Remove @gmod/binary-parser to avoid new Function eval/CSP violation (#…

…137)
GMOD · Aug 8, 2024 · 8675701 · 8675701
1 parent e90915a
commit 8675701
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Showing 25 changed files with 1,156 additions and 9,585 deletions.
diff --git a/eslint.config.mjs b/eslint.config.mjs
@@ -15,9 +15,6 @@ const compat = new FlatCompat({
 })
 
 export default [
-  {
-    ignores: ['src/binary-parser/*.js'],
-  },
   ...compat.extends(
     'plugin:@typescript-eslint/recommended',
     'plugin:@typescript-eslint/recommended-type-checked',
@@ -49,7 +46,12 @@ export default [
           ignoreRestSiblings: true,
         },
       ],
-
+      'no-console': [
+        'warn',
+        {
+          allow: ['error', 'warn'],
+        },
+      ],
       'no-underscore-dangle': 0,
       curly: 'error',
       '@typescript-eslint/no-explicit-any': 0,

diff --git a/example/index-debug.html b/example/index-debug.html
@@ -0,0 +1,49 @@
+<html>
+  <head>
+    <script src="cram-bundle.js"></script>
+    <script>
+      const { IndexedCramFile, CramFile, CraiIndex } = window.gmodCRAM
+
+      // open local files
+      const indexedFile = new IndexedCramFile({
+        cramUrl: 'volvox-sorted.cram',
+        index: new CraiIndex({
+          url: 'volvox-sorted.cram.crai',
+        }),
+        seqFetch: async (seqId, start, end) => {
+          return ''
+        },
+        checkSequenceMD5: false,
+      })
+
+      // example of fetching records from an indexed CRAM file.
+      // NOTE: only numeric IDs for the reference sequence are accepted.
+      // For indexedfasta the numeric ID is the order in which the sequence names appear in the header
+
+      // Wrap in an async and then run
+      run = async () => {
+        const records = await indexedFile.getRecordsForRange(0, 10000, 20000)
+        const r = []
+        records.forEach(record => {
+          console.log(`got a record named ${record.readName}`)
+          if (record.readFeatures != undefined) {
+            record.readFeatures.forEach(({ code, pos, refPos, ref, sub }) => {
+              if (code === 'X') {
+                r.push(
+                  `${record.readName} shows a base substitution at ${refPos}`,
+                )
+              }
+            })
+          }
+        })
+        document.getElementById('output').innerHTML = r.join('\n')
+      }
+
+      run()
+    </script>
+  </head>
+  <body>
+    <h1>Hello world</h1>
+    <pre id="output" />
+  </body>
+</html>
diff --git a/package.json b/package.json
@@ -22,7 +22,7 @@
   ],
   "scripts": {
     "test": "jest",
-    "lint": "eslint src test",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0 src test",
     "docs": "documentation readme --shallow src/indexedCramFile.ts --section=IndexedCramFile; documentation readme --shallow src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/craiIndex.ts --section=CraiIndex;  documentation readme --shallow errors.ts '--section=Exception Classes'; documentation readme --shallow src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/cramFile/record.ts --section=CramRecord",
     "prebuild": "npm run clean",
     "clean": "rimraf dist esm",
@@ -43,7 +43,6 @@
   ],
   "dependencies": {
     "@gmod/abortable-promise-cache": "^2.0.0",
-    "@gmod/binary-parser": "^1.3.5",
     "@jkbonfield/htscodecs": "^0.5.1",
     "buffer-crc32": "^1.0.0",
     "bzip2": "^0.1.1",
@@ -59,18 +58,18 @@
     "@types/long": "^4.0.0",
     "@types/md5": "^2.3.2",
     "@types/pako": "^1.0.3",
-    "@typescript-eslint/eslint-plugin": "^7.0.2",
-    "@typescript-eslint/parser": "^7.0.2",
+    "@typescript-eslint/eslint-plugin": "^8.0.0",
+    "@typescript-eslint/parser": "^8.0.0",
     "buffer": "^6.0.3",
     "documentation": "^14.0.3",
-    "eslint": "^9.0.0",
+    "eslint": "^9.8.0",
     "eslint-config-prettier": "^9.0.0",
     "eslint-plugin-prettier": "^5.1.3",
-    "eslint-plugin-unicorn": "^54.0.0",
+    "eslint-plugin-unicorn": "^55.0.0",
     "jest": "^29.3.1",
     "mock-fs": "^5.2.0",
     "prettier": "^3.2.5",
-    "rimraf": "^5.0.1",
+    "rimraf": "^6.0.1",
     "ts-jest": "^29.1.2",
     "typescript": "^5.0.3",
     "webpack": "^5.90.3",

diff --git a/src/cramFile/codecs/byteArrayLength.ts b/src/cramFile/codecs/byteArrayLength.ts
@@ -1,10 +1,9 @@
-import { tinyMemoize } from '../util'
-
 import CramCodec, { Cursors } from './_base'
 import { ByteArrayLengthEncoding, CramEncoding } from '../encoding'
 import CramSlice from '../slice'
 import { CramFileBlock } from '../file'
 import { DataType } from './dataSeriesTypes'
+import { tinyMemoize } from '../util'
 
 type CramCodecFactory = <TData extends DataType = DataType>(
   encodingData: CramEncoding,

diff --git a/src/cramFile/codecs/external.ts b/src/cramFile/codecs/external.ts
@@ -42,7 +42,7 @@ export default class ExternalCodec extends CramCodec<
     const contentBlock = blocksByContentId[blockContentId]
     if (!contentBlock) {
       throw new CramMalformedError(
-        `no block found with content ID ${blockContentId}`,
+        `no block found with content ID ${blockContentId}}`,
       )
     }
     const cursor = cursors.externalBlocks.getCursor(blockContentId)

diff --git a/src/cramFile/codecs/huffman.ts b/src/cramFile/codecs/huffman.ts
@@ -46,7 +46,8 @@ export default class HuffmanIntCodec extends CramCodec<
     this.buildCodes()
     this.buildCaches()
 
