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

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16 changes: 11 additions & 5 deletions dandischema/metadata.py
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
Expand Down