@apollo-annotation/shared 0.1.17 → 0.1.19

package/src/Checks/CDSCheck.ts

@@ -3,225 +3,225 @@ import {
   AnnotationFeatureSnapshot,
   CheckResultSnapshot,
 } from '@apollo-annotation/mst'
-import ObjectID from 'bson-objectid'
+// import ObjectID from 'bson-objectid'
 
-enum STOP_CODONS {
-  'TAG',
-  'TAA',
-  'TGA',
-}
+// enum STOP_CODONS {
+//   'TAG',
+//   'TAA',
+//   'TGA',
+// }
 
-const iupacComplements: Record<string, string | undefined> = {
-  G: 'C',
-  A: 'T',
-  T: 'A',
-  C: 'G',
-  R /* G or A */: 'Y',
-  Y /* T or C */: 'R',
-  M /* A or C */: 'K',
-  K /* G or T */: 'M',
-  S /* G or C */: 'S',
-  W /* A or T */: 'W',
-  H /* A or C or T */: 'D',
-  B /* G or T or C */: 'V',
-  V /* G or C or A */: 'B',
-  D /* G or A or T */: 'H',
-  N /* G or A or T or C */: 'N',
-}
+// const iupacComplements: Record<string, string | undefined> = {
+//   G: 'C',
+//   A: 'T',
+//   T: 'A',
+//   C: 'G',
+//   R /* G or A */: 'Y',
+//   Y /* T or C */: 'R',
+//   M /* A or C */: 'K',
+//   K /* G or T */: 'M',
+//   S /* G or C */: 'S',
+//   W /* A or T */: 'W',
+//   H /* A or C or T */: 'D',
+//   B /* G or T or C */: 'V',
+//   V /* G or C or A */: 'B',
+//   D /* G or A or T */: 'H',
+//   N /* G or A or T or C */: 'N',
+// }
 
-function reverseComplement(dna: string): string {
-  const complement: string[] = []
-  for (const nt of dna) {
-    const rc = iupacComplements[nt.toUpperCase()]
-    if (rc === undefined) {
-      throw new TypeError(`Cannot complement nucleotide: "${nt}"`)
-    }
-    if (nt === nt.toLowerCase()) {
-      complement.push(rc.toLowerCase())
-    } else {
-      complement.push(rc)
-    }
-  }
-  return complement.reverse().join('')
-}
+// function reverseComplement(dna: string): string {
+//   const complement: string[] = []
+//   for (const nt of dna) {
+//     const rc = iupacComplements[nt.toUpperCase()]
+//     if (rc === undefined) {
+//       throw new TypeError(`Cannot complement nucleotide: "${nt}"`)
+//     }
+//     if (nt === nt.toLowerCase()) {
+//       complement.push(rc.toLowerCase())
+//     } else {
+//       complement.push(rc)
+//     }
+//   }
+//   return complement.reverse().join('')
+// }
 
-async function getSequenceFromSingleFeature(
-  feature: AnnotationFeatureSnapshot,
-  getSequence: (start: number, end: number) => Promise<string>,
-) {
-  let seq = ''
-  if (
-    feature.discontinuousLocations !== undefined &&
-    feature.discontinuousLocations.length > 0
-  ) {
-    for (const loc of feature.discontinuousLocations) {
-      seq = seq + (await getSequence(loc.start, loc.end))
-    }
-  } else {
-    seq = await getSequence(feature.start, feature.end)
-  }
-  if (feature.strand === -1) {
-    return reverseComplement(seq)
-  }
-  return seq
-}
+// async function getSequenceFromSingleFeature(
+//   feature: AnnotationFeatureSnapshot,
+//   getSequence: (start: number, end: number) => Promise<string>,
+// ) {
+//   let seq = ''
+//   if (
+//     feature.discontinuousLocations !== undefined &&
+//     feature.discontinuousLocations.length > 0
+//   ) {
+//     for (const loc of feature.discontinuousLocations) {
+//       seq = seq + (await getSequence(loc.start, loc.end))
+//     }
+//   } else {
+//     seq = await getSequence(feature.start, feature.end)
+//   }
+//   if (feature.strand === -1) {
+//     return reverseComplement(seq)
+//   }
+//   return seq
+// }
 
