sha512-1Ge963tyEQWJJ+8qtXFU6wgmAVj9gweEjibUdbmcCEYsn38tVwRk8107rk2vzt6cfQcRr3SlZ8aQBqaD8aqf+Q==
 
+"bootstrap@>=4.5.3 <5.0.0":
+  version "4.6.0"
+  resolved "https://registry.yarnpkg.com/bootstrap/-/bootstrap-4.6.0.tgz#97b9f29ac98f98dfa43bf7468262d84392552fd7"
+  integrity sha512-Io55IuQY3kydzHtbGvQya3H+KorS/M9rSNyfCGCg9WZ4pyT/lCxIlpJgG1GXW/PswzC84Tr2fBYi+7+jFVQQBw==
+
 brace-expansion@^1.1.7:
   version "1.1.11"
   resolved "https://registry.yarnpkg.com/brace-expansion/-/brace-expansion-1.1.11.tgz#3c7fcbf529d87226f3d2f52b966ff5271eb441dd"
@@ -3826,6 +3831,14 @@ chalk@^4.0.0, chalk@~4.1.0:
     ansi-styles "^4.1.0"
     supports-color "^7.1.0"
 
+chalk@^4.1.0:
+  version "4.1.2"
+  resolved "https://registry.yarnpkg.com/chalk/-/chalk-4.1.2.tgz#aac4e2b7734a740867aeb16bf02aad556a1e7a01"
+  integrity sha512-oKnbhFyRIXpUuez8iBMmyEa4nbj4IOQyuhc/wy9kY7/WVPcwIO9VA668Pu8RkO7+0G76SLROeyw9CpQ061i4mA==
+  dependencies:
+    ansi-styles "^4.1.0"
+    supports-color "^7.1.0"
+
 char-regex@^1.0.2:
   version "1.0.2"
   resolved "https://registry.yarnpkg.com/char-regex/-/char-regex-1.0.2.tgz#d744358226217f981ed58f479b1d6bcc29545dcf"
@@ -4390,10 +4403,10 @@ connect@^3.7.0:
     parseurl "~1.3.3"
     utils-merge "1.0.1"
 
-consola@^2.10.1:
-  version "2.10.1"
-  resolved "https://registry.yarnpkg.com/consola/-/consola-2.10.1.tgz#4693edba714677c878d520e4c7e4f69306b4b927"
-  integrity sha512-4sxpH6SGFYLADfUip4vuY65f/gEogrzJoniVhNUYkJHtng0l8ZjnDCqxxrSVRHOHwKxsy8Vm5ONZh1wOR3/l/w==
+consola@^2.15.0:
+  version "2.15.3"
+  resolved "https://registry.yarnpkg.com/consola/-/consola-2.15.3.tgz#2e11f98d6a4be71ff72e0bdf07bd23e12cb61550"
+  integrity sha512-9vAdYbHj6x2fLKC4+oPH0kFzY/orMZyG2Aj+kNylHxKGJ/Ed4dpNyAQYwJOdqO4zdM7XpVHmyejQDcQHrnuXbw==
 
 console-browserify@^1.1.0:
   version "1.1.0"
@@ -10086,7 +10099,7 @@ node-fetch@^1.0.1:
     encoding "^0.1.11"
     is-stream "^1.0.1"
 
-node-fetch@^2.2.0:
+node-fetch@^2.2.0, node-fetch@^2.6.1:
   version "2.6.1"
   resolved "https://registry.yarnpkg.com/node-fetch/-/node-fetch-2.6.1.tgz#045bd323631f76ed2e2b55573394416b639a0052"
   integrity sha512-V4aYg89jEoVRxRb2fJdAg8FHvI7cEyYdVAh94HH0UIK8oJxUfkjlDQN9RbMx+bEjP7+ggMiFRprSti032Oipxw==
@@ -11691,6 +11704,11 @@ prettier@^2.3.0:
   resolved "https://registry.yarnpkg.com/prettier/-/prettier-2.3.0.tgz#b6a5bf1284026ae640f17f7ff5658a7567fc0d18"
   integrity sha512-kXtO4s0Lz/DW/IJ9QdWhAf7/NmPWQXkFr/r/WkR3vyI+0v8amTDxiaQSLzs8NBlytfLWX/7uQUMIW677yLKl4w==
 
