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[ENH] BEP031: Microscopy #1359

Merged
merged 75 commits into from
Jan 12, 2022
Merged

[ENH] BEP031: Microscopy #1359

merged 75 commits into from
Jan 12, 2022

Commits on Jul 28, 2021

  1. Added the microscopy Regex parts in the rules and added the function … 

    …IsMicroscopy called by IsBids in type.js
    @etiennebergeron
    etiennebergeron committed Jul 28, 2021
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  2. Added the different microscopy modality suffixes

    @etiennebergeron
    etiennebergeron committed Jul 28, 2021
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  3. Add back the enter removed by accident in phenotypic_rules.json

    @etiennebergeron
    etiennebergeron committed Jul 28, 2021
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Commits on Jul 29, 2021

  1. Created the file with the required metadata fields microscopy.json an… 

    …d modified json.js to call it
    @etiennebergeron
    etiennebergeron committed Jul 29, 2021
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Commits on Jul 30, 2021

  1. JSON field 'AcquisitionParameters' is now 'OtherAcquisitionParameters'

    @etiennebergeron
    etiennebergeron committed Jul 30, 2021
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Commits on Aug 3, 2021

  1. Added error codes 214 and 215 for missing samples files. Added the fi… 

    …le 'checkSamples.js' to check if the samples files are in the dataset. WIP; checkSamples considers for now that those files are always needed. Need to add the regex to find the sample entity. Modified 'fulLTest.js' to call 'checkSamples.js'.
    @etiennebergeron
    etiennebergeron committed Aug 3, 2021
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Commits on Aug 4, 2021

  1. Corrected a typo between the 'pet' and 'microscopy' paths.

    @etiennebergeron
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  2. Codes '216' and '217' added for 'PixelSizeUnits' and a missing recomm… 

    …ended JSON field respectively.
    @etiennebergeron
    etiennebergeron committed Aug 4, 2021
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  3. Removed code 214 since 'samples.json' is only recommended if samples.… 

    …tsv is there (already coded).
    @etiennebergeron
    etiennebergeron committed Aug 4, 2021
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  4. Modified 'checkSamples.js' to check 'samples.tsv' instead of JSON. Mi… 

    …ght not need this file, WIP. In 'microscopy.json', removed the recommended fields from the 'required' dict.
    @etiennebergeron
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Commits on Aug 5, 2021

  1. Modified again to check 'samples.tsv'.

    @etiennebergeron
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  2. The checkSamples method was working with 'samples.json', but not with… 

    … 'samples.tsv'. checkSamples deleted and its call in fullTest.js as well.
    @etiennebergeron
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  3. Didn't succeed to figure out how to detect samples.tsv. I restored th… 

    …e files 'fullTest.js', 'tsv.js' and 'validate.js'. I will work on something else and come back later on it.
    @etiennebergeron
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  4. Removed enters in fullTest.js.

    @etiennebergeron
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  5. Removed the warning for RECOMMENDED JSON fields missing. Doesn't seem… 

    … implemented yet for the other modalities.
    @etiennebergeron
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Commits on Aug 6, 2021

  1. Update bids-validator/utils/issues/list.js 

    Co-authored-by: mariehbourget <[email protected]>
    @etiennebergeron @mariehbourget
    etiennebergeron and mariehbourget authored Aug 6, 2021
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  2. Update bids-validator/validators/json/json.js 

    Co-authored-by: mariehbourget <[email protected]>
    @etiennebergeron @mariehbourget
    etiennebergeron and mariehbourget authored Aug 6, 2021
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  3. Changed the suffixes to uppercase in the rules and 'json.js'.

    @etiennebergeron
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  4. Merge branch 'bids-standard:master' into bep031

    @etiennebergeron
    etiennebergeron authored Aug 6, 2021
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  5. The entity 'sample' is REQUIRED in microscopy, so modified the regex … 

    …rules to suit that.
    @etiennebergeron
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Commits on Aug 9, 2021

  1. Added a new 'checkSamples.js' file, but this time based on 'checkRead… 

    …me.js'. The file is called in the fullTest only if the dataset has for modality 'Microscopy'.
    @etiennebergeron
    etiennebergeron committed Aug 9, 2021
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  2. Removed unnecessary import.

    @etiennebergeron
    etiennebergeron committed Aug 9, 2021
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Commits on Aug 11, 2021

  1. Added the rules related to the 'samples.tsv' file in 'tsv.js'. Added … 

    …the related errors in the 'list.js' file.
    @etiennebergeron
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Commits on Aug 12, 2021

  1. The PixelSizeUnits now needs to be in um. Currently using the existin… 

    …g error code: 55 where a JSON field's value is not equal to one of the allowed values, so the code 221 is deleted.
    @etiennebergeron
    etiennebergeron committed Aug 12, 2021
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Commits on Aug 19, 2021

  1. Merge branch 'bids-standard:master' into bep031

    @etiennebergeron
    etiennebergeron authored Aug 19, 2021
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Commits on Sep 16, 2021

  1. Added a dictionary 'microscopy_json' in the 'file_level_rules.json' t… 

    …o manage the JSON name rules separately. Modified 'type.js' to import this new dictionary. Put the <sample> entity optional at the session and top level.
    @etiennebergeron
    etiennebergeron committed Sep 16, 2021
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Commits on Sep 19, 2021

  1. Added the Regex rule for a file named _photo.jpg. Added the JSON fiel… 

    …ds 'Immersion', 'NumericalAperture', 'Magnification', 'ChunkTransformationMatrix' and 'ChunkTransformationMatrixAxis'.
    @etiennebergeron
    etiennebergeron committed Sep 19, 2021
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Commits on Sep 28, 2021

