IGVF-1936-change-ic-audit-mux

src/igvfd/audit/measurement_set.py

@@ -224,19 +224,33 @@ def audit_missing_institutional_certification(value, system):
  award = value.get('award', '')
  samples = value.get('samples', [])
 
+ sample_objects_to_check = []
  for sample in samples:
  sample_object = system.get('request').embed(sample, '@@object')
+ if 'MultiplexedSample' in sample_object['@type']:
+ multiplexed_sample_id = sample_object['@id']
+ multiplexed_phrase = f' that is multiplexed in {audit_link(path_to_text(multiplexed_sample_id), multiplexed_sample_id)}'
+ for mux_sample in sample_object['multiplexed_samples']:
+ mux_sample_object = system.get('request').embed(mux_sample, '@@object')
+ sample_objects_to_check.append((mux_sample_object, multiplexed_phrase))
+ else:
+ sample_objects_to_check.append((sample_object, ''))
+
+ for sample_tuple in sample_objects_to_check:
+ sample = sample_tuple[0]
+ multiplexed_phrase = sample_tuple[1]
  nic_labs = []
  nic_awards = []
- for nic in sample_object.get('institutional_certificates', []):
+ for nic in sample.get('institutional_certificates', []):
  nic_object = system.get('request').embed(nic, '@@object?skip_calculated=true')
  nic_labs.append(nic_object.get('lab', ''))
  nic_awards.append(nic_object.get('award', ''))
  if lab not in nic_labs or award not in nic_awards:
  detail = (
  f'Measurement set {audit_link(path_to_text(value["@id"]), value["@id"])} has '
- f'a sample {audit_link(path_to_text(sample), sample)} that lacks any `institutional_certificates` '
- f'issued to the lab that submitted this file set.'
+ f'a sample {audit_link(path_to_text(sample["@id"]), sample["@id"])}{multiplexed_phrase} '
+ f'that lacks any `institutional_certificates` issued to the lab '
+ f'that submitted this file set.'
  )
  yield AuditFailure(audit_message.get('audit_category', ''), f'{detail} {audit_message.get("audit_description", "")}', level=audit_message.get('audit_level', ''))
 

src/igvfd/mappings/measurement_set.json

@@ -1,6 +1,6 @@
 {
- "hash": "352b45520f2fbb50256a2a7ce8b7ef62",
- "index_name": "measurement_set_352b4552",
+ "hash": "860efa91714167146eaeab6130a6c665",
+ "index_name": "measurement_set_860efa91",
  "item_type": "measurement_set",
  "mapping": {
  "dynamic_templates": [

src/igvfd/mappings/multiplexed_sample.json

@@ -1,6 +1,6 @@
 {
- "hash": "fb8479a35acfd8440c65f8dea5192f00",
- "index_name": "multiplexed_sample_fb8479a3",
+ "hash": "5a0b11c7af0b9e512e1e5cc00f0f502e",
+ "index_name": "multiplexed_sample_5a0b11c7",
  "item_type": "multiplexed_sample",
  "mapping": {
  "dynamic_templates": [

src/igvfd/tests/test_audit_measurement_set.py

@@ -278,6 +278,7 @@ def test_audit_missing_institutional_certification(
  assay_term_mpra,
  other_lab,
  tissue,
+ multiplexed_sample,
  human_donor,
  assay_term_chip,
  institutional_certificate,
@@ -344,7 +345,31 @@ def test_audit_missing_institutional_certification(
  for error in res.json['audit'].get('NOT_COMPLIANT', [])
  )
 
+ # If the Measurement Set studies a Multiplexed Sample,
+ # its input samples are checked for their NIC.
+ testapp.patch_json(
+ measurement_set['@id'],
+ {
+ 'samples': [multiplexed_sample['@id']]
+ }
+ )
+ res = testapp.get(measurement_set['@id'] + '@@audit')
+ assert any(
+ error['category'] == 'missing NIH certification'
+ for error in res.json['audit'].get('NOT_COMPLIANT', [])
+ )
+ assert any(
+ f'multiplexed in [{multiplexed_sample["accession"]}]' in error['detail']
+ for error in res.json['audit'].get('NOT_COMPLIANT', [])
+ )
+
  # No flag if the NIC's lab and award match the Measurement Set.
+ testapp.patch_json(
+ measurement_set['@id'],
+ {
+ 'samples': [tissue['@id']]
+ }
+ )
  testapp.patch_json(
  institutional_certificate['@id'],
  {

src/igvfd/types/sample.py

@@ -972,6 +972,24 @@ def sources(self, request, multiplexed_samples):
  def construct_library_sets(self, request, multiplexed_samples):
  return collect_multiplexed_samples_prop(request, multiplexed_samples, 'construct_library_sets')
 
+ @calculated_property(
+ schema={
+ 'title': 'Institutional Certificates',
+ 'type': 'array',
+ 'description': 'The institutional certificates of the samples included in this multiplexed sample.',
+ 'minItems': 1,
+ 'uniqueItems': True,
+ 'notSubmittable': True,
+ 'items': {
+ 'title': 'Institutional Certificate',
+ 'type': 'string',
+ 'linkTo': 'InstitutionalCertificate'
+ }
+ }
+ )
+ def institutional_certificates(self, request, multiplexed_samples):
+ return collect_multiplexed_samples_prop(request, multiplexed_samples, 'institutional_certificates')
+
  @calculated_property(
  schema={
  'title': 'Classifications',