Merge branch 'release_24.1' into release_24.2

lib/galaxy/managers/jobs.py

@@ -346,7 +346,7 @@ def get_job_console_output(
 
     def stop(self, job, message=None):
         if not job.finished:
-            job.mark_deleted(self.app.config.track_jobs_in_database)
+            job.mark_deleted(self.app.config.track_jobs_in_database, message)
             session = self.app.model.session
             with transaction(session):
                 session.commit()
@@ -393,7 +393,12 @@ def populate_input_data_input_id(path, key, value):
                 current_case = param_dump
                 for p in path:
                     current_case = current_case[p]
-                src = current_case["src"]
+                src = current_case.get("src")
+                if src is None:
+                    # just a parameter named id.
+                    # TODO: dispatch on tool parameter type instead of values,
+                    # maybe with tool state variant
+                    return key, value
                 current_case = param
                 for i, p in enumerate(path):
                     if p == "values" and i == len(path) - 2:

lib/galaxy/model/__init__.py

@@ -1903,7 +1903,7 @@ def mark_stopped(self, track_jobs_in_database=False):
         else:
             self.state = Job.states.STOPPED
 
-    def mark_deleted(self, track_jobs_in_database=False):
+    def mark_deleted(self, track_jobs_in_database=False, message=None):
         """
         Mark this job as deleted, and mark any output datasets as discarded.
         """
@@ -1914,7 +1914,8 @@ def mark_deleted(self, track_jobs_in_database=False):
             self.state = Job.states.DELETING
         else:
             self.state = Job.states.DELETED
-        self.info = "Job output deleted by user before job completed."
+        info = message or "Job output deleted by user before job completed."
+        self.info = info
         for jtoda in self.output_datasets:
             output_hda = jtoda.dataset
             output_hda.deleted = True
@@ -1924,7 +1925,7 @@ def mark_deleted(self, track_jobs_in_database=False):
                 shared_hda.deleted = True
                 shared_hda.blurb = "deleted"
                 shared_hda.peek = "Job deleted"
-                shared_hda.info = "Job output deleted by user before job completed"
+                shared_hda.info = info
 
     def mark_failed(self, info="Job execution failed", blurb=None, peek=None):
         """
@@ -3708,6 +3709,10 @@ def active_contents(self):
         """Return all active contents ordered by hid."""
         return self.contents_iter(types=["dataset", "dataset_collection"], deleted=False, visible=True)
 
+    @property
+    def visible_contents(self):
+        return self.contents_iter(types=["dataset", "dataset_collection"], visible=True)
+
     def contents_iter(self, **kwds):
         """
         Fetch filtered list of contents of history.
@@ -5012,11 +5017,16 @@ def display_name(self):
     def display_info(self):
         return self.datatype.display_info(self)
 
-    def get_converted_files_by_type(self, file_type):
+    def get_converted_files_by_type(self, file_type, include_errored=False):
         for assoc in self.implicitly_converted_datasets:
             if not assoc.deleted and assoc.type == file_type:
                 item = assoc.dataset or assoc.dataset_ldda
-                if not item.deleted and item.state in Dataset.valid_input_states:
+                valid_states = (
+                    (Dataset.states.ERROR, *Dataset.valid_input_states)
+                    if include_errored
+                    else Dataset.valid_input_states
+                )
+                if not item.deleted and item.state in valid_states:
                     return item
         return None
 
@@ -5031,7 +5041,7 @@ def get_converted_dataset_deps(self, trans, target_ext):
             depends_list = []
         return {dep: self.get_converted_dataset(trans, dep) for dep in depends_list}
 
-    def get_converted_dataset(self, trans, target_ext, target_context=None, history=None):
+    def get_converted_dataset(self, trans, target_ext, target_context=None, history=None, include_errored=False):
         """
         Return converted dataset(s) if they exist, along with a dict of dependencies.
         If not converted yet, do so and return None (the first time). If unconvertible, raise exception.
@@ -5043,7 +5053,7 @@ def get_converted_dataset(self, trans, target_ext, target_context=None, history=
         converted_dataset = self.get_metadata_dataset(target_ext)
         if converted_dataset:
             return converted_dataset
-        converted_dataset = self.get_converted_files_by_type(target_ext)
+        converted_dataset = self.get_converted_files_by_type(target_ext, include_errored=include_errored)
         if converted_dataset:
             return converted_dataset
         deps = {}
@@ -5267,7 +5277,8 @@ def convert_dataset(self, trans, target_type):
 
