{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":44561280,"defaultBranch":"cwl-1.0","name":"galaxy","ownerLogin":"common-workflow-lab","currentUserCanPush":false,"isFork":true,"isEmpty":false,"createdAt":"2015-10-19T20:14:00.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/53422574?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1719494837.0","currentOid":""},"activityList":{"items":[{"before":"114c45614f2c9cdc79a022ca4b451fa0d844b093","after":"42ce7c6fbdff135391f32a2c91533a56e3b6f4a2","ref":"refs/heads/cwl-1.0","pushedAt":"2024-07-27T18:36:03.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"nsoranzo","name":"Nicola Soranzo","path":"/nsoranzo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4924623?s=80&v=4"},"commit":{"message":"Fix ``test_composite_datatype_stage_upload1`` test\n\nCan be squashed into commit \"Record unnamed_outputs as job outputs, wait for job outputs in staging function\" .\n\nFix the following traceback:\n\n```\nself = <galaxy_test.api.test_tools_upload.TestToolsUpload object at 0x7f309146b550>\nhistory_id = '333add226b1f5083'\n\n    @skip_without_datatype(\"velvet\")\n    def test_composite_datatype_stage_upload1(self, history_id: str) -> None:\n        job = {\n            \"input1\": {\n                \"class\": \"File\",\n                \"format\": \"velvet\",\n                \"composite_data\": [\n                    \"test-data/simple_line.txt\",\n                    \"test-data/simple_line_alternative.txt\",\n                    \"test-data/simple_line_x2.txt\",\n                ],\n            }\n        }\n>       stage_inputs(self.galaxy_interactor, history_id, job, use_path_paste=False, use_fetch_api=False)\n\nlib/galaxy_test/api/test_tools_upload.py:497:\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _\nlib/galaxy_test/base/populators.py:3181: in stage_inputs\n    return InteractorStaging(galaxy_interactor, use_fetch_api=use_fetch_api).stage(\nlib/galaxy/tool_util/client/staging.py:264: in stage\n    return galactic_job_json(\nlib/galaxy/tool_util/cwl/util.py:392: in galactic_job_json\n    replace_keys[key] = replacement_item(value)\nlib/galaxy/tool_util/cwl/util.py:220: in replacement_item\n    return replacement_file(value)\nlib/galaxy/tool_util/cwl/util.py:251: in replacement_file\n    rval_c = upload_file_with_composite_data(None, composite_data, filetype=filetype, **kwd)\nlib/galaxy/tool_util/cwl/util.py:190: in upload_file_with_composite_data\n    return response_to_hda(target, upload_response)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _\n\ntarget = <galaxy.tool_util.cwl.util.FileUploadTarget object at 0x7f30044f61c0>\nupload_response = {'implicit_collections': [], 'jobs': [{'create_time': '2024-04-02T13:19:27.579575', 'exit_code': None, 'galaxy_version...ats': ['http://edamontology.org/format_1915'], 'data_type': 'galaxy.datatypes.data.Data', 'deleted': False, ...}], ...}\n\n    def response_to_hda(target: UploadTarget, upload_response: Dict[str, Any]) -> Dict[str, str]:\n>       dataset = next(iter(upload_response[\"outputs\"].values()))\nE       AttributeError: 'list' object has no attribute 'values'\n\nlib/galaxy/tool_util/cwl/util.py:160: AttributeError\n```","shortMessageHtmlLink":"Fix <code>test_composite_datatype_stage_upload1</code> test"}},{"before":"d4904040570be175994b8311ed2e9ba1529a8bc3","after":"114c45614f2c9cdc79a022ca4b451fa0d844b093","ref":"refs/heads/cwl-1.0","pushedAt":"2024-07-21T18:55:54.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"nsoranzo","name":"Nicola Soranzo","path":"/nsoranzo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4924623?s=80&v=4"},"commit":{"message":"Fix ``test_composite_datatype_stage_upload1`` test\n\nCan be squashed into commit \"Record unnamed_outputs as job outputs, wait for job outputs in staging function\" .