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Add a script to correct incorrectly saved list in parameter file #1034

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cmadjar
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@cmadjar cmadjar commented Jan 16, 2024

Description

This adds a tool script to correct the list values incorrectly saved in parameter_file table due to a bug in the python insert query that has been resolved by #1025.

Close #1033

Notes for existing projects

If you have been any of the python pipeline to insert MRI data (bids_import.py or the dcm2bids pipeline) then, it is very likely that some of the list were improperly saved in parameter_file. The following command can be run from the root directory of the LORIS-MRI code:

python tools/correct_lists_incorrectly_saved_in_parameter_file.py -p database_config.py

Note: this is not necessary if you have been only using the perl dcm2mnc insertion pipeline.

@cmadjar cmadjar changed the base branch from main to 24.1-release January 17, 2024 14:25
@cmadjar cmadjar merged commit c167954 into aces:24.1-release Jan 17, 2024
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cmadjar added a commit that referenced this pull request Jan 18, 2024
* Update VERSION to 24.1.13

* Fixes for parameter file value lists (#1025)

* rm conversion to str on value list

* add check to ensure list is not empty

* Add method to check and skip duplicate content uploads to S3 - for 24.1-release (#1037)

* get Kim's code on 24.1-release branch

* fix flake8

* fix flake8

* remove pyblake2 from pip requirements.txt file as LORIS-MRI uses hashlib now (#1038)

* update version to 24.1.14 for bug fix release (#1039)

* Add a script to correct incorrectly saved list in parameter file (#1034)

* query parameter_file for the lists incorrectly saved

* finalize the update query

* finalize script help section

---------

Co-authored-by: breen0074 <[email protected]>
cmadjar added a commit that referenced this pull request Mar 15, 2024
* Update VERSION to 24.1.13

* Fixes for parameter file value lists (#1025)

* rm conversion to str on value list

* add check to ensure list is not empty

* Add method to check and skip duplicate content uploads to S3 - for 24.1-release (#1037)

* get Kim's code on 24.1-release branch

* fix flake8

* fix flake8

* remove pyblake2 from pip requirements.txt file as LORIS-MRI uses hashlib now (#1038)

* update version to 24.1.14 for bug fix release (#1039)

* Add a script to correct incorrectly saved list in parameter file (#1034)

* query parameter_file for the lists incorrectly saved

* finalize the update query

* finalize script help section

* [EEG BIDS] Support assembly_bids source for datasets (LORIS 24.1) (#1046)

* [EEG BIDS] Support assembly_bids source for datasets

* flake8

* Add executable permission

* QA comment

* Add support for config prePackagedDownloadPath and EEGChunksPath

* Update the bids_import script logic to explicitely add the --no-copy option

* fix incorrect conflict resolution

* fix incorrect conflict resolution

* bids_import.py - Missing short option fix

---------

Co-authored-by: breen0074 <[email protected]>
Co-authored-by: Laetitia Fesselier <[email protected]>
cmadjar added a commit that referenced this pull request Mar 15, 2024
* Update VERSION to 24.1.13

* Fixes for parameter file value lists (#1025)

* rm conversion to str on value list

* add check to ensure list is not empty

* Add method to check and skip duplicate content uploads to S3 - for 24.1-release (#1037)

* get Kim's code on 24.1-release branch

* fix flake8

* fix flake8

* remove pyblake2 from pip requirements.txt file as LORIS-MRI uses hashlib now (#1038)

* update version to 24.1.14 for bug fix release (#1039)

* Add a script to correct incorrectly saved list in parameter file (#1034)

* query parameter_file for the lists incorrectly saved

* finalize the update query

* finalize script help section

* [EEG BIDS] Support assembly_bids source for datasets (LORIS 24.1) (#1046)

* [EEG BIDS] Support assembly_bids source for datasets

* flake8

* Add executable permission

* QA comment

* Add support for config prePackagedDownloadPath and EEGChunksPath

* Update the bids_import script logic to explicitely add the --no-copy option

* fix flake8

* bids_import.py - Missing short option fix

---------

Co-authored-by: breen0074 <[email protected]>
Co-authored-by: Laetitia Fesselier <[email protected]>
cmadjar added a commit that referenced this pull request Mar 18, 2024
* Update VERSION to 24.1.13

* Fixes for parameter file value lists (#1025)

* rm conversion to str on value list

* add check to ensure list is not empty

* Add method to check and skip duplicate content uploads to S3 - for 24.1-release (#1037)

* get Kim's code on 24.1-release branch

* fix flake8

* fix flake8

* remove pyblake2 from pip requirements.txt file as LORIS-MRI uses hashlib now (#1038)

* update version to 24.1.14 for bug fix release (#1039)

* Add a script to correct incorrectly saved list in parameter file (#1034)

* query parameter_file for the lists incorrectly saved

* finalize the update query

* finalize script help section

* [EEG BIDS] Support assembly_bids source for datasets (LORIS 24.1) (#1046)

* [EEG BIDS] Support assembly_bids source for datasets

* flake8

* Add executable permission

* QA comment

* Add support for config prePackagedDownloadPath and EEGChunksPath

* Update the bids_import script logic to explicitely add the --no-copy option

* Update set file path override and chunks logic (#1050)

* Update set file path override and chunks logic

* flake8

* Update set file path override and chunks logic - bugfix (#1051)

---------

Co-authored-by: breen0074 <[email protected]>
Co-authored-by: Laetitia Fesselier <[email protected]>
cmadjar added a commit that referenced this pull request Mar 18, 2024
* Update VERSION to 24.1.13

* Fixes for parameter file value lists (#1025)

* rm conversion to str on value list

* add check to ensure list is not empty

* Add method to check and skip duplicate content uploads to S3 - for 24.1-release (#1037)

* get Kim's code on 24.1-release branch

* fix flake8

* fix flake8

* remove pyblake2 from pip requirements.txt file as LORIS-MRI uses hashlib now (#1038)

* update version to 24.1.14 for bug fix release (#1039)

* Add a script to correct incorrectly saved list in parameter file (#1034)

* query parameter_file for the lists incorrectly saved

* finalize the update query

* finalize script help section

* [EEG BIDS] Support assembly_bids source for datasets (LORIS 24.1) (#1046)

* [EEG BIDS] Support assembly_bids source for datasets

* flake8

* Add executable permission

* QA comment

* Add support for config prePackagedDownloadPath and EEGChunksPath

* Update the bids_import script logic to explicitely add the --no-copy option

* Update set file path override and chunks logic (#1050)

* Update set file path override and chunks logic

* flake8

* Update set file path override and chunks logic - bugfix (#1051)

* fix bad resolution

* fix bad resolution

---------

Co-authored-by: breen0074 <[email protected]>
Co-authored-by: Laetitia Fesselier <[email protected]>
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Create a script to correct the lists in parameter file that were incorrectly saved
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