Release 8 fixes by aditigopalan · Pull Request #169 · ncihtan/htan2-data-model

aditigopalan · 2026-04-14T17:34:36Z

Please refer to issues for description of reviews. You can ignore the docs files!

Please also review the docs for this branch here: https://htan2-data-model.readthedocs.io/en/release-8-fixes/

…issue 2) Remove TISSUE_SAMPLE_TYPE (caDSR:16391068) and its downstream conditional rules from the biospecimen schema. The field is no longer needed since frozen-sample tissue type is not captured here. Removes the tissue_sample_type_enum import, attribute, slot_usage entry, and the five rules that gated sectioning fields on it. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…t type (closes #168 issue 3) THERAPEUTIC_AGENTS was unconditionally required. Per the new spec, it (and REGIMEN_OR_LINE_OF_THERAPY) are only required when TREATMENT_TYPE is Chemotherapy, Concurrent Chemoradiation, or Pharmacotherapy. Replaces the single Pharmacotherapy rule with three explicit rules and adds THERAPEUTIC_AGENTS to slot_usage. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…issue 5) ECOG_PERFORMANCE_STATUS was always required, giving no way to report missing data. Add ECOG_PERFORMANCE_STATUS_IS_AVAILABLE (Yes/No/Unknown) as a required field and make ECOG_PERFORMANCE_STATUS conditionally required when IS_AVAILABLE is Yes. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

#168 issue 1) The model had no way to record that a tumor was not staged. Add TUMOR_STAGED (Yes/No/Unknown) as a required field and make CLINICAL_T_STAGE, CLINICAL_N_STAGE, CLINICAL_M_STAGE, and AJCC_STAGING_SYSTEM_EDITION conditionally required when TUMOR_STAGED is Yes. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…loses #168 issue 4) Add GleasonGradeGroupEnum (grade groups 1-5, caDSR:5918370) and an optional GLEASON_GRADE_GROUP slot to the Diagnosis class to support prostate cancer tumor grade reporting. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

#159) Sphinx slugifies heading IDs: lowercase + non-alphanumeric characters → dash. The link generator was using .lower() only, so enum names with underscores (e.g. tissue_or_organ_of_origin_uberon_enum) generated anchors like #tissue_or_organ_of_origin_uberon_enum that didn't match the rendered heading ID #tissue-or-organ-of-origin-uberon-enum, causing the broken link reported for SITE_OF_RESECTION_OR_BIOPSY. Regenerated all docs to apply the fix. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Auto-generated Python classes from LinkML schema updates. **Auto-generated by GitHub Actions workflow** [skip ci]

… values Replace numeric 1-5 values with proper caDSR permissible value names (Grade Group I-V) and update each description with the official caDSR text and per-value caDSR IDs (6051222, 6051013, 6051226, 6051227, 6051228). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

… caDSR text Keep permissible values 1-5; update each description to use the official caDSR grade group name and definition with per-value caDSR IDs (6051222, 6051013, 6051226, 6051227, 6051228). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…ta-model into release-8-fixes

Superseded by updated review on commit aa5840e

Superseded by updated review on commit 7465b8e

Auto-generated Python classes from LinkML schema updates. **Auto-generated by GitHub Actions workflow** [skip ci]

equals_string on a multivalued slot tests the entire collection rather than individual members, so rules never fired for combined treatment types like ["Chemotherapy", "Radiation Therapy"]. Replace equals_string with any_of/pattern semantics (matching the existing surgical/radiation rule style) and consolidate the Chemotherapy + Concurrent Chemoradiation rules into one since they share identical postconditions. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…ta-model into release-8-fixes

Superseded by updated review on commit 3977304

Auto-generated Python classes from LinkML schema updates. **Auto-generated by GitHub Actions workflow** [skip ci]

…attributes OFF_TREATMENT_REASON, REGIMEN_OR_LINE_OF_THERAPY, NUMBER_OF_CYCLES, and RESPONSE were required: true in attributes but immediately overridden to required: false in slot_usage. Set them to required: false at source so the attribute definition matches the effective behaviour; conditional enforcement is handled entirely by the rules block. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Auto-generated Python classes from LinkML schema updates. **Auto-generated by GitHub Actions workflow** [skip ci]

github-actions · 2026-04-14T19:56:14Z

✅ Python classes auto-updated!

The Python classes have been automatically regenerated and committed to this PR branch.

**Updated files:**
```
modules/Biospecimen/src/htan_biospecimen/datamodel/biospecimen.py

modules/Clinical/src/htan_clinical/datamodel/clinical.py
modules/DigitalPathology/src/htan_digitalpathology/datamodel/digital_pathology.py
modules/Imaging/src/htan_imaging/datamodel/imaging.py
modules/MultiplexMicroscopy/src/htan_multiplexmicroscopy/datamodel/multiplex_microscopy.py
modules/Sequencing/src/htan_sequencing/datamodel/sequencing.py
modules/SpatialOmics/src/htan_spatial/datamodel/spatial.py
modules/WES/src/htan_wes/datamodel/wes.py
modules/scRNA-seq/src/htan_scrna_seq/datamodel/scrna_seq.py
```

The generated classes are now up to date with the schema changes.

