From 60689aad3acecbd730156001673271a332f0346c Mon Sep 17 00:00:00 2001 From: simleo Date: Thu, 9 Nov 2023 14:56:20 +0100 Subject: [PATCH] convert encoding format for output files --- cwl/grepsort/grepsort.cwl | 1 + cwl/grepsort/sorttool.cwl | 1 + src/runcrate/convert.py | 9 + tests/data/grepsort-run-1/bag-info.txt | 6 +- ...e.158cac0a-3a3b-4716-b023-2f9d48de837a.txt | 20 + ...e.fb8f0a7a-121b-47e1-b955-75d213864598.txt | 20 - .../grepsort-run-1/metadata/manifest.json | 212 +++--- .../metadata/provenance/primary.cwlprov.json | 194 +++--- .../provenance/primary.cwlprov.jsonld | 640 +++++++++--------- .../metadata/provenance/primary.cwlprov.nt | 306 ++++----- .../metadata/provenance/primary.cwlprov.provn | 88 +-- .../metadata/provenance/primary.cwlprov.ttl | 170 ++--- .../metadata/provenance/primary.cwlprov.xml | 154 ++--- .../data/grepsort-run-1/snapshot/grepsort.cwl | 1 + .../data/grepsort-run-1/snapshot/sorttool.cwl | 1 + .../data/grepsort-run-1/tagmanifest-sha1.txt | 26 +- .../grepsort-run-1/tagmanifest-sha256.txt | 26 +- .../grepsort-run-1/tagmanifest-sha512.txt | 26 +- tests/data/grepsort-run-1/workflow/packed.cwl | 2 + .../workflow/primary-output.json | 3 +- tests/test_cwlprov_crate_builder.py | 4 + 21 files changed, 965 insertions(+), 945 deletions(-) create mode 100644 tests/data/grepsort-run-1/metadata/logs/engine.158cac0a-3a3b-4716-b023-2f9d48de837a.txt delete mode 100644 tests/data/grepsort-run-1/metadata/logs/engine.fb8f0a7a-121b-47e1-b955-75d213864598.txt diff --git a/cwl/grepsort/grepsort.cwl b/cwl/grepsort/grepsort.cwl index 88fd10d..b1b4faf 100644 --- a/cwl/grepsort/grepsort.cwl +++ b/cwl/grepsort/grepsort.cwl @@ -19,6 +19,7 @@ inputs: outputs: grepsort_out: type: File + format: "https://www.iana.org/assignments/media-types/text/plain" outputSource: sorted/sort_out steps: diff --git a/cwl/grepsort/sorttool.cwl b/cwl/grepsort/sorttool.cwl index 0fddb4f..e356ff7 100644 --- a/cwl/grepsort/sorttool.cwl +++ b/cwl/grepsort/sorttool.cwl @@ -20,6 +20,7 @@ inputs: outputs: sort_out: type: File + format: "https://www.iana.org/assignments/media-types/text/plain" outputBinding: glob: sort_out.txt stdout: sort_out.txt diff --git a/src/runcrate/convert.py b/src/runcrate/convert.py index ff48935..b189519 100644 --- a/src/runcrate/convert.py +++ b/src/runcrate/convert.py @@ -40,6 +40,7 @@ WORKFLOW_BASENAME = "packed.cwl" INPUTS_FILE_BASENAME = "primary-job.json" +OUTPUTS_FILE_BASENAME = "primary-output.json" MANIFEST_FILE = "manifest-sha1.txt" CWL_TYPE_MAP = { @@ -294,6 +295,7 @@ def build(self): self.add_action(crate, self.workflow_run) self.patch_workflow_input_collection(crate) self.add_inputs_file(crate) + self.add_output_formats(crate) return crate def add_root_metadata(self, crate): @@ -777,3 +779,10 @@ def add_inputs_file(self, crate): "name": "input object document", "encodingFormat": "application/json", }) + + def add_output_formats(self, crate): + path = self.root / "workflow" / OUTPUTS_FILE_BASENAME + if path.is_file(): + with open(path) as f: + data = json.load(f) + self._map_input_data(crate, data) diff --git a/tests/data/grepsort-run-1/bag-info.txt b/tests/data/grepsort-run-1/bag-info.txt index e9efc0c..81710c8 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 3.1.20230513155734 +Bag-Software-Agent: cwltool 3.1.20231020140205 BagIt-Profile-Identifier: https://w3id.org/ro/bagit/profile -Bagging-Date: 2023-05-26 +Bagging-Date: 2023-11-09 External-Description: Research Object of CWL workflow run -External-Identifier: arcp://uuid,c54a7289-731a-498b-9f08-3cc2bb801ba1/ +External-Identifier: arcp://uuid,8b3eb82c-de04-4dd0-b519-0354c0ce7cf5/ Payload-Oxum: 192.4 diff --git a/tests/data/grepsort-run-1/metadata/logs/engine.158cac0a-3a3b-4716-b023-2f9d48de837a.txt b/tests/data/grepsort-run-1/metadata/logs/engine.158cac0a-3a3b-4716-b023-2f9d48de837a.txt new file mode 100644 index 0000000..2ebc9bc --- /dev/null +++ b/tests/data/grepsort-run-1/metadata/logs/engine.158cac0a-3a3b-4716-b023-2f9d48de837a.txt @@ -0,0 +1,20 @@ +[2023-11-09T13:19:38,436.000000Z] [cwltool] /home/simleo/git/runcrate/venv/bin/cwltool --provenance ro grepsort.cwl params.yml +[2023-11-09T13:19:38,439.000000Z] Resolved 'grepsort.cwl' to 'file:///home/simleo/git/runcrate/cwl/grepsort/grepsort.cwl' +[2023-11-09T13:19:38,940.000000Z] [provenance] Adding to RO file:///home/simleo/git/runcrate/cwl/grepsort/lines.txt +[2023-11-09T13:19:38,940.000000Z] [provenance] Adding to RO file:///home/simleo/git/runcrate/cwl/grepsort/lines.aux +[2023-11-09T13:19:38,941.000000Z] [workflow ] start +[2023-11-09T13:19:38,942.000000Z] [workflow ] starting step grep +[2023-11-09T13:19:38,942.000000Z] [step grep] start +[2023-11-09T13:19:38,943.000000Z] [job grep] /tmp/mruwmsr2$ bash \ + -c \ + 'grep -f /tmp/b6vih64i/stg5a0c19bf-8d22-4f74-b973-641b81910030/lines.aux /tmp/b6vih64i/stg5a0c19bf-8d22-4f74-b973-641b81910030/lines.txt >grep_out.txt' +[2023-11-09T13:19:38,953.000000Z] [job grep] completed success +[2023-11-09T13:19:38,953.000000Z] [step grep] completed success +[2023-11-09T13:19:38,953.000000Z] [workflow ] starting step sorted +[2023-11-09T13:19:38,953.000000Z] [step sorted] start +[2023-11-09T13:19:38,954.000000Z] [job sorted] /tmp/w0c9z4je$ sort \ + /tmp/epamolr9/stgfc1b1b27-6041-4eb9-be0b-5ae94c510df3/grep_out.txt > /tmp/w0c9z4je/sort_out.txt +[2023-11-09T13:19:38,957.000000Z] [job sorted] completed success +[2023-11-09T13:19:38,957.000000Z] [step sorted] completed success +[2023-11-09T13:19:38,957.000000Z] [workflow ] completed success +[2023-11-09T13:19:38,987.000000Z] Final process status is success diff --git a/tests/data/grepsort-run-1/metadata/logs/engine.fb8f0a7a-121b-47e1-b955-75d213864598.txt b/tests/data/grepsort-run-1/metadata/logs/engine.fb8f0a7a-121b-47e1-b955-75d213864598.txt deleted file mode 100644 index f2f8d63..0000000 --- a/tests/data/grepsort-run-1/metadata/logs/engine.fb8f0a7a-121b-47e1-b955-75d213864598.txt +++ /dev/null @@ -1,20 +0,0 @@ -[2023-05-26T13:48:22,761.874199Z] [cwltool] /home/simleo/git/runcrate/venv/bin/cwltool --provenance grepsort-run-1 grepsort.cwl params.yml -[2023-05-26T13:48:22,763.775349Z] Resolved 'grepsort.cwl' to 'file:///home/simleo/git/runcrate/cwl/grepsort/grepsort.cwl' -[2023-05-26T13:48:23,857.358217Z] [provenance] Adding to RO file:///home/simleo/git/runcrate/cwl/grepsort/lines.txt -[2023-05-26T13:48:23,858.058929Z] [provenance] Adding to RO file:///home/simleo/git/runcrate/cwl/grepsort/lines.aux -[2023-05-26T13:48:23,860.283136Z] [workflow ] start -[2023-05-26T13:48:23,860.562325Z] [workflow ] starting step grep -[2023-05-26T13:48:23,860.731125Z] [step grep] start -[2023-05-26T13:48:23,862.983942Z] [job grep] /tmp/f9r41on_$ bash \ - -c \ - 'grep -f /tmp/iueonoei/stga889db5c-8b30-45b5-9826-287bfb970c74/lines.aux /tmp/iueonoei/stga889db5c-8b30-45b5-9826-287bfb970c74/lines.txt >grep_out.txt' -[2023-05-26T13:48:23,871.237516Z] [job grep] completed success -[2023-05-26T13:48:23,871.550560Z] [step grep] completed success -[2023-05-26T13:48:23,872.055531Z] [workflow ] starting step sorted -[2023-05-26T13:48:23,872.438669Z] [step sorted] start -[2023-05-26T13:48:23,874.803782Z] [job sorted] /tmp/7lf3aa84$ sort \ - /tmp/6h7ltdar/stg5551dd85-4192-4d88-a91f-7b2dfbff9740/grep_out.txt > /tmp/7lf3aa84/sort_out.txt -[2023-05-26T13:48:23,880.517006Z] [job sorted] completed success -[2023-05-26T13:48:23,880.779028Z] [step sorted] completed success -[2023-05-26T13:48:23,881.006241Z] [workflow ] completed success -[2023-05-26T13:48:23,940.695763Z] 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 9bf68dd..8ab89b5 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": "arcp://uuid,c54a7289-731a-498b-9f08-3cc2bb801ba1/metadata/" + "@base": "arcp://uuid,8b3eb82c-de04-4dd0-b519-0354c0ce7cf5/metadata/" }, "https://w3id.org/bundle/context" ], "id": "/", "conformsTo": "https://w3id.org/cwl/prov/0.6.0", "manifest": "manifest.json", - "createdOn": "2023-05-26T15:48:23.945518", + "createdOn": "2023-11-09T14:19:38.990187", "createdBy": { - "uri": "urn:uuid:fb8f0a7a-121b-47e1-b955-75d213864598", - "name": "cwltool 3.1.20230513155734" + "uri": "urn:uuid:158cac0a-3a3b-4716-b023-2f9d48de837a", + "name": "cwltool 3.1.20231020140205" }, "authoredBy": null, "aggregates": [ { "uri": "urn:hash::sha1:b64565ee76fcd5296c48314f858f8e4672c71439", "bundledAs": { - "uri": "arcp://uuid,c54a7289-731a-498b-9f08-3cc2bb801ba1/data/b6/b64565ee76fcd5296c48314f858f8e4672c71439", + "uri": "arcp://uuid,8b3eb82c-de04-4dd0-b519-0354c0ce7cf5/data/b6/b64565ee76fcd5296c48314f858f8e4672c71439", "folder": "/data/b6/", "filename": "b64565ee76fcd5296c48314f858f8e4672c71439" } @@ -26,7 +26,7 @@ { "uri": "urn:hash::sha1:c708d7ef841f7e1748436b8ef5670d0b2de1a227", "bundledAs": { - "uri": "arcp://uuid,c54a7289-731a-498b-9f08-3cc2bb801ba1/data/c7/c708d7ef841f7e1748436b8ef5670d0b2de1a227", + "uri": "arcp://uuid,8b3eb82c-de04-4dd0-b519-0354c0ce7cf5/data/c7/c708d7ef841f7e1748436b8ef5670d0b2de1a227", "folder": "/data/c7/", "filename": "c708d7ef841f7e1748436b8ef5670d0b2de1a227" } @@ -34,7 +34,7 @@ { "uri": "urn:hash::sha1:601203afd61ae8b19d9c639d8d16296c9039d9cc", "bundledAs": { - "uri": "arcp://uuid,c54a7289-731a-498b-9f08-3cc2bb801ba1/data/60/601203afd61ae8b19d9c639d8d16296c9039d9cc", + "uri": "arcp://uuid,8b3eb82c-de04-4dd0-b519-0354c0ce7cf5/data/60/601203afd61ae8b19d9c639d8d16296c9039d9cc", "folder": "/data/60/", "filename": "601203afd61ae8b19d9c639d8d16296c9039d9cc" } @@ -42,54 +42,78 @@ { "uri": "urn:hash::sha1:8292d6f0985a62d4abd624fc72aecb8132193d6e", "bundledAs": { - "uri": "arcp://uuid,c54a7289-731a-498b-9f08-3cc2bb801ba1/data/82/8292d6f0985a62d4abd624fc72aecb8132193d6e", + "uri": "arcp://uuid,8b3eb82c-de04-4dd0-b519-0354c0ce7cf5/data/82/8292d6f0985a62d4abd624fc72aecb8132193d6e", "folder": "/data/82/", "filename": "8292d6f0985a62d4abd624fc72aecb8132193d6e" } }, { - "uri": "../metadata/provenance/primary.cwlprov.nt", - "mediatype": "application/n-triples", + "uri": null, + "mediatype": null, + "conformsTo": null, + "createdOn": "2023-11-09T14:13:31.670223", + "bundledAs": null + }, + { + "uri": "../metadata/provenance/primary.cwlprov.json", + "mediatype": "application/json", "conformsTo": [ - "http://www.w3.org/TR/2013/REC-prov-o-20130430/", + "http://www.w3.org/Submission/2013/SUBM-prov-json-20130424/", "https://w3id.org/cwl/prov/0.6.0" ], - "createdOn": "2023-05-26T15:48:23.945671", + "createdOn": "2023-11-09T14:19:38.990293", "createdBy": { - "uri": "urn:uuid:fb8f0a7a-121b-47e1-b955-75d213864598", - "name": "cwltool 3.1.20230513155734" + "uri": "urn:uuid:158cac0a-3a3b-4716-b023-2f9d48de837a", + "name": "cwltool 3.1.20231020140205" } }, { - "uri": "../metadata/provenance/primary.cwlprov.xml", - "mediatype": "application/xml", - "conformsTo": [ - "http://www.w3.org/TR/2013/NOTE-prov-xml-20130430/", - "https://w3id.org/cwl/prov/0.6.0" - ], - "createdOn": "2023-05-26T15:48:23.945700", + "uri": "../workflow/primary-output.json", + "mediatype": "application/json", + "conformsTo": null, + "createdOn": "2023-11-09T14:19:38.990309", "createdBy": { - "uri": "urn:uuid:fb8f0a7a-121b-47e1-b955-75d213864598", - "name": "cwltool 3.1.20230513155734" + "uri": "urn:uuid:158cac0a-3a3b-4716-b023-2f9d48de837a", + "name": "cwltool 3.1.20231020140205" + } + }, + { + "uri": "../workflow/primary-job.json", + "mediatype": "application/json", + "conformsTo": null, + "createdOn": "2023-11-09T14:19:38.990326", + "createdBy": { + "uri": "urn:uuid:158cac0a-3a3b-4716-b023-2f9d48de837a", + "name": "cwltool 3.1.20231020140205" } }, { "uri": null, "mediatype": null, "conformsTo": null, - "createdOn": "2023-05-26T14:26:28.975371", + "createdOn": "2023-07-27T14:06:01.852007", "bundledAs": null }, { - "uri": "../workflow/primary-output.json", - "mediatype": "application/json", - "conformsTo": null, - "createdOn": "2023-05-26T15:48:23.945747", + "uri": "../metadata/provenance/primary.cwlprov.jsonld", + "mediatype": "application/ld+json", + "conformsTo": [ + "http://www.w3.org/TR/2013/REC-prov-o-20130430/", + "https://w3id.org/cwl/prov/0.6.0" + ], + "createdOn": "2023-11-09T14:19:38.990355", "createdBy": { - "uri": "urn:uuid:fb8f0a7a-121b-47e1-b955-75d213864598", - "name": "cwltool 3.1.20230513155734" + "uri": "urn:uuid:158cac0a-3a3b-4716-b023-2f9d48de837a", + "name": "cwltool 3.1.20231020140205" } }, + { + "uri": null, + "mediatype": null, + "conformsTo": null, + "createdOn": "2023-11-09T14:19:27.306106", + "bundledAs": null + }, { "uri": "../metadata/provenance/primary.cwlprov.ttl", "mediatype": "text/turtle; charset=\"UTF-8\"", @@ -97,46 +121,43 @@ "http://www.w3.org/TR/2013/REC-prov-o-20130430/", "https://w3id.org/cwl/prov/0.6.0" ], - "createdOn": "2023-05-26T15:48:23.945770", + "createdOn": "2023-11-09T14:19:38.990387", "createdBy": { - "uri": "urn:uuid:fb8f0a7a-121b-47e1-b955-75d213864598", - "name": "cwltool 3.1.20230513155734" + "uri": "urn:uuid:158cac0a-3a3b-4716-b023-2f9d48de837a", + "name": "cwltool 3.1.20231020140205" } }, { - "uri": "../metadata/provenance/primary.cwlprov.json", - "mediatype": "application/json", + "uri": "../metadata/provenance/primary.cwlprov.xml", + "mediatype": "application/xml", "conformsTo": [ - "http://www.w3.org/Submission/2013/SUBM-prov-json-20130424/", + "http://www.w3.org/TR/2013/NOTE-prov-xml-20130430/", "https://w3id.org/cwl/prov/0.6.0" ], - "createdOn": "2023-05-26T15:48:23.945794", + "createdOn": "2023-11-09T14:19:38.990400", "createdBy": { - "uri": "urn:uuid:fb8f0a7a-121b-47e1-b955-75d213864598", - "name": "cwltool 3.1.20230513155734" + "uri": "urn:uuid:158cac0a-3a3b-4716-b023-2f9d48de837a", + "name": "cwltool 3.1.20231020140205" } }, { - "uri": "../metadata/provenance/primary.cwlprov.jsonld", - "mediatype": "application/ld+json", - "conformsTo": [ - "http://www.w3.org/TR/2013/REC-prov-o-20130430/", - "https://w3id.org/cwl/prov/0.6.0" - ], - "createdOn": "2023-05-26T15:48:23.945817", + "uri": "../metadata/logs/engine.158cac0a-3a3b-4716-b023-2f9d48de837a.txt", + "mediatype": "text/plain; charset='UTF-8'", + "conformsTo": null, + "createdOn": "2023-11-09T14:19:38.990412", "createdBy": { - "uri": "urn:uuid:fb8f0a7a-121b-47e1-b955-75d213864598", - "name": "cwltool 3.1.20230513155734" + "uri": "urn:uuid:158cac0a-3a3b-4716-b023-2f9d48de837a", + "name": "cwltool 3.1.20231020140205" } }, { "uri": "../workflow/packed.cwl", "mediatype": "text/x+yaml; charset=\"UTF-8\"", "conformsTo": "https://w3id.org/cwl/", - "createdOn": "2023-05-26T15:48:23.945839", + "createdOn": "2023-11-09T14:19:38.990424", "createdBy": { - "uri": "urn:uuid:fb8f0a7a-121b-47e1-b955-75d213864598", - "name": "cwltool 3.1.20230513155734" + "uri": "urn:uuid:158cac0a-3a3b-4716-b023-2f9d48de837a", + "name": "cwltool 3.1.20231020140205" } }, { @@ -146,89 +167,68 @@ "http://www.w3.org/TR/2013/REC-prov-n-20130430/", "https://w3id.org/cwl/prov/0.6.0" ], - "createdOn": "2023-05-26T15:48:23.945861", + "createdOn": "2023-11-09T14:19:38.990436", "createdBy": { - "uri": "urn:uuid:fb8f0a7a-121b-47e1-b955-75d213864598", - "name": "cwltool 3.1.20230513155734" + "uri": "urn:uuid:158cac0a-3a3b-4716-b023-2f9d48de837a", + "name": "cwltool 3.1.20231020140205" } }, { - "uri": null, - "mediatype": null, - "conformsTo": null, - "createdOn": "2023-05-26T15:46:54.400481", - "bundledAs": null - }, - { - "uri": "../metadata/logs/engine.fb8f0a7a-121b-47e1-b955-75d213864598.txt", - "mediatype": "text/plain; charset=\"UTF-8\"", - "conformsTo": null, - "createdOn": "2023-05-26T15:48:23.945903", - "createdBy": { - "uri": "urn:uuid:fb8f0a7a-121b-47e1-b955-75d213864598", - "name": "cwltool 3.1.20230513155734" - } - }, - { - "uri": "../workflow/primary-job.json", - "mediatype": "application/json", - "conformsTo": null, - "createdOn": "2023-05-26T15:48:23.945925", + "uri": "../metadata/provenance/primary.cwlprov.nt", + "mediatype": "application/n-triples", + "conformsTo": [ + "http://www.w3.org/TR/2013/REC-prov-o-20130430/", + "https://w3id.org/cwl/prov/0.6.0" + ], + "createdOn": "2023-11-09T14:19:38.990448", "createdBy": { - "uri": "urn:uuid:fb8f0a7a-121b-47e1-b955-75d213864598", - "name": "cwltool 3.1.20230513155734" + "uri": "urn:uuid:158cac0a-3a3b-4716-b023-2f9d48de837a", + "name": "cwltool 3.1.20231020140205" } }, { - "uri": null, - "mediatype": null, - "conformsTo": null, - "createdOn": "2023-05-26T15:41:51.439214", - "bundledAs": null - }, - { - "uri": "urn:uuid:75476671-b37f-4269-bbe1-27b37d2939de", - "createdOn": "2023-05-26T15:48:23.860191", + "uri": "urn:uuid:33d87d69-c088-4dbc-a286-6b2898d78c33", + "createdOn": "2023-11-09T14:19:38.941902", "createdBy": { - "uri": "urn:uuid:fb8f0a7a-121b-47e1-b955-75d213864598", - "name": "cwltool 3.1.20230513155734" + "uri": "urn:uuid:158cac0a-3a3b-4716-b023-2f9d48de837a", + "name": "cwltool 3.1.20231020140205" } }, { - "uri": "urn:uuid:9862346a-7552-4d95-8029-6a70052e86af", - "createdOn": "2023-05-26T15:48:23.875037", + "uri": "urn:uuid:59e50eb7-e28f-43b4-a925-1e095bcb6260", + "createdOn": "2023-11-09T14:19:38.954876", "createdBy": { - "uri": "urn:uuid:fb8f0a7a-121b-47e1-b955-75d213864598", - "name": "cwltool 3.1.20230513155734" + "uri": "urn:uuid:158cac0a-3a3b-4716-b023-2f9d48de837a", + "name": "cwltool 3.1.20231020140205" } } ], "annotations": [ { - "uri": "urn:uuid:a6487511-23bc-4dc1-b241-21ea7a8c2bd9", - "about": "urn:uuid:c54a7289-731a-498b-9f08-3cc2bb801ba1", + "uri": "urn:uuid:4412a90c-6b56-4d0b-832f-a31f643e9e9c", + "about": "urn:uuid:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5", "content": "/", "oa:motivatedBy": { "@id": "oa:describing" } }, { - "uri": "urn:uuid:dbe156df-61b9-483c-8798-405484bd4206", - "about": "urn:uuid:c54a7289-731a-498b-9f08-3cc2bb801ba1", + "uri": "urn:uuid:43eb1ff5-0304-4f28-b567-b1e0ca21f3f9", + "about": "urn:uuid:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5", "content": [ - "provenance/primary.cwlprov.nt", - "provenance/primary.cwlprov.xml", - "provenance/primary.cwlprov.ttl", "provenance/primary.cwlprov.json", "provenance/primary.cwlprov.jsonld", - "provenance/primary.cwlprov.provn" + "provenance/primary.cwlprov.ttl", + "provenance/primary.cwlprov.xml", + "provenance/primary.cwlprov.provn", + "provenance/primary.cwlprov.nt" ], "oa:motivatedBy": { "@id": "http://www.w3.org/ns/prov#has_provenance" } }, { - "uri": "urn:uuid:4b717bb5-3806-4273-9822-223eb9c7c29c", + "uri": "urn:uuid:e1654687-823c-4ee1-859e-7ca6eafa830e", "about": "../workflow/packed.cwl", "content": null, "oa:motivatedBy": { @@ -236,8 +236,8 @@ } }, { - "uri": "urn:uuid:68506c5a-bff0-4b68-a399-c37040c80635", - "about": "urn:uuid:c54a7289-731a-498b-9f08-3cc2bb801ba1", + "uri": "urn:uuid:cc1804ed-9029-42ab-a16d-82e0401910b6", + "about": "urn:uuid:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5", "content": [ "../workflow/packed.cwl", "../workflow/primary-job.json" @@ -247,10 +247,10 @@ } }, { - "uri": "urn:uuid:0ee15f55-b287-4041-b581-60a3aabe39a0", - "about": "urn:uuid:fb8f0a7a-121b-47e1-b955-75d213864598", + "uri": "urn:uuid:29f9c5f7-49bf-4a62-9cf3-ccb97f33811a", + "about": "urn:uuid:158cac0a-3a3b-4716-b023-2f9d48de837a", "content": [ - "metadata/logs/engine.fb8f0a7a-121b-47e1-b955-75d213864598.txt" + "metadata/logs/engine.158cac0a-3a3b-4716-b023-2f9d48de837a.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 23b859f..f68de02 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,c54a7289-731a-498b-9f08-3cc2bb801ba1/", - "metadata": "arcp://uuid,c54a7289-731a-498b-9f08-3cc2bb801ba1/metadata/", - "provenance": "arcp://uuid,c54a7289-731a-498b-9f08-3cc2bb801ba1/metadata/provenance/", - "wf": "arcp://uuid,c54a7289-731a-498b-9f08-3cc2bb801ba1/workflow/packed.cwl#", - "input": "arcp://uuid,c54a7289-731a-498b-9f08-3cc2bb801ba1/workflow/primary-job.json#", + "researchobject": "arcp://uuid,8b3eb82c-de04-4dd0-b519-0354c0ce7cf5/", + "metadata": "arcp://uuid,8b3eb82c-de04-4dd0-b519-0354c0ce7cf5/metadata/", + "provenance": "arcp://uuid,8b3eb82c-de04-4dd0-b519-0354c0ce7cf5/metadata/provenance/", + "wf": "arcp://uuid,8b3eb82c-de04-4dd0-b519-0354c0ce7cf5/workflow/packed.cwl#", + "input": "arcp://uuid,8b3eb82c-de04-4dd0-b519-0354c0ce7cf5/workflow/primary-job.json#", "wf4ever": "http://purl.org/wf4ever/wf4ever#" }, "agent": { - "id:4cf6bce8-84b8-4135-a30f-7c4771980295": {}, - "id:fb8f0a7a-121b-47e1-b955-75d213864598": { + "id:f12047e2-01e6-4fbd-a1fc-c7de599d87e9": {}, + "id:158cac0a-3a3b-4716-b023-2f9d48de837a": { "prov:type": [ { - "$": "prov:SoftwareAgent", + "$": "wfprov:WorkflowEngine", "type": "prov:QUALIFIED_NAME" }, { - "$": "wfprov:WorkflowEngine", + "$": "prov:SoftwareAgent", "type": "prov:QUALIFIED_NAME" } ], - "prov:label": "cwltool 3.1.20230513155734" + "prov:label": "cwltool 3.1.20231020140205" } }, "wasStartedBy": { "_:id1": { - "prov:activity": "id:fb8f0a7a-121b-47e1-b955-75d213864598", - "prov:starter": "id:4cf6bce8-84b8-4135-a30f-7c4771980295", - "prov:time": "2023-05-26T15:48:23.831055" + "prov:activity": "id:158cac0a-3a3b-4716-b023-2f9d48de837a", + "prov:starter": "id:f12047e2-01e6-4fbd-a1fc-c7de599d87e9", + "prov:time": "2023-11-09T14:19:38.925857" }, "_:id3": { - "prov:activity": "id:c54a7289-731a-498b-9f08-3cc2bb801ba1", - "prov:starter": "id:fb8f0a7a-121b-47e1-b955-75d213864598", - "prov:time": "2023-05-26T15:48:23.831147" + "prov:activity": "id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5", + "prov:starter": "id:158cac0a-3a3b-4716-b023-2f9d48de837a", + "prov:time": "2023-11-09T14:19:38.925920" }, "_:id8": { - "prov:activity": "id:028ac876-8c5b-4289-b4fc-e8fd5aad93b2", - "prov:starter": "id:c54a7289-731a-498b-9f08-3cc2bb801ba1", - "prov:time": "2023-05-26T15:48:23.862572" + "prov:activity": "id:7360446d-1622-44fd-b37d-570fe6c9a9b4", + "prov:starter": "id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5", + "prov:time": "2023-11-09T14:19:38.943374" }, "_:id17": { - "prov:activity": "id:8cd1699b-2bef-46b7-9ac8-1cd4c8b43737", - "prov:starter": "id:c54a7289-731a-498b-9f08-3cc2bb801ba1", - "prov:time": "2023-05-26T15:48:23.874423" + "prov:activity": "id:74439271-abb9-43d7-ad9b-3bea9b25aa2a", + "prov:starter": "id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5", + "prov:time": "2023-11-09T14:19:38.954588" } }, "activity": { - "id:c54a7289-731a-498b-9f08-3cc2bb801ba1": { - "prov:startTime": "2023-05-26T15:48:23.831083", + "id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5": { + "prov:startTime": "2023-11-09T14:19:38.925882", "prov:type": { "$": "wfprov:WorkflowRun", "type": "prov:QUALIFIED_NAME" }, "prov:label": "Run of workflow/packed.cwl#main" }, - "id:028ac876-8c5b-4289-b4fc-e8fd5aad93b2": { + "id:7360446d-1622-44fd-b37d-570fe6c9a9b4": { "prov:type": { "$": "wfprov:ProcessRun", "type": "prov:QUALIFIED_NAME" }, "prov:label": "Run of workflow/packed.cwl#main/grep" }, - "id:8cd1699b-2bef-46b7-9ac8-1cd4c8b43737": { + "id:74439271-abb9-43d7-ad9b-3bea9b25aa2a": { "prov:type": { "$": "wfprov:ProcessRun", "type": "prov:QUALIFIED_NAME" @@ -80,18 +80,18 @@ }, "wasAssociatedWith": { "_:id2": { - "prov:activity": "id:c54a7289-731a-498b-9f08-3cc2bb801ba1", - "prov:agent": "id:fb8f0a7a-121b-47e1-b955-75d213864598", + "prov:activity": "id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5", + "prov:agent": "id:158cac0a-3a3b-4716-b023-2f9d48de837a", "prov:plan": "wf:main" }, "_:id7": { - "prov:activity": "id:028ac876-8c5b-4289-b4fc-e8fd5aad93b2", - "prov:agent": "id:fb8f0a7a-121b-47e1-b955-75d213864598", + "prov:activity": "id:7360446d-1622-44fd-b37d-570fe6c9a9b4", + "prov:agent": "id:158cac0a-3a3b-4716-b023-2f9d48de837a", "prov:plan": "wf:main/grep" }, "_:id16": { - "prov:activity": "id:8cd1699b-2bef-46b7-9ac8-1cd4c8b43737", - "prov:agent": "id:fb8f0a7a-121b-47e1-b955-75d213864598", + "prov:activity": "id:74439271-abb9-43d7-ad9b-3bea9b25aa2a", + "prov:agent": "id:158cac0a-3a3b-4716-b023-2f9d48de837a", "prov:plan": "wf:main/sorted" } }, @@ -112,39 +112,39 @@ }, { "wfdesc:hasSubProcess": { - "$": "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", + "$": "wfdesc:Process", "type": "prov:QUALIFIED_NAME" } ] @@ -163,14 +163,14 @@ } } ], - "id:da3f2ffa-1423-49e3-a90c-c0ad95ddbf38": { + "id:6cb836e0-cc64-4894-8db8-e6804466da38": { "prov:type": [ { - "$": "wf4ever:File", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "wfprov:Artifact", + "$": "wf4ever:File", "type": "prov:QUALIFIED_NAME" } ], @@ -178,17 +178,17 @@ "cwlprov:nameroot": "lines", "cwlprov:nameext": ".txt" }, - "id:75476671-b37f-4269-bbe1-27b37d2939de": { + "id:33d87d69-c088-4dbc-a286-6b2898d78c33": { "prov:value": false }, - "id:259e9cca-63a5-408a-9d31-4e72fd4bb1f2": { + "id:aafa8231-543f-4250-ad31-c72b00e3601d": { "prov:type": [ { - "$": "wf4ever:File", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "wfprov:Artifact", + "$": "wf4ever:File", "type": "prov:QUALIFIED_NAME" } ], @@ -202,14 +202,14 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:d5487918-49e0-44ae-8ccf-e3c9d77bdde9": { + "id:29cb3049-319f-4e7c-9004-d20bf21efd81": { "prov:type": [ { - "$": "wf4ever:File", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "wfprov:Artifact", + "$": "wf4ever:File", "type": "prov:QUALIFIED_NAME" } ], @@ -223,14 +223,14 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:8e3beb04-4d9d-4064-8ba9-d6a6da378257": { + "id:212bf964-9940-4f63-ac22-0e849d7d76ec": { "prov:type": [ { - "$": "wf4ever:File", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "wfprov:Artifact", + "$": "wf4ever:File", "type": "prov:QUALIFIED_NAME" } ], @@ -238,7 +238,7 @@ "cwlprov:nameroot": "grep_out", "cwlprov:nameext": ".txt" }, - "id:9862346a-7552-4d95-8029-6a70052e86af": { + "id:59e50eb7-e28f-43b4-a925-1e095bcb6260": { "prov:value": false }, "data:8292d6f0985a62d4abd624fc72aecb8132193d6e": { @@ -247,14 +247,14 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:f81f0901-a485-4a8b-b059-15de2f4f82f8": { + "id:3aaebe26-84d6-4428-adfa-156a969476a9": { "prov:type": [ { - "$": "wf4ever:File", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "wfprov:Artifact", + "$": "wf4ever:File", "type": "prov:QUALIFIED_NAME" } ], @@ -265,67 +265,67 @@ }, "specializationOf": { "_:id4": { - "prov:specificEntity": "id:da3f2ffa-1423-49e3-a90c-c0ad95ddbf38", + "prov:specificEntity": "id:6cb836e0-cc64-4894-8db8-e6804466da38", "prov:generalEntity": "data:b64565ee76fcd5296c48314f858f8e4672c71439" }, "_:id9": { - "prov:specificEntity": "id:259e9cca-63a5-408a-9d31-4e72fd4bb1f2", + "prov:specificEntity": "id:aafa8231-543f-4250-ad31-c72b00e3601d", "prov:generalEntity": "data:b64565ee76fcd5296c48314f858f8e4672c71439" }, "_:id10": { - "prov:specificEntity": "id:d5487918-49e0-44ae-8ccf-e3c9d77bdde9", + "prov:specificEntity": "id:29cb3049-319f-4e7c-9004-d20bf21efd81", "prov:generalEntity": "data:c708d7ef841f7e1748436b8ef5670d0b2de1a227" }, "_:id13": { - "prov:specificEntity": "id:8e3beb04-4d9d-4064-8ba9-d6a6da378257", + "prov:specificEntity": "id:212bf964-9940-4f63-ac22-0e849d7d76ec", "prov:generalEntity": "data:601203afd61ae8b19d9c639d8d16296c9039d9cc" }, "_:id20": { - "prov:specificEntity": "id:f81f0901-a485-4a8b-b059-15de2f4f82f8", + "prov:specificEntity": "id:3aaebe26-84d6-4428-adfa-156a969476a9", "prov:generalEntity": "data:8292d6f0985a62d4abd624fc72aecb8132193d6e" } }, "used": { "_:id5": { - "prov:activity": "id:c54a7289-731a-498b-9f08-3cc2bb801ba1", - "prov:entity": "id:da3f2ffa-1423-49e3-a90c-c0ad95ddbf38", - "prov:time": "2023-05-26T15:48:23.860079", + "prov:activity": "id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5", + "prov:entity": "id:6cb836e0-cc64-4894-8db8-e6804466da38", + "prov:time": "2023-11-09T14:19:38.941858", "prov:role": { "$": "wf:main/grepsort_in", "type": "prov:QUALIFIED_NAME" } }, "_:id6": { - "prov:activity": "id:c54a7289-731a-498b-9f08-3cc2bb801ba1", - "prov:entity": "id:75476671-b37f-4269-bbe1-27b37d2939de", - "prov:time": "2023-05-26T15:48:23.860200", + "prov:activity": "id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5", + "prov:entity": "id:33d87d69-c088-4dbc-a286-6b2898d78c33", + "prov:time": "2023-11-09T14:19:38.941908", "prov:role": { "$": "wf:main/reverse_sort", "type": "prov:QUALIFIED_NAME" } }, "_:id12": { - "prov:activity": "id:028ac876-8c5b-4289-b4fc-e8fd5aad93b2", - "prov:entity": "id:259e9cca-63a5-408a-9d31-4e72fd4bb1f2", - "prov:time": "2023-05-26T15:48:23.864081", + "prov:activity": "id:7360446d-1622-44fd-b37d-570fe6c9a9b4", + "prov:entity": "id:aafa8231-543f-4250-ad31-c72b00e3601d", + "prov:time": "2023-11-09T14:19:38.948188", "prov:role": { "$": "wf:main/grep/grep_in", "type": "prov:QUALIFIED_NAME" } }, "_:id18": { - "prov:activity": "id:8cd1699b-2bef-46b7-9ac8-1cd4c8b43737", - "prov:entity": "id:9862346a-7552-4d95-8029-6a70052e86af", - "prov:time": "2023-05-26T15:48:23.875053", + "prov:activity": "id:74439271-abb9-43d7-ad9b-3bea9b25aa2a", + "prov:entity": "id:59e50eb7-e28f-43b4-a925-1e095bcb6260", + "prov:time": "2023-11-09T14:19:38.954880", "prov:role": { "$": "wf:main/sorted/reverse", "type": "prov:QUALIFIED_NAME" } }, "_:id19": { - "prov:activity": "id:8cd1699b-2bef-46b7-9ac8-1cd4c8b43737", - "prov:entity": "id:8e3beb04-4d9d-4064-8ba9-d6a6da378257", - "prov:time": "2023-05-26T15:48:23.875160", + "prov:activity": "id:74439271-abb9-43d7-ad9b-3bea9b25aa2a", + "prov:entity": "id:212bf964-9940-4f63-ac22-0e849d7d76ec", + "prov:time": "2023-11-09T14:19:38.954920", "prov:role": { "$": "wf:main/sorted/sort_in", "type": "prov:QUALIFIED_NAME" @@ -334,8 +334,8 @@ }, "wasDerivedFrom": { "_:id11": { - "prov:generatedEntity": "id:d5487918-49e0-44ae-8ccf-e3c9d77bdde9", - "prov:usedEntity": "id:259e9cca-63a5-408a-9d31-4e72fd4bb1f2", + "prov:generatedEntity": "id:29cb3049-319f-4e7c-9004-d20bf21efd81", + "prov:usedEntity": "id:aafa8231-543f-4250-ad31-c72b00e3601d", "prov:type": { "$": "cwlprov:SecondaryFile", "type": "prov:QUALIFIED_NAME" @@ -344,27 +344,27 @@ }, "wasGeneratedBy": { "_:id14": { - "prov:entity": "id:8e3beb04-4d9d-4064-8ba9-d6a6da378257", - "prov:activity": "id:028ac876-8c5b-4289-b4fc-e8fd5aad93b2", - "prov:time": "2023-05-26T15:48:23.869987", + "prov:entity": "id:212bf964-9940-4f63-ac22-0e849d7d76ec", + "prov:activity": "id:7360446d-1622-44fd-b37d-570fe6c9a9b4", + "prov:time": "2023-11-09T14:19:38.952843", "prov:role": { "$": "wf:main/grep/grep_out", "type": "prov:QUALIFIED_NAME" } }, "_:id21": { - "prov:entity": "id:f81f0901-a485-4a8b-b059-15de2f4f82f8", - "prov:activity": "id:8cd1699b-2bef-46b7-9ac8-1cd4c8b43737", - "prov:time": "2023-05-26T15:48:23.879437", + "prov:entity": "id:3aaebe26-84d6-4428-adfa-156a969476a9", + "prov:activity": "id:74439271-abb9-43d7-ad9b-3bea9b25aa2a", + "prov:time": "2023-11-09T14:19:38.956812", "prov:role": { "$": "wf:main/sorted/sort_out", "type": "prov:QUALIFIED_NAME" } }, "_:id23": { - "prov:entity": "id:f81f0901-a485-4a8b-b059-15de2f4f82f8", - "prov:activity": "id:c54a7289-731a-498b-9f08-3cc2bb801ba1", - "prov:time": "2023-05-26T15:48:23.882012", + "prov:entity": "id:3aaebe26-84d6-4428-adfa-156a969476a9", + "prov:activity": "id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5", + "prov:time": "2023-11-09T14:19:38.958044", "prov:role": { "$": "wf:main/primary/grepsort_out", "type": "prov:QUALIFIED_NAME" @@ -373,19 +373,19 @@ }, "wasEndedBy": { "_:id15": { - "prov:activity": "id:028ac876-8c5b-4289-b4fc-e8fd5aad93b2", - "prov:ender": "id:c54a7289-731a-498b-9f08-3cc2bb801ba1", - "prov:time": "2023-05-26T15:48:23.869968" + "prov:activity": "id:7360446d-1622-44fd-b37d-570fe6c9a9b4", + "prov:ender": "id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5", + "prov:time": "2023-11-09T14:19:38.952841" }, "_:id22": { - "prov:activity": "id:8cd1699b-2bef-46b7-9ac8-1cd4c8b43737", - "prov:ender": "id:c54a7289-731a-498b-9f08-3cc2bb801ba1", - "prov:time": "2023-05-26T15:48:23.879428" + "prov:activity": "id:74439271-abb9-43d7-ad9b-3bea9b25aa2a", + "prov:ender": "id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5", + "prov:time": "2023-11-09T14:19:38.956810" }, "_:id24": { - "prov:activity": "id:c54a7289-731a-498b-9f08-3cc2bb801ba1", - "prov:ender": "id:fb8f0a7a-121b-47e1-b955-75d213864598", - "prov:time": "2023-05-26T15:48:23.882082" + "prov:activity": "id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5", + "prov:ender": "id:158cac0a-3a3b-4716-b023-2f9d48de837a", + "prov:time": "2023-11-09T14:19:38.958081" } } } \ 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 4e75bd7..659ad3b 100644 --- a/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.jsonld +++ b/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.jsonld @@ -1,195 +1,122 @@ [ { - "@id": "urn:uuid:8cd1699b-2bef-46b7-9ac8-1cd4c8b43737", + "@id": "arcp://uuid,8b3eb82c-de04-4dd0-b519-0354c0ce7cf5/workflow/packed.cwl#main/sorted", "@type": [ - "http://www.w3.org/ns/prov#Activity", - "http://purl.org/wf4ever/wfprov#ProcessRun" - ], - "http://www.w3.org/2000/01/rdf-schema#label": [ - { - "@value": "Run of workflow/packed.cwl#main/sorted" - } - ], - "http://www.w3.org/ns/prov#qualifiedAssociation": [ - { - "@id": "_:N7ba83f8002564d158a6518b30753b605" - } - ], - "http://www.w3.org/ns/prov#qualifiedEnd": [ - { - "@id": "_:N84f023af014e4930b2d738af79ddb3a8" - } - ], - "http://www.w3.org/ns/prov#qualifiedStart": [ - { - "@id": "_:Nf5ff53eda40d43b487eedcbde86b13b8" - } + "http://www.w3.org/ns/prov#Plan", + "http://www.w3.org/ns/prov#Entity", + "http://purl.org/wf4ever/wfdesc#Process" + ] + }, + { + "@id": "urn:uuid:6cb836e0-cc64-4894-8db8-e6804466da38", + "@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#qualifiedUsage": [ - { - "@id": "_:Nd423a3c2807a4cb38d66fa641bd437ab" - }, + "http://www.w3.org/ns/prov#specializationOf": [ { - "@id": "_:Nd4d20629c0bd439d8d01debcdebe1fcf" + "@id": "urn:hash::sha1:b64565ee76fcd5296c48314f858f8e4672c71439" } ], - "http://www.w3.org/ns/prov#wasAssociatedWith": [ + "https://w3id.org/cwl/prov#basename": [ { - "@id": "urn:uuid:fb8f0a7a-121b-47e1-b955-75d213864598" + "@value": "lines.txt" } - ] - }, - { - "@id": "_:Nf5ff53eda40d43b487eedcbde86b13b8", - "@type": [ - "http://www.w3.org/ns/prov#Start" ], - "http://www.w3.org/ns/prov#atTime": [ + "https://w3id.org/cwl/prov#nameext": [ { - "@type": "http://www.w3.org/2001/XMLSchema#dateTime", - "@value": "2023-05-26T15:48:23.874423" + "@value": ".txt" } ], - "http://www.w3.org/ns/prov#hadActivity": [ + "https://w3id.org/cwl/prov#nameroot": [ { - "@id": "urn:uuid:c54a7289-731a-498b-9f08-3cc2bb801ba1" + "@value": "lines" } ] }, { - "@id": "_:N7ba83f8002564d158a6518b30753b605", + "@id": "urn:hash::sha1:b64565ee76fcd5296c48314f858f8e4672c71439", "@type": [ - "http://www.w3.org/ns/prov#Association" - ], - "http://www.w3.org/ns/prov#hadPlan": [ - { - "@id": "arcp://uuid,c54a7289-731a-498b-9f08-3cc2bb801ba1/workflow/packed.cwl#main/sorted" - } + "http://www.w3.org/ns/prov#Entity", + "http://purl.org/wf4ever/wfprov#Artifact" ] }, { - "@id": "_:N84f023af014e4930b2d738af79ddb3a8", + "@id": "urn:uuid:29cb3049-319f-4e7c-9004-d20bf21efd81", "@type": [ - "http://www.w3.org/ns/prov#End" + "http://www.w3.org/ns/prov#Entity", + "http://purl.org/wf4ever/wfprov#Artifact", + "http://purl.org/wf4ever/wf4ever#File" ], - "http://www.w3.org/ns/prov#atTime": [ + "http://www.w3.org/ns/prov#qualifiedDerivation": [ { - "@type": "http://www.w3.org/2001/XMLSchema#dateTime", - "@value": "2023-05-26T15:48:23.879428" + "@id": "_:N2ebb67de4cdd43759a70fb57d54d851b" } ], - "http://www.w3.org/ns/prov#hadActivity": [ + "http://www.w3.org/ns/prov#specializationOf": [ { - "@id": "urn:uuid:c54a7289-731a-498b-9f08-3cc2bb801ba1" + "@id": "urn:hash::sha1:c708d7ef841f7e1748436b8ef5670d0b2de1a227" } - ] - }, - { - "@id": "_:Nd423a3c2807a4cb38d66fa641bd437ab", - "@type": [ - "http://www.w3.org/ns/prov#Usage" ], - "http://www.w3.org/ns/prov#atTime": [ + "https://w3id.org/cwl/prov#basename": [ { - "@type": "http://www.w3.org/2001/XMLSchema#dateTime", - "@value": "2023-05-26T15:48:23.875053" + "@value": "lines.aux" } ], - "http://www.w3.org/ns/prov#entity": [ + "https://w3id.org/cwl/prov#nameext": [ { - "@id": "urn:uuid:9862346a-7552-4d95-8029-6a70052e86af" + "@value": ".aux" } ], - "http://www.w3.org/ns/prov#hadRole": [ + "https://w3id.org/cwl/prov#nameroot": [ { - "@id": "arcp://uuid,c54a7289-731a-498b-9f08-3cc2bb801ba1/workflow/packed.cwl#main/sorted/reverse" + "@value": "lines" } ] }, { - "@id": "_:Nd4d20629c0bd439d8d01debcdebe1fcf", + "@id": "_:N2ebb67de4cdd43759a70fb57d54d851b", "@type": [ - "http://www.w3.org/ns/prov#Usage" - ], - "http://www.w3.org/ns/prov#atTime": [ - { - "@type": "http://www.w3.org/2001/XMLSchema#dateTime", - "@value": "2023-05-26T15:48:23.875160" - } + "http://www.w3.org/ns/prov#Derivation", + "https://w3id.org/cwl/prov#SecondaryFile" ], "http://www.w3.org/ns/prov#entity": [ { - "@id": "urn:uuid:8e3beb04-4d9d-4064-8ba9-d6a6da378257" - } - ], - "http://www.w3.org/ns/prov#hadRole": [ - { - "@id": "arcp://uuid,c54a7289-731a-498b-9f08-3cc2bb801ba1/workflow/packed.cwl#main/sorted/sort_in" + "@id": "urn:uuid:aafa8231-543f-4250-ad31-c72b00e3601d" } ] }, { - "@id": "urn:uuid:4cf6bce8-84b8-4135-a30f-7c4771980295", + "@id": "urn:hash::sha1:8292d6f0985a62d4abd624fc72aecb8132193d6e", "@type": [ - "http://www.w3.org/ns/prov#Agent" + "http://www.w3.org/ns/prov#Entity", + "http://purl.org/wf4ever/wfprov#Artifact" ] }, { - "@id": "arcp://uuid,c54a7289-731a-498b-9f08-3cc2bb801ba1/workflow/packed.cwl#main/sorted", + "@id": "arcp://uuid,8b3eb82c-de04-4dd0-b519-0354c0ce7cf5/workflow/packed.cwl#main", "@type": [ + "http://purl.org/wf4ever/wfdesc#Workflow", "http://www.w3.org/ns/prov#Entity", - "http://purl.org/wf4ever/wfdesc#Process", "http://www.w3.org/ns/prov#Plan" - ] - }, - { - "@id": "urn:uuid:fb8f0a7a-121b-47e1-b955-75d213864598", - "@type": [ - "http://www.w3.org/ns/prov#SoftwareAgent", - "http://www.w3.org/ns/prov#Agent", - "http://purl.org/wf4ever/wfprov#WorkflowEngine" - ], - "http://www.w3.org/2000/01/rdf-schema#label": [ - { - "@value": "cwltool 3.1.20230513155734" - } ], - "http://www.w3.org/ns/prov#qualifiedStart": [ - { - "@id": "_:Nbbc01a9f69b64c70893e076964f1d795" - } - ] - }, - { - "@id": "_:Nbbc01a9f69b64c70893e076964f1d795", - "@type": [ - "http://www.w3.org/ns/prov#Start" - ], - "http://www.w3.org/ns/prov#atTime": [ + "http://purl.org/wf4ever/wfdesc#hasSubProcess": [ { - "@type": "http://www.w3.org/2001/XMLSchema#dateTime", - "@value": "2023-05-26T15:48:23.831055" - } - ], - "http://www.w3.org/ns/prov#hadActivity": [ + "@id": "arcp://uuid,8b3eb82c-de04-4dd0-b519-0354c0ce7cf5/workflow/packed.cwl#main/sorted" + }, { - "@id": "urn:uuid:4cf6bce8-84b8-4135-a30f-7c4771980295" + "@id": "arcp://uuid,8b3eb82c-de04-4dd0-b519-0354c0ce7cf5/workflow/packed.cwl#main/grep" } - ] - }, - { - "@id": "urn:uuid:75476671-b37f-4269-bbe1-27b37d2939de", - "@type": [ - "http://www.w3.org/ns/prov#Entity" ], - "http://www.w3.org/ns/prov#value": [ + "http://www.w3.org/2000/01/rdf-schema#label": [ { - "@value": false + "@value": "Prospective provenance" } ] }, { - "@id": "urn:uuid:9862346a-7552-4d95-8029-6a70052e86af", + "@id": "urn:uuid:59e50eb7-e28f-43b4-a925-1e095bcb6260", "@type": [ "http://www.w3.org/ns/prov#Entity" ], @@ -200,14 +127,7 @@ ] }, { - "@id": "urn:hash::sha1:8292d6f0985a62d4abd624fc72aecb8132193d6e", - "@type": [ - "http://www.w3.org/ns/prov#Entity", - "http://purl.org/wf4ever/wfprov#Artifact" - ] - }, - { - "@id": "arcp://uuid,c54a7289-731a-498b-9f08-3cc2bb801ba1/workflow/packed.cwl#main/grep", + "@id": "arcp://uuid,8b3eb82c-de04-4dd0-b519-0354c0ce7cf5/workflow/packed.cwl#main/grep", "@type": [ "http://www.w3.org/ns/prov#Plan", "http://www.w3.org/ns/prov#Entity", @@ -215,94 +135,87 @@ ] }, { - "@id": "urn:hash::sha1:601203afd61ae8b19d9c639d8d16296c9039d9cc", + "@id": "urn:uuid:3aaebe26-84d6-4428-adfa-156a969476a9", "@type": [ - "http://purl.org/wf4ever/wfprov#Artifact", - "http://www.w3.org/ns/prov#Entity" - ] - }, - { - "@id": "urn:uuid:d5487918-49e0-44ae-8ccf-e3c9d77bdde9", - "@type": [ - "http://purl.org/wf4ever/wfprov#Artifact", + "http://purl.org/wf4ever/wf4ever#File", "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#qualifiedDerivation": [ + "http://www.w3.org/ns/prov#qualifiedGeneration": [ { - "@id": "_:Nec571c089f6045998caae98f91cefc61" + "@id": "_:N73375a8f2eae46d08c92ea5b23d2e82f" + }, + { + "@id": "_:Nde8d8dd5bfe640a3927d3e428e30ae1b" } ], "http://www.w3.org/ns/prov#specializationOf": [ { - "@id": "urn:hash::sha1:c708d7ef841f7e1748436b8ef5670d0b2de1a227" + "@id": "urn:hash::sha1:8292d6f0985a62d4abd624fc72aecb8132193d6e" } ], "https://w3id.org/cwl/prov#basename": [ { - "@value": "lines.aux" + "@value": "sort_out.txt" } ], "https://w3id.org/cwl/prov#nameext": [ { - "@value": ".aux" + "@value": ".txt" } ], "https://w3id.org/cwl/prov#nameroot": [ { - "@value": "lines" + "@value": "sort_out" } ] }, { - "@id": "_:Nec571c089f6045998caae98f91cefc61", + "@id": "_:N73375a8f2eae46d08c92ea5b23d2e82f", "@type": [ - "https://w3id.org/cwl/prov#SecondaryFile", - "http://www.w3.org/ns/prov#Derivation" + "http://www.w3.org/ns/prov#Generation" ], - "http://www.w3.org/ns/prov#entity": [ + "http://www.w3.org/ns/prov#activity": [ { - "@id": "urn:uuid:259e9cca-63a5-408a-9d31-4e72fd4bb1f2" + "@id": "urn:uuid:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5" + } + ], + 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"http://www.w3.org/ns/prov#qualifiedGeneration": [ + { + "@id": "_:N30b9baad4a564cc9be1ffc7c6f4fdfd3" } ], "http://www.w3.org/ns/prov#specializationOf": [ { - "@id": "urn:hash::sha1:8292d6f0985a62d4abd624fc72aecb8132193d6e" + "@id": "urn:hash::sha1:601203afd61ae8b19d9c639d8d16296c9039d9cc" } ], "https://w3id.org/cwl/prov#basename": [ { - "@value": "sort_out.txt" + "@value": "grep_out.txt" } ], "https://w3id.org/cwl/prov#nameext": [ @@ -683,51 +645,89 @@ ], "https://w3id.org/cwl/prov#nameroot": [ { - "@value": "sort_out" + "@value": "grep_out" } ] }, { - "@id": "_:N0382bd4eeb9a444cb6898ad2f7171bcf", + "@id": "_:N30b9baad4a564cc9be1ffc7c6f4fdfd3", "@type": [ "http://www.w3.org/ns/prov#Generation" ], "http://www.w3.org/ns/prov#activity": [ { - "@id": "urn:uuid:8cd1699b-2bef-46b7-9ac8-1cd4c8b43737" + "@id": "urn:uuid:7360446d-1622-44fd-b37d-570fe6c9a9b4" } ], "http://www.w3.org/ns/prov#atTime": [ { "@type": "http://www.w3.org/2001/XMLSchema#dateTime", - "@value": "2023-05-26T15:48:23.879437" + "@value": "2023-11-09T14:19:38.952843" } ], "http://www.w3.org/ns/prov#hadRole": [ { - "@id": "arcp://uuid,c54a7289-731a-498b-9f08-3cc2bb801ba1/workflow/packed.cwl#main/sorted/sort_out" + "@id": "arcp://uuid,8b3eb82c-de04-4dd0-b519-0354c0ce7cf5/workflow/packed.cwl#main/grep/grep_out" } ] }, { - "@id": "_:N1b990190bd044dc49b7f8b50df0748e2", + "@id": "urn:uuid:33d87d69-c088-4dbc-a286-6b2898d78c33", "@type": [ - "http://www.w3.org/ns/prov#Generation" + "http://www.w3.org/ns/prov#Entity" ], - "http://www.w3.org/ns/prov#activity": [ + "http://www.w3.org/ns/prov#value": [ + { + "@value": false + } + ] + }, + { + "@id": "urn:hash::sha1:c708d7ef841f7e1748436b8ef5670d0b2de1a227", + "@type": [ + "http://www.w3.org/ns/prov#Entity", + "http://purl.org/wf4ever/wfprov#Artifact" + ] + }, + { + "@id": "urn:hash::sha1:601203afd61ae8b19d9c639d8d16296c9039d9cc", + "@type": [ + "http://purl.org/wf4ever/wfprov#Artifact", + "http://www.w3.org/ns/prov#Entity" + ] + }, + { + "@id": "urn:uuid:158cac0a-3a3b-4716-b023-2f9d48de837a", + "@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/2000/01/rdf-schema#label": [ { - "@id": "urn:uuid:c54a7289-731a-498b-9f08-3cc2bb801ba1" + "@value": "cwltool 3.1.20231020140205" } ], + "http://www.w3.org/ns/prov#qualifiedStart": [ + { + "@id": "_:Na09fc5448eff40069653d8ee767d63aa" + } + ] + }, + { + "@id": "_:Na09fc5448eff40069653d8ee767d63aa", + "@type": [ + "http://www.w3.org/ns/prov#Start" + ], "http://www.w3.org/ns/prov#atTime": [ { "@type": "http://www.w3.org/2001/XMLSchema#dateTime", - "@value": "2023-05-26T15:48:23.882012" + "@value": "2023-11-09T14:19:38.925857" } ], - "http://www.w3.org/ns/prov#hadRole": [ + "http://www.w3.org/ns/prov#hadActivity": [ { - "@id": "arcp://uuid,c54a7289-731a-498b-9f08-3cc2bb801ba1/workflow/packed.cwl#main/primary/grepsort_out" + "@id": "urn:uuid:f12047e2-01e6-4fbd-a1fc-c7de599d87e9" } ] } 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 00599f1..66bf320 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 @@ - . - . -_:N8a33e1994d004760a0a1911ca4577f1e . -_:N167dd86d35a74c209d6adef2e126e300 . -_:N9f6b820a63af4216a2113dfcd3f5fcf9 . -_:Naa640848ade540c998c8cd72b15f02e6 "2023-05-26T15:48:23.879437"^^ . - . - "Prospective provenance"^^ . -_:Nb2f35dc1fc6f4392b664b6de7af9bcca . - . - . - . -_:N16a156f1ddc24deb9fef57ab892803f4 . - "lines.txt"^^ . - "2023-05-26T15:48:23.831083"^^ . + . +_:N8087a676400347f4b3bc50070259847b . + . + . + _:N997644aae7cd4ea5ba0b117e5abdcc1f . + _:N8087a676400347f4b3bc50070259847b . +_:Nebf3f1d978ee48499890158994f1e068 . +_:Ne42883012d5c408599e06425f2443db1 . + 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-_:N9121aa75f0b142d989a80e32e4e9c4a2 . -_:N16a156f1ddc24deb9fef57ab892803f4 "2023-05-26T15:48:23.831055"^^ . - ".txt"^^ . - . -_:N6b8e3c29f308420ea0801ddf652020bc . - . - _:N6b8e3c29f308420ea0801ddf652020bc . - . - . - . - . - "grep_out.txt"^^ . -_:N6f6b9f0ab34644c5bc78a82409b45ec6 . -_:N4d987c30d7f747b782ea8ebde3c9b342 . -_:Ndd8585618927478294d89d624655300f . - "grep_out"^^ . -_:N4a6edec203ba42b9b2ec3eb1fe45b6dc "2023-05-26T15:48:23.860200"^^ . - . - . - _:N46d3c971e8bd4bc2bca849e565994d7d . - . - . -_:N4a6edec203ba42b9b2ec3eb1fe45b6dc . - . - . - . -_:N6f6b9f0ab34644c5bc78a82409b45ec6 "2023-05-26T15:48:23.862572"^^ . - "lines"^^ . - . - . -_:N46d3c971e8bd4bc2bca849e565994d7d . - . - . - "false"^^ . - . - . -_:N9f6b820a63af4216a2113dfcd3f5fcf9 . -_:Nb2f35dc1fc6f4392b664b6de7af9bcca . -_:N46d3c971e8bd4bc2bca849e565994d7d "2023-05-26T15:48:23.879428"^^ . - . -_:N8a33e1994d004760a0a1911ca4577f1e "2023-05-26T15:48:23.882082"^^ . -_:N66d0e39d9eda422f80cd5fa0d6bf2338 . - "cwltool 3.1.20230513155734"^^ . - . -_:N0b60fb08f85e4dda98c33b55de3c5582 "2023-05-26T15:48:23.869987"^^ . -_:N01eb6ecabc23418297e8bc84ca69babb . -_:Naa640848ade540c998c8cd72b15f02e6 . -_:N4a6edec203ba42b9b2ec3eb1fe45b6dc . - _:Naa640848ade540c998c8cd72b15f02e6 . - . -_:Naa640848ade540c998c8cd72b15f02e6 . -_:N167dd86d35a74c209d6adef2e126e300 . - . -_:N0b60fb08f85e4dda98c33b55de3c5582 . - . -_:N8a33e1994d004760a0a1911ca4577f1e . - . - . - "lines"^^ . -_:N0b60fb08f85e4dda98c33b55de3c5582 . - _:N4b73fa30c512459fa1d5ca3e70b4ff21 . -_:N40d933920c674e58a9fd9de749761ef8 "2023-05-26T15:48:23.874423"^^ . - _:Ndd8585618927478294d89d624655300f . - _:N8a33e1994d004760a0a1911ca4577f1e . -_:Ndd8585618927478294d89d624655300f . - _:N66d0e39d9eda422f80cd5fa0d6bf2338 . - . - . - _:N01a3cb820a32478c96fa483a50214609 . - _:N4a6edec203ba42b9b2ec3eb1fe45b6dc . - _:Nb2f35dc1fc6f4392b664b6de7af9bcca . + . + . + . +_:Nfa32c8a1c3a5400bb6c8521e517ec239 "2023-11-09T14:19:38.956812"^^ . +_:N15240696327e4a0291de9729cf5f36d3 "2023-11-09T14:19:38.956810"^^ . +_:Ne42883012d5c408599e06425f2443db1 "2023-11-09T14:19:38.952841"^^ . + _:N15240696327e4a0291de9729cf5f36d3 . +_:Ndf9e5e55630e490c86edc567e34acbaa . + "lines.txt"^^ . + . + _:Nbdc5fe6ecb0f4b7aa71271250770c2dc . + . . - . -_:N0b60fb08f85e4dda98c33b55de3c5582 . -_:N01eb6ecabc23418297e8bc84ca69babb . -_:N46d3c971e8bd4bc2bca849e565994d7d . - . -_:N4b73fa30c512459fa1d5ca3e70b4ff21 . -_:N4d987c30d7f747b782ea8ebde3c9b342 . - "sort_out.txt"^^ . - _:N9121aa75f0b142d989a80e32e4e9c4a2 . -_:N66d0e39d9eda422f80cd5fa0d6bf2338 "2023-05-26T15:48:23.882012"^^ . -_:N167dd86d35a74c209d6adef2e126e300 "2023-05-26T15:48:23.875160"^^ . -_:N16a156f1ddc24deb9fef57ab892803f4 . -_:N9f6b820a63af4216a2113dfcd3f5fcf9 "2023-05-26T15:48:23.864081"^^ . -_:Nb2f35dc1fc6f4392b664b6de7af9bcca "2023-05-26T15:48:23.869968"^^ . - ".txt"^^ . - . - . - _:N9f6b820a63af4216a2113dfcd3f5fcf9 . + . + . + . + . + . + . +_:Ndf9e5e55630e490c86edc567e34acbaa . + . + . + _:Ne42883012d5c408599e06425f2443db1 . +_:N48f0fc72a2de47ef8e3ab10979b55430 . +_:N8087a676400347f4b3bc50070259847b "2023-11-09T14:19:38.954920"^^ . +_:Nfa32c8a1c3a5400bb6c8521e517ec239 . + _:N03a93bc1b5164e2c8305d72220ee18d1 . + _:N7ba8dcecffe24c4999e80292ebec8a85 . +_:N1c56ce5e0f7c40398f420fddf91cb305 . + . +_:N2a72706dc1cb4ee28c67805c7a23e30e "2023-11-09T14:19:38.941858"^^ . . -_:N01a3cb820a32478c96fa483a50214609 . -_:N9121aa75f0b142d989a80e32e4e9c4a2 "2023-05-26T15:48:23.860079"^^ . - . - _:N0b60fb08f85e4dda98c33b55de3c5582 . -_:N167dd86d35a74c209d6adef2e126e300 . - "lines.aux"^^ . -_:N01a3cb820a32478c96fa483a50214609 "2023-05-26T15:48:23.831147"^^ . - _:N16a156f1ddc24deb9fef57ab892803f4 . - . - . - "lines.txt"^^ . + . + . +_:Nfa32c8a1c3a5400bb6c8521e517ec239 . +_:N3c5f1f9035f948ea989916292a3bada0 "2023-11-09T14:19:38.958044"^^ . + "Run of workflow/packed.cwl#main/sorted"^^ . + . + . + ".txt"^^ . +_:Nfa32c8a1c3a5400bb6c8521e517ec239 . + ".aux"^^ . + "grep_out.txt"^^ . + . + . + _:Nebf3f1d978ee48499890158994f1e068 . +_:Nf5c10e4c58e045ba808192d9e02a5612 . +_:Nbdc5fe6ecb0f4b7aa71271250770c2dc . + . + . + "lines"^^ . +_:Nbdc5fe6ecb0f4b7aa71271250770c2dc . +_:Nebf3f1d978ee48499890158994f1e068 "2023-11-09T14:19:38.954880"^^ . +_:N7ba8dcecffe24c4999e80292ebec8a85 . + . + . +_:Ne42883012d5c408599e06425f2443db1 . +_:N73fb5c52e7ff41c2a76416299b02c236 . + "lines"^^ . +_:N3309213148744c3294d2a961ad257fee . + _:Nf5c10e4c58e045ba808192d9e02a5612 . + . +_:Nf5c10e4c58e045ba808192d9e02a5612 "2023-11-09T14:19:38.958081"^^ . + . + "Prospective provenance"^^ . +_:N8087a676400347f4b3bc50070259847b . +_:N1c56ce5e0f7c40398f420fddf91cb305 "2023-11-09T14:19:38.925857"^^ . +_:N2a72706dc1cb4ee28c67805c7a23e30e . + . + "cwltool 3.1.20231020140205"^^ . + "false"^^ . +_:N671956f550ce47a6b0daf6b187fa87b7 . + "false"^^ . . -_:N01a3cb820a32478c96fa483a50214609 . +_:Nebf3f1d978ee48499890158994f1e068 . +_:N3c5f1f9035f948ea989916292a3bada0 . +_:N73fb5c52e7ff41c2a76416299b02c236 . + _:Ndf9e5e55630e490c86edc567e34acbaa . + _:Nbb95d8c248f148dcbcac1e1ad993e15d . + . +_:N8087a676400347f4b3bc50070259847b . +_:Ndf9e5e55630e490c86edc567e34acbaa . + . +_:Nf5c10e4c58e045ba808192d9e02a5612 . + _:N1c56ce5e0f7c40398f420fddf91cb305 . +_:N671956f550ce47a6b0daf6b187fa87b7 . +_:N2a72706dc1cb4ee28c67805c7a23e30e . +_:N997644aae7cd4ea5ba0b117e5abdcc1f "2023-11-09T14:19:38.954588"^^ . + . +_:N2a72706dc1cb4ee28c67805c7a23e30e . +_:Nbb95d8c248f148dcbcac1e1ad993e15d . +_:N1c56ce5e0f7c40398f420fddf91cb305 . +_:N7ba8dcecffe24c4999e80292ebec8a85 . + . +_:N997644aae7cd4ea5ba0b117e5abdcc1f . . - . - _:N6f6b9f0ab34644c5bc78a82409b45ec6 . -_:N6b8e3c29f308420ea0801ddf652020bc . -_:N66d0e39d9eda422f80cd5fa0d6bf2338 . - . +_:N3c5f1f9035f948ea989916292a3bada0 . + . +_:N997644aae7cd4ea5ba0b117e5abdcc1f . + . +_:N15240696327e4a0291de9729cf5f36d3 . + . + . + "lines.txt"^^ . +_:N48f0fc72a2de47ef8e3ab10979b55430 . + _:N3c5f1f9035f948ea989916292a3bada0 . + . +_:N03a93bc1b5164e2c8305d72220ee18d1 . + . + . + _:N3309213148744c3294d2a961ad257fee . +_:N03a93bc1b5164e2c8305d72220ee18d1 . +_:N03a93bc1b5164e2c8305d72220ee18d1 "2023-11-09T14:19:38.925920"^^ . + ".txt"^^ . +_:N48f0fc72a2de47ef8e3ab10979b55430 "2023-11-09T14:19:38.948188"^^ . +_:N7ba8dcecffe24c4999e80292ebec8a85 . + . +_:N671956f550ce47a6b0daf6b187fa87b7 "2023-11-09T14:19:38.941908"^^ . +_:N671956f550ce47a6b0daf6b187fa87b7 . + _:Nfa32c8a1c3a5400bb6c8521e517ec239 . + . +_:N48f0fc72a2de47ef8e3ab10979b55430 . +_:N3c5f1f9035f948ea989916292a3bada0 . + . + _:N2a72706dc1cb4ee28c67805c7a23e30e . + . +_:Nebf3f1d978ee48499890158994f1e068 . +_:Nbb95d8c248f148dcbcac1e1ad993e15d "2023-11-09T14:19:38.943374"^^ . + ".txt"^^ . +_:N3309213148744c3294d2a961ad257fee . +_:N7ba8dcecffe24c4999e80292ebec8a85 "2023-11-09T14:19:38.952843"^^ . + _:N671956f550ce47a6b0daf6b187fa87b7 . + "lines.aux"^^ . + "Run of workflow/packed.cwl#main/grep"^^ . + _:N48f0fc72a2de47ef8e3ab10979b55430 . +_:Nbb95d8c248f148dcbcac1e1ad993e15d . + "sort_out.txt"^^ . + "lines"^^ . +_:N15240696327e4a0291de9729cf5f36d3 . + ".txt"^^ . + "grep_out"^^ . + "Run of workflow/packed.cwl#main"^^ . + _:N73fb5c52e7ff41c2a76416299b02c236 . + . + . + . + . + "sort_out"^^ . 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 5a17738..921a1c9 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:4cf6bce8-84b8-4135-a30f-7c4771980295) - agent(id:fb8f0a7a-121b-47e1-b955-75d213864598, [prov:type='prov:SoftwareAgent', prov:type='wfprov:WorkflowEngine', prov:label="cwltool 3.1.20230513155734"]) - wasStartedBy(id:fb8f0a7a-121b-47e1-b955-75d213864598, -, id:4cf6bce8-84b8-4135-a30f-7c4771980295, 2023-05-26T15:48:23.831055) - activity(id:c54a7289-731a-498b-9f08-3cc2bb801ba1, 2023-05-26T15:48:23.831083, -, [prov:type='wfprov:WorkflowRun', prov:label="Run of workflow/packed.cwl#main"]) - wasAssociatedWith(id:c54a7289-731a-498b-9f08-3cc2bb801ba1, id:fb8f0a7a-121b-47e1-b955-75d213864598, wf:main) - wasStartedBy(id:c54a7289-731a-498b-9f08-3cc2bb801ba1, -, id:fb8f0a7a-121b-47e1-b955-75d213864598, 2023-05-26T15:48:23.831147) + agent(id:f12047e2-01e6-4fbd-a1fc-c7de599d87e9) + agent(id:158cac0a-3a3b-4716-b023-2f9d48de837a, [prov:type='wfprov:WorkflowEngine', prov:type='prov:SoftwareAgent', prov:label="cwltool 3.1.20231020140205"]) + wasStartedBy(id:158cac0a-3a3b-4716-b023-2f9d48de837a, -, id:f12047e2-01e6-4fbd-a1fc-c7de599d87e9, 2023-11-09T14:19:38.925857) + activity(id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5, 2023-11-09T14:19:38.925882, -, [prov:type='wfprov:WorkflowRun', prov:label="Run of workflow/packed.cwl#main"]) + wasAssociatedWith(id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5, id:158cac0a-3a3b-4716-b023-2f9d48de837a, wf:main) + wasStartedBy(id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5, -, id:158cac0a-3a3b-4716-b023-2f9d48de837a, 2023-11-09T14:19:38.925920) entity(wf:main, [prov:type='wfdesc:Workflow', prov:type='prov:Plan', 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:da3f2ffa-1423-49e3-a90c-c0ad95ddbf38, [prov:type='wf4ever:File', prov:type='wfprov:Artifact', cwlprov:basename="lines.txt", cwlprov:nameroot="lines", cwlprov:nameext=".txt"]) - specializationOf(id:da3f2ffa-1423-49e3-a90c-c0ad95ddbf38, data:b64565ee76fcd5296c48314f858f8e4672c71439) - used(id:c54a7289-731a-498b-9f08-3cc2bb801ba1, id:da3f2ffa-1423-49e3-a90c-c0ad95ddbf38, 2023-05-26T15:48:23.860079, [prov:role='wf:main/grepsort_in']) - entity(id:75476671-b37f-4269-bbe1-27b37d2939de, [prov:value="0" %% xsd:boolean]) - used(id:c54a7289-731a-498b-9f08-3cc2bb801ba1, id:75476671-b37f-4269-bbe1-27b37d2939de, 2023-05-26T15:48:23.860200, [prov:role='wf:main/reverse_sort']) - activity(id:028ac876-8c5b-4289-b4fc-e8fd5aad93b2, -, -, [prov:type='wfprov:ProcessRun', prov:label="Run