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Trying jsonld simplification
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-30
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6 files changed

+39
-30
lines changed

‎examples/dcm2niix/code/exp1_merge_prov.py‎

Lines changed: 5 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
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from pyld import jsonld
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prov_files = [
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'prov/common.prov.jsonld',
7+
#'prov/common.prov.jsonld',
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'prov/software.prov.jsonld',
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'prov/environments.prov.jsonld',
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'sub_02/ses_20130717141500/anat/sub-02_ses-20130717141500_T1w.prov.jsonld',
@@ -19,11 +19,13 @@
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with open(prov_file, encoding = 'utf-8') as file:
2020
#expanded = json.dumps(jsonld.flatten(jsonld.expand(json.load(file)), ctx = context, options = {'processingMode': 'json-ld-1.1'}), indent = 2)
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#print(expanded)
22+
rdf_graph += f'# {prov_file}\n'
2223
rdf_graph += jsonld.normalize(
2324
json.load(file), {'algorithm': 'URDNA2015', 'format': 'application/n-quads'})
24-
print(rdf_graph)
25-
#graph.parse(data = expanded, format = 'json-ld')
25+
rdf_graph += '\n'
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27+
#graph.parse(data = expanded, format = 'json-ld')
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print(rdf_graph)
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"""

‎examples/dcm2niix/prov/environments.prov.jsonld‎

Lines changed: 8 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -1,12 +1,10 @@
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{
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"@context": "https://purl.org/nidash/bidsprov/context.json",
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"Records": {
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"Environments": [
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{
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"Id": "bids::prov/fedora",
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"Label": "Fedora release 36 (Thirty Six)",
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"OperatingSystem": " GNU/Linux 6.2.15-100.fc36.x86_64"
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}
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]
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}
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"@context": "https://raw.githubusercontent.com/bclenet/BEP028_BIDSprov/refs/heads/context/context.json",
3+
"Environments": [
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{
5+
"Id": "bids::prov/fedora",
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"Label": "Fedora release 36 (Thirty Six)",
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"OperatingSystem": " GNU/Linux 6.2.15-100.fc36.x86_64"
8+
}
9+
]
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}

