Merge pull request #1391 from lldelisle/wf_same_output_name

Try to fix planemo test workflow when output is collection with identical name

planemo/galaxy/activity.py

@@ -503,7 +503,7 @@ def outputs_dict(self):
 
     def download_output_to(self, ctx, dataset_details, output_directory, filename=None):
         if filename is None:
-            local_filename = sanitize_filename(dataset_details.get("cwl_file_name") or dataset_details.get("name"))
+            local_filename = f'{sanitize_filename(dataset_details.get("cwl_file_name") or dataset_details.get("name"))}__{dataset_details["uuid"]}'
         else:
             local_filename = filename
         destination = os.path.join(output_directory, local_filename)

tests/data/wf_same_name_outputs-tests.yml

@@ -0,0 +1,17 @@
+- doc: Test outline for Test-workflow
+  job:
+    input text file with numbers:
+      class: File
+      path: wf_same_name_outputs_input.txt
+      filetype: txt
+  outputs:
+    output:
+      element_tests:
+        split_file_000000.txt:
+          asserts:
+            has_n_lines:
+              n: 1
+        split_file_000001.txt:
+          asserts:
+            has_n_lines:
+              n: 2

tests/data/wf_same_name_outputs.ga

@@ -0,0 +1,167 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "Workflow with multiple output with identical names",
+    "format-version": "0.1",
+    "name": "Test workflow",
+    "steps": {
+        "0": {
+            "annotation": "input text file with numbers, one per line",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "input text file with numbers, one per line",
+                    "name": "input text file with numbers"
+                }
+            ],
+            "label": "input text file with numbers",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "left": 0,
+                "top": 46
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false, \"tag\": null}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "a659f5f4-cde9-46d5-8b9b-4dec7be29393",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "1": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0",
+            "errors": null,
+            "id": 1,
+            "input_connections": {
+                "split_parms|input": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "Split file",
+            "outputs": [
+                {
+                    "name": "list_output_txt",
+                    "type": "input"
+                }
+            ],
+            "position": {
+                "left": 280,
+                "top": 30
+            },
+            "post_job_actions": {
+                "HideDatasetActionlist_output_txt": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "list_output_txt"
+                }
+            },
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0",
+            "tool_shed_repository": {
+                "changeset_revision": "6cbe2f30c2d7",
+                "name": "split_file_to_collection",
+                "owner": "bgruening",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"split_parms\": {\"select_ftype\": \"txt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}, \"select_mode\": {\"mode\": \"chunk\", \"__current_case__\": 0, \"chunksize\": \"1\"}, \"newfilenames\": \"split_file\", \"select_allocate\": {\"allocate\": \"byrow\", \"__current_case__\": 2}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "0.5.0",
+            "type": "tool",
+            "uuid": "b0485dad-0939-489d-8a9d-877d847dc29f",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "2": {
+            "annotation": "",
+            "content_id": "param_value_from_file",
+            "errors": null,
+            "id": 2,
+            "input_connections": {
+                "input1": {
+                    "id": 1,
+                    "output_name": "list_output_txt"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "Parse parameter value",
+            "outputs": [
+                {
+                    "name": "integer_param",
+                    "type": "expression.json"
+                }
+            ],
+            "position": {
+                "left": 560,
+                "top": 0
+            },
+            "post_job_actions": {
+                "HideDatasetActiontext_param": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "text_param"
+                }
+            },
+            "tool_id": "param_value_from_file",
+            "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "0.1.0",
+            "type": "tool",
+            "uuid": "7a0d475f-e575-4a37-a2e8-5f5756694b39",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "3": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0",
+            "errors": null,
+            "id": 3,
+            "input_connections": {
+                "token_set_0|repeat_select|times": {
+                    "id": 2,
+                    "output_name": "integer_param"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "Create text file",
+            "outputs": [
+                {
+                    "name": "outfile",
+                    "type": "txt"
+                }
+            ],
+            "position": {
+                "left": 840,
+                "top": 42
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0",
+            "tool_shed_repository": {
+                "changeset_revision": "ddf54b12c295",
+                "name": "text_processing",
+                "owner": "bgruening",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"token_set\": [{\"__index__\": 0, \"line\": \"test\", \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.1.0",
+            "type": "tool",
+            "uuid": "5be7215e-3c3d-4302-91dd-e5f020a2c16b",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": "output",
+                    "output_name": "outfile",
+                    "uuid": "8b281401-fe43-4fd0-b835-532c3bba1b98"
+                }
+            ]
+        }
+    },
+    "tags": [],
+    "uuid": "3d858ad4-cd53-468c-8e51-860b31356343",
+    "version": 3
+}

tests/data/wf_same_name_outputs_input.txt

@@ -0,0 +1,2 @@
+1
+2

tests/test_cmd_test.py

@@ -368,3 +368,12 @@ def test_workflow_test_skipped_invocation(self):
             test_command = self.append_profile_argument_if_needed(test_command)
             test_command.append(test_artifact)
             self._check_exit_code(test_command, exit_code=0)
+
+    @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
+    def test_workflow_with_identical_output_names(self):
+        with self._isolate():
+            test_artifact = os.path.join(TEST_DATA_DIR, "wf_same_name_outputs.ga")
+            test_command = self._test_command()
+            test_command = self.append_profile_argument_if_needed(test_command)
+            test_command.append(test_artifact)
+            self._check_exit_code(test_command, exit_code=0)