wip

src/components/StrucvarClinvarCard/StrucvarClinvarCard.vue

@@ -6,8 +6,6 @@ import { computed, ref } from 'vue'
 
 import { type Strucvar } from '../../lib/genomicVars'
 import { roundIt } from '../../lib/utils'
-import { ResponseRecord as ClinvarSvRecord } from '../../pbs/annonars/clinvar/sv'
-import { AggregateClassificationSet } from '../../pbs/annonars/clinvar_data/clinvar_public'
 import DocsLink from '../DocsLink/DocsLink.vue'
 import {
   AGGREGATE_GERMLINE_REVIEW_STATUS_LABEL,
@@ -18,13 +16,14 @@ import {
   AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_STARS
 } from '../SeqvarClinvarCard/constants'
 import { clinsigColor } from '../SeqvarClinvarCard/helpers'
+import { StrucvarsClinvarResponseRecord } from '../../ext/annonars-api/src/lib'
 
 /** This component's props. */
 const props = defineProps<{
   /** Structural variant to display the card for. */
   strucvar?: Strucvar
   /** ClinVar records to display for. */
-  clinvarSvRecords?: ClinvarSvRecord[]
+  clinvarSvRecords?: StrucvarsClinvarResponseRecord[]
 }>()
 
 const vcvUrl = (vcv: string): string => {

src/components/StrucvarGeneListCard/StrucvarGeneListCard.vue

@@ -3,24 +3,21 @@ import { computed, ref, watch } from 'vue'
 import { onMounted } from 'vue'
 
 import { TX_EFFECT_LABELS } from '../../api/mehari/constants'
-import type { GeneTranscriptEffects } from '../../api/mehari/types'
 import { type Strucvar } from '../../lib/genomicVars'
-import { Record as GeneInfoRecord } from '../../pbs/annonars/genes/base'
-import { StoreState } from '../../stores'
 import DocsLink from '../DocsLink/DocsLink.vue'
 import GeneListEntry from './GeneListEntry.vue'
+import { StrucvarsGeneTranscriptEffects } from '../../ext/mehari-api/src/lib'
+import { GenesGeneInfoRecord } from '../../ext/annonars-api/src/lib'
 
 /** This component's props. */
 const props = withDefaults(
   defineProps<{
     /** Strucvar to be displayed for. */
     currentStrucvarRecord?: Strucvar
     /** The consequences to be displayed. */
-    csq?: GeneTranscriptEffects[]
+    csq?: StrucvarsGeneTranscriptEffects[]
     /** Gene info records to list for. */
-    genesInfos?: GeneInfoRecord[]
-    /** The state of the store that we display for. */
-    storeState?: StoreState
+    genesInfos?: GenesGeneInfoRecord[]
     /** The HGNC ID of the selected gene. */
     selectedGeneHgncId?: string
     /** Column width of the entry. */
@@ -30,7 +27,6 @@ const props = withDefaults(
     currentStrucvarRecord: undefined,
     csq: undefined,
     genesInfos: undefined,
-    storeState: StoreState.Initial,
     selectedGeneHgncId: undefined,
     entryColumnWidth: '280px'
   }
@@ -50,12 +46,12 @@ const itemsPerPage = ref<number>(10)
 const currentPage = ref<number>(1)
 
 /** Whether the list of genes is currently loading. */
-const isLoading = computed<boolean>(() => {
-  return (
-    props.storeState === undefined ||
-    [StoreState.Initial, StoreState.Loading].includes(props.storeState)
-  )
-})
+const isLoading = computed<boolean>(() => (
+  props.currentStrucvarRecord === undefined ||
+  props.genesInfos === undefined ||
+  props.selectedGeneHgncId === undefined ||
+  props.csq === undefined
+))
 
 /** Helper mapping from gene HGNC ID to worst transcript effect. */
 const hgncToEffect = computed<{ [key: string]: string }>(() => {

src/queries/annonars/genes.ts

@@ -1,8 +1,8 @@
 /**
  * Queries for gene queries and related powered by TanStack Query.
  */
-import { QueryClient, useQuery } from '@tanstack/vue-query'
-import { MaybeRefOrGetter, toValue } from 'vue'
+import { QueryClient, useQueries, useQuery } from '@tanstack/vue-query'
+import { MaybeRefOrGetter, toValue, computed } from 'vue'
 
