feat: add a flag for incidental findings (#1121) (#1466)

cases/vueapp/src/components/CaseDetail/CardAnnotations.vue

@@ -19,6 +19,7 @@ const svCommentsStore = useVariantCommentsStore()
 
 const flagIds = [
   'flag_bookmarked',
+  'flag_incidental',
   'flag_candidate',
   'flag_final_causative',
   'flag_for_validation',
@@ -42,6 +43,7 @@ const buildComputedAnnoCountByFlag = (theList: Map<string, any>) => {
   return computed<{ [flagId in FlagIds]: number }>(() => {
     const result = {
       flag_bookmarked: 0,
+      flag_incidental: 0,
       flag_candidate: 0,
       flag_final_causative: 0,
       flag_for_validation: 0,

cases/vueapp/src/components/CaseDetail/FlagIcon.vue

@@ -9,6 +9,7 @@ const props = defineProps<{
 <template>
   <span>
     <i-fa-solid-star v-if="flag === 'flag_bookmarked'" />
+    <i-mdi-dice-5 v-else-if="flag === 'flag_incidental'" />
     <i-fa-solid-flask v-else-if="flag === 'flag_for_validation'" />
     <i-fa-solid-heart v-else-if="flag === 'flag_candidate'" />
     <i-fa-solid-flag-checkered v-else-if="flag === 'flag_final_causative'" />

clinvar_export/serializers.py

@@ -415,6 +415,7 @@ class Meta:
                 "flag_molecular",
                 "flag_validation",
                 "flag_phenotype_match",
+                "flag_incidental",
                 "flag_summary",
             ]
         )

clinvar_export/tests/test_views_ajax.py

@@ -992,6 +992,7 @@ def test_query(self):
                         "flag_doesnt_segregate": False,
                         "flag_final_causative": False,
                         "flag_for_validation": False,
+                        "flag_incidental": False,
                         "flag_molecular": "",
                         "flag_no_disease_association": False,
                         "flag_phenotype_match": "",

maintenance/management/commands/repair_result_set.py

@@ -185,6 +185,7 @@ def _handle_case(self, case):  # noqa: C901
                     "flag_bookmarked",
                     "flag_segregates",
                     "flag_validation",
+                    "flag_incidental",
                     "flag_for_validation",
                     "flag_final_causative",
                     "flag_phenotype_match",

svs/migrations/0025_structuralvariantflags_flag_incidental.py

@@ -0,0 +1,18 @@
+# Generated by Django 3.2.24 on 2024-03-22 15:02
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("svs", "0024_clear_sv_queries"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="structuralvariantflags",
+            name="flag_incidental",
+            field=models.BooleanField(default=False),
+        ),
+    ]

svs/models/user_annos.py

@@ -116,6 +116,8 @@ class StructuralVariantFlags(HumanReadableMixin, _UserAnnotation):
     flag_segregates = models.BooleanField(default=False, null=False)
     #: Variant does not segregate
     flag_doesnt_segregate = models.BooleanField(default=False, null=False)
+    #: Variant is an incidental finding
+    flag_incidental = models.BooleanField(default=False, null=False)
 
     # Choice fields for gradual rating
 
@@ -155,6 +157,7 @@ def no_flags_set(self):
                 self.flag_no_disease_association,
                 self.flag_segregates,
                 self.flag_doesnt_segregate,
+                self.flag_incidental,
                 self.flag_molecular != "empty",
                 self.flag_visual != "empty",
                 self.flag_validation != "empty",

svs/serializers/user_annos.py

@@ -90,6 +90,7 @@ class Meta:
             "flag_molecular",
             "flag_validation",
             "flag_phenotype_match",
+            "flag_incidental",
             "flag_summary",
         )
         read_only_fields = ("sodar_uuid", "date_created", "date_modified", "case")

svs/tests/factories.py

@@ -247,6 +247,7 @@ class Meta:
     flag_no_disease_association = False
     flag_segregates = False
     flag_doesnt_segregate = False
+    flag_incidental = False
 
     flag_molecular = "empty"
     flag_visual = "empty"

svs/vueapp/src/stores/strucvarFlags/store.ts

@@ -18,6 +18,7 @@ type StructuralVariantFlags = any
 
 export const emptyFlagsTemplate = Object.freeze({
   flag_bookmarked: false,
+  flag_incidental: false,
   flag_for_validation: false,
   flag_candidate: false,
   flag_final_causative: false,

