94 lines
2.8 KiB
Python
94 lines
2.8 KiB
Python
from __future__ import annotations
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from pathlib import Path
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from openpyxl import Workbook
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from apps.web.vue3 import main
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def _write_config(input_dir: Path, pep: Path, cds: Path) -> None:
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workbook = Workbook()
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sheet = workbook.active
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sheet.title = "config"
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sheet.append(
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[
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"Species_Code",
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"Species_Role",
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"File_Type",
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"Original_File_Name",
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"Ref",
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]
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)
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sheet.append(["At", "reference", "pep", pep.name, True])
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sheet.append(["At", "reference", "cds", cds.name, True])
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workbook.save(input_dir / "config.xlsx")
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def test_execute_validation_accepts_config_resolved_reference_pep_and_cds(
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tmp_path: Path,
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monkeypatch,
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) -> None:
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input_root = tmp_path / "input"
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job_input = input_root / "job_at"
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external = tmp_path / "external"
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job_input.mkdir(parents=True)
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external.mkdir()
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pep = external / "Arabidopsis_thaliana.TAIR10.pep.all.fa"
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cds = external / "Arabidopsis_thaliana.TAIR10.cds.all.fa"
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pep.write_text(">AT1G01010\nMA\n", encoding="utf-8")
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cds.write_text(">AT1G01010\nATGGCT\n", encoding="utf-8")
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_write_config(job_input, pep, cds)
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monkeypatch.setattr(main, "INPUT_ROOT", input_root)
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monkeypatch.setenv("PLANTAI_REF_DATA_ROOT", str(external))
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available, source = main._reference_bundle_species_available(
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"job_at",
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"At",
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require_cds=True,
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)
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assert available is True
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assert source == str(job_input)
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def test_execute_validation_keeps_accepting_downloaded_reference_bundle(
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tmp_path: Path,
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monkeypatch,
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) -> None:
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input_root = tmp_path / "input"
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species_dir = input_root / "job_spinach" / "string_taxon_3562"
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species_dir.mkdir(parents=True)
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(species_dir / "string_taxon_3562.pep.fasta").write_text(">S1\nMA\n", encoding="utf-8")
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(species_dir / "string_taxon_3562.cds.fasta").write_text(">S1\nATGGCT\n", encoding="utf-8")
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monkeypatch.setattr(main, "INPUT_ROOT", input_root)
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available, source = main._reference_bundle_species_available(
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"job_spinach",
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"string_taxon_3562",
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require_cds=True,
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)
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assert available is True
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assert source == str(species_dir)
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def test_execute_validation_still_rejects_a_truly_incomplete_reference(
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tmp_path: Path,
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monkeypatch,
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) -> None:
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input_root = tmp_path / "input"
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species_dir = input_root / "job_incomplete" / "At"
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species_dir.mkdir(parents=True)
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(species_dir / "At.pep.fasta").write_text(">AT1G01010\nMA\n", encoding="utf-8")
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monkeypatch.setattr(main, "INPUT_ROOT", input_root)
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available, reason = main._reference_bundle_species_available(
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"job_incomplete",
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"At",
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require_cds=True,
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)
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assert available is False
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assert "missing CDS" in reason
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