-async function getSequenceFromMultipleFeatures(
-  features: AnnotationFeatureSnapshot[],
-  getSequence: (start: number, end: number) => Promise<string>,
-) {
-  const strands = features.map((feature) => feature.strand)
-  if (!strands.every((strand) => strand === strands[0])) {
-    throw new Error(
-      `Strands do not match in features: "${features
-        .map((f) => f._id)
-        .join(', ')}"`,
-    )
-  }
-  let seq = ''
-  for (const feature of features) {
-    seq = seq + (await getSequence(feature.start, feature.end))
-  }
-  if (strands[0] === -1) {
-    return reverseComplement(seq)
-  }
-  return seq
-}
+// async function getSequenceFromMultipleFeatures(
+//   features: AnnotationFeatureSnapshot[],
+//   getSequence: (start: number, end: number) => Promise<string>,
+// ) {
+//   const strands = features.map((feature) => feature.strand)
+//   if (!strands.every((strand) => strand === strands[0])) {
+//     throw new Error(
+//       `Strands do not match in features: "${features
+//         .map((f) => f._id)
+//         .join(', ')}"`,
+//     )
+//   }
+//   let seq = ''
+//   for (const feature of features) {
+//     seq = seq + (await getSequence(feature.start, feature.end))
+//   }
+//   if (strands[0] === -1) {
+//     return reverseComplement(seq)
+//   }
+//   return seq
+// }
 
-function splitSequenceInCodons(cds: string): string[] {
-  const codons: string[] = []
-  for (let i = 0; i <= cds.length - 3; i += 3) {
-    codons.push(cds.slice(i, i + 3))
-  }
-  return codons
-}
+// function splitSequenceInCodons(cds: string): string[] {
+//   const codons: string[] = []
+//   for (let i = 0; i <= cds.length - 3; i += 3) {
+//     codons.push(cds.slice(i, i + 3))
+//   }
+//   return codons
+// }
 
-function getOriginalCodonLocation(
-  feature: AnnotationFeatureSnapshot | AnnotationFeatureSnapshot[],
-  index: number,
-): [number, number] {
-  let lengthToStart = index * 3
-  let lengthToEnd = lengthToStart + 3
-  if (Array.isArray(feature)) {
-    let startLocation: number | undefined = undefined,
-      endLocation: number | undefined = undefined
-    for (const f of feature) {
-      const featureLength = f.end - f.start
-      if (startLocation === undefined && featureLength > lengthToStart) {
-        startLocation = f.start + lengthToStart
-      } else {
-        lengthToStart -= featureLength
-      }
-      if (endLocation === undefined && featureLength > lengthToEnd) {
-        endLocation = f.start + lengthToEnd
-      } else {
-        lengthToEnd -= featureLength
-      }
-      if (startLocation !== undefined && endLocation !== undefined) {
-        return [startLocation, endLocation]
-      }
-    }
-    throw new Error('Could not determine original CDS location')
-  } else {
-    if (
-      feature.discontinuousLocations !== undefined &&
-      feature.discontinuousLocations.length > 0
-    ) {
-      let startLocation: number | undefined = undefined,
-        endLocation: number | undefined = undefined
-      for (const loc of feature.discontinuousLocations) {
-        const locLength = loc.end - loc.start
-        if (startLocation === undefined && locLength > lengthToStart) {
-          startLocation = loc.start + lengthToStart
-        } else {
-          lengthToStart -= locLength
-        }
-        if (endLocation === undefined && locLength > lengthToEnd) {
-          endLocation = loc.start + lengthToEnd
-        } else {
-          lengthToEnd -= locLength
-        }
-        if (startLocation !== undefined && endLocation !== undefined) {
-          return [startLocation, endLocation]
-        }
-      }
-      throw new Error('Could not determine original CDS location')
-    } else {
-      return [feature.start + lengthToStart, feature.start + lengthToEnd]
-    }
-  }
-}
+// function getOriginalCodonLocation(
+//   feature: AnnotationFeatureSnapshot | AnnotationFeatureSnapshot[],
+//   index: number,
+// ): [number, number] {
+//   let lengthToStart = index * 3
+//   let lengthToEnd = lengthToStart + 3
+//   if (Array.isArray(feature)) {
+//     let startLocation: number | undefined = undefined,
+//       endLocation: number | undefined = undefined
+//     for (const f of feature) {
+//       const featureLength = f.end - f.start
+//       if (startLocation === undefined && featureLength > lengthToStart) {
+//         startLocation = f.start + lengthToStart
+//       } else {
+//         lengthToStart -= featureLength
+//       }
+//       if (endLocation === undefined && featureLength > lengthToEnd) {
+//         endLocation = f.start + lengthToEnd
+//       } else {
+//         lengthToEnd -= featureLength
+//       }
+//       if (startLocation !== undefined && endLocation !== undefined) {
+//         return [startLocation, endLocation]
+//       }
+//     }
+//     throw new Error('Could not determine original CDS location')
+//   } else {
+//     if (
+//       feature.discontinuousLocations !== undefined &&
+//       feature.discontinuousLocations.length > 0
+//     ) {
+//       let startLocation: number | undefined = undefined,
+//         endLocation: number | undefined = undefined
+//       for (const loc of feature.discontinuousLocations) {
+//         const locLength = loc.end - loc.start
+//         if (startLocation === undefined && locLength > lengthToStart) {
+//           startLocation = loc.start + lengthToStart
+//         } else {
+//           lengthToStart -= locLength
+//         }
+//         if (endLocation === undefined && locLength > lengthToEnd) {
+//           endLocation = loc.start + lengthToEnd
+//         } else {
+//           lengthToEnd -= locLength
+//         }
+//         if (startLocation !== undefined && endLocation !== undefined) {
+//           return [startLocation, endLocation]
+//         }
+//       }
+//       throw new Error('Could not determine original CDS location')
+//     } else {
+//       return [feature.start + lengthToStart, feature.start + lengthToEnd]
+//     }
+//   }
+// }
 