-    // if this is a degenerate zero-length huffman code, special-case the decoding
+    // if this is a degenerate zero-length huffman code, special-case the
+    // decoding
     if (this.sortedCodes[0].bitLength === 0) {
       this._decode = this._decodeZeroLengthCode
     }

diff --git a/src/cramFile/container/compressionScheme.ts b/src/cramFile/container/compressionScheme.ts
@@ -1,6 +1,6 @@
 import { instantiateCodec } from '../codecs'
 import CramCodec from '../codecs/_base'
-import { CramCompressionHeader, CramPreservationMap } from '../sectionParsers'
+import { CramCompressionHeader } from '../sectionParsers'
 import { CramEncoding } from '../encoding'
 import { CramMalformedError } from '../../errors'
 import {
@@ -95,12 +95,8 @@ export default class CramContainerCompressionScheme {
   public tagCodecCache: Record<string, CramCodec> = {}
   public tagEncoding: Record<string, CramEncoding> = {}
   public dataSeriesEncoding: DataSeriesEncodingMap
-  private preservation: CramPreservationMap
-  private _endPosition: number
-  private _size: number
 
   constructor(content: CramCompressionHeader) {
-    // Object.assign(this, content)
     // interpret some of the preservation map tags for convenient use
     this.readNamesIncluded = content.preservation.RN
     this.APdelta = content.preservation.AP
@@ -109,9 +105,6 @@ export default class CramContainerCompressionScheme {
     this.substitutionMatrix = parseSubstitutionMatrix(content.preservation.SM)
     this.dataSeriesEncoding = content.dataSeriesEncoding
     this.tagEncoding = content.tagEncoding
-    this.preservation = content.preservation
-    this._size = content._size
-    this._endPosition = content._endPosition
   }
 
   /**

diff --git a/src/cramFile/container/index.ts b/src/cramFile/container/index.ts
@@ -4,27 +4,29 @@ import { itf8Size, parseItem, tinyMemoize } from '../util'
 import CramSlice from '../slice'
 import CramContainerCompressionScheme from './compressionScheme'
 import CramFile from '../file'
+import { getSectionParsers } from '../sectionParsers'
 
 export default class CramContainer {
   constructor(
     public file: CramFile,
     public filePosition: number,
   ) {}
 
-  // memoize
   getHeader() {
     return this._readContainerHeader(this.filePosition)
   }
 
-  // memoize
   async getCompressionHeaderBlock() {
     const containerHeader = await this.getHeader()
 
-    // if there are no records in the container, there will be no compression header
-    if (!containerHeader.numRecords) {
+    // if there are no records in the container, there will be no compression
+    // header
+    if (!containerHeader?.numRecords) {
       return null
     }
-    const sectionParsers = await this.file.getSectionParsers()
+    const { majorVersion } = await this.file.getDefinition()
+    const sectionParsers = getSectionParsers(majorVersion)
+
     const block = await this.getFirstBlock()
     if (block === undefined) {
       return undefined
@@ -34,6 +36,7 @@ export default class CramContainer {
         `invalid content type ${block.contentType} in what is supposed to be the compression header block`,
       )
     }
+
     const content = parseItem(
       block.content,
       sectionParsers.cramCompressionHeader.parser,
@@ -48,16 +51,20 @@ export default class CramContainer {
 
   async getFirstBlock() {
     const containerHeader = await this.getHeader()
+    if (!containerHeader) {
+      return undefined
+    }
     return this.file.readBlock(containerHeader._endPosition)
   }
 
-  // parses the compression header data into a CramContainerCompressionScheme object
-  // memoize
+  // parses the compression header data into a CramContainerCompressionScheme
+  // object
   async getCompressionScheme() {
     const header = await this.getCompressionHeaderBlock()
     if (!header) {
       return undefined
     }
+
     return new CramContainerCompressionScheme(header.parsedContent)
   }
 
@@ -68,23 +75,27 @@ export default class CramContainer {
   }
 
   async _readContainerHeader(position: number) {
-    const sectionParsers = await this.file.getSectionParsers()
+    const { majorVersion } = await this.file.getDefinition()
+    const sectionParsers = getSectionParsers(majorVersion)
     const { cramContainerHeader1, cramContainerHeader2 } = sectionParsers
     const { size: fileSize } = await this.file.stat()
 
     if (position >= fileSize) {
+      console.warn(
+        `position:${position}>=fileSize:${fileSize} in cram container`,
+      )
       return undefined
     }
 
     // parse the container header. do it in 2 pieces because you cannot tell
     // how much to buffer until you read numLandmarks
     const bytes1 = Buffer.allocUnsafe(cramContainerHeader1.maxLength)
     await this.file.read(bytes1, 0, cramContainerHeader1.maxLength, position)
-    const header1 = parseItem(bytes1, cramContainerHeader1.parser) as any
+    const header1 = parseItem(bytes1, cramContainerHeader1.parser)
     const numLandmarksSize = itf8Size(header1.numLandmarks)
     if (position + header1.length >= fileSize) {
       console.warn(
-        `${this.file}: container header at ${position} indicates that the container has length ${header1.length}, which extends beyond the length of the file. Skipping this container.`,
+        `container header at ${position} indicates that the container has length ${header1.length}, which extends beyond the length of the file. Skipping this container.`,
       )
       return undefined
     }