fix: most recent mehari rest service causes unknown fields error (#249)…

… (#250)

package.json

@@ -106,5 +106,6 @@
     "vitest-canvas-mock": "^0.3.3",
     "vitest-fetch-mock": "^0.2.2",
     "vue-tsc": "^2.0.19"
-  }
+  },
+  "packageManager": "[email protected]+sha512.a6b2f7906b721bba3d67d4aff083df04dad64c399707841b7acf00f6b133b7ac24255f2652fa22ae3534329dc6180534e98d17432037ff6fd140556e2bb3137e"
 }

protos/mehari/txs.proto

@@ -23,6 +23,10 @@ message GeneToTxId {
     string gene_id = 1;
     // Vector of all transcript IDs.
     repeated string tx_ids = 2;
+    // Whether this gene has been filtered out because of missing transcripts.
+    optional bool filtered = 3;
+    // Reason for filtering.
+    optional uint32 filter_reason = 4;
 }
 
 // Container for the transcript-related database.
@@ -59,6 +63,8 @@ enum TranscriptTag {
     TRANSCRIPT_TAG_REF_SEQ_SELECT = 5;
     // Flagged as being a selenoprotein (UGA => selenon).
     TRANSCRIPT_TAG_SELENOPROTEIN = 6;
+    // Member of GENCODE Primary
+    TRANSCRIPT_TAG_GENCODE_PRIMARY = 7;
 }
 
 // Store information about a transcript.
@@ -81,6 +87,10 @@ message Transcript {
     optional int32 stop_codon = 8;
     // Alignments on the different genome builds.
     repeated GenomeAlignment genome_alignments = 9;
+    // Whether this transcript has an issue (e.g. MissingStopCodon), cf. `mehari::db::create::mod::Reason`.
+    optional bool filtered = 10;
+    // Reason for filtering.
+    optional uint32 filter_reason = 11;
 }
 
 // Enumeration for the known genome builds.

src/api/annonars/client.ts

@@ -112,7 +112,9 @@ export class AnnonarsClient {
     const responseJson = await response.json()
     if (responseJson?.genes && responseJson?.genes[hgncId]) {
       try {
-        return ClinvarPerGeneRecord.fromJson(responseJson.genes[hgncId])
+        return ClinvarPerGeneRecord.fromJson(responseJson.genes[hgncId], {
+          ignoreUnknownFields: true
+        })
       } catch (e) {
         throw new InvalidResponseContent(`failed to parse gene clinvar info response: ${e}`)
       }
@@ -176,7 +178,7 @@ export class AnnonarsClient {
       resultJsons.forEach((chunk: any) => {
         for (const value of Object.values(chunk.genes)) {
           // @ts-ignore
-          result.push(GeneInfoRecord.fromJson(value as JsonValue))
+          result.push(GeneInfoRecord.fromJson(value as JsonValue, { ignoreUnknownFields: true }))
         }
       })
       return result

src/api/annonars/types.ts

@@ -32,7 +32,9 @@ class ClinvarSvQueryResponse$Type {
   fromJson(apiResponse: ClinvarSvQueryResponse$Api): ClinvarSvQueryResponse {
     const records = apiResponse.records ?? []
     return {
-      records: records.map((value) => ClinvarStrucvarResponseRecord.fromJson(value))
+      records: records.map((value) =>
+        ClinvarStrucvarResponseRecord.fromJson(value, { ignoreUnknownFields: true })
+      )
     }
   }
 }
@@ -176,7 +178,7 @@ class GeneInfoResult$Type {
     return {
       genes: Object.values(apiResult.genes).map((gene$Api) =>
         // @ts-ignore
-        GeneInfoRecord.fromJson(gene$Api as JsonValue)
+        GeneInfoRecord.fromJson(gene$Api as JsonValue, { ignoreUnknownFields: true })
       )
     }
   }
@@ -278,27 +280,33 @@ class SeqvarInfoResult$Type {
         // @ts-ignore
         apiResult.dbsnp === null
           ? undefined // @ts-ignore
-          : DbsnpRecord.fromJson(apiResult.dbsnp as JsonValue),
+          : DbsnpRecord.fromJson(apiResult.dbsnp as JsonValue, { ignoreUnknownFields: true }),
       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),
+            GnomadMtdnaRecord.fromJson(apiResult.gnomad_mtdna as JsonValue, {
+              ignoreUnknownFields: true
+            }),
       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),
+            HelixmtdbRecord.fromJson(apiResult.helixmtdb as JsonValue, {
+              ignoreUnknownFields: true
+            }),
       ucscConservation: apiResult.ucsc_conservation.map((cons) => cons.records),
       clinvar:
         apiResult.clinvar === null
           ? undefined
           : // @ts-ignore
-            ExtractedVcvRecordList.fromJson(apiResult.clinvar as JsonValue)
+            ExtractedVcvRecordList.fromJson(apiResult.clinvar as JsonValue, {
+              ignoreUnknownFields: true
+            })
     }
   }
 }