 import {
   genesClinvarOptions,
@@ -13,55 +13,55 @@ import {
 /**
  * Query for gene-related information from Annonars.
  *
- * @params hgnc_id The HGNC ID to use.
+ * @params hgnc_ids The HGNC IDs to use.
  * @returns The query result.
  */
 export const useAnnonarsGenesInfoQuery = (
-  { hgnc_id }: { hgnc_id: MaybeRefOrGetter<string | undefined> },
+  { hgnc_ids }: { hgnc_ids: MaybeRefOrGetter<string[] | undefined> },
   queryClient?: QueryClient
 ) =>
   useQuery(
     {
       ...genesInfoOptions({
         // @ts-ignore // https://github.com/hey-api/openapi-ts/issues/653#issuecomment-2314847011
         query: () => ({
-          hgnc_id: toValue(hgnc_id)
+          hgnc_id: toValue(hgnc_ids) === undefined ? [] : toValue(hgnc_ids)?.join(",")
         })
       }),
       staleTime: Infinity, // static data so no need to refetch
-      enabled: () => !!toValue(hgnc_id)
+      enabled: () => !!toValue(hgnc_ids)
     },
     queryClient
   )
 
 /**
  * Query for clinvar-related information from Annonars.
  *
- * @params hgnc_id The HGNC ID to use.
+ * @params hgnc_ids The HGNC ID to use.
  * @returns The query result.
  */
 export const useAnnonarsGenesClinvarQuery = (
-  { hgnc_id }: { hgnc_id: MaybeRefOrGetter<string | undefined> },
+  { hgnc_ids }: { hgnc_ids: MaybeRefOrGetter<string[] | undefined> },
   queryClient?: QueryClient
 ) =>
   useQuery(
     {
       ...genesClinvarOptions({
         // @ts-ignore // https://github.com/hey-api/openapi-ts/issues/653#issuecomment-2314847011
         query: () => ({
-          hgnc_id: toValue(hgnc_id)
+          hgnc_id: toValue(hgnc_ids) === undefined ? [] : toValue(hgnc_ids)?.join(",")
         })
       }),
       staleTime: Infinity, // static data so no need to refetch
-      enabled: () => !!toValue(hgnc_id)
+      enabled: () => !!toValue(hgnc_ids)
     },
     queryClient
   )
 
 /**
  * Query for looking up genes.
  *
- * @params query The query to use.
+ * @params query The queries to use.
  * @returns The query result.
  */
 export const useAnnonarsGenesLookupQuery = (
@@ -77,7 +77,7 @@ export const useAnnonarsGenesLookupQuery = (
         })
       }),
       staleTime: Infinity, // static data so no need to refetch
-      enabled: () => !!toValue(query)
+      enabled: () => !!toValue(query)?.join(",")
     },
     queryClient
   )

src/queries/annonars/strucvars.ts

@@ -0,0 +1,68 @@
+/**
+ * Queries for strucvars information powered by TanStack Query.
+ */
+import { QueryClient, useQuery } from '@tanstack/vue-query'
+import { MaybeRefOrGetter, toValue } from 'vue'
+
+import { strucvarsClinvarQueryOptions } from '../../ext/annonars-api/src/lib/@tanstack/vue-query.gen'
+import { ClinvarExtractedVariationType } from '../../ext/annonars-api/src/lib'
+
+/**
+ * Query for overlapping ClinVar structural variants.
+ *
+ * @param genome_release The genome release to use.
+ * @param chromosome The chromosome to use.
+ * @param start The start position to use (1-based).
+ * @param stop The stop position to use (1-based).
+ * @param variation_types The variation types to use; optional.
+ * @param min_overlap The minimum overlap to use; optional.
+ * @param page_no The page number to use; optional.
+ * @param page_size The page size to use; optional.
+ * @returns The query result.
+ */
+export const useAnnonarsStrucvarsClinvarQuery = (
+  {
+    genome_release,
+    chromosome,
+    start,
+    stop,
+    variation_types,
+    min_overlap,
+    page_no,
+    page_size
+  }: {
+    genome_release: MaybeRefOrGetter<string | undefined>
+    chromosome: MaybeRefOrGetter<string | undefined>
+    start: MaybeRefOrGetter<number | undefined>
+    stop: MaybeRefOrGetter<number | undefined>
+    variation_types?: MaybeRefOrGetter<Array<ClinvarExtractedVariationType> | undefined>
+    min_overlap?: MaybeRefOrGetter<number | undefined>
+    page_no?: MaybeRefOrGetter<number | undefined>
+    page_size?: MaybeRefOrGetter<number | undefined>
+  },
+  queryClient?: QueryClient
+) =>
+  useQuery(
+    {
+      ...strucvarsClinvarQueryOptions({
+        // @ts-ignore // https://github.com/hey-api/openapi-ts/issues/653#issuecomment-2314847011
+        query: () => ({
+          genome_release: toValue(genome_release),
+          chromosome: toValue(chromosome),
+          start: toValue(start),
+          stop: toValue(stop),
+          variation_types: toValue(variation_types ?? (() => undefined)) === undefined ? undefined : toValue(variation_types)?.join(","),
+          min_overlap: toValue(min_overlap ?? (() => undefined)),
+          page_no: toValue(page_no ?? (() => undefined)),
+          page_size: toValue(page_size ?? (() => undefined))
+        })
+      }),
+      staleTime: Infinity, // static data so no need to refetch
+      enabled: () =>
+        !!toValue(genome_release) &&
+        !!toValue(chromosome) &&
+        !!toValue(start) &&
+        !!toValue(stop)
+    },
+    queryClient
+  )

