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Governance model integration and curator updates - #247

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Bankso merged 59 commits into
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study-duo-update
Jul 20, 2026
Merged

Governance model integration and curator updates#247
Bankso merged 59 commits into
mainfrom
study-duo-update

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@Bankso Bankso commented Apr 29, 2026 •
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Changelog

  • Added conditional attributes and valid values from governance collaboration on DUO
  • Updated make file and JSON schema generator script to use CSV. For the qc version of the model, we will still need to generate JSON-LD until we are no longer using schematic for validation.
  • Removed unused specimen information from File View template
  • Updated approach to assay-specific metadata: all file-level annotations will be incorporated into assay-specific schemas.
    • E.g., SequencingRNALevel1 will contain non-redundant attributes from FileView, SequencingLevel1, and SequencingRNALevel1. This ensures compatibility with the curator File View system
  • Updated Id and Key fields to use regex patterns that enforce alignment with CCKP docs

Bankso added 30 commits April 2, 2026 15:08
@Bankso
Move cv files to shared
bc2021d
@Bankso
Update duo from governance model
745fe28
@Bankso
Add governance-focused models
46218e4
@Bankso
Add updated governance attributes
affe79d
@Bankso
Update mapping.yaml
9eb952f
@Bankso
Update valid values
51255dd
@Bankso
Update all_valid_values.csv
fa7e429
@Bankso
Build model CSV
3eea5f5
@Bankso
Build JSON-LD
8522b0d
@Bankso
Add script to build JSON with curator
1cd13bc
@Bankso
Use curator-based JSON build tool
13ca6f2
@Bankso
Remove unused schemas
229f765
@Bankso
Remove outdated schemas
0a30990
@Bankso
Delete cckp_datacatalog.jsonld
b8a4128
@Bankso
Add json schemas from curator
b0ba90b
@Bankso
Rebuild JSON schemas with synapseclient 4.12
0334e96
@Bankso
Add base NGS Level 1 attributes to RNA Level 1
b4ce174
@Bankso
Build schemas from CSV, not JSON-LD
617fbfe
@Bankso
Remove unused functions
2bd316f 
It is no longer necessary to modify the columnType in this way
@Bankso
Make model
f3858c3
@Bankso
Integrate FileView attributes for curator adoption
c9f3de3
@Bankso
Update mc2.model.csv
dbcea81
@Bankso
Use file-specific data use codes attribute
ec6da3b 
Avoid needing to collect study information in file templates
@Bankso
Use File Data Use Codes attribute
faaffa3
@Bankso
Update mc2.model.csv
a42905d
@Bankso
Create SequencingRNALevel1.json
b5a8b6c
@Bankso
Use catalog-specific DUO attribute
09cee5b
@Bankso
Use DatasetView-specific DUO attribute
8483e25
@Bankso
Update docs link
7ca2f30
@Bankso
Use Study specific DUO attribute
9857dda 
Valid values included for conditional info
@Bankso Bankso added the major PR label for a major update label Apr 29, 2026
@Bankso Bankso mentioned this pull request Apr 29, 2026
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@Bankso
Bankso marked this pull request as ready for review June 24, 2026 23:00
@Bankso
Bankso requested a review from aditigopalan as a code owner June 24, 2026 23:00
@Bankso
Bankso requested a review from aditya-nath-sage June 24, 2026 23:05
aditya-nath-sage
aditya-nath-sage approved these changes Jun 25, 2026
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@aditya-nath-sage aditya-nath-sage left a comment

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LGTM!

@Bankso
Curator refactor (#253)
9e2a92b 
* Update to current curator CSV format

* Pattern rule is uri, not url

* Reformatting for curator model compliance

* Reformatting for curator model compliance (part 2)

* Update collection attributes

* Add primary_key property label and regex patterns

* Add common file attributes to file-based models

Enables use of a single JSON schema for each data type

* Collate CSVs

* Fix copy/paste error

* Remove old schema

* Add update curator JSON schemas

synapseclient version 4.12

* Update id pattern

* Update id pattern

* Update id pattern

* Update key patterns to align with ids

* Collate model

* Add updated JSON

* Update File Design description
This was referenced Jul 1, 2026
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@Bankso
Bankso merged commit 07e9620 into main Jul 20, 2026
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@Bankso
Bankso deleted the study-duo-update branch July 20, 2026 23:11
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@aditya-nath-sage aditya-nath-sage aditya-nath-sage approved these changes
@aditigopalan aditigopalan Awaiting requested review from aditigopalan

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@Bankso @aditya-nath-sage