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DM-14/DM-16 model fixes and File Data Use Codes (14.1.0) - #277
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Update qc_model/qc_attribute_mapping.csv to change the DatasetView attribute name from 'Data Use Codes' to 'Dataset Data Use Codes' for clarity/consistency.
…taset Doi) Source edits in modules/** with mc2.model.csv, mc2.model.jsonld, json_schemas, templates and all_valid_values.csv regenerated via make all. - Remove duplicate Tumor Type value Not-Applicable - Immunoassay casing in DataCatalog dataType - Publication Doi description uses https://doi.org/{doi} - DUO shorthands to official (US, RS, TS, IS, GS, DS) - DUO ID pattern widened to DUO:\d{7,8} - Strip leading/trailing whitespace from values - Dataset Doi not required in DatasetView Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Owner decision: dataType values stay lowercase. Revert the immunoassay -> Immunoassay rename in dataCatalog_data_type.csv and regenerate. The shared bts:Immunoassay JSON-LD node displayName may remain lowercase (known quirk, noted in the 14.0.1 release notes). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Added the 14.0.1 patch items (DM-16) on top of DM-14: Tumor Type 🤖 Generated with Claude Code |
File View and all file-level assay templates now use File Data Use Codes (pattern-validated DUO list, no conditional companion columns). Data Use Codes is retained for Study. Release notes renamed 14.0.1 -> 14.1.0. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
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October 26, 2026 23:34
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…investigators) and regenerate mc2_model from 14.1.0 (#278) * Split Tool/EducationalResource license and Grant investigator as lists, with legacy comma fallback Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * Regenerate cckp_portal.ttl: license and investigator no longer single-valued Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * Regenerate mc2_model LinkML and Turtle from mc2.model.csv 14.1.0 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * kg-pipeline: split a legacy comma-joined Grant.investigator with the person-name heuristic A plain comma split cut "Last, First" names (PEROU, CHARLES M) into two people. legacy_comma_separated takes a mode: "true" (comma) for the licenses, "person_names" (split_person_names, now in harmonize.py and shared with link_scdm) for Grant.investigator. On the extracted Grant table the result equals link_scdm.split_investigators for every row. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * kg-pipeline: keep each investigator as one item, same text in the comma and "|" forms Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * kg-pipeline: map File View data use codes to File Data Use Codes and keep resolving DUO terms Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * kg-pipeline: drop the tumorType crosswalk row for the removed Not-Applicable term Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * kg-pipeline: test build_triples for multivalued license and investigator cells Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * kg-pipeline: license and investigator stay comma-joined STRING columns (CCKP D-Q51) The CCKP cutover keeps these portal columns as text (license may become STRING_LIST later), so the annotation is renamed comma_separated and the descriptions say comma-joined text. The splitting rule is unchanged: a "|" cell splits on "|", otherwise on commas (licenses) or with the person-name heuristic (investigators). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
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Changes following review of PR #262. Releases as 14.1.0 (see
plans/release_14.1.0_notes.md).qc_model/qc_attribute_mapping.csvDatasetView attributeData Use CodesrenamedDataset Data Use Codes.Not-Applicabletumor type removed, DOI description (https://doi.org/{doi}), DUO shorthands aligned to official DUO, DUO ID pattern widened toDUO:\d{7,8}, trailing whitespace removed from source values,Dataset Doino longer required. DataCatalogdataTypestays lowercaseimmunoassay.File Data Use Codes: a pattern-validated DUO list with no controlled values and no conditional companion columns. File View and all 18 file-level assay templates use it instead ofData Use Codes(breaking for file manifests: the column header changes).Data Use Codesis kept for Study;DSP Data Use Codesfor DataDSP;Dataset Data Use Codesfor Dataset.mc2.model.csv,mc2.model.jsonld,json_schemas/,templates/.Deferred:
kg-pipelinestill maps the live annotation keyDataUseCodestoData Use Codes(and its generated LinkML schema/fixtures); to be updated once portal tables are re-annotated.Review: independent review found no correctness bugs.