fix: import fails with error 'intron_variant' (#2203)

backend/importer/management/commands/rebuild_variant_summary.py

@@ -16,15 +16,15 @@ class Command(BaseCommand):
 
     def add_arguments(self, parser):
         """Add the command's argument to the ``parser``."""
-        parser.add_argument("--async", help="Run the rebuild asynchronously.", action="store_false")
+        parser.add_argument("--async", help="Run the rebuild asynchronously.", action="store_true")
 
     @transaction.atomic
     def handle(self, *args, **options):
         """Perform rebuilding the statistics."""
         if options["async"]:
-            models.refresh_variants_smallvariantsummary()
-            msg = "Done rebuilding variant summary."
-        else:
             refresh_variants_smallvariantsummary.delay()
             msg = "Pushed rebuilding variant summary to background."
+        else:
+            models.refresh_variants_smallvariantsummary()
+            msg = "Done rebuilding variant summary."
         self.stdout.write(self.style.SUCCESS(msg))

backend/variants/forms.py

@@ -38,6 +38,16 @@
     "effect_3_prime_UTR_intron_variant": "3_prime_UTR_intron_variant",
     "effect_transcript_ablation": "transcript_ablation",
     "effect_upstream_gene_variant": "upstream_gene_variant",
+    # new mehari effects
+    "effect_coding_sequence_variant": "coding_sequence_variant",
+    "effect_conservative_inframe_deletion": "conservative_inframe_deletion",
+    "effect_conservative_inframe_insertion": "conservative_inframe_insertion",
+    "effect_intron_variant": "intron_variant",
+    "effect_splice_donor_5th_base_variant": "splice_donor_5th_base_variant",
+    "effect_splice_donor_region_variant": "splice_donor_region_variant",
+    "effect_splice_polypyrimidine_tract_variant": "splice_polypyrimidine_tract_variant",
+    "effect_start_retained_variant": "start_retained_variant",
+    "effect_transcript_amplification": "transcript_amplification",
 }
 
 FILTER_FORM_TRANSLATE_INHERITANCE = {

backend/variants/query_presets.py

@@ -571,6 +571,8 @@ class _ImpactPresets:
             "stop_lost",
             "structural_variant",
             "transcript_ablation",
+            # new mehari effects
+            "transcript_amplification",
         ],
     }
     #: Presets for "amino acid change and splicing" impact
@@ -604,6 +606,13 @@ class _ImpactPresets:
             "stop_lost",
             "structural_variant",
             "transcript_ablation",
+            # new mehari effects
+            "convervative_inframe_insertion",
+            "conservative_inframe_deletion",
+            "splice_donor_5th_base_variant",
+            "splice_donor_region_variant",
+            "splice_polypyrimidine_tract_variant",
+            "transcript_amplification",
         ],
     }
     #: Presets for "all coding and deep intronic" impact
@@ -639,6 +648,16 @@ class _ImpactPresets:
             "structural_variant",
             "synonymous_variant",
             "transcript_ablation",
+            # new mehari effects
+            "coding_sequence_variant",
+            "conservative_inframe_insertion",
+            "conservative_inframe_deletion",
+            "intron_variant",
+            "splice_donor_5th_base_variant",
+            "splice_donor_region_variant",
+            "splice_polypyrimidine_tract_variant",
+            "start_retained_variant",
+            "transcript_amplification",
         ],
     }
     #: Presets for "whole transcript" impact
@@ -683,6 +702,16 @@ class _ImpactPresets:
             "synonymous_variant",
             "transcript_ablation",
             "upstream_gene_variant",
+            # new mehari effects
+            "coding_sequence_variant",
+            "conservative_inframe_insertion",
+            "conservative_inframe_deletion",
+            "intron_variant",
+            "splice_donor_5th_base_variant",
+            "splice_donor_region_variant",
+            "splice_polypyrimidine_tract_variant",
+            "start_retained_variant",
+            "transcript_amplification",
         ],
     }
     #: Presets for "any" impact
@@ -728,6 +757,16 @@ class _ImpactPresets:
             "synonymous_variant",
             "transcript_ablation",
             "upstream_gene_variant",
+            # new mehari effects
+            "coding_sequence_variant",
+            "conservative_inframe_insertion",
+            "conservative_inframe_deletion",
+            "intron_variant",
+            "splice_donor_5th_base_variant",
+            "splice_donor_region_variant",
+            "splice_polypyrimidine_tract_variant",
+            "start_retained_variant",
+            "transcript_amplification",
         ],
     }
 

