@apollo-annotation/schemas 0.1.11

package/README.md

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+# apollo-schemas

package/package.json

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+{
+  "name": "@apollo-annotation/schemas",
+  "version": "0.1.11",
+  "main": "./dist/index.js",
+  "scripts": {
+    "build": "tsc"
+  },
+  "dependencies": {
+    "@nestjs/common": "^10.1.0",
+    "@nestjs/core": "^10.1.0",
+    "@nestjs/mongoose": "^10.0.0",
+    "mongoose": "^6.12.0",
+    "reflect-metadata": "^0.1.13",
+    "regenerator-runtime": "^0.13.9",
+    "rxjs": "^7.4.0",
+    "tslib": "^2.3.1"
+  },
+  "devDependencies": {
+    "@apollo-annotation/mst": "^0.1.11",
+    "@types/node": "^18.14.2",
+    "typescript": "^5.1.6"
+  },
+  "publishConfig": {
+    "access": "public"
+  }
+}

package/src/assembly.schema.ts

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+import { Prop, Schema, SchemaFactory } from '@nestjs/mongoose'
+import { Schema as MongooseSchema, Types } from 'mongoose'
+
+export type AssemblyDocument = Assembly & Document
+
+@Schema()
+export class Assembly {
+  @Prop({ required: true })
+  name: string
+
+  @Prop()
+  displayName: string
+
+  @Prop({ type: [String] })
+  aliases: string[]
+
+  @Prop()
+  description: string
+
+  @Prop()
+  status: number
+
+  @Prop()
+  user: string
+
+  @Prop({ type: { fa: String, fai: String, gzi: String } })
+  externalLocation: { fa: string; fai: string; gzi?: string }
+
+  @Prop({ type: [{ type: MongooseSchema.Types.ObjectId, ref: 'Check' }] })
+  checks: Types.ObjectId[]
+}
+
+export const AssemblySchema = SchemaFactory.createForClass(Assembly)

package/src/change.schema.ts

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+import { Prop, Schema, SchemaFactory } from '@nestjs/mongoose'
+import { Document, Schema as MongooseSchema } from 'mongoose'
+
+export type ChangeDocument = Change & Document
+
+@Schema({ timestamps: true })
+export class Change {
+  @Prop({ type: MongooseSchema.Types.ObjectId }) // We cannot use FK anymore because assembly is deleted outside of transaction concept
+  assembly: MongooseSchema.Types.ObjectId
+
+  @Prop({ required: true })
+  typeName: string
+
+  @Prop({ required: true, index: true })
+  changedIds: string[] // featureIds
+
+  @Prop({ type: JSON })
+  changes: unknown // serialized change
+
+  @Prop({ type: MongooseSchema.Types.ObjectId, ref: 'Change' })
+  reverts: Change
+
+  @Prop({ required: true, index: true })
+  user: string
+
+  @Prop()
+  sequence: number
+}
+
+export const ChangeSchema = SchemaFactory.createForClass(Change)

package/src/check.schema.ts

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+import { Prop, Schema, SchemaFactory } from '@nestjs/mongoose'
+import { HydratedDocument, Types } from 'mongoose'
+
+export interface CheckDocument extends HydratedDocument<Check> {
+  createdAt: Date
+  updatedAt: Date
+}
+
+@Schema({ timestamps: true })
+export class Check {
+  // Don't make this a @Prop since _id is already on a MongoDB document
+  _id: Types.ObjectId
+
+  @Prop()
+  name: string
+
+  @Prop()
+  default: boolean
+
+  @Prop()
+  version: number
+}
+export const CheckSchema = SchemaFactory.createForClass(Check)

