def test_metadata_clean_function(self):
test1 = "abc\tdef2"
test2 = """
abc\tdef!
"""
self.assertEqual(MetadataValidator.clean_value(test1), "abc def2")
self.assertEqual(MetadataValidator.clean_value(test2), "abc def")
def validate_metadata(self, data):
validator = MetadataValidator()
try:
validator.validate(data)
except MetadataValidationException as e:
raise serializers.ValidationError(e)
return data
def validate_metadata(self, data):
validator = MetadataValidator()
try:
validator.validate(data)
except MetadataValidationException as e:
print("ERROR in validation")
return data
return data
def generate_sample_data_content(files, pipeline_name, pipeline_github,
pipeline_version):
result = "SAMPLE_ID\tREQUEST_ID\tPROJECT_ID\tPATIENT_ID\tCOLLAB_ID\tSAMPLE_TYPE\tGENE_PANEL\tONCOTREE_CODE\tSAMPLE_CLASS\tSPECIMEN_PRESERVATION_TYPE\tSEX\tTISSUE_SITE\tIGO_ID\tRUN_MODE\tPIPELINE\tPIPELINE_GITHUB_LINK\tPIPELINE_VERSION\n"
ret_str = "metadata__sampleId"
query = Q(file__file_group_id=settings.IMPORT_FILE_GROUP)
query |= Q(file__file_group__slug="origin-unknown")
query |= Q(file__file_group__slug="fero-legacy-data")
query = query & Q(file__path__in=files)
samples = FileRepository.filter(
q=query).order_by(ret_str).distinct(ret_str).all()
for sample in samples:
metadata = sample.metadata
result += "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(
metadata.get(
"cmoSampleName",
format_sample_name(metadata["sampleName"],
metadata["specimenType"])),
metadata["requestId"],
get_project_id(metadata["requestId"]),
metadata["patientId"],
metadata["investigatorSampleId"],
MetadataValidator.clean_value(metadata["sampleClass"]),
MetadataValidator.clean_value(metadata["recipe"]),
MetadataValidator.clean_value(metadata["oncoTreeCode"]),
MetadataValidator.clean_value(metadata["specimenType"]),
MetadataValidator.clean_value(metadata["preservation"]),
MetadataValidator.clean_value(metadata["sex"]),
MetadataValidator.clean_value(metadata["tissueLocation"]),
metadata["sampleId"],
MetadataValidator.clean_value(metadata["runMode"]),
pipeline_name,
pipeline_github,
pipeline_version,
)
return result