backend/variants/query_schemas.py

@@ -92,6 +92,16 @@ class Effects(Enum):
     SYNONYMOUS_VARIANT = "synonymous_variant"
     TRANSCRIPT_ABLATION = "transcript_ablation"
     UPSTREAM_GENE_VARIANT = "upstream_gene_variant"
+    # new mehari effects
+    CODING_SEQUENCE_VARIANT = "coding_sequence_variant"
+    CONSERVATIVE_INFRAME_DELETION = "conservative_inframe_deletion"
+    CONSERVATIVE_INFRAME_INSERTION = "conservative_inframe_insertion"
+    INTRON_VARIANT = "intron_variant"
+    SPLICE_DONOR_5TH_BASE_VARIANT = "splice_donor_5th_base_variant"
+    SPLICE_DONOR_REGION_VARIANT = "splice_donor_region_variant"
+    SPLICE_POLYPYRIMIDINE_TRACT_VARIANT = "splice_polypyrimidine_tract_variant"
+    START_RETAINED_VARIANT = "start_retained_variant"
+    TRANSCRIPT_AMPLIFICATION = "transcript_amplification"
 
 
 @unique

backend/variants/schemas/case-query-v1.json

@@ -73,7 +73,16 @@
           "structural_variant",
           "synonymous_variant",
           "transcript_ablation",
-          "upstream_gene_variant"
+          "upstream_gene_variant",
+          "coding_sequence_variant",
+          "conservative_inframe_deletion",
+          "conservative_inframe_insertion",
+          "intron_variant",
+          "splice_donor_5th_base_variant",
+          "splice_donor_region_variant",
+          "splice_polypyrimidine_tract_variant",
+          "start_retained_variant",
+          "transcript_amplification"
         ]
       }
     },

backend/variants/tests/factories.py

@@ -187,6 +187,15 @@ class FormDataFactory(FormDataFactoryBase):
     effect_3_prime_UTR_intron_variant: bool = True
     effect_transcript_ablation: bool = True
     effect_upstream_gene_variant: bool = True
+    effect_coding_sequence_variant: bool = True
+    effect_conservative_inframe_deletion: bool = True
+    effect_conservative_inframe_insertion: bool = True
+    effect_intron_variant: bool = True
+    effect_splice_donor_5th_base_variant: bool = True
+    effect_splice_donor_region_variant: bool = True
+    effect_splice_polypyrimidine_tract_variant: bool = True
+    effect_start_retained_variant: bool = True
+    effect_transcript_amplification: bool = True
     gene_blocklist: str = ""
     genomic_region: str = ""
     gene_allowlist: str = ""

backend/variants/tests/test_ui.py

@@ -225,4 +225,14 @@ def assert_element_exists(self, kwargs, element_id, exists):
     "id_effect_structural_variant": False,
     "id_effect_transcript_ablation": False,
     "id_effect_complex_substitution": False,
+    # new mehari effects
+    "id_effect_coding_sequence_variant": False,
+    "id_effect_conservative_inframe_deletion": False,
+    "id_effect_conservative_inframe_insertion": False,
+    "id_effect_intron_variant": False,
+    "id_effect_splice_donor_5th_base_variant": False,
+    "id_effect_splice_donor_region_variant": False,
+    "id_effect_splice_polypyrimidine_tract_variant": False,
+    "id_effect_start_retained_variant": False,
+    "id_effect_transcript_amplification": False,
 }

frontend/src/seqvars/components/PresetsEditor/lib/consequence.ts

@@ -118,10 +118,10 @@ export const CONSEQUENCE_GROUP_INFOS: ConsequenceGroupInfo[] = [
       'stop_lost',
       'disruptive_inframe_deletion',
       'disruptive_inframe_insertion',
+      'coding_sequence_variant',
       'conservative_inframe_insertion',
       'conservative_inframe_deletion',
       'missense_variant',
-      'coding_sequence_variant',
     ],
   },
   {
@@ -145,10 +145,13 @@ export const CONSEQUENCE_GROUP_INFOS: ConsequenceGroupInfo[] = [
       'exon_loss_variant',
       'frameshift_variant',
       'start_lost',
+      'start_retained_variant',
       'stop_gained',
       'stop_lost',
+      'stop_retained_variant',
       'disruptive_inframe_deletion',
       'disruptive_inframe_insertion',
+      'coding_sequence_variant',
       'conservative_inframe_insertion',
       'conservative_inframe_deletion',
       'missense_variant',

