NF: Initial draft of a NIDM-FSL/FSL FEAT extractor

[mih]

This can now drive nidmfsl via the new metalad extractor interface.
Issues:

• How to link to files in the dataset rather than files in the result pack (that is not actually stored) Howto link up NIDMFSL metadata with other source incf-nidash/nidmresults-fsl#155
• Can we simplify the structure to a plain graph with a single list of documents Q re JSON-LD output structure incf-nidash/nidmresults-fsl#153
• Temporary files are created in the dataset, some might conflict with existing files nidmfsl run taints processed dataset incf-nidash/nidmresults-fsl#151
• Only works on a single contrast in a 2nd-level FEAT dir Permission denied crash on export incf-nidash/nidmresults-fsl#148
• Can give non-JSON compliant output Output not JSON-compliant incf-nidash/nidmresults-fsl#152
• adjust dependencies
• seems to fail to report results for all contrasts, but original nidm.json is confirmed to have all reports

Ping @cmaumet

Example metadata dump for a single file:

% datalad -f json_pp meta-dump --reporton files sub-16/2ndlvl.gfeat/cope10.feat/stats/zstat1.nii.gz

{
  "action": "meta_dump",
  "datalad_version": "0.12.0rc4.dev80",
  "dsid": "45ce9360-839d-11e9-a390-f0d5bf7b5561",
  "metadata": {
    "metalad_core": {
      "@id": "datalad:MD5E-s423417--8eafedd11afd04747dd518e5baa048cc.nii.gz",
      "contentbytesize": 423417
    },
    "metalad_fslfeat": {
      "@id": "datalad:MD5E-s423417--8eafedd11afd04747dd518e5baa048cc.nii.gz",
      "@type": "StatisticMap",
      "crypto:sha512": "882805bf4864b2b03bf0611bc26f9e9736c125a2cc2112eccd9b2320ef70bd97dcdb65cd1f27721f974f45a65de777f96de4becf0100566e09f73d52c9fdb75e",
      "dct:format": "image/nifti",
      "nidm:NIDM_0000085": "group mean",
      "nidm:NIDM_0000091": 1.0,
      "nidm:NIDM_0000093": Infinity,
      "nidm:NIDM_0000104": {
        "@id": "niiri:3e26e0d3-af8e-4f83-a3b7-16ad58bba97d"
      },
      "nidm:NIDM_0000123": {
        "@id": "obo:STATO_0000376"
      },
      "prov:atLocation": {
        "@type": "xsd:anyURI",
        "@value": "ZStatistic_10_T001.nii.gz"
      },
      "prov:wasGeneratedBy": {
        "@id": "niiri:fded5a9e-983e-4f96-b7b9-7d6a8d00e588"
      },
      "rdfs:label": "Z-Statistic Map: group mean"
    },
    "metalad_runprov": {
      "@id": "datalad:MD5E-s423417--8eafedd11afd04747dd518e5baa048cc.nii.gz",
      "@type": "entity",
      "prov:wasGeneratedBy": {
        "@id": "50fdaec13de7167452128a0c747250141df2e8c6"
      }
    }
  },
  "parentds": "/tmp/smallfsl",
  "path": "/tmp/smallfsl/sub-16/2ndlvl.gfeat/cope10.feat/stats/zstat1.nii.gz",
  "refcommit": "50fdaec13de7167452128a0c747250141df2e8c6",
  "status": "ok",
  "type": "file"
}

[codecov-io]

Codecov Report

Merging #102 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #102   +/-   ##
=======================================
  Coverage   86.21%   86.21%           
=======================================
  Files          17       17           
  Lines         943      943           
=======================================
  Hits          813      813           
  Misses        130      130

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