From 5fe9c91537a1ad532572af1173dfe2a10177fd48 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 30 Nov 2020 13:49:09 +0000
Subject: [PATCH 1/4] Cast ``ncores`` to str for ``subprocess.call()``

Fix https://github.com/galaxyproject/galaxy/issues/10824 .
---
 lib/galaxy/objectstore/s3.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py
index 327988be7be..1a4f4c3d36a 100644
--- a/lib/galaxy/objectstore/s3.py
+++ b/lib/galaxy/objectstore/s3.py
@@ -437,7 +437,7 @@ class S3ObjectStore(ObjectStore, CloudConfigMixin):
                 log.debug("Parallel pulled key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
                 ncores = multiprocessing.cpu_count()
                 url = key.generate_url(7200)
-                ret_code = subprocess.call(['axel', '-a', '-n', ncores, url])
+                ret_code = subprocess.call(['axel', '-a', '-n', str(ncores), url])
                 if ret_code == 0:
                     return True
             else:

From 018c3a7da99e264b6d68a380998e03da4ee39269 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Mon, 2 Nov 2020 20:38:05 +0100
Subject: [PATCH 2/4] implement auto-import

---
 client/src/components/Workflow/TrsImport.vue  | 62 +++++++++++++------
 .../components/Workflow/WorkflowImport.vue    |  5 +-
 client/src/components/Workflow/trsMixin.js    |  6 +-
 client/src/components/Workflow/utils.js       |  5 ++
 client/src/entry/analysis/AnalysisRouter.js   |  4 ++
 lib/galaxy/webapps/galaxy/api/workflows.py    | 15 +++--
 6 files changed, 69 insertions(+), 28 deletions(-)
 create mode 100644 client/src/components/Workflow/utils.js

diff --git a/client/src/components/Workflow/TrsImport.vue b/client/src/components/Workflow/TrsImport.vue
index 851b5dbe22b..6dc656ef4dd 100644
--- a/client/src/components/Workflow/TrsImport.vue
+++ b/client/src/components/Workflow/TrsImport.vue
@@ -1,22 +1,29 @@
 <template>
-    <b-card title="GA4GH Tool Registry Server (TRS) Workflow Import">
-        <b-alert :show="hasErrorMessage" variant="danger">{{ errorMessage }}</b-alert>
-        <div>
-            <b>TRS Server:</b>
-            <TrsServerSelection
-                :query-trs-server="queryTrsServer"
-                :query-trs-id="queryTrsId"
-                @onTrsSelection="onTrsSelection"
-                @onError="onTrsSelectionError"
-            />
-        </div>
-        <div>
-            <b>TRS ID:</b>
-            <b-form-input v-model="toolId" />
-        </div>
-
-        <trs-tool :trs-tool="trsTool" v-if="trsTool != null" @onImport="importVersion(trsTool.id, $event)" />
-    </b-card>
+    <div>
+        <b-card title="GA4GH Tool Registry Server (TRS) Workflow Import">
+            <b-alert :show="hasErrorMessage" variant="danger">{{ errorMessage }}</b-alert>
+            <div>
+                <b>TRS Server:</b>
+                <TrsServerSelection
+                    :query-trs-server="queryTrsServer"
+                    :query-trs-id="queryTrsId"
+                    @onTrsSelection="onTrsSelection"
+                    @onError="onTrsSelectionError"
+                />
+            </div>
+            <div v-if="isAutoImport" class="text-center my-2">
+                <b-spinner class="align-middle"></b-spinner>
+                <strong>Loading your Workflow...</strong>
+            </div>
+            <div v-else>
+                <div>
+                    <b>TRS ID:</b>
+                    <b-form-input v-model="toolId" />
+                </div>
+                <trs-tool :trs-tool="trsTool" v-if="trsTool" @onImport="importVersion(trsTool.id, $event)" />
+            </div>
+        </b-card>
+    </div>
 </template>
 
 <script>
@@ -24,6 +31,7 @@ import Vue from "vue";
 import BootstrapVue from "bootstrap-vue";
 import { Services } from "./services";
 import TrsMixin from "./trsMixin";
+import { Toast } from "ui/toast";
 
 Vue.use(BootstrapVue);
 
