From 1a2f45c64360cb891fd6fce3764860d920ed31b1 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 17 Jan 2023 17:10:32 -0500
Subject: [PATCH 01/31] Ensure that tool form is initialized before attempting
 updates triggered by history change emission

---
 client/src/components/Tool/ToolForm.vue | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/client/src/components/Tool/ToolForm.vue b/client/src/components/Tool/ToolForm.vue
index 2dc15868beb..ebb30af69bb 100644
--- a/client/src/components/Tool/ToolForm.vue
+++ b/client/src/components/Tool/ToolForm.vue
@@ -163,6 +163,7 @@ export default {
     data() {
         return {
             disabled: false,
+            initialized: false,
             showLoading: true,
             showForm: false,
             showEntryPoints: false,
@@ -225,7 +226,7 @@ export default {
     watch: {
         getLatestCreateTime() {
             const Galaxy = getGalaxyInstance();
-            if (Galaxy && Galaxy.currHistoryPanel) {
+            if (this.initialized && Galaxy && Galaxy.currHistoryPanel) {
                 console.debug("History change watcher detected a change.");
                 this.onHistoryChange();
             }
@@ -233,6 +234,7 @@ export default {
     },
     created() {
         this.requestTool().then(() => {
+            this.initialized = true;
             console.debug(`ToolForm::created - Started listening to history changes. [${this.id}]`);
         });
     },

From dde16032028f831197712a836bb5a9409aa005b3 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 22 Jan 2023 12:32:00 +0100
Subject: [PATCH 02/31] Fix re-enabling save button when invalid connections
 are resolved

---
 client/src/stores/workflowConnectionStore.ts     |  2 +-
 lib/galaxy_test/selenium/test_workflow_editor.py | 11 +++++++++++
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/client/src/stores/workflowConnectionStore.ts b/client/src/stores/workflowConnectionStore.ts
index 627f5df5525..7748a417e77 100644
--- a/client/src/stores/workflowConnectionStore.ts
+++ b/client/src/stores/workflowConnectionStore.ts
@@ -124,7 +124,7 @@ export const useConnectionStore = defineStore("workflowConnectionStore", {
             Vue.set(this.invalidConnections, connectionId, reason);
         },
         dropFromInvalidConnections(this: State, connectionId: string) {
-            this.invalidConnections[connectionId] = undefined;
+            Vue.delete(this.invalidConnections, connectionId);
         },
         removeConnection(this: State, terminal: InputTerminal | OutputTerminal | Connection["id"]) {
             const stepStore = useWorkflowStepStore();
diff --git a/lib/galaxy_test/selenium/test_workflow_editor.py b/lib/galaxy_test/selenium/test_workflow_editor.py
index f907926eb07..9be68ab210c 100644
--- a/lib/galaxy_test/selenium/test_workflow_editor.py
+++ b/lib/galaxy_test/selenium/test_workflow_editor.py
@@ -558,6 +558,17 @@ steps:
         editor.select_datatype(datatype="bam").wait_for_and_click()
         editor.node.output_data_row(output_name="out_file1", extension="bam").wait_for_visible()
         self.assert_connection_invalid("create_2#out_file1", "checksum#input")
+        save_button = self.components.workflow_editor.save_button
+        # Assert save button is disabled
+        assert save_button.has_class("disabled")
+        # Make connection valid again
+        editor.change_datatype.wait_for_and_click()
+        editor.select_datatype_text_search.wait_for_and_send_keys("tabular")
+        editor.select_datatype(datatype="tabular").wait_for_and_click()
+        # Assert connection is valid
+        self.assert_connected("create_2#out_file1", "checksum#input")
+        # Assert save button is enabled
+        assert not save_button.has_class("disabled")
 
     @selenium_test
     def test_change_datatype_post_job_action_lost_regression(self):

From e7443bbb01ce6c4c49141bcb8e298b36e93ef9a2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 23 Jan 2023 16:06:28 +0100
Subject: [PATCH 03/31] Use built-in download_to_file instead of relying on
 curl/wget for conda/involucro installs

Fixes https://github.com/galaxyproject/galaxy/issues/15355
---
 lib/galaxy/tool_util/deps/conda_util.py          |  6 ++----
 lib/galaxy/tool_util/deps/mulled/mulled_build.py | 11 +++++++----
 2 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/tool_util/deps/conda_util.py b/lib/galaxy/tool_util/deps/conda_util.py
index b5bdfd72473..bc91af0c433 100644
--- a/lib/galaxy/tool_util/deps/conda_util.py
+++ b/lib/galaxy/tool_util/deps/conda_util.py
@@ -24,6 +24,7 @@ import packaging.version
 
 from galaxy.util import (
     commands,
+    download_to_file,
     listify,
     shlex_join,
     smart_str,
@@ -483,16 +484,13 @@ def hash_conda_packages(conda_packages: Iterable[CondaTarget]) -> str:
 def install_conda(conda_context: CondaContext, force_conda_build: bool = False) -> int:
     with tempfile.NamedTemporaryFile(suffix=".sh", prefix="conda_install", delete=False) as temp:
         script_path = temp.name
-    download_cmd = commands.download_command(conda_link(), to=script_path)
     install_cmd = ["bash", script_path, "-b", "-p", conda_context.conda_prefix]
     package_targets = list(CONDA_PACKAGE_SPECS)
     if force_conda_build or conda_context.use_local:
         package_targets.extend(CONDA_BUILD_SPECS)
     log.info("Installing conda, this may take several minutes.")
     try:
-        exit_code = conda_context.shell_exec(download_cmd)
-        if exit_code:
-            return exit_code
+        download_to_file(conda_link(), script_path)
         exit_code = conda_context.shell_exec(install_cmd)
     except Exception:
         log.exception("Failed to install conda")
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_build.py b/lib/galaxy/tool_util/deps/mulled/mulled_build.py
index 7f99a829b3f..82ca88e156e 100644
--- a/lib/galaxy/tool_util/deps/mulled/mulled_build.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_build.py
@@ -29,6 +29,7 @@ from galaxy.tool_util.deps.conda_util import (
 from galaxy.tool_util.deps.docker_util import command_list as docker_command_list
 from galaxy.util import (
     commands,
+    download_to_file,
     safe_makedirs,
     shlex_join,
     unicodify,
@@ -428,10 +429,12 @@ def ensure_installed(involucro_context, auto_init):
 def install_involucro(involucro_context):
     install_path = os.path.abspath(involucro_context.involucro_bin)
     involucro_context.involucro_bin = install_path
-    download_cmd = commands.download_command(involucro_link(), to=install_path)
-    exit_code = involucro_context.shell_exec(download_cmd)
-    if exit_code:
-        return exit_code
+
+    try:
+        download_to_file(involucro_link(), install_path)
+    except Exception:
+        log.exception(f"Failed to download involucro from url '{involucro_link()}'")
+        return 1
     try:
         os.chmod(install_path, os.stat(install_path).st_mode | stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH)
         return 0

From ce93b01b116660760109e698072d083413b084e2 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 23 Jan 2023 15:08:32 -0500
Subject: [PATCH 04/31] Add metadata generation failed dataset details, when
 metadata fails

---
 client/src/components/History/Content/model/states.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/src/components/History/Content/model/states.js b/client/src/components/History/Content/model/states.js
index 150d990b228..2ddfcecbf9e 100644
--- a/client/src/components/History/Content/model/states.js
+++ b/client/src/components/History/Content/model/states.js
@@ -33,6 +33,7 @@ export const STATES = {
     /** metadata discovery/setting failed or errored (but otherwise ok) */
     failed_metadata: {
         status: "danger",
+        text: "Metadata generation failed.",
         icon: "exclamation-triangle",
     },
     /** was created without a tool */

From f2926ad41f28d569c1c7ae44c79d78c51737483e Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 24 Jan 2023 10:48:06 +0100
Subject: [PATCH 05/31] Fix reference to sample_tool_conf.xml

---
 .vscode/.test.env          | 2 +-
 .vscode/launch_gitpod.json | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.vscode/.test.env b/.vscode/.test.env
index 0fd4d77f2ed..8321bcadf92 100644
--- a/.vscode/.test.env
+++ b/.vscode/.test.env
@@ -1 +1 @@
-GALAXY_TEST_TOOL_CONF="lib/galaxy/config/sample/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
\ No newline at end of file
+GALAXY_TEST_TOOL_CONF="lib/galaxy/config/sample/tool_conf.xml.sample,test/functional/tools/sample_tool_conf.xml"
diff --git a/.vscode/launch_gitpod.json b/.vscode/launch_gitpod.json
index c9bee582dcd..ebab8a9437a 100644
--- a/.vscode/launch_gitpod.json
+++ b/.vscode/launch_gitpod.json
@@ -10,7 +10,7 @@
             "env": {
                 "GALAXY_CONFIG_FILE": "${workspaceFolder}/config/galaxy.yml",
                 "GALAXY_CONDA_AUTO_INIT": "false",
-                "GALAXY_CONFIG_TOOL_CONFIG_FILE": "lib/galaxy/config/sample/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml",
+                "GALAXY_CONFIG_TOOL_CONFIG_FILE": "lib/galaxy/config/sample/tool_conf.xml.sample,test/functional/tools/sample_tool_conf.xml",
                 "GALAXY_CONFIG_DATABASE_CONNECTION": "postgresql://localhost/galaxy"
             }
         },

From bb5ecb72a24b8b82753b093eaec6b13988ad2c8f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 24 Jan 2023 13:32:28 +0100
Subject: [PATCH 06/31] Reset confirmation state then unmounting workflow
 editor

Should fix https://github.com/galaxyproject/galaxy/issues/15366
---
 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 a682769f5ec..92ee4af0680 100644
--- a/client/src/components/Workflow/Editor/Index.vue
+++ b/client/src/components/Workflow/Editor/Index.vue
@@ -236,7 +236,7 @@ export default {
             required: true,
         },
     },
-    setup() {
+    setup(props, { emit }) {
         const { datatypes, datatypesMapper, datatypesMapperLoading } = useDatatypesMapper();
         const connectionsStore = useConnectionStore();
         const stepStore = useWorkflowStepStore();
@@ -260,6 +260,7 @@ export default {
         }
         onUnmounted(() => {
             resetStores();
+            emit("update:confirmation", false);
         });
         return {
             connectionsStore,

From e9cd987e90ec4400b0578d732fc5b203472a8728 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 24 Jan 2023 14:27:10 +0100
Subject: [PATCH 07/31] Allow configuring webpack devserver port

Should be useful when you're debugging against a live server and a local
instance.
---
 client/webpack.config.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/webpack.config.js b/client/webpack.config.js
index 06f773f8f3a..795db78e6f1 100644
--- a/client/webpack.config.js
+++ b/client/webpack.config.js
@@ -252,7 +252,7 @@ module.exports = (env = {}, argv = {}) => {
                 publicPath: "/static/dist",
             },
             hot: true,
-            port: 8081,
+            port: process.env.WEBPACK_PORT || 8081,
             host: "0.0.0.0",
             // proxy *everything* to the galaxy server.
             // someday, when we have a fully API-driven independent client, this