of workflow/packed.cwl#main/grep"]) - wasAssociatedWith(id:028ac876-8c5b-4289-b4fc-e8fd5aad93b2, id:fb8f0a7a-121b-47e1-b955-75d213864598, wf:main/grep) - wasStartedBy(id:028ac876-8c5b-4289-b4fc-e8fd5aad93b2, -, id:c54a7289-731a-498b-9f08-3cc2bb801ba1, 2023-05-26T15:48:23.862572) + entity(id:6cb836e0-cc64-4894-8db8-e6804466da38, [prov:type='wfprov:Artifact', prov:type='wf4ever:File', cwlprov:basename="lines.txt", cwlprov:nameroot="lines", cwlprov:nameext=".txt"]) + specializationOf(id:6cb836e0-cc64-4894-8db8-e6804466da38, data:b64565ee76fcd5296c48314f858f8e4672c71439) + used(id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5, id:6cb836e0-cc64-4894-8db8-e6804466da38, 2023-11-09T14:19:38.941858, [prov:role='wf:main/grepsort_in']) + entity(id:33d87d69-c088-4dbc-a286-6b2898d78c33, [prov:value="0" %% xsd:boolean]) + used(id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5, id:33d87d69-c088-4dbc-a286-6b2898d78c33, 2023-11-09T14:19:38.941908, [prov:role='wf:main/reverse_sort']) + activity(id:7360446d-1622-44fd-b37d-570fe6c9a9b4, -, -, [prov:type='wfprov:ProcessRun', prov:label="Run of workflow/packed.cwl#main/grep"]) + wasAssociatedWith(id:7360446d-1622-44fd-b37d-570fe6c9a9b4, id:158cac0a-3a3b-4716-b023-2f9d48de837a, wf:main/grep) + wasStartedBy(id:7360446d-1622-44fd-b37d-570fe6c9a9b4, -, id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5, 2023-11-09T14:19:38.943374) entity(data:b64565ee76fcd5296c48314f858f8e4672c71439, [prov:type='wfprov:Artifact']) - entity(id:259e9cca-63a5-408a-9d31-4e72fd4bb1f2, [prov:type='wf4ever:File', prov:type='wfprov:Artifact', cwlprov:basename="lines.txt", cwlprov:nameroot="lines", cwlprov:nameext=".txt"]) - specializationOf(id:259e9cca-63a5-408a-9d31-4e72fd4bb1f2, data:b64565ee76fcd5296c48314f858f8e4672c71439) + entity(id:aafa8231-543f-4250-ad31-c72b00e3601d, [prov:type='wfprov:Artifact', prov:type='wf4ever:File', cwlprov:basename="lines.txt", cwlprov:nameroot="lines", cwlprov:nameext=".txt"]) + specializationOf(id:aafa8231-543f-4250-ad31-c72b00e3601d, data:b64565ee76fcd5296c48314f858f8e4672c71439) entity(data:c708d7ef841f7e1748436b8ef5670d0b2de1a227, [prov:type='wfprov:Artifact']) - entity(id:d5487918-49e0-44ae-8ccf-e3c9d77bdde9, [prov:type='wf4ever:File', prov:type='wfprov:Artifact', cwlprov:basename="lines.aux", cwlprov:nameroot="lines", cwlprov:nameext=".aux"]) - specializationOf(id:d5487918-49e0-44ae-8ccf-e3c9d77bdde9, data:c708d7ef841f7e1748436b8ef5670d0b2de1a227) - wasDerivedFrom(id:d5487918-49e0-44ae-8ccf-e3c9d77bdde9, id:259e9cca-63a5-408a-9d31-4e72fd4bb1f2, -, -, -, [prov:type='cwlprov:SecondaryFile']) - used(id:028ac876-8c5b-4289-b4fc-e8fd5aad93b2, id:259e9cca-63a5-408a-9d31-4e72fd4bb1f2, 2023-05-26T15:48:23.864081, [prov:role='wf:main/grep/grep_in']) + entity(id:29cb3049-319f-4e7c-9004-d20bf21efd81, [prov:type='wfprov:Artifact', prov:type='wf4ever:File', cwlprov:basename="lines.aux", cwlprov:nameroot="lines", cwlprov:nameext=".aux"]) + specializationOf(id:29cb3049-319f-4e7c-9004-d20bf21efd81, data:c708d7ef841f7e1748436b8ef5670d0b2de1a227) + wasDerivedFrom(id:29cb3049-319f-4e7c-9004-d20bf21efd81, id:aafa8231-543f-4250-ad31-c72b00e3601d, -, -, -, [prov:type='cwlprov:SecondaryFile']) + used(id:7360446d-1622-44fd-b37d-570fe6c9a9b4, id:aafa8231-543f-4250-ad31-c72b00e3601d, 2023-11-09T14:19:38.948188, [prov:role='wf:main/grep/grep_in']) entity(data:601203afd61ae8b19d9c639d8d16296c9039d9cc, [prov:type='wfprov:Artifact']) - entity(id:8e3beb04-4d9d-4064-8ba9-d6a6da378257, [prov:type='wf4ever:File', prov:type='wfprov:Artifact', cwlprov:basename="grep_out.txt", cwlprov:nameroot="grep_out", cwlprov:nameext=".txt"]) - specializationOf(id:8e3beb04-4d9d-4064-8ba9-d6a6da378257, data:601203afd61ae8b19d9c639d8d16296c9039d9cc) - wasGeneratedBy(id:8e3beb04-4d9d-4064-8ba9-d6a6da378257, id:028ac876-8c5b-4289-b4fc-e8fd5aad93b2, 2023-05-26T15:48:23.869987, [prov:role='wf:main/grep/grep_out']) - wasEndedBy(id:028ac876-8c5b-4289-b4fc-e8fd5aad93b2, -, id:c54a7289-731a-498b-9f08-3cc2bb801ba1, 2023-05-26T15:48:23.869968) - activity(id:8cd1699b-2bef-46b7-9ac8-1cd4c8b43737, -, -, [prov:type='wfprov:ProcessRun', prov:label="Run of workflow/packed.cwl#main/sorted"]) - wasAssociatedWith(id:8cd1699b-2bef-46b7-9ac8-1cd4c8b43737, id:fb8f0a7a-121b-47e1-b955-75d213864598, wf:main/sorted) - wasStartedBy(id:8cd1699b-2bef-46b7-9ac8-1cd4c8b43737, -, id:c54a7289-731a-498b-9f08-3cc2bb801ba1, 2023-05-26T15:48:23.874423) - entity(id:9862346a-7552-4d95-8029-6a70052e86af, [prov:value="0" %% xsd:boolean]) - used(id:8cd1699b-2bef-46b7-9ac8-1cd4c8b43737, id:9862346a-7552-4d95-8029-6a70052e86af, 2023-05-26T15:48:23.875053, [prov:role='wf:main/sorted/reverse']) - used(id:8cd1699b-2bef-46b7-9ac8-1cd4c8b43737, id:8e3beb04-4d9d-4064-8ba9-d6a6da378257, 2023-05-26T15:48:23.875160, [prov:role='wf:main/sorted/sort_in']) + entity(id:212bf964-9940-4f63-ac22-0e849d7d76ec, [prov:type='wfprov:Artifact', prov:type='wf4ever:File', cwlprov:basename="grep_out.txt", cwlprov:nameroot="grep_out", cwlprov:nameext=".txt"]) + specializationOf(id:212bf964-9940-4f63-ac22-0e849d7d76ec, data:601203afd61ae8b19d9c639d8d16296c9039d9cc) + wasGeneratedBy(id:212bf964-9940-4f63-ac22-0e849d7d76ec, id:7360446d-1622-44fd-b37d-570fe6c9a9b4, 2023-11-09T14:19:38.952843, [prov:role='wf:main/grep/grep_out']) + wasEndedBy(id:7360446d-1622-44fd-b37d-570fe6c9a9b4, -, id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5, 2023-11-09T14:19:38.952841) + activity(id:74439271-abb9-43d7-ad9b-3bea9b25aa2a, -, -, [prov:type='wfprov:ProcessRun', prov:label="Run of workflow/packed.cwl#main/sorted"]) + wasAssociatedWith(id:74439271-abb9-43d7-ad9b-3bea9b25aa2a, id:158cac0a-3a3b-4716-b023-2f9d48de837a, wf:main/sorted) + wasStartedBy(id:74439271-abb9-43d7-ad9b-3bea9b25aa2a, -, id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5, 2023-11-09T14:19:38.954588) + entity(id:59e50eb7-e28f-43b4-a925-1e095bcb6260, [prov:value="0" %% xsd:boolean]) + used(id:74439271-abb9-43d7-ad9b-3bea9b25aa2a, id:59e50eb7-e28f-43b4-a925-1e095bcb6260, 2023-11-09T14:19:38.954880, [prov:role='wf:main/sorted/reverse']) + used(id:74439271-abb9-43d7-ad9b-3bea9b25aa2a, id:212bf964-9940-4f63-ac22-0e849d7d76ec, 2023-11-09T14:19:38.954920, [prov:role='wf:main/sorted/sort_in']) entity(data:8292d6f0985a62d4abd624fc72aecb8132193d6e, [prov:type='wfprov:Artifact']) - entity(id:f81f0901-a485-4a8b-b059-15de2f4f82f8, [prov:type='wf4ever:File', prov:type='wfprov:Artifact', cwlprov:basename="sort_out.txt", cwlprov:nameroot="sort_out", cwlprov:nameext=".txt"]) - specializationOf(id:f81f0901-a485-4a8b-b059-15de2f4f82f8, data:8292d6f0985a62d4abd624fc72aecb8132193d6e) - wasGeneratedBy(id:f81f0901-a485-4a8b-b059-15de2f4f82f8, id:8cd1699b-2bef-46b7-9ac8-1cd4c8b43737, 2023-05-26T15:48:23.879437, [prov:role='wf:main/sorted/sort_out']) - wasEndedBy(id:8cd1699b-2bef-46b7-9ac8-1cd4c8b43737, -, id:c54a7289-731a-498b-9f08-3cc2bb801ba1, 2023-05-26T15:48:23.879428) - wasGeneratedBy(id:f81f0901-a485-4a8b-b059-15de2f4f82f8, id:c54a7289-731a-498b-9f08-3cc2bb801ba1, 2023-05-26T15:48:23.882012, [prov:role='wf:main/primary/grepsort_out']) - wasEndedBy(id:c54a7289-731a-498b-9f08-3cc2bb801ba1, -, id:fb8f0a7a-121b-47e1-b955-75d213864598, 2023-05-26T15:48:23.882082) + entity(id:3aaebe26-84d6-4428-adfa-156a969476a9, [prov:type='wfprov:Artifact', prov:type='wf4ever:File', cwlprov:basename="sort_out.txt", cwlprov:nameroot="sort_out", cwlprov:nameext=".txt"]) + specializationOf(id:3aaebe26-84d6-4428-adfa-156a969476a9, data:8292d6f0985a62d4abd624fc72aecb8132193d6e) + wasGeneratedBy(id:3aaebe26-84d6-4428-adfa-156a969476a9, id:74439271-abb9-43d7-ad9b-3bea9b25aa2a, 2023-11-09T14:19:38.956812, [prov:role='wf:main/sorted/sort_out']) + wasEndedBy(id:74439271-abb9-43d7-ad9b-3bea9b25aa2a, -, id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5, 2023-11-09T14:19:38.956810) + wasGeneratedBy(id:3aaebe26-84d6-4428-adfa-156a969476a9, id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5, 2023-11-09T14:19:38.958044, [prov:role='wf:main/primary/grepsort_out']) + wasEndedBy(id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5, -, id:158cac0a-3a3b-4716-b023-2f9d48de837a, 2023-11-09T14:19:38.958081) 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 9fc464f..d46c3d3 100644 --- a/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.ttl +++ b/tests/data/grepsort-run-1/metadata/provenance/primary.cwlprov.ttl @@ -3,34 +3,34 @@ @prefix id: . @prefix prov: . @prefix rdfs: . -@prefix wf: . +@prefix wf: . @prefix wf4ever: . @prefix wfdesc: . @prefix wfprov: . @prefix xsd: . -id:d5487918-49e0-44ae-8ccf-e3c9d77bdde9 a wf4ever:File, +id:29cb3049-319f-4e7c-9004-d20bf21efd81 a wf4ever:File, wfprov:Artifact, prov:Entity ; prov:qualifiedDerivation [ a prov:Derivation, cwlprov:SecondaryFile ; - prov:entity id:259e9cca-63a5-408a-9d31-4e72fd4bb1f2 ] ; + prov:entity id:aafa8231-543f-4250-ad31-c72b00e3601d ] ; prov:specializationOf data:c708d7ef841f7e1748436b8ef5670d0b2de1a227 ; cwlprov:basename "lines.aux"^^xsd:string ; cwlprov:nameext ".aux"^^xsd:string ; cwlprov:nameroot "lines"^^xsd:string . -id:f81f0901-a485-4a8b-b059-15de2f4f82f8 a wf4ever:File, +id:3aaebe26-84d6-4428-adfa-156a969476a9 a wf4ever:File, wfprov:Artifact, prov:Entity ; prov:qualifiedGeneration [ a prov:Generation ; - prov:activity id:c54a7289-731a-498b-9f08-3cc2bb801ba1 ; - prov:atTime "2023-05-26T15:48:23.882012"^^xsd:dateTime ; - prov:hadRole ], + prov:activity id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5 ; + prov:atTime "2023-11-09T14:19:38.958044"^^xsd:dateTime ; + prov:hadRole ], [ a prov:Generation ; - prov:activity id:8cd1699b-2bef-46b7-9ac8-1cd4c8b43737 ; - prov:atTime "2023-05-26T15:48:23.879437"^^xsd:dateTime ; - prov:hadRole ] ; + prov:activity id:74439271-abb9-43d7-ad9b-3bea9b25aa2a ; + prov:atTime "2023-11-09T14:19:38.956812"^^xsd:dateTime ; + prov:hadRole ] ; prov:specializationOf data:8292d6f0985a62d4abd624fc72aecb8132193d6e ; cwlprov:basename "sort_out.txt"^^xsd:string ; cwlprov:nameext ".txt"^^xsd:string ; @@ -40,8 +40,8 @@ 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 . @@ -52,65 +52,25 @@ data:8292d6f0985a62d4abd624fc72aecb8132193d6e a wfprov:Artifact, data:c708d7ef841f7e1748436b8ef5670d0b2de1a227 a wfprov:Artifact, prov:Entity . -id:028ac876-8c5b-4289-b4fc-e8fd5aad93b2 a wfprov:ProcessRun, - prov:Activity ; - rdfs:label "Run of workflow/packed.cwl#main/grep"^^xsd:string ; - prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; - prov:qualifiedEnd [ a prov:End ; - prov:atTime "2023-05-26T15:48:23.869968"^^xsd:dateTime ; - prov:hadActivity id:c54a7289-731a-498b-9f08-3cc2bb801ba1 ] ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2023-05-26T15:48:23.862572"^^xsd:dateTime ; - prov:hadActivity id:c54a7289-731a-498b-9f08-3cc2bb801ba1 ] ; - prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2023-05-26T15:48:23.864081"^^xsd:dateTime ; - prov:entity id:259e9cca-63a5-408a-9d31-4e72fd4bb1f2 ; - prov:hadRole ] ; - prov:wasAssociatedWith id:fb8f0a7a-121b-47e1-b955-75d213864598 . - -id:4cf6bce8-84b8-4135-a30f-7c4771980295 a prov:Agent . - -id:75476671-b37f-4269-bbe1-27b37d2939de a prov:Entity ; - prov:value false . - -id:8cd1699b-2bef-46b7-9ac8-1cd4c8b43737 a wfprov:ProcessRun, - prov:Activity ; - rdfs:label "Run of workflow/packed.cwl#main/sorted"^^xsd:string ; - prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; - prov:qualifiedEnd [ a prov:End ; - prov:atTime "2023-05-26T15:48:23.879428"^^xsd:dateTime ; - prov:hadActivity id:c54a7289-731a-498b-9f08-3cc2bb801ba1 ] ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2023-05-26T15:48:23.874423"^^xsd:dateTime ; - prov:hadActivity id:c54a7289-731a-498b-9f08-3cc2bb801ba1 ] ; - prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2023-05-26T15:48:23.875053"^^xsd:dateTime ; - prov:entity id:9862346a-7552-4d95-8029-6a70052e86af ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2023-05-26T15:48:23.875160"^^xsd:dateTime ; - prov:entity id:8e3beb04-4d9d-4064-8ba9-d6a6da378257 ; - prov:hadRole ] ; - prov:wasAssociatedWith id:fb8f0a7a-121b-47e1-b955-75d213864598 . - -id:8e3beb04-4d9d-4064-8ba9-d6a6da378257 a wf4ever:File, +id:212bf964-9940-4f63-ac22-0e849d7d76ec a wf4ever:File, wfprov:Artifact, prov:Entity ; prov:qualifiedGeneration [ a prov:Generation ; - prov:activity id:028ac876-8c5b-4289-b4fc-e8fd5aad93b2 ; - prov:atTime "2023-05-26T15:48:23.869987"^^xsd:dateTime ; - prov:hadRole ] ; + prov:activity id:7360446d-1622-44fd-b37d-570fe6c9a9b4 ; + prov:atTime "2023-11-09T14:19:38.952843"^^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:9862346a-7552-4d95-8029-6a70052e86af a prov:Entity ; +id:33d87d69-c088-4dbc-a286-6b2898d78c33 a prov:Entity ; + prov:value false . + +id:59e50eb7-e28f-43b4-a925-1e095bcb6260 a prov:Entity ; prov:value false . -id:da3f2ffa-1423-49e3-a90c-c0ad95ddbf38 a wf4ever:File, +id:6cb836e0-cc64-4894-8db8-e6804466da38 a wf4ever:File, wfprov:Artifact, prov:Entity ; prov:specializationOf data:b64565ee76fcd5296c48314f858f8e4672c71439 ; @@ -118,18 +78,58 @@ id:da3f2ffa-1423-49e3-a90c-c0ad95ddbf38 a wf4ever:File, cwlprov:nameext ".txt"^^xsd:string ; cwlprov:nameroot "lines"^^xsd:string . - a wfdesc:Process, +id:7360446d-1622-44fd-b37d-570fe6c9a9b4 a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of workflow/packed.cwl#main/grep"^^xsd:string ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedEnd [ a prov:End ; + prov:atTime "2023-11-09T14:19:38.952841"^^xsd:dateTime ; + prov:hadActivity id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5 ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2023-11-09T14:19:38.943374"^^xsd:dateTime ; + prov:hadActivity id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5 ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2023-11-09T14:19:38.948188"^^xsd:dateTime ; + prov:entity id:aafa8231-543f-4250-ad31-c72b00e3601d ; + prov:hadRole ] ; + prov:wasAssociatedWith id:158cac0a-3a3b-4716-b023-2f9d48de837a . + +id:74439271-abb9-43d7-ad9b-3bea9b25aa2a a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of workflow/packed.cwl#main/sorted"^^xsd:string ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedEnd [ a prov:End ; + prov:atTime "2023-11-09T14:19:38.956810"^^xsd:dateTime ; + prov:hadActivity id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5 ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2023-11-09T14:19:38.954588"^^xsd:dateTime ; + prov:hadActivity id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5 ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2023-11-09T14:19:38.954880"^^xsd:dateTime ; + prov:entity id:59e50eb7-e28f-43b4-a925-1e095bcb6260 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2023-11-09T14:19:38.954920"^^xsd:dateTime ; + prov:entity id:212bf964-9940-4f63-ac22-0e849d7d76ec ; + prov:hadRole ] ; + prov:wasAssociatedWith id:158cac0a-3a3b-4716-b023-2f9d48de837a . + +id:f12047e2-01e6-4fbd-a1fc-c7de599d87e9 a prov:Agent . + + 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:259e9cca-63a5-408a-9d31-4e72fd4bb1f2 a wf4ever:File, +id:aafa8231-543f-4250-ad31-c72b00e3601d a wf4ever:File, wfprov:Artifact, prov:Entity ; prov:specializationOf data:b64565ee76fcd5296c48314f858f8e4672c71439 ; @@ -137,33 +137,33 @@ id:259e9cca-63a5-408a-9d31-4e72fd4bb1f2 a wf4ever:File, cwlprov:nameext ".txt"^^xsd:string ; cwlprov:nameroot "lines"^^xsd:string . -id:c54a7289-731a-498b-9f08-3cc2bb801ba1 a wfprov:WorkflowRun, +id:158cac0a-3a3b-4716-b023-2f9d48de837a a wfprov:WorkflowEngine, + prov:Agent, + prov:SoftwareAgent ; + rdfs:label "cwltool 3.1.20231020140205"^^xsd:string ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2023-11-09T14:19:38.925857"^^xsd:dateTime ; + prov:hadActivity id:f12047e2-01e6-4fbd-a1fc-c7de599d87e9 ] . + +id:8b3eb82c-de04-4dd0-b519-0354c0ce7cf5 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 "2023-05-26T15:48:23.882082"^^xsd:dateTime ; - prov:hadActivity id:fb8f0a7a-121b-47e1-b955-75d213864598 ] ; + prov:atTime "2023-11-09T14:19:38.958081"^^xsd:dateTime ; + prov:hadActivity id:158cac0a-3a3b-4716-b023-2f9d48de837a ] ; prov:qualifiedStart [ a prov:Start ; - prov:atTime "2023-05-26T15:48:23.831147"^^xsd:dateTime ; - prov:hadActivity id:fb8f0a7a-121b-47e1-b955-75d213864598 ] ; + prov:atTime "2023-11-09T14:19:38.925920"^^xsd:dateTime ; + prov:hadActivity id:158cac0a-3a3b-4716-b023-2f9d48de837a ] ; prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2023-05-26T15:48:23.860200"^^xsd:dateTime ; - prov:entity id:75476671-b37f-4269-bbe1-27b37d2939de ; - prov:hadRole ], + prov:atTime "2023-11-09T14:19:38.941858"^^xsd:dateTime ; + prov:entity id:6cb836e0-cc64-4894-8db8-e6804466da38 ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2023-05-26T15:48:23.860079"^^xsd:dateTime ; - prov:entity id:da3f2ffa-1423-49e3-a90c-c0ad95ddbf38 ; - prov:hadRole ] ; - prov:startedAtTime "2023-05-26T15:48:23.831083"^^xsd:dateTime ; - prov:wasAssociatedWith id:fb8f0a7a-121b-47e1-b955-75d213864598 . - -id:fb8f0a7a-121b-47e1-b955-75d213864598 a wfprov:WorkflowEngine, - prov:Agent, - prov:SoftwareAgent ; - rdfs:label "cwltool 3.1.20230513155734"^^xsd:string ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2023-05-26T15:48:23.831055"^^xsd:dateTime ; - prov:hadActivity id:4cf6bce8-84b8-4135-a30f-7c4771980295 ] . + prov:atTime "2023-11-09T14:19:38.941908"^^xsd:dateTime ; + prov:entity id:33d87d69-c088-4dbc-a286-6b2898d78c33 ; + prov:hadRole ] ; + prov:startedAtTime "2023-11-09T14:19:38.925882"^^xsd:dateTime ; + prov:wasAssociatedWith id:158cac0a-3a3b-4716-b023-2f9d48de837a . 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 c8e3b3b..b8a3b9f 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 3.1.20230513155734 + + + + cwltool 3.1.20231020140205 wfprov:WorkflowEngine - - - 2023-05-26T15:48:23.831055 + + + 2023-11-09T14:19:38.925857 - - 2023-05-26T15:48:23.831083 + + 2023-11-09T14:19:38.925882 Run of workflow/packed.cwl#main wfprov:WorkflowRun - - + + - - - 2023-05-26T15:48:23.831147 + + + 2023-11-09T14:19:38.925920 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 - + - - - 2023-05-26T15:48:23.860079 + + + 2023-11-09T14:19:38.941858 wf:main/grepsort_in - + false - - - 2023-05-26T15:48:23.860200 + + + 2023-11-09T14:19:38.941908 wf:main/reverse_sort - + Run of workflow/packed.cwl#main/grep wfprov:ProcessRun - - + + - - - 2023-05-26T15:48:23.862572 + + + 2023-11-09T14:19:38.943374 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 - - - 2023-05-26T15:48:23.864081 + + + 2023-11-09T14:19:38.948188 wf:main/grep/grep_in wfprov:Artifact - + wf4ever:File wfprov:Artifact grep_out.txt @@ -136,53 +136,53 @@ grep_out - + - - - 2023-05-26T15:48:23.869987 + + + 2023-11-09T14:19:38.952843 wf:main/grep/grep_out - - - 2023-05-26T15:48:23.869968 + + + 2023-11-09T14:19:38.952841 - + Run of workflow/packed.cwl#main/sorted wfprov:ProcessRun - - + + - - - 2023-05-26T15:48:23.874423 + + + 2023-11-09T14:19:38.954588 - + false - - - 2023-05-26T15:48:23.875053 + + + 2023-11-09T14:19:38.954880 wf:main/sorted/reverse - - - 2023-05-26T15:48:23.875160 + + + 2023-11-09T14:19:38.954920 wf:main/sorted/sort_in wfprov:Artifact - + wf4ever:File wfprov:Artifact sort_out.txt @@ -190,29 +190,29 @@ sort_out - + - - - 2023-05-26T15:48:23.879437 + + + 2023-11-09T14:19:38.956812 wf:main/sorted/sort_out - - - 2023-05-26T15:48:23.879428 + + + 2023-11-09T14:19:38.956810 - - - 2023-05-26T15:48:23.882012 + + + 2023-11-09T14:19:38.958044 wf:main/primary/grepsort_out - - - 2023-05-26T15:48:23.882082 + + + 2023-11-09T14:19:38.958081 diff --git a/tests/data/grepsort-run-1/snapshot/grepsort.cwl b/tests/data/grepsort-run-1/snapshot/grepsort.cwl index 88fd10d..b1b4faf 100644 --- a/tests/data/grepsort-run-1/snapshot/grepsort.cwl +++ b/tests/data/grepsort-run-1/snapshot/grepsort.cwl @@ -19,6 +19,7 @@ inputs: outputs: grepsort_out: type: File + format: "https://www.iana.org/assignments/media-types/text/plain" outputSource: sorted/sort_out steps: diff --git a/tests/data/grepsort-run-1/snapshot/sorttool.cwl b/tests/data/grepsort-run-1/snapshot/sorttool.cwl index 0fddb4f..e356ff7 100644 --- a/tests/data/grepsort-run-1/snapshot/sorttool.cwl +++ b/tests/data/grepsort-run-1/snapshot/sorttool.cwl @@ -20,6 +20,7 @@ inputs: outputs: sort_out: type: File + format: "https://www.iana.org/assignments/media-types/text/plain" outputBinding: glob: sort_out.txt stdout: sort_out.txt diff --git a/tests/data/grepsort-run-1/tagmanifest-sha1.txt b/tests/data/grepsort-run-1/tagmanifest-sha1.txt index 4188bf0..39f38cf 100644 --- a/tests/data/grepsort-run-1/tagmanifest-sha1.txt +++ b/tests/data/grepsort-run-1/tagmanifest-sha1.txt @@ -1,15 +1,15 @@ -416dffad85cbeb64b8d8b8e57975f63b33cdc95a workflow/packed.cwl +c5b7d9f8068acd082341e7a0e7eaa2cb84b34b33 workflow/packed.cwl adeeed935d1e6d141fda6fd72619106ef07fa4ee workflow/primary-job.json -88c5cdba4a190de6778cea96013df4268e15f8dc metadata/provenance/primary.cwlprov.xml -3023daec0b2415a2a1715f1c5ff5be4edf918660 metadata/provenance/primary.cwlprov.provn -904c3e9bf67c549355d4ef2713b17ca15c36f004 metadata/provenance/primary.cwlprov.json -b51d6b16116a76c97739b7512e6048cda928d92a metadata/provenance/primary.cwlprov.ttl -579b1e653d5610465d2bae6e16305413a311d022 metadata/provenance/primary.cwlprov.nt -0a95befdb8124c86a4fb7a3ecb12a481752fed3f metadata/provenance/primary.cwlprov.jsonld -64f60aa7e1df0744f2d9e49b0d830521df28d81b workflow/primary-output.json -c9a5474805659078290b7aefa9e25dd6c47a997d snapshot/grepsort.cwl +4b5db56447b189851861151c735b02b51b7cf761 metadata/provenance/primary.cwlprov.xml +4f647e053ead83e9f0bc7bf8a655ded162a05744 metadata/provenance/primary.cwlprov.provn +7150b1aad65670c3faecd0ea270f537c9382445e metadata/provenance/primary.cwlprov.json +4244ced471826a57a0784d32aa26824adefeadb1 