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[ENH] State of the schema sprint #1075

Merged
merged 139 commits into from
Apr 28, 2022
Merged

[ENH] State of the schema sprint #1075

merged 139 commits into from
Apr 28, 2022

Commits on Feb 24, 2022

  1. SCHEMA: Encode first two MR metadata tables as "sidecars.yml" (#1016)

    Co-authored-by: Christopher J. Markiewicz <[email protected]>
    tsalo and effigies authored Feb 24, 2022
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  3. Add anatomical MRI rules.

    tsalo committed Feb 24, 2022
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  5. Fix formatting.

    tsalo committed Feb 24, 2022
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Commits on Mar 3, 2022

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Commits on Mar 17, 2022

  1. Address review.

    tsalo committed Mar 17, 2022
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  2. Merge pull request #1017 from tsalo/tsalo-tables

    [SCHEMA] Define YAML tables for MRI common metadata fields and anatomy data
    effigies authored Mar 17, 2022
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Commits on Apr 7, 2022

  1. [SCHEMA] Define YAML tables for DWI/ASL/(i)EEG/micr/beh metadata (#1029)

    * Draft ASL and DWI metadata table rules.
    
    * Add description addendum.
    
    * Define metadata for the behavioral modality.
    
    * Whoops, separate beh and continuous data.
    
    * Add EEG.
    
    * Add iEEG.
    
    * Fix.
    
    * Add microscopy.
    
    * Split up the existing sidecars file.
    
    * Fix issues.
    
    * Update micr.yaml
    
    * Update entities.yaml
    tsalo authored Apr 7, 2022
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  3. Merge gh-1027

    Squashed commit of the following:
    
    commit ee5ff05
    Author: anthony galassi <[email protected]>
    Date:   Thu Apr 7 15:48:02 2022 -0400
    
        moved pet stuff to src/schema/rules/sidecars/pet.yaml
    
    commit d00e683
    Author: Anthony Galassi <[email protected]>
    Date:   Fri Mar 18 09:40:55 2022 -0400
    
        Update src/schema/rules/sidecars.yml
    
    commit 928eea2
    Author: Anthony Galassi <[email protected]>
    Date:   Thu Mar 17 15:42:10 2022 -0400
    
        Add backticks
    
        Added backticks
    
    commit 50b0ae0
    Author: anthony galassi <[email protected]>
    Date:   Tue Mar 15 12:34:42 2022 -0400
    
        fixed level addendum's, removed quotes for selector in PETMRISequenceSpecifics to make linter happy
    
    commit 4a177c0
    Author: anthony galassi <[email protected]>
    Date:   Mon Mar 14 15:59:54 2022 -0400
    
        fixed n - 1 yaml errors, 1 remaining
    
    commit 6e40318
    Author: Anthony Galassi <[email protected]>
    Date:   Mon Mar 14 15:49:29 2022 -0400
    
        Update src/schema/rules/sidecars.yml
    
        change addendum -> level_addendum per commit suggestion.
    
        Co-authored-by: Taylor Salo <[email protected]>
    
    commit a4fb377
    Merge: 41bc816 c5f89c6
    Author: Anthony Galassi <[email protected]>
    Date:   Mon Mar 14 15:17:00 2022 -0400
    
        Merge branch 'schema/sidecar_validation' into bendhouseart-tables
    
    commit 41bc816
    Author: anthony galassi <[email protected]>
    Date:   Thu Mar 10 15:49:58 2022 -0500
    
        fixed yaml formatting
    bendhouseart authored and effigies committed Apr 7, 2022
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Commits on Apr 8, 2022

  1. [SCHEMA] Add MEG, func, and fmap metadata tables (#1054)

    * Add MEG.
    
    * Add fmap file.
    
    * Add func file.
    
    * Fix a couple of things.
    