\n\nFix the following traceback:\n\n```\nself = <galaxy_test.api.test_tools_upload.TestToolsUpload object at 0x7f309146b550>\nhistory_id = '333add226b1f5083'\n\n    @skip_without_datatype(\"velvet\")\n    def test_composite_datatype_stage_upload1(self, history_id: str) -> None:\n        job = {\n            \"input1\": {\n                \"class\": \"File\",\n                \"format\": \"velvet\",\n                \"composite_data\": [\n                    \"test-data/simple_line.txt\",\n                    \"test-data/simple_line_alternative.txt\",\n                    \"test-data/simple_line_x2.txt\",\n                ],\n            }\n        }\n>       stage_inputs(self.galaxy_interactor, history_id, job, use_path_paste=False, use_fetch_api=False)\n\nlib/galaxy_test/api/test_tools_upload.py:497:\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _\nlib/galaxy_test/base/populators.py:3181: in stage_inputs\n    return InteractorStaging(galaxy_interactor, use_fetch_api=use_fetch_api).stage(\nlib/galaxy/tool_util/client/staging.py:264: in stage\n    return galactic_job_json(\nlib/galaxy/tool_util/cwl/util.py:392: in galactic_job_json\n    replace_keys[key] = replacement_item(value)\nlib/galaxy/tool_util/cwl/util.py:220: in replacement_item\n    return replacement_file(value)\nlib/galaxy/tool_util/cwl/util.py:251: in replacement_file\n    rval_c = upload_file_with_composite_data(None, composite_data, filetype=filetype, **kwd)\nlib/galaxy/tool_util/cwl/util.py:190: in upload_file_with_composite_data\n    return response_to_hda(target, upload_response)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _\n\ntarget = <galaxy.tool_util.cwl.util.FileUploadTarget object at 0x7f30044f61c0>\nupload_response = {'implicit_collections': [], 'jobs': [{'create_time': '2024-04-02T13:19:27.579575', 'exit_code': None, 'galaxy_version...ats': ['http://edamontology.org/format_1915'], 'data_type': 'galaxy.datatypes.data.Data', 'deleted': False, ...}], ...}\n\n    def response_to_hda(target: UploadTarget, upload_response: Dict[str, Any]) -> Dict[str, str]:\n>       dataset = next(iter(upload_response[\"outputs\"].values()))\nE       AttributeError: 'list' object has no attribute 'values'\n\nlib/galaxy/tool_util/cwl/util.py:160: AttributeError\n```","shortMessageHtmlLink":"Fix <code>test_composite_datatype_stage_upload1</code> test"}},{"before":"a5cc09147330928bb6abec0f0b832cbb0ba6ffa9","after":"d4904040570be175994b8311ed2e9ba1529a8bc3","ref":"refs/heads/cwl-1.0","pushedAt":"2024-07-15T18:27:31.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"nsoranzo","name":"Nicola Soranzo","path":"/nsoranzo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4924623?s=80&v=4"},"commit":{"message":"Fix ``test_composite_datatype_stage_upload1`` test\n\nCan be squashed into commit \"Record unnamed_outputs as job outputs, wait for job outputs in staging function\" .\n\nFix the following traceback:\n\n```\nself = <galaxy_test.api.test_tools_upload.TestToolsUpload object at 0x7f309146b550>\nhistory_id = '333add226b1f5083'\n\n    @skip_without_datatype(\"velvet\")\n    def test_composite_datatype_stage_upload1(self, history_id: str) -> None:\n        job = {\n            \"input1\": {\n                \"class\": \"File\",\n                \"format\": \"velvet\",\n                \"composite_data\": [\n                    \"test-data/simple_line.txt\",\n                    \"test-data/simple_line_alternative.txt\",\n                    \"test-data/simple_line_x2.txt\",\n                ],\n            }\n        }\n>       stage_inputs(self.galaxy_interactor, history_id, job, use_path_paste=False, use_fetch_api=False)\n\nlib/galaxy_test/api/test_tools_upload.py:497:\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _\nlib/galaxy_test/base/populators.py:3181: in stage_inputs\n    return InteractorStaging(galaxy_interactor, use_fetch_api=use_fetch_api).stage(\nlib/galaxy/tool_util/client/staging.py:264: in stage\n    return galactic_job_json(\nlib/galaxy/tool_util/cwl/util.py:392: in galactic_job_json\n    replace_keys[key] = replacement_item(value)\nlib/galaxy/tool_util/cwl/util.py:220: in replacement_item\n    return replacement_file(value)\nlib/galaxy/tool_util/cwl/util.py:251: in replacement_file\n    rval_c = upload_file_with_composite_data(None, composite_data, filetype=filetype, **kwd)\nlib/galaxy/tool_util/cwl/util.py:190: in upload_file_with_composite_data\n    return response_to_hda(target, upload_response)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _\n\ntarget = <galaxy.tool_util.cwl.util.FileUploadTarget object at 0x7f30044f61c0>\nupload_response = {'implicit_collections': [], 'jobs': [{'create_time': '2024-04-02T13:19:27.579575', 'exit_code': None, 'galaxy_version...ats': ['http://edamontology.org/format_1915'], 'data_type': 'galaxy.datatypes.data.Data', 'deleted': False, ...}], ...