-async function checkCDS(
-  feature: AnnotationFeatureSnapshot | AnnotationFeatureSnapshot[],
-  getSequence: (start: number, end: number) => Promise<string>,
-): Promise<CheckResultSnapshot[]> {
-  const checkResults: CheckResultSnapshot[] = []
-  let _id: string,
-    ids: string[],
-    start: number,
-    end: number,
-    refSeq: string,
-    sequence: string
-  if (Array.isArray(feature)) {
-    sequence = await getSequenceFromMultipleFeatures(feature, getSequence)
-    ids = feature.map((f) => f._id)
-    _id = ids.join(',')
-    ;[{ refSeq, start }] = feature
-    const lastFeature = feature.at(-1)
-    if (!lastFeature) {
-      throw new Error('Zero-length feature array encountered')
-    }
-    ;({ end } = lastFeature)
-  } else {
-    sequence = await getSequenceFromSingleFeature(feature, getSequence)
-    ;({ _id, end, refSeq, start } = feature)
-    ids = [_id]
-  }
-  const codons = splitSequenceInCodons(sequence)
-  if (sequence.length % 3 === 0) {
-    const lastCodon = codons.pop() // Last codon is supposed to be a stop
-    if (!lastCodon) {
-      throw new Error(`No sequence found for feature "${_id}"`)
-    }
-    if (!(lastCodon.toUpperCase() in STOP_CODONS)) {
-      checkResults.push({
-        _id: new ObjectID().toHexString(),
-        name: 'MissingStopCodonCheck',
-        ids,
-        refSeq: refSeq.toString(),
-        start: end,
-        end,
-        message: `Feature "${_id}" is missing a stop codon`,
-      })
-    }
-  } else {
-    checkResults.push({
-      _id: new ObjectID().toHexString(),
-      name: 'MultipleOfThreeCheck',
-      ids,
-      refSeq: refSeq.toString(),
-      start,
-      end,
-      message: `The coding sequence for feature "${_id}" is not a multiple of three`,
-    })
-  }
-  for (const [idx, codon] of codons.entries()) {
-    const [codonStart, codonEnd] = getOriginalCodonLocation(feature, idx)
-    if (codon.toUpperCase() in STOP_CODONS) {
-      checkResults.push({
-        _id: new ObjectID().toHexString(),
-        name: 'InternalStopCodonCheck',
-        ids,
-        refSeq: refSeq.toString(),
-        start: codonStart,
-        end: codonEnd,
-        message: `The coding sequence for feature "${_id}" has an internal stop codon`,
-      })
-    }
-  }
-  return checkResults
-}
+// async function checkCDS(
+//   feature: AnnotationFeatureSnapshot | AnnotationFeatureSnapshot[],
+//   getSequence: (start: number, end: number) => Promise<string>,
+// ): Promise<CheckResultSnapshot[]> {
+//   const checkResults: CheckResultSnapshot[] = []
+//   let _id: string,
+//     ids: string[],
+//     start: number,
+//     end: number,
+//     refSeq: string,
+//     sequence: string
+//   if (Array.isArray(feature)) {
+//     sequence = await getSequenceFromMultipleFeatures(feature, getSequence)
+//     ids = feature.map((f) => f._id)
+//     _id = ids.join(',')
+//     ;[{ refSeq, start }] = feature
+//     const lastFeature = feature.at(-1)
+//     if (!lastFeature) {
+//       throw new Error('Zero-length feature array encountered')
+//     }
+//     ;({ end } = lastFeature)
+//   } else {
+//     sequence = await getSequenceFromSingleFeature(feature, getSequence)
+//     ;({ _id, end, refSeq, start } = feature)
+//     ids = [_id]
+//   }
+//   const codons = splitSequenceInCodons(sequence)
+//   if (sequence.length % 3 === 0) {
+//     const lastCodon = codons.pop() // Last codon is supposed to be a stop
+//     if (!lastCodon) {
+//       throw new Error(`No sequence found for feature "${_id}"`)
+//     }
+//     if (!(lastCodon.toUpperCase() in STOP_CODONS)) {
+//       checkResults.push({
+//         _id: new ObjectID().toHexString(),
+//         name: 'MissingStopCodonCheck',
+//         ids,
+//         refSeq: refSeq.toString(),
+//         start: end,
+//         end,
+//         message: `Feature "${_id}" is missing a stop codon`,
+//       })
+//     }
+//   } else {
+//     checkResults.push({
+//       _id: new ObjectID().toHexString(),
+//       name: 'MultipleOfThreeCheck',
+//       ids,
+//       refSeq: refSeq.toString(),
+//       start,
+//       end,
+//       message: `The coding sequence for feature "${_id}" is not a multiple of three`,
+//     })
+//   }
+//   for (const [idx, codon] of codons.entries()) {
+//     const [codonStart, codonEnd] = getOriginalCodonLocation(feature, idx)
+//     if (codon.toUpperCase() in STOP_CODONS) {
+//       checkResults.push({
+//         _id: new ObjectID().toHexString(),
+//         name: 'InternalStopCodonCheck',
+//         ids,
+//         refSeq: refSeq.toString(),
+//         start: codonStart,
+//         end: codonEnd,
+//         message: `The coding sequence for feature "${_id}" has an internal stop codon`,
+//       })
+//     }
+//   }
+//   return checkResults
+// }
 
