Additional case where parsing can be not strict

Author: garrettjstevens

packages/apollo-collaboration-server/package.json

@@ -44,7 +44,7 @@
     "@apollo-annotation/shared": "workspace:^",
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
-    "@gmod/gff": "^2.0.0",
+    "@gmod/gff": "^2.1.0",
     "@gmod/indexedfasta": "^5.0.2",
     "@jbrowse/core": "^4.1.1",
     "@jbrowse/mobx-state-tree": "^5.5.0",

packages/apollo-collaboration-server/src/files/files.service.ts

@@ -105,15 +105,25 @@ export class FilesService {
 
   parseGFF3(
     stream: ReadableStream<Uint8Array>,
-    options?: { bufferSize?: number },
+    options?: {
+      bufferSize?: number
+      errorCallback?(erroreMessage: string): void
+    },
   ): ReadableStream<GFF3Feature> {
+    // eslint-disable-next-line @typescript-eslint/unbound-method
+    const { errorCallback } = options ?? {}
     return stream.pipeThrough(
       new TransformStream(
         new GFFTransformer({
           parseSequences: false,
           parseComments: false,
           parseDirectives: false,
           parseFeatures: true,
+          errorCallback: errorCallback
+            ? (errorMessage: string) => {
+                errorCallback(errorMessage)
+              }
+            : undefined,
           ...options,
         }),
       ),

packages/apollo-common/package.json

@@ -20,7 +20,7 @@
   },
   "devDependencies": {
     "@apollo-annotation/mst": "workspace:^",
-    "@gmod/gff": "^2.0.0",
+    "@gmod/gff": "^2.1.0",
     "@nestjs/common": "^10.1.0",
     "@nestjs/core": "^10.1.0",
     "@types/node": "^24.10.9",

packages/apollo-common/src/Operation.ts

@@ -47,7 +47,10 @@ export interface ServerDataStore {
     getFileHandle(file: FileDocument): GenericFilehandle
     parseGFF3(
       stream: ReadableStream<Uint8Array>,
-      parseOptions?: { bufferSize?: number },
+      parseOptions?: {
+        bufferSize?: number
+        errorCallback?(errorMessage: string): void
+      },
     ): ReadableStream<GFF3Feature>
     create(createFileDto: CreateFileDto): void
     remove(id: string): void

packages/apollo-shared/package.json

@@ -15,7 +15,7 @@
     "@apollo-annotation/common": "workspace:^",
     "@apollo-annotation/mst": "workspace:^",
     "@apollo-annotation/schemas": "workspace:^",
-    "@gmod/gff": "^2.0.0",
+    "@gmod/gff": "^2.1.0",
     "@gmod/indexedfasta": "^5.0.2",
     "@jbrowse/core": "^4.1.1",
     "bson-objectid": "^2.0.4",

packages/apollo-shared/src/Changes/AddFeaturesFromFileChange.ts

@@ -88,14 +88,28 @@ export class AddFeaturesFromFileChange extends FromFileBaseChange {
       }
       logger.debug?.(`FileId "${fileId}", checksum "${fileDoc.checksum}"`)
 
+      let errorCount = 0
+      // eslint-disable-next-line unicorn/consistent-function-scoping
+      const errorLogger = (error: unknown) => {
+        if (errorCount <= 99) {
+          logger.warn('Error parsing or adding feature')
+          logger.warn(error)
+          if (errorCount === 99) {
+            logger.warn(
+              'Reached 100 feature errors, omitting further warnings from log',
+            )
+          }
+        }
+        errorCount++
+      }
+
       // Read data from compressed file and parse the content
       const { bufferSize = 10_000, strict = true } = parseOptions ?? {}
       const featureStream = filesService.parseGFF3(
         filesService.getFileStream(fileDoc),
-        { bufferSize },
+        { bufferSize, errorCallback: strict ? undefined : errorLogger },
       )
       let featureCount = 0
-      let errorCount = 0
       for await (const gff3Feature of featureStream) {
         // Add new feature into database
         try {
@@ -105,16 +119,7 @@ export class AddFeaturesFromFileChange extends FromFileBaseChange {
           if (strict || featureCount === 0) {
             throw error
           }
-          if (errorCount <= 99) {
-            logger.warn('Error parsing feature')
-            logger.warn(error)
-            if (errorCount === 99) {
-              logger.warn(
-                'Reached 100 parsing errors, omitting further warnings from log',
-              )
-            }
-          }
-          errorCount++
+          errorLogger(error)
         }
         featureCount++
         if (featureCount % 1000 === 0) {

