Add Genome Quality Metrics

[JeanMainguy]

Adds support for loading genome quality metrics (CheckM/CheckM2 scores, assembly statistics) into typed Genome table columns, with data integrity protection to prevent accidental overwrites.

Key Changes

Database Schema

• Added 14 optional columns to GenomeBase: CheckM/CheckM2 metrics, assembly stats, genome metadata

New CLI Command

# Add quality metrics (errors if changing existing values)
pangbank_db add-quality-metrics genome_quality_metrics.tsv

# Force overwrite (with warnings)
pangbank_db add-quality-metrics genome_quality_metrics.tsv --force

Can be added also with the command add-collection-release.
The file should be added in the input JSON as follow:

"genome_quality_metrics": {
  "file": "/path/to/genome_quality_metrics.tsv"
}

Data Integrity

• Default: Raises error when attempting to change existing values
• --force flag: Allows overwrites with warning logs
• Idempotent: Re-applying same values succeeds
• Initial imports via add-collection-release allow setting values

Implementation

• Dynamic Pydantic model introspection (no hardcoded mappings)
• Automatic type conversion (int, float, str)
• Required field protection
• New columns work automatically

[Copilot]

Pull request overview

Adds support for ingesting genome quality metrics (typed columns on Genome) and per-release genome statuses (new GenomeStatus table), including CLI commands and end-to-end functional tests to validate the import pipeline.

Changes:

• Extended Genome schema with optional quality/assembly/statistics columns and added Alembic migration.
• Introduced GenomeStatus model + migration, API exposure on genome endpoints, and a CLI command to add statuses to an existing release.
• Added functional and unit tests covering quality-metric import, status import, and API response shape.

Reviewed changes

Copilot reviewed 21 out of 21 changed files in this pull request and generated 11 comments.

Show a summary per file

File	Description
pangbank_api/models.py	Adds GenomeStatus* models/relationships and new optional quality-metric columns on GenomeBase.
alembic/versions/1b2d64350ce4_add_genome_status_table.py	Creates genomestatus table with uniqueness constraint + indexes.
alembic/versions/765d642f1d8c_add_new_optional_columns_in_genome_table.py	Adds new nullable quality/assembly columns to genome table.
pangbank_api/manage_db/input_models.py	Updates JSON input model to accept genome_quality_metrics and genome_statuses.
pangbank_api/manage_db/utils.py	Validates optional quality-metrics file and status files exist for add-collection-release.
pangbank_api/manage_db/genome_metadata.py	Adds dynamic column filtering/type conversion and updater for typed Genome quality metrics.
pangbank_api/manage_db/genome_status.py	New loader for genome status files + insert logic into DB.
pangbank_api/manage_db/pangbank_db.py	Wires quality-metrics + statuses into add-collection-release; adds add-genome-statuses and add-quality-metrics CLI commands.
pangbank_api/manage_db/collections.py	Removes now-unused genome_metadata_sources linkage from release creation.
pangbank_api/crud/genomes.py	Extends genome public representation to include statuses.
pangbank_api/routers/genomes.py	Updates response models to include statuses (via GenomePublic).
tests/routers/test_genomes.py	Adds API tests asserting statuses is included and empty when absent.
tests/manage_db/test_genome_status.py	New tests for parsing status files and adding statuses to releases.
tests/manage_db/test_genome_metadata.py	Adds tests for type conversion and overwrite protection/idempotency behavior.
tests/manage_db/test_collection.py	Updates tests for changed create_collection_release signature.
tests/functional/test_functional_pangbank_db.py	New end-to-end functional test covering import (taxonomy, genomes, pangenomes, statuses, quality metrics).
tests/functional/run_functional_test.py	Adds a standalone runner to generate data and run the functional workflow.
tests/functional/README.md	Documents how to run and interpret functional tests and generated data structure.
tests/functional/__init__.py	Marks functional tests package.
pyproject.toml	Registers functional pytest marker.
README.md	Documents new JSON inputs and new CLI commands (quality metrics + genome statuses).

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.