From 31d31cb74f3e1a4bfabd772458c4a551c801a264 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 24 Jan 2023 12:44:10 +0100
Subject: [PATCH 08/31] Extend terminal test

---
 client/src/components/Workflow/Editor/modules/terminals.test.ts | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/src/components/Workflow/Editor/modules/terminals.test.ts b/client/src/components/Workflow/Editor/modules/terminals.test.ts
index 4d41492bc86..00cdd99954c 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.test.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.test.ts
@@ -102,6 +102,7 @@ describe("canAccept", () => {
         dataIn.connect(collectionOut);
         expect(dataIn.mapOver).toEqual({ collectionType: "list", isCollection: true, rank: 1 });
         expect(dataIn.canAccept(collectionOut).canAccept).toBe(false);
+        expect(dataIn.canAccept(collectionOut).reason).toBe("Input already filled with another connection, delete it before connecting another output.");
         dataIn.disconnect(collectionOut);
         expect(dataIn.canAccept(collectionOut).canAccept).toBe(true);
         expect(dataIn.mapOver).toEqual(NULL_COLLECTION_TYPE_DESCRIPTION);

From bd25f11a5d8a638355a984e00a7a5c43813cb51c Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 24 Jan 2023 08:55:22 -0500
Subject: [PATCH 09/31] Have webpack dev server write files to disk by default
 -- this should be equivalent to the old watch mode

---
 client/webpack.config.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/webpack.config.js b/client/webpack.config.js
index 795db78e6f1..aa12a065163 100644
--- a/client/webpack.config.js
+++ b/client/webpack.config.js
@@ -250,6 +250,7 @@ module.exports = (env = {}, argv = {}) => {
             allowedHosts: process.env.GITPOD_WORKSPACE_ID ? "all" : "auto",
             devMiddleware: {
                 publicPath: "/static/dist",
+                writeToDisk: true,
             },
             hot: true,
             port: process.env.WEBPACK_PORT || 8081,

From 6c99486d8f2096a6c34bf8c4f0be6302ca06a527 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 24 Jan 2023 09:04:53 -0500
Subject: [PATCH 10/31] Client README updates

---
 client/README.md | 29 +++++++++++++----------------
 1 file changed, 13 insertions(+), 16 deletions(-)

diff --git a/client/README.md b/client/README.md
index 15fad423884..9b23e47280c 100644
--- a/client/README.md
+++ b/client/README.md
@@ -53,24 +53,12 @@ and these should not be committed.
 When you're actively developing, it is convenient to have the client
 automatically rebuild every time you save a file. You can do this using:
 
-    make client-watch
-
-This will first stage client dependencies, initiate a build, and then will
-watch for changes in any of the galaxy client source files.  When a file is
-changed, the client will automatically rebuild, after which you can refresh
-your browser to see changes.
-
-For even more rapid development you can use the webpack development server,
-which takes advantage of hot module replacement (HMR). This technique allows
-swapping out of javascript modules while the application is running without
-requiring a full page reload most of the time, at least in the more modern
-parts of the application.
-
-The command below starts a special webpack dev server after a client
-build.
-
     make client-dev-server
 
+Or, with the package scripts from this `client` directory:
+    
+    yarn run develop
+
 This will start up an extra client development server running on port 8081.
 Open your browser to http://localhost:8081 (instead of the default 8080 that
 Galaxy would run on), and you should see Galaxy like normal.  Except now, when
@@ -86,6 +74,10 @@ Sometimes you want to run your local UI against a remote Galaxy server. This is
 
     CHANGE_ORIGIN=true GALAXY_URL="https://usegalaxy.org/" make client-dev-server
 
+You can also specify a particular port to bind the dev server to:
+
+    WEBPACK_PORT=8083 yarn run develop
+
 ## Running a Separate Server
 
 When developing the client it can be helpful to run a local server for the
@@ -94,6 +86,11 @@ commands. This command will run galaxy without building the client:
 
     make skip-client
 
+Or by setting the following environment variable and running Galaxy however you
+prefer:
+
+    GALAXY_SKIP_CLIENT_BUILD=1 ./run.sh
+
 ## Changing Styles/CSS
 
 Galaxy uses Sass for its styling, which is a superset of CSS that compiles down

From 56a2ace72d2218d086129b3222878329f7f783ee Mon Sep 17 00:00:00 2001
From: Anup Kumar <kumara@informatik.uni-freiburg.de>
Date: Thu, 12 Jan 2023 11:49:08 +0100
Subject: [PATCH 11/31] Update interactivetool_ml_jupyter_notebook.xml

Add changes to GPU Jupyterlab tool based on Jupytool
---
 .../interactivetool_ml_jupyter_notebook.xml   | 245 ++++++++++++++----
 1 file changed, 197 insertions(+), 48 deletions(-)

