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Fix: Staging area validator incorrectly fails on supplementary LungMAP file #27

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Merged
ncalvanese1 merged 2 commits into from
Oct 29, 2025
Merged

Fix: Staging area validator incorrectly fails on supplementary LungMAP file #27

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20ba1c4
Require metadata files contain a provenance
dsotirho-ucsc Oct 15, 2025
96db216
Identify suupplementary file CGM by ontology
dsotirho-ucsc Oct 15, 2025
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38 changes: 22 additions & 16 deletions hca/staging_area_validator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -209,31 +209,37 @@ def validate_metadata_file(self, blob: gcs.Blob) -> None:
metadata_id, metadata_version = metadata_file[:-5].split("_")
file_json = self.download_blob_as_json(blob)
self.validate_file_json(file_json, blob.name)
if provenance := file_json.get("provenance"):
assert metadata_id == provenance["document_id"]
provenance = file_json["provenance"]
assert metadata_id == provenance["document_id"]
if metadata_file := self.metadata_files.get(metadata_id):
metadata_file["name"].add(blob.name)
metadata_file["metadata_versions"].add(metadata_version)
metadata_file["found_metadata"] = True
if metadata_type.endswith("_file"):
metadata_file["data_file_name"] = file_json["file_core"]["file_name"]
metadata_file["found_data_file"] = False
if metadata_type == "supplementary_file" and file_json.get(
"provenance", {}
).get("submitter_id"):
try:
self.validate_file_description(file_json.get("file_description"))
except Exception as e:
self.file_errors[blob.name] = e
metadata_file["valid_stratification"] = False
log.error("Invalid file_description in %s.", blob.name)
else:
metadata_file["valid_stratification"] = True
if metadata_type == "supplementary_file" and "submitter_id" in provenance:
content_description = file_json["file_core"].get(
"content_description", []
)
if any(
"matrix" in v.lower()
for cd in content_description
for v in cd.values()
):
try:
self.validate_stratification(file_json.get("file_description"))
except Exception as e:
self.file_errors[blob.name] = e
metadata_file["valid_stratification"] = False
log.error("Invalid file_description in %s.", blob.name)
else:
metadata_file["valid_stratification"] = True
else:
self.extra_files.append(blob.name)

def validate_file_description(self, file_description: str) -> None:
if not file_description:
def validate_stratification(self, stratification: str) -> None:
if not stratification:
return
strata = [
{
Expand All @@ -242,7 +248,7 @@ def validate_file_description(self, file_description: str) -> None:
point.split("=") for point in stratum.split(";")
)
}
for stratum in file_description.split("\n")
for stratum in stratification.split("\n")
]
log.debug(strata)
valid_keys = [
Expand Down