src/api/mehari/client.ts

@@ -132,7 +132,7 @@ export class MehariClient {
     }
     try {
       const responseJson = await response.json()
-      return GeneTranscriptsResponse.fromJson(responseJson)
+      return GeneTranscriptsResponse.fromJson(responseJson, { ignoreUnknownFields: true })
     } catch (e) {
       throw new InvalidResponseContent(`Failed to parse transcript response: ${e}`)
     }

src/components/GeneClinvarCard/ClinvarFreqPlot.stories.ts

@@ -10,9 +10,13 @@ import geneClinvarTgdsJson from './fixture.clinvarPerGene.TGDS.json'
 // as in the tests fails with "process is not defined" error in the browser.
 
 // @ts-ignore
-const clinvarPerGeneTgds = ClinvarPerGeneRecord.fromJson(geneClinvarTgdsJson as JsonValue)
+const clinvarPerGeneTgds = ClinvarPerGeneRecord.fromJson(geneClinvarTgdsJson as JsonValue, {
+  ignoreUnknownFields: true
+})
 // @ts-ignore
-const clinvarPerGeneBrca1 = ClinvarPerGeneRecord.fromJson(geneClinvarBrca1Json as JsonValue)
+const clinvarPerGeneBrca1 = ClinvarPerGeneRecord.fromJson(geneClinvarBrca1Json as JsonValue, {
+  ignoreUnknownFields: true
+})
 
 const meta = {
   title: 'Gene/Clinvar/ClinvarFreqPlot',

src/components/GeneClinvarCard/GeneClinvarCard.stories.ts

@@ -17,19 +17,33 @@ import genesTxsTgdsJson38 from './fixture.genesTxs.TGDS.38.json'
 // as in the tests fails with "process is not defined" error in the browser.
 
 // @ts-ignore
-const clinvarPerGeneTgds = ClinvarPerGeneRecord.fromJson(geneClinvarTgdsJson as JsonValue)
+const clinvarPerGeneTgds = ClinvarPerGeneRecord.fromJson(geneClinvarTgdsJson as JsonValue, {
+  ignoreUnknownFields: true
+})
 // @ts-ignore
-const clinvarPerGeneBrca1 = ClinvarPerGeneRecord.fromJson(geneClinvarBrca1Json as JsonValue)
+const clinvarPerGeneBrca1 = ClinvarPerGeneRecord.fromJson(geneClinvarBrca1Json as JsonValue, {
+  ignoreUnknownFields: true
+})
 // @ts-ignore
-const genesTxsTgds37 = GeneTranscriptsResponse.fromJson(genesTxsTgdsJson37 as JsonValue)
+const genesTxsTgds37 = GeneTranscriptsResponse.fromJson(genesTxsTgdsJson37 as JsonValue, {
+  ignoreUnknownFields: true
+})
 // @ts-ignore
-const genesTxsTgds38 = GeneTranscriptsResponse.fromJson(genesTxsTgdsJson38 as JsonValue)
+const genesTxsTgds38 = GeneTranscriptsResponse.fromJson(genesTxsTgdsJson38 as JsonValue, {
+  ignoreUnknownFields: true
+})
 // @ts-ignore
-const genesTxsBrca137 = GeneTranscriptsResponse.fromJson(genesTxsBrca1Json37 as JsonValue)
+const genesTxsBrca137 = GeneTranscriptsResponse.fromJson(genesTxsBrca1Json37 as JsonValue, {
+  ignoreUnknownFields: true
+})
 // @ts-ignore
-const geneInfoTgds = GeneInfoRecord.fromJson(geneInfoTgdsJson as JsonValue)
+const geneInfoTgds = GeneInfoRecord.fromJson(geneInfoTgdsJson as JsonValue, {
+  ignoreUnknownFields: true
+})
 // @ts-ignore
-const geneInfoBrca1 = GeneInfoRecord.fromJson(geneInfoBrca1Json as JsonValue)
+const geneInfoBrca1 = GeneInfoRecord.fromJson(geneInfoBrca1Json as JsonValue, {
+  ignoreUnknownFields: true
+})
 
