Merge branch 'release_24.0' into release_24.1

lib/galaxy/job_execution/setup.py

@@ -213,22 +213,26 @@ def get_input_dataset_fnames(self, ds: DatasetInstance) -> List[str]:
         for value in ds.metadata.values():
             if isinstance(value, MetadataFile):
                 filenames.append(value.get_file_name())
+        if ds.dataset and ds.dataset.extra_files_path_exists():
+            filenames.append(ds.dataset.extra_files_path)
         return filenames
 
-    def get_input_fnames(self) -> List[str]:
+    def get_input_datasets(self) -> List[DatasetInstance]:
         job = self.job
+        return [
+            da.dataset for da in job.input_datasets + job.input_library_datasets if da.dataset
+        ]  # da is JobToInputDatasetAssociation object
+
+    def get_input_fnames(self) -> List[str]:
         filenames = []
-        for da in job.input_datasets + job.input_library_datasets:  # da is JobToInputDatasetAssociation object
-            if da.dataset:
-                filenames.extend(self.get_input_dataset_fnames(da.dataset))
+        for ds in self.get_input_datasets():
+            filenames.extend(self.get_input_dataset_fnames(ds))
         return filenames
 
     def get_input_paths(self) -> List[DatasetPath]:
-        job = self.job
         paths = []
-        for da in job.input_datasets + job.input_library_datasets:  # da is JobToInputDatasetAssociation object
-            if da.dataset:
-                paths.append(self.get_input_path(da.dataset))
+        for ds in self.get_input_datasets():
+            paths.append(self.get_input_path(ds))
         return paths
 
     def get_input_path(self, dataset: DatasetInstance) -> DatasetPath:

lib/galaxy/jobs/splitters/basic.py

@@ -13,7 +13,7 @@ def set_basic_defaults(job_wrapper):
 
 
 def do_split(job_wrapper):
-    if len(job_wrapper.job_io.get_input_fnames()) > 1 or len(job_wrapper.job_io.get_output_fnames()) > 1:
+    if len(job_wrapper.job_io.get_input_datasets()) > 1 or len(job_wrapper.job_io.get_output_fnames()) > 1:
         log.error("The basic splitter is not capable of handling jobs with multiple inputs or outputs.")
         raise Exception("Job Splitting Failed, the basic splitter only handles tools with one input and one output")
     # add in the missing information for splitting the one input and merging the one output

lib/galaxy/managers/users.py

@@ -616,7 +616,7 @@ def get_reset_token(self, trans, email):
         reset_user = get_user_by_email(trans.sa_session, email, self.app.model.User)
         if not reset_user and email != email.lower():
             reset_user = self._get_user_by_email_case_insensitive(trans.sa_session, email)
-        if reset_user:
+        if reset_user and not reset_user.deleted:
             prt = self.app.model.PasswordResetToken(reset_user)
             trans.sa_session.add(prt)
             with transaction(trans.sa_session):

lib/galaxy/managers/workflows.py

@@ -1416,7 +1416,7 @@ def _workflow_to_dict_export(self, trans, stored=None, workflow=None, internal=F
         If `allow_upgrade`, the workflow and sub-workflows might use updated tool versions when refactoring.
         """
         annotation_str = ""
-        tag_str = ""
+        tags_list = []
         annotation_owner = None
         if stored is not None:
             if stored.id:
@@ -1427,7 +1427,7 @@ def _workflow_to_dict_export(self, trans, stored=None, workflow=None, internal=F
                     or self.get_item_annotation_str(trans.sa_session, annotation_owner, stored)
                     or ""
                 )
-                tag_str = stored.make_tag_string_list()
+                tags_list = stored.make_tag_string_list()
             else:
                 # dry run with flushed workflow objects, just use the annotation
                 annotations = stored.annotations
@@ -1440,7 +1440,7 @@ def _workflow_to_dict_export(self, trans, stored=None, workflow=None, internal=F
         data["format-version"] = "0.1"
         data["name"] = workflow.name
         data["annotation"] = annotation_str
-        data["tags"] = tag_str
+        data["tags"] = tags_list
         if workflow.uuid is not None:
             data["uuid"] = str(workflow.uuid)
         steps: Dict[int, Dict[str, Any]] = {}