diff --git a/tools/interactive/interactivetool_ml_jupyter_notebook.xml b/tools/interactive/interactivetool_ml_jupyter_notebook.xml
index f11cec41589..5d19185d4ef 100644
--- a/tools/interactive/interactivetool_ml_jupyter_notebook.xml
+++ b/tools/interactive/interactivetool_ml_jupyter_notebook.xml
@@ -1,6 +1,6 @@
 <tool id="interactive_tool_ml_jupyter_notebook" tool_type="interactive" name="GPU enabled Interactive Jupyter Notebook for Machine Learning" version="@VERSION@" profile="22.01">
     <macros>
-        <token name="@VERSION@">0.1</token>
+        <token name="@VERSION@">0.2</token>
     </macros>
     <requirements>
         <container type="docker">docker.io/anupkumar/docker-ml-jupyterlab:galaxy-integration-@VERSION@</container>
@@ -19,71 +19,221 @@
         <environment_variable name="DISABLE_AUTH">true</environment_variable>
         <environment_variable name="API_KEY" inject="api_key" />
     </environment_variables>
-    <command detect_errors="aggressive"><![CDATA[
-        #import re
+    <configfiles>
+        <inputs name="inputs" filename="galaxy_inputs.json" data_style="staging_path_and_source_path"/>
+        <configfile name="staging_script" filename="staging_script.py"><![CDATA[
+import json, os, shutil
+import os.path
+galaxy_inputs = "galaxy_inputs.json"
+galaxy_inputs_raw = "galaxy_inputs_raw.json"
+base_staging_path = "jupyter"
+base_data_staging_path = "galaxy_inputs"
+data_staging_path = os.path.join(base_staging_path, base_data_staging_path)
+os.makedirs(data_staging_path, exist_ok=True)
+shutil.copyfile(galaxy_inputs, os.path.join(data_staging_path, galaxy_inputs_raw))
+galaxy_input_dict = {}
+for user_input in json.load(open(galaxy_inputs, "r")).get("user_inputs", []):
+    input_values = user_input['input_type']['input_value']
+    input_name = user_input["input_name"]
+    assert input_name not in galaxy_input_dict, ValueError("Each name can only be used once, but a duplicate was found: %s" % (input_name))
+    if 'dataset' in user_input['input_type']['input_type_selector']:
+        input_values2 = []
+        if not isinstance(input_values, list):
+            input_values = [input_values]
+        for input_value_dict in input_values:
+            path, filename = os.path.split(input_value_dict['staging_path'])
+            input_value_dict2 = {"path": os.path.join(base_data_staging_path, input_name, path, filename), "metadata_files": []}
+            path = os.path.join(data_staging_path, input_name, path)
+            os.makedirs(path, exist_ok=True)
+            try:
+                os.symlink(input_value_dict['source_path'], os.path.join(path, filename))
+            except FileExistsError:
+                pass
+            for metadata_value_dict in input_value_dict['metadata_files']:
+                path, filename = os.path.split(metadata_value_dict['staging_path'])
+                input_value_dict2["metadata_files"].append(os.path.join(base_data_staging_path, input_name, path, filename))
+                path = os.path.join(data_staging_path, input_name, path)
+                os.makedirs(path, exist_ok=True)
+                try:
+                    os.symlink(metadata_value_dict['source_path'], os.path.join(path, filename))
+                except FileExistsError:
+                    pass
+            input_values2.append(input_value_dict2)
+        input_values = input_values2
+    galaxy_input_dict[input_name] = input_values
+with open(os.path.join(data_staging_path, galaxy_inputs), "w") as fh:
+    json.dump(galaxy_input_dict, fh)
+]]>
+        </configfile>
+        <configfile name="galaxy_input_startup_script"><![CDATA[
+import json, os
+from galaxy_ie_helpers import get
+from galaxy_ie_helpers import put
+from galaxy_ie_helpers import get_galaxy_connection
+HISTORY_ID = os.environ.get('HISTORY_ID', None)
+try:
+    GALAXY_INPUTS = json.load(open(os.path.join(os.environ.get("GALAXY_WORKING_DIR", ""), "jupyter", "galaxy_inputs", "galaxy_inputs.json")))
+except FileNotFoundError:
+    GALAXY_INPUTS = {}
+        ]]>
+    </configfile>
+    </configfiles>
+    
+    <command><![CDATA[
+        python staging_script.py &&
         export GALAXY_WORKING_DIR=`pwd` &&
-        mkdir -p ./jupyter/outputs/ &&
-        mkdir -p ./jupyter/data &&
-        mkdir -p ./jupyter/notebooks &&
-        mkdir -p ./jupyter/elyra &&
-
-        #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
-        ln -sf '$input' './jupyter/data/${cleaned_name}' &&
-
-        ## change into the directory where the notebooks are located
+        mkdir -p ./jupyter/outputs &&
+        mkdir -p ./jupyter/galaxy_inputs &&
         cd ./jupyter/ &&
         export HOME=/home/\$NB_USER/ &&
         export PATH=/home/\$NB_USER/.local/bin:\$PATH &&
+        cp '${galaxy_input_startup_script}' /home/\$NB_USER/.ipython/profile_default/startup/02-load.py &&
+        #set $output_notebook_name = 'jupyterlab_notebook.ipynb'
         #if $mode.mode_select == 'scratch':
-            ## copy all notebooks, workflows and data
-            cp /home/\$NB_USER/home_page.ipynb ./ &&
-            cp /home/\$NB_USER/notebooks/*.ipynb ./notebooks/ &&
-            cp /home/\$NB_USER/elyra/*.* ./elyra/ &&
-            cp /home/\$NB_USER/data/*.tsv ./data/ &&
-            ## provide all rights to copied files
-            chown -R \$NB_USER:users `pwd` &&
-            chown \$NB_USER ./home_page.ipynb &&
-            chown \$NB_USER ./notebooks/ &&
-            chown \$NB_USER ./notebooks/*.ipynb &&
-            chown \$NB_USER ./elyra/ &&
-            chown \$NB_USER ./elyra/*.* &&
-            jupyter trust ./home_page.ipynb &&
-            jupyter trust ./notebooks/*.ipynb &&
-            jupyter trust ./elyra/*.ipynb &&
-            jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True
+            cp -r /home/\$NB_USER/data ./ &&
+            cp -r /home/\$NB_USER/elyra ./ &&
+            cp -r /home/\$NB_USER/notebooks ./ &&
+            cp -r /home/\$NB_USER/usecases ./ &&
+            cp -r /home/\$NB_USER/home_page.ipynb ./ &&
+            jupyter lab --no-browser --NotebookApp.shutdown_button=True
         #else:
-            #set $noteboook_name = re.sub('[^\w\-\.\s]', '_', str($mode.ipynb.element_identifier))
-            cp '$mode.ipynb' './${noteboook_name}.ipynb' &&
-            jupyter trust './${noteboook_name}.ipynb' &&
+            #import re
+            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier))
+            #if not $cleaned_name.endswith(".ipynb"'$jupyter_notebook'):
+                #set $cleaned_name = "%s.ipynb" % $cleaned_name
+            #end if
+            cp '$mode.ipynb' '${cleaned_name}' &&
+            jupyter trust '${cleaned_name}' &&
+
             #if $mode.run_it:
-                jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors  ./*.ipynb &&
-                #set $noteboook_name = 'ipython_galaxy_notebook'
+                jupyter nbconvert --to notebook --execute --output '${output_notebook_name}' --allow-errors '${cleaned_name}' &&
+                cp '${output_notebook_name}' '$jupyter_notebook'
             #else:
-                jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
+                #set $output_notebook_name = $cleaned_name
+                jupyter lab --no-browser --NotebookApp.shutdown_button=True
             #end if
-            cp './${noteboook_name}.ipynb' '$jupyter_notebook'
         #end if
     ]]>
     </command>
     <inputs>
-
         <conditional name="mode">
-            <param name="mode_select" type="select" label="Do you already have a notebook?" help="If not, no problem we will provide you with a default one.">
-                <option value="scratch">Start with a fresh notebook</option>
-                <option value="previous">Load a previous notebook</option>
+            <param name="mode_select" type="select" label="Do you already have a notebook?" help="Select a set of default notebooks or load an existing one.">
+                <option value="scratch">Start with default notebooks</option>
+                <option value="previous">Load an existing notebook</option>
             </param>
             <when value="scratch"/>
             <when value="previous">
-                <param name="ipynb" type="data" format="ipynb" label="IPython Notebook"/>
-                <param name="run_it" type="boolean" truevalue="true" falsevalue="false" label="Execute notebook and return a new one."
-                    help="This option is useful in workflows when you just want to execute a notebook and not dive into the webfrontend."/>
+                <param name="ipynb" type="data" format="ipynb" label="IPython Notebook" required="true"/>
+                <param name="run_it" type="boolean" truevalue="true" falsevalue="false" label="Execute notebook and return a new one." help="This option is useful in workflows when you just want to execute a notebook and not dive into the webfrontend."/>
             </when>
         </conditional>
-        <param name="input" type="data" optional="true" label="Include data into the environment"/>
-
+        <repeat name="user_inputs" title="User inputs">
+            <param name="input_name" type="text" value="" label="Name for parameter" optional="False" help="Required. ASCII letters and numbers only.">
+                <validator type="empty_field" message="Name is required"/>
+                <sanitizer>
+                    <valid initial="string.ascii_letters,string.digits"/>
+                </sanitizer>
+            </param>
+            <param name="description" type="text" label="Additional optional description" optional="true"/>
+            <conditional name="input_type">
+                <param name="input_type_selector" type="select" label="Choose the input type">
+                    <option value="dataset" selected="true">Dataset</option>
+                    <option value="dataset_multiple">Multiple datasets</option>
+                    <option value="dataset_collection">Dataset collection</option>
+                    <option value="dataset_collection_list">Dataset collection (list)</option>
+                    <option value="dataset_collection_paired">Dataset collection (paired)</option>
+                    <option value="dataset_collection_list_paired">Dataset collection (list:paired)</option>
+                    <option value="text">Text</option>
+                    <option value="integer">Integer</option>
+                    <option value="float">Floating point</option>
+                    <option value="boolean">Boolean</option>
+                    <option value="color">Color selector</option>
+                    <option value="dataset_optional" selected="true">Optional Dataset</option>
+                    <option value="dataset_multiple_optional">Optional Multiple datasets</option>
+                    <option value="dataset_collection_optional">Optional Dataset collection</option>
+                    <option value="dataset_collection_list_optional">Optional Dataset collection (list)</option>
+                    <option value="dataset_collection_paired_optional">Optional Dataset collection (paired)</option>
+                    <option value="dataset_collection_list_paired_optional">Optional Dataset collection (list:paired)</option>
+                    <option value="text_optional">Optional Text</option>
+                    <option value="integer_optional">Optional Integer</option>
+                    <option value="float_optional">Optional Floating point</option>
+                    <option value="boolean_optional">Optional Boolean</option>
+                    <option value="color_optional">Optional Color selector</option>
+                </param>
+                <when value="dataset">
+                    <param name="input_value" type="data" format="data" label="Select value" multiple="false" optional="false"/>
+                </when>
+                <when value="dataset_multiple">
+                    <param name="input_value" type="data" format="data" label="Select value" multiple="true" optional="false"/>
+                </when>
+                <when value="dataset_collection">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" optional="false"/>
+                </when>
+                <when value="dataset_collection_list">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" collection_type="list" optional="false"/>
+                </when>
+                <when value="dataset_collection_paired">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" collection_type="paired" optional="false"/>
+                </when>
+                <when value="dataset_collection_list_paired">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" collection_type="list:paired" optional="false"/>
+                </when>
+                <when value="text">
+                    <param name="input_value" type="text" value="" label="Select value" optional="false"/>
+                </when>
+                <when value="integer">
+                    <param name="input_value" type="integer" value="" label="Select value" optional="false"/>
+                </when>
+                <when value="float">
+                    <param name="input_value" type="float" value="" label="Select value" optional="false"/>
+                </when>
+                <when value="boolean">
+                    <param name="input_value" type="boolean" truevalue="true" falsevalue="false" label="Select value" optional="false"/>
+                </when>
+                <when value="color">
+                    <param name="input_value" type="color" label="Select value" optional="false"/>
+                </when>
+                <when value="dataset_optional">
+                    <param name="input_value" type="data" format="data" label="Select value" multiple="false" optional="true"/>
+                </when>
+                <when value="dataset_multiple_optional">
+                    <param name="input_value" type="data" format="data" label="Select value" multiple="true" optional="true"/>
+                </when>
+                <when value="dataset_collection_optional">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" optional="true"/>
+                </when>
+                <when value="dataset_collection_list_optional">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" collection_type="list" optional="true"/>
+                </when>
+                <when value="dataset_collection_paired_optional">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" collection_type="paired" optional="true"/>
+                </when>
+                <when value="dataset_collection_list_paired_optional">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" collection_type="list:paired" optional="true"/>
+                </when>
+                <when value="text_optional">
+                    <param name="input_value" type="text" value="" label="Select value" optional="true"/>
+                </when>
+                <when value="integer_optional">
+                    <param name="input_value" type="integer" value="" label="Select value" optional="true"/>
+                </when>
+                <when value="float_optional">
+                    <param name="input_value" type="float" value="" label="Select value" optional="true"/>
+                </when>
+                <when value="boolean_optional">
+                    <param name="input_value" type="boolean" truevalue="true" falsevalue="false" label="Select value" optional="true"/>
+                </when>
+                <when value="color_optional">
+                    <param name="input_value" type="color" label="Select value" optional="true"/>
+                </when>
+            </conditional>
+        </repeat>
     </inputs>
     <outputs>
-        <data name="jupyter_notebook" format="ipynb" label="Executed Notebook" />
+        <data name="jupyter_notebook" format="ipynb" label="Executed GPU JupyterLab Notebook"/>
+        <collection name="output_collection" type="list" label="GPU JupyterLab notebook output collection">
+            <discover_datasets pattern="__designation_and_ext__" directory="jupyter/outputs" visible="false"/>
+        </collection>
     </outputs>
     <tests>
         <test expect_num_outputs="1">
@@ -97,10 +247,9 @@
         JupyterLab is a next-generation web-based user interface for Project Jupyter. JupyterLab enables you to work with documents and activities such as Jupyter notebooks, text editors,
         terminals, and custom components in a flexible, integrated, and extensible manner.
 
-        Galaxy offers you to use Jupyter Lab directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to
+        Galaxy offers you to use JupyterLab directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to
         do the heavy lifting such as performing computation on GPUs and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in Jupyter Lab.
 
-        You can start with a new Jupyter Lab notebook from scratch and wait until the job starts running. Running job will provide you a link which can be opened in the same or another
-        browser tab. This link opens Jupyter Lab notebook which can be used to prototype machine learning solutions.
+        You can start with a new JupyterLab notebook from scratch and wait until the job starts running. Running job will provide you a link which can be opened in the same or another browser tab. This link opens JupyterLab notebook which can be used to prototype machine learning solutions.
     ]]></help>
 </tool>

From 5ab06841dab4bfcb46fd8cdeab266b0f0d82380b Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 24 Jan 2023 16:23:39 -0500
Subject: [PATCH 12/31] Attempt to force result order?

---
 client/webpack.config.js | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/client/webpack.config.js b/client/webpack.config.js
index 795db78e6f1..3389ffb1529 100644
--- a/client/webpack.config.js
+++ b/client/webpack.config.js
@@ -28,6 +28,9 @@ const modulesExcludedFromLibs = [
 
 const buildDate = new Date();
 
+const dns = require('node:dns');
+dns.setDefaultResultOrder('ipv4first');
+
 module.exports = (env = {}, argv = {}) => {
     // environment name based on -d, -p, webpack flag
     const targetEnv = process.env.NODE_ENV == "production" || argv.mode == "production" ? "production" : "development";

From 7674416df0c1cb0c6e73bc3d881aab904b090329 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 24 Jan 2023 16:38:00 -0500
Subject: [PATCH 13/31] Swap default binding from localhost to explicit ipv4
 loopback

---
 client/webpack.config.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/client/webpack.config.js b/client/webpack.config.js
index 3389ffb1529..e4729ccc555 100644
--- a/client/webpack.config.js
+++ b/client/webpack.config.js
@@ -28,9 +28,6 @@ const modulesExcludedFromLibs = [
 
 const buildDate = new Date();
 
-const dns = require('node:dns');
-dns.setDefaultResultOrder('ipv4first');
-
 module.exports = (env = {}, argv = {}) => {
     // environment name based on -d, -p, webpack flag
     const targetEnv = process.env.NODE_ENV == "production" || argv.mode == "production" ? "production" : "development";
@@ -262,7 +259,10 @@ module.exports = (env = {}, argv = {}) => {
             // can be a more limited set -- e.g. `/api`, `/auth`
             proxy: {
                 "**": {
-                    target: process.env.GALAXY_URL || "http://localhost:8080",
+                    // We explicitly use ipv4 loopback instead of localhost to
+                    // avoid ipv6/ipv4 resolution order issues; this should
+                    // align with Galaxy's default.
+                    target: process.env.GALAXY_URL || "http://127.0.0.1:8080",
                     secure: process.env.CHANGE_ORIGIN ? !process.env.CHANGE_ORIGIN : true,
                     changeOrigin: !!process.env.CHANGE_ORIGIN,
                     logLevel: "debug",

From 9a6ee51d28fc278b241efbbd7790efe5439439b4 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 24 Jan 2023 12:25:28 -0500
Subject: [PATCH 14/31] Fix workflow editing route for workflows created from
 history

