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Merge pull request #18456 from arash77/subworkflows_tags_fix
[24.0] Fix subwofklow tags serialization type
This commit is contained in:
Marius van den Beek
@@ -1413,7 +1413,7 @@ class WorkflowContentsManager(UsesAnnotations):
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If `allow_upgrade`, the workflow and sub-workflows might use updated tool versions when refactoring.
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"""
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annotation_str = ""
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tag_str = ""
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tags_list = []
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annotation_owner = None
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if stored is not None:
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if stored.id:
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@@ -1424,7 +1424,7 @@ class WorkflowContentsManager(UsesAnnotations):
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or self.get_item_annotation_str(trans.sa_session, annotation_owner, stored)
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or ""
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)
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tag_str = stored.make_tag_string_list()
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tags_list = stored.make_tag_string_list()
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else:
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# dry run with flushed workflow objects, just use the annotation
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annotations = stored.annotations
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@@ -1437,7 +1437,7 @@ class WorkflowContentsManager(UsesAnnotations):
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data["format-version"] = "0.1"
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data["name"] = workflow.name
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data["annotation"] = annotation_str
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data["tags"] = tag_str
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data["tags"] = tags_list
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if workflow.uuid is not None:
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data["uuid"] = str(workflow.uuid)
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steps: Dict[int, Dict[str, Any]] = {}
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@@ -7621,6 +7621,13 @@ outer_input:
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invocation_ids = [i["id"] for i in all_invocations_for_user.json()]
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return invocation_ids
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def test_subworkflow_tags(self):
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workflow = self.workflow_populator.load_workflow_from_resource("test_subworkflow_with_tags")
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workflow_id = self.workflow_populator.create_workflow(workflow)
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downloaded_workflow = self._download_workflow(workflow_id)
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subworkflow = downloaded_workflow["steps"]["1"]["subworkflow"]
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assert subworkflow["tags"] == []
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class TestAdminWorkflowsApi(BaseWorkflowsApiTestCase):
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require_admin_user = True
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@@ -0,0 +1,134 @@
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{
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"a_galaxy_workflow": "true",
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"annotation": "Test main ",
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"comments": [],
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"format-version": "0.1",
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"name": "Unnamed Workflow",
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"report": {
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"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"
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},
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"steps": {
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"0": {
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"annotation": "",
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"content_id": null,
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"errors": null,
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"id": 0,
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"input_connections": {},
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"inputs": [],
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"label": null,
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"name": "Input dataset",
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"outputs": [],
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"position": {
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"left": 0,
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"top": 0
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},
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"tool_id": null,
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"tool_state": "{\"optional\": false, \"tag\": null}",
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"tool_version": null,
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"type": "data_input",
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"uuid": "967583e9-d2a6-444a-ba31-6fb749d03f9e",
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"when": null,
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"workflow_outputs": []
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},
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"1": {
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"annotation": "",
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"id": 1,
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"input_connections": {
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"0:Input dataset": {
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"id": 0,
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"input_subworkflow_step_id": 0,
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"output_name": "output"
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}
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},
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"inputs": [],
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"label": null,
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"name": "Workflow with tags",
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"outputs": [],
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"position": {
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"left": 249,
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"top": 51
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},
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"subworkflow": {
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"a_galaxy_workflow": "true",
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"annotation": "",
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"comments": [],
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"format-version": "0.1",
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"name": "Workflow with tags",
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"report": {
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"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"
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},
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"steps": {
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"0": {
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"annotation": "",
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"content_id": null,
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"errors": null,
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"id": 0,
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"input_connections": {},
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"inputs": [],
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"label": null,
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"name": "Input dataset",
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"outputs": [],
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"position": {
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"left": 0,
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"top": 0.0
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},
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"tool_id": null,
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"tool_state": "{\"optional\": false, \"tag\": null}",
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"tool_version": null,
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"type": "data_input",
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"uuid": "eca9b088-ff50-4253-8387-01512f03ff2f",
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"when": null,
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"workflow_outputs": []
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},
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"1": {
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"annotation": "",
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"content_id": "addValue",
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"errors": null,
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"id": 1,
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"input_connections": {
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"input": {
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"id": 0,
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"output_name": "output"
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}
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},
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"inputs": [
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{
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"description": "runtime parameter for tool Add column",
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"name": "input"
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}
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],
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"label": null,
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"name": "Add column",
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"outputs": [
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{
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"name": "out_file1",
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"type": "input"
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}
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],
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"position": {
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"left": 123,
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"top": 112.0
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},
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"post_job_actions": {},
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"tool_id": "addValue",
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"tool_state": "{\"exp\": \"1\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"iterate\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
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"tool_version": "1.0.0",
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"type": "tool",
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"uuid": "7016e754-149b-402a-bb17-eb6cd4b1ab0a",
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"when": null,
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"workflow_outputs": []
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}
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},
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"uuid": "c33370a9-188f-4af8-bfcc-137c577c79ba"
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},
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"tool_id": null,
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"type": "subworkflow",
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"uuid": "90bdcd13-418a-49da-847e-02926942bf4b",
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"when": null,
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"workflow_outputs": []
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}
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},
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"tags": [],
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"uuid": "64d7fac3-6402-412b-9db6-490ffc18e129",
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"version": 1
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}
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