+pretty-bytes@^5.6.0:
+  version "5.6.0"
+  resolved "https://registry.yarnpkg.com/pretty-bytes/-/pretty-bytes-5.6.0.tgz#356256f643804773c82f64723fe78c92c62beaeb"
+  integrity sha512-FFw039TmrBqFK8ma/7OL3sDz/VytdtJr044/QUJtH0wK9lb9jLq9tJyIxUwtQJHwar2BqtiA4iCWSwo9JLkzFg==
+
 pretty-format@^25.2.1, pretty-format@^25.5.0:
   version "25.5.0"
   resolved "https://registry.yarnpkg.com/pretty-format/-/pretty-format-25.5.0.tgz#7873c1d774f682c34b8d48b6743a2bf2ac55791a"

From 059f3776e6441cf073cd9ee871e5f162b09f77e4 Mon Sep 17 00:00:00 2001
From: Mason Houtz <nerdinacan@gmail.com>
Date: Tue, 17 Aug 2021 13:56:31 -0700
Subject: [PATCH 213/218] cleanup, removed some non-essential edits

---
 client/src/components/History/ContentFilters.vue            | 2 +-
 client/src/components/History/ContentItem/ContentItem.js    | 5 ++---
 .../src/components/History/ContentItem/Dataset/Dataset.vue  | 2 --
 .../components/History/ContentItem/Dataset/DatasetUI.vue    | 2 +-
 client/src/components/History/ContentItem/index.js          | 3 +++
 client/src/components/History/CurrentHistoryPanel.vue       | 1 -
 .../providers/ContentProvider/aggregateCacheUpdates.js      | 6 ------
 .../providers/ContentProvider/processContentStreams.js      | 3 +--
 client/src/components/History/providers/DatasetProvider.js  | 0
 9 files changed, 8 insertions(+), 16 deletions(-)
 delete mode 100644 client/src/components/History/providers/DatasetProvider.js

diff --git a/client/src/components/History/ContentFilters.vue b/client/src/components/History/ContentFilters.vue
index 03c9536728f..da1663d41b8 100644
--- a/client/src/components/History/ContentFilters.vue
+++ b/client/src/components/History/ContentFilters.vue
@@ -1,7 +1,7 @@
 <template>
     <b-input-group v-if="params">
         <DebouncedInput v-model.trim="filterText" v-slot="{ value, input }">
-            <b-form-input size="sm" :value="value" @input="input" :placeholder="'Content Filter' | localize" />
+            <b-form-input size="sm" :value="value" @input="input" :placeholder="'Search Filter' | localize" />
         </DebouncedInput>
 
         <b-input-group-append>
diff --git a/client/src/components/History/ContentItem/ContentItem.js b/client/src/components/History/ContentItem/ContentItem.js
index b39fd514d4e..1dd82051f2a 100644
--- a/client/src/components/History/ContentItem/ContentItem.js
+++ b/client/src/components/History/ContentItem/ContentItem.js
@@ -13,7 +13,6 @@ import Dataset from "./Dataset";
 import DatasetCollection from "./DatasetCollection";
 import Subdataset from "./Subdataset";
 import Subcollection from "./Subcollection";
-import "./styles.scss";
 
