Merge branch 'release_20.09' into release_21.01

client/src/components/Panels/ToolBoxWorkflow.vue

@@ -40,6 +40,7 @@
                     v-if="hasWorkflowSection"
                     :category="workflowSection"
                     :key="workflowSection.name"
+                    section-name="workflows"
                     operation-icon="fa fa-files-o"
                     operation-title="Insert individual steps."
                     :query-filter="query"

client/src/components/Workflow/Editor/Node.vue

@@ -321,7 +321,7 @@ export default {
         },
         setData(data) {
             this.config_form = data.config_form;
-            this.content_id = this.config_form?.id;
+            this.content_id = data.config_form?.id || data.content_id;
             this.tool_state = data.tool_state;
             this.errors = data.errors;
             this.annotation = data.annotation;

lib/galaxy/selenium/navigation.yml

@@ -406,6 +406,9 @@ workflow_editor:
     tool_menu: '.toolMenuContainer'
     tool_menu_section_link: '.tool-menu-section-${section_name} a span'
     tool_menu_item_link: 'a.tool-menu-item-${item_name}'
+    workflow_link:
+      type: xpath
+      selector: '//a[contains(., "${workflow_title}")]'
 
     connect_icon: 'div.ui-form-element[tour_id="${name}"] .ui-form-connected-icon'
     collapse_icon: 'div.ui-form-element[tour_id="${name}"] .ui-form-collapsible-icon'

lib/galaxy/tools/execute.py

@@ -31,7 +31,7 @@ def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, colle
     Execute a tool and return object containing summary (output data, number of
     failures, etc...).
     """
-    if max_num_jobs:
+    if max_num_jobs is not None:
         assert invocation_step is not None
     if rerun_remap_job_id:
         assert invocation_step is None
@@ -93,7 +93,7 @@ def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, colle
     execution_slice = None
 
     for i, execution_slice in enumerate(execution_tracker.new_execution_slices()):
-        if max_num_jobs and jobs_executed >= max_num_jobs:
+        if max_num_jobs is not None and jobs_executed >= max_num_jobs:
             has_remaining_jobs = True
             break
         else:

lib/galaxy/tools/toolbox/base.py

@@ -319,9 +319,13 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
 
     def get_shed_config_dict_by_filename(self, filename):
         filename = os.path.abspath(filename)
+        dynamic_tool_conf_paths = []
         for shed_config_dict in self._dynamic_tool_confs:
-            if shed_config_dict['config_filename'] == filename:
+            dynamic_tool_conf_path = os.path.abspath(shed_config_dict['config_filename'])
+            dynamic_tool_conf_paths.append(dynamic_tool_conf_path)
+            if dynamic_tool_conf_path == filename:
                 return shed_config_dict
+        log.warning("'{}' not among installable tool config files ({})".format(filename, ', '.join(dynamic_tool_conf_paths)))
         return None
 
     def update_shed_config(self, shed_conf):

lib/galaxy/workflow/run.py

@@ -173,7 +173,12 @@ class WorkflowInvoker:
 
         remaining_steps = self.progress.remaining_steps()
         delayed_steps = False
+        max_jobs_per_iteration_reached = False
         for (step, workflow_invocation_step) in remaining_steps:
+            max_jobs_to_schedule = self.progress.maximum_jobs_to_schedule_or_none
+            if max_jobs_to_schedule is not None and max_jobs_to_schedule <= 0:
+                max_jobs_per_iteration_reached = True
+                break
             step_delayed = False
             step_timer = ExecutionTimer()
             try:
@@ -208,7 +213,7 @@ class WorkflowInvoker:
             if not step_delayed:
                 log.debug(f"Workflow step {step.id} of invocation {workflow_invocation.id} invoked {step_timer}")
 