varfish/tests/drf_spectacular/varfish_api_schema.yaml

@@ -10872,6 +10872,8 @@ components:
           type: boolean
         flag_bookmarked:
           type: boolean
+        flag_incidental:
+          type: boolean
         flag_candidate:
           type: boolean
         flag_doesnt_segregate:
@@ -12711,6 +12713,8 @@ components:
           type: boolean
         flag_bookmarked:
           type: boolean
+        flag_incidental:
+          type: boolean
         flag_candidate:
           type: boolean
         flag_doesnt_segregate:
@@ -13287,6 +13291,8 @@ components:
           maxLength: 512
         flag_bookmarked:
           type: boolean
+        flag_incidental:
+          type: boolean
         flag_candidate:
           type: boolean
         flag_final_causative:
@@ -13476,6 +13482,8 @@ components:
           $ref: '#/components/schemas/VariantRatingEnum'
         flag_phenotype_match:
           $ref: '#/components/schemas/VariantRatingEnum'
+        flag_incidental:
+          type: boolean
         flag_summary:
           $ref: '#/components/schemas/VariantRatingEnum'
     PatchedTargetBedFile:
@@ -14361,6 +14369,8 @@ components:
           maxLength: 512
         flag_bookmarked:
           type: boolean
+        flag_incidental:
+          type: boolean
         flag_candidate:
           type: boolean
         flag_final_causative:
@@ -14940,6 +14950,8 @@ components:
           $ref: '#/components/schemas/VariantRatingEnum'
         flag_phenotype_match:
           $ref: '#/components/schemas/VariantRatingEnum'
+        flag_incidental:
+          type: boolean
         flag_summary:
           $ref: '#/components/schemas/VariantRatingEnum'
       required:

varfish/vueapp/components.d.ts

@@ -25,6 +25,9 @@ declare module 'vue' {
     IFaSolidCode: typeof import('~icons/fa-solid/code')['default']
     IFaSolidComment: typeof import('~icons/fa-solid/comment')['default']
     IFaSolidDatabase: typeof import('~icons/fa-solid/database')['default']
+    IFaSolidDice: typeof import('~icons/fa-solid/dice')['default']
+    IFaSolidDice5Outline: typeof import('~icons/fa-solid/dice5-outline')['default']
+    IFaSolidDiceFive: typeof import('~icons/fa-solid/dice-five')['default']
     IFaSolidExclamationCircle: typeof import('~icons/fa-solid/exclamation-circle')['default']
     IFaSolidFlagCheckered: typeof import('~icons/fa-solid/flag-checkered')['default']
     IFaSolidFlask: typeof import('~icons/fa-solid/flask')['default']
@@ -71,6 +74,8 @@ declare module 'vue' {
     IMdiContentCopy: typeof import('~icons/mdi/content-copy')['default']
     IMdiDelete: typeof import('~icons/mdi/delete')['default']
     IMdiDeleteForever: typeof import('~icons/mdi/delete-forever')['default']
+    IMdiDice5: typeof import('~icons/mdi/dice5')['default']
+    IMdiDice5Outline: typeof import('~icons/mdi/dice5-outline')['default']
     IMdiDoNotDisturbOn: typeof import('~icons/mdi/do-not-disturb-on')['default']
     IMdiDotsHorizontal: typeof import('~icons/mdi/dots-horizontal')['default']
     IMdiDownload: typeof import('~icons/mdi/download')['default']
@@ -99,6 +104,8 @@ declare module 'vue' {
     IMdiPodium: typeof import('~icons/mdi/podium')['default']
     IMdiRefresh: typeof import('~icons/mdi/refresh')['default']
     IMdiSquareEditOutline: typeof import('~icons/mdi/square-edit-outline')['default']
+    IMdiTableColumnWidth: typeof import('~icons/mdi/table-column-width')['default']
+    IMdiTableMergeCells: typeof import('~icons/mdi/table-merge-cells')['default']
     IMdiToggleSwitchOutline: typeof import('~icons/mdi/toggle-switch-outline')['default']
     IMdiTools: typeof import('~icons/mdi/tools')['default']
     IMdiUndoVariant: typeof import('~icons/mdi/undo-variant')['default']

