Revert "IGVF-1903-missing-MPRA-design"

src/igvfd/audit/construct_library_set.py

@@ -33,7 +33,7 @@ def audit_construct_library_set_associated_phenotypes(value, system):
                 f'has phenotype-associated variants listed in its `selection_criteria`, '
                 f'but no phenotype term specified in `associated_phenotypes`.'
             )
-            yield AuditFailure(audit_message.get('audit_category', ''), f'{detail} {audit_message.get("audit_description", "")}', level=audit_message.get('audit_level', ''))
+            yield AuditFailure(audit_message.get('audit_category', ''), f'{detail} {audit_message.get("audit_description", "")})', level=audit_message.get('audit_level', ''))
 
 
 @audit_checker('ConstructLibrarySet', frame='object')
@@ -55,7 +55,7 @@ def audit_construct_library_set_plasmid_map(value, system):
     )
     documents = value.get('documents', [])
     if documents == []:
-        yield AuditFailure(audit_message.get('audit_category', ''), f'{detail} {audit_message.get("audit_description", "")}', level=audit_message.get('audit_level', ''))
+        yield AuditFailure(audit_message.get('audit_category', ''), f'{detail} {audit_message.get("audit_description", "")})', level=audit_message.get('audit_level', ''))
     else:
         for document in documents:
             document_obj = system.get('request').embed(document, '@@object?skip_calculated=true')
@@ -65,7 +65,7 @@ def audit_construct_library_set_plasmid_map(value, system):
             else:
                 continue
         if map_counter == 0:
-            yield AuditFailure(audit_message.get('audit_category', ''), f'{detail} {audit_message.get("audit_description", "")}', level=audit_message.get('audit_level', ''))
+            yield AuditFailure(audit_message.get('audit_category', ''), f'{detail} {audit_message.get("audit_description", "")})', level=audit_message.get('audit_level', ''))
 
 
 @audit_checker('ConstructLibrarySet', frame='object')
@@ -93,43 +93,30 @@ def audit_construct_library_set_scope(value, system):
 
 
 @audit_checker('ConstructLibrarySet', frame='object')
-def audit_integrated_content_files(value, system):
+def audit_construct_library_set_guide_design(value, system):
     '''
     [
         {
             "audit_description": "Guide libraries are expected to link to an integrated content file of guide RNA sequences.",
             "audit_category": "missing guide RNA sequences",
             "audit_level": "NOT_COMPLIANT"
-        },
-        {
-            "audit_description": "Reporter libraries are expected to link to an integrated content file of MPRA sequence designs.",
-            "audit_category": "missing MPRA sequence designs",
-            "audit_level": "NOT_COMPLIANT"
         }
     ]
     '''
-    audit_message_guide = get_audit_message(audit_integrated_content_files, index=0)
-    audit_message_reporter = get_audit_message(audit_integrated_content_files, index=1)
-    library_expectation = {
-        'guide library': ('guide RNA sequences', audit_message_guide),
-        'reporter library': ('MPRA sequence designs', audit_message_reporter),
-    }
-    integrated_content_files = value.get('integrated_content_files', '')
-    library_type = value.get('file_set_type', '')
-    if library_type in library_expectation:
-        file_expectation = library_expectation[library_type][0]
-        audit_message = library_expectation[library_type][1]
+    audit_message = get_audit_message(audit_construct_library_set_guide_design)
+    if value.get('file_set_type', '') == 'guide library':
+        integrated_content_files = value.get('integrated_content_files', '')
         if integrated_content_files:
             files = [system.get('request').embed(file, '@@object?skip_calculated=true')
                      for file in integrated_content_files]
-            if not ([file for file in files if file['content_type'] == file_expectation]):
+            if not ([file for file in files if file['content_type'] == 'guide RNA sequences']):
                 detail = (f'Construct library set {audit_link(path_to_text(value["@id"]), value["@id"])} has no '
-                          f'linked files in `integrated_content_files` with `content_type` {file_expectation}.')
-                yield AuditFailure(audit_message.get('audit_category', ''), f'{detail} {audit_message.get("audit_description", "")}', level=audit_message.get('audit_level', ''))
+                          f'linked files in `integrated_content_files` with `content_type` "guide RNA sequences".')
+                yield AuditFailure(audit_message.get('audit_category', ''), f'{detail} {audit_message.get("audit_description", "")})', level=audit_message.get('audit_level', ''))
         else:
             detail = (f'Construct library set {audit_link(path_to_text(value["@id"]), value["@id"])} has no '
                       f'`integrated_content_files`.')
-            yield AuditFailure(audit_message.get('audit_category', ''), f'{detail} {audit_message.get("audit_description", "")}', level=audit_message.get('audit_level', ''))
+            yield AuditFailure(audit_message.get('audit_category', ''), f'{detail} {audit_message.get("audit_description", "")})', level=audit_message.get('audit_level', ''))
 