lib/galaxy/workflow/refactor/execute.py

@@ -531,6 +531,9 @@ def _patch_step(self, execution, step, step_def):
                 if upgrade_input["name"] == input_name:
                     matching_input = upgrade_input
                     break
+                elif step.when_expression and f"inputs.{input_name}" in step.when_expression:
+                    # TODO: eventually track step inputs more formally
+                    matching_input = upgrade_input
 
             # In the future check parameter type, format, mapping status...
             if matching_input is None:

lib/galaxy_test/api/test_workflows.py

@@ -7704,6 +7704,13 @@ def _all_user_invocation_ids(self):
         invocation_ids = [i["id"] for i in all_invocations_for_user.json()]
         return invocation_ids
 
+    def test_subworkflow_tags(self):
+        workflow = self.workflow_populator.load_workflow_from_resource("test_subworkflow_with_tags")
+        workflow_id = self.workflow_populator.create_workflow(workflow)
+        downloaded_workflow = self._download_workflow(workflow_id)
+        subworkflow = downloaded_workflow["steps"]["1"]["subworkflow"]
+        assert subworkflow["tags"] == []
+
 
 class TestAdminWorkflowsApi(BaseWorkflowsApiTestCase):
     require_admin_user = True

lib/galaxy_test/base/data/test_subworkflow_with_tags.ga

@@ -0,0 +1,134 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "Test main ",
+    "comments": [],
+    "format-version": "0.1",
+    "name": "Unnamed Workflow",
+    "report": {
+        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+    },
+    "steps": {
+        "0": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [],
+            "label": null,
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "left": 0,
+                "top": 0
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false, \"tag\": null}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "967583e9-d2a6-444a-ba31-6fb749d03f9e",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "1": {
+            "annotation": "",
+            "id": 1,
+            "input_connections": {
+                "0:Input dataset": {
+                    "id": 0,
+                    "input_subworkflow_step_id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "Workflow with tags",
+            "outputs": [],
+            "position": {
+                "left": 249,
+                "top": 51
+            },
+            "subworkflow": {
+                "a_galaxy_workflow": "true",
+                "annotation": "",
+                "comments": [],
+                "format-version": "0.1",
+                "name": "Workflow with tags",
+                "report": {
+                    "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                },
+                "steps": {
+                    "0": {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 0.0
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "eca9b088-ff50-4253-8387-01512f03ff2f",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    "1": {
+                        "annotation": "",
+                        "content_id": "addValue",
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Add column",
+                                "name": "input"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Add column",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 123,
+                            "top": 112.0
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "addValue",
+                        "tool_state": "{\"exp\": \"1\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"iterate\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "7016e754-149b-402a-bb17-eb6cd4b1ab0a",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                },
+                "uuid": "c33370a9-188f-4af8-bfcc-137c577c79ba"
+            },
+            "tool_id": null,
+            "type": "subworkflow",
+            "uuid": "90bdcd13-418a-49da-847e-02926942bf4b",
+            "when": null,
+            "workflow_outputs": []
+        }
+    },
+    "tags": [],
+    "uuid": "64d7fac3-6402-412b-9db6-490ffc18e129",
+    "version": 1
+}

lib/tool_shed/webapp/templates/galaxy_client_app.mako

@@ -72,7 +72,7 @@ ${ h.dumps( dictionary, indent=( 2 if trans.debug else 0 ) ) }
 
 <%def name="config_plausible_analytics(plausible_server, plausible_domain)">
     %if plausible_server and plausible_domain:
-        <script async defer data-domain="${plausible_domain}" src="${plausible_server}/js/plausible.js"></script>
+        <script async defer data-domain="${plausible_domain}" src="${plausible_server}/js/script.js"></script>
     %else:
         <script>console.warn("Missing plausible server or plausible domain");</script>
     %endif