‎examples/dcm2niix/prov/experiment_1/merged_provenance.ttl‎

Lines changed: 23 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -1,43 +1,52 @@
1-
<bids::prov/dcm2niix> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Agent> .
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# prov/software.prov.jsonld
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<bids::prov/dcm2niix> <http://www.w3.org/2000/01/rdf-schema#label> "dcm2niix" .
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<bids::prov/fmriprep> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Agent> .
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<bids::prov/fmriprep> <http://www.w3.org/2000/01/rdf-schema#label> "fmriprep" .
4+
_:c14n0 <http://www.w3.org/ns/prov#Agent> <bids::prov/dcm2niix> .
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_:c14n0 <http://www.w3.org/ns/prov#Agent> <bids::prov/fmriprep> .
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# prov/environments.prov.jsonld
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<bids::prov/fedora> <http://www.w3.org/2000/01/rdf-schema#label> "Fedora release 36 (Thirty Six)" .
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<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Entity> .
9+
_:c14n0 <http://www.w3.org/ns/prov#Entity> <bids::prov/fedora> .
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11+
# sub_02/ses_20130717141500/anat/sub-02_ses-20130717141500_T1w.prov.jsonld
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<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm> <http://www.w3.org/2000/01/rdf-schema#label> "N2D_0001.dcm" .
8-
<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Entity> .
913
<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm> <http://www.w3.org/2000/01/rdf-schema#label> "N2D_0002.dcm" .
10-
<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Entity> .
1114
<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm> <http://www.w3.org/2000/01/rdf-schema#label> "N2D_0003.dcm" .
12-
<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Entity> .
1315
<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json> <http://www.w3.org/2000/01/rdf-schema#label> "sub-02_ses-20130717141500_T1w.json" .
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<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json> <http://www.w3.org/ns/prov#wasGeneratedBy> <urn:conversion-00f3a18f> .
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<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Entity> .
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<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii> <http://www.w3.org/2000/01/rdf-schema#label> "sub-02_ses-20130717141500_T1w.nii" .
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<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii> <http://www.w3.org/ns/prov#wasGeneratedBy> <urn:conversion-00f3a18f> .
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<urn:conversion-00f3a18f> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> .
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<urn:conversion-00f3a18f> <http://www.w3.org/2000/01/rdf-schema#label> "Conversion" .
2020
<urn:conversion-00f3a18f> <http://www.w3.org/ns/prov#used> <bids::prov/fedora> .
2121
<urn:conversion-00f3a18f> <http://www.w3.org/ns/prov#used> <bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm> .
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<urn:conversion-00f3a18f> <http://www.w3.org/ns/prov#used> <bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm> .
2323
<urn:conversion-00f3a18f> <http://www.w3.org/ns/prov#used> <bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm> .
2424
<urn:conversion-00f3a18f> <http://www.w3.org/ns/prov#wasAssociatedWith> <bids::prov/dcm2niix> .
25-
<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Entity> .
25+
_:c14n0 <http://www.w3.org/ns/prov#Activity> <urn:conversion-00f3a18f> .
26+
_:c14n0 <http://www.w3.org/ns/prov#Entity> <bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm> .
27+
_:c14n0 <http://www.w3.org/ns/prov#Entity> <bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm> .
28+
_:c14n0 <http://www.w3.org/ns/prov#Entity> <bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm> .
29+
_:c14n0 <http://www.w3.org/ns/prov#Entity> <bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json> .
30+
_:c14n0 <http://www.w3.org/ns/prov#Entity> <bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii> .
31+
32+
# sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.jsonld
2633
<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586> <http://www.w3.org/2000/01/rdf-schema#label> "MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586" .
27-
<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Entity> .
2834
<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588> <http://www.w3.org/2000/01/rdf-schema#label> "MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588" .
29-
<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Entity> .
3035
<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590> <http://www.w3.org/2000/01/rdf-schema#label> "MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590" .
31-
<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Entity> .
3236
<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json> <http://www.w3.org/2000/01/rdf-schema#label> "sub-02_ses-20140425155335_task-oneback_run-1_bold.json" .
3337
<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json> <http://www.w3.org/ns/prov#wasGeneratedBy> <urn:conversion-5a66f5be> .
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<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.nii> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Entity> .
3538
<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.nii> <http://www.w3.org/2000/01/rdf-schema#label> "sub-02_ses-20140425155335_task-oneback_run-1_bold.nii" .
3639
<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.nii> <http://www.w3.org/ns/prov#wasGeneratedBy> <urn:conversion-5a66f5be> .
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<urn:conversion-5a66f5be> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> .
3840
<urn:conversion-5a66f5be> <http://www.w3.org/2000/01/rdf-schema#label> "Conversion" .
3941
<urn:conversion-5a66f5be> <http://www.w3.org/ns/prov#used> <bids::prov/fedora> .
4042
<urn:conversion-5a66f5be> <http://www.w3.org/ns/prov#used> <bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586> .
4143
<urn:conversion-5a66f5be> <http://www.w3.org/ns/prov#used> <bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588> .
4244
<urn:conversion-5a66f5be> <http://www.w3.org/ns/prov#used> <bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590> .
4345
<urn:conversion-5a66f5be> <http://www.w3.org/ns/prov#wasAssociatedWith> <bids::prov/dcm2niix> .
46+
_:c14n0 <http://www.w3.org/ns/prov#Activity> <urn:conversion-5a66f5be> .
47+
_:c14n0 <http://www.w3.org/ns/prov#Entity> <bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586> .
48+
_:c14n0 <http://www.w3.org/ns/prov#Entity> <bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588> .
49+
_:c14n0 <http://www.w3.org/ns/prov#Entity> <bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590> .
50+
_:c14n0 <http://www.w3.org/ns/prov#Entity> <bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json> .
51+
_:c14n0 <http://www.w3.org/ns/prov#Entity> <bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.nii> .
52+

‎examples/dcm2niix/prov/software.prov.jsonld‎

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{
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"@context": "https://purl.org/nidash/bidsprov/context.json",
2+
"@context": "https://raw.githubusercontent.com/bclenet/BEP028_BIDSprov/refs/heads/context/context.json",
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"Records": {
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"Software": [
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{

‎examples/dcm2niix/sub_02/ses_20130717141500/anat/sub-02_ses-20130717141500_T1w.prov.jsonld‎

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@@ -1,5 +1,5 @@
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{
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"@context": "https://purl.org/nidash/bidsprov/context.json",
2+
"@context": "https://raw.githubusercontent.com/bclenet/BEP028_BIDSprov/refs/heads/context/context.json",
33
"Records": {
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"Activities": [
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{

‎examples/dcm2niix/sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.jsonld‎

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@@ -1,5 +1,5 @@
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{
2-
"@context": "https://purl.org/nidash/bidsprov/context.json",
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"@context": "https://raw.githubusercontent.com/bclenet/BEP028_BIDSprov/refs/heads/context/context.json",
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"Records": {
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"Activities": [
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{

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