 export default {
     template: `
@@ -59,8 +58,8 @@ export default {
             if (this.suppressFocus) {
                 return;
             }
-            const scrollContainer = this.$el.closest(".scroller");
-            const el = scrollContainer.querySelector(`[tabindex="${index}"]`);
+            const ul = this.$el.closest(".scroller");
+            const el = ul.querySelector(`[tabindex="${index}"]`);
             if (el) {
                 el.focus();
             }
diff --git a/client/src/components/History/ContentItem/Dataset/Dataset.vue b/client/src/components/History/ContentItem/Dataset/Dataset.vue
index 14b3c358276..cc00d07b0d4 100644
--- a/client/src/components/History/ContentItem/Dataset/Dataset.vue
+++ b/client/src/components/History/ContentItem/Dataset/Dataset.vue
@@ -4,7 +4,6 @@
         v-bind="$attrs"
         v-on="$listeners"
         :dataset="dataset"
-        :row-key="rowKey"
         @update:dataset="onUpdate"
         @delete="onDelete"
         @undelete="onUndelete"
@@ -27,7 +26,6 @@ export default {
     },
     props: {
         item: { type: Object, required: true },
-        rowKey: { type: [Number, String], required: false, default: "" },
     },
     computed: {
         dataset() {
diff --git a/client/src/components/History/ContentItem/Dataset/DatasetUI.vue b/client/src/components/History/ContentItem/Dataset/DatasetUI.vue
index 2b15be928e9..e36d2c8d2e1 100644
--- a/client/src/components/History/ContentItem/Dataset/DatasetUI.vue
+++ b/client/src/components/History/ContentItem/Dataset/DatasetUI.vue
@@ -8,7 +8,7 @@ either through the props, and make updates through the events -->
 <template>
     <div
         class="dataset history-content"
-        :data-content-type-id="typeId"
+        :id="typeId"
         :class="{ expanded, collapsed, selected }"
         :data-state="dataset.state"
         @keydown.arrow-left.self.stop="$emit('update:expanded', false)"
diff --git a/client/src/components/History/ContentItem/index.js b/client/src/components/History/ContentItem/index.js
index 5543ce9497a..32d866ab9d0 100644
--- a/client/src/components/History/ContentItem/index.js
+++ b/client/src/components/History/ContentItem/index.js
@@ -1,6 +1,9 @@
 /**
  * Scrolling components for history contents and collection contents.
  */
+
+import "./styles.scss";
+
 export { default as ContentItem } from "./ContentItem";
 export { default as CollectionContentItem } from "./CollectionContentItem";
 export { default as HistoryContentItem } from "./HistoryContentItem";
diff --git a/client/src/components/History/CurrentHistoryPanel.vue b/client/src/components/History/CurrentHistoryPanel.vue
index b54c8619a55..86011f0b5a4 100644
--- a/client/src/components/History/CurrentHistoryPanel.vue
+++ b/client/src/components/History/CurrentHistoryPanel.vue
@@ -12,7 +12,6 @@
                 </template>
             </HistoryPanel>
 
-            <!-- still loading -->
             <div v-else class="flex-grow-1 loadingBackground h-100">
                 <span class="sr-only" v-localize>Loading History...</span>
             </div>
diff --git a/client/src/components/History/providers/ContentProvider/aggregateCacheUpdates.js b/client/src/components/History/providers/ContentProvider/aggregateCacheUpdates.js
index 41bcad3d798..8024fd20b7b 100644
--- a/client/src/components/History/providers/ContentProvider/aggregateCacheUpdates.js
+++ b/client/src/components/History/providers/ContentProvider/aggregateCacheUpdates.js
@@ -38,11 +38,6 @@ export const aggregateCacheUpdates = (monitor, cfg = {}) => (src$) => {
         keyField = "hid",
         keyDirection = SEEK.DESC,
 
-        // interval in which we create new monitors
-        // if we chunk the inputs then we won't make as many
-        // might be easier on memory
-        // inputChunk = Math.floor(pageSize / 2),
-
         // reduces duplicate updates to the skiplist
         // which can be expensive
         updateGroupLifetime = 2 * debouncePeriod,
@@ -59,7 +54,6 @@ export const aggregateCacheUpdates = (monitor, cfg = {}) => (src$) => {
     // avoids creating a new monitor for every single key emission
     // chunk to ceiling if descending, floor if ascending
     const monitorInputKey$ = targetKey$.pipe(
-        // chunk(inputChunk, keyDirection == SEEK.DESC, "monitorInputKey"),
         distinctUntilChanged(),
         show(debug, (key) => console.log("monitorInputKey", key)),
     );
diff --git a/client/src/components/History/providers/ContentProvider/processContentStreams.js b/client/src/components/History/providers/ContentProvider/processContentStreams.js
index 6b28650ee2b..79baa25a528 100644
--- a/client/src/components/History/providers/ContentProvider/processContentStreams.js
+++ b/client/src/components/History/providers/ContentProvider/processContentStreams.js
@@ -23,7 +23,7 @@ import { Subject } from "rxjs";
  */
 // prettier-ignore
 export function processContentStreams(payloadOperator, sources = {}, settings = {}) {
-    const { debouncePeriod, debug = true } = settings;
+    const { debouncePeriod, debug = false } = settings;
 