 const meta = {
   title: 'Gene/Clinvar/GeneClinvarCard',

src/pbs/mehari/txs.ts

@@ -59,6 +59,18 @@ export interface GeneToTxId {
    * @generated from protobuf field: repeated string tx_ids = 2;
    */
   txIds: string[]
+  /**
+   * Whether this gene has been filtered out because of missing transcripts.
+   *
+   * @generated from protobuf field: optional bool filtered = 3;
+   */
+  filtered?: boolean
+  /**
+   * Reason for filtering.
+   *
+   * @generated from protobuf field: optional uint32 filter_reason = 4;
+   */
+  filterReason?: number
 }
 /**
  * Container for the transcript-related database.
@@ -139,6 +151,18 @@ export interface Transcript {
    * @generated from protobuf field: repeated mehari.txs.GenomeAlignment genome_alignments = 9;
    */
   genomeAlignments: GenomeAlignment[]
+  /**
+   * Whether this transcript has an issue (e.g. MissingStopCodon), cf. `mehari::db::create::mod::Reason`.
+   *
+   * @generated from protobuf field: optional bool filtered = 10;
+   */
+  filtered?: boolean
+  /**
+   * Reason for filtering.
+   *
+   * @generated from protobuf field: optional uint32 filter_reason = 11;
+   */
+  filterReason?: number
 }
 /**
  * Store information about a transcript aligning to a genome.
@@ -329,7 +353,13 @@ export enum TranscriptTag {
    *
    * @generated from protobuf enum value: TRANSCRIPT_TAG_SELENOPROTEIN = 6;
    */
-  TRANSCRIPT_TAG_SELENOPROTEIN = 6
+  TRANSCRIPT_TAG_SELENOPROTEIN = 6,
+  /**
+   * Member of GENCODE Primary
+   *
+   * @generated from protobuf enum value: TRANSCRIPT_TAG_GENCODE_PRIMARY = 7;
+   */
+  TRANSCRIPT_TAG_GENCODE_PRIMARY = 7
 }
 /**
  * Enumeration for the known genome builds.
@@ -495,7 +525,9 @@ class GeneToTxId$Type extends MessageType<GeneToTxId> {
         kind: 'scalar',
         repeat: 2 /*RepeatType.UNPACKED*/,
         T: 9 /*ScalarType.STRING*/
-      }
+      },
+      { no: 3, name: 'filtered', kind: 'scalar', opt: true, T: 8 /*ScalarType.BOOL*/ },
+      { no: 4, name: 'filter_reason', kind: 'scalar', opt: true, T: 13 /*ScalarType.UINT32*/ }
     ])
   }
   create(value?: PartialMessage<GeneToTxId>): GeneToTxId {
@@ -522,6 +554,12 @@ class GeneToTxId$Type extends MessageType<GeneToTxId> {
         case /* repeated string tx_ids */ 2:
           message.txIds.push(reader.string())
           break
+        case /* optional bool filtered */ 3:
+          message.filtered = reader.bool()
+          break
+        case /* optional uint32 filter_reason */ 4:
+          message.filterReason = reader.uint32()
+          break
         default:
           const u = options.readUnknownField
           if (u === 'throw')
@@ -551,6 +589,11 @@ class GeneToTxId$Type extends MessageType<GeneToTxId> {
     /* repeated string tx_ids = 2; */
     for (let i = 0; i < message.txIds.length; i++)
       writer.tag(2, WireType.LengthDelimited).string(message.txIds[i])
+    /* optional bool filtered = 3; */
+    if (message.filtered !== undefined) writer.tag(3, WireType.Varint).bool(message.filtered)
+    /* optional uint32 filter_reason = 4; */
+    if (message.filterReason !== undefined)
+      writer.tag(4, WireType.Varint).uint32(message.filterReason)
     const u = options.writeUnknownFields
     if (u !== false) (u == true ? UnknownFieldHandler.onWrite : u)(this.typeName, message, writer)
     return writer
@@ -680,7 +723,9 @@ class Transcript$Type extends MessageType<Transcript> {
         kind: 'message',
         repeat: 1 /*RepeatType.PACKED*/,
         T: () => GenomeAlignment
-      }
+      },
+      { no: 10, name: 'filtered', kind: 'scalar', opt: true, T: 8 /*ScalarType.BOOL*/ },
+      { no: 11, name: 'filter_reason', kind: 'scalar', opt: true, T: 13 /*ScalarType.UINT32*/ }
     ])
   }
   create(value?: PartialMessage<Transcript>): Transcript {
@@ -737,6 +782,12 @@ class Transcript$Type extends MessageType<Transcript> {
             GenomeAlignment.internalBinaryRead(reader, reader.uint32(), options)
           )
           break
+        case /* optional bool filtered */ 10:
+          message.filtered = reader.bool()
+          break
+        case /* optional uint32 filter_reason */ 11:
+          message.filterReason = reader.uint32()
+          break
         default:
           const u = options.readUnknownField
           if (u === 'throw')
@@ -790,6 +841,11 @@ class Transcript$Type extends MessageType<Transcript> {
         writer.tag(9, WireType.LengthDelimited).fork(),
         options
       ).join()
+    /* optional bool filtered = 10; */
+    if (message.filtered !== undefined) writer.tag(10, WireType.Varint).bool(message.filtered)
+    /* optional uint32 filter_reason = 11; */
+    if (message.filterReason !== undefined)
+      writer.tag(11, WireType.Varint).uint32(message.filterReason)
     const u = options.writeUnknownFields
     if (u !== false) (u == true ? UnknownFieldHandler.onWrite : u)(this.typeName, message, writer)
     return writer