PozhidayevaDarya

Looks great; the only thing I don't see in this PR is the ECOG performance availability but it looks like Kristen responded that it should be: caDSR (#5943795)
"The data element name is "ECOG Score Performed" and the permissible values are 'Known' and 'Unknown."

adamjtaylor

This is a little hard to parse, but I think this looks like it is implemented correctly. Minor comments but approved without changes.

docs/*.md are generated by scripts/generate_table_docs.py during the ReadTheDocs build (.readthedocs.yaml). They do not need to be committed. Restoring to pre-fix state; the slug fix in the script is what matters. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…ta-model into release-8-fixes

Superseded by updated review on commit 9730d25

Auto-generated Python classes from LinkML schema updates. **Auto-generated by GitHub Actions workflow** [skip ci]

github-actions · 2026-04-15T14:13:58Z

✅ Python classes auto-updated!

The Python classes have been automatically regenerated and committed to this PR branch.

**Updated files:**
```
modules/Biospecimen/src/htan_biospecimen/datamodel/biospecimen.py

modules/Clinical/src/htan_clinical/datamodel/clinical.py
modules/DigitalPathology/src/htan_digitalpathology/datamodel/digital_pathology.py
modules/Imaging/src/htan_imaging/datamodel/imaging.py
modules/MultiplexMicroscopy/src/htan_multiplexmicroscopy/datamodel/multiplex_microscopy.py
modules/Sequencing/src/htan_sequencing/datamodel/sequencing.py
modules/SpatialOmics/src/htan_spatial/datamodel/spatial.py
modules/WES/src/htan_wes/datamodel/wes.py
modules/scRNA-seq/src/htan_scrna_seq/datamodel/scrna_seq.py
```

The generated classes are now up to date with the schema changes.

Adds .gitattributes so GitHub collapses generated Python dataclasses and JSON schemas in PR diffs. Reviewers can still expand them but they won't clutter the default diff view. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…DSR text Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…ta-model into release-8-fixes

Superseded by updated review on commit 0be154e

…resence: PRESENT minimum_value is a slot definition keyword and is not valid inside a slot_conditions precondition block in LinkML rules. Replace with value_presence: PRESENT, which is the correct LinkML 1.3 keyword for expressing "when this field has a value" in rule preconditions. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Superseded by updated review on commit aa09c71

github-actions · 2026-04-15T14:26:14Z

✅ Python classes auto-updated!

The Python classes have been automatically regenerated and committed to this PR branch.

**Updated files:**
```
modules/Biospecimen/src/htan_biospecimen/datamodel/biospecimen.py

modules/Clinical/src/htan_clinical/datamodel/clinical.py
modules/DigitalPathology/src/htan_digitalpathology/datamodel/digital_pathology.py
modules/Imaging/src/htan_imaging/datamodel/imaging.py
modules/MultiplexMicroscopy/src/htan_multiplexmicroscopy/datamodel/multiplex_microscopy.py
modules/Sequencing/src/htan_sequencing/datamodel/sequencing.py
modules/SpatialOmics/src/htan_spatial/datamodel/spatial.py
modules/WES/src/htan_wes/datamodel/wes.py
modules/scRNA-seq/src/htan_scrna_seq/datamodel/scrna_seq.py
```

The generated classes are now up to date with the schema changes.

Superseded by updated review on commit 1506546

github-actions · 2026-04-15T14:27:54Z

✅ Python classes auto-updated!

The Python classes have been automatically regenerated and committed to this PR branch.

**Updated files:**
```
modules/Biospecimen/src/htan_biospecimen/datamodel/biospecimen.py

modules/Clinical/src/htan_clinical/datamodel/clinical.py
modules/DigitalPathology/src/htan_digitalpathology/datamodel/digital_pathology.py
modules/Imaging/src/htan_imaging/datamodel/imaging.py
modules/MultiplexMicroscopy/src/htan_multiplexmicroscopy/datamodel/multiplex_microscopy.py
modules/Sequencing/src/htan_sequencing/datamodel/sequencing.py
modules/SpatialOmics/src/htan_spatial/datamodel/spatial.py
modules/WES/src/htan_wes/datamodel/wes.py
modules/scRNA-seq/src/htan_scrna_seq/datamodel/scrna_seq.py
```

The generated classes are now up to date with the schema changes.

Auto-generated Python classes from LinkML schema updates. **Auto-generated by GitHub Actions workflow** [skip ci]

github-actions · 2026-04-15T14:32:02Z

✅ Python classes auto-updated!

The Python classes have been automatically regenerated and committed to this PR branch.

**Updated files:**
```
modules/Biospecimen/src/htan_biospecimen/datamodel/biospecimen.py

modules/Clinical/src/htan_clinical/datamodel/clinical.py
modules/DigitalPathology/src/htan_digitalpathology/datamodel/digital_pathology.py
modules/Imaging/src/htan_imaging/datamodel/imaging.py
modules/MultiplexMicroscopy/src/htan_multiplexmicroscopy/datamodel/multiplex_microscopy.py
modules/Sequencing/src/htan_sequencing/datamodel/sequencing.py
modules/SpatialOmics/src/htan_spatial/datamodel/spatial.py
modules/WES/src/htan_wes/datamodel/wes.py
modules/scRNA-seq/src/htan_scrna_seq/datamodel/scrna_seq.py
```

The generated classes are now up to date with the schema changes.

aditigopalan and others added 7 commits April 14, 2026 13:22

Merge 0b7a7d1 into 7215196

729d0ce

This comment was marked as resolved.

