feat: adding store/seqvarInfo, api/viguno, more api/annonars (#50)

src/api/annonars/client.ts

@@ -1,6 +1,7 @@
 import { chunks } from '@reactgular/chunks'
 
 import type { LinearStrucvar, Seqvar } from '../../lib/genomicVars'
+import { ClinvarPerGeneRecord } from '../../pbs/annonars/clinvar/per_gene'
 import { Record as GeneInfoRecord } from '../../pbs/annonars/genes/base'
 import { GeneInfoResult } from './types'
 
@@ -61,7 +62,7 @@ export class AnnonarsClient {
    * @param hgncId
    * @returns
    */
-  async fetchGeneClinvarInfo(hgncId: string): Promise<any> {
+  async fetchGeneClinvarInfo(hgncId: string): Promise<ClinvarPerGeneRecord> {
     const response = await fetch(`${this.apiBaseUrl}genes/clinvar?hgnc_id=${hgncId}`, {
       method: 'GET'
     })

src/api/annonars/types.ts

@@ -1,7 +1,174 @@
+import { JsonValue } from '@protobuf-ts/runtime'
+
+import { Record as ClinvarRecord } from '../../pbs/annonars/clinvar/minimal'
+import { Record as UcscConservationRecord } from '../../pbs/annonars/cons/base'
+import { Record as DbsnpRecord } from '../../pbs/annonars/dbsnp/base'
 import { Record as GeneInfoRecord } from '../../pbs/annonars/genes/base'
+import { Record as Gnomad2Record } from '../../pbs/annonars/gnomad/gnomad2'
+import { Record as Gnomad3Record } from '../../pbs/annonars/gnomad/gnomad3'
+import { Record as Gnomad4Record } from '../../pbs/annonars/gnomad/gnomad4'
+import { Record as GnomadMtdnaRecord } from '../../pbs/annonars/gnomad/mtdna'
+import { Record as HelixmtdbRecord } from '../../pbs/annonars/helixmtdb/base'
 