 export class CDSCheck extends Check {
   name = 'CDSCheck'
@@ -229,47 +229,49 @@ export class CDSCheck extends Check {
   default = true
 
   async checkFeature(
-    feature: AnnotationFeatureSnapshot,
-    getSequence: (start: number, end: number) => Promise<string>,
+    _feature: AnnotationFeatureSnapshot,
+    _getSequence: (start: number, end: number) => Promise<string>,
   ): Promise<CheckResultSnapshot[]> {
-    if (feature.type === 'CDS') {
-      return checkCDS(feature, getSequence)
-    }
+    await Promise.resolve()
+    return []
+    // if (feature.type === 'CDS') {
+    //   return checkCDS(feature, getSequence)
+    // }
 
-    if (!feature.children) {
-      return []
-    }
+    // if (!feature.children) {
+    //   return []
+    // }
 
-    if (feature.type !== 'mRNA') {
-      const checkResults: CheckResultSnapshot[] = []
-      for (const child of Object.values(feature.children)) {
-        checkResults.push(...(await this.checkFeature(child, getSequence)))
-      }
-      return checkResults
-    }
+    // if (feature.type !== 'mRNA') {
+    //   const checkResults: CheckResultSnapshot[] = []
+    //   for (const child of Object.values(feature.children)) {
+    //     checkResults.push(...(await this.checkFeature(child, getSequence)))
+    //   }
+    //   return checkResults
+    // }
 
