fixed bug

beacon/__main__.py

@@ -103,9 +103,9 @@ def main(path=None):
         # TODO: add the CA chain
 
     # Load ontologies
-    LOG.info("Loading ontologies... (this might take a while)")
-    ontologies.load_obo()
-    LOG.info("Finished loading the ontologies...")
+    #LOG.info("Loading ontologies... (this might take a while)")
+    #ontologies.load_obo()
+    #LOG.info("Finished loading the ontologies...")
 
     # Run beacon
     if path:

beacon/db/filters.py

@@ -147,7 +147,11 @@ def apply_alphanumeric_filter(query: dict, filter: AlphanumericFilter, collectio
     LOG.debug(filter.value)
     formatted_value = format_value(filter.value)
     formatted_operator = format_operator(filter.operator)
-    if isinstance(formatted_value,str):
+    if collection == 'g_variants':
+        formatted_value = format_value(filter.value)
+        formatted_operator = format_operator(filter.operator)
+        query[filter.id] = { formatted_operator: formatted_value }
+    elif isinstance(formatted_value,str):
         if formatted_operator == "$eq":
             if '%' in filter.value:
                 if collection == 'individuals':

beacon/db/g_variants.py

@@ -72,6 +72,7 @@ def generate_position_filter_end(key: str, value: List[int]) -> List[Alphanumeri
 
 
 def apply_request_parameters(query: Dict[str, List[dict]], qparams: RequestParams):
+    collection = 'g_variants'
     LOG.debug("Request parameters len = {}".format(len(qparams.query.request_parameters)))
     if len(qparams.query.request_parameters) > 0 and "$and" not in query:
         query["$and"] = []
@@ -81,20 +82,20 @@ def apply_request_parameters(query: Dict[str, List[dict]], qparams: RequestParam
                 v = v.split(',')
             filters = generate_position_filter_start(k, v)
             for filter in filters:
-                query["$and"].append(apply_alphanumeric_filter({}, filter))
+                query["$and"].append(apply_alphanumeric_filter({}, filter, collection))
         elif k == "end":
             if isinstance(v, str):
                 v = v.split(',')
             filters = generate_position_filter_end(k, v)
             for filter in filters:
-                query["$and"].append(apply_alphanumeric_filter({}, filter))
+                query["$and"].append(apply_alphanumeric_filter({}, filter, collection))
         elif k == "variantMinLength" or k == "variantMaxLength" or k == "mateName":
             continue
         else:
             query["$and"].append(apply_alphanumeric_filter({}, AlphanumericFilter(
                 id=VARIANTS_PROPERTY_MAP[k],
                 value=v
-            )))
+            ), collection))
     return query