     // clean incoming source streams
     const parent$ = sources.parent$.pipe(
@@ -35,7 +35,6 @@ export function processContentStreams(payloadOperator, sources = {}, settings =
         show(debug, (params) => console.log('processContentStreams: params changed', params)),
     );
     const pos$ = sources.scrollPos$.pipe(
-        // debounceTime(debouncePeriod),
         show(debug, (pos) => console.log('processContentStreams: pos changed', pos)),
         distinctUntilChanged(ScrollPos.equals),
     );
diff --git a/client/src/components/History/providers/DatasetProvider.js b/client/src/components/History/providers/DatasetProvider.js
deleted file mode 100644
index e69de29bb2d..00000000000

From 622ce6e64fdf5787fcb796037c14dfb063ef73bc Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Wed, 18 Aug 2021 16:21:41 +0200
Subject: [PATCH 214/218] Refactor

---
 lib/galaxy/managers/group_roles.py           | 11 +++++------
 lib/galaxy/webapps/galaxy/api/group_roles.py | 15 +++++++++++----
 2 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/managers/group_roles.py b/lib/galaxy/managers/group_roles.py
index e6a484c26e9..2a149dd7df9 100644
--- a/lib/galaxy/managers/group_roles.py
+++ b/lib/galaxy/managers/group_roles.py
@@ -37,10 +37,9 @@ class GroupRolesManager:
         group = self._get_group(trans, group_id)
         role = self._get_role(trans, role_id)
         group_role = self._get_group_role(trans, group, role)
-        if group_role is None:
+        if not group_role:
             raise ObjectNotFound(f"Role {role.name} not in group {group.name}")
         return role
-        # return self._serialize_group_role(group_id, role)
 
     def update(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, group_id: EncodedDatabaseIdField):
         """
@@ -50,7 +49,7 @@ class GroupRolesManager:
         group = self._get_group(trans, group_id)
         role = self._get_role(trans, role_id)
         group_role = self._get_group_role(trans, group, role)
-        if group_role is None:
+        if not group_role:
             self._add_role_to_group(trans, group, role)
         return role
 
@@ -62,7 +61,7 @@ class GroupRolesManager:
         group = self._get_group(trans, group_id)
         role = self._get_role(trans, role_id)
         group_role = self._get_group_role(trans, group, role)
-        if group_role is None:
+        if not group_role:
             raise ObjectNotFound(f"Role {role.name} not in group {group.name}")
         self._remove_role_from_group(trans, group_role)
         return role
@@ -70,14 +69,14 @@ class GroupRolesManager:
     def _get_group(self, trans: ProvidesAppContext, encoded_group_id: EncodedDatabaseIdField) -> Any:
         decoded_group_id = decode_id(self._app, encoded_group_id)
         group = trans.sa_session.query(model.Group).get(decoded_group_id)
-        if group is None:
+        if not group:
             raise ObjectNotFound(f"Group with id {encoded_group_id} was not found.")
         return group
 
     def _get_role(self, trans: ProvidesAppContext, encoded_role_id: EncodedDatabaseIdField) -> model.Role:
         decoded_role_id = decode_id(self._app, encoded_role_id)
         role = trans.sa_session.query(model.Role).get(decoded_role_id)
-        if role is None:
+        if not role:
             raise ObjectNotFound(f"Role with id {encoded_role_id} was not found.")
         return role
 
diff --git a/lib/galaxy/webapps/galaxy/api/group_roles.py b/lib/galaxy/webapps/galaxy/api/group_roles.py
index 4d73f0f511a..2aeebfdf53a 100644
--- a/lib/galaxy/webapps/galaxy/api/group_roles.py
+++ b/lib/galaxy/webapps/galaxy/api/group_roles.py
@@ -62,28 +62,35 @@ class FastAPIGroupRoles:
     @router.get('/api/groups/{group_id}/roles',
                 require_admin=True,
                 summary='Displays a collection (list) of groups.')
-    def index(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam) -> GroupRoleListModel:
+    def index(self, trans: ProvidesAppContext = DependsOnTrans,
+              group_id: EncodedDatabaseIdField = GroupIDParam) -> GroupRoleListModel:
         group_roles = self.manager.index(trans, group_id)
         return GroupRoleListModel(__root__=[group_role_to_model(trans, group_id, gr.role) for gr in group_roles])
 