-/** Interface for gene info result. */
+/**
+ * Interface for gene info result.
+ */
 export interface GeneInfoResult {
   /** Gehe information per HGNC ID. */
   genes: GeneInfoRecord[]
 }
+
+/**
+ * Interface for seqvar info query as returned by API.
+ */
+export interface SeqvarInfoQuery$Api {
+  genome_release: string
+  chromosome: string
+  pos: number
+  reference: string
+  alternative: string
+}
+
+/**
+ * Interface for seqvar info query.
+ */
+export interface SeqvarInfoQuery {
+  genomeRelease: string
+  chromosome: string
+  pos: number
+  reference: string
+  alternative: string
+}
+
+/**
+ * Helper class to convert `SeqvarInfoQuery$Api` to `SeqvarInfoQuery`.
+ */
+class SeqvarInfoQuery$Type {
+  fromJson(apiQuery: SeqvarInfoQuery$Api): SeqvarInfoQuery {
+    return {
+      genomeRelease: apiQuery.genome_release,
+      chromosome: apiQuery.chromosome,
+      pos: apiQuery.pos,
+      reference: apiQuery.reference,
+      alternative: apiQuery.alternative
+    }
+  }
+}
+
+/**
+ * Helper instance to convert `SeqvarInfoQuery$Api` to `SeqvarInfoQuery`.
+ */
+export const SeqvarInfoQuery = new SeqvarInfoQuery$Type()
+
+/**
+ * Interface for seqvar info query result as returned by API.
+ */
+export interface SeqvarInfoResult$Api {
+  cadd: { [key: string]: number | string | boolean | null } | null
+  dbsnp: DbsnpRecord | null
+  dbnsfp: { [key: string]: number | string | boolean | null } | null
+  dbscsnv: { [key: string]: number | string | boolean | null } | null
+  gnomad_mtdna: GnomadMtdnaRecord | null
+  gnomad_exomes: Gnomad2Record | Gnomad3Record | Gnomad4Record | null
+  gnomad_genomes: Gnomad2Record | Gnomad3Record | Gnomad4Record | null
+  helixmtdb: HelixmtdbRecord | null
+  ucsc_conservation: UcscConservationRecord[]
+  clinvar: null
+}
+
+/**
+ * Interface for seqvar info result.
+ */
+export interface SeqvarInfoResult {
+  cadd?: { [key: string]: number | string | boolean | null }
+  dbsnp?: DbsnpRecord
+  dbnsfp?: { [key: string]: number | string | boolean | null }
+  dbscsnv?: { [key: string]: number | string | boolean | null }
+  gnomadMtdna?: GnomadMtdnaRecord
+  gnomadExomes?: Gnomad2Record | Gnomad3Record | Gnomad4Record
+  gnomadGenomes?: Gnomad2Record | Gnomad3Record | Gnomad4Record
+  helixmtdb?: HelixmtdbRecord
+  ucscConservation: UcscConservationRecord[]
+  clinvar?: ClinvarRecord
+}
+
+/**
+ * Helper to convert
+ */
+
+/**
+ * Helper class to convert `SeqvarInfoResult$Api` to `SeqvarInfoResult`.
+ */
+class SeqvarInfoResult$Type {
+  fromJson(apiResult: SeqvarInfoResult$Api): SeqvarInfoResult {
+    return {
+      cadd: apiResult.cadd === null ? undefined : apiResult.cadd,
+      dbsnp:
+        // @ts-ignore
+        apiResult.dbsnp === null
+          ? undefined // @ts-ignore
+          : DbsnpRecord.fromJson(apiResult.dbsnp as JsonValue),
+      dbnsfp: apiResult.dbnsfp === null ? undefined : apiResult.dbnsfp,
+      dbscsnv: apiResult.dbscsnv === null ? undefined : apiResult.dbscsnv,
+      gnomadMtdna:
+        apiResult.gnomad_mtdna === null
+          ? undefined
+          : // @ts-ignore
+            GnomadMtdnaRecord.fromJson(apiResult.gnomad_mtdna as JsonValue),
+      gnomadExomes: apiResult.gnomad_exomes === null ? undefined : apiResult.gnomad_exomes,
+      gnomadGenomes: apiResult.gnomad_genomes === null ? undefined : apiResult.gnomad_genomes,
+      helixmtdb:
+        apiResult.helixmtdb === null
+          ? undefined
+          : // @ts-ignore
+            HelixmtdbRecord.fromJson(apiResult.helixmtdb as JsonValue),
+      ucscConservation: apiResult.ucsc_conservation,
+      clinvar:
+        apiResult.clinvar === null
+          ? undefined
+          : // @ts-ignore
+            ClinvarRecord.fromJson(apiResult.clinvar as JsonValue)
+    }
+  }
+}
+
+/**
+ * Helper instance to convert `SeqvarInfoResult$Api` to `SeqvarInfoResult`.
+ */
+export const SeqvarInfoResult = new SeqvarInfoResult$Type()
+
+/**
+ * Interface for seqvar info query response as returned by API.
+ */
+export interface SeqvarInfoResponse$Api {
+  server_version: string
+  query: SeqvarInfoQuery$Api
+  result: SeqvarInfoResult$Api
+}
+
+/**
+ * Interface for seqvar info query result.
+ */
+export interface SeqvarInfoResponse {
+  serverVersion: string
+  query: SeqvarInfoQuery
+  result: SeqvarInfoResult
+}
+
+/**
+ * Helper class to convert `SeqvarInfoResponse$Api` to `SeqvarInfoResponse`.
+ */
+class SeqvarInfoResponse$Type {
+  static fromJson(apiResponse: SeqvarInfoResponse$Api): SeqvarInfoResponse {
+    return {
+      serverVersion: apiResponse.server_version,
+      query: SeqvarInfoQuery.fromJson(apiResponse.query),
+      result: SeqvarInfoResult.fromJson(apiResponse.result)
+    }
+  }
+}
+
+/**
+ * Helper instance to convert `SeqvarInfoResponse$Api` to `SeqvarInfoResponse`.
+ */
+export const SeqvarInfoResponse = new SeqvarInfoResponse$Type()