-    const cdsChildren = Object.values(feature.children).filter(
-      (child) => child.type === 'CDS',
-    )
-    if (cdsChildren.length === 0) {
-      throw new Error(`mRNA "${feature._id}" has no CDS children`)
-    }
-    const cdsChildrenWithDiscontinuousLocations = cdsChildren.filter(
-      (child) =>
-        child.discontinuousLocations && child.discontinuousLocations.length > 0,
-    )
-    if (cdsChildrenWithDiscontinuousLocations.length === 0) {
-      return checkCDS(cdsChildren, getSequence)
-    }
-    if (cdsChildrenWithDiscontinuousLocations.length === cdsChildren.length) {
-      const checkResults: CheckResultSnapshot[] = []
-      for (const child of cdsChildren) {
-        checkResults.push(...(await this.checkFeature(child, getSequence)))
-      }
-      return checkResults
-    }
-    throw new Error(
-      `Mix of CDS with and without discontinuous locations found in mRNA "${feature._id}"`,
-    )
+    // const cdsChildren = Object.values(feature.children).filter(
+    //   (child) => child.type === 'CDS',
+    // )
+    // if (cdsChildren.length === 0) {
+    //   throw new Error(`mRNA "${feature._id}" has no CDS children`)
+    // }
+    // const cdsChildrenWithDiscontinuousLocations = cdsChildren.filter(
+    //   (child) =>
+    //     child.discontinuousLocations && child.discontinuousLocations.length > 0,
+    // )
+    // if (cdsChildrenWithDiscontinuousLocations.length === 0) {
+    //   return checkCDS(cdsChildren, getSequence)
+    // }
+    // if (cdsChildrenWithDiscontinuousLocations.length === cdsChildren.length) {
+    //   const checkResults: CheckResultSnapshot[] = []
+    //   for (const child of cdsChildren) {
+    //     checkResults.push(...(await this.checkFeature(child, getSequence)))
+    //   }
+    //   return checkResults
+    // }
+    // throw new Error(
+    //   `Mix of CDS with and without discontinuous locations found in mRNA "${feature._id}"`,
+    // )
   }
 }

package/src/Common/jwtPayload.ts

@@ -3,7 +3,7 @@ import jwtDecode from 'jwt-decode'
 export interface JWTPayload {
   username: string
   email: string
-  role?: 'admin' | 'user' | 'readOnly'
+  role?: 'admin' | 'user' | 'readOnly' | 'none'
   id: string
 }
 

package/src/GFF3/gff3ToAnnotationFeature.test.ts

@@ -0,0 +1,49 @@
+/* eslint-disable @typescript-eslint/no-floating-promises */
+import { strict as assert } from 'node:assert'
+import { describe, it } from 'node:test'
+import gff from '@gmod/gff'
+
+import { gff3ToAnnotationFeature } from './gff3ToAnnotationFeature'
+import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+
+const testCases: [string, string, AnnotationFeatureSnapshot][] = [
+  [
+    'a feature with no children',
+    'ctgA	example	remark	1000	2000	.	.	.	Name=Remark:hga;Alias=hga\n',
+    {
+      _id: '66c51f3e002c683eaf98a223',
+      refSeq: 'ctgA',
+      type: 'remark',
+      min: 999,
+      max: 2000,
+      attributes: {
+        gff_source: ['example'],
+        gff_name: ['Remark:hga'],
+        gff_alias: ['hga'],
+      },
+    },
+  ],
+]
+
+function compareFeatures(
+  feature1: AnnotationFeatureSnapshot,
+  feature2: AnnotationFeatureSnapshot,
+) {
+  assert.deepEqual(
+    { ...feature1, _id: undefined },
+    { ...feature2, _id: undefined },
+  )
+}
+
+describe('gff3ToAnnotationFeature', () => {
+  for (const testCase of testCases) {
+    const [description, featureLine, convertedFeature] = testCase
+    it(`converts ${description}`, () => {
+      const gff3Feature = gff.parseStringSync(featureLine, {
+        parseSequences: false,
+      })
+      const feature = gff3ToAnnotationFeature(gff3Feature[0])
+      compareFeatures(convertedFeature, feature)
+    })
+  }
+})