Merge pull request #6570 from mvdbeek/fix_auto_labelling_and_output_recovery

[18.01] Use subworkflow index when setting auto-label

lib/galaxy/workflow/modules.py

@@ -361,7 +361,7 @@ class SubWorkflowModule(WorkflowModule):
         subworkflow_progress = subworkflow_invoker.progress
         outputs = {}
         for workflow_output in subworkflow.workflow_outputs:
-            workflow_output_label = workflow_output.label or "%s:%s" % (step.order_index, workflow_output.output_name)
+            workflow_output_label = workflow_output.label or "%s:%s" % (workflow_output.workflow_step.order_index, workflow_output.output_name)
             replacement = subworkflow_progress.get_replacement_workflow_output(workflow_output)
             outputs[workflow_output_label] = replacement
         progress.set_step_outputs(invocation_step, outputs)

test/api/test_workflows.py

@@ -65,6 +65,47 @@ steps:
             $link: nested_workflow#workflow_output
 """
 
+NESTED_WORKFLOW_AUTO_LABELS = """
+class: GalaxyWorkflow
+inputs:
+  - id: outer_input
+outputs:
+  - id: outer_output
+    source: second_cat#out_file1
+steps:
+  - tool_id: cat1
+    label: first_cat
+    state:
+      input1:
+        $link: outer_input
+  - run:
+      class: GalaxyWorkflow
+      inputs:
+        - id: inner_input
+      outputs:
+        - source: 1#out_file1
+      steps:
+        - tool_id: random_lines1
+          state:
+            num_lines: 1
+            input:
+              $link: inner_input
+            seed_source:
+              seed_source_selector: set_seed
+              seed: asdf
+    label: nested_workflow
+    connect:
+      inner_input: first_cat#out_file1
+  - tool_id: cat1
+    label: second_cat
+    state:
+      input1:
+        $link: nested_workflow#1:out_file1
+      queries:
+        - input2:
+            $link: nested_workflow#1:out_file1
+"""
+
 
 class BaseWorkflowsApiTestCase(api.ApiTestCase):
     # TODO: Find a new file for this class.
@@ -1002,6 +1043,23 @@ test_data:
         content = self.dataset_populator.get_history_dataset_content(history_id)
         self.assertEqual("chr5\t131424298\t131424460\tCCDS4149.1_cds_0_0_chr5_131424299_f\t0\t+\nchr5\t131424298\t131424460\tCCDS4149.1_cds_0_0_chr5_131424299_f\t0\t+\n", content)
 
+    def test_run_subworkflow_auto_labels(self):
+            history_id = self.dataset_populator.new_history()
+            workflow_run_description = """%s
+
+test_data:
+  outer_input:
+    value: 1.bed
+    type: File
+""" % NESTED_WORKFLOW_AUTO_LABELS
+            job_summary = self._run_jobs(workflow_run_description, history_id=history_id)
+            assert len(job_summary.jobs) == 4, "4 jobs expected, got %d jobs" % len(job_summary.jobs)
+
+            content = self.dataset_populator.get_history_dataset_content(history_id)
+            self.assertEqual(
+                "chr5\t131424298\t131424460\tCCDS4149.1_cds_0_0_chr5_131424299_f\t0\t+\nchr5\t131424298\t131424460\tCCDS4149.1_cds_0_0_chr5_131424299_f\t0\t+\n",
+                content)
+
     @skip_without_tool("cat1")
     @skip_without_tool("collection_paired_test")
     def test_workflow_run_zip_collections(self):

test/base/workflows_format_2/converter.py

@@ -133,7 +133,7 @@ def _python_to_workflow(as_python, conversion_context):
         if "label" in output and "id" in output:
             raise Exception("label and id are aliases for outputs, may only define one")
         if "label" not in output and "id" not in output:
-            raise Exception("Output must define a label.")
+            label = ""
 
         raw_label = output.pop("label", None)
         raw_id = output.pop("id", None)