@apollo-annotation/common 0.3.12 → 1.0.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/common",
-  "version": "0.3.12",
+  "version": "1.0.0",
   "repository": {
     "type": "git",
     "url": "https://github.com/GMOD/Apollo3.git",
@@ -13,13 +13,13 @@
     "build": "tsc --build"
   },
   "dependencies": {
-    "@apollo-annotation/schemas": "^0.3.12",
+    "@apollo-annotation/schemas": "^1.0.0",
     "@jbrowse/core": "^4.1.1",
     "bson-objectid": "^2.0.4",
     "tslib": "^2.3.1"
   },
   "devDependencies": {
-    "@apollo-annotation/mst": "^0.3.12",
+    "@apollo-annotation/mst": "^1.0.0",
     "@gmod/gff": "^2.1.0",
     "@nestjs/common": "^10.1.0",
     "@nestjs/core": "^10.1.0",

package/src/Change.ts

@@ -1,57 +1,31 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
-import type {
-  AnnotationFeature,
-  AnnotationFeatureSnapshot,
-  ApolloAssemblyI,
-  BackendDriverType,
-  CheckResultI,
-  CheckResultSnapshot,
-} from '@apollo-annotation/mst'
-import type { AppRootModel, Region } from '@jbrowse/core/util'
+import type { LoggerService } from '@nestjs/common'
 
 import { changeRegistry } from './ChangeTypeRegistry.js'
-import {
-  type BackendDataStore,
-  Operation,
-  type OperationOptions,
-  type SerializedOperation,
-} from './Operation.js'
 
-export interface ClientDataStore {
-  typeName: 'Client'
-  assemblies: Map<string | number, ApolloAssemblyI>
-  checkResults: Map<string | number, CheckResultI>
-  internetAccounts: AppRootModel['internetAccounts']
-  getInternetAccount(
-    assemblyName?: string,
-    internetAccountId?: string,
-  ): AppRootModel['internetAccounts'][0]
-  loadFeatures(regions: Region[]): Promise<void>
-  loadRefSeq(regions: Region[]): void
-  getFeature(featureId: string): AnnotationFeature | undefined
-  addFeature(assemblyId: string, feature: AnnotationFeatureSnapshot): void
-  deleteFeature(featureId: string): void
-  deleteAssembly(assemblyId: string): void
-  addCheckResults(checkResults: CheckResultSnapshot[]): void
-  addAssembly(
-    assemblyId: string,
-    backendDriverType?: BackendDriverType,
-  ): ApolloAssemblyI
-  clearCheckResults(): void
+export interface SerializedChange {
+  typeName: string
 }
 
-export type SerializedChange = SerializedOperation
-export type ChangeOptions = OperationOptions
-
-export type DataStore = BackendDataStore | ClientDataStore
+export interface ChangeOptions {
+  logger: LoggerService
+}
 
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 export function isChange(thing: any): thing is Change {
-  return (thing as Change).executeOnClient !== undefined
+  return (thing as Change).getInverse !== undefined
 }
 
-export abstract class Change extends Operation {
+export abstract class Change {
+  protected logger: LoggerService
+  abstract typeName: string
+
+  constructor(json: SerializedChange, options?: ChangeOptions) {
+    this.logger = options?.logger ?? console
+  }
+
+  abstract toJSON(): SerializedChange
+
   /**
    * If a non-empty string, a snackbar will display in JBrowse with this message
    * when a successful response is received from the server.
@@ -61,25 +35,10 @@ export abstract class Change extends Operation {
     return ''
   }
 
-  static fromJSON(json: SerializedOperation, options?: ChangeOptions): Change {
+  static fromJSON(json: SerializedChange, options?: ChangeOptions): Change {
     const ChangeType = changeRegistry.getChangeType(json.typeName)
     return new ChangeType(json, options?.logger && { logger: options.logger })
   }
 