     @router.get('/api/groups/{group_id}/roles/{role_id}',
                 require_admin=True,
                 summary='Displays information about a group role.')
-    def show(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam, role_id: EncodedDatabaseIdField = RoleIDParam) -> GroupRoleModel:
+    def show(self, trans: ProvidesAppContext = DependsOnTrans,
+             group_id: EncodedDatabaseIdField = GroupIDParam,
+             role_id: EncodedDatabaseIdField = RoleIDParam) -> GroupRoleModel:
         role = self.manager.show(trans, role_id, group_id)
         return group_role_to_model(trans, group_id, role)
 
     @router.put('/api/groups/{group_id}/roles/{role_id}',
                 require_admin=True,
                 summary='Adds a role to a group')
-    def update(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam, role_id: EncodedDatabaseIdField = RoleIDParam) -> GroupRoleModel:
+    def update(self, trans: ProvidesAppContext = DependsOnTrans,
+               group_id: EncodedDatabaseIdField = GroupIDParam,
+               role_id: EncodedDatabaseIdField = RoleIDParam) -> GroupRoleModel:
         role = self.manager.update(trans, role_id, group_id)
         return group_role_to_model(trans, group_id, role)
 
     @router.delete('/api/groups/{group_id}/roles/{role_id}',
                    require_admin=True,
                    summary='Removes a role from a group')
-    def delete(self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam, role_id: EncodedDatabaseIdField = RoleIDParam) -> GroupRoleModel:
+    def delete(self, trans: ProvidesAppContext = DependsOnTrans,
+               group_id: EncodedDatabaseIdField = GroupIDParam,
+               role_id: EncodedDatabaseIdField = RoleIDParam) -> GroupRoleModel:
         role = self.manager.delete(trans, role_id, group_id)
         return group_role_to_model(trans, group_id, role)
 

From 84fa44a12451ec71d01ee3ec01c2777dc1e79b34 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Wed, 18 Aug 2021 18:44:06 +0200
Subject: [PATCH 215/218] webpack dev server on remote galaxy server

---
 client/README.md         | 4 ++++
 client/webpack.config.js | 2 ++
 2 files changed, 6 insertions(+)

diff --git a/client/README.md b/client/README.md
index e091c142848..1483f95d857 100644
--- a/client/README.md
+++ b/client/README.md
@@ -83,6 +83,10 @@ environment variable:
 
     GALAXY_URL="http://localhost:8000" make client-dev-server
 
+Sometimes you want to run your UI against a remote Galaxy server. This is also possible, if you enable `CHANGE_ORIGIN` flag 
+
+    CHANGE_ORIGIN=true GALAXY_URL="https://usegalaxy.org/" make client-dev-server
+
 ## Changing Styles/CSS
 
 Galaxy uses Sass for its styling, which is a superset of CSS that compiles down
diff --git a/client/webpack.config.js b/client/webpack.config.js
index 1fd253866ae..4eb2694f59c 100644
--- a/client/webpack.config.js
+++ b/client/webpack.config.js
@@ -232,6 +232,8 @@ module.exports = (env = {}, argv = {}) => {
             proxy: {
                 "/": {
                     target: process.env.GALAXY_URL || "http://localhost:8080",
+                    secure: process.env.CHANGE_ORIGIN ? !process.env.CHANGE_ORIGIN : true,
+                    changeOrigin: !!process.env.CHANGE_ORIGIN,
                 },
             },
         },

From d96ee3c14c0e02c386a630c0e2e8e364d18cc5b7 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Wed, 18 Aug 2021 18:47:35 +0200
Subject: [PATCH 216/218] wording

---
 client/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/README.md b/client/README.md
index 1483f95d857..1295ec3a169 100644
--- a/client/README.md
+++ b/client/README.md
@@ -83,7 +83,7 @@ environment variable:
 
     GALAXY_URL="http://localhost:8000" make client-dev-server
 
-Sometimes you want to run your UI against a remote Galaxy server. This is also possible, if you enable `CHANGE_ORIGIN` flag 
+Sometimes you want to run your local UI against a remote Galaxy server. This is also possible, if you enable `CHANGE_ORIGIN` flag 
 
     CHANGE_ORIGIN=true GALAXY_URL="https://usegalaxy.org/" make client-dev-server
 

From 853d7e978d765cf0fefe8f8285e62a9a4b451287 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 18 Aug 2021 12:52:06 -0400
Subject: [PATCH 217/218] API test case to ensure dataset names get escaped
 during tool evaluation.

