[Bug]: Directories as Entities in FSL

[bclenet]

batch name and line

For example here :

BEP028_BIDSprov/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.html

Line 306 in 05d9728

mkdir -p tsplot ; /usr/local/packages/fsl-5.0.8/bin/tsplot . -f filtered_func_data -o tsplot

What happened?

Parsing the following FSL commands
mkdir -p tsplot ; /usr/local/packages/fsl-5.0.8/bin/tsplot . -f filtered_func_data -o tsplot

creates the following Entities records :

{
    "@id": "urn:f48b9d90-4542-4e86-a17f-230fb813fba2",
    "Label": "tsplot",
    "AtLocation": "tsplot",
    "GeneratedBy": "urn:7bd4ef46-e596-482c-9e4d-7c5154719873",
    "digest": {
      "sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
    }
},
{
    "@id": "urn:ec0e91e7-0d5a-4651-8771-0d8218963f1c",
    "Label": "tsplot",
    "AtLocation": "tsplot",
    "GeneratedBy": "urn:550ce33c-c8c6-470f-ad14-5f94187fffa6",
    "digest": {
      "sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
    }
}

Describe the expected ground-truth ?

A directory is not defined as an Entity by the spec. We could either :

• ignore command lines dealing with directories (as done here:

  BEP028_BIDSprov/bids_prov/afni/afni_parser.py

  Line 292 in 05d9728

  dropline_begin = ["#", "cd", "printf", "\\rm", "$cmd", 'touch', 'sleep',

  )
• use a priori knowledge of files creates by the command line in the directory, and create Entities accordingly (as done here : https://github.com/bids-standard/BEP028_BIDSprov/blob/master/bids_prov/spm/spm_config.yml)

What soft is concerned

FSL