feat: map diagnosis facet term values to display value (#4722)

[frano-m]

Closes #4722.

This pull request introduces a new mapping for diagnosis term IDs to human-readable names, and updates the application to display these improved labels throughout the UI. The main focus is on enhancing the clarity of diagnosis-related data by showing both the name and the ontology ID (e.g., "Autism (OMIM:209850)") wherever diagnosis terms appear. The most important changes are grouped below:

Diagnosis Term Mapping Infrastructure:

• Added a script (scripts/lookup-diagnosis-terms.ts) to fetch HP and OMIM term names from authoritative sources and generate a mapping of diagnosis term IDs to their display names. This script outputs a JS constant used by the app.
• Introduced DIAGNOSIS_DISPLAY_VALUE in site-config/anvil-cmg/dev/index/common/diagnosis.ts (referenced, not shown) and imported it into utility files for use in value mapping.

UI Integration and Value Mapping:

• Added the mapDiagnosisValue function in site-config/anvil-cmg/dev/index/common/utils.ts to map diagnosis term IDs to their display names (with fallback to raw value if unmapped).
• Updated the diagnoses cell builder in app/viewModelBuilders/azul/anvil-cmg/common/viewModelBuilders.ts to display mapped diagnosis values in table cells.
• Updated the select category configuration for diagnoses in site-config/anvil-cmg/dev/config.ts to use mapDiagnosisValue, ensuring consistent labeling in filters and selectors.

Codebase Cleanup and Imports:

• Cleaned up and reorganized imports in several files to reflect the new mapping utility and remove unused or redundant imports. [1] [2] [3] [4]

These changes collectively ensure that all diagnosis terms shown in the UI are now much more user-friendly and informative, improving both accessibility and user experience.

[Copilot]

Pull request overview

Adds a diagnosis code → human-readable label mapping to the AnVIL CMG site config so diagnosis facet values can be displayed as friendly names rather than raw HP/OMIM IDs.

Changes:

• Introduces an auto-generated DIAGNOSIS_DISPLAY_VALUE lookup for HP/OMIM term IDs.
• Adds mapDiagnosisValue and wires it into the diagnosis select category configuration.
• Adds a generator script (scripts/lookup-diagnosis-terms.ts) to build/update the mapping from authoritative sources.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 3 comments.

File	Description
site-config/anvil-cmg/dev/index/common/utils.ts	Adds mapDiagnosisValue using the new diagnosis display mapping.
site-config/anvil-cmg/dev/index/common/diagnosis.ts	New generated dictionary mapping HP/OMIM IDs to display names.
site-config/anvil-cmg/dev/config.ts	Applies diagnosis value mapping in the diagnosis select category configuration and refactors imports.
scripts/lookup-diagnosis-terms.ts	New script to generate the diagnosis mapping from Azul + HPO/OMIM sources.

Comments suppressed due to low confidence (1)

site-config/anvil-cmg/dev/config.ts:90

• Diagnosis mapping is only applied to diagnoses.disease, but diagnoses.phenotype is also a diagnosis facet and the mapping dictionary/script covers phenotype IDs too. If the intent is to make diagnosis facets human-readable, apply the same mapSelectCategoryValue(mapDiagnosisValue) to the DIAGNOSIS_PHENOTYPE category as well (or clarify why phenotype is excluded).

            {
              key: ANVIL_CMG_CATEGORY_KEY.DIAGNOSE_DISEASE,
              label: ANVIL_CMG_CATEGORY_LABEL.DIAGNOSE_DISEASE,
              mapSelectCategoryValue: mapSelectCategoryValue(mapDiagnosisValue),
            },
            {
              key: ANVIL_CMG_CATEGORY_KEY.DONOR_ORGANISM_TYPE,
              label: ANVIL_CMG_CATEGORY_LABEL.DONOR_ORGANISM_TYPE,
            },
            {
              key: ANVIL_CMG_CATEGORY_KEY.DIAGNOSIS_PHENOTYPE,
              label: ANVIL_CMG_CATEGORY_LABEL.DIAGNOSIS_PHENOTYPE,
            },

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[Copilot]

Pull request overview

Copilot reviewed 5 out of 5 changed files in this pull request and generated 4 comments.

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