kemal
e518ea03d5
Readers for IDAT v3, BPM (locus entries v4-v8), CSV manifest, EGT (data blocks 5-9) and GTC v3-v5 (plus a layout-preserving GTC writer); sample-sheet validation (IN-001..IN-014), IDAT discovery and pairing (IN-020..IN-022), message catalogue and exit codes (CLI-014/016), JSON Lines logging (CLI-007/008), atomic writes (CLI-011), run manifest, and `simurg inspect`. Validation (docs/validation/P1.md): GTC, BPM and EGT readers agree exactly with Illumina BeadArrayFiles on GSA v4 / GDA v1 files; GTCs round-trip byte-identically; BPM and CSV manifests are consistent.
46 lines
1.8 KiB
Python
46 lines
1.8 KiB
Python
"""Shared test configuration.
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Tests marked ``data`` need files fetched by ``scripts/fetch_data.sh p0``; tests marked ``oracle`` need
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reference repositories under ``refs/`` (``scripts/bootstrap_refs.sh``). Both are skipped when absent.
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"""
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from __future__ import annotations
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import sys
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from pathlib import Path
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import pytest
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ROOT = Path(__file__).resolve().parents[1]
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DATA = ROOT / "data" / "p0"
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REFS = ROOT / "refs"
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GSA = DATA / "gsa_v4_pgx"
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GSA_BPM = GSA / "GSA-PGx-48v4-0_20079540_E2_bpm" / "GSA-PGx-48v4-0_20079540_E2.bpm"
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GSA_CSV = GSA / "GSA-PGx-48v4-0_20079540_E2_csv" / "GSA-PGx-48v4-0_20079540_E2.csv"
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GSA_EGT = GSA / "GSA-PGx-48v4-0_20079540_E2_ClusterFile" / "GSA-PGx-48v4-0_20079540_E2_ClusterFile.egt"
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GSA_IDATS = GSA / "idats_Demo_36" / "idats_Demo_36"
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GDA_EGT = DATA / "gda_v1" / "infinium-global-diversity-array-8-v1-0-D1-cluster-file" / "GDA-8v1-0_D1_ClusterFile.egt"
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GDA_BPM = DATA / "gda_v1" / "infinium-global-diversity-array-8-v1-0-D1-manifest-file-bpm" / "GDA-8v1-0_D1.bpm"
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GDA_SHEET = DATA / "gda_v1" / "infinium-global-diversity-array-8-v1-0_D1_SampleSheet_Demo_36.csv"
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BIOC_IDATS = DATA / "bioc" / "IlluminaDataTestFiles_1.50.0" / "IlluminaDataTestFiles" / "inst" / "extdata" / "idat"
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ORACLE_GTCS = DATA / "oracle" / "gsa_gtc_gtc2vcf"
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def need(*paths: Path) -> None:
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missing = [p for p in paths if not p.exists()]
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if missing:
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pytest.skip(f"missing test data: {missing[0]} (run scripts/fetch_data.sh p0)")
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@pytest.fixture(scope="session")
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def beadarrayfiles(): # type: ignore[no-untyped-def]
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"""Illumina BeadArrayFiles (BSD-2) as an oracle."""
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path = REFS / "BeadArrayFiles"
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if not (path / "module").is_dir():
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pytest.skip("refs/BeadArrayFiles not present (run scripts/bootstrap_refs.sh)")
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sys.path.insert(0, str(path))
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import module # type: ignore[import-not-found]
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return module
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