small cleanup

cancervariants · Nov 14, 2024 · 4b01496 · 4b01496
1 parent 4dccbf4
commit 4b01496
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Showing 3 changed files with 8 additions and 5 deletions.
diff --git a/src/metakb/load_data.py b/src/metakb/load_data.py
@@ -412,8 +412,9 @@ def _add_study(tx: ManagedTransaction, study_in: dict) -> None:
         rel_line += f"MERGE (s) -[:IS_REPORTED_IN] -> ({name})\n"
 
     allele_origin = study.get("alleleOriginQualifier")
-    study["alleleOriginQualifier"] = allele_origin
-    match_line += "SET s.alleleOriginQualifier=$alleleOriginQualifier\n"
+    if allele_origin:
+        study["alleleOriginQualifier"] = allele_origin
+        match_line += "SET s.alleleOriginQualifier=$alleleOriginQualifier\n"
 
     gene_context_id = study.get("geneContextQualifier", {}).get("id")
     if gene_context_id:
@@ -452,7 +453,7 @@ def _add_study(tx: ManagedTransaction, study_in: dict) -> None:
     rel_line += "MERGE (s) -[:HAS_TUMOR_TYPE] -> (tt)\n"
 
     query = f"""
-    MERGE (s:{study_type}:Statement {{ {study_keys} }})
+    MERGE (s:{study_type}:StudyStatement:Statement {{ {study_keys} }})
     {match_line}
     {rel_line}
     """

diff --git a/src/metakb/query.py b/src/metakb/query.py
@@ -158,7 +158,7 @@ async def search_studies(
         >>> result = qh.search_studies("BRAF V600E")
         >>> result.study_ids[:3]
         ['moa.assertion:944', 'moa.assertion:911', 'moa.assertion:865']
-        >>> result.studies[0].reportedIn[0].url
+        >>> result.studies[0].reportedIn[0].urls[0]
         'https://www.accessdata.fda.gov/drugsatfda_docs/label/2020/202429s019lbl.pdf'
 
         Variation, disease, therapy, and gene terms are resolved via their respective

diff --git a/tests/unit/database/test_database.py b/tests/unit/database/test_database.py
@@ -547,7 +547,9 @@ def test_study_rules(
     check_relation_count("Statement", "Method", "IS_SPECIFIED_BY", max_rels=None)
     check_relation_count("Statement", "Gene", "HAS_GENE_CONTEXT", max_rels=None)
 
-    expected_node_labels = [{"Statement", "VariantTherapeuticResponseStudyStatement"}]
+    expected_node_labels = [
+        {"Statement", "StudyStatement", "VariantTherapeuticResponseStudyStatement"}
+    ]
     check_node_labels("Statement", expected_node_labels, 1)
 
     cite_query = """