    * Update func.yaml
    tsalo authored Apr 8, 2022
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Commits on Apr 12, 2022

  1. Draft ASL validation file.

    tsalo committed Apr 12, 2022
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  2. Fix level.

    tsalo committed Apr 12, 2022
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  3. Reorder based on code.

    tsalo committed Apr 12, 2022
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  4. Add 196 and reorder selectors.

    tsalo committed Apr 12, 2022
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  5. Add a few DWI and events rules.

    tsalo committed Apr 12, 2022
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  6. started adding special_errors corresponding to columne 'Reason' Valid…

    …ator Issues google sheet
    bendhouseart committed Apr 12, 2022
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  7. Fix linter issues.

    tsalo committed Apr 12, 2022
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  8. Add a few more rules.

    tsalo committed Apr 12, 2022
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Commits on Apr 13, 2022

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  4. fixed formatting issues

    bendhouseart committed Apr 13, 2022
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  6. missed 3 of em

    bendhouseart committed Apr 13, 2022
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  8. Fix line length.

    tsalo committed Apr 13, 2022
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  12. SCHEMA add MEG channels.tsv

    effigies committed Apr 13, 2022
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  15. Define task columns

    effigies committed Apr 13, 2022
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  17. Update src/schema/rules/tabular_data/eeg.yaml

    Co-authored-by: Taylor Salo <[email protected]>
    effigies and tsalo committed Apr 13, 2022
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  18. Add a few more rules.

    tsalo committed Apr 13, 2022
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  20. Merge pull request #1061 from effigies/schema/tsv-task

    SCHEMA: Specify column requirement levels for several tabular files
    effigies authored Apr 13, 2022
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Commits on Apr 14, 2022

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  3. lint fixes for pet.yaml

    rwblair committed Apr 14, 2022
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  6. Merge pull request #1066 from tsalo/schema-sprint-taylor-2

    Replace `addendum` with `description_addendum`
    effigies authored Apr 14, 2022
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  8. remove nifti_header schemam

    rwblair committed Apr 14, 2022
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  9. Merge pull request #1070 from rwblair/schema/pet_tsv

    [SCHEMA] Define blood.tsv columns
    effigies authored Apr 14, 2022
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  12. Update src/schema/rules/sidecars/asl_validation.yaml

    Co-authored-by: Chris Markiewicz <[email protected]>
    tsalo and effigies authored Apr 14, 2022
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  13. Switch to new context terms.

    tsalo committed Apr 14, 2022
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  14. More.

    tsalo committed Apr 14, 2022
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  15. [SCHEMA] Add datatypes field to datatype rule files (#1012)

    * Add datatypes field to datatype rule files.
    
    * Update src/schema/rules/datatypes/meg.yaml
    
    Co-authored-by: Chris Markiewicz <[email protected]>
    
    Co-authored-by: Chris Markiewicz <[email protected]>
    tsalo and effigies authored Apr 14, 2022
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  16. Use YAML schema types.

    tsalo committed Apr 14, 2022
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  18. Merge branch 'schema-sprint' of github.com:bids-standard/bids-specifi…

    …cation into schema/common_derivatives
    rwblair committed Apr 14, 2022
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  19. Update mri.yaml

    removed ::
    bendhouseart authored Apr 14, 2022
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  20. Update func.yaml

    removed ::
    bendhouseart authored Apr 14, 2022
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  21. Update asl.yaml

    bendhouseart authored Apr 14, 2022
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  24. Merge pull request #1063 from bendhouseart/schema-sprint

    [SCHEMA] Correlating existing validator issues to schema entries
    effigies authored Apr 14, 2022
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  25. Merge pull request #1074 from effigies/name-tables

    SCHEMA: Convert datatype lists to objects
    effigies authored Apr 14, 2022
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  26. Merge branch 'schema-sprint' of github.com:bids-standard/bids-specifi…

    …cation into schema/common_derivatives
    rwblair committed Apr 14, 2022
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  27. Hostile takeover

    effigies authored Apr 14, 2022
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  28. Merge branch 'schema/common_derivatives' of github.com:rwblair/bids-s…

    …pecification into schema/common_derivatives
    rwblair committed Apr 14, 2022
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Commits on Apr 15, 2022

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  4. lint nifti_header.yaml

    rwblair authored and effigies committed Apr 15, 2022
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  5. lint fixes for nifti_header.yaml

    rwblair authored and effigies committed Apr 15, 2022
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  8. Flesh out context object

    effigies committed Apr 15, 2022
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  10. Add dataset.modalities

    effigies committed Apr 15, 2022
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  11. Add json object

    effigies committed Apr 15, 2022
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  13. Back to JSON schema

    effigies committed Apr 15, 2022
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  14. Add aslcontext and events

    effigies committed Apr 15, 2022
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  18. Comment context

    effigies committed Apr 15, 2022
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  20. Apply suggestions from code review

