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Count only for the first hit for subject or tissue within filename #173

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Count only for the first hit for subject or tissue within filename #173

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ed02dec
Count only for the first hit for subject or tissue within filename
yarikoptic Apr 6, 2023
d22ac9c
Fix logic to count only if not yet present
yarikoptic Apr 19, 2023
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16 changes: 11 additions & 5 deletions dandischema/metadata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -311,13 +311,16 @@ def _add_asset_to_stats(assetmeta: Dict[str, Any], stats: _stats_type) -> None:
stats = _get_samples(value, stats, hierarchy)
break

# which components already found, so we do not count more than
# once in some incorrectly named datasets
found: Dict[str, str] = {}
for part in Path(assetmeta["path"]).name.split(".")[0].split("_"):
if part.startswith("sub-"):
subject = part.replace("sub-", "")
if not found.get("subject") and part.startswith("sub-"):
found["subject"] = subject = part.split("sub-", 1)[1]
if subject not in stats["subjects"]:
stats["subjects"].append(subject)
if part.startswith("sample-"):
sample = part.replace("sample-", "")
if not found.get("sample") and part.startswith("sample-"):
found["sample"] = sample = part.replace("sample-", "")
if sample not in stats["tissuesample"]:
stats["tissuesample"].append(sample)

Expand All @@ -338,10 +341,13 @@ def aggregate_assets_summary(metadata: Iterable[Dict[str, Any]]) -> dict:
stats: _stats_type = {}
for meta in metadata:
_add_asset_to_stats(meta, stats)

stats["numberOfBytes"] = stats.get("numberOfBytes", 0)
stats["numberOfFiles"] = stats.get("numberOfFiles", 0)
stats["numberOfSubjects"] = len(stats.pop("subjects", [])) or None
if stats["numberOfSubjects"]:
# Must not happen. If does -- a bug in software
assert stats["numberOfFiles"]
assert stats["numberOfSubjects"] <= stats["numberOfFiles"]
stats["numberOfSamples"] = (
len(stats.pop("tissuesample", [])) + len(stats.pop("slice", []))
) or None
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