adapt esummary response handling to new data format

for details see https://ftp.ncbi.nlm.nih.gov/pub/clinvar/release_notes/20240129WebRelease.pdf

genie.py

@@ -225,7 +225,7 @@ def find_specific_variation(variation_id: str | int) -> ClinVarVariation:
         var.id = int(variation_id)
         try:
             var.title = data['title']
-            var.clinical_significance = data['clinical_significance']['description']
+            var.clinical_significance = data['germline_classification']['description']
             var.accession = data['accession']
             var.obj_type = data['obj_type']
             var.cdna_change = data['variation_set'][0]['cdna_change']
@@ -254,6 +254,7 @@ def esummary_request(variation_id: int):
                     logging.debug(
                         f'esummary request took: {(time.time() - start_time) * 1000:.0f}ms')
                     response = json.loads(esummary_response.read())
+                    ClinVarAPI.check_esummary_version(response)
                     return response
             except Exception as e:
                 logging.debug(
@@ -263,6 +264,14 @@ def esummary_request(variation_id: int):
         logging.error(f'esummary request failed 10 times.')
         sys.exit(1)
 
+    @staticmethod
+    def check_esummary_version(response):
+        version = response['header']['version']
+        if version != '0.3':
+            logging.error(
+                'unsupported esummary version {version}. Please contact the Genie maintainer for an update.')
+            sys.exit(1)
+
     @staticmethod
     def get_variation_accession_version(variation_id: str | int) -> ClinVarVariation:
         # e.g: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=clinvar&rettype=vcv&is_variationid&id=125889