Merge pull request #22 from CanDIG/bugfix/htsget-pruning

Bugfix/htsget pruning

query_server/query_operations.py

@@ -204,7 +204,7 @@ def query(treatment="", primary_site="", chemotherapy="", immunotherapy="", horm
 
     # Now we combine this with HTSGet, if any
     genomic_query = []
-    genomic_query_info = None
+    # genomic_query_info = None
     if gene != "" or chrom != "":
         try:
             if gene != "":
@@ -220,14 +220,16 @@ def query(treatment="", primary_site="", chemotherapy="", immunotherapy="", horm
             for specimen in specimen_query['items']:
                 specimen_mapping[specimen['submitter_sample_id']] = (specimen['submitter_donor_id'], specimen['tumour_normal_designation'])
 
-            # handovers = htsget['results']['beaconHandovers']
-            genomic_query_info = htsget['query_info']
-            for cohort in genomic_query_info:
-               sample_ids = genomic_query_info[cohort]
-               print(f"cohort {cohort} has samples {sample_ids}")
+            # genomic_query_info contains ALL matches from every dataset
+            # This is meant to be used to fill out the summary stats ONLY
+            # However, that part isn't covered in this PR (it's in DIG-1372 (https://candig.atlassian.net/browse/DIG-1372))
+            # and does not yet function
+            # genomic_query_info = htsget['query_info']
+            # for cohort in genomic_query_info:
+            #    sample_ids = genomic_query_info[cohort]
+
             htsget_found_donors = {}
             for response in htsget['response']:
-                genomic_query = response['caseLevelData']
                 for case_data in response['caseLevelData']:
                     if 'biosampleId' not in case_data:
                         print(f"Could not parse htsget response for {case_data}")
@@ -247,13 +249,22 @@ def query(treatment="", primary_site="", chemotherapy="", immunotherapy="", horm
                         htsget_found_donors[case_data['donor_id']] = 1
                     else:
                         print(f"Could not parse biosampleId for {case_data}")
-                        case_data['program_id'] = ""
-                        case_data['donor_id'] = ""
+                        case_data['program_id'] = None
+                        case_data['donor_id'] = None
                         case_data['submitter_specimen_id'] = case_data['biosampleId']
                         case_data['tumour_normal_designation'] = 'Tumour'
                     case_data['position'] = response['variation']['location']['interval']['start']['value']
             # Filter clinical results based on genomic results
             donors = [donor for donor in donors if donor['submitter_donor_id'] in htsget_found_donors]
+            katsu_allowed_donors = {}
+            for donor in donors:
+                katsu_allowed_donors[f"{donor['program_id']}~{donor['submitter_donor_id']}"] = 1
+            for response in htsget['response']:
+                for case_data in response['caseLevelData']:
+                    if ('donor_id' in case_data and 'program_id' in case_data and
+                        f"{case_data['program_id']}~{case_data['donor_id']}" in katsu_allowed_donors):
+                        genomic_query.append(case_data)
+
         except Exception as ex:
             print(ex)
 
@@ -278,7 +289,7 @@ def query(treatment="", primary_site="", chemotherapy="", immunotherapy="", horm
     full_data['summary'] = summary_stats
     full_data['next'] = None
     full_data['prev'] = None
-    full_data['genomic_query_info'] = genomic_query_info
+    # full_data['genomic_query_info'] = genomic_query_info
 
     # Add prev and next parameters to the repsonse, appending a session ID.
     # Essentially we want to go session ID -> list of donors