IGVF-3599-add-gene-activity

src/igvfd/audit/pseudobulk_set.py

@@ -123,19 +123,20 @@ def audit_pseudobulk_set_input_file_set_type(value, system):
     '''
     [
         {
-            "audit_description": "Pseudobulk sets are expected to have input curated sets with `file_set_type` of `external sequencing data` only.",
+            "audit_description": "Pseudobulk sets are expected to have input curated sets with `file_set_type` of `external sequencing data` or `genes` only.",
             "audit_category": "unexpected input file set type",
             "audit_level": "ERROR"
         }
     ]
     '''
     audit_message = get_audit_message(audit_pseudobulk_set_input_file_set_type, index=0)
+    accepted_curated_set_file_set_types = ['external sequencing data', 'genes']
     if value.get('input_file_sets', []):
         for input_file_set in value.get('input_file_sets', []):
             input_file_set_object = system.get('request').embed(
                 input_file_set, '@@object_with_select_calculated_properties?field=@type')
             if input_file_set_object['@type'][0] == 'CuratedSet':
-                if input_file_set_object.get('file_set_type') != 'external sequencing data':
+                if input_file_set_object.get('file_set_type') not in accepted_curated_set_file_set_types:
                     detail = (
                         f'Pseudobulk set {audit_link(path_to_text(value["@id"]), value["@id"])} '
                         f'has curated set {audit_link(path_to_text(input_file_set), input_file_set)} in input file sets '

src/igvfd/mappings/pseudobulk_set.json

@@ -1,6 +1,6 @@
 {
-    "hash": "a2b43ca56457e055bd8caa73cbec496f",
-    "index_name": "pseudobulk_set_a2b43ca5",
+    "hash": "3437d4c4240b11c4f1e64c5feaac016b",
+    "index_name": "pseudobulk_set_3437d4c4",
     "item_type": "pseudobulk_set",
     "mapping": {
         "dynamic_templates": [

src/igvfd/tests/test_audit_pseudobulk_set.py

@@ -118,6 +118,26 @@ def test_audit_pseudobulk_set_input_file_set_type(
     )
 
 
+def test_audit_pseudobulk_set_input_file_set_type_genes(
+    testapp,
+    pseudobulk_set_base,
+    curated_set_genome
+):
+    testapp.patch_json(
+        curated_set_genome['@id'],
+        {'file_set_type': 'genes'}
+    )
+    testapp.patch_json(
+        pseudobulk_set_base['@id'],
+        {'input_file_sets': [curated_set_genome['@id']]}
+    )
+    res = testapp.get(pseudobulk_set_base['@id'] + '@@audit')
+    assert all(
+        error['category'] != 'unexpected input file set type'
+        for error in res.json['audit'].get('ERROR', [])
+    )
+
+
 def test_audit_pseudobulk_set_mixed_classifications(
     testapp,
     pseudobulk_set_base,