diff --git a/cwl/grepsort/greptool.cwl b/cwl/grepsort/greptool.cwl index 04fff08..e94fdab 100644 --- a/cwl/grepsort/greptool.cwl +++ b/cwl/grepsort/greptool.cwl @@ -1,6 +1,10 @@ class: CommandLineTool cwlVersion: v1.0 +hints: + - class: ResourceRequirement + ramMin: 64 + baseCommand: ["bash", "-c"] inputs: diff --git a/src/runcrate/convert.py b/src/runcrate/convert.py index 0dd842b..164ae6b 100644 --- a/src/runcrate/convert.py +++ b/src/runcrate/convert.py @@ -341,6 +341,13 @@ def add_tool(self, crate, workflow, cwl_tool): properties["@type"] = ["SoftwareSourceCode", "ComputationalWorkflow", "HowTo"] else: properties["@type"] = "SoftwareApplication" + if hasattr(cwl_tool, "hints") and cwl_tool.hints: + hints_map = {_["class"]: _ for _ in cwl_tool.hints} + rreq = hints_map.get("ResourceRequirement") + if rreq: + ramMin = rreq.get("ramMin") + if ramMin: + properties["memoryRequirements"] = f"{int(ramMin)} MiB" tool = crate.add(ContextEntity(crate, tool_id, properties=properties)) tool["input"] = self.add_params(crate, cwl_tool.inputs) tool["output"] = self.add_params(crate, cwl_tool.outputs) diff --git a/tests/data/grepsort-run-1/bag-info.txt b/tests/data/grepsort-run-1/bag-info.txt index 467ebfe..2646bc9 100644 --- a/tests/data/grepsort-run-1/bag-info.txt +++ b/tests/data/grepsort-run-1/bag-info.txt @@ -1,6 +1,6 @@ -Bag-Software-Agent: cwltool 3.1.20220802125926 +Bag-Software-Agent: cwltool 3.1.20230425144158 BagIt-Profile-Identifier: https://w3id.org/ro/bagit/profile -Bagging-Date: 2022-12-09 +Bagging-Date: 2023-05-11 External-Description: Research Object of CWL workflow run -External-Identifier: arcp://uuid,e442628c-e95b-48f5-b5c2-ae2f266a7fbe/ +External-Identifier: arcp://uuid,a59b2ee0-e2cf-4f8c-b6ed-193fb588c154/ Payload-Oxum: 192.4 diff --git a/tests/data/grepsort-run-1/metadata/logs/engine.c8915798-6b30-42c9-a29f-83ad8866310d.txt b/tests/data/grepsort-run-1/metadata/logs/engine.c8915798-6b30-42c9-a29f-83ad8866310d.txt deleted file mode 100644 index 734d298..0000000 --- a/tests/data/grepsort-run-1/metadata/logs/engine.c8915798-6b30-42c9-a29f-83ad8866310d.txt +++ /dev/null @@ -1,20 +0,0 @@ -[2022-12-09T13:57:45,145.927668Z] [cwltool] /home/simleo/git/runcrate/venv/bin/cwltool --provenance ro grepsort.cwl params.yml -[2022-12-09T13:57:45,147.553682Z] Resolved 'grepsort.cwl' to 'file:///home/simleo/sandbox/try_cwl/secondaryfiles_wf/grepsort.cwl' -[2022-12-09T13:57:45,744.498253Z] [provenance] Adding to RO file:///home/simleo/sandbox/try_cwl/secondaryfiles_wf/lines.txt -[2022-12-09T13:57:45,745.075941Z] [provenance] Adding to RO file:///home/simleo/sandbox/try_cwl/secondaryfiles_wf/lines.aux -[2022-12-09T13:57:45,746.627569Z] [workflow ] start -[2022-12-09T13:57:45,746.865988Z] [workflow ] starting step grep -[2022-12-09T13:57:45,747.010708Z] [step grep] start -[2022-12-09T13:57:45,749.337673Z] [job grep] /tmp/a2mr5sql$ bash \ - -c \ - 'grep -f /tmp/g3mho05k/stg172cfbf3-036f-46b5-ad87-7a3c8559c751/lines.aux /tmp/g3mho05k/stg172cfbf3-036f-46b5-ad87-7a3c8559c751/lines.txt >grep_out.txt' -[2022-12-09T13:57:45,756.167650Z] [job grep] completed success -[2022-12-09T13:57:45,756.421804Z] [step grep] completed success -[2022-12-09T13:57:45,756.950855Z] [workflow ] starting step sorted -[2022-12-09T13:57:45,757.264614Z] [step sorted] start -[2022-12-09T13:57:45,759.635210Z] [job sorted] /tmp/40aw38sy$ sort \ - /tmp/sylqrrh1/stg3b3e37fb-c003-4c65-8685-850bc5c8a939/grep_out.txt > /tmp/40aw38sy/sort_out.txt -[2022-12-09T13:57:45,765.366316Z] [job sorted] completed success -[2022-12-09T13:57:45,765.622616Z] [step sorted] completed success -[2022-12-09T13:57:45,765.789509Z] [workflow ] completed success -[2022-12-09T13:57:45,818.056822Z] Final process status is success diff --git a/tests/data/grepsort-run-1/metadata/logs/engine.f66f5014-d8d8-4544-bc78-ab0ac7cb1e36.txt b/tests/data/grepsort-run-1/metadata/logs/engine.f66f5014-d8d8-4544-bc78-ab0ac7cb1e36.txt new file mode 100644 index 0000000..1ac695d --- /dev/null +++ b/tests/data/grepsort-run-1/metadata/logs/engine.f66f5014-d8d8-4544-bc78-ab0ac7cb1e36.txt @@ -0,0 +1,20 @@ +[2023-05-11T12:54:09,213.033438Z] [cwltool] /tmp/venv/bin/cwltool --provenance ro grepsort.cwl params.yml +[2023-05-11T12:54:09,214.917898Z] Resolved 'grepsort.cwl' to 'file:///home/simleo/git/runcrate/cwl/grepsort/grepsort.cwl' +[2023-05-11T12:54:09,810.973883Z] [provenance] Adding to RO file:///home/simleo/git/runcrate/cwl/grepsort/lines.txt +[2023-05-11T12:54:09,811.661243Z] [provenance] Adding to RO file:///home/simleo/git/runcrate/cwl/grepsort/lines.aux +[2023-05-11T12:54:09,814.031839Z] [workflow ] start +[2023-05-11T12:54:09,814.396143Z] [workflow ] starting step grep +[2023-05-11T12:54:09,814.627886Z] [step grep] start +[2023-05-11T12:54:09,817.400694Z] [job grep] /tmp/_i2f82au$ bash \ + -c \ + 'grep -f /tmp/26d8jeyl/stgc839385b-f723-4ab7-a7bc-a8c62ddb6ed7/lines.aux /tmp/26d8jeyl/stgc839385b-f723-4ab7-a7bc-a8c62ddb6ed7/lines.txt >grep_out.txt' +[2023-05-11T12:54:09,825.176477Z] [job grep] completed success +[2023-05-11T12:54:09,825.467348Z] [step grep] completed success +[2023-05-11T12:54:09,825.929165Z] [workflow ] starting step sorted +[2023-05-11T12:54:09,826.179743Z] [step sorted] start +[2023-05-11T12:54:09,828.734159Z] [job sorted] /tmp/0yah5kc_$ sort \ + /tmp/e1qxjn80/stgf144cefc-21a6-4547-a687-9617dde38166/grep_out.txt > /tmp/0yah5kc_/sort_out.txt +[2023-05-11T12:54:09,834.231853Z] [job sorted] completed success +[2023-05-11T12:54:09,834.487200Z] [step sorted] completed success +[2023-05-11T12:54:09,834.689617Z] [workflow ] completed success +[2023-05-11T12:54:09,899.184704Z] Final process status is success diff --git a/tests/data/grepsort-run-1/metadata/manifest.json b/tests/data/grepsort-run-1/metadata/manifest.json index 7593a5b..cfbdc6d 100644 --- a/tests/data/grepsort-run-1/metadata/manifest.json +++ b/tests/data/grepsort-run-1/metadata/manifest.json @@ -1,24 +1,24 @@ { "@context": [ { - "@base": 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+ }, + { + "uri": "urn:uuid:929dfcb7-37af-4e41-863f-a9bf80555239", + "createdOn": "2023-05-11T14:54:09.813935", "createdBy": { - "uri": "urn:uuid:c8915798-6b30-42c9-a29f-83ad8866310d", - "name": "cwltool 3.1.20220802125926" + "uri": "urn:uuid:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36", + "name": "cwltool 3.1.20230425144158" } }, { - "uri": "urn:uuid:fd907908-a40c-472c-b479-dfc7f61b0f65", - "createdOn": "2022-12-09T14:57:45.759832", + "uri": "urn:uuid:600e9be9-eaea-4dbc-9948-b0bf01481b0a", + "createdOn": "2023-05-11T14:54:09.829044", "createdBy": { - "uri": "urn:uuid:c8915798-6b30-42c9-a29f-83ad8866310d", - "name": "cwltool 3.1.20220802125926" + "uri": "urn:uuid:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36", + "name": "cwltool 3.1.20230425144158" } } ], "annotations": [ { - "uri": "urn:uuid:c4d0f086-bef0-408e-878b-3d8cb9db8372", - "about": "urn:uuid:e442628c-e95b-48f5-b5c2-ae2f266a7fbe", + "uri": "urn:uuid:f221346f-3fdc-4a15-a6ee-c2297e88bf3a", + "about": "urn:uuid:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154", "content": "/", "oa:motivatedBy": { "@id": "oa:describing" } }, { - "uri": "urn:uuid:8ad2918c-f3ab-426c-bfbc-c76a9b678470", - "about": "urn:uuid:e442628c-e95b-48f5-b5c2-ae2f266a7fbe", + "uri": "urn:uuid:242a7028-e069-494c-a6ee-0b57fc7f9d1f", + "about": "urn:uuid:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154", "content": [ - "provenance/primary.cwlprov.provn", - "provenance/primary.cwlprov.xml", - "provenance/primary.cwlprov.json", "provenance/primary.cwlprov.ttl", + "provenance/primary.cwlprov.json", + "provenance/primary.cwlprov.xml", "provenance/primary.cwlprov.jsonld", - "provenance/primary.cwlprov.nt" + "provenance/primary.cwlprov.nt", + "provenance/primary.cwlprov.provn" ], "oa:motivatedBy": { "@id": "http://www.w3.org/ns/prov#has_provenance" } }, { - "uri": "urn:uuid:ad890a55-99cd-4c75-b448-6b13e36d8b2c", + "uri": "urn:uuid:b81c95ab-65d4-41bc-b548-2159d8eafc31", "about": "../workflow/packed.cwl", "content": null, "oa:motivatedBy": { @@ -236,8 +236,8 @@ } }, { - "uri": "urn:uuid:da9a55af-566a-474a-b63f-d37229cdd44c", - "about": "urn:uuid:e442628c-e95b-48f5-b5c2-ae2f266a7fbe", + "uri": "urn:uuid:7a08b1d3-71ea-406e-af0f-8a92f53579f9", + "about": "urn:uuid:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154", "content": [ "../workflow/packed.cwl", "../workflow/primary-job.json" @@ -247,10 +247,10 @@ } }, { - "uri": "urn:uuid:fbbe272d-8f48-43f7-acb8-d2640e8bc762", - "about": "urn:uuid:c8915798-6b30-42c9-a29f-83ad8866310d", + "uri": "urn:uuid:6f65e1ed-b496-46f8-a2b8-77abfe16e2b0", + "about": "urn:uuid:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36", "content": [ - "metadata/logs/engine.c8915798-6b30-42c9-a29f-83ad8866310d.txt" + "metadata/logs/engine.f66f5014-d8d8-4544-bc78-ab0ac7cb1e36.txt" ], "oa:motivatedBy": { "@id": "https://w3id.org/cwl/prov#log" diff --git a/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.json b/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.json index 09c91cf..132842b 100644 --- a/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.json +++ b/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.json @@ -9,68 +9,68 @@ "id": "urn:uuid:", "data": "urn:hash::sha1:", "sha256": "nih:sha-256;", - "researchobject": "arcp://uuid,e442628c-e95b-48f5-b5c2-ae2f266a7fbe/", - "metadata": "arcp://uuid,e442628c-e95b-48f5-b5c2-ae2f266a7fbe/metadata/", - "provenance": "arcp://uuid,e442628c-e95b-48f5-b5c2-ae2f266a7fbe/metadata/provenance/", - "wf": "arcp://uuid,e442628c-e95b-48f5-b5c2-ae2f266a7fbe/workflow/packed.cwl#", - "input": "arcp://uuid,e442628c-e95b-48f5-b5c2-ae2f266a7fbe/workflow/primary-job.json#", + "researchobject": "arcp://uuid,a59b2ee0-e2cf-4f8c-b6ed-193fb588c154/", + "metadata": "arcp://uuid,a59b2ee0-e2cf-4f8c-b6ed-193fb588c154/metadata/", + "provenance": "arcp://uuid,a59b2ee0-e2cf-4f8c-b6ed-193fb588c154/metadata/provenance/", + "wf": "arcp://uuid,a59b2ee0-e2cf-4f8c-b6ed-193fb588c154/workflow/packed.cwl#", + "input": "arcp://uuid,a59b2ee0-e2cf-4f8c-b6ed-193fb588c154/workflow/primary-job.json#", "wf4ever": "http://purl.org/wf4ever/wf4ever#" }, "agent": { - "id:dbc054dc-3fde-4ae4-9812-f92df6589666": {}, - "id:c8915798-6b30-42c9-a29f-83ad8866310d": { + "id:07bc4dab-678d-4290-b119-363995f3d4ac": {}, + "id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36": { "prov:type": [ { - "$": "prov:SoftwareAgent", + "$": "wfprov:WorkflowEngine", "type": "prov:QUALIFIED_NAME" }, { - "$": "wfprov:WorkflowEngine", + "$": "prov:SoftwareAgent", "type": "prov:QUALIFIED_NAME" } ], - "prov:label": "cwltool 3.1.20220802125926" + "prov:label": "cwltool 3.1.20230425144158" } }, "wasStartedBy": { "_:id1": { - "prov:activity": "id:c8915798-6b30-42c9-a29f-83ad8866310d", - "prov:starter": "id:dbc054dc-3fde-4ae4-9812-f92df6589666", - "prov:time": "2022-12-09T14:57:45.717548" + "prov:activity": "id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36", + "prov:starter": "id:07bc4dab-678d-4290-b119-363995f3d4ac", + "prov:time": "2023-05-11T14:54:09.781736" }, "_:id3": { - "prov:activity": "id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe", - "prov:starter": "id:c8915798-6b30-42c9-a29f-83ad8866310d", - "prov:time": "2022-12-09T14:57:45.717640" + "prov:activity": "id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154", + "prov:starter": "id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36", + "prov:time": "2023-05-11T14:54:09.781827" }, "_:id8": { - "prov:activity": "id:15826194-2534-4654-924a-55386c53db47", - "prov:starter": "id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe", - "prov:time": "2022-12-09T14:57:45.748935" + "prov:activity": "id:4d7e2fbb-89c6-4575-8005-336cc021766b", + "prov:starter": "id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154", + "prov:time": "2023-05-11T14:54:09.816978" }, "_:id17": { - "prov:activity": "id:230af7c3-a8e0-4b20-ae98-925868e3c332", - "prov:starter": "id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe", - "prov:time": "2022-12-09T14:57:45.759218" + "prov:activity": "id:ba7a4132-7149-484b-b29b-3f5716e6ef5f", + "prov:starter": "id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154", + "prov:time": "2023-05-11T14:54:09.828159" } }, "activity": { - "id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe": { - "prov:startTime": "2022-12-09T14:57:45.717577", + "id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154": { + "prov:startTime": "2023-05-11T14:54:09.781765", "prov:type": { "$": "wfprov:WorkflowRun", "type": "prov:QUALIFIED_NAME" }, "prov:label": "Run of workflow/packed.cwl#main" }, - "id:15826194-2534-4654-924a-55386c53db47": { + "id:4d7e2fbb-89c6-4575-8005-336cc021766b": { "prov:type": { "$": "wfprov:ProcessRun", "type": "prov:QUALIFIED_NAME" }, "prov:label": "Run of workflow/packed.cwl#main/grep" }, - "id:230af7c3-a8e0-4b20-ae98-925868e3c332": { + "id:ba7a4132-7149-484b-b29b-3f5716e6ef5f": { "prov:type": { "$": "wfprov:ProcessRun", "type": "prov:QUALIFIED_NAME" @@ -80,18 +80,18 @@ }, "wasAssociatedWith": { "_:id2": { - "prov:activity": "id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe", - "prov:agent": "id:c8915798-6b30-42c9-a29f-83ad8866310d", + "prov:activity": "id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154", + "prov:agent": "id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36", "prov:plan": "wf:main" }, "_:id7": { - "prov:activity": "id:15826194-2534-4654-924a-55386c53db47", - "prov:agent": "id:c8915798-6b30-42c9-a29f-83ad8866310d", + "prov:activity": "id:4d7e2fbb-89c6-4575-8005-336cc021766b", + "prov:agent": "id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36", "prov:plan": "wf:main/grep" }, "_:id16": { - "prov:activity": "id:230af7c3-a8e0-4b20-ae98-925868e3c332", - "prov:agent": "id:c8915798-6b30-42c9-a29f-83ad8866310d", + "prov:activity": "id:ba7a4132-7149-484b-b29b-3f5716e6ef5f", + "prov:agent": "id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36", "prov:plan": "wf:main/sorted" } }, @@ -112,39 +112,39 @@ }, { "wfdesc:hasSubProcess": { - "$": "wf:main/sorted", + "$": "wf:main/grep", "type": "prov:QUALIFIED_NAME" }, "prov:label": "Prospective provenance" }, { "wfdesc:hasSubProcess": { - "$": "wf:main/grep", + "$": "wf:main/sorted", "type": "prov:QUALIFIED_NAME" }, "prov:label": "Prospective provenance" } ], - "wf:main/sorted": { + "wf:main/grep": { "prov:type": [ { - "$": "wfdesc:Process", + "$": "prov:Plan", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Plan", + "$": "wfdesc:Process", "type": "prov:QUALIFIED_NAME" } ] }, - "wf:main/grep": { + "wf:main/sorted": { "prov:type": [ { - "$": "wfdesc:Process", + "$": "prov:Plan", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Plan", + "$": "wfdesc:Process", "type": "prov:QUALIFIED_NAME" } ] @@ -163,7 +163,7 @@ } } ], - "id:5790fe8b-da2b-4e87-9a73-2eff75d27e50": { + "id:fc5f1254-379c-45b1-8f2c-3acfe0d52067": { "prov:type": [ { "$": "wfprov:Artifact", @@ -178,10 +178,10 @@ "cwlprov:nameroot": "lines", "cwlprov:nameext": ".txt" }, - "id:6751988b-0f91-4271-8c79-d4c06b599ffe": { + "id:929dfcb7-37af-4e41-863f-a9bf80555239": { "prov:value": false }, - "id:79847ff5-502b-4795-8204-11dffb82044e": { + "id:f420bbdc-3c19-4b07-8762-38fd82178c48": { "prov:type": [ { "$": "wfprov:Artifact", @@ -202,7 +202,7 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:7498296b-d276-46b9-abf4-013068cc82b0": { + "id:f8a3035b-7d0f-4695-88be-b21554668854": { "prov:type": [ { "$": "wfprov:Artifact", @@ -223,7 +223,7 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:afadeff0-99ee-4574-bde1-d2585ee5701a": { + "id:72844ffc-c823-4466-bf31-af3a13c6efdc": { "prov:type": [ { "$": "wfprov:Artifact", @@ -238,7 +238,7 @@ "cwlprov:nameroot": "grep_out", "cwlprov:nameext": ".txt" }, - "id:fd907908-a40c-472c-b479-dfc7f61b0f65": { + "id:600e9be9-eaea-4dbc-9948-b0bf01481b0a": { "prov:value": false }, "data:8292d6f0985a62d4abd624fc72aecb8132193d6e": { @@ -247,7 +247,7 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:a41171df-a9d0-4f5f-8179-be34451bda0e": { + "id:b59b8a30-d974-4703-96b0-cc2b9a47bbf1": { "prov:type": [ { "$": "wfprov:Artifact", @@ -265,67 +265,67 @@ }, "specializationOf": { "_:id4": { - "prov:specificEntity": "id:5790fe8b-da2b-4e87-9a73-2eff75d27e50", + "prov:specificEntity": "id:fc5f1254-379c-45b1-8f2c-3acfe0d52067", "prov:generalEntity": "data:b64565ee76fcd5296c48314f858f8e4672c71439" }, "_:id9": { - "prov:specificEntity": "id:79847ff5-502b-4795-8204-11dffb82044e", + "prov:specificEntity": "id:f420bbdc-3c19-4b07-8762-38fd82178c48", "prov:generalEntity": "data:b64565ee76fcd5296c48314f858f8e4672c71439" }, "_:id10": { - "prov:specificEntity": "id:7498296b-d276-46b9-abf4-013068cc82b0", + "prov:specificEntity": "id:f8a3035b-7d0f-4695-88be-b21554668854", "prov:generalEntity": "data:c708d7ef841f7e1748436b8ef5670d0b2de1a227" }, "_:id13": { - "prov:specificEntity": "id:afadeff0-99ee-4574-bde1-d2585ee5701a", + "prov:specificEntity": "id:72844ffc-c823-4466-bf31-af3a13c6efdc", "prov:generalEntity": "data:601203afd61ae8b19d9c639d8d16296c9039d9cc" }, "_:id20": { - "prov:specificEntity": "id:a41171df-a9d0-4f5f-8179-be34451bda0e", + "prov:specificEntity": "id:b59b8a30-d974-4703-96b0-cc2b9a47bbf1", "prov:generalEntity": "data:8292d6f0985a62d4abd624fc72aecb8132193d6e" } }, "used": { "_:id5": { - "prov:activity": "id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe", - "prov:entity": "id:5790fe8b-da2b-4e87-9a73-2eff75d27e50", - "prov:time": "2022-12-09T14:57:45.746490", + "prov:activity": "id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154", + "prov:entity": "id:fc5f1254-379c-45b1-8f2c-3acfe0d52067", + "prov:time": "2023-05-11T14:54:09.813821", "prov:role": { "$": "wf:main/grepsort_in", "type": "prov:QUALIFIED_NAME" } }, "_:id6": { - "prov:activity": "id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe", - "prov:entity": "id:6751988b-0f91-4271-8c79-d4c06b599ffe", - "prov:time": "2022-12-09T14:57:45.746575", + "prov:activity": "id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154", + "prov:entity": "id:929dfcb7-37af-4e41-863f-a9bf80555239", + "prov:time": "2023-05-11T14:54:09.813943", "prov:role": { "$": "wf:main/reverse_sort", "type": "prov:QUALIFIED_NAME" } }, "_:id12": { - "prov:activity": "id:15826194-2534-4654-924a-55386c53db47", - "prov:entity": "id:79847ff5-502b-4795-8204-11dffb82044e", - "prov:time": "2022-12-09T14:57:45.750152", + "prov:activity": "id:4d7e2fbb-89c6-4575-8005-336cc021766b", + "prov:entity": "id:f420bbdc-3c19-4b07-8762-38fd82178c48", + "prov:time": "2023-05-11T14:54:09.818401", "prov:role": { "$": "wf:main/grep/grep_in", "type": "prov:QUALIFIED_NAME" } }, "_:id18": { - "prov:activity": "id:230af7c3-a8e0-4b20-ae98-925868e3c332", - "prov:entity": "id:fd907908-a40c-472c-b479-dfc7f61b0f65", - "prov:time": "2022-12-09T14:57:45.759848", + "prov:activity": "id:ba7a4132-7149-484b-b29b-3f5716e6ef5f", + "prov:entity": "id:600e9be9-eaea-4dbc-9948-b0bf01481b0a", + "prov:time": "2023-05-11T14:54:09.829063", "prov:role": { "$": "wf:main/sorted/reverse", "type": "prov:QUALIFIED_NAME" } }, "_:id19": { - "prov:activity": "id:230af7c3-a8e0-4b20-ae98-925868e3c332", - "prov:entity": "id:afadeff0-99ee-4574-bde1-d2585ee5701a", - "prov:time": "2022-12-09T14:57:45.759940", + "prov:activity": "id:ba7a4132-7149-484b-b29b-3f5716e6ef5f", + "prov:entity": "id:72844ffc-c823-4466-bf31-af3a13c6efdc", + "prov:time": "2023-05-11T14:54:09.829169", "prov:role": { "$": "wf:main/sorted/sort_in", "type": "prov:QUALIFIED_NAME" @@ -334,8 +334,8 @@ }, "wasDerivedFrom": { "_:id11": { - "prov:generatedEntity": "id:7498296b-d276-46b9-abf4-013068cc82b0", - "prov:usedEntity": "id:79847ff5-502b-4795-8204-11dffb82044e", + "prov:generatedEntity": "id:f8a3035b-7d0f-4695-88be-b21554668854", + "prov:usedEntity": "id:f420bbdc-3c19-4b07-8762-38fd82178c48", "prov:type": { "$": "cwlprov:SecondaryFile", "type": "prov:QUALIFIED_NAME" @@ -344,27 +344,27 @@ }, "wasGeneratedBy": { "_:id14": { - "prov:entity": "id:afadeff0-99ee-4574-bde1-d2585ee5701a", - "prov:activity": "id:15826194-2534-4654-924a-55386c53db47", - "prov:time": "2022-12-09T14:57:45.755224", + "prov:entity": "id:72844ffc-c823-4466-bf31-af3a13c6efdc", + "prov:activity": "id:4d7e2fbb-89c6-4575-8005-336cc021766b", + "prov:time": "2023-05-11T14:54:09.824121", "prov:role": { "$": "wf:main/grep/grep_out", "type": "prov:QUALIFIED_NAME" } }, "_:id21": { - "prov:entity": "id:a41171df-a9d0-4f5f-8179-be34451bda0e", - "prov:activity": "id:230af7c3-a8e0-4b20-ae98-925868e3c332", - "prov:time": "2022-12-09T14:57:45.764426", + "prov:entity": "id:b59b8a30-d974-4703-96b0-cc2b9a47bbf1", + "prov:activity": "id:ba7a4132-7149-484b-b29b-3f5716e6ef5f", + "prov:time": "2023-05-11T14:54:09.833103", "prov:role": { "$": "wf:main/sorted/sort_out", "type": "prov:QUALIFIED_NAME" } }, "_:id23": { - "prov:entity": "id:a41171df-a9d0-4f5f-8179-be34451bda0e", - "prov:activity": "id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe", - "prov:time": "2022-12-09T14:57:45.766778", + "prov:entity": "id:b59b8a30-d974-4703-96b0-cc2b9a47bbf1", + "prov:activity": "id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154", + "prov:time": "2023-05-11T14:54:09.835606", "prov:role": { "$": "wf:main/primary/grepsort_out", "type": "prov:QUALIFIED_NAME" @@ -373,19 +373,19 @@ }, "wasEndedBy": { "_:id15": { - "prov:activity": "id:15826194-2534-4654-924a-55386c53db47", - "prov:ender": "id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe", - "prov:time": "2022-12-09T14:57:45.755214" + "prov:activity": "id:4d7e2fbb-89c6-4575-8005-336cc021766b", + "prov:ender": "id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154", + "prov:time": "2023-05-11T14:54:09.824109" }, "_:id22": { - "prov:activity": "id:230af7c3-a8e0-4b20-ae98-925868e3c332", - "prov:ender": "id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe", - "prov:time": "2022-12-09T14:57:45.764417" + "prov:activity": "id:ba7a4132-7149-484b-b29b-3f5716e6ef5f", + "prov:ender": "id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154", + "prov:time": "2023-05-11T14:54:09.833094" }, "_:id24": { - "prov:activity": "id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe", - "prov:ender": "id:c8915798-6b30-42c9-a29f-83ad8866310d", - "prov:time": "2022-12-09T14:57:45.766852" + "prov:activity": "id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154", + "prov:ender": "id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36", + "prov:time": "2023-05-11T14:54:09.835672" } } } \ No newline at end of file diff --git a/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.jsonld b/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.jsonld index e07a473..0c4ea19 100644 --- a/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.jsonld +++ b/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.jsonld @@ -1,246 +1,214 @@ [ { - "@id": "urn:hash::sha1:c708d7ef841f7e1748436b8ef5670d0b2de1a227", + "@id": "arcp://uuid,a59b2ee0-e2cf-4f8c-b6ed-193fb588c154/workflow/packed.cwl#main/sorted", "@type": [ - "http://purl.org/wf4ever/wfprov#Artifact", + "http://www.w3.org/ns/prov#Plan", + "http://purl.org/wf4ever/wfdesc#Process", "http://www.w3.org/ns/prov#Entity" ] }, { - "@id": "urn:uuid:a41171df-a9d0-4f5f-8179-be34451bda0e", + "@id": "urn:uuid:ba7a4132-7149-484b-b29b-3f5716e6ef5f", "@type": [ - "http://www.w3.org/ns/prov#Entity", - "http://purl.org/wf4ever/wf4ever#File", - "http://purl.org/wf4ever/wfprov#Artifact" - ], - "http://www.w3.org/ns/prov#qualifiedGeneration": [ - { - "@id": "_:N24d2e3e83edd4f919a9facefae4820bf" - }, - { - "@id": "_:N15622c774c2949168017006fd14924bb" - } + "http://purl.org/wf4ever/wfprov#ProcessRun", + "http://www.w3.org/ns/prov#Activity" ], - "http://www.w3.org/ns/prov#specializationOf": [ + "http://www.w3.org/2000/01/rdf-schema#label": [ { - "@id": "urn:hash::sha1:8292d6f0985a62d4abd624fc72aecb8132193d6e" + "@value": "Run of workflow/packed.cwl#main/sorted" } ], - "https://w3id.org/cwl/prov#basename": [ + "http://www.w3.org/ns/prov#qualifiedAssociation": [ { - "@value": "sort_out.txt" + "@id": "_:N220a2b25f04b4826a6457ecf0e38d398" } ], - "https://w3id.org/cwl/prov#nameext": [ + "http://www.w3.org/ns/prov#qualifiedEnd": [ { - "@value": ".txt" + "@id": "_:N807269ad26584a8abb9fb9ad5adf9b3f" } ], - "https://w3id.org/cwl/prov#nameroot": [ + "http://www.w3.org/ns/prov#qualifiedStart": [ { - "@value": "sort_out" + "@id": "_:Nd1390f54ae38440b83cad086f09077ce" } - ] - }, - { - "@id": "_:N24d2e3e83edd4f919a9facefae4820bf", - "@type": [ - "http://www.w3.org/ns/prov#Generation" ], - "http://www.w3.org/ns/prov#activity": [ + "http://www.w3.org/ns/prov#qualifiedUsage": [ { - "@id": "urn:uuid:e442628c-e95b-48f5-b5c2-ae2f266a7fbe" - } - ], - "http://www.w3.org/ns/prov#atTime": [ + "@id": "_:N2b8929e37dfa4c22926eec9ee05bc170" + }, { - "@type": "http://www.w3.org/2001/XMLSchema#dateTime", - "@value": "2022-12-09T14:57:45.766778" + "@id": "_:Nb988851f37af4c6fa3c74394ccf443c8" } ], - "http://www.w3.org/ns/prov#hadRole": [ + "http://www.w3.org/ns/prov#wasAssociatedWith": [ { - "@id": "arcp://uuid,e442628c-e95b-48f5-b5c2-ae2f266a7fbe/workflow/packed.cwl#main/primary/grepsort_out" + "@id": "urn:uuid:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36" } ] }, { - "@id": "_:N15622c774c2949168017006fd14924bb", + "@id": "_:N220a2b25f04b4826a6457ecf0e38d398", "@type": [ - "http://www.w3.org/ns/prov#Generation" - ], - "http://www.w3.org/ns/prov#activity": [ - { - "@id": "urn:uuid:230af7c3-a8e0-4b20-ae98-925868e3c332" - } - ], - "http://www.w3.org/ns/prov#atTime": [ - { - "@type": "http://www.w3.org/2001/XMLSchema#dateTime", - "@value": "2022-12-09T14:57:45.764426" - } + "http://www.w3.org/ns/prov#Association" ], - "http://www.w3.org/ns/prov#hadRole": [ + "http://www.w3.org/ns/prov#hadPlan": [ { - "@id": "arcp://uuid,e442628c-e95b-48f5-b5c2-ae2f266a7fbe/workflow/packed.cwl#main/sorted/sort_out" + "@id": "arcp://uuid,a59b2ee0-e2cf-4f8c-b6ed-193fb588c154/workflow/packed.cwl#main/sorted" } ] }, { - "@id": "arcp://uuid,e442628c-e95b-48f5-b5c2-ae2f266a7fbe/workflow/packed.cwl#main/grep", - "@type": [ - "http://www.w3.org/ns/prov#Entity", - "http://purl.org/wf4ever/wfdesc#Process", - "http://www.w3.org/ns/prov#Plan" - ] - }, - { - "@id": "urn:uuid:dbc054dc-3fde-4ae4-9812-f92df6589666", + "@id": "_:Nd1390f54ae38440b83cad086f09077ce", "@type": [ - "http://www.w3.org/ns/prov#Agent" - ] - }, - { - "@id": "urn:uuid:c8915798-6b30-42c9-a29f-83ad8866310d", - "@type": [ - "http://www.w3.org/ns/prov#SoftwareAgent", - "http://purl.org/wf4ever/wfprov#WorkflowEngine", - "http://www.w3.org/ns/prov#Agent" + "http://www.w3.org/ns/prov#Start" ], - "http://www.w3.org/2000/01/rdf-schema#label": [ + "http://www.w3.org/ns/prov#atTime": [ { - "@value": "cwltool 3.1.20220802125926" + "@type": "http://www.w3.org/2001/XMLSchema#dateTime", + "@value": "2023-05-11T14:54:09.828159" } ], - "http://www.w3.org/ns/prov#qualifiedStart": [ + "http://www.w3.org/ns/prov#hadActivity": [ { - "@id": "_:Nc60d190e48804f1ca46c9438820ec391" + "@id": "urn:uuid:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154" } ] }, { - "@id": "_:Nc60d190e48804f1ca46c9438820ec391", + "@id": "_:N807269ad26584a8abb9fb9ad5adf9b3f", "@type": [ - "http://www.w3.org/ns/prov#Start" + "http://www.w3.org/ns/prov#End" ], "http://www.w3.org/ns/prov#atTime": [ { "@type": "http://www.w3.org/2001/XMLSchema#dateTime", - "@value": "2022-12-09T14:57:45.717548" + "@value": "2023-05-11T14:54:09.833094" } ], "http://www.w3.org/ns/prov#hadActivity": [ { - "@id": "urn:uuid:dbc054dc-3fde-4ae4-9812-f92df6589666" + "@id": "urn:uuid:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154" } ] }, { - "@id": "urn:uuid:15826194-2534-4654-924a-55386c53db47", + "@id": "_:N2b8929e37dfa4c22926eec9ee05bc170", "@type": [ - "http://www.w3.org/ns/prov#Activity", - "http://purl.org/wf4ever/wfprov#ProcessRun" + "http://www.w3.org/ns/prov#Usage" ], - "http://www.w3.org/2000/01/rdf-schema#label": [ + "http://www.w3.org/ns/prov#atTime": [ { - "@value": "Run of workflow/packed.cwl#main/grep" + "@type": "http://www.w3.org/2001/XMLSchema#dateTime", + "@value": "2023-05-11T14:54:09.829063" } ], - "http://www.w3.org/ns/prov#qualifiedAssociation": [ + "http://www.w3.org/ns/prov#entity": [ { - "@id": "_:N1b5d694b79344b73a6dce37849794d91" + "@id": "urn:uuid:600e9be9-eaea-4dbc-9948-b0bf01481b0a" } ], - "http://www.w3.org/ns/prov#qualifiedEnd": [ + "http://www.w3.org/ns/prov#hadRole": [ { - "@id": "_:N9e6eb88c80c74ba5bfc28b2dfdae2b37" + "@id": "arcp://uuid,a59b2ee0-e2cf-4f8c-b6ed-193fb588c154/workflow/packed.cwl#main/sorted/reverse" } + ] + }, + { + "@id": "_:Nb988851f37af4c6fa3c74394ccf443c8", + "@type": [ + "http://www.w3.org/ns/prov#Usage" ], - "http://www.w3.org/ns/prov#qualifiedStart": [ + "http://www.w3.org/ns/prov#atTime": [ { - "@id": "_:N8e8bc148c16a4c32b965fabb2f4aaa69" + "@type": "http://www.w3.org/2001/XMLSchema#dateTime", + "@value": "2023-05-11T14:54:09.829169" } ], - "http://www.w3.org/ns/prov#qualifiedUsage": [ + "http://www.w3.org/ns/prov#entity": [ { - "@id": "_:N380d6ffa500e463d8378a45821c53ffb" + "@id": "urn:uuid:72844ffc-c823-4466-bf31-af3a13c6efdc" } ], - "http://www.w3.org/ns/prov#wasAssociatedWith": [ + "http://www.w3.org/ns/prov#hadRole": [ { - "@id": "urn:uuid:c8915798-6b30-42c9-a29f-83ad8866310d" + "@id": "arcp://uuid,a59b2ee0-e2cf-4f8c-b6ed-193fb588c154/workflow/packed.cwl#main/sorted/sort_in" } ] }, { - "@id": "_:N9e6eb88c80c74ba5bfc28b2dfdae2b37", + "@id": "arcp://uuid,a59b2ee0-e2cf-4f8c-b6ed-193fb588c154/workflow/packed.cwl#main", "@type": [ - "http://www.w3.org/ns/prov#End" + "http://www.w3.org/ns/prov#Plan", + "http://www.w3.org/ns/prov#Entity", + "http://purl.org/wf4ever/wfdesc#Workflow" ], - "http://www.w3.org/ns/prov#atTime": [ + "http://purl.org/wf4ever/wfdesc#hasSubProcess": [ { - "@type": "http://www.w3.org/2001/XMLSchema#dateTime", - "@value": "2022-12-09T14:57:45.755214" + "@id": "arcp://uuid,a59b2ee0-e2cf-4f8c-b6ed-193fb588c154/workflow/packed.cwl#main/sorted" + }, + { + "@id": "arcp://uuid,a59b2ee0-e2cf-4f8c-b6ed-193fb588c154/workflow/packed.cwl#main/grep" } ], - "http://www.w3.org/ns/prov#hadActivity": [ + "http://www.w3.org/2000/01/rdf-schema#label": [ { - "@id": "urn:uuid:e442628c-e95b-48f5-b5c2-ae2f266a7fbe" + "@value": "Prospective provenance" } ] }, { - "@id": "_:N1b5d694b79344b73a6dce37849794d91", + "@id": "arcp://uuid,a59b2ee0-e2cf-4f8c-b6ed-193fb588c154/workflow/packed.cwl#main/grep", "@type": [ - "http://www.w3.org/ns/prov#Association" - ], - "http://www.w3.org/ns/prov#hadPlan": [ - { - "@id": "arcp://uuid,e442628c-e95b-48f5-b5c2-ae2f266a7fbe/workflow/packed.cwl#main/grep" - } + "http://www.w3.org/ns/prov#Plan", + "http://www.w3.org/ns/prov#Entity", + "http://purl.org/wf4ever/wfdesc#Process" ] }, { - "@id": "_:N8e8bc148c16a4c32b965fabb2f4aaa69", + "@id": "urn:hash::sha1:8292d6f0985a62d4abd624fc72aecb8132193d6e", "@type": [ - "http://www.w3.org/ns/prov#Start" + "http://purl.org/wf4ever/wfprov#Artifact", + "http://www.w3.org/ns/prov#Entity" + ] + }, + { + "@id": "urn:uuid:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36", + "@type": [ + "http://purl.org/wf4ever/wfprov#WorkflowEngine", + "http://www.w3.org/ns/prov#SoftwareAgent", + "http://www.w3.org/ns/prov#Agent" ], - "http://www.w3.org/ns/prov#atTime": [ + "http://www.w3.org/2000/01/rdf-schema#label": [ { - "@type": "http://www.w3.org/2001/XMLSchema#dateTime", - "@value": "2022-12-09T14:57:45.748935" + "@value": "cwltool 3.1.20230425144158" } ], - "http://www.w3.org/ns/prov#hadActivity": [ + "http://www.w3.org/ns/prov#qualifiedStart": [ { - "@id": "urn:uuid:e442628c-e95b-48f5-b5c2-ae2f266a7fbe" + "@id": "_:N23eb0ae665f14edf9bba1d4e485bfec3" } ] }, { - "@id": "_:N380d6ffa500e463d8378a45821c53ffb", + "@id": "_:N23eb0ae665f14edf9bba1d4e485bfec3", "@type": [ - "http://www.w3.org/ns/prov#Usage" + "http://www.w3.org/ns/prov#Start" ], "http://www.w3.org/ns/prov#atTime": [ { "@type": "http://www.w3.org/2001/XMLSchema#dateTime", - "@value": "2022-12-09T14:57:45.750152" + "@value": "2023-05-11T14:54:09.781736" } ], - "http://www.w3.org/ns/prov#entity": [ - { - "@id": "urn:uuid:79847ff5-502b-4795-8204-11dffb82044e" - } - ], - "http://www.w3.org/ns/prov#hadRole": [ + "http://www.w3.org/ns/prov#hadActivity": [ { - "@id": "arcp://uuid,e442628c-e95b-48f5-b5c2-ae2f266a7fbe/workflow/packed.cwl#main/grep/grep_in" + "@id": "urn:uuid:07bc4dab-678d-4290-b119-363995f3d4ac" } ] }, { - "@id": "urn:uuid:6751988b-0f91-4271-8c79-d4c06b599ffe", + "@id": "urn:uuid:929dfcb7-37af-4e41-863f-a9bf80555239", "@type": [ "http://www.w3.org/ns/prov#Entity" ], @@ -251,11 +219,11 @@ ] }, { - "@id": "urn:uuid:5790fe8b-da2b-4e87-9a73-2eff75d27e50", + "@id": "urn:uuid:f420bbdc-3c19-4b07-8762-38fd82178c48", "@type": [ - "http://purl.org/wf4ever/wf4ever#File", + "http://www.w3.org/ns/prov#Entity", "http://purl.org/wf4ever/wfprov#Artifact", - "http://www.w3.org/ns/prov#Entity" + "http://purl.org/wf4ever/wf4ever#File" ], "http://www.w3.org/ns/prov#specializationOf": [ { @@ -279,77 +247,125 @@ ] }, { - "@id": "urn:hash::sha1:8292d6f0985a62d4abd624fc72aecb8132193d6e", + "@id": "urn:hash::sha1:601203afd61ae8b19d9c639d8d16296c9039d9cc", "@type": [ "http://www.w3.org/ns/prov#Entity", "http://purl.org/wf4ever/wfprov#Artifact" ] }, { - "@id": "urn:uuid:7498296b-d276-46b9-abf4-013068cc82b0", + "@id": "urn:hash::sha1:b64565ee76fcd5296c48314f858f8e4672c71439", + "@type": [ + "http://purl.org/wf4ever/wfprov#Artifact", + "http://www.w3.org/ns/prov#Entity" + ] + }, + { + "@id": "urn:uuid:72844ffc-c823-4466-bf31-af3a13c6efdc", "@type": [ "http://purl.org/wf4ever/wfprov#Artifact", "http://purl.org/wf4ever/wf4ever#File", "http://www.w3.org/ns/prov#Entity" ], - "http://www.w3.org/ns/prov#qualifiedDerivation": [ + "http://www.w3.org/ns/prov#qualifiedGeneration": [ { - "@id": "_:Ne8d5364e4ba64e47826766477400937a" + "@id": "_:N8565765c9b0f4ce78cc8021dc67f5629" } ], "http://www.w3.org/ns/prov#specializationOf": [ { - "@id": "urn:hash::sha1:c708d7ef841f7e1748436b8ef5670d0b2de1a227" + "@id": "urn:hash::sha1:601203afd61ae8b19d9c639d8d16296c9039d9cc" } ], "https://w3id.org/cwl/prov#basename": [ { - "@value": "lines.aux" + "@value": "grep_out.txt" } ], "https://w3id.org/cwl/prov#nameext": [ { - "@value": ".aux" + "@value": ".txt" } ], "https://w3id.org/cwl/prov#nameroot": [ { - "@value": "lines" + "@value": "grep_out" } ] }, { - "@id": "_:Ne8d5364e4ba64e47826766477400937a", + "@id": "_:N8565765c9b0f4ce78cc8021dc67f5629", "@type": [ - "http://www.w3.org/ns/prov#Derivation", - "https://w3id.org/cwl/prov#SecondaryFile" + "http://www.w3.org/ns/prov#Generation" ], - "http://www.w3.org/ns/prov#entity": [ + "http://www.w3.org/ns/prov#activity": [ + { + "@id": "urn:uuid:4d7e2fbb-89c6-4575-8005-336cc021766b" + } + ], + "http://www.w3.org/ns/prov#atTime": [ + { + "@type": "http://www.w3.org/2001/XMLSchema#dateTime", + "@value": "2023-05-11T14:54:09.824121" + } + ], + "http://www.w3.org/ns/prov#hadRole": [ { - "@id": "urn:uuid:79847ff5-502b-4795-8204-11dffb82044e" + "@id": "arcp://uuid,a59b2ee0-e2cf-4f8c-b6ed-193fb588c154/workflow/packed.cwl#main/grep/grep_out" } ] }, { - "@id": "urn:uuid:afadeff0-99ee-4574-bde1-d2585ee5701a", + "@id": "urn:uuid:fc5f1254-379c-45b1-8f2c-3acfe0d52067", "@type": [ - "http://purl.org/wf4ever/wfprov#Artifact", + "http://purl.org/wf4ever/wf4ever#File", "http://www.w3.org/ns/prov#Entity", + 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} ] }, { - "@id": "_:N50d45cfd1b4c418a9e81bcd6a863abe5", + "@id": "_:N964273fe467349d3a4f2e4758007e4d5", "@type": [ - "http://www.w3.org/ns/prov#Start" - ], - "http://www.w3.org/ns/prov#atTime": [ - { - "@type": "http://www.w3.org/2001/XMLSchema#dateTime", - "@value": "2022-12-09T14:57:45.759218" - } + "http://www.w3.org/ns/prov#Association" ], - "http://www.w3.org/ns/prov#hadActivity": [ + "http://www.w3.org/ns/prov#hadPlan": [ { - "@id": "urn:uuid:e442628c-e95b-48f5-b5c2-ae2f266a7fbe" + "@id": "arcp://uuid,a59b2ee0-e2cf-4f8c-b6ed-193fb588c154/workflow/packed.cwl#main" } ] }, { - "@id": "_:N947f7d45f3fe43998ffea9f6aa65f91c", + "@id": "_:N737433e0937a4f1296899132a24aed8d", "@type": [ - "http://www.w3.org/ns/prov#Association" + "http://www.w3.org/ns/prov#End" ], - "http://www.w3.org/ns/prov#hadPlan": [ + "http://www.w3.org/ns/prov#atTime": [ + { + "@type": "http://www.w3.org/2001/XMLSchema#dateTime", + "@value": "2023-05-11T14:54:09.835672" + } + ], + "http://www.w3.org/ns/prov#hadActivity": [ { - "@id": "arcp://uuid,e442628c-e95b-48f5-b5c2-ae2f266a7fbe/workflow/packed.cwl#main/sorted" + "@id": "urn:uuid:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36" } ] } diff --git a/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.nt b/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.nt index 1108529..eedec98 100644 --- a/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.nt +++ b/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.nt @@ -1,158 +1,158 @@ - . -_:N05d866c14ba74df097bf98e3dab0f5cb "2022-12-09T14:57:45.759848"^^ . - _:N672738b03a5c406c9a8642bc13781231 . -_:N746c8a74ddd9432587676f611904abf2 . - "cwltool 3.1.20220802125926"^^ . - _:Ndef590de423148219c761479113feb1d . -_:Ndef590de423148219c761479113feb1d "2022-12-09T14:57:45.750152"^^ . -_:N05d866c14ba74df097bf98e3dab0f5cb . -_:Nb4afb78c9e1c48ec963f7d6ba2822230 . - "grep_out.txt"^^ . - . -_:N468aa8ac692c497d8ee6a38f55e5a987 . -_:N0ff17fb1fb0344a9a34d6282e1952849 . - "lines"^^ . -_:Ndef590de423148219c761479113feb1d . -_:N916706c36f2b4a1ea32bd2cfbc2b6785 . - _:N8c4c2134d57a45afbd6d7d3f1aaa5b8e . - _:N2e4195272d2b48b4b9dc89f2f67ef656 . -_:N8cf27afbb51043d3ac318f402cb9dc6f . -_:N5640eee8a6be464288acc6c273f390a7 . -_:N2834f478e02a45cbb8a8b110e003b0df . - . - _:N5e5b247c626e4b49b8cf6459492db593 . - "lines.txt"^^ . - "grep_out"^^ . - . - "2022-12-09T14:57:45.717577"^^ . -_:N8c4c2134d57a45afbd6d7d3f1aaa5b8e . -_:N2e4195272d2b48b4b9dc89f2f67ef656 . -_:N2834f478e02a45cbb8a8b110e003b0df . - . -_:Nbdfe68ba23e24bef8d27165ba5a2c960 . - . - . - . - . -_:N672738b03a5c406c9a8642bc13781231 "2022-12-09T14:57:45.755214"^^ . - "Prospective provenance"^^ . - _:Nd208c7a35d9f4996b88f6113ba20fb6c . - . - "false"^^ . - _:N5640eee8a6be464288acc6c273f390a7 . - . - _:N05d866c14ba74df097bf98e3dab0f5cb . -_:N507792325b884e169fb5e92ae7bae3c0 . - ".aux"^^ . - . - _:Nbdfe68ba23e24bef8d27165ba5a2c960 . -_:N746c8a74ddd9432587676f611904abf2 "2022-12-09T14:57:45.764417"^^ . - . -_:N51dcfa9322494ea1a49180d1a26af38a . -_:Nd208c7a35d9f4996b88f6113ba20fb6c . - . - . -_:N8c4c2134d57a45afbd6d7d3f1aaa5b8e . -_:N8cf27afbb51043d3ac318f402cb9dc6f "2022-12-09T14:57:45.717640"^^ . -_:N79a7be97a2b249b68d0ff77a4f7f1cd1 . - . - . - . - ".txt"^^ . - . -_:N507792325b884e169fb5e92ae7bae3c0 . - . -_:N2834f478e02a45cbb8a8b110e003b0df "2022-12-09T14:57:45.748935"^^ . - . -_:N0ff17fb1fb0344a9a34d6282e1952849 . - . - _:N8cf27afbb51043d3ac318f402cb9dc6f . - _:N746c8a74ddd9432587676f611904abf2 . - . - ".txt"^^ . - . - "sort_out.txt"^^ . - . -_:N5640eee8a6be464288acc6c273f390a7 "2022-12-09T14:57:45.746575"^^ . -_:Nd208c7a35d9f4996b88f6113ba20fb6c "2022-12-09T14:57:45.746490"^^ . -_:N51dcfa9322494ea1a49180d1a26af38a . -_:N672738b03a5c406c9a8642bc13781231 . - . - _:N916706c36f2b4a1ea32bd2cfbc2b6785 . - . - "sort_out"^^ . - . - . -_:Nd208c7a35d9f4996b88f6113ba20fb6c . - . +_:Naac30689366e4430a1908ccb3a252ba2 . +_:N54e41a97aa6f4e8a84ca71bb28943105 "2023-05-11T14:54:09.829169"^^ . . - . -_:N5640eee8a6be464288acc6c273f390a7 . - . - . - . -_:N916706c36f2b4a1ea32bd2cfbc2b6785 . -_:N0ff17fb1fb0344a9a34d6282e1952849 "2022-12-09T14:57:45.759940"^^ . -_:N2e4195272d2b48b4b9dc89f2f67ef656 "2022-12-09T14:57:45.717548"^^ . - _:N507792325b884e169fb5e92ae7bae3c0 . - "Run of workflow/packed.cwl#main"^^ . -_:N746c8a74ddd9432587676f611904abf2 . - . - "lines"^^ . - "lines.txt"^^ . -_:N468aa8ac692c497d8ee6a38f55e5a987 . -_:N5640eee8a6be464288acc6c273f390a7 . - . - . - . -_:N05d866c14ba74df097bf98e3dab0f5cb . -_:N79a7be97a2b249b68d0ff77a4f7f1cd1 . -_:N8c4c2134d57a45afbd6d7d3f1aaa5b8e "2022-12-09T14:57:45.766778"^^ . -_:Nbdfe68ba23e24bef8d27165ba5a2c960 . -_:N51dcfa9322494ea1a49180d1a26af38a . - _:N51dcfa9322494ea1a49180d1a26af38a . -_:N8c4c2134d57a45afbd6d7d3f1aaa5b8e . -_:Nb4afb78c9e1c48ec963f7d6ba2822230 . - "lines"^^ . - . - _:Nb4afb78c9e1c48ec963f7d6ba2822230 . - "Run of workflow/packed.cwl#main/sorted"^^ . -_:N5e5b247c626e4b49b8cf6459492db593 . + _:Nc6cdc1111319443080197f2eda15e287 . + . + . + _:N8b9966d12fc142f2a1061d0f33d09f97 . +_:N54e41a97aa6f4e8a84ca71bb28943105 . + . +_:N4e4e1579db974536a5089b2e2d34d07a . +_:N8b9966d12fc142f2a1061d0f33d09f97 "2023-05-11T14:54:09.818401"^^ . +_:Naac30689366e4430a1908ccb3a252ba2 . + . + . +_:Naf2d07ef96c642c7b7be3dc6efd0df6f "2023-05-11T14:54:09.824109"^^ . + "Run of workflow/packed.cwl#main/sorted"^^ . + . +_:N6180e2a4e7bd4e7d9a12f5278dd453da . + . + "false"^^ . . -_:N468aa8ac692c497d8ee6a38f55e5a987 . - . -_:Ndef590de423148219c761479113feb1d . - _:N0ff17fb1fb0344a9a34d6282e1952849 . - . - . - . - . - . -_:N5e5b247c626e4b49b8cf6459492db593 . - . - "Run of workflow/packed.cwl#main/grep"^^ . -_:N79a7be97a2b249b68d0ff77a4f7f1cd1 "2022-12-09T14:57:45.764426"^^ . - . - ".txt"^^ . -_:N05d866c14ba74df097bf98e3dab0f5cb . -_:N8cf27afbb51043d3ac318f402cb9dc6f . - . -_:N79a7be97a2b249b68d0ff77a4f7f1cd1 . - . - "lines.aux"^^ . -_:N672738b03a5c406c9a8642bc13781231 . - _:N468aa8ac692c497d8ee6a38f55e5a987 . - . - "false"^^ . - _:N2834f478e02a45cbb8a8b110e003b0df . -_:Nb4afb78c9e1c48ec963f7d6ba2822230 "2022-12-09T14:57:45.766852"^^ . - . -_:N5e5b247c626e4b49b8cf6459492db593 "2022-12-09T14:57:45.759218"^^ . -_:N2e4195272d2b48b4b9dc89f2f67ef656 . -_:N0ff17fb1fb0344a9a34d6282e1952849 . - ".txt"^^ . - . -_:N51dcfa9322494ea1a49180d1a26af38a "2022-12-09T14:57:45.755224"^^ . - _:N79a7be97a2b249b68d0ff77a4f7f1cd1 . -_:Nd208c7a35d9f4996b88f6113ba20fb6c . -_:Ndef590de423148219c761479113feb1d . + ".txt"^^ . + . + _:N9d020df8e6b74b96a48657590d929acc . + _:Nb75adf186f784e6b9d8db358069bbf87 . + . +_:N1baa303656244263bd7c429fd7ecb9b5 . + . + . + ".txt"^^ . + _:N6180e2a4e7bd4e7d9a12f5278dd453da . +_:N0d7a84a5be8c445d8a77d856e5e472ad . + . +_:Naac30689366e4430a1908ccb3a252ba2 . + . +_:N7601b25ea3904865a551e326d4e5c6f4 . +_:N9d020df8e6b74b96a48657590d929acc . + . + . +_:N153e9e08e7b2450c8ffc3444bf050d96 . + . +_:Nc6cdc1111319443080197f2eda15e287 . + . + . + _:N6415c2eed0204d0b894f7db3bb63225e . +_:N706c7b50ff0740009d6d44b3dacd8b50 . + . +_:N1baa303656244263bd7c429fd7ecb9b5 "2023-05-11T14:54:09.813821"^^ . + _:N54e41a97aa6f4e8a84ca71bb28943105 . + "lines"^^ . +_:N4e4e1579db974536a5089b2e2d34d07a . + . + . + . +_:Nc6cdc1111319443080197f2eda15e287 . +_:N706c7b50ff0740009d6d44b3dacd8b50 . + ".aux"^^ . + _:N3651e095cd8947df8b663ed2254c6a61 . + _:N7601b25ea3904865a551e326d4e5c6f4 . + "grep_out"^^ . +_:N4e4e1579db974536a5089b2e2d34d07a "2023-05-11T14:54:09.835606"^^ . +_:N4e4e1579db974536a5089b2e2d34d07a . +_:Nb75adf186f784e6b9d8db358069bbf87 . + . + . +_:N7601b25ea3904865a551e326d4e5c6f4 "2023-05-11T14:54:09.781736"^^ . + . +_:N6180e2a4e7bd4e7d9a12f5278dd453da . + . + . + "lines"^^ . +_:N7601b25ea3904865a551e326d4e5c6f4 . + . + _:N917e67b0692443bb88b955d98069ad45 . +_:N153e9e08e7b2450c8ffc3444bf050d96 "2023-05-11T14:54:09.824121"^^ . +_:N6415c2eed0204d0b894f7db3bb63225e . + . +_:N9d020df8e6b74b96a48657590d929acc . +_:Nb75adf186f784e6b9d8db358069bbf87 . + . +_:N854713727bfb4892a4ef6dd8b7e4212f "2023-05-11T14:54:09.835672"^^ . +_:N1baa303656244263bd7c429fd7ecb9b5 . + . + . + . +_:Naf2d07ef96c642c7b7be3dc6efd0df6f . +_:N1929d020c0494cecb14fc1f3a7e770fc . + "false"^^ . + "lines.txt"^^ . + . + . +_:N8b9966d12fc142f2a1061d0f33d09f97 . +_:N3651e095cd8947df8b663ed2254c6a61 . +_:N1929d020c0494cecb14fc1f3a7e770fc "2023-05-11T14:54:09.833094"^^ . + "Prospective provenance"^^ . + "lines"^^ . + "cwltool 3.1.20230425144158"^^ . + . + "sort_out.txt"^^ . +_:N8b9966d12fc142f2a1061d0f33d09f97 . +_:N706c7b50ff0740009d6d44b3dacd8b50 "2023-05-11T14:54:09.828159"^^ . +_:N8b9966d12fc142f2a1061d0f33d09f97 . + . +_:N917e67b0692443bb88b955d98069ad45 . + . + "lines.txt"^^ . + _:N854713727bfb4892a4ef6dd8b7e4212f . +_:N153e9e08e7b2450c8ffc3444bf050d96 . + . +_:Naf2d07ef96c642c7b7be3dc6efd0df6f . +_:N6180e2a4e7bd4e7d9a12f5278dd453da "2023-05-11T14:54:09.833103"^^ . + "2023-05-11T14:54:09.781765"^^ . +_:N153e9e08e7b2450c8ffc3444bf050d96 . + . +_:N3651e095cd8947df8b663ed2254c6a61 . +_:Nb75adf186f784e6b9d8db358069bbf87 . + _:N1929d020c0494cecb14fc1f3a7e770fc . +_:N0d7a84a5be8c445d8a77d856e5e472ad . +_:N1baa303656244263bd7c429fd7ecb9b5 . + _:N153e9e08e7b2450c8ffc3444bf050d96 . + "Run of workflow/packed.cwl#main"^^ . +_:N9d020df8e6b74b96a48657590d929acc . +_:N917e67b0692443bb88b955d98069ad45 . +_:N6415c2eed0204d0b894f7db3bb63225e "2023-05-11T14:54:09.781827"^^ . + . + . + . +_:N854713727bfb4892a4ef6dd8b7e4212f . +_:N854713727bfb4892a4ef6dd8b7e4212f . + ".txt"^^ . + . + _:Naf2d07ef96c642c7b7be3dc6efd0df6f . + "grep_out.txt"^^ . + _:N1baa303656244263bd7c429fd7ecb9b5 . + . +_:N9d020df8e6b74b96a48657590d929acc "2023-05-11T14:54:09.813943"^^ . + . +_:N54e41a97aa6f4e8a84ca71bb28943105 . + "Run of workflow/packed.cwl#main/grep"^^ . + _:Naac30689366e4430a1908ccb3a252ba2 . + . +_:N54e41a97aa6f4e8a84ca71bb28943105 . +_:Nc6cdc1111319443080197f2eda15e287 "2023-05-11T14:54:09.816978"^^ . + . +_:N1929d020c0494cecb14fc1f3a7e770fc . + . + . + . + _:N0d7a84a5be8c445d8a77d856e5e472ad . + ".txt"^^ . +_:Naac30689366e4430a1908ccb3a252ba2 "2023-05-11T14:54:09.829063"^^ . + _:N706c7b50ff0740009d6d44b3dacd8b50 . +_:N6180e2a4e7bd4e7d9a12f5278dd453da . + "sort_out"^^ . + _:N4e4e1579db974536a5089b2e2d34d07a . +_:N6415c2eed0204d0b894f7db3bb63225e . + . + "lines.aux"^^ . diff --git a/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.provn b/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.provn index ebb0bca..8868e4e 100644 --- a/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.provn +++ b/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.provn @@ -8,57 +8,57 @@ document prefix id prefix data prefix sha256 - prefix researchobject - prefix metadata - prefix provenance - prefix wf - prefix input + prefix researchobject + prefix metadata + prefix provenance + prefix wf + prefix input prefix wf4ever - agent(id:dbc054dc-3fde-4ae4-9812-f92df6589666) - agent(id:c8915798-6b30-42c9-a29f-83ad8866310d, [prov:type='prov:SoftwareAgent', prov:type='wfprov:WorkflowEngine', prov:label="cwltool 3.1.20220802125926"]) - wasStartedBy(id:c8915798-6b30-42c9-a29f-83ad8866310d, -, id:dbc054dc-3fde-4ae4-9812-f92df6589666, 2022-12-09T14:57:45.717548) - activity(id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe, 2022-12-09T14:57:45.717577, -, [prov:type='wfprov:WorkflowRun', prov:label="Run of workflow/packed.cwl#main"]) - wasAssociatedWith(id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe, id:c8915798-6b30-42c9-a29f-83ad8866310d, wf:main) - wasStartedBy(id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe, -, id:c8915798-6b30-42c9-a29f-83ad8866310d, 2022-12-09T14:57:45.717640) + agent(id:07bc4dab-678d-4290-b119-363995f3d4ac) + agent(id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36, [prov:type='wfprov:WorkflowEngine', prov:type='prov:SoftwareAgent', prov:label="cwltool 3.1.20230425144158"]) + wasStartedBy(id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36, -, id:07bc4dab-678d-4290-b119-363995f3d4ac, 2023-05-11T14:54:09.781736) + activity(id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154, 2023-05-11T14:54:09.781765, -, [prov:type='wfprov:WorkflowRun', prov:label="Run of workflow/packed.cwl#main"]) + wasAssociatedWith(id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154, id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36, wf:main) + wasStartedBy(id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154, -, id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36, 2023-05-11T14:54:09.781827) entity(wf:main, [prov:type='prov:Plan', prov:type='wfdesc:Workflow', prov:label="Prospective provenance"]) - entity(wf:main/sorted, [prov:type='wfdesc:Process', prov:type='prov:Plan']) - entity(wf:main, [wfdesc:hasSubProcess='wf:main/sorted', prov:label="Prospective provenance"]) - entity(wf:main/grep, [prov:type='wfdesc:Process', prov:type='prov:Plan']) + entity(wf:main/grep, [prov:type='prov:Plan', prov:type='wfdesc:Process']) entity(wf:main, [wfdesc:hasSubProcess='wf:main/grep', prov:label="Prospective provenance"]) + entity(wf:main/sorted, [prov:type='prov:Plan', prov:type='wfdesc:Process']) + entity(wf:main, [wfdesc:hasSubProcess='wf:main/sorted', prov:label="Prospective provenance"]) entity(data:b64565ee76fcd5296c48314f858f8e4672c71439, [prov:type='wfprov:Artifact']) - entity(id:5790fe8b-da2b-4e87-9a73-2eff75d27e50, [prov:type='wfprov:Artifact', prov:type='wf4ever:File', cwlprov:basename="lines.txt", cwlprov:nameroot="lines", cwlprov:nameext=".txt"]) - specializationOf(id:5790fe8b-da2b-4e87-9a73-2eff75d27e50, data:b64565ee76fcd5296c48314f858f8e4672c71439) - used(id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe, id:5790fe8b-da2b-4e87-9a73-2eff75d27e50, 2022-12-09T14:57:45.746490, [prov:role='wf:main/grepsort_in']) - entity(id:6751988b-0f91-4271-8c79-d4c06b599ffe, [prov:value="0" %% xsd:boolean]) - used(id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe, id:6751988b-0f91-4271-8c79-d4c06b599ffe, 2022-12-09T14:57:45.746575, [prov:role='wf:main/reverse_sort']) - activity(id:15826194-2534-4654-924a-55386c53db47, -, -, [prov:type='wfprov:ProcessRun', prov:label="Run of workflow/packed.cwl#main/grep"]) - wasAssociatedWith(id:15826194-2534-4654-924a-55386c53db47, id:c8915798-6b30-42c9-a29f-83ad8866310d, wf:main/grep) - wasStartedBy(id:15826194-2534-4654-924a-55386c53db47, -, id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe, 2022-12-09T14:57:45.748935) + entity(id:fc5f1254-379c-45b1-8f2c-3acfe0d52067, [prov:type='wfprov:Artifact', prov:type='wf4ever:File', cwlprov:basename="lines.txt", cwlprov:nameroot="lines", cwlprov:nameext=".txt"]) + specializationOf(id:fc5f1254-379c-45b1-8f2c-3acfe0d52067, data:b64565ee76fcd5296c48314f858f8e4672c71439) + used(id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154, id:fc5f1254-379c-45b1-8f2c-3acfe0d52067, 2023-05-11T14:54:09.813821, [prov:role='wf:main/grepsort_in']) + entity(id:929dfcb7-37af-4e41-863f-a9bf80555239, [prov:value="0" %% xsd:boolean]) + used(id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154, id:929dfcb7-37af-4e41-863f-a9bf80555239, 2023-05-11T14:54:09.813943, [prov:role='wf:main/reverse_sort']) + activity(id:4d7e2fbb-89c6-4575-8005-336cc021766b, -, -, [prov:type='wfprov:ProcessRun', prov:label="Run of workflow/packed.cwl#main/grep"]) + wasAssociatedWith(id:4d7e2fbb-89c6-4575-8005-336cc021766b, id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36, wf:main/grep) + wasStartedBy(id:4d7e2fbb-89c6-4575-8005-336cc021766b, -, id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154, 2023-05-11T14:54:09.816978) entity(data:b64565ee76fcd5296c48314f858f8e4672c71439, [prov:type='wfprov:Artifact']) - entity(id:79847ff5-502b-4795-8204-11dffb82044e, [prov:type='wfprov:Artifact', prov:type='wf4ever:File', cwlprov:basename="lines.txt", cwlprov:nameroot="lines", cwlprov:nameext=".txt"]) - specializationOf(id:79847ff5-502b-4795-8204-11dffb82044e, data:b64565ee76fcd5296c48314f858f8e4672c71439) + entity(id:f420bbdc-3c19-4b07-8762-38fd82178c48, [prov:type='wfprov:Artifact', prov:type='wf4ever:File', cwlprov:basename="lines.txt", cwlprov:nameroot="lines", cwlprov:nameext=".txt"]) + specializationOf(id:f420bbdc-3c19-4b07-8762-38fd82178c48, data:b64565ee76fcd5296c48314f858f8e4672c71439) entity(data:c708d7ef841f7e1748436b8ef5670d0b2de1a227, [prov:type='wfprov:Artifact']) - entity(id:7498296b-d276-46b9-abf4-013068cc82b0, [prov:type='wfprov:Artifact', prov:type='wf4ever:File', cwlprov:basename="lines.aux", cwlprov:nameroot="lines", cwlprov:nameext=".aux"]) - specializationOf(id:7498296b-d276-46b9-abf4-013068cc82b0, data:c708d7ef841f7e1748436b8ef5670d0b2de1a227) - wasDerivedFrom(id:7498296b-d276-46b9-abf4-013068cc82b0, id:79847ff5-502b-4795-8204-11dffb82044e, -, -, -, [prov:type='cwlprov:SecondaryFile']) - used(id:15826194-2534-4654-924a-55386c53db47, id:79847ff5-502b-4795-8204-11dffb82044e, 