I think other sanitization properties aren't testing that model properties are escaped.
---
 lib/galaxy_test/api/test_tools.py           | 36 ++++++++++++++++++++-
 test/functional/tools/model_attributes.xml  | 15 +++++++++
 test/functional/tools/samples_tool_conf.xml |  1 +
 3 files changed, 51 insertions(+), 1 deletion(-)
 create mode 100644 test/functional/tools/model_attributes.xml

diff --git a/lib/galaxy_test/api/test_tools.py b/lib/galaxy_test/api/test_tools.py
index 4d93a920943..1d583c4d6da 100644
--- a/lib/galaxy_test/api/test_tools.py
+++ b/lib/galaxy_test/api/test_tools.py
@@ -6,7 +6,7 @@ import zipfile
 from io import BytesIO
 
 import pytest
-from requests import get
+from requests import get, put
 
 from galaxy.util import galaxy_root_path
 from galaxy_test.base import rules_test_data
@@ -308,6 +308,40 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         self._assert_has_keys(tool_info, "inputs", "outputs", "panel_section_id")
         return tool_info
 
+    @skip_without_tool("model_attributes")
+    @uses_test_history(require_new=False)
+    def test_model_attributes_sanitization(self, history_id):
+        cool_name_with_quote = "cool name with a quo\"te"
+        cool_name_without_quote = "cool name with a quo__dq__te"
+
+        current_user = self._get("users/current").json()
+        user_info_url = self._api_url(f"users/{current_user['id']}/information/inputs", use_key=True)
+        put_response = put(user_info_url, data=json.dumps({"address_0|desc": cool_name_with_quote}))
+        put_response.raise_for_status()
+
+        response = get(user_info_url).json()
+        self.assertEqual(len(response["addresses"]), 1)
+        self.assertEqual(response["addresses"][0]["desc"], cool_name_with_quote)
+
+        hda1 = self.dataset_populator.new_dataset(history_id, content='1\t2\t3', name=cool_name_with_quote)
+        assert hda1["name"] == cool_name_with_quote
+
+        rval = self._run(
+            tool_id="model_attributes",
+            inputs={"input1": dataset_to_param(hda1)},
+            history_id=history_id,
+            assert_ok=True,
+            wait_for_job=True,
+        )
+        sanitized_dataset_name = self.dataset_populator.get_history_dataset_content(history_id, dataset=rval["outputs"][0])
+        assert sanitized_dataset_name.strip() == cool_name_without_quote
+
+        sanitized_email = self.dataset_populator.get_history_dataset_content(history_id, dataset=rval["outputs"][1])
+        assert '"' not in sanitized_email
+
+        sanitized_address = self.dataset_populator.get_history_dataset_content(history_id, dataset=rval["outputs"][2])
+        assert sanitized_address.strip() == cool_name_without_quote
+
     @skip_without_tool("composite_output")
     def test_test_data_filepath_security(self):
         test_data_response = self._get(f"tools/{'composite_output'}/test_data_path?filename=../CONTRIBUTORS.md", admin=True)
diff --git a/test/functional/tools/model_attributes.xml b/test/functional/tools/model_attributes.xml
new file mode 100644
index 00000000000..a43b3de501f
--- /dev/null
+++ b/test/functional/tools/model_attributes.xml
@@ -0,0 +1,15 @@
+<tool id="model_attributes" name="model_attributes" version="0.1.0">
+    <command><![CDATA[
+        echo '$input1.name' > "$out_file1";
+        echo '$__user__.email' > "$out_file2";
+        echo '$__user__.addresses[0].desc' > "$out_file3";
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" label="Dataset with a name to output"/>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+        <data name="out_file2" format="txt" />
+        <data name="out_file3" format="txt" />
+    </outputs>
+</tool>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 7c82aca504e..9bef64673f0 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -195,6 +195,7 @@
   <tool file="cheetah_problem_unbound_var.xml" />
   <tool file="cheetah_problem_unbound_var_input.xml" />
   <tool file="cheetah_problem_syntax_error.xml" />
+  <tool file="model_attributes.xml" />
   <tool file="python_environment_problem.xml" />
   <tool file="config_vars.xml" />
 