-  async execute(backend: DataStore): Promise<unknown> {
-    const backendType = backend.typeName
-    if (backendType === 'LocalGFF3' || backendType === 'Server') {
-      return super.execute(backend)
-    }
-    if (backendType === 'Client') {
-      return this.executeOnClient(backend)
-    }
-    throw new Error(
-      `no change implementation for backend type '${backendType}'`,
-    )
-  }
-
-  abstract executeOnClient(backend: ClientDataStore): Promise<void>
-
   abstract getInverse(): Change
 }

package/src/Validation.ts

@@ -4,7 +4,7 @@ import type { ExecutionContext } from '@nestjs/common'
 import type { Reflector } from '@nestjs/core'
 import type { ClientSession, Model } from 'mongoose'
 
-import type { Change, ClientDataStore } from './Change.js'
+import type { Change } from './Change.js'
 
 export interface Context {
   context: ExecutionContext
@@ -26,10 +26,7 @@ export abstract class Validation {
     return { validationName: this.name }
   }
 
-  async frontendPostValidate(
-    _change: Change,
-    _dataStore: ClientDataStore,
-  ): Promise<ValidationResult> {
+  async frontendPostValidate(_change: Change): Promise<ValidationResult> {
     return { validationName: this.name }
   }
 

package/src/index.ts

@@ -5,6 +5,4 @@ export * from './ChangeTypeRegistry.js'
 export * from './Check.js'
 export * from './CheckRegistry.js'
 export * from './FeatureChange.js'
-export * from './Operation.js'
-export * from './OperationTypeRegistry.js'
 export * from './Validation.js'

package/dist/Operation.d.ts

@@ -1,64 +0,0 @@
-import type { FileHandle } from 'node:fs/promises';
-import type { AssemblyDocument, CheckDocument, FeatureDocument, FileDocument, JBrowseConfigDocument, RefSeqChunkDocument, RefSeqDocument, UserDocument } from '@apollo-annotation/schemas';
-import type { GFF3Feature } from '@gmod/gff';
-import type { LoggerService } from '@nestjs/common';
-import type { GenericFilehandle } from 'generic-filehandle2';
-import type { ClientSession, Model } from 'mongoose';
-export interface LocalGFF3DataStore {
-    typeName: 'LocalGFF3';
-    gff3Handle: FileHandle;
-}
-interface CreateFileDto {
-    readonly _id: string;
-    readonly basename: string;
-    readonly checksum: string;
-    readonly type: 'text/x-gff3' | 'text/x-fasta';
-    readonly user: string;
-}
-export interface ServerDataStore {
-    typeName: 'Server';
-    featureModel: Model<FeatureDocument>;
-    assemblyModel: Model<AssemblyDocument>;
-    refSeqModel: Model<RefSeqDocument>;
-    refSeqChunkModel: Model<RefSeqChunkDocument>;
-    checkModel: Model<CheckDocument>;
-    fileModel: Model<FileDocument>;
-    userModel: Model<UserDocument>;
-    jbrowseConfigModel: Model<JBrowseConfigDocument>;
-    session: ClientSession;
-    filesService: {
-        getFileStream(file: FileDocument): ReadableStream<Uint8Array>;
-        getFileHandle(file: FileDocument): GenericFilehandle;
-        parseGFF3(stream: ReadableStream<Uint8Array>, parseOptions?: {
-            bufferSize?: number;
-            errorCallback?(errorMessage: string): void;
-        }): ReadableStream<GFF3Feature>;
-        create(createFileDto: CreateFileDto): void;
-        remove(id: string): void;
-    };
-    pluginsService: {
-        evaluateExtensionPoint(extensionPointName: string, extendee: unknown, props?: Record<string, unknown>): void;
-    };
-    counterService: {
-        getNextSequenceValue(sequenceName: string): Promise<number>;
-    };
-    user: string;
-}
-export interface SerializedOperation {
-    typeName: string;
-}
-export type BackendDataStore = ServerDataStore | LocalGFF3DataStore;
-export interface OperationOptions {
-    logger: LoggerService;
-}
-export declare abstract class Operation implements SerializedOperation {
-    protected logger: LoggerService;
-    abstract typeName: string;
-    constructor(json: SerializedOperation, options?: OperationOptions);
-    abstract toJSON(): SerializedOperation;
-    execute(backend: BackendDataStore): Promise<unknown>;
-    abstract executeOnServer(backend: ServerDataStore): