Merge pull request #343 from bento-platform/fix/table_summary

Fix/table summary

chord_metadata_service/chord/views_search.py

@@ -5,7 +5,6 @@
 
 from bento_lib.responses import errors
 from bento_lib.search import build_search_response, postgres
-from collections import Counter
 from datetime import datetime
 from django.db import connection
 from django.db.models import Count, F
@@ -14,6 +13,7 @@
 from django.conf import settings
 from django.views.decorators.cache import cache_page
 from psycopg2 import sql
+from chord_metadata_service.restapi.utils import get_field_bins, queryset_stats_for_field
 from rest_framework.decorators import api_view, permission_classes
 from rest_framework.permissions import AllowAny
 from rest_framework.response import Response
@@ -179,68 +179,30 @@ def mcodepacket_table_summary(table):
 
 
 def phenopacket_table_summary(table):
-    phenopackets = Phenopacket.objects.filter(table=table)  # TODO
+    phenopacket_qs = Phenopacket.objects.filter(table=table)  # TODO
 
-    diseases_counter = Counter()
-    phenotypic_features_counter = Counter()
-
-    biosamples_set = set()
-    individuals_set = set()
-
-    biosamples_cs = Counter()
-    biosamples_taxonomy = Counter()
-
-    individuals_sex = Counter()
-    individuals_k_sex = Counter()
-    individuals_taxonomy = Counter()
-
-    def count_individual(ind):
-        individuals_set.add(ind.id)
-        individuals_sex.update((ind.sex,))
-        individuals_k_sex.update((ind.karyotypic_sex,))
-        if ind.taxonomy is not None:
-            individuals_taxonomy.update((ind.taxonomy["id"],))
-
-    for p in phenopackets.prefetch_related("biosamples"):
-        for b in p.biosamples.all():
-            biosamples_set.add(b.id)
-            biosamples_cs.update((b.is_control_sample,))
-
-            if b.taxonomy is not None:
-                biosamples_taxonomy.update((b.taxonomy["id"],))
-
-            if b.individual is not None:
-                count_individual(b.individual)
-
-            for pf in b.phenotypic_features.all():
-                phenotypic_features_counter.update((pf.pftype["id"],))
-
-        for d in p.diseases.all():
-            diseases_counter.update((d.term["id"],))
-
-        for pf in p.phenotypic_features.all():
-            phenotypic_features_counter.update((pf.pftype["id"],))
-
-        # Currently, phenopacket subject is required so we can assume it's not None
-        count_individual(p.subject)
+    # Sex related fields stats are precomputed here and post processed later
+    # to include missing values inferred from the schema
+    individuals_sex = queryset_stats_for_field(phenopacket_qs, "subject__sex")
+    individuals_k_sex = queryset_stats_for_field(phenopacket_qs, "subject__karyotypic_sex")
 
     return Response({
-        "count": phenopackets.count(),
+        "count": phenopacket_qs.count(),
         "data_type_specific": {
             "biosamples": {
-                "count": len(biosamples_set),
-                "is_control_sample": dict(biosamples_cs),
-                "taxonomy": dict(biosamples_taxonomy),
+                "count": phenopacket_qs.values("biosamples__id").count(),
+                "is_control_sample": queryset_stats_for_field(phenopacket_qs, "biosamples__is_control_sample"),
+                "taxonomy": queryset_stats_for_field(phenopacket_qs, "biosamples__taxonomy__label"),
             },
-            "diseases": dict(diseases_counter),
+            "diseases": queryset_stats_for_field(phenopacket_qs, "diseases__term__label"),
             "individuals": {
-                "count": len(individuals_set),
-                "sex": {k: individuals_sex[k] for k in (s[0] for s in Individual.SEX)},
-                "karyotypic_sex": {k: individuals_k_sex[k] for k in (s[0] for s in Individual.KARYOTYPIC_SEX)},
-                "taxonomy": dict(individuals_taxonomy),
-                # TODO: age histogram
+                "count": phenopacket_qs.values("subject__id").count(),
+                "sex": {k: individuals_sex.get(k, 0) for k in (s[0] for s in Individual.SEX)},
+                "karyotypic_sex": {k: individuals_k_sex.get(k, 0) for k in (s[0] for s in Individual.KARYOTYPIC_SEX)},
+                "taxonomy": queryset_stats_for_field(phenopacket_qs, "subject__taxonomy__label"),
+                "age": get_field_bins(phenopacket_qs, "subject__age_numeric", 10),
             },
-            "phenotypic_features": dict(phenotypic_features_counter),
+            "phenotypic_features": queryset_stats_for_field(phenopacket_qs, "phenotypic_features__pftype__label"),
         }
     })
 

chord_metadata_service/restapi/utils.py

@@ -215,7 +215,11 @@ def queryset_stats_for_field(queryset, field: str, add_missing=False) -> Mapping
         if key is None:
             continue
 
-        key = key.strip()
+        if not isinstance(key, str):
+            key = str(key)
+        else:
+            key = key.strip()
+
         if key == "":
             continue