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Commits on Oct 25, 2018
  1. Add version-independent DOI

    stain committed Oct 25, 2018
  2. Add cwlprov 0.6.0

    stain committed Oct 25, 2018
  3. 0.6.0 example from cwltool 1.0.20181012180214

    stain committed Oct 25, 2018
    adds metadata/logs/
  4. Tidy up versions

    stain committed Oct 25, 2018
  5. cwlprov 0.5.0 example

    stain committed Oct 25, 2018
    Made with cwltool 1.0.20180912090223
Commits on Oct 5, 2018
  1. add cwlprov-py

    stain committed Oct 5, 2018
Commits on Sep 10, 2018
  1. Update README.md

    stain committed Sep 10, 2018
  2. Update README.md

    stain committed Sep 10, 2018
Commits on Aug 22, 2018
  1. json syntax ..

    stain committed Aug 22, 2018
  2. markdown tweaks

    stain committed Aug 22, 2018
  3. about directories

    stain committed Aug 22, 2018
  4. 0.4.0 in preparation

    stain committed Aug 22, 2018
Commits on Aug 21, 2018
  1. CWLProv 0.4.0 example

    stain committed Aug 21, 2018
    Made using cwltool c7c269b6fc18ebcc9ddefa2c248957ea4b255186
    
    (venv3) stain@biggie:~/src/cwltool/tests/wf$ cwltool --provenance revsort-run-1 revsort.cwl revsort-job.json
    /home/stain/src/cwltool/venv3/bin/cwltool 1.0.20180821160715
    [provenance] Temporary research object: /tmp/tmpyc_yuzf9
    Resolved 'revsort.cwl' to 'file:///home/stain/src/cwltool/tests/wf/revsort.cwl'
    [provenance] Added packed workflow: workflow/packed.cwl
    [provenance] Creator ORCID: https://orcid.org/0000-0001-9842-9718
    File not previously registered in RO: CommentedMap([('class', 'File'), ('location', 'file:///home/stain/src/cwltool/tests/wf/whale.txt'), ('size', 1111), ('basename', 'whale.txt'), ('nameroot', 'whale'), ('nameext', '.txt')])
    [provenance] Added data file /tmp/tmpyc_yuzf9/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376
    [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376
    [provenance] Generated customised job file: workflow/primary-job.json
    [provenance] Added data file /tmp/tmpyc_yuzf9/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376
    [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376
    [workflow ] start
    [workflow ] starting step rev
    [step rev] start
    [job rev] /tmp/tmpx3z3n9n2$ docker \
        run \
        -i \
        --volume=/tmp/tmpx3z3n9n2:/var/spool/cwl:rw \
        --volume=/tmp/tmprwflmw_5:/tmp:rw \
        --volume=/home/stain/src/cwltool/tests/wf/whale.txt:/var/lib/cwl/stg09e0b3db-b46e-4be5-8cdb-c21edff5856a/whale.txt:ro \
        --workdir=/var/spool/cwl \
        --read-only=true \
        --log-driver=none \
        --user=1000:1000 \