templates/galaxy_client_app.mako

@@ -73,7 +73,7 @@ ${ h.dumps( dictionary, indent=( 2 if trans.debug else 0 ) ) }
 
 <%def name="config_plausible_analytics(plausible_server, plausible_domain)">
     %if plausible_server and plausible_domain:
-        <script async defer data-domain="${plausible_domain}" src="${plausible_server}/js/plausible.js"></script>
+        <script async defer data-domain="${plausible_domain}" src="${plausible_server}/js/script.js"></script>
         <script>window.plausible = window.plausible || function() { (window.plausible.q = window.plausible.q || []).push(arguments) }</script>
     %else:
         <script>

templates/js-app.mako

@@ -22,10 +22,10 @@
             | ${app.config.brand}
             %endif
         </title>
-        
+
         ## relative href for site root
         <link rel="index" href="${ h.url_for( '/' ) }"/>
-        
+
         ## TODO: use loaders to move everything but the essentials below the fold
         ${ h.dist_css(
             'base',
@@ -86,10 +86,10 @@
         ${ galaxy_client.config_google_analytics(app.config.ga_code) }
     %endif
     %if app.config.plausible_server and app.config.plausible_domain:
-            ${ galaxy_client.config_plausible_analytics(app.config.plausible_server, app.config.plausible_domain) }
+        ${ galaxy_client.config_plausible_analytics(app.config.plausible_server, app.config.plausible_domain) }
     %endif
     %if app.config.matomo_server and app.config.matomo_site_id:
-            ${ galaxy_client.config_matomo_analytics(app.config.matomo_server, app.config.matomo_site_id) }
+        ${ galaxy_client.config_matomo_analytics(app.config.matomo_server, app.config.matomo_site_id) }
     %endif
 </%def>
 

test/integration/test_workflow_refactoring.py

@@ -537,6 +537,35 @@ def test_tool_version_upgrade_no_state_change(self):
         assert len(action_executions[0].messages) == 0
         assert self._latest_workflow.step_by_label("the_step").tool_version == "0.2"
 
+    def test_tool_version_upgrade_keeps_when_expression(self):
+        self.workflow_populator.upload_yaml_workflow(
+            """
+class: GalaxyWorkflow
+inputs:
+  the_bool:
+    type: boolean
+steps:
+  the_step:
+    tool_id: multiple_versions
+    tool_version: '0.1'
+    in:
+      when: the_bool
+    state:
+      inttest: 0
+    when: $(inputs.when)
+"""
+        )
+        assert self._latest_workflow.step_by_label("the_step").tool_version == "0.1"
+        actions: ActionsJson = [
+            {"action_type": "upgrade_tool", "step": {"label": "the_step"}},
+        ]
+        action_executions = self._refactor(actions).action_executions
+        assert len(action_executions) == 1
+        assert len(action_executions[0].messages) == 0
+        step = self._latest_workflow.step_by_label("the_step")
+        assert step.tool_version == "0.2"
+        assert step.when_expression
+
     def test_tool_version_upgrade_state_added(self):
         self.workflow_populator.upload_yaml_workflow(
             """

test/unit/app/managers/test_UserManager.py

@@ -232,6 +232,16 @@ def validate_send_email(frm, to, subject, body, config, html=None):
                 mock_unique_id.assert_called_once()
         assert result is None
 
+    def test_reset_email_user_deleted(self):
+        self.trans.app.config.allow_user_deletion = True
+        self.log("should not produce the password reset email if user is deleted")
+        user_email = "[email protected]"
+        user = self.user_manager.create(email=user_email, username="nopassword")
+        self.user_manager.delete(user)
+        assert user.deleted is True
+        message = self.user_manager.send_reset_email(self.trans, {"email": user_email})
+        assert message == "Failed to produce password reset token. User not found."
+
     def test_get_user_by_identity(self):
         # return None if username/email not found
         assert self.user_manager.get_user_by_identity("xyz") is None