metadata/provenance/primary.cwlprov.ttl +bbdd79f5f58de97351b98abc3414a948c8bcab5b metadata/provenance/primary.cwlprov.nt +efcbda0a5da8e60c23f7e739678b39d00ec12501 metadata/provenance/primary.cwlprov.jsonld +3c8d42231d1fae6e3b7632587514184cea75bfd1 workflow/primary-output.json +d92e46b8f89cd2153fd2c606468a253c11b19087 snapshot/grepsort.cwl 368b85477ec6619b0369fc35503971199456cd15 snapshot/greptool.cwl -9e6fd331579bf88e7b10d7870b4c926f4fcd7cd5 snapshot/sorttool.cwl -b1ee8d61649bfb9c068387ea8aa7203e501073ff metadata/logs/engine.fb8f0a7a-121b-47e1-b955-75d213864598.txt -db990a700941409626a6a7997109bc26ebc9e944 metadata/manifest.json -5e083af3d5121c7d6ca415b58e0c6ff083f9783d bag-info.txt +3a5c1a8152bd4587457479f32c24d65a8535aa0d snapshot/sorttool.cwl +911b5925f1d5ac1570c73c9788623c37c1ed5a8a metadata/logs/engine.158cac0a-3a3b-4716-b023-2f9d48de837a.txt +aa67e635cb2dfc54ade4d4f9bf7b0ef1c6b1a744 metadata/manifest.json +cca4e9077dd13ad872c14d96b5a1455b5fe91d66 bag-info.txt diff --git a/tests/data/grepsort-run-1/tagmanifest-sha256.txt b/tests/data/grepsort-run-1/tagmanifest-sha256.txt index 136c0b6..c4a0dba 100644 --- a/tests/data/grepsort-run-1/tagmanifest-sha256.txt +++ b/tests/data/grepsort-run-1/tagmanifest-sha256.txt @@ -1,15 +1,15 @@ -bb769f586082c3a6d61f660f773991b6dd838af594d7c0e127cfd9b64005cf88 workflow/packed.cwl +434a812d6549d1fce450cfcc2a1bc77931891897b70306fb0e7b20c92831270a workflow/packed.cwl cc9f6f6f599e24901397820affc253b1d01f8f4f137174292bf4cea566320782 workflow/primary-job.json -b8b7af5b29fdbe5c1cfa24ac3d9a2ecfc7fd8be36819f01b9773c932314e46ac metadata/provenance/primary.cwlprov.xml -7dc62b0564260ce69ab345a03cd897d4e43a17745e049832fe3a2b5b90d3c85f metadata/provenance/primary.cwlprov.provn -259dbffc64e04aa5014d3f3456cf01483d5a2aec189d44c20cf5a9bc64b3a2d6 metadata/provenance/primary.cwlprov.json -1aa1a46a7b750860894ba339634e5b4ac032a2f04d2e5a6816b818b7fb11e857 metadata/provenance/primary.cwlprov.ttl -5f92793b87ee5303c2d3bb992bf1edccdb5c1f9ddf8e6e82437105a9324a9865 metadata/provenance/primary.cwlprov.nt -5d71799600c61044ce20657dec7bbb553a4c01b96d5f146f1b663c3895e0ee22 metadata/provenance/primary.cwlprov.jsonld -fa765307471d1bba0eb9a88df7edff1c23ca0a8bf11a059484fd96c707edd67d workflow/primary-output.json -1461b99ca972c8ba2ba641a0b143a91793b30f2a5df359835ccab70fae5dd032 snapshot/grepsort.cwl +74def51cbc2e0c29d2408717e74db8c2e2ce8ce86200548248993cc541086ffb metadata/provenance/primary.cwlprov.xml +26bef8a0a96ae0d08e40eb97f0d8728adb7121153bf03cc40c6b8c523a5a21da metadata/provenance/primary.cwlprov.provn +0e329011e443271b94e6cb382f29b8729802a32ec618e8a29a1d6180ffb86731 metadata/provenance/primary.cwlprov.json +e51747dc8ea86741c3f677e68a1ba12234411c9e4b15f89afe68aa160c821e9a metadata/provenance/primary.cwlprov.ttl +8147120e89529141bca895f212976f928fd97b460ba563fca7a8a9dd744c16ac metadata/provenance/primary.cwlprov.nt +033ca4bb821ae1baada5737b9280ef9128610ddca9ee22c346d891fc6cdc4c6c metadata/provenance/primary.cwlprov.jsonld +f1e017f6cf37a7d2989e104849b9f593969cd65075efffb33dcbe65351fa13ad workflow/primary-output.json +53b91ac0cbe8b4c0a2f91f47eea9080f1aab2eb50d50397d8920eaeae3f1f3fb snapshot/grepsort.cwl 8a8a2f5b4f23e13b79c550740d3f94330c64ba77af3bc0b3449545cf32ecbb91 snapshot/greptool.cwl -87c9204a0b39da00e5b8fa712cc5060833155ede139c175c76ae040b0829b8f1 snapshot/sorttool.cwl -a498d26d353ab6cdf733d48297246136c324fb13b9c85fcbe75f31cb392d0343 metadata/logs/engine.fb8f0a7a-121b-47e1-b955-75d213864598.txt -75668472aff14533c3bf882b653a22311935bf88270034d413b147a553bbf274 metadata/manifest.json -748afe5a5a36a12ab41c7a4864283ea6d9f071f10485cd4a5e1ce30284274425 bag-info.txt +0f7c7844de53c52ba941e47d14bb8a5f1b09e7595e47bf4d0eaf95d4472ab690 snapshot/sorttool.cwl +dd20d6c7e32f5f699258046e35b07a3be1ac4e89afb91f53b2d18c503c3e9954 metadata/logs/engine.158cac0a-3a3b-4716-b023-2f9d48de837a.txt +bd5e079597fa4706c9814b5f1d2fdc9bb98aa406459f1153db0a3856ef5a1008 metadata/manifest.json +3d212c1b1629822af37ad6bc44dc2088200c38f38f9d11ea1de946e1de41a84c bag-info.txt diff --git a/tests/data/grepsort-run-1/tagmanifest-sha512.txt b/tests/data/grepsort-run-1/tagmanifest-sha512.txt index 6b23cdd..037f18e 100644 --- a/tests/data/grepsort-run-1/tagmanifest-sha512.txt +++ b/tests/data/grepsort-run-1/tagmanifest-sha512.txt @@ -1,15 +1,15 @@ -a7ba0dd9402632483d1e4aa2c11dce07555e92c0563648a679e41c141d281f3f31f688c012bf2f39f056a1256cb570c1d0e7bc3e89bded055599ce9eba9ffd02 workflow/packed.cwl +1669370708cc6b1a7f1bf44459b12cbe8ae009e9a1fa57c7cf02909bd9ac157de84ada678c191caa47430ff02a32534e71388c8bfccdd3386205380b0f282337 workflow/packed.cwl eff9f0b0ebac2410a3eb6bd02c9e25464d6a3ae78d067a9a55db3ebbba8c0009108807b1a6a19d2c7789c01090a6d43055be940c48582effd2b96a7cd6810bc9 workflow/primary-job.json -af4ecf71e903f6a0a24d8ce78847f0ca9ed4b66ada7609fb2c7fa62541c761a0785915bac14407eb2c229d1841a29f3ddd43903121146c59b2e521a3cf71cdb4 metadata/provenance/primary.cwlprov.xml -42562694b48de698a3bf4a490348b1fd17cfa79f9f33d85b7d22d2ffde2d466063692d7947074e786b7ea39cbca89a483c55ef5390e163f6418398e5633d8418 metadata/provenance/primary.cwlprov.provn -6d1bcfd858d66554b40ac5eda76f48f129ce0673d00f79350ddaf3b3dfb5d969cbc91adcc05fa7ced78623e610d64b0ae0327afa980d0b669244673a09fa0b41 metadata/provenance/primary.cwlprov.json -a53e3f5c83aaf8de7c4ec7adccfb7d59d0c40311d70e913b0a266358a797ba6b5e3eda86cf54bd45265ac550acf95c5daf0d054457b6634d3b6d047989d97cf8 metadata/provenance/primary.cwlprov.ttl -309538e0acea57a034888c970571d82d0445dbc024f0a431dcea4f88d31e164bda8f65c798a2be97e88c286b7f647ea2f9768056b7da2d207b4d64152cee0633 metadata/provenance/primary.cwlprov.nt -1d8dc4bc1771676b68a5b24e663e71b7d6807ca75b4568d73eda7b3c55bb8226a011cd702ee8af3341a40636e7dd9eae77c1b5e76417daa6d0847c58a135d0bf metadata/provenance/primary.cwlprov.jsonld -738c51196e5e49a246ae5f41bffb8a6217bd4cc4befa96fbc5f6bc77ae1877bbd0f6e26ad9952389e30da20a83eb3c69c5297291b714af44e2cfcfbe4a4ea4af workflow/primary-output.json -a88699fc73da60621a6c9c1ef345ddc9e371f292b55f54a81a8ee1b714f2c045f4cf33436cab1923c7763d35cc769a6b922d4446608cd2be3b93fec631eb6ddf snapshot/grepsort.cwl +b699186de20f3de2ac20b7a48387e3ffbe85484a9dbc9bf69b891e321ac829f721c8d2f7917491e94daef9f3e96e6eb2bcd7a97f6affd3e13a48ec27398a044d metadata/provenance/primary.cwlprov.xml +345aaa5888e400f711c3ada3fcd9e5871806d51ec317797ccddf46fb3c3c694b87fe4c80c75e4d0f83a7ccac3a9356290ecb96570695f03cf775a8b192faa8e1 metadata/provenance/primary.cwlprov.provn +a1bc479c90d4353f54d19084bc3ea736512a85229d4edca399da12ad2bde2a9f2fa6d3a068085a43ee7d3ea72c2044cab2b849027a2f1ea8e745b0b0ddd8a087 metadata/provenance/primary.cwlprov.json +c8bb656320b5981a7859bb07558506ab72a319717bf560f592851771372a82c82eeb9bb1e8001d27991248b152a3a07c29d41d20f22bb37d895f3a0d7fa7b5b3 metadata/provenance/primary.cwlprov.ttl +2ef6dd7045d57ae7133f4a8dc6bc04a506070ea99277f51bc4222ff612a37d0e7857a45e8bc2055c0492840ea571b0d8b81ad42e65db2d00368da79f614af6df metadata/provenance/primary.cwlprov.nt +f5d9748c3d47130a5a2d4a6b97db2a5bfc9ec86e2d78e436ad59edc5c9a4d4a101a7a3b49fec34b7121245112175054497a8e3ecd4e250bc86c39e45e459d437 metadata/provenance/primary.cwlprov.jsonld +3593edae29a274634fdddf09826694f5897799f0462c0857d6b4227d00b2ae3d30eefa493cf42be2eb75dc1ab6d7387744dddd02fc262722d9b46cf79d545283 workflow/primary-output.json +aac26ec0a6f728cc0f3100c7ede0fd39d8e87973cda51a5dcddbdc26cbe5c1b391a188b66bafdc2ef6416591c2829868c69f5b0dd34dfa4f0eeda774b03a007a snapshot/grepsort.cwl 3fcf2e264180fb8580adf10896eef69cd28f58e2f568f0757bb724868deac7d6000b955b80aaa96a2b9e872b0a31ef5e39cdf44343f7988510cb64526bc04e29 snapshot/greptool.cwl -a3bc8816b11f43c935eaece944f26f827376a9bc4cb6c4093f36c6791f4ad07b368a3c64b29cdec996c2f936ef7b2830b009ffccbe5de64598ada5c0e35c0115 snapshot/sorttool.cwl -8a76f1cab8e6926f4fb340b0e254a51128dba05c3de4725d9cfab663c6888fb98b06ac8dfd69c6a183ab22d444f0f6e9bbeb69b6e8400d8703b26ef5a93b8653 metadata/logs/engine.fb8f0a7a-121b-47e1-b955-75d213864598.txt -0814b5ddd0ac941758363a54b53671f4b0cf0d2e69d134428f349b2624d918e23deffc33ffe2886d5948cd9b0a519d3656544b5be84f6f49b405df5064d387ab metadata/manifest.json -051e7e72b77767e49e97c6d5aeb068644bd0d5b36cb5445788012d514adcd82911754bc6dc076c3a20888281899c24a25964cff2599f550bd6675fa35476957e bag-info.txt +9df79d641652f80db0f709372219940ebf8d0823430ce50fa3e1c5377afab4b248bdb7308b351557763709eaf4d9d7f07370879a0562f73680a9da4a1ee38eef snapshot/sorttool.cwl +1263ad6db58d2ddfff413860629ec1d7075f8be72952675663c37943478608b1e445290f76c027192e9169a67362440d381c821860d88bc904bbfa1c30e73a29 metadata/logs/engine.158cac0a-3a3b-4716-b023-2f9d48de837a.txt +720f8cfe8896a874700aa5a72cf11012286a7f1463cce6b1ddc380963b3fe8f39ee8c6d720a3dd2fa523d1e9bbab2677203ca1cd6d9d6d58f890c5d69d6c9916 metadata/manifest.json +ec993cea1afaf50504d2bfc552a55be21486330c32ae75b743ab0061d2a54ddc95e6efac2a50d4d51388239233986223d5fa7987395b702d828f4d495f2e0c61 bag-info.txt diff --git a/tests/data/grepsort-run-1/workflow/packed.cwl b/tests/data/grepsort-run-1/workflow/packed.cwl index 20a9399..fde86b5 100644 --- a/tests/data/grepsort-run-1/workflow/packed.cwl +++ b/tests/data/grepsort-run-1/workflow/packed.cwl @@ -67,6 +67,7 @@ "outputs": [ { "type": "File", + "format": "https://www.iana.org/assignments/media-types/text/plain", "outputSource": "#main/sorted/sort_out", "id": "#main/grepsort_out" } @@ -150,6 +151,7 @@ "outputs": [ { "type": "File", + "format": "https://www.iana.org/assignments/media-types/text/plain", "outputBinding": { "glob": "sort_out.txt" }, diff --git a/tests/data/grepsort-run-1/workflow/primary-output.json b/tests/data/grepsort-run-1/workflow/primary-output.json index 0d478ea..a7e9049 100644 --- a/tests/data/grepsort-run-1/workflow/primary-output.json +++ b/tests/data/grepsort-run-1/workflow/primary-output.json @@ -7,7 +7,8 @@ "class": "File", "checksum": "sha1$8292d6f0985a62d4abd624fc72aecb8132193d6e", "size": 58, + "format": "https://www.iana.org/assignments/media-types/text/plain", "http://commonwl.org/cwltool#generation": 0, - "@id": "urn:uuid:f81f0901-a485-4a8b-b059-15de2f4f82f8" + "@id": "urn:uuid:3aaebe26-84d6-4428-adfa-156a969476a9" } } diff --git a/tests/test_cwlprov_crate_builder.py b/tests/test_cwlprov_crate_builder.py index 0f6404d..7a7ae9e 100644 --- a/tests/test_cwlprov_crate_builder.py +++ b/tests/test_cwlprov_crate_builder.py @@ -878,6 +878,10 @@ def test_secondary_files(data_dir, tmpdir): assert main_file.id in collection_parts aux_file = [v for k, v in collection_parts.items() if k != main_file.id][0] assert set(grep_collection["exampleOfWork"]) == {grep_in, grepsort_in} + wf_results = wf_action["result"] + assert len(wf_results) == 1 + sort_out = wf_results[0] + assert "encodingFormat" in sort_out # file contents text_main = (root / "data/b6/b64565ee76fcd5296c48314f858f8e4672c71439").read_text() text_aux = (root / "data/c7/c708d7ef841f7e1748436b8ef5670d0b2de1a227").read_text()