        --rm \
        --env=TMPDIR=/tmp \
        --env=HOME=/var/spool/cwl \
        debian:8 \
        rev \
        /var/lib/cwl/stg09e0b3db-b46e-4be5-8cdb-c21edff5856a/whale.txt > /tmp/tmpx3z3n9n2/output.txt
    [provenance] Added data file /tmp/tmpyc_yuzf9/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376
    [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376
    [provenance] Added data file /tmp/tmpyc_yuzf9/data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f
    [provenance] Relative path for data file data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f
    [job rev] completed success
    [step rev] completed success
    [workflow ] starting step sorted
    [step sorted] start
    [job sorted] /tmp/tmpj2ar3bx5$ docker \
        run \
        -i \
        --volume=/tmp/tmpj2ar3bx5:/var/spool/cwl:rw \
        --volume=/tmp/tmpa07xmc89:/tmp:rw \
        --volume=/tmp/tmpx3z3n9n2/output.txt:/var/lib/cwl/stg3a577a45-dd07-4fe1-8701-2de7e5d07c1f/output.txt:ro \
        --workdir=/var/spool/cwl \
        --read-only=true \
        --log-driver=none \
        --user=1000:1000 \
        --rm \
        --env=TMPDIR=/tmp \
        --env=HOME=/var/spool/cwl \
        debian:8 \
        sort \
        --reverse \
        /var/lib/cwl/stg3a577a45-dd07-4fe1-8701-2de7e5d07c1f/output.txt > /tmp/tmpj2ar3bx5/output.txt
    [provenance] Added data file /tmp/tmpyc_yuzf9/data/b9/b9214658cc453331b62c2282b772a5c063dbd284
    [provenance] Relative path for data file data/b9/b9214658cc453331b62c2282b772a5c063dbd284
    [job sorted] completed success
    [step sorted] completed success
    [workflow ] completed success
    [provenance] added provenance: [<QualifiedName: provenance:primary.cwlprov.xml>, <QualifiedName: provenance:primary.cwlprov.provn>, <QualifiedName: provenance:primary.cwlprov.json>, <QualifiedName: provenance:primary.cwlprov.ttl>, <QualifiedName: provenance:primary.cwlprov.nt>, <QualifiedName: provenance:primary.cwlprov.jsonld>]
    {
        "output": {
            "location": "file:///home/stain/src/cwltool/tests/wf/output.txt",
            "basename": "output.txt",
            "class": "File",
            "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",
            "size": 1111,
            "@id": "urn:uuid:e8b03590-527b-494f-9003-124fb6862983",
            "path": "/home/stain/src/cwltool/tests/wf/output.txt"
        }
    }
    Final process status is success
    [provenance] Finalizing Research Object
    [provenance] Generated bagit metadata: /tmp/tmpyc_yuzf9
    [provenance] Research Object saved to /home/stain/src/cwltool/tests/wf/revsort-run-1
Commits on Jul 9, 2018
  1. Markdown typos