From 341658c1eeb87b3068b7d2267c954e04c3fce366 Mon Sep 17 00:00:00 2001
From: Mason Houtz <nerdinacan@gmail.com>
Date: Wed, 18 Aug 2021 13:01:22 -0700
Subject: [PATCH 218/218] started fixing selenium tests in workflow_run tests

---
 client/src/components/History/EditorMenu.vue  |  2 +
 .../src/components/History/HistoriesMenu.vue  |  2 +-
 client/src/components/History/History.vue     |  1 +
 .../src/components/History/HistoryDetails.vue |  6 ++-
 lib/galaxy/selenium/navigates_galaxy.py       | 45 +++++++++++++------
 lib/galaxy/selenium/navigation.yml            |  2 +
 6 files changed, 41 insertions(+), 17 deletions(-)

diff --git a/client/src/components/History/EditorMenu.vue b/client/src/components/History/EditorMenu.vue
index a3c84878860..8ab53810e1b 100644
--- a/client/src/components/History/EditorMenu.vue
+++ b/client/src/components/History/EditorMenu.vue
@@ -6,6 +6,7 @@
             :pressed="editing"
             icon="pen"
             @click="$emit('update:editing', !editing)"
+            data-description="history editor toggle"
         />
 
         <template v-if="editing">
@@ -16,6 +17,7 @@
                 :class="{ disabled: !valid }"
                 icon="save"
                 @click="$emit('save')"
+                data-description="history editor save button"
             />
 
             <!-- revert -->
diff --git a/client/src/components/History/HistoriesMenu.vue b/client/src/components/History/HistoriesMenu.vue
index 8e88a20cf3a..f9cb8d3d047 100644
--- a/client/src/components/History/HistoriesMenu.vue
+++ b/client/src/components/History/HistoriesMenu.vue
@@ -28,7 +28,7 @@
                 <span v-localize>Change the Current History</span>
             </b-dropdown-item>
 
-            <b-dropdown-item @click="$emit('createNewHistory')">
+            <b-dropdown-item data-description="create new history" @click="$emit('createNewHistory')">
                 <Icon class="mr-1" icon="plus" />
                 <span v-localize>Create a New History</span>
             </b-dropdown-item>
diff --git a/client/src/components/History/History.vue b/client/src/components/History/History.vue
index 48b1013848c..516147616a0 100644
--- a/client/src/components/History/History.vue
+++ b/client/src/components/History/History.vue
@@ -82,6 +82,7 @@
                                     :selected="isSelected(item)"
                                     @update:selected="setSelected(item, $event)"
                                     @viewCollection="$emit('viewCollection', item)"
+                                    :data-hid="item.hid"
                                 />
                             </template>
                         </Scroller>
diff --git a/client/src/components/History/HistoryDetails.vue b/client/src/components/History/HistoryDetails.vue
index a9bc27bf1e7..c443219632e 100644
--- a/client/src/components/History/HistoryDetails.vue
+++ b/client/src/components/History/HistoryDetails.vue
@@ -5,8 +5,8 @@ Emit new History model object when done via .sync syntax
 
 <template>
     <section class="history-details d-flex">
-        <div class="flex-grow-1">
-            <h3>{{ historyName || "(History Name)" }}</h3>
+        <div class="flex-grow-1 overflow-hidden">
+            <h3 data-description="history name display">{{ historyName || "(History Name)" }}</h3>
             <h5 class="history-size">{{ history.size | niceFileSize }}</h5>
 
             <!-- display title, annotation, tags -->
@@ -23,6 +23,7 @@ Emit new History model object when done via .sync syntax
                     placeholder="History Name"
                     trim
                     max-rows="4"
+                    data-description="history name input"
                 ></b-textarea>
 
                 <b-textarea
@@ -31,6 +32,7 @@ Emit new History model object when done via .sync syntax
                     placeholder="Annotation (optional)"
                     trim
                     max-rows="4"
+                    data-description="history annotation input"
                 ></b-textarea>
 
