153 lines
4.5 KiB
Python
153 lines
4.5 KiB
Python
"""Tests for the workflow report entry point."""
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import json
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from pathlib import Path
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from workflow_glue import report
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class _NullContext:
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"""Minimal context manager used by report section and tab stubs."""
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def __enter__(self):
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return self
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def __exit__(self, exc_type, exc, tb):
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return False
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class _FakeReport:
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"""Small stand-in for the ezcharts report wrapper."""
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def __init__(self, *args, **kwargs):
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self.sections = []
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def add_section(self, title, key):
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self.sections.append((title, key))
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return _NullContext()
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def write(self, path):
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Path(path).write_text("report ok\n", encoding="utf-8")
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class _FakeTabs:
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"""Small stand-in for the tab layout helper."""
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def add_tab(self, label):
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return _NullContext()
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def _write(path, text):
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path.write_text(text, encoding="utf-8")
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return path
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def test_report_main_accepts_optional_file_sentinels(monkeypatch, tmp_path):
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"""The report entry point should tolerate null-object sentinel files."""
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tables = []
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monkeypatch.setattr(report.labs, "LabsReport", _FakeReport)
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monkeypatch.setattr(report, "Tabs", _FakeTabs)
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monkeypatch.setattr(report, "p", lambda *args, **kwargs: None)
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monkeypatch.setattr(report, "pre", lambda *args, **kwargs: None)
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monkeypatch.setattr(report, "_create_warning_banner", lambda *args, **kwargs: None)
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monkeypatch.setattr(report.fastcat, "SeqSummary", lambda *args, **kwargs: None)
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monkeypatch.setattr(
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report.DataTable,
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"from_pandas",
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staticmethod(lambda table, *args, **kwargs: tables.append(table.copy())),
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)
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metadata = _write(
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tmp_path / "metadata.json",
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json.dumps([{"alias": "sampleA", "has_stats": False}]),
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)
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params = _write(tmp_path / "params.json", "{}")
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versions = tmp_path / "versions"
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versions.mkdir()
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_write(versions / "versions.txt", "tool,1.0\n")
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cohort = tmp_path / "cohort"
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cohort.mkdir()
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reference = cohort / "reference"
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reference.mkdir()
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_write(
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reference / "annotation_reference_summary.json",
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json.dumps({
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"seqname_overlap": ["chr1"],
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"only_in_annotation": ["chrMissing"],
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"only_in_reference": ["chrExtra"],
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"annotation": {
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"kept_records": 10,
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"excluded_unstranded_records": 2,
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"sanitised_attribute_records": 1,
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"unstranded_examples": ["chr1\tsim\ttranscript\t1\t4\t.\t.\t."],
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},
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"reference_build_hints": ["GRCh38"],
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"annotation_build_hints": [],
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"reference_provider_hints": [],
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"annotation_provider_hints": [],
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"warnings": ["Warning: Some seqnames are present in the annotation."],
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}),
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)
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samples = tmp_path / "samples"
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samples.mkdir()
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(samples / "OPTIONAL_FILE").touch()
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sqanti = tmp_path / "sqanti"
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sqanti.mkdir()
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(sqanti / "OPTIONAL_FILE").touch()
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alignment_stats = tmp_path / "alignment_stats"
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alignment_stats.mkdir()
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(alignment_stats / "OPTIONAL_FILE").touch()
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out_report = tmp_path / "wf-transcriptomes-report.html"
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args = report.argparser().parse_args(
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[
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str(out_report),
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"--metadata",
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str(metadata),
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"--alignment_stats_dir",
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str(alignment_stats),
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"--cohort_dir",
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str(cohort),
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"--samples_dir",
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str(samples),
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"--sqanti_dir",
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str(sqanti),
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"--versions",
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str(versions),
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"--params",
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str(params),
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]
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)
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report.main(args)
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assert out_report.exists()
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assert any("Overlapping seqnames" in table.to_string() for table in tables)
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assert any(
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"Annotation attributes sanitised" in table.to_string() for table in tables
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)
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assert any("GRCh38" in table.to_string() for table in tables)
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def test_pychopper_tables_uses_sample_directory_names(tmp_path):
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"""Pychopper summaries should be keyed by sample alias."""
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pychopper_dir = tmp_path / "pychopper"
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sample_dir = pychopper_dir / "sampleA_pychopper_output"
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sample_dir.mkdir(parents=True)
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_write(
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sample_dir / "pychopper_summary.tsv",
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"Classification\tValue\nFull length\t10\nUnclassified\t2\n",
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)
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tables = report._pychopper_tables(pychopper_dir)
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assert list(tables) == ["sampleA"]
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assert list(tables["sampleA"]["Classification"]) == [
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"Full length",
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"Unclassified",
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]
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