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

diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py
index 8c8038c6384..b5e8861a911 100644
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -711,8 +711,8 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
                 'You can <a href="%s" target="_parent">edit</a> or <a href="%s" target="_parent">run</a> the workflow.'
                 % (
                     escape(workflow_name),
-                    url_for(controller="workflow", action="editor", id=workflow_id),
-                    url_for(controller="workflows", action="run", id=workflow_id),
+                    url_for("/workflows/edit?id=%s" % workflow_id),
+                    url_for("/workflows/run?id=%s" % workflow_id),
                 )
             )
 

From 71fbbfe0d232ccd77bd58f98f53398d330dbf987 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 24 Jan 2023 20:35:54 -0500
Subject: [PATCH 15/31] Use fstrings instead of % style composition

---
 lib/galaxy/webapps/galaxy/controllers/workflow.py | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py
index b5e8861a911..88fae496993 100644
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -706,14 +706,11 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
             )
             # Index page with message
             workflow_id = trans.security.encode_id(stored_workflow.id)
+            edit_url = url_for(f"/workflows/edit?id={workflow_id}")
+            run_url = url_for(f"/workflows/run?id={workflow_id}")
             return trans.show_message(
-                'Workflow "%s" created from current history. '
-                'You can <a href="%s" target="_parent">edit</a> or <a href="%s" target="_parent">run</a> the workflow.'
-                % (
-                    escape(workflow_name),
-                    url_for("/workflows/edit?id=%s" % workflow_id),
-                    url_for("/workflows/run?id=%s" % workflow_id),
-                )
+                f'Workflow "{escape(workflow_name)}" created from current history. '
+                f'You can <a href="{edit_url}" target="_parent">edit</a> or <a href="{run_url}" target="_parent">run</a> the workflow.'
             )
 
     def get_item(self, trans, id):

From c72af2b045b837cf231a7989d09451ae5992582d Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 25 Jan 2023 10:35:03 +0100
Subject: [PATCH 16/31] fix broken fetch

---
 client/src/composables/datatypes.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/composables/datatypes.ts b/client/src/composables/datatypes.ts
index 88a38f045f4..cb29633e4ec 100644
--- a/client/src/composables/datatypes.ts
+++ b/client/src/composables/datatypes.ts
@@ -29,7 +29,7 @@ export function useDetailedDatatypes() {
 
     async function getDatatypes() {
         try {
-            const datatypesPromise = datatypesFetcher({ extension_only: true });
+            const datatypesPromise = datatypesFetcher({ extension_only: false });
             const datatypeEDAMFormatsPromise = edamFormatsFetcher({});
             const datatypeEDAMDataPromise = edamDataFetcher({});
 

From 32961aca6bf68e877dd427c9855509aedb7b414b Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 25 Jan 2023 12:58:27 +0100
Subject: [PATCH 17/31] fix zoom and refactor

---
 .../Workflow/Editor/WorkflowGraph.vue         |  5 +-
 .../Workflow/Editor/ZoomControl.vue           | 85 +++++++------------
 .../composables/{useZoom.ts => d3Zoom.ts}     | 18 +---
 .../Workflow/Editor/modules/zoomLevels.ts     | 59 +++++++++++++
 4 files changed, 97 insertions(+), 70 deletions(-)
 rename client/src/components/Workflow/Editor/composables/{useZoom.ts => d3Zoom.ts} (76%)
 create mode 100644 client/src/components/Workflow/Editor/modules/zoomLevels.ts

diff --git a/client/src/components/Workflow/Editor/WorkflowGraph.vue b/client/src/components/Workflow/Editor/WorkflowGraph.vue
index 2dfdb7841bc..3dc2aa26b14 100644
--- a/client/src/components/Workflow/Editor/WorkflowGraph.vue
+++ b/client/src/components/Workflow/Editor/WorkflowGraph.vue
@@ -48,9 +48,10 @@ import { useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
 import type { TerminalPosition } from "@/stores/workflowEditorStateStore";
 import { DatatypesMapperModel } from "@/components/Datatypes/model";
 import { useWorkflowStepStore, type Step } from "@/stores/workflowStepStore";
-import { useZoom } from "./composables/useZoom";
+import { useD3Zoom } from "./composables/d3Zoom";
 import type { XYPosition } from "@/stores/workflowEditorStateStore";
 import type { OutputTerminals } from "./modules/terminals";
+import { minZoom, maxZoom } from "./modules/zoomLevels";
 
 const emit = defineEmits(["transform", "graph-offset", "onRemove", "scrollTo"]);
 const props = defineProps({
@@ -67,7 +68,7 @@ const canvas: Ref<HTMLElement | null> = ref(null);
 
 const elementBounding = useElementBounding(canvas, { windowResize: false, windowScroll: false });
 const scroll = useScroll(canvas);
-const { transform, panBy, setZoom, moveTo } = useZoom(1, 0.2, 5, canvas, scroll);
+const { transform, panBy, setZoom, moveTo } = useD3Zoom(1, minZoom, maxZoom, canvas, scroll);
 
 const isDragging = ref(false);
 provide("isDragging", isDragging);
diff --git a/client/src/components/Workflow/Editor/ZoomControl.vue b/client/src/components/Workflow/Editor/ZoomControl.vue
index 755d89343e4..081ec21fa7a 100644
--- a/client/src/components/Workflow/Editor/ZoomControl.vue
+++ b/client/src/components/Workflow/Editor/ZoomControl.vue
@@ -1,8 +1,38 @@
+<script lang="ts" setup>
+import Vue, { computed } from "vue";
+import BootstrapVue from "bootstrap-vue";
+import { getZoomInLevel, getZoomOutLevel, isMinZoom, isMaxZoom } from "./modules/zoomLevels";
+
+Vue.use(BootstrapVue);
+
+const props = defineProps({
+    zoomLevel: { type: Number, default: 1 },
+});
+
+const emit = defineEmits<{
+    (e: "onZoom", zoom: number): void;
+}>();
+
+const zoomDefault = 1;
+const zoomPercentage = computed(() => Math.round(props.zoomLevel * 100));
+
+function onZoomIn() {
+    emit("onZoom", getZoomInLevel(props.zoomLevel));
+}
+
+function onZoomOut() {
+    emit("onZoom", getZoomOutLevel(props.zoomLevel));
+}
+
+function onZoomReset() {
+    emit("onZoom", zoomDefault);
+}
+</script>
+
 <template>
     <span class="zoom-control float-right btn-group-horizontal">
         <b-button
-            v-b-tooltip.hover
-            :disabled="isMin"
+            :disabled="isMinZoom(props.zoomLevel)"
             role="button"
             class="fa fa-minus"
             title="Zoom Out"
@@ -21,8 +51,7 @@
             {{ zoomPercentage }}%
         </b-button>
         <b-button
-            v-b-tooltip.hover
-            :disabled="isMax"
+            :disabled="isMaxZoom(props.zoomLevel)"
             role="button"
             class="fa fa-plus"
             title="Zoom In"
@@ -32,54 +61,6 @@
     </span>
 </template>
 
-<script lang="ts" setup>
-import Vue, { computed } from "vue";
-import BootstrapVue from "bootstrap-vue";
-
-Vue.use(BootstrapVue);
-
-const props = withDefaults(
-    defineProps<{
-        zoomLevel: number;
-    }>(),
-    {
-        zoomLevel: 1,
-    }
-);
-const emit = defineEmits(["onZoom"]);
-
-const zoomDefault = 1;
-const zoomLevels = [0.1, 0.2, 0.25, 0.33, 0.5, 0.67, 0.75, 0.8, 0.9, 1, 1.1, 1.25, 1.33, 1.5, 2, 2.5, 3, 4, 5];
-const isMin = computed(() => Math.round(props.zoomLevel * 100) == Math.round(zoomLevels[0] * 100));
-const isMax = computed(() => Math.round(props.zoomLevel * 100) == Math.round(zoomLevels.at(-1)! * 100));
-const zoomPercentage = computed(() => Math.round(props.zoomLevel * 100));
-const index = computed(() => {
-    let index = zoomLevels.indexOf(props.zoomLevel);
-    if (index < 0) {
-        const closest = zoomLevels.reduce((prev, curr) => {
-            return Math.abs(curr - props.zoomLevel) < Math.abs(prev - props.zoomLevel) ? curr : prev;
-        });
-        index = zoomLevels.indexOf(closest);
-    }
-    return index;
-});
-function onZoomIn() {
-    const zoomLevel = zoomLevels[index.value + 1];
-    if (zoomLevel) {
-        emit("onZoom", zoomLevel);
-    }
-}
-function onZoomOut() {
-    const zoomLevel = zoomLevels[index.value - 1];
-    if (zoomLevel) {
-        emit("onZoom", zoomLevel);
-    }
-}
-function onZoomReset() {
-    emit("onZoom", zoomDefault);
-}
-</script>
-
 <style scoped>
 .zoom-reset {
     width: 4rem;
diff --git a/client/src/components/Workflow/Editor/composables/useZoom.ts b/client/src/components/Workflow/Editor/composables/d3Zoom.ts
similarity index 76%
rename from client/src/components/Workflow/Editor/composables/useZoom.ts
rename to client/src/components/Workflow/Editor/composables/d3Zoom.ts
index 76beceb2e4b..17df1fc74dd 100644
--- a/client/src/components/Workflow/Editor/composables/useZoom.ts
+++ b/client/src/components/Workflow/Editor/composables/d3Zoom.ts
@@ -1,6 +1,6 @@
 import { zoom, zoomIdentity, type D3ZoomEvent } from "d3-zoom";
 import { ref, watch } from "vue";
-import { pointer, select } from "d3-selection";
+import { select } from "d3-selection";
 import type { Ref } from "vue";
 import type { XYPosition } from "@/stores/workflowEditorStateStore";
 import type { UseScrollReturn } from "@vueuse/core";
@@ -12,7 +12,7 @@ const filter = (event: any) => {
     return !preventZoom;
 };
 