varfish/vueapp/src/varfish/components/FlagsCard/FlagsCard.vue

@@ -28,6 +28,8 @@ const flagsSubmitted = computed(() => {
   return (
     flagsToSubmit.value.flag_bookmarked ===
       props.flagsStore.flags.flag_bookmarked &&
+    flagsToSubmit.value.flag_incidental ===
+      props.flagsStore.flags.flag_incidental &&
     flagsToSubmit.value.flag_for_validation ===
       props.flagsStore.flags.flag_for_validation &&
     flagsToSubmit.value.flag_candidate ===
@@ -54,6 +56,7 @@ const flagsSubmitted = computed(() => {
 const resetFlags = async () => {
   if (props.flagsStore.flags) {
     flagsToSubmit.value.flag_bookmarked = props.flagsStore.flags.flag_bookmarked
+    flagsToSubmit.value.flag_incidental = props.flagsStore.flags.flag_incidental
     flagsToSubmit.value.flag_for_validation =
       props.flagsStore.flags.flag_for_validation
     flagsToSubmit.value.flag_candidate = props.flagsStore.flags.flag_candidate

varfish/vueapp/src/varfish/components/FlagsCard/constants.ts

@@ -4,6 +4,7 @@ export interface BooleanFlagSpec {
   icon: string
   key:
     | 'flag_bookmarked'
+    | 'flag_incidental'
     | 'flag_for_validation'
     | 'flag_candidate'
     | 'flag_final_causative'
@@ -24,6 +25,11 @@ export const BOOLEAN_FLAGS: BooleanFlagSpec[] = [
     icon: 'mdi-flask-empty',
     key: 'flag_for_validation',
   },
+  {
+    label: 'incidental finding',
+    icon: 'mdi-dice-5',
+    key: 'flag_incidental',
+  },
   {
     label: 'candidate',
     icon: 'mdi-cards-heart',

variants/file_export.py

@@ -145,6 +145,7 @@ def to_str(val):
     ("flag_no_disease_association", "Flag: selected for no known disease association", str),
     ("flag_segregates", "Flag: selected as segregating variant", str),
     ("flag_doesnt_segregate", "Flag: selected as not segregating variant", str),
+    ("flag_incidental", "Flag: selected as incidental finding", str),
     ("flag_molecular", "Rating: variant is molecular", str),
     ("flag_visual", "Rating: visual inspection of alignment", str),
     ("flag_validation", "Rating: validation result", str),

variants/migrations/0071_smallvariantflags_flag_molecular.py

@@ -4,16 +4,6 @@
 
 from django.db import migrations, models
 
-from variants.models import SmallVariantComment, SmallVariantFlags
-
-
-# Was in migration 0062 before. Didn't work anymore, because of the new field in SmallVariantFlags
-def update_chromosome_no_in_existing_flags_and_comments(apps, schema_editor):
-    if not schema_editor.connection.alias == "default":
-        return
-    for o in list(SmallVariantFlags.objects.all()) + list(SmallVariantComment.objects.all()):
-        o.save()
-
 
 class Migration(migrations.Migration):
     dependencies = [
@@ -35,6 +25,4 @@ class Migration(migrations.Migration):
                 max_length=32,
             ),
         ),
-        # Was in migration 0062 before. Didn't work anymore, because of the new field in SmallVariantFlags
-        migrations.RunPython(update_chromosome_no_in_existing_flags_and_comments),
     ]

variants/migrations/0102_auto_20240322_1502.py

@@ -0,0 +1,37 @@
+# Generated by Django 3.2.24 on 2024-03-22 15:02
+
+from django.db import migrations, models
+
+from variants.models import SmallVariantComment, SmallVariantFlags
+
+
+# Was in migration 0062 before. Didn't work anymore, because of the new field in SmallVariantFlags
+# Was in migration 0071 before
+def update_chromosome_no_in_existing_flags_and_comments(apps, schema_editor):
+    if not schema_editor.connection.alias == "default":
+        return
+    for o in list(SmallVariantFlags.objects.all()) + list(SmallVariantComment.objects.all()):
+        o.save()
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("variants", "0101_auto_20240301_1141_not_null_sodar_field"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="flagsetcpresets",
+            name="flag_incidental",
+            field=models.BooleanField(default=True),
+        ),
+        migrations.AddField(
+            model_name="smallvariantflags",
+            name="flag_incidental",
+            field=models.BooleanField(default=False),
+        ),
+        # Was in migration 0062 before. Didn't work anymore, because of the new field in SmallVariantFlags
+        # Was in migration 0071 before
+        migrations.RunPython(update_chromosome_no_in_existing_flags_and_comments),
+    ]

