def _matches(cookie: Cookie, context: HgiContext) -> bool:
"""
Matches if the creation of the data object in iRODS has been observed but the reference has been set to one that we
are not interested in. The order of these events is not considered.
"""
if not was_creation_observed(cookie.enrichments):
return False
reference = extract_latest_metadata_key_value_known_in_irods(cookie.enrichments, IRODS_REFERENCE_KEY)
if reference is None:
# No update to reference yet
return False
if len(reference) != 1:
# Multiple values for reference is unexpected
return False
reference_species_groups = re.match(_REFERENCE_EXTRACTION_PATTERN, list(reference)[0])
if reference_species_groups is None:
# Reference is in unexpected format
return False
reference_species = reference_species_groups.group(1)
# Read uninteresting references from file every time to (easily) support live updates to this list
with open(KNOWN_UNINTERESTING_REFERENCES_PATH, "r") as file:
uninteresting_references = file.read().splitlines()
return reference_species in uninteresting_references
def test_not_in_irods_enrichment_or_irods_update(self):
enrichments = [
Enrichment(IRODS_ENRICHMENT, datetime(1, 1, 1), UNINTERESTING_DATA_OBJECT_AS_METADATA),
Enrichment(
IRODS_UPDATE_ENRICHMENT, datetime(2, 2, 2),
Metadata(UNINTERESTING_DATA_OBJECT_MODIFICATION_AS_METADATA))
]
self.enrichment_collection.add(enrichments)
self.assertIsNone(extract_latest_metadata_key_value_known_in_irods(self.enrichment_collection, _METADATA_KEY))
def test_in_irods_enrichments(self):
enrichments = [
Enrichment(IRODS_ENRICHMENT, datetime(1, 1, 1), self.interesting_data_objects_as_metadata[0]),
Enrichment(IRODS_ENRICHMENT, datetime(2, 2, 2), self.interesting_data_objects_as_metadata[1]),
Enrichment(IRODS_ENRICHMENT, datetime(3, 3, 3), UNINTERESTING_DATA_OBJECT_AS_METADATA),
]
self.enrichment_collection.add(enrichments)
value = extract_latest_metadata_key_value_known_in_irods(self.enrichment_collection, _METADATA_KEY)
self.assertEqual(len(list(value)), 1)
self.assertIn(3, value)
def test_in_irods_enrichments_and_irods_update_enrichments_when_most_recent_from_irods_update_enrichment(self):
enrichments = [
Enrichment(IRODS_UPDATE_ENRICHMENT, datetime(1, 1, 1), self.interesting_modifications_as_metadata[0]),
Enrichment(IRODS_ENRICHMENT, datetime(2, 2, 2), self.interesting_data_objects_as_metadata[0]),
Enrichment(IRODS_ENRICHMENT, datetime(3, 3, 3), UNINTERESTING_DATA_OBJECT_AS_METADATA),
Enrichment(IRODS_ENRICHMENT, datetime(4, 4, 4), self.interesting_data_objects_as_metadata[1]),
Enrichment(IRODS_UPDATE_ENRICHMENT, datetime(5, 5, 5), self.interesting_modifications_as_metadata[1])
]
self.enrichment_collection.add(enrichments)
value = extract_latest_metadata_key_value_known_in_irods(self.enrichment_collection, _METADATA_KEY)
self.assertEqual(len(list(value)), 1)
self.assertIn(1, value)
def _matches(cookie: Cookie, context: HgiContext) -> bool:
"""
Matches if the creation has been observed and the manual QC has been set to an incorrect value. The order of these
events is not considered.
"""
if not was_creation_observed(cookie.enrichments):
return False
manual_qc = extract_latest_metadata_key_value_known_in_irods(cookie.enrichments, IRODS_MANUAL_QC_KEY)
if manual_qc is None:
# No update to manual QC yet
return False
if len(manual_qc) != 1:
# Multiple values for manual QC is unexpected
return False
return INCORRECT_MANUAL_QC_VALUE in manual_qc
def test_not_in_irods_enrichment(self):
enrichment = Enrichment(IRODS_ENRICHMENT, datetime(1, 1, 1), UNINTERESTING_DATA_OBJECT_AS_METADATA)
self.enrichment_collection.add(enrichment)
self.assertIsNone(extract_latest_metadata_key_value_known_in_irods(self.enrichment_collection, _METADATA_KEY))
def test_no_irods_related_enrichments(self):
self.enrichment_collection.add(Enrichment("other", datetime(1, 1, 1), Metadata()))
self.assertIsNone(extract_latest_metadata_key_value_known_in_irods(self.enrichment_collection, _METADATA_KEY))
def test_no_enrichments(self):
self.assertIsNone(extract_latest_metadata_key_value_known_in_irods(self.enrichment_collection, _METADATA_KEY))
