Propagate input annotations to primary.cwlprov files

[RenskeW]

Propagate structured annotations for files and directories (e.g. Schema.org, but also CWL-specific metadata fields) to the provenance graph. In addition, annotations under the cwlprov:prov field should be incorporated in the RDF graph as well.

Step 1: If 'label' is specified in input object, it is added as an annotation to the file entity it corresponds to.

Example:

file: 
  class: File
  path: ./file.tsv
  label: file_label

This would be represented in the cwlprov provenance like this:

id:92fc295f-f6cb-444b-8ffe-0f604b127858 a wf4ever:File,
        wfprov:Artifact,
        prov:Entity ;
    rdfs:label "file_label"^^xsd:string ;
    prov:specializationOf data:86ec86fdbbe70863a78453f69349568f9d1f14a1 ;
    cwlprov:basename "file.tsv"^^xsd:string ;
    cwlprov:nameext ".tsv"^^xsd:string ;
    cwlprov:nameroot "file"^^xsd:string .

See here for the full example RO.

Step 2: Values of doc, format, label, intent are propagated to RDF provenance graph.

EXAMPLE RO: https://github.com/RenskeW/cwlprov-provenance/tree/930cc268da77c5aa3739a2f7f87b94e076b144e6/cwlprov_rdf_examples

Mapping to Schema.org terms:

• doc: https://schema.org/description
• label: https://schema.org/name
• format: https://schema.org/encodingFormat
• intent: https://schema.org/featureList

TODO:

• Propagate annotations for File
• Propagate annotations for Directory
• Add support for annotations of type CommentedSeq
• Propagate annotations under cwlprov:prov
• Propagate values of doc, intent, label, and intent fields to RDF
• inputs should be copied into data/ , not be broken symlinks
• improve code coverage
• Fix double entries in provenance (optionally)

[codecov]

Codecov Report

Attention: 16 lines in your changes are missing coverage. Please review.

Comparison is base (bcdbeaf) 83.80% compared to head (dea0b8e) 83.92%.

Files	Patch %	Lines
cwltool/cwlprov/provenance_profile.py	71.69%	11 Missing and 4 partials ⚠️
cwltool/singularity.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1678      +/-   ##
==========================================
+ Coverage   83.80%   83.92%   +0.11%     
==========================================
  Files          46       46              
  Lines        8221     8266      +45     
  Branches     2182     2201      +19     
==========================================
+ Hits         6890     6937      +47     
+ Misses        854      850       -4     
- Partials      477      479       +2     

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[mr-c]

Thank you for this @RenskeW ! can you make format and push the changes?

[mr-c]

@RenskeW Thanks!

Checking https://www.commonwl.org/v1.2/CommandLineTool.html#File we see that label is not one of the fields present here in the CWL standards. So we'll need to use a namespaced field name, for which I recommend that you choose one of the schema.org properties like https://schema.org/name as it is linked to rdfs:label and is modeled as equivalent to dcterms:title.

After you make that change, can you add a s:name to one of the input objects used in the cwlprov tests? You'll need to add a $namespaces dictionary to document the s prefix if the corresponding CWL description lacks that. Then you can add a check to one of the cwlprov tests to look for the rdfs:label in the resulting CWLProv RO.

[mr-c]

(maybe in CWL v1.3 we will add a label field to File)

[lgtm-com]

This pull request introduces 1 alert when merging 99fc196 into c23a9ed - view on LGTM.com

new alerts:

• 1 for Variable defined multiple times

[lgtm-com]

This pull request introduces 1 alert when merging c6e7385 into b21b0c1 - view on LGTM.com

new alerts:

• 1 for Variable defined multiple times

[RenskeW]

isinstance(dataset[annotation], list), isinstance(dataset[annotation], MutableMapping)

[RenskeW]

MutableSequence = list

[lgtm-com]

This pull request introduces 2 alerts when merging bf34ca6 into bb41504 - view on LGTM.com

new alerts:

• 2 for Incomplete URL substring sanitization

[RenskeW]

First step in propagating metadata under cwlprov:prov to provenance as well.

[lgtm-com]

This pull request introduces 2 alerts when merging 70d184f into bb41504 - view on LGTM.com

new alerts:

• 2 for Incomplete URL substring sanitization

[cwl-bot]

This pull request has been mentioned on Common Workflow Language Discourse. There might be relevant details there:

https://cwl.discourse.group/t/equivalent-to-file-metadata-for-local-environment/782/2

[RenskeW]

@mr-c here is a hand-annotated example of the new RDF provenance graph, including the CWL metadata fields:

https://github.com/RenskeW/cwlprov-provenance/blob/d0b69c24e57b6db9e7d061f9512ba35e842c9cc5/cwlprov_rdf_examples/scenario1/ro/metadata/provenance/primary.cwlprov.ttl

There is a separate example, containing propagation of annotation of input parameter values (e.g. an input File), to CWLprov RDF, here:

https://github.com/RenskeW/cwlprov-provenance/tree/930cc268da77c5aa3739a2f7f87b94e076b144e6/prov_data_annotations/example1