2022-12-09T14:57:45.750152, [prov:role='wf:main/grep/grep_in']) + entity(id:f8a3035b-7d0f-4695-88be-b21554668854, [prov:type='wfprov:Artifact', prov:type='wf4ever:File', cwlprov:basename="lines.aux", cwlprov:nameroot="lines", cwlprov:nameext=".aux"]) + specializationOf(id:f8a3035b-7d0f-4695-88be-b21554668854, data:c708d7ef841f7e1748436b8ef5670d0b2de1a227) + wasDerivedFrom(id:f8a3035b-7d0f-4695-88be-b21554668854, id:f420bbdc-3c19-4b07-8762-38fd82178c48, -, -, -, [prov:type='cwlprov:SecondaryFile']) + used(id:4d7e2fbb-89c6-4575-8005-336cc021766b, id:f420bbdc-3c19-4b07-8762-38fd82178c48, 2023-05-11T14:54:09.818401, [prov:role='wf:main/grep/grep_in']) entity(data:601203afd61ae8b19d9c639d8d16296c9039d9cc, [prov:type='wfprov:Artifact']) - entity(id:afadeff0-99ee-4574-bde1-d2585ee5701a, [prov:type='wfprov:Artifact', prov:type='wf4ever:File', cwlprov:basename="grep_out.txt", cwlprov:nameroot="grep_out", cwlprov:nameext=".txt"]) - specializationOf(id:afadeff0-99ee-4574-bde1-d2585ee5701a, data:601203afd61ae8b19d9c639d8d16296c9039d9cc) - wasGeneratedBy(id:afadeff0-99ee-4574-bde1-d2585ee5701a, id:15826194-2534-4654-924a-55386c53db47, 2022-12-09T14:57:45.755224, [prov:role='wf:main/grep/grep_out']) - wasEndedBy(id:15826194-2534-4654-924a-55386c53db47, -, id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe, 2022-12-09T14:57:45.755214) - activity(id:230af7c3-a8e0-4b20-ae98-925868e3c332, -, -, [prov:type='wfprov:ProcessRun', prov:label="Run of workflow/packed.cwl#main/sorted"]) - wasAssociatedWith(id:230af7c3-a8e0-4b20-ae98-925868e3c332, id:c8915798-6b30-42c9-a29f-83ad8866310d, wf:main/sorted) - wasStartedBy(id:230af7c3-a8e0-4b20-ae98-925868e3c332, -, id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe, 2022-12-09T14:57:45.759218) - entity(id:fd907908-a40c-472c-b479-dfc7f61b0f65, [prov:value="0" %% xsd:boolean]) - used(id:230af7c3-a8e0-4b20-ae98-925868e3c332, id:fd907908-a40c-472c-b479-dfc7f61b0f65, 2022-12-09T14:57:45.759848, [prov:role='wf:main/sorted/reverse']) - used(id:230af7c3-a8e0-4b20-ae98-925868e3c332, id:afadeff0-99ee-4574-bde1-d2585ee5701a, 2022-12-09T14:57:45.759940, [prov:role='wf:main/sorted/sort_in']) + entity(id:72844ffc-c823-4466-bf31-af3a13c6efdc, [prov:type='wfprov:Artifact', prov:type='wf4ever:File', cwlprov:basename="grep_out.txt", cwlprov:nameroot="grep_out", cwlprov:nameext=".txt"]) + specializationOf(id:72844ffc-c823-4466-bf31-af3a13c6efdc, data:601203afd61ae8b19d9c639d8d16296c9039d9cc) + wasGeneratedBy(id:72844ffc-c823-4466-bf31-af3a13c6efdc, id:4d7e2fbb-89c6-4575-8005-336cc021766b, 2023-05-11T14:54:09.824121, [prov:role='wf:main/grep/grep_out']) + wasEndedBy(id:4d7e2fbb-89c6-4575-8005-336cc021766b, -, id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154, 2023-05-11T14:54:09.824109) + activity(id:ba7a4132-7149-484b-b29b-3f5716e6ef5f, -, -, [prov:type='wfprov:ProcessRun', prov:label="Run of workflow/packed.cwl#main/sorted"]) + wasAssociatedWith(id:ba7a4132-7149-484b-b29b-3f5716e6ef5f, id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36, wf:main/sorted) + wasStartedBy(id:ba7a4132-7149-484b-b29b-3f5716e6ef5f, -, id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154, 2023-05-11T14:54:09.828159) + entity(id:600e9be9-eaea-4dbc-9948-b0bf01481b0a, [prov:value="0" %% xsd:boolean]) + used(id:ba7a4132-7149-484b-b29b-3f5716e6ef5f, id:600e9be9-eaea-4dbc-9948-b0bf01481b0a, 2023-05-11T14:54:09.829063, [prov:role='wf:main/sorted/reverse']) + used(id:ba7a4132-7149-484b-b29b-3f5716e6ef5f, id:72844ffc-c823-4466-bf31-af3a13c6efdc, 2023-05-11T14:54:09.829169, [prov:role='wf:main/sorted/sort_in']) entity(data:8292d6f0985a62d4abd624fc72aecb8132193d6e, [prov:type='wfprov:Artifact']) - entity(id:a41171df-a9d0-4f5f-8179-be34451bda0e, [prov:type='wfprov:Artifact', prov:type='wf4ever:File', cwlprov:basename="sort_out.txt", cwlprov:nameroot="sort_out", cwlprov:nameext=".txt"]) - specializationOf(id:a41171df-a9d0-4f5f-8179-be34451bda0e, data:8292d6f0985a62d4abd624fc72aecb8132193d6e) - wasGeneratedBy(id:a41171df-a9d0-4f5f-8179-be34451bda0e, id:230af7c3-a8e0-4b20-ae98-925868e3c332, 2022-12-09T14:57:45.764426, [prov:role='wf:main/sorted/sort_out']) - wasEndedBy(id:230af7c3-a8e0-4b20-ae98-925868e3c332, -, id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe, 2022-12-09T14:57:45.764417) - wasGeneratedBy(id:a41171df-a9d0-4f5f-8179-be34451bda0e, id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe, 2022-12-09T14:57:45.766778, [prov:role='wf:main/primary/grepsort_out']) - wasEndedBy(id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe, -, id:c8915798-6b30-42c9-a29f-83ad8866310d, 2022-12-09T14:57:45.766852) + entity(id:b59b8a30-d974-4703-96b0-cc2b9a47bbf1, [prov:type='wfprov:Artifact', prov:type='wf4ever:File', cwlprov:basename="sort_out.txt", cwlprov:nameroot="sort_out", cwlprov:nameext=".txt"]) + specializationOf(id:b59b8a30-d974-4703-96b0-cc2b9a47bbf1, data:8292d6f0985a62d4abd624fc72aecb8132193d6e) + wasGeneratedBy(id:b59b8a30-d974-4703-96b0-cc2b9a47bbf1, id:ba7a4132-7149-484b-b29b-3f5716e6ef5f, 2023-05-11T14:54:09.833103, [prov:role='wf:main/sorted/sort_out']) + wasEndedBy(id:ba7a4132-7149-484b-b29b-3f5716e6ef5f, -, id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154, 2023-05-11T14:54:09.833094) + wasGeneratedBy(id:b59b8a30-d974-4703-96b0-cc2b9a47bbf1, id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154, 2023-05-11T14:54:09.835606, [prov:role='wf:main/primary/grepsort_out']) + wasEndedBy(id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154, -, id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36, 2023-05-11T14:54:09.835672) endDocument \ No newline at end of file diff --git a/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.ttl b/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.ttl index 83b7156..2ed3176 100644 --- a/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.ttl +++ b/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.ttl @@ -3,45 +3,45 @@ @prefix id: . @prefix prov: . @prefix rdfs: . -@prefix wf: . +@prefix wf: . @prefix wf4ever: . @prefix wfdesc: . @prefix wfprov: . @prefix xsd: . -id:7498296b-d276-46b9-abf4-013068cc82b0 a wf4ever:File, - wfprov:Artifact, - prov:Entity ; - prov:qualifiedDerivation [ a prov:Derivation, - cwlprov:SecondaryFile ; - prov:entity id:79847ff5-502b-4795-8204-11dffb82044e ] ; - prov:specializationOf data:c708d7ef841f7e1748436b8ef5670d0b2de1a227 ; - cwlprov:basename "lines.aux"^^xsd:string ; - cwlprov:nameext ".aux"^^xsd:string ; - cwlprov:nameroot "lines"^^xsd:string . - -id:a41171df-a9d0-4f5f-8179-be34451bda0e a wf4ever:File, +id:b59b8a30-d974-4703-96b0-cc2b9a47bbf1 a wf4ever:File, wfprov:Artifact, prov:Entity ; prov:qualifiedGeneration [ a prov:Generation ; - prov:activity id:230af7c3-a8e0-4b20-ae98-925868e3c332 ; - prov:atTime "2022-12-09T14:57:45.764426"^^xsd:dateTime ; - prov:hadRole ], + prov:activity id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154 ; + prov:atTime "2023-05-11T14:54:09.835606"^^xsd:dateTime ; + prov:hadRole ], [ a prov:Generation ; - prov:activity id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe ; - prov:atTime "2022-12-09T14:57:45.766778"^^xsd:dateTime ; - prov:hadRole ] ; + prov:activity id:ba7a4132-7149-484b-b29b-3f5716e6ef5f ; + prov:atTime "2023-05-11T14:54:09.833103"^^xsd:dateTime ; + prov:hadRole ] ; prov:specializationOf data:8292d6f0985a62d4abd624fc72aecb8132193d6e ; cwlprov:basename "sort_out.txt"^^xsd:string ; cwlprov:nameext ".txt"^^xsd:string ; cwlprov:nameroot "sort_out"^^xsd:string . +id:f8a3035b-7d0f-4695-88be-b21554668854 a wf4ever:File, + wfprov:Artifact, + prov:Entity ; + prov:qualifiedDerivation [ a prov:Derivation, + cwlprov:SecondaryFile ; + prov:entity id:f420bbdc-3c19-4b07-8762-38fd82178c48 ] ; + prov:specializationOf data:c708d7ef841f7e1748436b8ef5670d0b2de1a227 ; + cwlprov:basename "lines.aux"^^xsd:string ; + cwlprov:nameext ".aux"^^xsd:string ; + cwlprov:nameroot "lines"^^xsd:string . + wf:main a wfdesc:Workflow, prov:Entity, prov:Plan ; rdfs:label "Prospective provenance"^^xsd:string ; - wfdesc:hasSubProcess , - . + wfdesc:hasSubProcess , + . data:601203afd61ae8b19d9c639d8d16296c9039d9cc a wfprov:Artifact, prov:Entity . @@ -52,45 +52,65 @@ data:8292d6f0985a62d4abd624fc72aecb8132193d6e a wfprov:Artifact, data:c708d7ef841f7e1748436b8ef5670d0b2de1a227 a wfprov:Artifact, prov:Entity . -id:15826194-2534-4654-924a-55386c53db47 a wfprov:ProcessRun, +id:07bc4dab-678d-4290-b119-363995f3d4ac a prov:Agent . + +id:4d7e2fbb-89c6-4575-8005-336cc021766b a wfprov:ProcessRun, prov:Activity ; rdfs:label "Run of workflow/packed.cwl#main/grep"^^xsd:string ; prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; + prov:hadPlan ] ; prov:qualifiedEnd [ a prov:End ; - prov:atTime "2022-12-09T14:57:45.755214"^^xsd:dateTime ; - prov:hadActivity id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe ] ; + prov:atTime "2023-05-11T14:54:09.824109"^^xsd:dateTime ; + prov:hadActivity id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154 ] ; prov:qualifiedStart [ a prov:Start ; - prov:atTime "2022-12-09T14:57:45.748935"^^xsd:dateTime ; - prov:hadActivity id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe ] ; + prov:atTime "2023-05-11T14:54:09.816978"^^xsd:dateTime ; + prov:hadActivity id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154 ] ; prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-12-09T14:57:45.750152"^^xsd:dateTime ; - prov:entity id:79847ff5-502b-4795-8204-11dffb82044e ; - prov:hadRole ] ; - prov:wasAssociatedWith id:c8915798-6b30-42c9-a29f-83ad8866310d . + prov:atTime "2023-05-11T14:54:09.818401"^^xsd:dateTime ; + prov:entity id:f420bbdc-3c19-4b07-8762-38fd82178c48 ; + prov:hadRole ] ; + prov:wasAssociatedWith id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36 . + +id:600e9be9-eaea-4dbc-9948-b0bf01481b0a a prov:Entity ; + prov:value false . + +id:72844ffc-c823-4466-bf31-af3a13c6efdc a wf4ever:File, + wfprov:Artifact, + prov:Entity ; + prov:qualifiedGeneration [ a prov:Generation ; + prov:activity id:4d7e2fbb-89c6-4575-8005-336cc021766b ; + prov:atTime "2023-05-11T14:54:09.824121"^^xsd:dateTime ; + prov:hadRole ] ; + prov:specializationOf data:601203afd61ae8b19d9c639d8d16296c9039d9cc ; + cwlprov:basename "grep_out.txt"^^xsd:string ; + cwlprov:nameext ".txt"^^xsd:string ; + cwlprov:nameroot "grep_out"^^xsd:string . -id:230af7c3-a8e0-4b20-ae98-925868e3c332 a wfprov:ProcessRun, +id:929dfcb7-37af-4e41-863f-a9bf80555239 a prov:Entity ; + prov:value false . + +id:ba7a4132-7149-484b-b29b-3f5716e6ef5f a wfprov:ProcessRun, prov:Activity ; rdfs:label "Run of workflow/packed.cwl#main/sorted"^^xsd:string ; prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; + prov:hadPlan ] ; prov:qualifiedEnd [ a prov:End ; - prov:atTime "2022-12-09T14:57:45.764417"^^xsd:dateTime ; - prov:hadActivity id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe ] ; + prov:atTime "2023-05-11T14:54:09.833094"^^xsd:dateTime ; + prov:hadActivity id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154 ] ; prov:qualifiedStart [ a prov:Start ; - prov:atTime "2022-12-09T14:57:45.759218"^^xsd:dateTime ; - prov:hadActivity id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe ] ; + prov:atTime "2023-05-11T14:54:09.828159"^^xsd:dateTime ; + prov:hadActivity id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154 ] ; prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-12-09T14:57:45.759848"^^xsd:dateTime ; - prov:entity id:fd907908-a40c-472c-b479-dfc7f61b0f65 ; - prov:hadRole ], + prov:atTime "2023-05-11T14:54:09.829063"^^xsd:dateTime ; + prov:entity id:600e9be9-eaea-4dbc-9948-b0bf01481b0a ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-12-09T14:57:45.759940"^^xsd:dateTime ; - prov:entity id:afadeff0-99ee-4574-bde1-d2585ee5701a ; - prov:hadRole ] ; - prov:wasAssociatedWith id:c8915798-6b30-42c9-a29f-83ad8866310d . + prov:atTime "2023-05-11T14:54:09.829169"^^xsd:dateTime ; + prov:entity id:72844ffc-c823-4466-bf31-af3a13c6efdc ; + prov:hadRole ] ; + prov:wasAssociatedWith id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36 . -id:5790fe8b-da2b-4e87-9a73-2eff75d27e50 a wf4ever:File, +id:fc5f1254-379c-45b1-8f2c-3acfe0d52067 a wf4ever:File, wfprov:Artifact, prov:Entity ; prov:specializationOf data:b64565ee76fcd5296c48314f858f8e4672c71439 ; @@ -98,38 +118,18 @@ id:5790fe8b-da2b-4e87-9a73-2eff75d27e50 a wf4ever:File, cwlprov:nameext ".txt"^^xsd:string ; cwlprov:nameroot "lines"^^xsd:string . -id:6751988b-0f91-4271-8c79-d4c06b599ffe a prov:Entity ; - prov:value false . - -id:afadeff0-99ee-4574-bde1-d2585ee5701a a wf4ever:File, - wfprov:Artifact, - prov:Entity ; - prov:qualifiedGeneration [ a prov:Generation ; - prov:activity id:15826194-2534-4654-924a-55386c53db47 ; - prov:atTime "2022-12-09T14:57:45.755224"^^xsd:dateTime ; - prov:hadRole ] ; - prov:specializationOf data:601203afd61ae8b19d9c639d8d16296c9039d9cc ; - cwlprov:basename "grep_out.txt"^^xsd:string ; - cwlprov:nameext ".txt"^^xsd:string ; - cwlprov:nameroot "grep_out"^^xsd:string . - -id:dbc054dc-3fde-4ae4-9812-f92df6589666 a prov:Agent . - -id:fd907908-a40c-472c-b479-dfc7f61b0f65 a prov:Entity ; - prov:value false . - - a wfdesc:Process, + a wfdesc:Process, prov:Entity, prov:Plan . - a wfdesc:Process, + a wfdesc:Process, prov:Entity, prov:Plan . data:b64565ee76fcd5296c48314f858f8e4672c71439 a wfprov:Artifact, prov:Entity . -id:79847ff5-502b-4795-8204-11dffb82044e a wf4ever:File, +id:f420bbdc-3c19-4b07-8762-38fd82178c48 a wf4ever:File, wfprov:Artifact, prov:Entity ; prov:specializationOf data:b64565ee76fcd5296c48314f858f8e4672c71439 ; @@ -137,33 +137,33 @@ id:79847ff5-502b-4795-8204-11dffb82044e a wf4ever:File, cwlprov:nameext ".txt"^^xsd:string ; cwlprov:nameroot "lines"^^xsd:string . -id:c8915798-6b30-42c9-a29f-83ad8866310d a wfprov:WorkflowEngine, - prov:Agent, - prov:SoftwareAgent ; - rdfs:label "cwltool 3.1.20220802125926"^^xsd:string ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2022-12-09T14:57:45.717548"^^xsd:dateTime ; - prov:hadActivity id:dbc054dc-3fde-4ae4-9812-f92df6589666 ] . - -id:e442628c-e95b-48f5-b5c2-ae2f266a7fbe a wfprov:WorkflowRun, +id:a59b2ee0-e2cf-4f8c-b6ed-193fb588c154 a wfprov:WorkflowRun, prov:Activity ; rdfs:label "Run of workflow/packed.cwl#main"^^xsd:string ; prov:qualifiedAssociation [ a prov:Association ; prov:hadPlan wf:main ] ; prov:qualifiedEnd [ a prov:End ; - prov:atTime "2022-12-09T14:57:45.766852"^^xsd:dateTime ; - prov:hadActivity id:c8915798-6b30-42c9-a29f-83ad8866310d ] ; + prov:atTime "2023-05-11T14:54:09.835672"^^xsd:dateTime ; + prov:hadActivity id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36 ] ; prov:qualifiedStart [ a prov:Start ; - prov:atTime "2022-12-09T14:57:45.717640"^^xsd:dateTime ; - prov:hadActivity id:c8915798-6b30-42c9-a29f-83ad8866310d ] ; + prov:atTime "2023-05-11T14:54:09.781827"^^xsd:dateTime ; + prov:hadActivity id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36 ] ; prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-12-09T14:57:45.746490"^^xsd:dateTime ; - prov:entity id:5790fe8b-da2b-4e87-9a73-2eff75d27e50 ; - prov:hadRole ], + prov:atTime "2023-05-11T14:54:09.813943"^^xsd:dateTime ; + prov:entity id:929dfcb7-37af-4e41-863f-a9bf80555239 ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-12-09T14:57:45.746575"^^xsd:dateTime ; - prov:entity id:6751988b-0f91-4271-8c79-d4c06b599ffe ; - prov:hadRole ] ; - prov:startedAtTime "2022-12-09T14:57:45.717577"^^xsd:dateTime ; - prov:wasAssociatedWith id:c8915798-6b30-42c9-a29f-83ad8866310d . + prov:atTime "2023-05-11T14:54:09.813821"^^xsd:dateTime ; + prov:entity id:fc5f1254-379c-45b1-8f2c-3acfe0d52067 ; + prov:hadRole ] ; + prov:startedAtTime "2023-05-11T14:54:09.781765"^^xsd:dateTime ; + prov:wasAssociatedWith id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36 . + +id:f66f5014-d8d8-4544-bc78-ab0ac7cb1e36 a wfprov:WorkflowEngine, + prov:Agent, + prov:SoftwareAgent ; + rdfs:label "cwltool 3.1.20230425144158"^^xsd:string ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2023-05-11T14:54:09.781736"^^xsd:dateTime ; + prov:hadActivity id:07bc4dab-678d-4290-b119-363995f3d4ac ] . diff --git a/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.xml b/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.xml index a6d130b..16a6346 100644 --- a/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.xml +++ b/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.xml @@ -1,52 +1,52 @@ - - - - cwltool 3.1.20220802125926 + + + + cwltool 3.1.20230425144158 wfprov:WorkflowEngine - - - 2022-12-09T14:57:45.717548 + + + 2023-05-11T14:54:09.781736 - - 2022-12-09T14:57:45.717577 + + 2023-05-11T14:54:09.781765 Run of workflow/packed.cwl#main wfprov:WorkflowRun - - + + - - - 2022-12-09T14:57:45.717640 + + + 2023-05-11T14:54:09.781827 Prospective provenance wfdesc:Workflow - + wfdesc:Process Prospective provenance - wf:main/sorted + wf:main/grep - + wfdesc:Process Prospective provenance - wf:main/grep + wf:main/sorted wfprov:Artifact - + wf4ever:File wfprov:Artifact lines.txt @@ -54,42 +54,42 @@ lines - + - - - 2022-12-09T14:57:45.746490 + + + 2023-05-11T14:54:09.813821 wf:main/grepsort_in - + false - - - 2022-12-09T14:57:45.746575 + + + 2023-05-11T14:54:09.813943 wf:main/reverse_sort - + Run of workflow/packed.cwl#main/grep wfprov:ProcessRun - - + + - - - 2022-12-09T14:57:45.748935 + + + 2023-05-11T14:54:09.816978 wfprov:Artifact - + wf4ever:File wfprov:Artifact lines.txt @@ -97,13 +97,13 @@ lines - + wfprov:Artifact - + wf4ever:File wfprov:Artifact lines.aux @@ -111,24 +111,24 @@ lines - + - - + + cwlprov:SecondaryFile - - - 2022-12-09T14:57:45.750152 + + + 2023-05-11T14:54:09.818401 wf:main/grep/grep_in wfprov:Artifact - + wf4ever:File wfprov:Artifact grep_out.txt @@ -136,53 +136,53 @@ grep_out - + - - - 2022-12-09T14:57:45.755224 + + + 2023-05-11T14:54:09.824121 wf:main/grep/grep_out - - - 2022-12-09T14:57:45.755214 + + + 2023-05-11T14:54:09.824109 - + Run of workflow/packed.cwl#main/sorted wfprov:ProcessRun - - + + - - - 2022-12-09T14:57:45.759218 + + + 2023-05-11T14:54:09.828159 - + false - - - 2022-12-09T14:57:45.759848 + + + 2023-05-11T14:54:09.829063 wf:main/sorted/reverse - - - 2022-12-09T14:57:45.759940 + + + 2023-05-11T14:54:09.829169 wf:main/sorted/sort_in wfprov:Artifact - + wf4ever:File wfprov:Artifact sort_out.txt @@ -190,29 +190,29 @@ sort_out - + - - - 2022-12-09T14:57:45.764426 + + + 2023-05-11T14:54:09.833103 wf:main/sorted/sort_out - - - 2022-12-09T14:57:45.764417 + + + 2023-05-11T14:54:09.833094 - - - 2022-12-09T14:57:45.766778 + + + 2023-05-11T14:54:09.835606 wf:main/primary/grepsort_out - - - 2022-12-09T14:57:45.766852 + + + 2023-05-11T14:54:09.835672 diff --git a/tests/data/grepsort-run-1/snapshot/greptool.cwl b/tests/data/grepsort-run-1/snapshot/greptool.cwl index 04fff08..e94fdab 100644 --- a/tests/data/grepsort-run-1/snapshot/greptool.cwl +++ b/tests/data/grepsort-run-1/snapshot/greptool.cwl @@ -1,6 +1,10 @@ class: CommandLineTool cwlVersion: v1.0 +hints: + - class: ResourceRequirement + ramMin: 64 + baseCommand: ["bash", "-c"] inputs: diff --git a/tests/data/grepsort-run-1/tagmanifest-sha1.txt b/tests/data/grepsort-run-1/tagmanifest-sha1.txt index ec8115f..415178f 100644 --- a/tests/data/grepsort-run-1/tagmanifest-sha1.txt +++ b/tests/data/grepsort-run-1/tagmanifest-sha1.txt @@ -1,15 +1,15 @@ -87823bb034718ff2c8f372d554fc453336458237 workflow/packed.cwl +23f922b3818a6870ac529470fe7cf79786d22f8c workflow/packed.cwl adeeed935d1e6d141fda6fd72619106ef07fa4ee workflow/primary-job.json -bcb75606fee3f2d66491dadc389eec5542e9ced5 metadata/provenance/primary.cwlprov.xml -d26fcc6d1b94be63af626146098b33d7063c8e76 metadata/provenance/primary.cwlprov.provn -dc1078bb2bd896a0a258866478ce411b48437d0d metadata/provenance/primary.cwlprov.json -28def5960d2c9284478c00b2925f809226155f55 metadata/provenance/primary.cwlprov.ttl -aab564e98509e0ee2c4b003a4d39ac775f909fa1 metadata/provenance/primary.cwlprov.nt -fc96790ecc861238ea008bcd610afe82742f5d2c metadata/provenance/primary.cwlprov.jsonld -7512c0a7cd52dbffb62ed781d8e14d682a07db34 workflow/primary-output.json +b1b58ac9a3a18e3d0e41ca31101eb3a32a4c48fe