Merge pull request #18456 from arash77/subworkflows_tags_fix (6b8c7f75) · Commits · NDIP / Galaxy

lib/galaxy/managers/workflows.py

+3 −3

Original line number	Diff line number	Diff line
		@@ -1413,7 +1413,7 @@ class WorkflowContentsManager(UsesAnnotations):
		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:
		@@ -1424,7 +1424,7 @@ class WorkflowContentsManager(UsesAnnotations):
		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
		@@ -1437,7 +1437,7 @@ class WorkflowContentsManager(UsesAnnotations):
		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_test/api/test_workflows.py

+7 −0

Original line number	Diff line number	Diff line
		@@ -7621,6 +7621,13 @@ outer_input:
		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 → 100644

+134 −0

Original line number	Diff line number	Diff line
		{
		"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
		}
		No newline at end of file