-export function useZoom(
+export function useD3Zoom(
     k: number,
     minZoom: number,
     maxZoom: number,
@@ -29,20 +29,6 @@ export function useZoom(
                 .translate(transform.value.x, transform.value.y)
                 .scale(transform.value.k);
             d3Zoom.transform(d3Selection, updatedTransform);
-
-            d3Selection
-                .on("wheel", (event) => {
-                    const currentZoom = d3Selection.property("__zoom").k || 1;
-
-                    const pinchDelta =
-                        -event.deltaY * (event.deltaMode === 1 ? 0.05 : event.deltaMode ? 1 : 0.002) * 10;
-                    const point = pointer(event);
-                    point[0] += scroll.x.value;
-                    point[1] += scroll.y.value;
-                    const zoom = currentZoom * 2 ** pinchDelta;
-                    d3Zoom.scaleTo(d3Selection, zoom, point);
-                })
-                .on("wheel.zoom", null);
         }
 
         d3Zoom.on("zoom", (event: D3ZoomEvent<HTMLElement, unknown>) => {
diff --git a/client/src/components/Workflow/Editor/modules/zoomLevels.ts b/client/src/components/Workflow/Editor/modules/zoomLevels.ts
new file mode 100644
index 00000000000..79048cfe720
--- /dev/null
+++ b/client/src/components/Workflow/Editor/modules/zoomLevels.ts
@@ -0,0 +1,59 @@
+export const zoomLevels = [
+    0.1, 0.2, 0.25, 0.33, 0.5, 0.67, 0.75, 0.8, 0.9, 1, 1.1, 1.25, 1.33, 1.5, 2, 2.5, 3, 4, 5,
+] as const;
+
+export type ZoomLevel = (typeof zoomLevels)[number];
+
+export const minZoom = zoomLevels[0];
+export const maxZoom = zoomLevels[zoomLevels.length - 1];
+
+/**
+ * Finds the closest snapped zoom level
+ * @param zoom decimal number indicating current zoom multiplier
+ * @returns snapped zoom level
+ */
+export function getSnappedZoom(zoom: number): ZoomLevel {
+    return zoomLevels.reduce((a, b) => {
+        return Math.abs(b - zoom) < Math.abs(a - zoom) ? b : a;
+    });
+}
+
+/**
+ * Gets the next largest zoom level
+ * @param zoom decimal number indicating current zoom multiplier
+ * @returns snapped zoom level
+ */
+export function getZoomInLevel(zoom: number): ZoomLevel {
+    const snapped = getSnappedZoom(zoom);
+    const index = zoomLevels.indexOf(snapped);
+
+    if (index === zoomLevels.length - 1) {
+        return snapped;
+    } else {
+        return zoomLevels[index + 1];
+    }
+}
+
+/**
+ * Get the next smaller zoom level
+ * @param zoom decimal number indicating current zoom multiplier
+ * @returns snapped zoom level
+ */
+export function getZoomOutLevel(zoom: number): ZoomLevel {
+    const snapped = getSnappedZoom(zoom);
+    const index = zoomLevels.indexOf(snapped);
+
+    if (index === 0) {
+        return snapped;
+    } else {
+        return zoomLevels[index - 1];
+    }
+}
+
+export function isMinZoom(zoom: number): boolean {
+    return zoom === minZoom;
+}
+
+export function isMaxZoom(zoom: number): boolean {
+    return zoom === maxZoom;
+}

From b413bfa189e57ab8cb96f47b7f76b402983cc212 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 25 Jan 2023 13:24:20 +0100
Subject: [PATCH 18/31] Redirect anonymous users on histories/list

---
 client/src/components/Grid/GridHistory.vue | 10 +---------
 client/src/components/Grid/history-list.js |  9 ++-------
 client/src/entry/analysis/router.js        | 11 ++++++-----
 3 files changed, 9 insertions(+), 21 deletions(-)

diff --git a/client/src/components/Grid/GridHistory.vue b/client/src/components/Grid/GridHistory.vue
index 8f91a6af438..c00cf5641ae 100644
--- a/client/src/components/Grid/GridHistory.vue
+++ b/client/src/components/Grid/GridHistory.vue
@@ -5,16 +5,8 @@
 <script>
 import HistoryList from "./history-list";
 export default {
-    props: {
-        actionId: {
-            type: String,
-            default: null,
-        },
-    },
     mounted() {
-        new HistoryList.View({
-            action_id: this.actionId,
-        }).$el.appendTo(this.$refs.target);
+        new HistoryList.View().$el.appendTo(this.$refs.target);
     },
 };
 </script>
diff --git a/client/src/components/Grid/history-list.js b/client/src/components/Grid/history-list.js
index e8a768413af..42b8c21ff2c 100644
--- a/client/src/components/Grid/history-list.js
+++ b/client/src/components/Grid/history-list.js
@@ -62,15 +62,10 @@ var View = Backbone.View.extend({
     initialize: function (options) {
         const Galaxy = getGalaxyInstance();
         LoadingIndicator.markViewAsLoading(this);
-
-        if (options.action_id == "list_published") {
-            this.active_tab = "shared";
-        } else if (options.action_id == "list") {
-            this.active_tab = "user";
-        }
+        this.active_tab = "user";
         this.model = new Backbone.Model();
         Utils.get({
-            url: `${getAppRoot()}history/${options.action_id}?${$.param(Galaxy.params)}`,
+            url: `${getAppRoot()}history/list?${$.param(Galaxy.params)}`,
             success: (response) => {
                 this.model.set(response);
                 this.render();
diff --git a/client/src/entry/analysis/router.js b/client/src/entry/analysis/router.js
index 56e2bdac7e9..558e962322f 100644
--- a/client/src/entry/analysis/router.js
+++ b/client/src/entry/analysis/router.js
@@ -235,6 +235,12 @@ export function getRouter(Galaxy) {
                         component: HistoryPublishedList,
                         props: true,
                     },
+                    {
+                        path: "histories/list",
+                        component: GridHistory,
+                        props: true,
+                        redirect: redirectAnon(),
+                    },
                     {
                         path: "histories/:historyId/export",
                         get component() {
@@ -242,11 +248,6 @@ export function getRouter(Galaxy) {
                         },
                         props: true,
                     },
-                    {
-                        path: "histories/:actionId",
-                        component: GridHistory,
-                        props: true,
-                    },
                     {
                         path: "interactivetool_entry_points/list",
                         component: InteractiveTools,

From e192896011172272749b10feddc6d213193c09e8 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 25 Jan 2023 09:06:24 -0500
Subject: [PATCH 19/31] Content updates to client readme, some grammatical and
 other changes.

---
 client/README.md | 64 ++++++++++++++++++++++++------------------------
 1 file changed, 32 insertions(+), 32 deletions(-)

diff --git a/client/README.md b/client/README.md
index 9b23e47280c..c3dde023c79 100644
--- a/client/README.md
+++ b/client/README.md
@@ -1,19 +1,19 @@
 # Client Build System
 
 Installs, stages, and builds the client-side scripts necessary for running the
-Galaxy webapp. When started through `run.sh` or any other method that utilizes
-`scripts/common_startup.sh`, Galaxy will (since 18.09) _automatically_ build
-the client as a part of server startup, when it detects changes, unless that
+Galaxy web client. When started through `run.sh` or any other method that
+utilizes `scripts/common_startup.sh`, Galaxy will (since 18.09) _automatically_
+build the client as a part of server startup when it detects changes unless that
 functionality is explicitly disabled.
 
-The base dependencies used are Node.js and Yarn. Galaxy now includes these in
-the virtual environment, and they can be accessed by activating that with `.
-.venv/bin/activate` from the Galaxy root directory.
+The base dependencies used are Node.js and Yarn. Galaxy includes appropriate
+versions of these in the virtual environment, and they can be accessed by
+activating that with `. .venv/bin/activate` from the Galaxy root directory.
 
-If you'd like to install your own dependencies, on OSX the easiest way to get
-set up is using `homebrew` and the command `brew install nodejs yarn`. More
-information, including instructions for other platforms, is available at
-[https://nodejs.org](https://nodejs.org) and
+If you'd like to install your dependencies external to Galaxy, on OSX the
+easiest way to get set up is using `homebrew` and the command `brew install
+nodejs yarn`. More information, including instructions for other platforms, is
+available at [https://nodejs.org](https://nodejs.org) and
 [https://yarnpkg.com/](https://yarnpkg.com).
 
 The Galaxy client build has necessarily grown more complex in the past several
@@ -27,11 +27,11 @@ directly on Gitter at
 
 There are many moving parts to the client build system, but the entry point for
 most people is the 'client' rule in the Makefile at the root of the Galaxy
-repository. Execute the following to perform a complete build suitable for
-local development, including dependency staging, style building, script
-processing, and bundling. This is a development-specific build which includes
-extra debugging features, and excludes several production optimizations made
-during the build process.
+repository. Execute the following to perform a complete build suitable for local
+development, including dependency staging, style building, script processing,
+and bundling. This is a development-specific build that includes extra debugging
+features and excludes several production optimizations made during the build
+process.
 
     make client
 
@@ -56,21 +56,21 @@ automatically rebuild every time you save a file. You can do this using:
     make client-dev-server
 
 Or, with the package scripts from this `client` directory:
-    
+
     yarn run develop
 
-This will start up an extra client development server running on port 8081.
-Open your browser to http://localhost:8081 (instead of the default 8080 that
-Galaxy would run on), and you should see Galaxy like normal.  Except now, when
-you change client code it'll automatically rebuild *and* reload the relevant
-portion of the application for you. Lastly, if you
-are running Galaxy at a location other than the default, you can specify a
-different proxy target (in this example, port 8000) using the GALAXY_URL
-environment variable:
+This will start up an extra client development server running on port 8081. Open
+your browser to `http://localhost:8081` (instead of the default 8080 that Galaxy
+would run on), and you should see Galaxy like normal.  Except now, when you
+change client code it'll automatically rebuild _and_ reload the relevant portion
+of the application for you. Lastly, if you are running Galaxy at a location
+other than the default, you can specify a different proxy target (in this
+example, port 8000) using the GALAXY_URL environment variable:
 
     GALAXY_URL="http://localhost:8000" make client-dev-server
 
-Sometimes you want to run your local 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
 
@@ -93,11 +93,11 @@ prefer:
 
 ## Changing Styles/CSS
 
-Galaxy uses Sass for its styling, which is a superset of CSS that compiles down
+Galaxy uses Sass for globally applied styling, which is a superset of CSS that compiles down
 to regular CSS. Most Galaxy styling source (.scss) files are kept in
-`client/src/style/scss`. There are additionally style blocks alongside some Vue
-components -- styles that are particular to that individual component and do
-not apply site-wide.
+`client/src/style/scss`. There are additionaly style blocks alongside some Vue
+components -- styles that are particular to that individual component and do not
+apply site-wide.
 
 On build, the compiled css bundle is served at `/static/style/base.css`.
 
@@ -139,8 +139,8 @@ directory. This is what happens during a complete client build.
 
 During client-side development, it is more convenient to have granular testing
 options. The various testing scripts are defined inside package.json within the
-client folder, and are called with `yarn` as demonstrated in the
-following commands.
+client folder, and are called with `yarn` as demonstrated in the following
+commands.
 
 This is what CI is going to run, and also what 'make client-test' invokes,
 executing all the client tests:
@@ -151,7 +151,7 @@ You can also bypass qunit and single-run all of the jest tests like so:
 
      yarn run jest
 
-Or, if you really want to run just the qunit tests:
+Or, if you want to run just the qunit tests:
 
     yarn run qunit
 

From 2c69c96dfd441678714b433477807aa3f29968af Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 25 Jan 2023 09:13:35 -0500
Subject: [PATCH 20/31] Update run_tests_help w/ client targets

---
 doc/source/dev/run_tests_help.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/source/dev/run_tests_help.txt b/doc/source/dev/run_tests_help.txt
index 4e002913339..5e646326027 100644
--- a/doc/source/dev/run_tests_help.txt
+++ b/doc/source/dev/run_tests_help.txt
@@ -75,8 +75,8 @@ Run a specific selenium test (under Linux or Mac OS X after installing geckodriv
 
 Run a selenium test against a running server while watching client (fastest iterating on client tests):
     ./run.sh & # run Galaxy on 8080
-    make client-watch & # watch for client changes
-    export GALAXY_TEST_EXTERNAL=http://localhost:8080/  # Target tests at server.
+    make client-dev-server & # watch for client changes
+    export GALAXY_TEST_EXTERNAL=http://localhost:8081/  # Target tests at server.
     . .venv/bin/activate # source the virtualenv so can skip run_tests.sh.
     pytest lib/galaxy_test/selenium/test_workflow_editor.py::TestWorkflowEditor::test_data_input
 

From 741aec7aa90eef081b5a04578c4d0447d383e6ea Mon Sep 17 00:00:00 2001
From: Dannon <dannon.baker@gmail.com>
Date: Wed, 25 Jan 2023 09:22:27 -0500
Subject: [PATCH 21/31] Apply suggestions from code review

Thanks @nsoranzo!