    Co-authored-by: Chris Markiewicz <[email protected]>
    tsalo and effigies authored Apr 15, 2022
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  21. associated --> associations

    tsalo committed Apr 15, 2022
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  22. seq --> array

    tsalo committed Apr 15, 2022
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  24. Revert extra change.

    tsalo committed Apr 15, 2022
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  25. Merge pull request #1069 from effigies/schema/context

    SCHEMA: Create context schema in meta/
    effigies authored Apr 15, 2022
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  26. Merge pull request #1060 from tsalo/schema-sprint-taylor

    Start drafting validation rules for ASL data
    effigies authored Apr 15, 2022
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  27. generate common_derivatives datatypes from all other existing datatyp…

    …es. Add anatomical volumetric, mask and segmentation derivatives
    rwblair committed Apr 15, 2022
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  29. Latin

    effigies committed Apr 15, 2022
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  30. Update src/schema/rules/datatypes/derivatives.yaml

    Co-authored-by: Taylor Salo <[email protected]>
    rwblair and tsalo authored Apr 15, 2022
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  31. STY: fix YAML lint

    effigies committed Apr 15, 2022
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  34. Make path a selector

    rwblair authored and effigies committed Apr 15, 2022
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  37. Implement gh-1068

    effigies committed Apr 15, 2022
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  38. STY: indent 2

    effigies committed Apr 15, 2022
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  39. Tag issues 113 and 128

    effigies committed Apr 15, 2022
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  40. Use curly-bracket syntax

    effigies committed Apr 15, 2022
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  41. Merge branch 'schema-sprint' of github.com:bids-standard/bids-specifi…

    …cation into schema/common_derivatives
    rwblair committed Apr 15, 2022
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  42. ---

    effigies committed Apr 15, 2022
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  43. YAML: syntax error

    effigies committed Apr 15, 2022
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  44. Conform to issue syntax

    effigies committed Apr 15, 2022
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  45. Conform schema/rules for sidecars and tabular_data

    Did my best to conform all these rules to the sprint standard decisions.
    ericearl committed Apr 15, 2022
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  50. Merge pull request #1078 from ericearl/fix/conform-schema

    [SCHEMA] Conform the schema/rules files consistently
    effigies authored Apr 15, 2022
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  51. Merge branch 'schema-sprint' of github.com:bids-standard/bids-specifi…

    …cation into schema/common_derivatives
    rwblair committed Apr 15, 2022
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  52. STY: pacify yaml linter

    effigies committed Apr 15, 2022
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  56. add missing periods and use full entity name in dataype common imagin…

    …g derivatives
    
    add missing comma in tabular common_derivatives
    rwblair committed Apr 15, 2022
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Commits on Apr 16, 2022

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Commits on Apr 18, 2022

  1. change to _ref in schema

    rwblair committed Apr 18, 2022
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  2. Merge pull request #1064 from effigies/schema/dataset_description

    [RTM] SCHEMA: Encode requirement levels for dataset_description and genetic_info
    effigies authored Apr 18, 2022
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Commits on Apr 19, 2022

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Commits on Apr 20, 2022

  1. Revert "change to _ref in schema"

    This reverts commit d9e38fa.
    rwblair committed Apr 20, 2022
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  4. yamllint asl_validation

    rwblair committed Apr 20, 2022
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  5. Merge branch 'schema-sprint' of github.com:bids-standard/bids-specifi…

    …cation into schema/common_derivatives
    rwblair committed Apr 20, 2022
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Commits on Apr 21, 2022

  1. Merge pull request #1072 from rwblair/schema/common_derivatives

    [SCHEMA] Define common derivatives rules
    rwblair authored Apr 21, 2022
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Commits on Apr 25, 2022

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Commits on Apr 28, 2022

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  2. Merge pull request #1094 from rwblair/schema/convert-checks-to-js

    SCHEMA convert selectors and checks to javascript
    rwblair authored Apr 28, 2022
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