variants/models/presets.py

@@ -235,6 +235,7 @@ class FlagsEtcPresets(PresetBase):
     clinvar_include_pathogenic = models.BooleanField(null=False, default=True)
     clinvar_include_uncertain_significance = models.BooleanField(null=False, default=True)
     flag_bookmarked = models.BooleanField(null=False, default=True)
+    flag_incidental = models.BooleanField(null=False, default=True)
     flag_candidate = models.BooleanField(null=False, default=True)
     flag_doesnt_segregate = models.BooleanField(null=False, default=True)
     flag_final_causative = models.BooleanField(null=False, default=True)

variants/models/userannos.py

@@ -211,6 +211,8 @@ class SmallVariantFlags(GetGeneSymbolsMixin, HumanReadableMixin, models.Model):
 
     #: Bookmarked: saved for later
     flag_bookmarked = models.BooleanField(default=False, null=False)
+    #: Incidental finding
+    flag_incidental = models.BooleanField(default=False, null=False)
     #: Candidate variant
     flag_candidate = models.BooleanField(default=False, null=False)
     #: Finally selected causative variant
@@ -261,6 +263,7 @@ def no_flags_set(self):
         return not any(
             (
                 self.flag_bookmarked,
+                self.flag_incidental,
                 self.flag_candidate,
                 self.flag_final_causative,
                 self.flag_for_validation,

variants/queries.py

@@ -1210,6 +1210,7 @@ def __init__(self, *args, **kwargs):
                 [
                     func.count(SmallVariantFlags.sa.id).label("flag_count"),
                     func.bool_or(SmallVariantFlags.sa.flag_bookmarked).label("flag_bookmarked"),
+                    func.bool_or(SmallVariantFlags.sa.flag_incidental).label("flag_incidental"),
                     func.bool_or(SmallVariantFlags.sa.flag_candidate).label("flag_candidate"),
                     func.bool_or(SmallVariantFlags.sa.flag_segregates).label("flag_segregates"),
                     func.bool_or(SmallVariantFlags.sa.flag_doesnt_segregate).label(
@@ -1256,6 +1257,7 @@ def extend_fields(self, _query_parts):
         return [
             self.subquery.c.flag_count,
             self.subquery.c.flag_bookmarked,
+            self.subquery.c.flag_incidental,
             self.subquery.c.flag_candidate,
             self.subquery.c.flag_segregates,
             self.subquery.c.flag_doesnt_segregate,

variants/query_presets.py

@@ -914,6 +914,7 @@ class _FlagsEtcPresets:
         "clinvar_include_pathogenic": True,
         "clinvar_include_uncertain_significance": False,
         "flag_bookmarked": True,
+        "flag_incidental": True,
         "flag_candidate": True,
         "flag_doesnt_segregate": True,
         "flag_final_causative": True,
@@ -949,6 +950,7 @@ class _FlagsEtcPresets:
     #: Presets for the "Clinvar only" flags etc. settings
     clinvar_only: typing.Dict[str, typing.Any] = {
         "flag_bookmarked": True,
+        "flag_incidental": True,
         "flag_candidate": True,
         "flag_doesnt_segregate": True,
         "flag_final_causative": True,
@@ -989,6 +991,7 @@ class _FlagsEtcPresets:
         "clinvar_include_pathogenic": True,
         "clinvar_include_uncertain_significance": False,
         "flag_bookmarked": True,
+        "flag_incidental": True,
         "flag_candidate": True,
         "flag_doesnt_segregate": True,
         "flag_final_causative": True,

variants/query_schemas.py

@@ -200,6 +200,7 @@ class CaseQueryV1:
 
     flag_simple_empty: bool = True
     flag_bookmarked: bool = True
+    flag_incidental: bool = True
     flag_candidate: bool = True
     flag_doesnt_segregate: bool = True
     flag_final_causative: bool = True
@@ -343,6 +344,7 @@ def convert(self, case: Case, query: CaseQueryV1) -> typing.Dict[str, typing.Any
             "clinvar_include_pathogenic": query.clinvar_include_pathogenic,
             "flag_simple_empty": query.flag_simple_empty,
             "flag_bookmarked": query.flag_bookmarked,
+            "flag_incidental": query.flag_incidental,
             "flag_candidate": query.flag_candidate,
             "flag_doesnt_segregate": query.flag_doesnt_segregate,
             "flag_final_causative": query.flag_final_causative,