@@ -38,6 +46,14 @@ export default {
             type: String,
             default: null,
         },
+        queryTrsVersionId: {
+            type: String,
+            default: null,
+        },
+        isRun: {
+            type: Boolean,
+            default: false,
+        },
     },
     created() {
         this.services = new Services();
@@ -49,6 +65,7 @@ export default {
             toolId: null,
             trsTool: null,
             errorMessage: null,
+            isAutoImport: this.queryTrsVersionId && this.queryTrsServer && this.queryTrsId,
         };
     },
     computed: {
@@ -80,6 +97,15 @@ export default {
                 .then((tool) => {
                     this.trsTool = tool;
                     this.errorMessage = null;
+                    if (this.isAutoImport) {
+                        const version = this.trsTool.versions.find((version) => version.id === this.queryTrsVersionId);
+                        if (version) {
+                            this.importVersion(this.trsTool.id, version, this.isRun);
+                        } else {
+                            Toast.warning(`Specified version: ${this.queryTrsVersionId} doesn't exist`);
+                            this.isAutoImport = false;
+                        }
+                    }
                 })
                 .catch((errorMessage) => {
                     this.trsTool = null;
diff --git a/client/src/components/Workflow/WorkflowImport.vue b/client/src/components/Workflow/WorkflowImport.vue
index 1dec22910db..d5fa827e36b 100644
--- a/client/src/components/Workflow/WorkflowImport.vue
+++ b/client/src/components/Workflow/WorkflowImport.vue
@@ -31,6 +31,7 @@ import { getGalaxyInstance } from "app";
 import axios from "axios";
 import Vue from "vue";
 import BootstrapVue from "bootstrap-vue";
+import { redirectOnImport } from "./utils";
 
 Vue.use(BootstrapVue);
 
@@ -67,9 +68,7 @@ export default {
                 axios
                     .post(`${getAppRoot()}api/workflows`, formData)
                     .then((response) => {
-                        window.location = `${getAppRoot()}workflows/list?message=${
-                            response.data.message
-                        }&status=success`;
+                        redirectOnImport(getAppRoot(), response.data);
                     })
                     .catch((error) => {
                         const message = error.response.data && error.response.data.err_msg;
diff --git a/client/src/components/Workflow/trsMixin.js b/client/src/components/Workflow/trsMixin.js
index 44dbde859f9..dfd944df435 100644
--- a/client/src/components/Workflow/trsMixin.js
+++ b/client/src/components/Workflow/trsMixin.js
@@ -1,6 +1,7 @@
 import { getAppRoot } from "onload/loadConfig";
 import TrsServerSelection from "./TrsServerSelection";
 import TrsTool from "./TrsTool";
+import { redirectOnImport } from "./utils";
 
 export default {
     components: {
@@ -8,12 +9,11 @@ export default {
         TrsTool,
     },
     methods: {
-        importVersion(toolId, version) {
+        importVersion(toolId, version, isRunFormRedirect = false) {
             this.services
                 .importTrsTool(this.trsSelection.id, toolId, version.name)
                 .then((response_data) => {
-                    // copied from the WorkflowImport, de-duplicate somehow
-                    window.location = `${getAppRoot()}workflows/list?message=${response_data.message}&status=success`;
+                    redirectOnImport(getAppRoot(), response_data, isRunFormRedirect);
                 })
                 .catch((errorMessage) => {
                     this.errorMessage = errorMessage || "Import failed for an unknown reason.";
diff --git a/client/src/components/Workflow/utils.js b/client/src/components/Workflow/utils.js
new file mode 100644
index 00000000000..03c8d7634be
--- /dev/null
+++ b/client/src/components/Workflow/utils.js
@@ -0,0 +1,5 @@
+export function redirectOnImport(appRoot, response, isRunFormRedirect = false) {
+    isRunFormRedirect
+        ? (window.location = `${appRoot}workflows/run?id=${response.id}`)
+        : (window.location = `${appRoot}workflows/list?message=${response.message}&status=success`);
+}
diff --git a/client/src/entry/analysis/AnalysisRouter.js b/client/src/entry/analysis/AnalysisRouter.js
index 883dd19bc57..bbf017ab8a6 100644
--- a/client/src/entry/analysis/AnalysisRouter.js
+++ b/client/src/entry/analysis/AnalysisRouter.js
@@ -342,9 +342,13 @@ export const getAnalysisRouter = (Galaxy) =>
         show_workflows_trs_import: function () {
             const queryTrsServer = QueryStringParsing.get("trs_server");
             const queryTrsId = QueryStringParsing.get("trs_id");
+            const queryTrsVersionId = QueryStringParsing.get("trs_version");
+            const isRun = QueryStringParsing.get("run_form") === "true";
             const propsData = {
                 queryTrsServer,
                 queryTrsId,
+                queryTrsVersionId,
+                isRun,
             };
             this._display_vue_helper(TrsImport, propsData);
         },
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 066515a2107..b90addd8918 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -678,14 +678,21 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
             raise exceptions.MessageException("The data content is missing.")
         raw_workflow_description = self.__normalize_workflow(trans, data)
         workflow, missing_tool_tups = self._workflow_from_dict(trans, raw_workflow_description, source=source)
+        workflow_id = workflow.id
         workflow = workflow.latest_workflow
+
+        response = {"message": "Workflow '%s' imported successfully." % escape(workflow.name), "status": "success",
+                    "id": trans.security.encode_id(workflow_id)}
         if workflow.has_errors:
-            return {"message": "Imported, but some steps in this workflow have validation errors.", "status": "error"}
+            response["message"] = "Imported, but some steps in this workflow have validation errors."
+            response["status"] = "error"
         elif len(workflow.steps) == 0:
-            return {"message": "Imported, but this workflow has no steps.", "status": "error"}
+            response["message"] = "Imported, but this workflow has no steps."
+            response["status"] = "error"
         elif workflow.has_cycles:
-            return {"message": "Imported, but this workflow contains cycles.", "status": "error"}
-        return {"message": "Workflow '%s' imported successfully." % escape(workflow.name), "status": "success"}
+            response["message"] = "Imported, but this workflow contains cycles."
+            response["status"] = "error"
+        return response
 