  1. Entities order modified; <chunk> at the end.

    @etiennebergeron
    etiennebergeron committed Sep 28, 2021
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Commits on Oct 1, 2021

  1. Merge branch 'master' into bep031

    @mariehbourget
    mariehbourget authored Oct 1, 2021
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Commits on Oct 13, 2021

  1. Modified tsv.js for samples.tsv ; now two different subjects can have a 

    sample named the same way without raising an error.
    @etiennebergeron
    etiennebergeron committed Oct 13, 2021
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  2. Merge branch 'bep031' of https://github.com/neuropoly/bids-validator … 

    …into HEAD

Merging the bep031 branch (after master update) and the HEAD I was
working on to add the samples.tsv feature.
    @etiennebergeron
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Commits on Oct 21, 2021

  1. Completed the JSON fields ('TissueDeformationScaling' and 'SampleEnvi… 

    …ronment') and the suffix 'uCT' modifications on the validator.
    @etiennebergeron
    etiennebergeron committed Oct 21, 2021
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Commits on Oct 23, 2021

  1. Merge branch 'bids-standard:master' into bep031

    @etiennebergeron
    etiennebergeron authored Oct 23, 2021
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Commits on Nov 4, 2021

  1. Merge branch 'master' of github.com:bids-standard/bids-validator into… 

    … bep031
    @rwblair
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Commits on Dec 5, 2021

  1. Resolve some issues that mentioned in BEP031 pr changes document

    @konantian
    konantian committed Dec 5, 2021
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  2. Resolve comments from PR

    @konantian
    konantian committed Dec 5, 2021
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Commits on Dec 6, 2021

  1. Fix microscopy regexp

    @konantian
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  2. Merge branch 'bep031' into main-pr-changes

    @konantian
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Commits on Dec 7, 2021

  1. Remove "ChunkTransformationMatrix" from the recommended list

    @konantian
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Commits on Dec 8, 2021

  1. Add regexp for _photo ext in microscopy

    @konantian
    konantian committed Dec 8, 2021
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  2. Revert changes

    @konantian
    konantian committed Dec 8, 2021
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  3. Merge pull request #2 from neuropoly/main-pr-changes 

    Resolve some issues that mentioned in BEP031 pr changes document
    @konantian
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Commits on Dec 20, 2021

  1. 1. Add Check for consistency for PixelSize between JSON and OME-TIFF … 

    …metadata

2. Add Check for consistency with optional OME-TIFF metadata if present for Immersion, NumericalAperture and Magnification
3. Add check for ChunkTransformationMatrix field in the JSON file
    @konantian
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Commits on Dec 21, 2021

  1. Resolve comments

    @konantian
    konantian committed Dec 21, 2021
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Commits on Dec 23, 2021

  1. Resolve comments

    @konantian
    konantian committed Dec 23, 2021
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  2. Resolve comments

    @konantian
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Commits on Dec 24, 2021

  1. Resolve comments

    @konantian
    konantian committed Dec 24, 2021
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  2. Rename folder ometiff to microscopy

    @konantian
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  3. Merge pull request #3 from neuropoly/bep031-consistency-check 

    Bep031 consistency check
    @konantian
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Commits on Dec 27, 2021

  1. 1. Update regex rules for microscopy 

    2. Update microscopy schema json
3. Code optimization for tsv.js
    @konantian
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  2. Update regex for matrix field check

    @konantian
    konantian committed Dec 27, 2021
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Commits on Dec 28, 2021

  1. Bug fix

    @konantian
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  2. Merge pull request #4 from neuropoly/bep031-minor-changes 

    Resolve PR comments
    @konantian
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Commits on Dec 29, 2021

  1. Update the error message when sample type is not valid

    @konantian
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Commits on Jan 2, 2022

  1. 1. Add validation for tiff and big tiff 

    2. Add validation for inconsistent tiff type and extension
    @konantian
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Commits on Jan 3, 2022

  1. Change an error to warning

    @konantian
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  2. Merge pull request #5 from neuropoly/bep031-tiff-validation 

    Validation for Tiff and BigTiff
    @konantian
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  3. Merge branch 'master' into bep031

    @konantian
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Commits on Jan 6, 2022

  1. Update validation for OME namespace

    @konantian
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  2. add tests for checkJSONAndField

    @rwblair
    rwblair committed Jan 6, 2022
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  3. add tests for checkSample.js

    @rwblair
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  4. add tests for microscopy validate.js and test data

    @rwblair
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  5. add param docs to readFile function

    @rwblair
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  6. generate error if magic number is incorrect on tiff file

    @rwblair
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Commits on Jan 7, 2022

  1. Fix code style

    @konantian
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  2. Merge pull request #6 from neuropoly/bep031-update-namespace 

    Update validation for OME namespace
    @konantian
    konantian authored Jan 7, 2022
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  3. move new dependencies into validator package.json

    @rwblair
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  4. have micro json check use old sidecar generation function

    @rwblair
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  5. Merge branch 'bep031' of github.com:neuropoly/bids-validator into HEAD

    @rwblair
    rwblair committed Jan 7, 2022
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  6. rearrange logic for samples.tsv validation. Add tests.

    @rwblair
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  7. updated package-lock to reflect package.json changes.

    @rwblair
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Commits on Jan 11, 2022

  1. have microscopy json check return empty list if no other issues found

    @rwblair
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Commits on Jan 12, 2022

  1. set esbuild buffer size env in bin/bids-validator when we are using e… 

    …sbuild-runner
    @rwblair
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  2. added babel runtime to web package.json, maybe it was just my setup b… 

    …eing wonky.
    @rwblair
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  3. Merge pull request #7 from bids-standard/bep031_review_updates 

    Bep031 review updates
    @mariehbourget
    mariehbourget authored Jan 12, 2022
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