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Save full peak file path key under the peak_file key of SpectrumDataset instead of just the file name. #69

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Save full peak file path key under the peak_file key of SpectrumDataset instead of just the file name. #69

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2 changes: 1 addition & 1 deletion depthcharge/data/parsers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -197,7 +197,7 @@ def iter_batches(self, batch_size: int | None) -> pa.RecordBatch:
parsed = processor(parsed)

entry = {
"peak_file": self.peak_file.name,
"peak_file": str(self.peak_file.resolve()),
"scan_id": str(parsed.scan_id),
"ms_level": parsed.ms_level,
"precursor_mz": parsed.precursor_mz,
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4 changes: 2 additions & 2 deletions tests/unit_tests/test_data/test_datasets.py
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Expand Up @@ -47,7 +47,7 @@ def test_indexing(tokenizer, mgf_small, tmp_path):

spec = dataset[0]
assert len(spec) == 7
assert spec["peak_file"] == ["small.mgf"]
assert spec["peak_file"] == [str(mgf_small.resolve())]
assert spec["scan_id"] == ["0"]
assert spec["ms_level"].item() == 2
assert (spec["precursor_mz"].item() - 416.2448) < 0.001
Expand Down Expand Up @@ -123,7 +123,7 @@ def test_load(tokenizer, tmp_path, mgf_small):
dataset = SpectrumDataset.from_lance(db_path, 1)
spec = dataset[0]
assert len(spec) == 8
assert spec["peak_file"] == ["small.mgf"]
assert spec["peak_file"] == [str(mgf_small.resolve())]
assert spec["scan_id"] == ["0"]
assert spec["ms_level"] == 2
assert (spec["precursor_mz"] - 416.2448) < 0.001
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2 changes: 1 addition & 1 deletion tests/unit_tests/test_data/test_parsers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@ def test_mgf_and_base(mgf_small):
)
expected = pl.DataFrame(
{
"peak_file": [mgf_small.name] * 2,
"peak_file": [str(mgf_small.resolve())] * 2,
"scan_id": ["0", "1"],
"ms_level": [2, 2],
"precursor_mz": [416.24474357, 257.464565],
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