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 client/README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/README.md b/client/README.md
index c3dde023c79..3045a31b16a 100644
--- a/client/README.md
+++ b/client/README.md
@@ -70,7 +70,7 @@ example, port 8000) using the GALAXY_URL environment variable:
     GALAXY_URL="http://localhost:8000" make client-dev-server
 
 Sometimes you want to run your local UI against a remote Galaxy server. This is
-also possible if you enable `CHANGE_ORIGIN` flag:
+also possible if you set the `CHANGE_ORIGIN` environment variable:
 
     CHANGE_ORIGIN=true GALAXY_URL="https://usegalaxy.org/" make client-dev-server
 
@@ -95,7 +95,7 @@ prefer:
 
 Galaxy uses Sass for globally applied styling, which is a superset of CSS that compiles down
 to regular CSS. Most Galaxy styling source (.scss) files are kept in
-`client/src/style/scss`. There are additionaly style blocks alongside some Vue
+`client/src/style/scss`. There are additional style blocks alongside some Vue
 components -- styles that are particular to that individual component and do not
 apply site-wide.
 

From a8e5702e3cb01e07a55886c1e32f1cb465c6167f Mon Sep 17 00:00:00 2001
From: Assunta DeSanto <assuntad23@gmail.com>
Date: Wed, 25 Jan 2023 12:53:06 -0500
Subject: [PATCH 22/31] Adding more directive to the tooltip

---
 client/src/components/Workflow/Editor/modules/terminals.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Workflow/Editor/modules/terminals.ts b/client/src/components/Workflow/Editor/modules/terminals.ts
index 4efe198c526..cdb3538e69c 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.ts
@@ -367,7 +367,7 @@ export class InvalidInputTerminal extends BaseInputTerminal {
     }
 
     attachable(terminal: BaseOutputTerminal) {
-        return new ConnectionAcceptable(false, "Cannot attach to invalid input.");
+        return new ConnectionAcceptable(false, "Cannot attach to invalid input. Disconnect this input.");
     }
 }
 

From d683d1a50a82da2a545856b988f2dbc72f13a928 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 25 Jan 2023 16:50:38 -0500
Subject: [PATCH 23/31] Add hint to indicate that retrying to auto-detect the
 metadata might succeed

---
 client/src/components/History/Content/model/states.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/History/Content/model/states.js b/client/src/components/History/Content/model/states.js
index 2ddfcecbf9e..f37800d8282 100644
--- a/client/src/components/History/Content/model/states.js
+++ b/client/src/components/History/Content/model/states.js
@@ -33,7 +33,7 @@ export const STATES = {
     /** metadata discovery/setting failed or errored (but otherwise ok) */
     failed_metadata: {
         status: "danger",
-        text: "Metadata generation failed.",
+        text: "Metadata generation failed. Please retry.",
         icon: "exclamation-triangle",
     },
     /** was created without a tool */

From 9a0bb385b8876ac0914d5a803cf1f13ffb9a1083 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 26 Jan 2023 11:33:43 +0100
Subject: [PATCH 24/31] Fix dataset options text

On show, explicitly state that we will be switching to the history to avoid confusion.

On copy, explicitly state that it will be copied to the current history.
---
 client/src/components/Dataset/DatasetName.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Dataset/DatasetName.vue b/client/src/components/Dataset/DatasetName.vue
index 1625cd497ac..9751155ea3d 100644
--- a/client/src/components/Dataset/DatasetName.vue
+++ b/client/src/components/Dataset/DatasetName.vue
@@ -22,11 +22,11 @@
         <div class="dropdown-menu" aria-labelledby="dataset-dropdown">
             <a class="dropdown-item" href="#" @click.prevent="showDataset">
                 <span class="fa fa-eye fa-fw mr-1" />
-                <span>Show in History</span>
+                <span>Switch to History containing dataset</span>
             </a>
             <a class="dropdown-item" href="#" @click.prevent="copyDataset">
                 <span class="fa fa-copy fa-fw mr-1" />
-                <span>Copy to History</span>
+                <span>Copy to current History</span>
             </a>
         </div>
     </div>

From 005fdafc23de3abf4b0e7761ca14d8789079dc35 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 25 Jan 2023 22:29:14 +0100
Subject: [PATCH 25/31] Split up node map over into input map over

Fixes https://github.com/galaxyproject/galaxy/issues/15369 ...
this was a real pain, and it definitely needs more tests.
---
 .../Workflow/Editor/TerminalConnector.vue     |  6 ++-
 .../Workflow/Editor/modules/terminals.test.ts |  8 ++-
 .../Workflow/Editor/modules/terminals.ts      | 53 ++++++++++++++-----
 client/src/stores/workflowStepStore.ts        | 18 ++++++-
 4 files changed, 67 insertions(+), 18 deletions(-)

diff --git a/client/src/components/Workflow/Editor/TerminalConnector.vue b/client/src/components/Workflow/Editor/TerminalConnector.vue
index 9700c452dd3..5830982e5d0 100644
--- a/client/src/components/Workflow/Editor/TerminalConnector.vue
+++ b/client/src/components/Workflow/Editor/TerminalConnector.vue
@@ -23,7 +23,11 @@ const props = defineProps<{
 const stepStore = useWorkflowStepStore();
 const connectionStore = useConnectionStore();
 const outputIsMappedOver = computed(() => stepStore.stepMapOver[props.connection.output.stepId]?.isCollection);
-const inputIsMappedOver = computed(() => stepStore.stepMapOver[props.connection.input.stepId]?.isCollection);
+const inputIsMappedOver = computed(
+    () =>
+        stepStore.stepInputMapOver[props.connection.input.stepId] &&
+        stepStore.stepInputMapOver[props.connection.input.stepId][props.connection.input.name]?.isCollection
+);
 const outputIsOptional = computed(() => {
     return Boolean(
         stepStore.getStep(props.connection.output.stepId)?.when ||
diff --git a/client/src/components/Workflow/Editor/modules/terminals.test.ts b/client/src/components/Workflow/Editor/modules/terminals.test.ts
index 00cdd99954c..dd46474b686 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.test.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.test.ts
@@ -102,7 +102,9 @@ describe("canAccept", () => {
         dataIn.connect(collectionOut);
         expect(dataIn.mapOver).toEqual({ collectionType: "list", isCollection: true, rank: 1 });
         expect(dataIn.canAccept(collectionOut).canAccept).toBe(false);
-        expect(dataIn.canAccept(collectionOut).reason).toBe("Input already filled with another connection, delete it before connecting another output.");
+        expect(dataIn.canAccept(collectionOut).reason).toBe(
+            "Input already filled with another connection, delete it before connecting another output."
+        );
         dataIn.disconnect(collectionOut);
         expect(dataIn.canAccept(collectionOut).canAccept).toBe(true);
         expect(dataIn.mapOver).toEqual(NULL_COLLECTION_TYPE_DESCRIPTION);
@@ -262,14 +264,16 @@ describe("canAccept", () => {
         dataIn.connect(collectionOut);
         dataInTwo.connect(dataOut);
         expect(dataIn.mapOver).toEqual({ collectionType: "list", isCollection: true, rank: 1 });
+        expect(dataIn.localMapOver).toEqual({ collectionType: "list", isCollection: true, rank: 1 });
         //
         dataIn.disconnect(collectionOut);
         // this is weird and not particularly robust, if you save and reload this will most likely not be constrained
         // TODO: avoid this if possible ...
         expect(dataIn.mapOver).toEqual({ collectionType: "list", isCollection: true, rank: 1 });
+        expect(dataIn.localMapOver).toEqual({ collectionType: "list", isCollection: true, rank: 1 });
         expect(dataIn.canAccept(simpleDataOut).canAccept).toBe(false);
         expect(dataIn.canAccept(simpleDataOut).reason).toBe(
-            "Cannot attach non-collection outputs to mapped over inputs, consider disconnecting inputs and outputs to reset this input's mapping."
+            "Cannot attach non-collection output to mapped over input, consider disconnecting inputs and outputs to reset this input's mapping."
         );
     });
     // TODO: test mapOver reset when constraint removed
diff --git a/client/src/components/Workflow/Editor/modules/terminals.ts b/client/src/components/Workflow/Editor/modules/terminals.ts
index 4efe198c526..249bd89fe55 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.ts
@@ -18,6 +18,7 @@ import type {
     TerminalSource,
 } from "@/stores/workflowStepStore";
 import type { DatatypesMapperModel } from "@/components/Datatypes/model";
+import Vue from "vue";
 
 export class ConnectionAcceptable {
     reason: string | null;
@@ -53,6 +54,7 @@ class Terminal extends EventEmitter {
     stepId: number;
     terminalType: "input" | "output";
     datatypesMapper: DatatypesMapperModel;
+    localMapOver: CollectionTypeDescriptor;
 
     constructor(attr: BaseTerminalArgs) {
         super();
@@ -63,6 +65,7 @@ class Terminal extends EventEmitter {
         this.multiple = false;
         this.terminalType = "input";
         this.datatypesMapper = attr.datatypesMapper;
+        this.localMapOver = NULL_COLLECTION_TYPE_DESCRIPTION;
     }
     public get id() {
         return `node-${this.stepId}-${this.terminalType}-${this.name}`;
@@ -105,10 +108,12 @@ class Terminal extends EventEmitter {
             outputVal = val.effectiveMapOver(description);
         }
         const effectiveMapOver = this._effectiveMapOver(outputVal);
+        if (!this.localMapOver.equal(effectiveMapOver)) {
+            this.stepStore.changeStepInputMapOver(this.stepId, this.name, effectiveMapOver);
+            this.localMapOver = effectiveMapOver;
+        }
         if (!this.mapOver.equal(effectiveMapOver)) {
             this.stepStore.changeStepMapOver(this.stepId, effectiveMapOver);
-            // TODO: do we even need to listen for this?
-            this.emit("changeMapOver", outputVal);
         }
     }
     _effectiveMapOver(otherCollectionType: CollectionTypeDescriptor) {
@@ -119,8 +124,7 @@ class Terminal extends EventEmitter {
     }
     resetMapping(connection?: Connection) {
         this.stepStore.changeStepMapOver(this.stepId, NULL_COLLECTION_TYPE_DESCRIPTION);
-        // necessary ?
-        this.emit("changeMapOver", this.mapOver);
+        this.stepStore.resetStepInputMapOver(this.stepId);
     }
     hasConnectedMappedInputTerminals() {
         // check if step has connected and mapped input terminals ... should maybe be on step/node ?
@@ -150,7 +154,7 @@ class Terminal extends EventEmitter {
         // No output terminals are counting on this being mapped
         // over if connected inputs are still mapped over or if none
         // of the outputs are connected...
-        const reset = this.hasConnectedMappedInputTerminals() || !this.hasConnectedOutputTerminals();
+        const reset = !this.hasConnectedOutputTerminals();
         if (reset) {
             this.resetMapping(connection);
         }
@@ -160,12 +164,18 @@ class Terminal extends EventEmitter {
 class BaseInputTerminal extends Terminal {
     datatypes: InputTerminalInputs["datatypes"];
     optional: InputTerminalInputs["optional"];
+    localMapOver: CollectionTypeDescriptor;
 
