Merge pull request #20 from CanDIG/bugfix/genomic-completeness

Bugfix: Missing data and completeness data

query_server/query_operations.py

@@ -64,25 +64,27 @@ def get_summary_stats(donors, headers):
         # A donor's date of birth is defined as the (negative) interval between actual DOB and the date of first diagnosis
         # So we just use that info
         donors_by_id[donor["submitter_donor_id"]] = donor
-        age = abs(donor['date_of_birth']['month_interval']) // 12
-        age = age // 10 * 10
-        if age < 20:
-            add_or_increment(age_at_diagnosis, '0-19 Years')
-        elif age > 79:
-            add_or_increment(age_at_diagnosis, '80+ Years')
-        else:
-            add_or_increment(age_at_diagnosis, f'{age}-{age+9} Years')
+        if donor['date_of_birth'] and donor['date_of_birth']['month_interval']:
+            age = abs(donor['date_of_birth']['month_interval']) // 12
+            age = age // 10 * 10
+            if age < 20:
+                add_or_increment(age_at_diagnosis, '0-19 Years')
+            elif age > 79:
+                add_or_increment(age_at_diagnosis, '80+ Years')
+            else:
+                add_or_increment(age_at_diagnosis, f'{age}-{age+9} Years')
 
         # Cancer types
-        for cancer_type in donor['primary_site']:
-            if cancer_type in cancer_type_count:
-                cancer_type_count[cancer_type] += 1
-            else:
-                cancer_type_count[cancer_type] = 1
+        if donor['primary_site']:
+            for cancer_type in donor['primary_site']:
+                if cancer_type in cancer_type_count:
+                    cancer_type_count[cancer_type] += 1
+                else:
+                    cancer_type_count[cancer_type] = 1
         program_id = donor['program_id']
         if program_id in patients_per_cohort:
             patients_per_cohort[program_id] += 1
-        else:
+        elif program_id is not None:
             patients_per_cohort[program_id] = 1
 
     # Treatment types
@@ -285,6 +287,12 @@ def query(treatment="", primary_site="", chemotherapy="", immunotherapy="", horm
 
 @app.route('/genomic_completeness')
 def genomic_completeness():
+    # Add a service token to the headers so that Katsu will know this is from the query service:
+    headers = {}
+    for k in request.headers.keys():
+        headers[k] = request.headers[k]
+    headers["X-Service-Token"] = config.SERVICE_TOKEN
+
     params = { 'page_size': PAGE_SIZE }
     url = f"{config.KATSU_URL}/v2/authorized/sample_registrations/"
     r = safe_get_request_json(requests.get(f"{url}?{urllib.parse.urlencode(params)}",
@@ -302,7 +310,7 @@ def genomic_completeness():
         # Check with HTSGet to see whether or not this sample is complete
         r = requests.get(f"{config.HTSGET_URL}/htsget/v1/samples/{sample_id}",
             # Reuse their bearer token
-            headers=request.headers)
+            headers=headers)
         if r.ok:
             r_json = r.json()
             retVal[program_id]