[CLE] Removed the need for local uta

Author: dameyerdave

.gitignore

@@ -29,3 +29,5 @@ svip_api/api/static
 
 /node_modules
 *.orig
+
+Pipfile*

docker-compose.dev.yml

@@ -14,9 +14,6 @@ services:
   db:
     ports:
       - '30432:5432' # dev access port
-  local_uta:
-    ports:
-      - '15032:5432'
   redis:
     ports:
       - '${REDIS_PORT}:${REDIS_PORT}'

docker-compose.yml

@@ -30,9 +30,7 @@ services:
     depends_on:
       - db
       - redis
-      - local_uta
     environment:
-      - UTA_DB_URL=postgresql://anonymous@local_uta/uta/uta_20171026
       - HGVS_SEQREPO_DIR=/usr/local/share/seqrepo/latest
       - PYTHONUNBUFFERED=1
     env_file:
@@ -49,15 +47,6 @@ services:
       - ./service_config/postgres:/docker-entrypoint-initdb.d
     env_file:
       - .env
-  local_uta:
-    # image: biocommons/uta:uta_20190928
-    image: biocommons/uta:uta_20171026
-    hostname: local_uta
-    restart: unless-stopped
-    volumes:
-      - '/usr/local/share/seqrepo:/usr/local/share/seqrepo'
-    environment:
-      - POSTGRES_HOST_AUTH_METHOD=trust
   redis:
     image: 'redis:alpine'
     hostname: redis

svip_api/api/views/svip.py

@@ -1,13 +1,9 @@
 import django_filters
-import hgvs.assemblymapper
-import hgvs.dataproviders.uta
-import hgvs.normalizer
 import hgvs.parser
 from django.contrib.auth.models import User
 from django.contrib.postgres.aggregates import ArrayAgg
 from django.db.models import Prefetch, Q
 from django.http import JsonResponse
-from hgvs.exceptions import HGVSParseError
 from rest_framework import viewsets, permissions, filters, status
 from rest_framework.decorators import action
 from rest_framework.exceptions import PermissionDenied
@@ -63,19 +59,19 @@ def get_queryset(self):
             q = VariantInSVIP.objects.all()
 
         q = (q
-            .select_related('variant')
-            .prefetch_related(
-            Prefetch('diseaseinsvip_set', queryset=(
-                DiseaseInSVIP.objects
-                    .select_related('disease', 'svip_variant', 'svip_variant__variant')
-                    .prefetch_related(
-                    'sample_set'
-                )
-            )),
-            # Prefetch('diseaseinsvip_set', queryset=DiseaseInSVIP.objects.prefetch_related('sample_set')),
-            # 'diseaseinsvip_set', 'diseaseinsvip_set__sample_set'
-        )
-        )
+             .select_related('variant')
+             .prefetch_related(
+                 Prefetch('diseaseinsvip_set', queryset=(
+                     DiseaseInSVIP.objects
+                     .select_related('disease', 'svip_variant', 'svip_variant__variant')
+                     .prefetch_related(
+                         'sample_set'
+                     )
+                 )),
+                 # Prefetch('diseaseinsvip_set', queryset=DiseaseInSVIP.objects.prefetch_related('sample_set')),
+                 # 'diseaseinsvip_set', 'diseaseinsvip_set__sample_set'
+             )
+             )
 
         return q
 
@@ -136,8 +132,8 @@ class CurationRequestViewSet(viewsets.ModelViewSet):
     serializer_class = CurationRequestSerializer
     queryset = (
         CurationRequest.objects
-            .prefetch_related('variant', 'variant__gene', 'submission')
-            .order_by('-created_on')
+        .prefetch_related('variant', 'variant__gene', 'submission')
+        .order_by('-created_on')
     )
 
 
@@ -273,9 +269,9 @@ def all_references(self, request):
             'references': {
                 x['references']: x['recs'] for x in (
                     CurationEntry.objects
-                        .select_related('variant', 'variant__gene')
-                        .values('references')
-                        .annotate(recs=ArrayAgg(json_build_fields(
+                    .select_related('variant', 'variant__gene')
+                    .values('references')
+                    .annotate(recs=ArrayAgg(json_build_fields(
                         id='id', variant_id='variant__id', gene_id='variant__gene__id', etype='type_of_evidence'
                     )))
                 )
@@ -286,13 +282,13 @@ def get_queryset(self):
         # pre-select variant and gene data to prevent thousands of queries
         return (
             CurationEntry.objects.authed_curation_set(self.request.user)
-                .select_related('owner', 'variant', 'variant__gene', 'disease')
-                .prefetch_related(
+            .select_related('owner', 'variant', 'variant__gene', 'disease')
+            .prefetch_related(
                 'extra_variants',
                 'extra_variants__gene',
                 'disease'
             )
-                .order_by('created_on')
+            .order_by('created_on')
         )
 
 
@@ -410,11 +406,7 @@ def bulk_submit(self, request):
 # hgvs stuff
 
 # these shared assembly mappers will allow us to convert HGVS g. variants to c. and p. later on
-hdp = hgvs.dataproviders.uta.connect()
-hgnorm = hgvs.normalizer.Normalizer(hdp)
 hgvsparser = hgvs.parser.Parser()
-am = hgvs.assemblymapper.AssemblyMapper(
-    hdp, assembly_name='GRCh37', normalize=True)
 
 AC_MAP = {
     '1': 'NC_000001',
@@ -458,8 +450,8 @@ class SubmittedVariantViewSet(viewsets.ModelViewSet):
         'chromosome', 'pos', 'ref', 'alt', 'status'
     )
     ordering_fields = filter_fields + \
-                      ('created_on', 'processed_on', 'batch', 'owner',
-                       'canonical_only', 'for_curation_request')
+        ('created_on', 'processed_on', 'batch', 'owner',
+         'canonical_only', 'for_curation_request')
     search_fields = ('chromosome', 'pos', 'ref', 'alt',)
 
     permission_classes = (IsSubmitter,)
@@ -469,6 +461,7 @@ class SubmittedVariantViewSet(viewsets.ModelViewSet):
     @action(methods=['GET'], detail=False)
     def map_hgvs(self, request):
         try:
+            raise NotImplementedError('Please implement map_hgvs correctly')
             # removes all sorts of weird unicode characters that, e.g., SVIP, adds for formatting purposes
             sanitized_hgvs = request.GET['hgvs_str'].strip().encode(
                 "ascii", errors='ignore').decode("utf8")
@@ -479,7 +472,7 @@ def map_hgvs(self, request):
             if result.type == 'c':
                 lifted = True
                 result = am.c_to_g(result)
-        except HGVSParseError as ex:
+        except Exception as ex:
             return JsonResponse({'error': str(ex)}, status=status.HTTP_400_BAD_REQUEST)
 
         return JsonResponse({