packages/jbrowse-plugin-apollo/package.json

@@ -51,7 +51,7 @@
     "@apollo-annotation/shared": "workspace:^",
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
-    "@gmod/gff": "^2.0.0",
+    "@gmod/gff": "^2.1.0",
     "@jbrowse/plugin-authentication": "^4.1.1",
     "@jbrowse/plugin-linear-genome-view": "^4.1.1",
     "@mui/icons-material": "^7.3.7",

yarn.lock

@@ -372,7 +372,7 @@ __metadata:
     "@apollo-annotation/shared": "workspace:^"
     "@emotion/react": "npm:^11.10.6"
     "@emotion/styled": "npm:^11.10.6"
-    "@gmod/gff": "npm:^2.0.0"
+    "@gmod/gff": "npm:^2.1.0"
     "@gmod/indexedfasta": "npm:^5.0.2"
     "@jbrowse/core": "npm:^4.1.1"
     "@jbrowse/mobx-state-tree": "npm:^5.5.0"
@@ -453,7 +453,7 @@ __metadata:
   dependencies:
     "@apollo-annotation/mst": "workspace:^"
     "@apollo-annotation/schemas": "workspace:^"
-    "@gmod/gff": "npm:^2.0.0"
+    "@gmod/gff": "npm:^2.1.0"
     "@jbrowse/core": "npm:^4.1.1"
     "@nestjs/common": "npm:^10.1.0"
     "@nestjs/core": "npm:^10.1.0"
@@ -490,7 +490,7 @@ __metadata:
     "@babel/preset-env": "npm:^7.28.6"
     "@emotion/react": "npm:^11.10.6"
     "@emotion/styled": "npm:^11.10.6"
-    "@gmod/gff": "npm:^2.0.0"
+    "@gmod/gff": "npm:^2.1.0"
     "@jbrowse/cli": "npm:^4.1.1"
     "@jbrowse/core": "npm:^4.1.1"
     "@jbrowse/development-tools": "npm:^2.2.1"
@@ -617,7 +617,7 @@ __metadata:
     "@apollo-annotation/common": "workspace:^"
     "@apollo-annotation/mst": "workspace:^"
     "@apollo-annotation/schemas": "workspace:^"
-    "@gmod/gff": "npm:^2.0.0"
+    "@gmod/gff": "npm:^2.1.0"
     "@gmod/indexedfasta": "npm:^5.0.2"
     "@jbrowse/core": "npm:^4.1.1"
     "@jbrowse/mobx-state-tree": "npm:^5.5.0"
@@ -7186,10 +7186,10 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@gmod/gff@npm:^2.0.0":
-  version: 2.0.0
-  resolution: "@gmod/gff@npm:2.0.0"
-  checksum: 10c0/f8a40c0eb84eeffcea49aa65e0656a12e8810fb0525b61272be443c9d45790a00ae84ad19808c5f30acd8a69714b04bcaacd5c469a65e8f6ae36920bf6ccca00
+"@gmod/gff@npm:^2.1.0":
+  version: 2.1.0
+  resolution: "@gmod/gff@npm:2.1.0"
+  checksum: 10c0/0f83d5cbbfe6338d89d5f0939c4c35f72d4f13085522d01e777e72ee614ea1aa9ccdca6a7df05bde4cccae99f8cd2b8d04b9c27197f88442810bda508e0ab6cc
   languageName: node
   linkType: hard