Merge pull request #14 from EGA-archive/iso8601duration

Refactoring the iso8601duration alphanumeric filter
EGA-archive · Nov 18, 2024 · dc9fd97 · dc9fd97
2 parents 7a17f2a + 918e9c8
commit dc9fd97
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Showing 2 changed files with 27 additions and 7 deletions.
diff --git a/beacon/conf/conf.py b/beacon/conf/conf.py
@@ -26,7 +26,7 @@
 default_beacon_granularity = "record" # boolean, count or record
 security_levels = ['PUBLIC', 'REGISTERED', 'CONTROLLED']
 documentation_url = 'https://b2ri-documentation-demo.ega-archive.org/'
-alphanumeric_terms = ['libraryStrategy', 'molecularAttributes.geneIds', 'diseases.ageOfOnset.iso8601duration', 'molecularAttributes.aminoacidChanges']
+alphanumeric_terms = ['libraryStrategy', 'molecularAttributes.geneIds', 'diseases.ageOfOnset.iso8601duration', 'molecularAttributes.aminoacidChanges','phenotypicFeatures.onset.iso8601duration']
 cors_urls = ["http://localhost:3000","https://cancer-beacon-demo.ega-archive.org", "https://beacon-network-demo2.ega-archive.org", "https://beacon.ega-archive.org"]
 
 

diff --git a/beacon/connections/mongo/filters.py b/beacon/connections/mongo/filters.py
@@ -938,18 +938,21 @@ def apply_alphanumeric_filter(self, query: dict, filter: AlphanumericFilter, col
                         age_in_number = age_in_number+char
                     except Exception:# pragma: no cover
                         continue
-                new_age_list=[]
+                new_age_list=''
 
                 if "=" in filter.operator:
                     z = int(age_in_number)# pragma: no cover
                 else:
                     z = int(age_in_number)+1
                 while z < 150:
                     newagechar="P"+str(z)+"Y"
-                    new_age_list.append(newagechar)
+                    if new_age_list == '':
+                        new_age_list+=newagechar
+                    else:
+                        new_age_list+='|'+newagechar
                     z+=1
                 dict_in={}
-                dict_in["$in"]=new_age_list
+                dict_in["$regex"]=new_age_list
                 query[filter.id] = dict_in
                 query=cross_query(self, query, scope, collection, {}, dataset)
             elif '<' in filter.operator:
@@ -960,17 +963,34 @@ def apply_alphanumeric_filter(self, query: dict, filter: AlphanumericFilter, col
                         age_in_number = age_in_number+char
                     except Exception:# pragma: no cover
                         continue
-                new_age_list=[]
+                new_age_list=''
                 if "=" in filter.operator:
                     z = int(age_in_number)# pragma: no cover
                 else:
                     z = int(age_in_number)-1
                 while z > 0:
                     newagechar="P"+str(z)+"Y"
-                    new_age_list.append(newagechar)
+                    if new_age_list == '':
+                        new_age_list+=newagechar
+                    else:
+                        new_age_list+='|'+newagechar
                     z-=1
                 dict_in={}
-                dict_in["$in"]=new_age_list
+                dict_in["$regex"]=new_age_list
+                query[filter.id] = dict_in
+                query=cross_query(self, query, scope, collection, {}, dataset)
+            elif '=' in filter.operator:
+                age_in_number=""
+                for char in filter.value:
+                    try:
+                        int(char)
+                        age_in_number = age_in_number+char
+                    except Exception:# pragma: no cover
+                        continue
+                z = int(age_in_number)# pragma: no cover
+                newagechar="P"+str(z)+"Y"
+                dict_in={}
+                dict_in["$regex"]=newagechar
                 query[filter.id] = dict_in
                 query=cross_query(self, query, scope, collection, {}, dataset)
         else: