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New @id generation for parsers and other bug corrections #142

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New @id generation for parsers and other bug corrections #142

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bclenet
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@bclenet bclenet commented Oct 4, 2024 •
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This PR addresses the following topics:

  • Closes [Bug]: RRID should be replaced by AltIdentifier #137, closes [Bug]: RRID of SPM is used for all software in the examples #138 about RRIDs of Software records
  • new strategies for @id generation :
    • for Agents, @id is set to the value of Label + a random alphanumeric string
    • for Activities, @id is set to the value of Label + a random alphanumeric string
    • for Entities, @id is set using the value of AtLocation to generate a bids: id. It is set to an uuri if AtLocation is not set or not suitable for an urn value
  • launcher for nidm examples makes BIDS compliant paths for files that are part of BIDS dataset, or derivatives
  • correction of some function descriptions for AFNI and FSL
  • some other unreferenced bugs for all parsers

GitHub Actions Bot and others added 22 commits June 10, 2024 08:47
automated nidm example computation from github action
c7a2197
@bclenet
Merge branch 'bids-standard:master' into master
c7372d4
@bclenet
Replacing RRID by AltIdentifier
dd2f163
@bclenet
Dealing with RRIDs for AltIdentifier
acef62b
@bclenet
[TEST] updates for RRID handling
79b41a1
@bclenet
Updating parsers after changes in default_graph
777f59c
automated nidm example computation from github action
19f0262
@bclenet
New strategies for Id generation
3846692
@bclenet
Sanitizing URIs for Entities from AFNI provenance
a63a41d
@bclenet
Cleaning SPM paths before parsing nidm examples
db87417
@bclenet
AFNI entity URIs
f142cfc
@bclenet
Entity ids
11003ec
@bclenet
Correcting some function descriptions doe AFNI
c85e427
@bclenet
AFni description functions + SPM c1xxx bug
3b84ca9
@bclenet
Allowing '--' for FSL parameter keys
7bcf386
@bclenet
[BUG] multiple space chars causing wrong entities for FSL parser
5b9d420
@bclenet
Safer URNs for all parsers
f740415
automated nidm example computation from github action
6aa1fcf
@bclenet
[BUG] Agent ids on all parsers
8be9c48
@bclenet
Issue with c1xxx ids
fd70559
@bclenet
[Launch Nidm Examples] Changing file names for ds000052 bids dataset
9ca3535
automated nidm example computation from github action
d35cd57
@cmaumet
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cmaumet commented Oct 8, 2024

Discussed with @bclenet, this is ready to review

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Successfully merging this pull request may close these issues.

[Bug]: RRID of SPM is used for all software in the examples [Bug]: RRID should be replaced by AltIdentifier
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