src/queries/mehari/geneTranscripts.ts

@@ -1,8 +1,8 @@
 /**
  * Queries for Mehari gene transcripts by TanStack Query.
  */
-import { QueryClient, useQuery } from '@tanstack/vue-query'
-import { MaybeRefOrGetter, toValue } from 'vue'
+import { QueryClient, useQueries, useQuery } from '@tanstack/vue-query'
+import { MaybeRefOrGetter, toValue, computed } from 'vue'
 
 import { genesTranscriptsListOptions } from '../../ext/mehari-api/src/lib/@tanstack/vue-query.gen'
 

src/queries/mehari/strucvars.ts

@@ -0,0 +1,57 @@
+/**
+ * Queries for seqvars information powered by TanStack Query.
+ */
+import { QueryClient, useQuery } from '@tanstack/vue-query'
+import { MaybeRefOrGetter, toValue } from 'vue'
+
+import { strucvarsCsqOptions } from '../../ext/mehari-api/src/lib/@tanstack/vue-query.gen'
+import { StrucvarsSvType } from '../../ext/mehari-api/src/lib'
+
+/**
+ * Query for the consequence of a seqvar.
+ *
+ * @param genome_release The genome release to use.
+ * @param chromosome The chromosome to use.
+ * @param position The position to use.
+ * @param reference The reference to use.
+ * @param alternative The alternative to use.
+ * @param hgnc_id The HGNC ID to use; optional.
+ * @returns The query result.
+ */
+export const useMehariStrucvarsCsqQuery = (
+  {
+    genome_release,
+    chromosome,
+    start,
+    stop,
+    sv_type,
+  }: {
+    genome_release: MaybeRefOrGetter<string | undefined>
+    chromosome: MaybeRefOrGetter<string | undefined>
+    start: MaybeRefOrGetter<number | undefined>
+    stop?: MaybeRefOrGetter<number | undefined>
+    sv_type: MaybeRefOrGetter<StrucvarsSvType | undefined>
+  },
+  queryClient?: QueryClient
+) =>
+  useQuery(
+    {
+      ...strucvarsCsqOptions({
+        // @ts-ignore // https://github.com/hey-api/openapi-ts/issues/653#issuecomment-2314847011
+        query: () => ({
+          genome_release: toValue(genome_release),
+          chromosome: toValue(chromosome),
+          start: toValue(start),
+          stop: toValue(stop ?? (() => undefined)),
+          sv_type: toValue(sv_type)
+        })
+      }),
+      staleTime: Infinity, // static data so no need to refetch
+      enabled: () =>
+        !!toValue(genome_release) &&
+        !!toValue(chromosome) &&
+        !!toValue(start) &&
+        !!toValue(sv_type)
+    },
+    queryClient
+  )

src/queries/viguno/genes.ts

@@ -1,8 +1,8 @@
 /**
  * Queries for HPO queries and related powered by TanStack Query.
  */
-import { QueryClient, useQuery } from '@tanstack/vue-query'
-import { MaybeRefOrGetter, toValue } from 'vue'
+import { QueryClient, useQueries, useQuery } from '@tanstack/vue-query'
+import { MaybeRefOrGetter, toValue, computed } from 'vue'
 
 import { hpoGenesOptions } from '../../ext/viguno-api/src/lib/@tanstack/vue-query.gen'