Feature/transfer new view spec branch#25
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…r builder, processor, database, models, and stats tracking.
…d platform are not None
…ocessing, and memory-optimized JSON serialization, introducing new configuration options and a build timeout.
…sing TermAccessionNumber
…safety and configuration management
…improved type safety and validation
…r improved readability and performance
…ataBatch, enhancing performance and memory efficiency
… a typo in the postCreateCommand grep pattern.
…CH_VCS_PRETEND_VERSION` from Dockerfile build commands.
…rror handling - Introduced ArcBuildData class for structured data handling during ARC building. - Enhanced Database class with validation methods to handle missing required columns and NULL values. - Updated InvestigationRow, StudyRow, AssayRow, PublicationRow, and ContactRow models to include spec_field for better metadata management. - Improved error logging for missing required columns and NULL values during database streaming. - Modified main entry point to accept command line arguments more flexibly. - Updated integration and unit tests to cover new validation logic and ensure robustness. - Refactored test cases to align with new model structures and validation rules.
…ust validation tests for required fields
…tion; update tests accordingly
…o use SQLAlchemy's select API.
… new validation tests
- Refactor environment files to include a new debug configuration.
- Change log level in the main config to DEBUG for better traceability.
- Modify SQL queries to use `literal_column("*")` for selecting all columns.
- Introduce validation tests to ensure correct handling of NULL values and spec overrides.
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This pull request refactors the sql_to_arc component to use SQLAlchemy, enabling multi-database support via connection strings and introducing a modular architecture with Pydantic-based data models. The update also improves the development environment with SOPS-based secret management and a more resilient database initialization workflow. Feedback was provided regarding the use of echo in the Docker Compose configuration, which could introduce unwanted newlines in the client key file.
…pdate README code block for better readability
…command syntax in docker-compose
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