 
 @audit_checker('ConstructLibrarySet', frame='object')
@@ -160,4 +147,4 @@ def audit_construct_library_set_orf_gene(value, system):
                 f'Construct library set {audit_link(path_to_text(value["@id"]), value["@id"])} '
                 f'has a `small_scale_gene_list` which does not match the genes of its associated `orf_list`.'
             )
-            yield AuditFailure(audit_message.get('audit_category', ''), f'{detail} {audit_message.get("audit_description", "")}', level=audit_message.get('audit_level', ''))
+            yield AuditFailure(audit_message.get('audit_category', ''), f'{detail} {audit_message.get("audit_description", "")})', level=audit_message.get('audit_level', ''))

src/igvfd/mappings/construct_library_set.json

@@ -1,6 +1,6 @@
 {
-    "hash": "b8a3872fe50e49f54571b421dade990c",
-    "index_name": "construct_library_set_b8a3872f",
+    "hash": "589aee3185664ed4d88efdd4ecb42d57",
+    "index_name": "construct_library_set_589aee31",
     "item_type": "construct_library_set",
     "mapping": {
         "dynamic_templates": [

src/igvfd/tests/test_audit_construct_library_set.py

@@ -210,35 +210,6 @@ def test_audit_construct_library_set_guide_library_guide_rna_sequences(
         for error in res.json['audit'].get('NOT_COMPLIANT', []))
 
 
-def test_audit_construct_library_set_mpra_sequence_designs(
-    testapp,
-    construct_library_set_reporter,
-    tabular_file
-):
-    res = testapp.get(construct_library_set_reporter['@id'] + '@@audit')
-    assert any(
-        error['category'] == 'missing MPRA sequence designs'
-        for error in res.json['audit'].get('NOT_COMPLIANT', [])
-    )
-    testapp.patch_json(
-        construct_library_set_reporter['@id'],
-        {'integrated_content_files': [tabular_file['@id']]}
-    )
-    res = testapp.get(construct_library_set_reporter['@id'] + '@@audit')
-    assert any(
-        error['category'] == 'missing MPRA sequence designs'
-        for error in res.json['audit'].get('NOT_COMPLIANT', [])
-    )
-    testapp.patch_json(
-        tabular_file['@id'],
-        {'content_type': 'MPRA sequence designs'}
-    )
-    res = testapp.get(construct_library_set_reporter['@id'] + '@@audit')
-    assert all(
-        error['category'] != 'missing MPRA sequence designs'
-        for error in res.json['audit'].get('NOT_COMPLIANT', []))
-
-
 def test_audit_unexpected_virtual_sample(
     testapp,
     construct_library_set_genome_wide,

src/igvfd/types/file_set.py

@@ -99,7 +99,6 @@ class FileSet(Item):
         'samples.disease_terms',
         'samples.treatments',
         'samples.modifications',
-        'samples.construct_library_sets',
         'donors',
     ]
 

src/igvfd/types/sample.py

@@ -100,7 +100,7 @@ class Sample(Item):
         'lab',
         'sources',
         'sample_terms',
-        'construct_library_sets',
+        'treatments'
     ]
 
     set_status_up = [
@@ -772,7 +772,11 @@ class WholeOrganism(Biosample):
     item_type = 'whole_organism'
     schema = load_schema('igvfd:schemas/whole_organism.json')
     embedded_with_frame = Biosample.embedded_with_frame
-    audit_inherit = Biosample.audit_inherit
+    audit_inherit = Biosample.audit_inherit + [
+        'disease_terms',
+        'treatments',
+        'modifications',
+    ]
     set_status_up = Biosample.set_status_up + []
     set_status_down = Biosample.set_status_down + []