}\n\n    def response_to_hda(target: UploadTarget, upload_response: Dict[str, Any]) -> Dict[str, str]:\n>       dataset = next(iter(upload_response[\"outputs\"].values()))\nE       AttributeError: 'list' object has no attribute 'values'\n\nlib/galaxy/tool_util/cwl/util.py:160: AttributeError\n```","shortMessageHtmlLink":"Fix <code>test_composite_datatype_stage_upload1</code> test"}},{"before":"68648a0aa66fae2acd2f776a892883a5078e9c0e","after":"a5cc09147330928bb6abec0f0b832cbb0ba6ffa9","ref":"refs/heads/cwl-1.0","pushedAt":"2024-07-13T16:51:10.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"nsoranzo","name":"Nicola Soranzo","path":"/nsoranzo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4924623?s=80&v=4"},"commit":{"message":"Fix ``test_composite_datatype_stage_upload1`` test\n\nCan be squashed into commit \"Record unnamed_outputs as job outputs, wait for job outputs in staging function\" .\n\nFix the following traceback:\n\n```\nself = <galaxy_test.api.test_tools_upload.TestToolsUpload object at 0x7f309146b550>\nhistory_id = '333add226b1f5083'\n\n    @skip_without_datatype(\"velvet\")\n    def test_composite_datatype_stage_upload1(self, history_id: str) -> None:\n        job = {\n            \"input1\": {\n                \"class\": \"File\",\n                \"format\": \"velvet\",\n                \"composite_data\": [\n                    \"test-data/simple_line.txt\",\n                    \"test-data/simple_line_alternative.txt\",\n                    \"test-data/simple_line_x2.txt\",\n                ],\n            }\n        }\n>       stage_inputs(self.galaxy_interactor, history_id, job, use_path_paste=False, use_fetch_api=False)\n\nlib/galaxy_test/api/test_tools_upload.py:497:\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _\nlib/galaxy_test/base/populators.py:3181: in stage_inputs\n    return InteractorStaging(galaxy_interactor, use_fetch_api=use_fetch_api).stage(\nlib/galaxy/tool_util/client/staging.py:264: in stage\n    return galactic_job_json(\nlib/galaxy/tool_util/cwl/util.py:392: in galactic_job_json\n    replace_keys[key] = replacement_item(value)\nlib/galaxy/tool_util/cwl/util.py:220: in replacement_item\n    return replacement_file(value)\nlib/galaxy/tool_util/cwl/util.py:251: in replacement_file\n    rval_c = upload_file_with_composite_data(None, composite_data, filetype=filetype, **kwd)\nlib/galaxy/tool_util/cwl/util.py:190: in upload_file_with_composite_data\n    return response_to_hda(target, upload_response)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _\n\ntarget = <galaxy.tool_util.cwl.util.FileUploadTarget object at 0x7f30044f61c0>\nupload_response = {'implicit_collections': [], 'jobs': [{'create_time': '2024-04-02T13:19:27.579575', 'exit_code': None, 'galaxy_version...ats': ['http://edamontology.org/format_1915'], 'data_type': 'galaxy.datatypes.data.Data', 'deleted': False, ...}], ...}\n\n    def response_to_hda(target: UploadTarget, upload_response: Dict[str, Any]) -> Dict[str, str]:\n>       dataset = next(iter(upload_response[\"outputs\"].values()))\nE       AttributeError: 'list' object has no attribute 'values'\n\nlib/galaxy/tool_util/cwl/util.py:160: AttributeError\n```","shortMessageHtmlLink":"Fix <code>test_composite_datatype_stage_upload1</code> test"}},{"before":"072ed0138d0be770441333686ffea4d6dd626ecd","after":"68648a0aa66fae2acd2f776a892883a5078e9c0e","ref":"refs/heads/cwl-1.0","pushedAt":"2024-07-12T12:35:03.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"nsoranzo","name":"Nicola Soranzo","path":"/nsoranzo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4924623?s=80&v=4"},"commit":{"message":"Fix ``test_composite_datatype_stage_upload1`` test\n\nCan be squashed into commit \"Record unnamed_outputs as job outputs, wait for job outputs in staging function\" .\n\nFix the following traceback:\n\n```\nself = <galaxy_test.api.test_tools_upload.TestToolsUpload object at 0x7f309146b550>\nhistory_id = '333add226b1f5083'\n\n    @skip_without_datatype(\"velvet\")\n    def test_composite_datatype_stage_upload1(self, history_id: str) -> None:\n        job = {\n            \"input1\": {\n                \"class\": \"File\",\n                \"format\": \"velvet\",\n                \"composite_data\": [\n                    \"test-data/simple_line.txt\",\n                    \"test-data/simple_line_alternative.txt\",\n                    \"test-data/simple_line_x2.txt\",\n                ],\n            }\n        }\n>       stage_inputs(self.galaxy_interactor, history_id, job, use_path_paste=False, use_fetch_api=False)\n\nlib/galaxy_test/api/test_tools_upload.py:497:\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _\nlib/galaxy_test/base/populators.py:3181: in stage_inputs\n    return InteractorStaging(galaxy_interactor, use_fetch_api=use_fetch_api).stage(\nlib/galaxy/tool_util/client/staging.py:264: in stage\n    return galactic_job_json(\nlib/galaxy/tool_util/cwl/util.py:392: in galactic_job_json\n    replace_keys[key] = replacement_item(value)\nlib/galaxy/tool_util/cwl/util.py:220: in replacement_item\n    return replacement_file(value)\nlib/galaxy/tool_util/cwl/util.py:251: in replacement_file\n    rval_c = upload_file_with_composite_data(None, composite_data, filetype=filetype, **kwd)\nlib/galaxy/tool_util/cwl/util.py:190: in upload_file_with_composite_data\n    return response_to_hda(target, upload_response)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _\n\ntarget = <galaxy.tool_util.cwl.util.FileUploadTarget object at 0x7f30044f61c0>\nupload_response = {'implicit_collections': [], 'jobs': [{'create_time': '2024-04-02T13:19:27.579575', 'exit_code': None, 'galaxy_version...ats': ['http://edamontology.org/format_1915'], 'data_type': 'galaxy.datatypes.data.Data', 'deleted': False, ...}], ...}\n\n    def response_to_hda(target: UploadTarget, upload_response: Dict[str, Any]) -> Dict[str, str]:\n>       dataset = next(iter(upload_response[\"outputs\"].values()))\nE       AttributeError: 'list' object has no attribute 'values'\n\nlib/galaxy/tool_util/cwl/util.py:160: AttributeError\n```","shortMessageHtmlLink":"Fix <code>test_composite_datatype_stage_upload1</code> test"}},{"before":"707b31b0591771f8827a6b2061a1ba6628f429de","after":null,"ref":"refs/heads/h5py_and_typos","pushedAt":"2024-06-27T13:27:17.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"mr-c","name":"Michael R. 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\"class\": \"File\",\n                \"format\": \"velvet\",\n                \"composite_data\": [\n                    \"test-data/simple_line.txt\",\n                    \"test-data/simple_line_alternative.txt\",\n                    \"test-data/simple_line_x2.txt\",\n                ],\n            }\n        }\n>       stage_inputs(self.galaxy_interactor, history_id, job, use_path_paste=False, use_fetch_api=False)\n\nlib/galaxy_test/api/test_tools_upload.py:497:\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _\nlib/galaxy_test/base/populators.py:3181: in stage_inputs\n    return InteractorStaging(galaxy_interactor, use_fetch_api=use_fetch_api).stage(\nlib/galaxy/tool_util/client/staging.py:264: in stage\n    return galactic_job_json(\nlib/galaxy/tool_util/cwl/util.py:392: in galactic_job_json\n    replace_keys[key] = replacement_item(value)\nlib/galaxy/tool_util/cwl/util.py:220: in replacement_item\n    return replacement_file(value)\nlib/galaxy/tool_util/cwl/util.py:251: in replacement_file\n    rval_c = upload_file_with_composite_data(None, composite_data, filetype=filetype, **kwd)\nlib/galaxy/tool_util/cwl/util.py:190: in upload_file_with_composite_data\n    return response_to_hda(target, upload_response)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _\n\ntarget = <galaxy.tool_util.cwl.util.FileUploadTarget object at 0x7f30044f61c0>\nupload_response = {'implicit_collections': [], 'jobs': [{'create_time': '2024-04-02T13:19:27.579575', 'exit_code': None, 'galaxy_version...ats': ['http://edamontology.org/format_1915'], 'data_type': 'galaxy.datatypes.data.Data', 'deleted': False, ...}], ...}\n\n    def response_to_hda(target: UploadTarget, upload_response: Dict[str, Any]) -> Dict[str, str]:\n>       dataset = next(iter(upload_response[\"outputs\"].values()))\nE       AttributeError: 'list' object has no attribute 'values'\n\nlib/galaxy/tool_util/cwl/util.py:160: AttributeError\n```","shortMessageHtmlLink":"Fix <code>test_composite_datatype_stage_upload1</code> test"}},{"before":"31b4746f6300159cb30326292f62a3b9a3368aa6","after":"58a1c4c58ef20d5ae0ea597ec3c5ed004100d78f","ref":"refs/heads/cwl-1.0","pushedAt":"2024-04-02T13:05:15.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"nsoranzo","name":"Nicola Soranzo","path":"/nsoranzo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4924623?s=80&v=4"},"commit":{"message":"Fix directory unpacking","shortMessageHtmlLink":"Fix directory unpacking"}},{"before":"7dd1002631396c42fd07016af8b039501844808a","after":"31b4746f6300159cb30326292f62a3b9a3368aa6","ref":"refs/heads/cwl-1.0","pushedAt":"2024-03-06T19:04:11.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"nsoranzo","name":"Nicola 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