Sign in to view

chore: auto-generate Python classes from schema changes

13797d6

Auto-generated Python classes from LinkML schema updates. **Auto-generated by GitHub Actions workflow** [skip ci]

This comment was marked as outdated.

Sign in to view

aditigopalan and others added 3 commits April 14, 2026 13:58

Merge branch 'release-8-fixes' of https://github.com/ncihtan/htan2-da…

aa5840e

…ta-model into release-8-fixes

This comment was marked as resolved.

Sign in to view

aditigopalan added 2 commits April 14, 2026 14:05

Removing unnecessary cadsr annotations from gleason_grade_group

7465b8e

Merge 7465b8e into 7215196

7db7b92

This comment was marked as resolved.

Sign in to view

This comment was marked as outdated.

Sign in to view

chore: auto-generate Python classes from schema changes

e25e81f

Auto-generated Python classes from LinkML schema updates. **Auto-generated by GitHub Actions workflow** [skip ci]

This comment was marked as outdated.

Sign in to view

aditigopalan and others added 3 commits April 14, 2026 14:17

Merge branch 'release-8-fixes' of https://github.com/ncihtan/htan2-da…

3977304

…ta-model into release-8-fixes

Merge 3977304 into 7215196

9825f08

This comment was marked as resolved.

Sign in to view

chore: auto-generate Python classes from schema changes

e19d151

Auto-generated Python classes from LinkML schema updates. **Auto-generated by GitHub Actions workflow** [skip ci]

This comment was marked as outdated.

Sign in to view

chore: auto-generate Python classes from schema changes

e7d9840

Auto-generated Python classes from LinkML schema updates. **Auto-generated by GitHub Actions workflow** [skip ci]

PozhidayevaDarya approved these changes Apr 14, 2026

View reviewed changes

adamjtaylor approved these changes Apr 15, 2026

View reviewed changes

Comment thread docs/biospecimen.md

Comment thread modules/Biospecimen/domains/biospecimen.yaml Outdated

Comment thread modules/Biospecimen/domains/biospecimen.yaml

Comment thread modules/Biospecimen/src/htan_biospecimen/datamodel/biospecimen.py Outdated

aditigopalan and others added 3 commits April 15, 2026 10:06

Merge branch 'release-8-fixes' of https://github.com/ncihtan/htan2-da…

9730d25

…ta-model into release-8-fixes

Merge 9730d25 into 7215196

632a5d7

This comment was marked as outdated.

Sign in to view

chore: auto-generate Python classes from schema changes

4f427ee

Auto-generated Python classes from LinkML schema updates. **Auto-generated by GitHub Actions workflow** [skip ci]

aditigopalan and others added 3 commits April 15, 2026 10:15

fix(biospecimen): update IS_TISSUE_SECTION description to official ca…

b929087

…DSR text Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Merge branch 'release-8-fixes' of https://github.com/ncihtan/htan2-da…

0be154e

…ta-model into release-8-fixes

aditigopalan mentioned this pull request Apr 15, 2026

Investigate JSON Schema ordering of attributes #170

Open

This comment was marked as outdated.

Sign in to view

aditigopalan added 2 commits April 15, 2026 10:25

TISSUE_SECTION permissible value descriptions updated

1506546

Merge 1506546 into 7215196

59dfef6

This comment was marked as outdated.

Sign in to view

chore: auto-generate Python classes from schema changes

2c0c401

Auto-generated Python classes from LinkML schema updates. **Auto-generated by GitHub Actions workflow** [skip ci]

aditigopalan merged commit 278bc9c into main Apr 15, 2026

aditigopalan deleted the release-8-fixes branch April 15, 2026 14:46

Conversation

aditigopalan commented Apr 14, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

This comment was marked as resolved.

Uh oh!

This comment was marked as outdated.

This comment was marked as resolved.

Uh oh!

This comment was marked as resolved.

Uh oh!

This comment was marked as outdated.

This comment was marked as outdated.

This comment was marked as resolved.

Uh oh!

This comment was marked as outdated.

github-actions Bot commented Apr 14, 2026

Uh oh!

PozhidayevaDarya left a comment

Choose a reason for hiding this comment

Uh oh!

adamjtaylor left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

This comment was marked as outdated.

Uh oh!

github-actions Bot commented Apr 15, 2026

Uh oh!

This comment was marked as outdated.

Uh oh!

This comment was marked as outdated.

Uh oh!

github-actions Bot commented Apr 15, 2026

Uh oh!

This comment was marked as outdated.

Uh oh!

github-actions Bot commented Apr 15, 2026

Uh oh!

github-actions Bot commented Apr 15, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

aditigopalan commented Apr 14, 2026 •

edited

Loading