Add profile-level generic assay aggregation

[dippindots]

Part of: cBioPortal/GSoC#131 and #7940
Frontend PR: cBioPortal/cbioportal-frontend#5596

Summary

Adds backend support for the Generic Assay frequency/counts table in Study View by introducing a profile-level aggregation path for Generic Assay data and wiring Generic Assay row selections into Study View filtering.

This keeps the existing entity-filtered Generic Assay count behavior intact while enabling the new cohort-level table for binary and categorical Generic Assay profiles.

What changed

New profile-level Generic Assay counts path

• Extended the Generic Assay counts request shape to accept profileType
• Added a new profile-level aggregation query in the ClickHouse Generic Assay mapper
• Routed column-store Generic Assay count requests to:
  • existing entity-filter path when genericAssayDataFilters are present
  • new profile-level path when profileType is provided

Study View filter integration

• Added genericAssaySelectionFilters to Study View filter models/context
• Wired Generic Assay table row selections into Study View cohort filtering
• Added SQL support so selected Generic Assay rows restrict the cohort the same way other Study View components do

Counting semantics

• Supports both sample-level and patient-level Generic Assay profiles
• Uses exact case-insensitive matching for selected Generic Assay values
• Preserves existing NA denominator semantics on the legacy/entity-filter count path
• Computes profile-scoped totals for the new profile-level aggregation path
• Fixed bin-count aggregation so patient-level profiles use patient-level counting/NA totals instead of sample-level counting

Follow-up cleanup and hardening

• Tightened Generic Assay selection validation to reject blank profileType, stableId, and value
• Refactored Generic Assay selection validation helpers for readability
• Removed the dead intercepted Generic Assay request-attribute path from the column-store controller
• Cleaned up Sonar-reported test issues, including deprecated test wiring and unused constants

Backend flow

1. Study View sends POST /api/generic-assay-data-counts/fetch
2. If genericAssayDataFilters are present, backend uses the existing entity-filter count path
3. If no entity filters are present and profileType is provided, backend uses the new profile-level aggregation path
4. If users select rows in the Generic Assay table, those selections are stored in genericAssaySelectionFilters
5. Study View filtering SQL converts those selections into cohort restrictions and all downstream aggregations recompute against the filtered cohort

Validation / tests

Added or updated focused coverage for:

• column-store Generic Assay controller routing and request validation
• Generic Assay selection validation
• Generic Assay selection matching behavior
• profile-level Generic Assay count aggregation
• sample-level and patient-level Generic Assay bin-count aggregation
• restored skipped Study View controller test annotation coverage

[sonarqubecloud]

Quality Gate passed

Issues
6 New issues
0 Accepted issues

Measures
0 Security Hotspots
74.3% Coverage on New Code
8.6% Duplication on New Code

See analysis details on SonarQube Cloud