     constructor(attr: InputTerminalArgs) {
         super(attr);
         this.datatypes = attr.input.datatypes;
         this.multiple = attr.input.multiple;
         this.optional = attr.input.optional;
+        if (this.stepStore.stepInputMapOver[this.stepId] && this.stepStore.stepInputMapOver[this.stepId][this.name]) {
+            this.localMapOver = this.stepStore.stepInputMapOver[this.stepId][this.name];
+        } else {
+            this.localMapOver = NULL_COLLECTION_TYPE_DESCRIPTION;
+        }
     }
     connect(other: BaseOutputTerminal): void {
         super.connect(other);
@@ -174,9 +184,15 @@ class BaseInputTerminal extends Terminal {
     setDefaultMapOver(other: BaseOutputTerminal) {
         const otherCollectionType = this._otherCollectionType(other);
         if (otherCollectionType.isCollection) {
-            this.setMapOver(otherCollectionType);
+            return this.setMapOver(otherCollectionType);
         }
     }
+    getStepMapOver() {
+        this.getConnectedTerminals().forEach((other) => {
+            this.setDefaultMapOver(other);
+        });
+    }
+
     canAccept(outputTerminal: BaseOutputTerminal) {
         if (this.stepId == outputTerminal.stepId) {
             return new ConnectionAcceptable(false, "Cannot connect output to input of same step.");
@@ -201,6 +217,7 @@ class BaseInputTerminal extends Terminal {
     }
     resetMapping(connection?: Connection) {
         super.resetMapping(connection);
+        this.stepStore.changeStepInputMapOver(this.stepId, this.name, NULL_COLLECTION_TYPE_DESCRIPTION);
         const outputStepIds = this._getOutputTerminals().map((outputTerminal) => outputTerminal.stepId);
         if (connection) {
             outputStepIds.push(connection.output.stepId);
@@ -360,10 +377,12 @@ interface InvalidInputTerminalArgs extends InputTerminalArgs {
 
 export class InvalidInputTerminal extends BaseInputTerminal {
     valid: false;
+    localMapOver: CollectionTypeDescriptor;
 
     constructor(attr: InvalidInputTerminalArgs) {
         super(attr);
         this.valid = false;
+        this.localMapOver = NULL_COLLECTION_TYPE_DESCRIPTION;
     }
 
     attachable(terminal: BaseOutputTerminal) {
@@ -378,7 +397,11 @@ export class InputTerminal extends BaseInputTerminal {
     constructor(attr: InputTerminalArgs) {
         super(attr);
         this.collection = false;
-        this.getConnectedTerminals().map((other) => this.setDefaultMapOver(other));
+        this.getStepMapOver();
+    }
+
+    isMappedOver(): boolean {
+        return Boolean(this.localMapOver.isCollection);
     }
 
     attachable(other: BaseOutputTerminal) {
@@ -435,11 +458,13 @@ export class InputTerminal extends BaseInputTerminal {
                     }
                 }
             }
-        } else if (mapOver.isCollection) {
-            return new ConnectionAcceptable(
-                false,
-                "Cannot attach non-collection outputs to mapped over inputs, consider disconnecting inputs and outputs to reset this input's mapping."
-            );
+        } else {
+            if (this.localMapOver.isCollection) {
+                return new ConnectionAcceptable(
+                    false,
+                    "Cannot attach non-collection output to mapped over input, consider disconnecting inputs and outputs to reset this input's mapping."
+                );
+            }
         }
         return this._producesAcceptableDatatypeAndOptionalness(other);
     }
@@ -455,7 +480,7 @@ export class InputParameterTerminal extends BaseInputTerminal {
     constructor(attr: InputParameterTerminalArgs) {
         super(attr);
         this.type = attr.type;
-        this.getConnectedTerminals().map((other) => this.setDefaultMapOver(other));
+        this.getStepMapOver();
     }
 
     effectiveType(parameterType: string) {
@@ -490,7 +515,7 @@ export class InputCollectionTerminal extends BaseInputTerminal {
         if (!this.collectionTypes.length) {
             this.collectionTypes.push(ANY_COLLECTION_TYPE_DESCRIPTION);
         }
-        this.getConnectedTerminals().map((other) => this.setDefaultMapOver(other));
+        this.getStepMapOver();
     }
     _effectiveMapOver(otherCollectionType: CollectionTypeDescriptor) {
         const collectionTypes = this.collectionTypes;
diff --git a/client/src/stores/workflowStepStore.ts b/client/src/stores/workflowStepStore.ts
index 95e4fbe687c..655f6735c7d 100644
--- a/client/src/stores/workflowStepStore.ts
+++ b/client/src/stores/workflowStepStore.ts
@@ -8,6 +8,7 @@ interface State {
     steps: { [index: string]: Step };
     stepIndex: number;
     stepMapOver: { [index: number]: CollectionTypeDescriptor };
+    stepInputMapOver: StepInputMapOver;
 }
 
 interface StepPosition {
@@ -133,10 +134,15 @@ interface WorkflowOutputs {
     };
 }
 
+interface StepInputMapOver {
+    [index: number]: { [index: string]: CollectionTypeDescriptor };
+}
+
 export const useWorkflowStepStore = defineStore("workflowStepStore", {
     state: (): State => ({
         steps: {} as Steps,
         stepMapOver: {} as { [index: number]: CollectionTypeDescriptor },
+        stepInputMapOver: {} as StepInputMapOver,
         stepIndex: -1,
     }),
     getters: {
@@ -211,7 +217,17 @@ export const useWorkflowStepStore = defineStore("workflowStepStore", {
             this.steps[step.id.toString()] = step;
         },
         changeStepMapOver(stepId: number, mapOver: CollectionTypeDescriptor) {
-            this.stepMapOver[stepId] = mapOver;
+            Vue.set(this.stepMapOver, stepId, mapOver);
+        },
+        resetStepInputMapOver(stepId: number) {
+            Vue.set(this.stepInputMapOver, stepId, {});
+        },
+        changeStepInputMapOver(stepId: number, inputName: string, mapOver: CollectionTypeDescriptor) {
+            if (this.stepInputMapOver[stepId]) {
+                Vue.set(this.stepInputMapOver[stepId], inputName, mapOver);
+            } else {
+                Vue.set(this.stepInputMapOver, stepId, { [inputName]: mapOver });
+            }
         },
         addConnection(connection: Connection) {
             const inputStep = this.getStep(connection.input.stepId);

From a6456b4c3b766587063e1044eef594f6732930f1 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 26 Jan 2023 13:30:04 +0100
Subject: [PATCH 26/31] Add test for connecting to non-mapped over input

---
 .../Workflow/Editor/modules/terminals.test.ts | 71 ++++++++++++++-----
 1 file changed, 55 insertions(+), 16 deletions(-)

diff --git a/client/src/components/Workflow/Editor/modules/terminals.test.ts b/client/src/components/Workflow/Editor/modules/terminals.test.ts
index dd46474b686..3c18f160e8d 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.test.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.test.ts
@@ -271,28 +271,67 @@ describe("canAccept", () => {
         // TODO: avoid this if possible ...
         expect(dataIn.mapOver).toEqual({ collectionType: "list", isCollection: true, rank: 1 });
         expect(dataIn.localMapOver).toEqual({ collectionType: "list", isCollection: true, rank: 1 });
+        expect(dataIn.localMapOver.isCollection).toBe(true);
         expect(dataIn.canAccept(simpleDataOut).canAccept).toBe(false);
         expect(dataIn.canAccept(simpleDataOut).reason).toBe(
             "Cannot attach non-collection output to mapped over input, consider disconnecting inputs and outputs to reset this input's mapping."
         );
-    });
-    // TODO: test mapOver reset when constraint removed
-    it("resets mapOver when constraint is lifted", () => {
-        const collectionOut = terminals["list input"]["output"] as OutputCollectionTerminal;
-        const dataIn = terminals["simple data"]["input"] as InputTerminal;
-        const dataOut = terminals["simple data"]["out_file1"] as OutputTerminal;
-        const dataInTwo = terminals["simple data 2"]["input"] as InputTerminal;
-        dataIn.connect(collectionOut);
-        dataInTwo.connect(dataOut);
-        expect(dataIn.mapOver).toEqual({ collectionType: "list", isCollection: true, rank: 1 });
-        //
-        dataIn.disconnect(collectionOut);
-        // this is weird and not particularly robust, if you save and reload this will most likely not be constrained
-        // TODO: avoid this if possible ...
-        expect(dataIn.mapOver).toEqual({ collectionType: "list", isCollection: true, rank: 1 });
         dataInTwo.disconnect(dataOut);
-        expect(dataIn.mapOver).toEqual(NULL_COLLECTION_TYPE_DESCRIPTION);
+        // terminal isn't a reactive class in any way (worth a thought doing, but difficult!), the following happens when a new terminal is built
+        // in useTerminal.ts
+        const rebuiltDataIn = terminalFactory(
+            dataIn.stepId,
+            advancedSteps[dataIn.stepId].inputs[0],
+            testDatatypesMapper
+        );
+        expect(rebuiltDataIn.localMapOver.isCollection).toBe(false);
+        expect(rebuiltDataIn.canAccept(simpleDataOut).canAccept).toBe(true);
     });
+    it("accepts attaching dataset to non-mapped over input for a mapped over step", () => {
+        const collectionOut = terminals["list input"]["output"] as OutputCollectionTerminal;
+        const simpleDataOut = terminals["data input"]["output"] as OutputTerminal;
+        const otherDataIn = terminals["simple data"]["input"] as InputTerminal;
+        const multiSimpleInputOne = terminals["multiple simple data"]["input1"] as InputTerminal;
+        const multiSimpleInputTwo = terminals["multiple simple data"]["queries_0|input2"] as InputTerminal;
+        const multiSimpleOut = terminals["multiple simple data"]["out_file1"] as OutputTerminal;
+        // map over simple input
+        multiSimpleInputOne.connect(collectionOut);
+        // constrain input by connecting an output to same step
+        otherDataIn.connect(multiSimpleOut);
+        // can connect a simple input to the non mapped-over input of the mapped-over step
+        expect(multiSimpleInputTwo.canAccept(simpleDataOut).canAccept).toBe(true);
+        // can also connect a connection of the same map over state
+        expect(multiSimpleInputTwo.canAccept(collectionOut).canAccept).toBe(true);
+        // cannot connect connection of deeper nesting
+        const listListOut = terminals["list:list input"]["output"] as OutputCollectionTerminal;
+        expect(multiSimpleInputTwo.canAccept(listListOut).canAccept).toBe(false);
+        expect(multiSimpleInputTwo.canAccept(listListOut).reason).toBe(
+            "Can't map over this input with output collection type - other inputs have an incompatible map over collection type. Disconnect inputs (and potentially outputs) and retry."
+        );
+        // disconnect, map over should be maintained
+        multiSimpleInputOne.disconnect(collectionOut);
+        expect(multiSimpleInputOne.localMapOver.isCollection).toBe(true);
+        expect(multiSimpleInputOne.canAccept(simpleDataOut).canAccept).toBe(false);
+        expect(multiSimpleInputOne.canAccept(simpleDataOut).reason).toBe(
+            "Cannot attach non-collection output to mapped over input, consider disconnecting inputs and outputs to reset this input's mapping."
+        );
+    }),
+        it("resets mapOver when constraint is lifted", () => {
+            const collectionOut = terminals["list input"]["output"] as OutputCollectionTerminal;
+            const dataIn = terminals["simple data"]["input"] as InputTerminal;
+            const dataOut = terminals["simple data"]["out_file1"] as OutputTerminal;
+            const dataInTwo = terminals["simple data 2"]["input"] as InputTerminal;
+            dataIn.connect(collectionOut);
+            dataInTwo.connect(dataOut);
+            expect(dataIn.mapOver).toEqual({ collectionType: "list", isCollection: true, rank: 1 });
+            //
+            dataIn.disconnect(collectionOut);
+            // this is weird and not particularly robust, if you save and reload this will most likely not be constrained
+            // TODO: avoid this if possible ...
+            expect(dataIn.mapOver).toEqual({ collectionType: "list", isCollection: true, rank: 1 });
+            dataInTwo.disconnect(dataOut);
+            expect(dataIn.mapOver).toEqual(NULL_COLLECTION_TYPE_DESCRIPTION);
+        });
     it("rejects connecting incompatible connection types", () => {
         const pairedOut = terminals["paired input"]["output"] as OutputCollectionTerminal;
         const collectionIn = terminals["list collection input"]["input1"] as InputCollectionTerminal;

