Move standard references to TSV-backed package data and remove DB models

[Ulthran]

Motivation

• Make HostSpecies, SampleType and machine-prefix mappings authoritative, file-backed TSVs that are easy to reference from other projects.
• Remove duplication in the database and provide lightweight Python wrappers so other services can import the canonical lists without DB access.
• Expose machine prefix → machine type mapping for programmatic use.

Description

• Add sample_registry/standards.py implementing dataclasses and loader/wrapper classes (StandardSampleTypes, StandardHostSpeciesList, MachineTypeMappings) that read packaged TSVs via importlib.resources and expose accessors like get(), names(), values(), and as_dict().
• Add TSV reference data under sample_registry/data/ (standard_sample_types.tsv, standard_host_species.tsv, machine_types.tsv) and a root machine_types.tsv for easy URL access, and add sample_registry/data to package data in pyproject.toml (include data/*.tsv).
• Remove the StandardSampleType and StandardHostSpecies ORM models from sample_registry/models.py and delete the database initialization / registration logic that wrote these tables from sample_registry/db.py, sample_registry/register.py, and sample_registry/registrar.py.
• Update runtime code to use the TSV-backed data: sample_registry/registrar.py now uses MACHINE_TYPE_MAPPINGS for machines, and sample_registry/app.py uses STANDARD_SAMPLE_TYPES and STANDARD_HOST_SPECIES for stats and counts.
• Update tests to remove DB-driven standard registration checks and add tests/test_standards.py to validate TSV loading and mappings.

Testing

• Ran the test suite with pytest -q; test collection failed with ModuleNotFoundError: No module named 'flask_sqlalchemy', so automated tests did not complete.

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Codex Task

[codecov]

Codecov Report

❌ Patch coverage is 77.19298% with 26 lines in your changes missing coverage. Please review.
✅ Project coverage is 60.13%. Comparing base (167adba) to head (4b2e898).

Files with missing lines	Patch %	Lines
sample_registry/app.py	0.00%	14 Missing ⚠️
sample_registry/standards.py	87.50%	12 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #62      +/-   ##
==========================================
- Coverage   60.23%   60.13%   -0.11%     
==========================================
  Files           8        9       +1     
  Lines         757      765       +8     
==========================================
+ Hits          456      460       +4     
- Misses        301      305       +4     

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[Copilot]

Pull request overview

This PR refactors the standard reference data (sample types, host species, and machine type mappings) from database-backed storage to TSV file-backed storage. This change makes the reference data authoritative, file-backed, and easily importable by other services without requiring database access.

Changes:

• Added sample_registry/standards.py with dataclasses and loader classes for TSV-backed reference data
• Added TSV reference files in sample_registry/data/ directory and duplicates at repository root for URL access
• Removed StandardSampleType and StandardHostSpecies ORM models and related database initialization code
• Updated runtime code to use TSV-backed data instead of database queries

Reviewed changes

Copilot reviewed 15 out of 15 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
sample_registry/standards.py	New module implementing dataclasses and loaders for TSV-backed standard reference data
sample_registry/data/standard_sample_types.tsv	TSV file containing standard sample type reference data
sample_registry/data/standard_host_species.tsv	TSV file containing standard host species reference data
sample_registry/data/machine_types.tsv	TSV file containing machine prefix to type mappings
sample_registry/data/init.py	Package initialization for data directory
machine_types.tsv	Duplicate of machine_types.tsv at repository root for easy URL access
sample_registry/models.py	Removed StandardSampleType and StandardHostSpecies ORM models
sample_registry/db.py	Removed database initialization functions for standard types
sample_registry/registrar.py	Updated to use MACHINE_TYPE_MAPPINGS from TSV-backed data
sample_registry/register.py	Removed register_sample_types and register_host_species functions
sample_registry/app.py	Updated stats endpoint to query using TSV-backed standard lists instead of database joins
tests/test_standards.py	New tests validating TSV loading and data access
tests/test_registrar.py	Removed tests for DB-backed standard type registration
tests/test_register.py	Removed tests for DB-backed standard type registration
pyproject.toml	Added sample_registry.data package and data/*.tsv to package data; removed obsolete console scripts

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[Copilot]

The values() method returns all machine types from the dictionary, which can contain duplicates if multiple prefixes map to the same machine type. In machine_types.tsv, both "M" and "SH" map to "Illumina-MiSeq". This causes duplicate entries in the argparse choices when SampleRegistry.machines is used (see sample_registry/register.py lines 120 and 142). Consider returning unique values by using set() or modifying the return to be distinct.

Suggested change

	return list(self._by_prefix.values())
	# Return unique machine types, preserving insertion order
	return list(dict.fromkeys(self._by_prefix.values()))