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Intialize Provenance Tracking #423

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omar-rifai
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@omar-rifai omar-rifai commented Sep 16, 2021 •
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WIP towards a traceability feature for Clinica:

  • Define data model for PROV concepts
  • Serialize and de-serialize json-ld documents
  • Compose prov modules with pipelines
  • Log all attributes defined in BIDS prov
  • Homogenize inputs and outputs of all pipelines for use in prov

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pep8speaks commented Sep 16, 2021 •
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Hello @omar-rifai! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

Line 26:10: E111 indentation is not a multiple of four
Line 26:10: E117 over-indented
Line 33:55: E231 missing whitespace after ','
Line 33:98: W291 trailing whitespace

Comment last updated at 2022-03-14 16:07:38 UTC

@omar-rifai omar-rifai force-pushed the feat_init_traceability branch 2 times, most recently from c34018d to 3d25540 Compare September 23, 2021 07:51
@omar-rifai omar-rifai force-pushed the feat_init_traceability branch from 9207166 to 7eafeb3 Compare December 29, 2021 15:51
@ghisvail
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ghisvail commented Jan 5, 2022

You gonna have to rebase onto the latest dev to pass CI

@omar-rifai omar-rifai force-pushed the feat_init_traceability branch from b1b69cb to 44bb79d Compare February 7, 2022 13:34
@omar-rifai omar-rifai force-pushed the feat_init_traceability branch from 5a4690d to ce07366 Compare February 23, 2022 15:52
omar-rifai added 23 commits March 14, 2022 10:28
@omar-rifai
Init traceability feature
5dc0d02
@omar-rifai
Add function to create new provenance files
b1bc38e
@omar-rifai
Update clinica_file_reader call
9c0ee0d
@omar-rifai
Add data model
aa0cb6f
@omar-rifai
rename files
6b28410
@omar-rifai
Update prov with Data Model
8fdf9e7
@omar-rifai
Fix typing with list
47f9ce5
@omar-rifai
Fix various issues
a3ef086
@omar-rifai
Rename prov extraction functions
bd4636b
@omar-rifai
Deserialize json-ld
5dc8475
@omar-rifai
Update record data model and serialization/deserialization
8f384c5
@omar-rifai
Clean up unused code
d32e06f
@omar-rifai
fix conflict in rebase
126ce0b
@omar-rifai
Update prov jsonld representation
672c28c
@omar-rifai
manually lint code
39a2064
@omar-rifai
Start extending workflow to other pipelines
46b9892
@omar-rifai
Connect provenance through nipype nodes
f2c5300
@omar-rifai
Add context to provenance
fdf8ed7
@omar-rifai
specify error type in try catch
203d84d
@omar-rifai
Revert changes in clinica/utils/ after architecture change
cb31dd1
@omar-rifai
Homogenize the funcs get_input_fields() get_output_fields()
4687211
@omar-rifai
Remove unused imports
ddc82c8
@omar-rifai
Lint __init__ file in engine
54b3ffe
@omar-rifai omar-rifai force-pushed the feat_init_traceability branch from 931d9a9 to 07204cc Compare March 14, 2022 16:07
@omar-rifai omar-rifai changed the title Feat init traceability Intialize Provenance Tracking Jul 8, 2022
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3 participants

@omar-rifai @pep8speaks @ghisvail