frontend/src/variants/components/FilterForm/EffectPane.fields.js

@@ -143,6 +143,41 @@ export const detailedEffectGroups = Object.freeze([
         explanation:
           'A tandem duplication where the individual regions are in the same orientation.',
       },
+      {
+        id: 'coding_sequence_variant',
+        label: 'coding variant',
+        so: 'SO:0001580',
+        explanation:
+          'A sequence variant that changes the coding sequence.',
+      },
+      {
+        id: 'conservative_inframe_insertion',
+        label: 'conservative in-frame insertion',
+        so: 'SO:0001823',
+        explanation:
+          'An inframe increase in cds length that inserts bases into the coding sequence without changing the amino acid sequence.',
+      },
+      {
+        id: 'conservative_inframe_deletion',
+        label: 'conservative in-frame deletion',
+        so: 'SO:0001825',
+        explanation:
+          'An inframe decrease in cds length that deletes bases from the coding sequence without changing the amino acid sequence.',
+      },
+      {
+        id: 'start_retained_variant',
+        label: 'start retained',
+        so: 'SO:0002019',
+        explanation:
+          'A sequence variant where at least one base in the start codon is changed, but the start remains.',
+      },
+      {
+        id: 'transcript_amplification',
+        label: 'transcript amplification',
+        so: 'SO:0001889',
+        explanation:
+          'A feature amplification of a region containing a transcript.',
+      },
     ],
   },
   {
@@ -178,9 +213,14 @@ export const detailedEffectGroups = Object.freeze([
         id: 'exon_loss_variant',
         label: 'exon loss',
         so: 'SO:0001572',
-        explanation:
-          'A sequence variant whereby an exon is lost from the transcript.',
+        explanation: 'A sequence variant whereby an exon is lost from the transcript.',
       },
+      {
+        id: 'intron_variant',
+        label: 'intron variant',
+        so: 'SO:0001627',
+        explanation: 'A transcript variant occurring within an intron.',
+      }
     ],
   },
   {
@@ -250,6 +290,27 @@ export const detailedEffectGroups = Object.freeze([
         explanation:
           'A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.',
       },
+      {
+        id: 'splice_donor_5th_base_variant',
+        label: 'splice donor 5th base',
+        so: 'SO:0001787',
+        explanation:
+          'A splice variant that changes the 5th base of the 5 base pair region at the 5\' end of an intron.',
+      },
+      {
+        id: 'splice_donor_region_variant',
+        label: 'splice donor region',
+        so: 'SO:0001789',
+        explanation:
+          'A sequence variant that changes the 5 base pair region at the 5\' end of an intron.',
+      },
+      {
+        id: 'splice_polypyrimidine_tract_variant',
+        label: 'splice polypyrimidine tract',
+        so: 'SO:0001624',
+        explanation:
+          'A variant that changes the polypyrimidine tract of a splice site.',
+      },
     ],
   },
   {
@@ -307,19 +368,34 @@ const _effectGroups = {
     'stop_lost',
     'structural_variant',
     'transcript_ablation',
+    'coding_sequence_variant',
+    'conservative_inframe_insertion',
+    'conservative_inframe_deletion',
+    'transcript_amplification',
   ],
   splicing: [
     'splice_acceptor_variant',
     'splice_donor_variant',
     'splice_region_variant',
+    'splice_donor_5th_base_variant',
+    'splice_donor_region_variant',
+    'splice_polypyrimidine_tract_variant',
+  ],
+  coding: [
+    'stop_retained_variant',
+    'synonymous_variant',
+    'coding_sequence_variant',
+    'conservative_inframe_insertion',
+    'conservative_inframe_deletion',
+    'start_retained_variant',
   ],
-  coding: ['stop_retained_variant', 'synonymous_variant'],
   utr_intronic: [
     'coding_transcript_intron_variant',
     '5_prime_UTR_exon_variant',
     '5_prime_UTR_intron_variant',
     '3_prime_UTR_exon_variant',
     '3_prime_UTR_intron_variant',
+    'intron_variant',
   ],
   noncoding: [
     'downstream_gene_variant',

frontend/src/variants/components/FilterForm/EffectPane.vue

@@ -359,13 +359,13 @@ defineExpose({
         <div class="row">
           <div
             v-for="group in detailedEffectGroups"
-            class="col-xl-3 col-lg-4 pl-0 pr-0 mt-3"
+            class="col-xl-3 col-lg-4 mt-3"
           >
             <strong>{{ group.title }}</strong>
             <br />
             <div
               v-for="field in group.fields"
-              class="custom-control custom-checkbox custom-control-inline"
+              class="d-flex custom-control custom-checkbox custom-control-inline"
               :title="`${field.explanation} [${field.so}]`"
             >
               <input