                 <HistoryTags class="mt-3" :history="history" />
diff --git a/lib/galaxy/selenium/navigates_galaxy.py b/lib/galaxy/selenium/navigates_galaxy.py
index a588542594a..9da66468f5f 100644
--- a/lib/galaxy/selenium/navigates_galaxy.py
+++ b/lib/galaxy/selenium/navigates_galaxy.py
@@ -372,9 +372,12 @@ class NavigatesGalaxy(HasDriver):
         return history_item_selector
 
     def history_panel_wait_for_hid_state(self, hid, state, allowed_force_refreshes=0, multi_history_panel=False):
-        history_item_selector = self.history_panel_wait_for_hid_visible(hid, allowed_force_refreshes=allowed_force_refreshes, multi_history_panel=multi_history_panel)
-        # history_item_selector_state = history_item_selector.with_class(f"state-{state}")
-        history_item_selector_state = history_item_selector.with_data("state", state)
+        if self.is_beta_history():
+            history_item_selector_state = self.components.history_panel.item.by_state_and_hid(state='ok', hid=hid)
+        else:
+            history_item_selector = self.history_panel_wait_for_hid_visible(hid, allowed_force_refreshes=allowed_force_refreshes, multi_history_panel=multi_history_panel)
+            # history_item_selector_state = history_item_selector.with_class(f"state-{state}")
+            history_item_selector_state = history_item_selector.with_data("state", state)
         try:
             self.history_item_wait_for(history_item_selector_state, allowed_force_refreshes)
         except self.TimeoutException as e:
@@ -1245,8 +1248,18 @@ class NavigatesGalaxy(HasDriver):
     def is_beta_history(self):
         return not self.components.history_panel.beta.is_absent
 
+    # avoids problematic ID and classes on markup
+    def beta_element(self, attribute_value, attribute_name="data-description"):
+        return self.components.history_panel.by_attribute(name=attribute_name, value=attribute_value)
+
     def history_click_create_new(self):
-        self.components.history_panel.new_history_button.wait_for_and_click()
+        if not self.is_beta_history():
+            self.components.history_panel.new_history_button.wait_for_and_click()
+        else:
+            dropdown = self.beta_element("histories operation menu")
+            dropdown.wait_for_and_click()
+            option = self.beta_element("create new history")
+            option.wait_for_and_click()
 
     def history_panel_click_copy_elements(self):
         if self.is_beta_history():
@@ -1287,21 +1300,25 @@ class NavigatesGalaxy(HasDriver):
             time.sleep(.5)
 
     def history_panel_rename(self, new_name):
-        editable_text_input_element = self.history_panel_click_to_rename()
         if self.is_beta_history():
+            toggle = self.beta_element("history editor toggle")
+            toggle.wait_for_and_click()
+            editable_text_input_element = self.beta_element("history name input").wait_for_visible()
+            self.sleep_for_seconds(1)
             editable_text_input_element.clear()
-        editable_text_input_element.send_keys(new_name)
-        self.send_enter(editable_text_input_element)
+            editable_text_input_element.send_keys(new_name)
+            self.send_enter(editable_text_input_element)
+            save_button = self.beta_element("history editor save button")
+            save_button.wait_for_and_click()
+        else:
+            editable_text_input_element = self.history_panel_click_to_rename()
+            editable_text_input_element.send_keys(new_name)
+            self.send_enter(editable_text_input_element)
 
     def history_panel_click_to_rename(self):
         history_panel = self.components.history_panel
-        if self.is_beta_history():
-            name = history_panel.name_beta
-            edit = history_panel.name_edit_input_beta
-        else:
-            name = history_panel.name
-            edit = history_panel.name_edit_input
-
+        name = history_panel.name
+        edit = history_panel.name_edit_input
         name.wait_for_and_click()
         return edit.wait_for_visible()
 
diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index dcd5300db0d..4f766f55b91 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -116,6 +116,7 @@ history_panel:
       # These now appear other places :_( - e.g. in the invocation view so we'll try
       # prefixing ids with #current-history-panel but obviously we need to switch to classes or data
       _: '#current-history-panel #${history_content_type}-${id}'
+      by_state_and_hid: '.beta.history .listing [data-hid="${hid}"][data-state="${state}"]'
 
       title: '${_} .content-title'
       hid: '${_} .hid'
@@ -168,6 +169,7 @@ history_panel:
 
   selectors:
     beta: 'section.history'
+    by_attribute: '.beta.history [${name}="${value}"]'
     _: '#current-history-panel'
     search: '#current-history-panel input.search-query'
     refresh_button: '.history-refresh-button'