package/src/checkResult.schema.ts

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+import type { CheckResultSnapshot } from '@apollo-annotation/mst'
+import { Prop, Schema, SchemaFactory } from '@nestjs/mongoose'
+import { HydratedDocument, Schema as MongooseSchema, Types } from 'mongoose'
+
+export type CheckResultDocument = HydratedDocument<CheckResult>
+
+@Schema()
+export class CheckResult
+  implements Omit<CheckResultSnapshot, '_id' | 'ids' | 'refSeq'>
+{
+  // Don't make this a @Prop since _id is already on a MongoDB document
+  _id: Types.ObjectId
+
+  @Prop()
+  name: string
+
+  @Prop({ type: [MongooseSchema.Types.ObjectId], required: true, index: true })
+  ids: Types.ObjectId[]
+
+  @Prop({
+    required: true,
+    index: true,
+    type: MongooseSchema.Types.ObjectId,
+    ref: 'RefSeq',
+  })
+  refSeq: Types.ObjectId
+
+  @Prop({ required: true })
+  start: number
+
+  @Prop({ required: true })
+  end: number
+
+  @Prop({ default: false })
+  ignored: boolean
+
+  @Prop()
+  message: string
+}
+export const CheckResultSchema = SchemaFactory.createForClass(CheckResult)
+
+CheckResultSchema.index({ refSeq: 1, start: 1 })
+CheckResultSchema.index({ refSeq: 1, end: 1 })

package/src/counter.schema.ts

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+import { Prop, Schema, SchemaFactory } from '@nestjs/mongoose'
+import { Document } from 'mongoose'
+
+export type CounterDocument = Counter & Document
+
+@Schema()
+export class Counter {
+  @Prop({ default: 0, required: true })
+  sequenceValue: number
+
+  @Prop({ required: true })
+  id: string
+}
+
+export const CounterSchema = SchemaFactory.createForClass(Counter)

package/src/export.schema.ts

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+import { Prop, Schema, SchemaFactory } from '@nestjs/mongoose'
+import { Document, Schema as MongooseSchema, Types } from 'mongoose'
+
+export type ExportDocument = Export & Document
+
+@Schema({ timestamps: true })
+export class Export {
+  @Prop({
+    type: MongooseSchema.Types.ObjectId,
+    ref: 'Assembly',
+    required: true,
+  })
+  assembly: Types.ObjectId
+}
+
+export const ExportSchema = SchemaFactory.createForClass(Export)
+
+ExportSchema.index({ createdAt: 1 }, { expireAfterSeconds: 300 })

package/src/feature.schema.ts

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+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import { Prop, Schema, SchemaFactory } from '@nestjs/mongoose'
+import { HydratedDocument, Schema as MongooseSchema, Types } from 'mongoose'
+
+export interface FeatureDocument extends HydratedDocument<Feature> {
+  createdAt?: Date
+  updatedAt?: Date
+}
+
+@Schema({ timestamps: true })
+export class Feature
+  implements Omit<AnnotationFeatureSnapshot, '_id' | 'children' | 'refSeq'>
+{
+  // Don't make this a @Prop since _id is already on a MongoDB document
+  _id: Types.ObjectId
+
+  // Here we store feature ID if it's given in attributes, otherwise gffId = _id as string
+  @Prop()
+  gffId: string
+
+  @Prop({
+    required: true,
+    index: true,
+    type: MongooseSchema.Types.ObjectId,
+    ref: 'RefSeq',
+  })
+  refSeq: Types.ObjectId
+
+  @Prop({ type: [String], required: true, index: true })
+  allIds: string[]
+
+  @Prop({ required: true })
+  type: string
+
+  @Prop({ required: true })
+  start: number
+
+  @Prop({ required: true })
+  end: number
+
+  @Prop()
+  discontinuousLocations?: { start: number; end: number; phase?: 0 | 1 | 2 }[]
+
+  @Prop()
+  strand?: 1 | -1
+
+  @Prop()
+  score?: number
+
+  @Prop()
+  phase?: 0 | 1 | 2
+
+  @Prop({ type: Map, of: [String] })
+  attributes?: Record<string, string[]>
+
+  // This is not a @Prop because it needs to be a recursive reference to the
+  // schema, which is done with Schema.add below
+  children?: Map<string, Feature>
+
+  @Prop()
+  status: number
+
+  @Prop()
+  user: string
+}
+export const FeatureSchema = SchemaFactory.createForClass(Feature)
+
+FeatureSchema.add({ children: { type: Map, of: FeatureSchema } })
+
+FeatureSchema.index({ refSeq: 1, start: 1 })
+FeatureSchema.index({ refSeq: 1, end: 1 })
+FeatureSchema.index({ '$**': 'text' })

