Feature/transfer new view spec branch#25

Merged

Zalfsten merged 30 commits into

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feature/transfer_new_view_spec_branch

Mar 31, 2026

Commits on Feb 2, 2026

refactor: Reimplement SQL-to-ARC conversion with dedicated modules for builder, processor, database, models, and stats tracking.
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feat: add syncing of Python dependencies with uv in load-env script
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fix: update import statements for ARC to include 'import-not-found' type ignore
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test: add assertions to verify assay measurement, technology type, and platform are not None
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feat: Refactor ARC generation to use batched streaming, concurrent processing, and memory-optimized JSON serialization, introducing new configuration options and a build timeout.
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Merge branch 'main' into feature/transfer_optimizations
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fix: enhance assertions in assay tests to check for None before accessing TermAccessionNumber
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feat: update data models and tests to use Pydantic for improved type safety and configuration management
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feat: optimize data fetching by using streaming and grouping for related data
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feat: refactor data models and mapping functions to use Pydantic for improved type safety and validation
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refactor: replace SQLAlchemy Table constructs with raw SQL queries for improved readability and performance
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Commits on Feb 3, 2026

Commits on Feb 4, 2026

refactor: Centralize `SETUPTOOLS_SCM_PRETEND_VERSION` and remove `HATCH_VCS_PRETEND_VERSION` from Dockerfile build commands.
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Commits on Feb 24, 2026

Commits on Mar 2, 2026

Commits on Mar 4, 2026

feat: Add database schema validation and refactor streaming queries to use SQLAlchemy's select API.
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Commits on Mar 19, 2026

feat: Update environment configurations and enhance SQL handling with new validation tests
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Commits on Mar 25, 2026

Merge branch 'main' into feature/transfer_new_view_spec_branch
Zalfsten
committed