metadata/provenance/primary.cwlprov.xml +3166a17d39aa3b87d7ff6daa56628ba693c7decb metadata/provenance/primary.cwlprov.provn +555f3eb6244879a01568f375d2168142e594b546 metadata/provenance/primary.cwlprov.json +dc7b1945e8f632d9645781581a87368beb8499e9 metadata/provenance/primary.cwlprov.ttl +00810defdfee13daee0c2f02987f5fb3ee3b269d metadata/provenance/primary.cwlprov.nt +321c58fe7b762987959b8aba952b53a1474c4fee metadata/provenance/primary.cwlprov.jsonld +e0962e7390fe42de91ed4da935a879f69e718230 workflow/primary-output.json d833b3e023ad41139b6f2d03cd2fb3fd56c23668 snapshot/grepsort.cwl -3f94b445f9f12fc56e055e8f4f5d4234560b3ac9 snapshot/greptool.cwl +c5405099be3b5f462fa15387720aad1f7c9f762c snapshot/greptool.cwl 602d182b8e5fd172f77425b99f07fcc4c7d5ece8 snapshot/sorttool.cwl -ca8cab8d276d4f907802fed6b35d352f7641ce82 metadata/logs/engine.c8915798-6b30-42c9-a29f-83ad8866310d.txt -82518a00491fbf7ace8272055d2efa433700d9b3 metadata/manifest.json -464f0ff0448fd56c89ec9f5300fb89dea1e8ac27 bag-info.txt +7b3bd2593e0940dfa9f550c8482795b8a15142a1 metadata/logs/engine.f66f5014-d8d8-4544-bc78-ab0ac7cb1e36.txt +cc7a6c6f14be2d6277414bb68cd8e498ef1933c2 metadata/manifest.json +2d409822d3db92a457b9ebc19df4d094db7bd094 bag-info.txt diff --git a/tests/data/grepsort-run-1/tagmanifest-sha256.txt b/tests/data/grepsort-run-1/tagmanifest-sha256.txt index 7c55a33..aa21743 100644 --- a/tests/data/grepsort-run-1/tagmanifest-sha256.txt +++ b/tests/data/grepsort-run-1/tagmanifest-sha256.txt @@ -1,15 +1,15 @@ -878bdfa28b10dc86a106dad423f5bb4306fef85df77a81b06a964f1400fa7b22 workflow/packed.cwl +76f754a2d1ef82433c64e49fcadc71f5811472f8877b0539e87cbe93068fec63 workflow/packed.cwl cc9f6f6f599e24901397820affc253b1d01f8f4f137174292bf4cea566320782 workflow/primary-job.json -ae3b04473e4229c511f9649bdfcc17a5d842930d4255fb53bcb4908db040a37e metadata/provenance/primary.cwlprov.xml -9d312902781dce549839de48707dc2372b90714f193701bcc4a0bf1c1488c3e0 metadata/provenance/primary.cwlprov.provn -38d5863041be2300fe5b6000be1f17c0e795e70fc1870a0fc5e0dfb9480c063d metadata/provenance/primary.cwlprov.json -e962a9f0c92782a1eb464b127dcd37e3453e29176b54961ed824a26cac7772cc metadata/provenance/primary.cwlprov.ttl -c4055a09805a39524b9d3f4c7edf303957043c9a2de2341dd3f0ab402e6fe787 metadata/provenance/primary.cwlprov.nt -6fe2b77da65e48c3691bf6037aac1018a488660a6a6a57cec3ad0e099ee9fa52 metadata/provenance/primary.cwlprov.jsonld -aa12e03f91d5247c1d3652af59859a43094b65aa1ef0e71e300bec40593ea24a workflow/primary-output.json +843fadc7dcb3e6705e6cf497c2b30d1e04defa6670cdcbbe67dd65c4c121eeb8 metadata/provenance/primary.cwlprov.xml +ce1f1c90ce2a20fbeb771a66af4fe6855153b36d0a78dfa2b32dc12f42dc0a35 metadata/provenance/primary.cwlprov.provn +de7758fd477632ba72a1eb336101a8353cce9af0ebb29053990acc15f95d40f5 metadata/provenance/primary.cwlprov.json +1c98943e9c9b7b13df86efc7d608d265ef11bc1251577b9e9522963ec1ffc5cd metadata/provenance/primary.cwlprov.ttl +181a37ea6e53d8a308de0bc52c432b11c409743c5220583edfe8558ba60f7d8b metadata/provenance/primary.cwlprov.nt +318b789c83ec43f0edb606bbdaa829bf2ee6173b6d7f2ab9c689ce0e2703e894 metadata/provenance/primary.cwlprov.jsonld +3e554fb8d0d66648ee1d00aa2daaa9f0e4812b18eadc93b089efd62857c73c9b workflow/primary-output.json 7993132441cdc80df1077563a5ac57304f47d2817383dfb8954bcf823db208c7 snapshot/grepsort.cwl -aa50fb2c05b438b84a4b12c03a354bdb81ebef6bfd7758f96598c6f577409d00 snapshot/greptool.cwl +6bab7ffa73fca1ab7ae731ff7c4fc8542d5e534275bf7d732a768eb5452bc666 snapshot/greptool.cwl f17285267ea30d9a7d59cf01631021a4f0e12b0b36cd609ee5cf5ab3212fcdf8 snapshot/sorttool.cwl -803c8a5bc7978aa8b095060fb1d91c482e81bce257ba36ed1d17f5bd7192cda3 metadata/logs/engine.c8915798-6b30-42c9-a29f-83ad8866310d.txt -bd4c4bd18683e9269a7052a8e2cf60a244663a19a8b7cea974b6e8fc491b3502 metadata/manifest.json -ab148cba9ccce5696ef2ef0a4c5e45fa74d55bd4e496804a3ddbd6b9b7f083c6 bag-info.txt +0a2888bccce6341ee8c197030100f4c944570bf217828649c41159eef8791272 metadata/logs/engine.f66f5014-d8d8-4544-bc78-ab0ac7cb1e36.txt +61883826498315f9ed4bed04cf9b7fe1eeab17c7b47614b2c49f8518adea9a35 metadata/manifest.json +4963febb6b066f73406fead752b844b2d75f6b70281ab787d178d3324ee6ad83 bag-info.txt diff --git a/tests/data/grepsort-run-1/tagmanifest-sha512.txt b/tests/data/grepsort-run-1/tagmanifest-sha512.txt index 981a6ee..1c1b579 100644 --- a/tests/data/grepsort-run-1/tagmanifest-sha512.txt +++ b/tests/data/grepsort-run-1/tagmanifest-sha512.txt @@ -1,15 +1,15 @@ -73352dd7f5ff7fbc8327e6998287644c9678b62681092fbd94e739282b0f12bf6e2627376152a28050d138fe763d46aa076ff2ef06ff84efc60cdd1d85db4014 workflow/packed.cwl +636ff3ddb82c7b0c68de768c368d9dc77603929ba7a5bcd9bf6c5523cf219fb73d60616e9813429a4482e44e84d8f7e1656c6e2a8d235da2080ffa11e225b1eb workflow/packed.cwl eff9f0b0ebac2410a3eb6bd02c9e25464d6a3ae78d067a9a55db3ebbba8c0009108807b1a6a19d2c7789c01090a6d43055be940c48582effd2b96a7cd6810bc9 workflow/primary-job.json -2611a30bc9f8c7b5c23012d2116d045cc1c9a8460ba6b85e7dd244b74533d691e742f146032116c831e6894b805df30e9f64bab95db9c8839251baba2371f569 metadata/provenance/primary.cwlprov.xml -5c4fa2c1218c2597e02e9de5e323cd8eaa4460704de7d6677cc803c7f37552010aab949e77a2d634088b036fa9f0d7ef3cc4dc4c1fa9eb4c7e1291ab59f940b8 metadata/provenance/primary.cwlprov.provn -bcde149f50c9a58ecf6c96a506bfd37486d79f08aea13e51b5d5924d5c8e3e23edb4dee240e0ce1fa3e67482ecdeef6d262df3e39f81ac2e97d1393cbe46d8bf metadata/provenance/primary.cwlprov.json -0478f0237569faba836f56dc20433542d0f6d45ae5e4d21a85392085b3f89db32e3efb1ce61ef13a182ee2925478f8988769c148e6e84f32101551ccf6c059b3 metadata/provenance/primary.cwlprov.ttl -26ac411cf2f8605bf96281c8c3372dc77272c24ff5d464f4e87b9170ea250a928cd4c53a5a34a675fe819815c9ce0e0f3e741d415a1bbe3462fa99234868cc16 metadata/provenance/primary.cwlprov.nt -277f714fbc2cb0075ef2944a53a5bb63bacb81813b566362df315a45e4c25adb29499d9821f98e61bd88747727dad6e2595ab4016e64fa93191a2f5ea4092a51 metadata/provenance/primary.cwlprov.jsonld -069c6a31e08b9ab8a163df1fd579cc04af8279563e00278cd848329756514165d8e0c1fefbb51a6e9b2fe506bb08c8595a4feb22509b8ab3181f7d98b915e77f workflow/primary-output.json +0df27b901aba3e2b43861913f4ebc18ec858f4eb84779952ca120a9990cf498301070445e8c7c9b97f4ba2309aee1f39a17efd7ef590be78f328c2563f4aefb1 metadata/provenance/primary.cwlprov.xml +8e03ea9958995d1a744740810fc616271992579ec3d8e9f00e7099f4a1a17780005d130a83bde71ca678910993eff85d5ec405154cea4cb81742577c234cdeac metadata/provenance/primary.cwlprov.provn +ec4505348ff884b1635dfecfb89a554f801216677e15ba6ca81f9d111d85d2f2d5f48b2f1e2f3af5abb4582cf40403714fa6dff59d516e8de56aabb43979b4b7 metadata/provenance/primary.cwlprov.json +8aea4acf6e8073fac9693c581e016b66b30635b51fb116d3969b764006737f31a2fb912228848a90c5d3ba34d1282de5622c49f9ee81349c7624455e12fc690e metadata/provenance/primary.cwlprov.ttl +421c3305310c6909aa0f61006bf32b17032727890c200dd6566e811ab3a1988df307e63a498d460191486c5556c77db0919b3d50ff3f7a7e9bd77c8c0eab1aaa metadata/provenance/primary.cwlprov.nt +871f32099a2410006e2ff94158ef63743bbece7c98f01c37d6589a4b622d971bb88502f5f57d786405693d53e8d3081b5babc4e595fd5349521bbe8a1569bfbe metadata/provenance/primary.cwlprov.jsonld +19ccb4554098c33c9a11226f2e0f651989b3d2d774c2bd2d80b93c56596d734d05329b16d38d6fa5740c2e8c815eaf3b8178f5883c2a1b89ae2d50351d38045e workflow/primary-output.json a15611e241162303925de6428c71ea2ff1f8d9167ed430859998883d08fbe3a7928f0cf7f84b03f2622f8b83b14e798ea4f10a1ad75537225fc8c44953b338b8 snapshot/grepsort.cwl -aaac385e5bc8d2b25a3d29e59aaf07c7b099ff5632723a1175f5bc44c6a0c8450b8139c15887f4c462c89cd5119299dda70fb147132e7562bf12c5a3cbffd1dd snapshot/greptool.cwl +9884040151226af0a19bbb6f1002289cbb24a9a7158f8cf4a4469a3d14be93f67c7d7fc97f59338a69cca15b841fb9b71b608b07a0e3c2def96aeed73392d724 snapshot/greptool.cwl fb0d7a3f79fb3ece4bbffa74f555648c2607f994fec5c8173a2497493c337ef2c1847f9c27cbcf19dc5f366476d8cffc4b04fcb0e9c16328a78419b9b1e4fcd7 snapshot/sorttool.cwl -0faec3171a5ab337bb282a846633a6a269ef218bb4d5162d87c00c8dc9095c8c319604c14e839523ea5125025d503a3a1cefac2042981dca00271ab12c972792 metadata/logs/engine.c8915798-6b30-42c9-a29f-83ad8866310d.txt -18c38a84a3539206b1e8ddde878afd565bd4a1a4bfdf8b57ea73ed0fd53060adcf0da13ba4e87c8957337dd776055c8ffdded640f28011d4798adac203307e90 metadata/manifest.json -2f27cb445f8e2e8b9d1ede0a155a7338cc80b92da9ab9f41a6f2ac92fc96e32d684b79e5623e255f09c38fdcd00365c1f78261a7ef5ec9e3dc8adc03e69de275 bag-info.txt +20683a166b7f4462653b48a5f588836c7d81bc5628e877d80e43d767029cd732f62b8c7f4cb0fde43d66e8f2bce4885674e484a1b693a8bfe6def09fe4b37c73 metadata/logs/engine.f66f5014-d8d8-4544-bc78-ab0ac7cb1e36.txt +119de2a08267d83320fab7c7fb448e533c396086dd7e0e16c0545c579ab5cff5582a9248bad491fbd0f67e9307975973e6555827b978d543b749dee4c06d37c1 metadata/manifest.json +d6266839d73641acfdbb69b4cf86ea3d31189027edb9305439f618a2f9f1cff062321727e88eb5f9b4e2c06e218005b9bbd1c8a47aab3872254972e87697077a bag-info.txt diff --git a/tests/data/grepsort-run-1/workflow/packed.cwl b/tests/data/grepsort-run-1/workflow/packed.cwl index 9d0b7d3..4627ff4 100644 --- a/tests/data/grepsort-run-1/workflow/packed.cwl +++ b/tests/data/grepsort-run-1/workflow/packed.cwl @@ -59,6 +59,12 @@ }, { "class": "CommandLineTool", + "hints": [ + { + "class": "ResourceRequirement", + "ramMin": 64 + } + ], "baseCommand": [ "bash", "-c" diff --git a/tests/data/grepsort-run-1/workflow/primary-output.json b/tests/data/grepsort-run-1/workflow/primary-output.json index 34be20e..7b1e1a0 100644 --- a/tests/data/grepsort-run-1/workflow/primary-output.json +++ b/tests/data/grepsort-run-1/workflow/primary-output.json @@ -8,6 +8,6 @@ "checksum": "sha1$8292d6f0985a62d4abd624fc72aecb8132193d6e", "size": 58, "http://commonwl.org/cwltool#generation": 0, - "@id": "urn:uuid:a41171df-a9d0-4f5f-8179-be34451bda0e" + "@id": "urn:uuid:b59b8a30-d974-4703-96b0-cc2b9a47bbf1" } } diff --git a/tests/test_cwlprov_crate_builder.py b/tests/test_cwlprov_crate_builder.py index c206718..5af38a2 100644 --- a/tests/test_cwlprov_crate_builder.py +++ b/tests/test_cwlprov_crate_builder.py @@ -817,6 +817,7 @@ def test_secondary_files(data_dir, tmpdir): "packed.cwl#sorttool.cwl", } greptool = wf_tools["packed.cwl#greptool.cwl"] + assert greptool["memoryRequirements"] == "64 MiB" assert len(greptool["input"]) == 1 grep_in = greptool["input"][0] assert grep_in["additionalType"] == "Collection"