From 83f6463e46a0d2c6d88e02ca01af6a81994e2953 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 26 Jan 2023 09:04:45 -0500
Subject: [PATCH 27/31] Minor touchups to client readme

---
 client/README.md | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/client/README.md b/client/README.md
index 3045a31b16a..8b015c9ce7e 100644
--- a/client/README.md
+++ b/client/README.md
@@ -93,16 +93,16 @@ prefer:
 
 ## Changing Styles/CSS
 
-Galaxy uses Sass for globally applied styling, which is a superset of CSS that compiles down
-to regular CSS. Most Galaxy styling source (.scss) files are kept in
-`client/src/style/scss`. There are additional style blocks alongside some Vue
-components -- styles that are particular to that individual component and do not
+Galaxy uses Sass for globally applied styling, which is a superset of CSS that
+compiles down to regular CSS. Most Galaxy styling source (.scss) files are kept
+in `client/src/style/scss`. Many components will also have local style blocks
+containing styles that are particular to that individual component and do not
 apply site-wide.
 
 On build, the compiled css bundle is served at `/static/style/base.css`.
 
-As mentioned above, `make client` will rebuild styles, as a part of the webpack
-build. For iterative development, "Watch Mode" rebuilds as described above do
+As mentioned above, `make client` will rebuild styles as a part of the webpack
+build. For iterative development "Watch Mode" rebuilds as described above do
 include style changes.
 
 ## Client-Side Unit Testing

From becd483b5062470d06598558208e337d396f0815 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 26 Jan 2023 09:38:51 -0500
Subject: [PATCH 28/31] Fix test definition

---
 .../Workflow/Editor/modules/terminals.test.ts | 34 +++++++++----------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/client/src/components/Workflow/Editor/modules/terminals.test.ts b/client/src/components/Workflow/Editor/modules/terminals.test.ts
index 3c18f160e8d..1ab09b97a25 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.test.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.test.ts
@@ -315,23 +315,23 @@ describe("canAccept", () => {
         expect(multiSimpleInputOne.canAccept(simpleDataOut).reason).toBe(
             "Cannot attach non-collection output to mapped over input, consider disconnecting inputs and outputs to reset this input's mapping."
         );
-    }),
-        it("resets mapOver when constraint is lifted", () => {
-            const collectionOut = terminals["list input"]["output"] as OutputCollectionTerminal;
-            const dataIn = terminals["simple data"]["input"] as InputTerminal;
-            const dataOut = terminals["simple data"]["out_file1"] as OutputTerminal;
-            const dataInTwo = terminals["simple data 2"]["input"] as InputTerminal;
-            dataIn.connect(collectionOut);
-            dataInTwo.connect(dataOut);
-            expect(dataIn.mapOver).toEqual({ collectionType: "list", isCollection: true, rank: 1 });
-            //
-            dataIn.disconnect(collectionOut);
-            // this is weird and not particularly robust, if you save and reload this will most likely not be constrained
-            // TODO: avoid this if possible ...
-            expect(dataIn.mapOver).toEqual({ collectionType: "list", isCollection: true, rank: 1 });
-            dataInTwo.disconnect(dataOut);
-            expect(dataIn.mapOver).toEqual(NULL_COLLECTION_TYPE_DESCRIPTION);
-        });
+    });
+    it("resets mapOver when constraint is lifted", () => {
+        const collectionOut = terminals["list input"]["output"] as OutputCollectionTerminal;
+        const dataIn = terminals["simple data"]["input"] as InputTerminal;
+        const dataOut = terminals["simple data"]["out_file1"] as OutputTerminal;
+        const dataInTwo = terminals["simple data 2"]["input"] as InputTerminal;
+        dataIn.connect(collectionOut);
+        dataInTwo.connect(dataOut);
+        expect(dataIn.mapOver).toEqual({ collectionType: "list", isCollection: true, rank: 1 });
+        //
+        dataIn.disconnect(collectionOut);
+        // this is weird and not particularly robust, if you save and reload this will most likely not be constrained
+        // TODO: avoid this if possible ...
+        expect(dataIn.mapOver).toEqual({ collectionType: "list", isCollection: true, rank: 1 });
+        dataInTwo.disconnect(dataOut);
+        expect(dataIn.mapOver).toEqual(NULL_COLLECTION_TYPE_DESCRIPTION);
+    });
     it("rejects connecting incompatible connection types", () => {
         const pairedOut = terminals["paired input"]["output"] as OutputCollectionTerminal;
         const collectionIn = terminals["list collection input"]["input1"] as InputCollectionTerminal;

From 8118c1906e9f86a1e00e921ff25bda0304c200e0 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 26 Jan 2023 15:54:11 +0100
Subject: [PATCH 29/31] Don't display tooltip of connection is acceptable

---
 .../src/components/Workflow/Editor/modules/terminals.test.ts | 2 ++
 client/src/components/Workflow/Editor/modules/terminals.ts   | 5 +++--
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Workflow/Editor/modules/terminals.test.ts b/client/src/components/Workflow/Editor/modules/terminals.test.ts
index 4d41492bc86..5abb667c019 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.test.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.test.ts
@@ -205,6 +205,8 @@ describe("canAccept", () => {
         const integerInputParam = terminals["multi data"]["advanced|advanced_threshold"] as InputParameterTerminal;
         const integerOutputParam = terminals["integer parameter input"]["output"] as OutputParameterTerminal;
         expect(integerInputParam.canAccept(integerOutputParam).canAccept).toBe(true);
+        // regression test for https://github.com/galaxyproject/galaxy/issues/15417
+        expect(integerInputParam.canAccept(integerOutputParam).reason).toBe(null);
     });
     it("rejects text to integer parameter connection", () => {
         const integerInputParam = terminals["multi data"]["advanced|advanced_threshold"] as InputParameterTerminal;
diff --git a/client/src/components/Workflow/Editor/modules/terminals.ts b/client/src/components/Workflow/Editor/modules/terminals.ts
index 4efe198c526..eff12488333 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.ts
@@ -465,9 +465,10 @@ export class InputParameterTerminal extends BaseInputTerminal {
         const effectiveThisType = this.effectiveType(this.type);
         const otherType = ("type" in other && other.type) || "data";
         const effectiveOtherType = this.effectiveType(otherType);
+        const canAccept = effectiveThisType === effectiveOtherType
         return new ConnectionAcceptable(
-            effectiveThisType == effectiveOtherType,
-            `Cannot attach a ${effectiveOtherType} parameter to a ${effectiveThisType} input`
+            canAccept,
+            canAccept ? null: `Cannot attach a ${effectiveOtherType} parameter to a ${effectiveThisType} input`
         );
     }
 }

From addc0159f043d92fcb7952ea66f076b084d5a44d Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 26 Jan 2023 09:56:11 -0500
Subject: [PATCH 30/31] Commas are confusing

---
 client/README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/README.md b/client/README.md
index 8b015c9ce7e..aec3f0f8622 100644
--- a/client/README.md
+++ b/client/README.md
@@ -102,7 +102,7 @@ apply site-wide.
 On build, the compiled css bundle is served at `/static/style/base.css`.
 
 As mentioned above, `make client` will rebuild styles as a part of the webpack
-build. For iterative development "Watch Mode" rebuilds as described above do
+build. For iterative development, "Watch Mode" rebuilds as described above do
 include style changes.
 
 ## Client-Side Unit Testing
@@ -139,7 +139,7 @@ directory. This is what happens during a complete client build.
 
 During client-side development, it is more convenient to have granular testing
 options. The various testing scripts are defined inside package.json within the
-client folder, and are called with `yarn` as demonstrated in the following
+client folder and are called with `yarn` as demonstrated in the following
 commands.
 
 This is what CI is going to run, and also what 'make client-test' invokes,

From f4cebe9a66227fe45d8ebc171def5e57d8766ac8 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 26 Jan 2023 10:28:36 -0500
Subject: [PATCH 31/31] Sort tool sections in a way that works for both Chrome
 and Firefox. We should refactor this whole thing and pull the state into a
 separate store.

---
 .../src/components/Panels/Common/ToolSection.vue | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/client/src/components/Panels/Common/ToolSection.vue b/client/src/components/Panels/Common/ToolSection.vue
index f02fc438f18..c57738e49e3 100644
--- a/client/src/components/Panels/Common/ToolSection.vue
+++ b/client/src/components/Panels/Common/ToolSection.vue
@@ -137,9 +137,19 @@ export default {
                 this.config.toolbox_auto_sort === true &&
                 !this.category.elems.some((el) => el.text !== undefined && el.text !== "")
             ) {
-                return Object.entries(
-                    [...this.category.elems].sort((a, b) => a.name.toLowerCase() > b.name.toLowerCase())
-                );
+                const elements = [...this.category.elems];
+                const sorted = elements.sort((a, b) => {
+                    const aNameLower = a.name.toLowerCase();
+                    const bNameLower = b.name.toLowerCase();
+                    if (aNameLower > bNameLower) {
+                        return 1;
+                    } else if (aNameLower < bNameLower) {
+                        return -1;
+                    } else {
+                        return 0;
+                    }
+                });
+                return Object.entries(sorted);
             } else {
                 return Object.entries(this.category.elems);
             }