package/src/file.schema.ts

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+import { Prop, Schema, SchemaFactory } from '@nestjs/mongoose'
+import { Document } from 'mongoose'
+
+export type FileDocument = File & Document
+
+@Schema()
+export class File {
+  @Prop({ required: true })
+  basename: string
+
+  @Prop({ required: true })
+  checksum: string
+
+  @Prop({ required: true, enum: ['text/x-gff3', 'text/x-fasta'] })
+  type: 'text/x-gff3' | 'text/x-fasta'
+}
+
+export const FileSchema = SchemaFactory.createForClass(File)

package/src/index.ts

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+export * from './assembly.schema'
+export * from './change.schema'
+export * from './check.schema'
+export * from './checkResult.schema'
+export * from './counter.schema'
+export * from './export.schema'
+export * from './feature.schema'
+export * from './file.schema'
+export * from './refSeq.schema'
+export * from './refSeqChunk.schema'
+export * from './user.schema'

package/src/refSeq.schema.ts

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+import { Prop, Schema, SchemaFactory } from '@nestjs/mongoose'
+import { Document, Schema as MongooseSchema, Types } from 'mongoose'
+
+import { Assembly } from './assembly.schema'
+
+export type RefSeqDocument = RefSeq & Document
+
+@Schema()
+export class RefSeq {
+  // Don't make this a @Prop since _id is already on a MongoDB document
+  _id: Types.ObjectId
+
+  @Prop({
+    type: MongooseSchema.Types.ObjectId,
+    ref: 'Assembly',
+    required: true,
+    index: true,
+  })
+  assembly: Assembly
+
+  @Prop({ required: true })
+  name: string
+
+  @Prop()
+  description: string
+
+  @Prop({ required: true })
+  length: number
+
+  @Prop({ default: 256 * 1024 /* 256 KiB */ })
+  chunkSize: number
+
+  @Prop()
+  status: number
+
+  @Prop()
+  user: string
+}
+
+export const RefSeqSchema = SchemaFactory.createForClass(RefSeq)

package/src/refSeqChunk.schema.ts

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+import { Prop, Schema, SchemaFactory } from '@nestjs/mongoose'
+import { Document, Schema as MongooseSchema } from 'mongoose'
+
+import { RefSeq } from './refSeq.schema'
+
+export type RefSeqChunkDocument = RefSeqChunk & Document
+
+@Schema()
+export class RefSeqChunk {
+  @Prop({
+    type: MongooseSchema.Types.ObjectId,
+    ref: 'RefSeq',
+    required: true,
+    index: true,
+  })
+  refSeq: RefSeq
+
+  @Prop({ required: true })
+  n: number
+
+  @Prop({ required: true })
+  sequence: string
+
+  @Prop()
+  status: number
+
+  @Prop()
+  user: string
+}
+
+export const RefSeqChunkSchema = SchemaFactory.createForClass(RefSeqChunk)

package/src/user.schema.ts

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+import { Prop, Schema, SchemaFactory } from '@nestjs/mongoose'
+import { Document } from 'mongoose'
+
+export type UserDocument = User & Document
+
+export type Role = 'readOnly' | 'admin' | 'user'
+
+@Schema({ timestamps: true })
+export class User {
+  @Prop({ required: true })
+  username: string
+
+  @Prop({ required: true, unique: true })
+  email: string
+
+  @Prop({ type: String, enum: ['readOnly', 'admin', 'user'] })
+  role: Role
+}
+
+export const UserSchema = SchemaFactory.createForClass(User)

package/tsconfig.json

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+{
+  "extends": "../../tsconfig.json",
+  "compilerOptions": {
+    "composite": true,
+    "incremental": true,
+    "outDir": "./dist",
+    "rootDir": "./src",
+    "target": "ES2022",
+    "lib": ["ES2022", "DOM"],
+    "module": "CommonJS",
+    "tsBuildInfoFile": "./dist/tsconfig.tsbuildinfo",
+    "experimentalDecorators": true,
+    "emitDecoratorMetadata": true,
+    "strictPropertyInitialization": false,
+  },
+  "include": ["./src"],
+}