    stain committed Jul 9, 2018
Commits on Jul 5, 2018
  1. RST -> Markdown fun

    stain committed Jul 5, 2018
  2. simplify

    stain committed Jul 5, 2018
  3. newer revsort run

    stain committed Jul 5, 2018
    Made using 0afceced3f76d55e726e6f037b108696bce198a8 to get correct
    manifest.json
  4. Add overview

    stain committed Jul 5, 2018
  5. CWLProv BagIt Profile

    stain committed Jul 5, 2018
  6. README: Some markdown typos

    stain committed Jul 5, 2018
  7. Run of tests/wf/revsort.cwl

    stain committed Jul 5, 2018
    using cwltool 2ba677ac25c90e9400c6b0d0d324fe7e11cb5fed
    
    (venv3) stain@biggie:~/src/cwltool/tests/wf$ cwltool --provenance revsort-run-1 revsort.cwl revsort-job.json
    /home/stain/src/cwltool/venv3/bin/cwltool 1.0.20180703025338
    [provenance] Temporary research object: /tmp/tmpbt18ylo4
    Resolved 'revsort.cwl' to 'file:///home/stain/src/cwltool/tests/wf/revsort.cwl'
    [provenance] Added packed workflow: workflow/packed.cwl
    [provenance] Creator ORCID: https://orcid.org/0000-0001-9842-9718
    [provenance] Added data file /tmp/tmpbt18ylo4/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376
    [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376
    [provenance] Generated customised job file: workflow/primary-job.json
    [workflow ] start
    [workflow ] starting step rev
    [step rev] start
    ['docker', 'pull', 'debian:8']
    8: Pulling from library/debian
    1c7fe136a31e: Pull complete
    Digest: sha256:d68fe870fe9c7d71d98cf575c42e7c4c3e024c42581eaa116041aa6092430662
    Status: Downloaded newer image for debian:8
    [job rev] /tmp/tmp5qanhyfp$ docker \
        run \
        -i \
        --volume=/tmp/tmp5qanhyfp:/var/spool/cwl:rw \
        --volume=/tmp/tmpf21younq:/tmp:rw \
        --volume=/home/stain/src/cwltool/tests/wf/whale.txt:/var/lib/cwl/stg74d29f02-7b02-41ef-894c-6496a9e9ba3a/whale.txt:ro \
        --workdir=/var/spool/cwl \
        --read-only=true \
        --log-driver=none \
        --user=1000:1000 \
        --rm \
        --env=TMPDIR=/tmp \
        --env=HOME=/var/spool/cwl \
        debian:8 \
        rev \
        /var/lib/cwl/stg74d29f02-7b02-41ef-894c-6496a9e9ba3a/whale.txt > /tmp/tmp5qanhyfp/output.txt
    [provenance] Used data w/o checksum file:///home/stain/src/cwltool/tests/wf/whale.txt
    [provenance] Added data file /tmp/tmpbt18ylo4/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376
    [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376
    [provenance] Added data file /tmp/tmpbt18ylo4/data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f
    [provenance] Relative path for data file data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f
    [provenance] Adding output file data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f to RO
    [job rev] completed success
    [step rev] completed success
    [workflow ] starting step sorted
    [step sorted] start
    [job sorted] /tmp/tmp3p_j0x30$ docker \
        run \
        -i \
        --volume=/tmp/tmp3p_j0x30:/var/spool/cwl:rw \
        --volume=/tmp/tmppzojjjh8:/tmp:rw \
        --volume=/tmp/tmp5qanhyfp/output.txt:/var/lib/cwl/stgbe4e20ff-95cd-445b-a1c5-8fcda3dcaace/output.txt:ro \
        --workdir=/var/spool/cwl \
        --read-only=true \
        --log-driver=none \
        --user=1000:1000 \
        --rm \
        --env=TMPDIR=/tmp \
        --env=HOME=/var/spool/cwl \
        debian:8 \
        sort \
        --reverse \
        /var/lib/cwl/stgbe4e20ff-95cd-445b-a1c5-8fcda3dcaace/output.txt > /tmp/tmp3p_j0x30/output.txt
    [provenance] Used data w/ checksum sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f
    [provenance] Added data file /tmp/tmpbt18ylo4/data/b9/b9214658cc453331b62c2282b772a5c063dbd284
    [provenance] Relative path for data file data/b9/b9214658cc453331b62c2282b772a5c063dbd284
    [provenance] Adding output file data/b9/b9214658cc453331b62c2282b772a5c063dbd284 to RO
    [job sorted] completed success
    [step sorted] completed success
    [workflow ] completed success
    [provenance] Added data file /tmp/tmpbt18ylo4/data/b9/b9214658cc453331b62c2282b772a5c063dbd284
    [provenance] Relative path for data file data/b9/b9214658cc453331b62c2282b772a5c063dbd284
    [provenance] Adding output file data/b9/b9214658cc453331b62c2282b772a5c063dbd284 to RO
    [provenance] added all tag files
    {
        "output": {
            "path": "/home/stain/src/cwltool/tests/wf/output.txt",
            "class": "File",
            "size": 1111,
            "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",
            "basename": "output.txt",
            "location": "file:///home/stain/src/cwltool/tests/wf/output.txt"
        }
    }
    Final process status is success
    [provenance] Finalizing Research Object
    [provenance] Generated bagit metadata: /tmp/tmpbt18ylo4
    [provenance] Research Object saved to /home/stain/src/cwltool/tests/wf/revsort-run-1
  8. CWLProv README

    stain committed Jul 5, 2018
  9. NOTICE with copyright

    stain committed Jul 5, 2018
  10. Rename to LICENSE.txt

    stain committed Jul 5, 2018
  11. Initial commit

    stain committed Jul 5, 2018