     def __api_import_new_workflow(self, trans, payload, **kwd):
         data = payload['workflow']

From bf78fdfc76be76f4f58a2fe05bc18bff9dc8e9c9 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Wed, 25 Nov 2020 14:09:45 +0100
Subject: [PATCH 3/4] show "please register" warning on TRS import

---
 client/src/components/Workflow/TrsImport.vue | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Workflow/TrsImport.vue b/client/src/components/Workflow/TrsImport.vue
index 6dc656ef4dd..04a22a1ec57 100644
--- a/client/src/components/Workflow/TrsImport.vue
+++ b/client/src/components/Workflow/TrsImport.vue
@@ -1,6 +1,6 @@
 <template>
     <div>
-        <b-card title="GA4GH Tool Registry Server (TRS) Workflow Import">
+        <b-card v-if="!isAnonymous" title="GA4GH Tool Registry Server (TRS) Workflow Import">
             <b-alert :show="hasErrorMessage" variant="danger">{{ errorMessage }}</b-alert>
             <div>
                 <b>TRS Server:</b>
@@ -11,7 +11,7 @@
                     @onError="onTrsSelectionError"
                 />
             </div>
-            <div v-if="isAutoImport" class="text-center my-2">
+            <div v-if="isAutoImport && !hasErrorMessage" class="text-center my-2">
                 <b-spinner class="align-middle"></b-spinner>
                 <strong>Loading your Workflow...</strong>
             </div>
@@ -23,6 +23,9 @@
                 <trs-tool :trs-tool="trsTool" v-if="trsTool" @onImport="importVersion(trsTool.id, $event)" />
             </div>
         </b-card>
+        <b-alert v-else show variant="danger" class="text-center my-2"
+            >Anonymous user cannot import workflows, please register or log in</b-alert
+        >
     </div>
 </template>
 
@@ -32,6 +35,7 @@ import BootstrapVue from "bootstrap-vue";
 import { Services } from "./services";
 import TrsMixin from "./trsMixin";
 import { Toast } from "ui/toast";
+import { getGalaxyInstance } from "app";
 
 Vue.use(BootstrapVue);
 
@@ -72,6 +76,9 @@ export default {
         hasErrorMessage() {
             return this.errorMessage != null;
         },
+        isAnonymous() {
+            return getGalaxyInstance().user.isAnonymous();
+        },
     },
     watch: {
         toolId: function () {

From 7d1569ed472d7381bcacecbbee883cbc97d97a01 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 30 Nov 2020 16:48:42 +0000
Subject: [PATCH 4/4] Update `sphinx-markdown-tables` to fix conflict

`sphinx-markdown-tables` 0.0.12 had a strict pin which is causing a conflict
error with the new pip 20.3:

```
ERROR: Cannot install -r ./lib/galaxy/dependencies/dev-requirements.txt (line 55) and markdown==3.1.1 because these package versions have conflicting dependencies.

ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies
The conflict is caused by:
    The user requested markdown==3.1.1
    The user requested markdown==3.1.1
    sphinx-markdown-tables 0.0.12 depends on markdown==3.0.1

To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict
```

See https://github.com/galaxyproject/galaxy/pull/10825/checks?check_run_id=1474883413
---
 .../dependencies/pipfiles/default/pinned-dev-requirements.txt   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
index 1b53e2b2826..9a382962cbd 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
@@ -52,7 +52,7 @@ scandir==1.10.0 ; python_version < '3.5'
 selenium==3.141.0
 six==1.11.0
 snowballstemmer==2.0.0
-sphinx-markdown-tables==0.0.12
+sphinx-markdown-tables==0.0.13
 sphinx-rtd-theme==0.4.3
 sphinx==1.8.5
 sphinxcontrib-websupport==1.1.2