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Merge pull request #163 from bclenet/merge
Module to merge provenance
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‎bids_prov/README.md‎

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@@ -15,21 +15,18 @@ python launch_parser_on_nidm.py --input_dir input_examples --output_dir output_r
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Your `output_results` directory tree will be generated by itself. A folder is created for each parser and each example contains the input file, the jsonld and the associated png.
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### Notes
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All scripts provide a `--help` flag, to get an overview of possible parameters and default values
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Here is an example
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```bash
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>> python -m bids_prov.visualize --help
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Usage: visualize.py [OPTIONS] [FILENAMES]...
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### Parser entry points
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Options:
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-o, --output_file TEXT
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--omit-details omit the following low level details : {'Activity':
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('startedAtTime', 'endedAtTime'), 'Entity':
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('atLocation', 'generatedAt')}
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The following parser python modules provide entry points for direct use in a terminal:
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--help Show this message and exit.
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```
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* `bids_prov.afni_parser`
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* `bids_prov.fsl_parser`
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* `bids_prov.spm_parser`
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> [!NOTE]
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> All scripts provide a `--help` flag, to get an overview of possible parameters and default values.
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Here are examples:
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```bash
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>> python -m bids_prov.spm_parser --help
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-o, --output-file TEXT [required]
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-c, --context-url TEXT
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--help Show this message and exit.
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```
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```
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### Visualize provenance as a graph
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The `bids_prov.visualize` module allows to generate an image showing provenance contained in a JSON-LD file as a graph.
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```bash
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>> python -m bids_prov.visualize --help
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usage: visualize.py [-h] --input_file INPUT_FILE [--output_file OUTPUT_FILE]
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options:
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-h, --help show this help message and exit
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--input_file INPUT_FILE
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input BIDSprov data as a .jsonld file
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--output_file OUTPUT_FILE
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output .png file showing BIDSprov graph
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```
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This is a generated graph, form the spm_default_batch example.
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![](examples/from_parsers/spm/spm_default_batch.png)
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### Merge provenance provenance records
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The `bids_prov.merge` module allows to merge provenance records contained in a BIDS dataset into a single JSON-LD file.
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```bash
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>> python -m bids_prov.merge --help
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usage: merge.py [-h] [--dataset DATASET] [--derivative] --output_file
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OUTPUT_FILE [--group GROUP]
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options:
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-h, --help show this help message and exit
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--dataset DATASET, -d DATASET
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The path to the input BIDS dataset.
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--derivative Set this option to specify the dataset is a BIDS
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derivative dataset.
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--output_file OUTPUT_FILE, -o OUTPUT_FILE
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Output JSON-LD file containing the provenance graph
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for the input dataset.
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--group GROUP, -g GROUP
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Provenance group for which to extract the metadata.
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```
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In the example of the following BIDS dataset:
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```
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.
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├── dataset_description.json
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├── prov/
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│ ├── prov-fmriprep_act.json
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│ ├── prov-fmriprep_ent.json
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│ ├── prov-fmriprep_env.json
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│ └── prov-fmriprep_soft.json
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├── README.md
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└── sub-001/
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├── anat
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│ ├── sub-001_T1w_brainmask.nii.gz
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│ ├── sub-001_T1w_dtissue.nii.gz
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│ ├── sub-001_T1w_label-aparcaseg_roi.nii.gz
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│ ├── sub-001_T1w_label-aseg_roi.nii.gz
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│ ├── sub-001_T1w_preproc.nii.gz
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│ ├── sub-001_T1w_space-MNI152NLin2009cAsym_brainmask.nii.gz
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│ ├── sub-001_T1w_space-MNI152NLin2009cAsym_dtissue.nii.gz
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│ └── sub-001_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz
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└── func
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├── sub-001_task-MGT_run-01_bold_confounds.tsv
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├── sub-001_task-MGT_run-01_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
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├── sub-001_task-MGT_run-01_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
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├── sub-001_task-MGT_run-01_bold_space-T1w_label-aparcaseg_roi.nii.gz
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├── sub-001_task-MGT_run-01_bold_space-T1w_label-aseg_roi.nii.gz
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├── sub-001_task-MGT_run-02_bold_confounds.tsv
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├── sub-001_task-MGT_run-02_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
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├── sub-001_task-MGT_run-02_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
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├── sub-001_task-MGT_run-02_bold_space-T1w_label-aparcaseg_roi.nii.gz
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├── sub-001_task-MGT_run-02_bold_space-T1w_label-aseg_roi.nii.gz
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├── sub-001_task-MGT_run-03_bold_confounds.tsv
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├── sub-001_task-MGT_run-03_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
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├── sub-001_task-MGT_run-03_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
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├── sub-001_task-MGT_run-03_bold_space-T1w_label-aparcaseg_roi.nii.gz
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├── sub-001_task-MGT_run-03_bold_space-T1w_label-aseg_roi.nii.gz
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├── sub-001_task-MGT_run-04_bold_confounds.tsv
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├── sub-001_task-MGT_run-04_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
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├── sub-001_task-MGT_run-04_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
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├── sub-001_task-MGT_run-04_bold_space-T1w_label-aparcaseg_roi.nii.gz
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└── sub-001_task-MGT_run-04_bold_space-T1w_label-aseg_roi.nii.gz
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```
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Launching this command from the root dir of the dataset:
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```shell
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python -m bids_prov.merge -d . -o prov/prov-fmriprep_all.jsonld
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```
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will look through all the sidecar JSON files, the `dataset_description.json`, and the `prov/*` files to extract provenance metadata, and merge it into the `prov/prov-fmriprep_all.jsonld` file as a JSON-LD RDF graph.
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Note that it is possible to extract provenance metadata for all provenance groups or for one provenance group only. Also note that it is important to set the `--derivative` option to parse BIDS derivative datasets.

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