         # Get converted dataset; this will start the conversion if necessary.
         try:
-            converted_dataset = self.get_converted_dataset(trans, target_type)
+            # Include errored datasets here, we let user chose to retry or view error
+            converted_dataset = self.get_converted_dataset(trans, target_type, include_errored=True)
         except NoConverterException:
             return self.conversion_messages.NO_CONVERTER
         except ConverterDependencyException as dep_error:

lib/galaxy/workflow/extract.py

@@ -283,7 +283,7 @@ def __summarize(self):
         # just grab the implicitly mapped jobs and handle in second pass. Second pass is
         # needed because cannot allow selection of individual datasets from an implicit
         # mapping during extraction - you get the collection or nothing.
-        for content in self.history.active_contents:
+        for content in self.history.visible_contents:
             self.__summarize_content(content)
 
     def __summarize_content(self, content):

lib/galaxy_test/api/test_jobs.py

@@ -1062,6 +1062,24 @@ def test_delete_job(self, history_id):
         self._assert_status_code_is(empty_search_response, 200)
         assert len(empty_search_response.json()) == 0
 
+    @pytest.mark.require_new_history
+    def test_delete_job_with_message(self, history_id):
+        input_dataset_id = self.__history_with_ok_dataset(history_id)
+        inputs = json.dumps({"input1": {"src": "hda", "id": input_dataset_id}})
+        search_payload = self._search_payload(history_id=history_id, tool_id="cat1", inputs=inputs)
+        # create a job
+        tool_response = self._post("tools", data=search_payload).json()
+        job_id = tool_response["jobs"][0]["id"]
+        output_dataset_id = tool_response["outputs"][0]["id"]
+        # delete the job with message
+        expected_message = "test message"
+        delete_job_response = self._delete(f"jobs/{job_id}", data={"message": expected_message}, json=True)
+        self._assert_status_code_is(delete_job_response, 200)
+        # Check the output dataset is deleted and the info field contains the message
+        dataset_details = self._get(f"histories/{history_id}/contents/{output_dataset_id}").json()
+        assert dataset_details["deleted"] is True
+        assert dataset_details["misc_info"] == expected_message
+
     @pytest.mark.require_new_history
     def test_destination_params(self, history_id):
         dataset_id = self.__history_with_ok_dataset(history_id)

templates/webapps/galaxy/workflow/build_from_current_history.mako

@@ -88,7 +88,7 @@ into a workflow will be shown in gray.</p>
     <div class="warningmark">${warning}</div>
 %endfor
 
-<form method="post" action="${h.url_for(controller='workflow', action='build_from_current_history')}">
+<form method="post" action="${h.url_for(controller='workflow', action='build_from_current_history', history_id=trans.security.encode_id(history.id))}">
 <div class='form-row'>
     <label>Workflow name</label>
     <input name="workflow_name" type="text" value="Workflow constructed from history '${ util.unicodify( history.name )}'" size="60"/>
@@ -112,6 +112,7 @@ into a workflow will be shown in gray.</p>
     <%
     cls = "toolForm"
     tool_name = "Unknown"
+    checked_job = "checked" if any(True for d in datasets if not d[1].deleted) else ""
     if hasattr( job, 'is_fake' ) and job.is_fake:
         cls += " toolFormDisabled"
         disabled = True
@@ -142,7 +143,10 @@ into a workflow will be shown in gray.</p>
                     %if disabled:
                         <div style="font-style: italic; color: gray">${disabled_why}</div>
                     %else:
-                        <div><input type="checkbox" name="job_ids" value="${job.id}" checked="true" />Include "${tool_name}" in workflow</div>
+                        <div><input type="checkbox" name="job_ids" value="${job.id}" ${checked_job} />Include "${tool_name}" in workflow</div>
+                        %if not checked_job:
+                            ${ render_msg( "All job outputs have been deleted", status="info" ) }
+                        %endif
                         %if tool_version_warning:
                             ${ render_msg( tool_version_warning, status="warning" ) }
                         %endif

test/unit/workflows/test_extract_summary.py

@@ -121,6 +121,10 @@ def __init__(self):
     def active_contents(self):
         return self.active_datasets
 
+    @property
+    def visible_contents(self):
+        return self.active_contents
+
 
 class MockTrans:
     def __init__(self, history):