-        if delayed_steps:
+        if delayed_steps or max_jobs_per_iteration_reached:
             state = model.WorkflowInvocation.states.READY
         else:
             state = model.WorkflowInvocation.states.SCHEDULED

lib/galaxy_test/selenium/test_workflow_editor.py

@@ -2,6 +2,7 @@ import json
 
 from galaxy_test.base.workflow_fixtures import (
     WORKFLOW_NESTED_SIMPLE,
+    WORKFLOW_OPTIONAL_TRUE_INPUT_COLLECTION,
     WORKFLOW_SIMPLE_CAT_TWICE,
     WORKFLOW_SIMPLE_MAPPING,
     WORKFLOW_WITH_INVALID_STATE,
@@ -358,6 +359,36 @@ steps:
         self.assert_modal_has_text("Using version '0.2' instead of version '0.0.1'")
         self.screenshot("workflow_editor_tool_upgrade")
 
+    @selenium_test
+    def test_editor_embed_workflow(self):
+        workflow_populator = self.workflow_populator
+        child_workflow_name = self._get_random_name()
+        workflow_populator.upload_yaml_workflow(WORKFLOW_OPTIONAL_TRUE_INPUT_COLLECTION, name=child_workflow_name)
+        parent_workflow_id = workflow_populator.upload_yaml_workflow("""class: GalaxyWorkflow
+inputs: []
+steps:
+  - tool_id: multiple_versions
+    tool_version: 0.1
+    label: multiple_versions
+    state:
+      foo: bar
+        """)
+        self.workflow_index_open()
+        self.workflow_index_click_option("Edit")
+        editor = self.components.workflow_editor
+        editor.canvas_body.wait_for_visible()
+        editor.tool_menu.wait_for_visible()
+        editor.tool_menu_section_link(section_name="workflows").wait_for_and_click()
+        editor.workflow_link(workflow_title=child_workflow_name).wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.assert_has_changes_and_save()
+        self.sleep_for(self.wait_types.UX_RENDER)
+        workflow = self.workflow_populator.download_workflow(parent_workflow_id)
+        subworkflow_step = workflow['steps']['1']
+        assert subworkflow_step['name'] == child_workflow_name
+        assert subworkflow_step['type'] == 'subworkflow'
+        assert subworkflow_step['subworkflow']['a_galaxy_workflow'] == 'true'
+
     @selenium_test
     def test_editor_invalid_tool_state(self):
         workflow_populator = self.workflow_populator

test/integration/test_workflow_scheduling_options.py

@@ -61,7 +61,7 @@ class MaximumWorkflowJobsPerSchedulingIterationTestCase(integration_util.Integra
     def handle_galaxy_config_kwds(cls, config):
         config["maximum_workflow_jobs_per_scheduling_iteration"] = 1
 
-    def test(self):
+    def test_collection_explicit_and_implicit(self):
         workflow_id = self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 steps:
@@ -89,3 +89,40 @@ steps:
             self.workflow_populator.wait_for_workflow(history_id, workflow_id, invocation_id)
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             self.assertEqual("a\nc\nb\nd\ne\ng\nf\nh\n", self.dataset_populator.get_history_dataset_content(history_id, hid=0))
+
+    def test_scheduling_rounds(self):
+        with self.dataset_populator.test_history() as history_id:
+            invocation_response = self.workflow_populator.run_workflow("""
+class: GalaxyWorkflow
+inputs:
+  input1: data
+  text_input: text
+steps:
+  first_cat:
+    tool_id: cat1
+    in:
+      input1: input1
+  second_cat:
+    tool_id: cat1
+    in:
+      input1: first_cat/out_file1
+  collection_creates_dynamic_list_of_pairs:
+    tool_id: collection_creates_dynamic_list_of_pairs
+    in:
+      file: second_cat/out_file1
+  count_multi_file:
+    tool_id: count_multi_file
+    in:
+      input1: collection_creates_dynamic_list_of_pairs/list_output
+outputs:
+  wf_output_1:
+    outputSource: collection_creates_dynamic_list_of_pairs/list_output
+""", test_data="""
+input1:
+  value: 1.fasta
+  type: File
+  name: fasta1
+text_input: foo
+""", history_id=history_id)
+            invocation = self._get("/invocations/{}".format(invocation_response.invocation_id)).json()
+            assert 'wf_output_1' in invocation['output_collections']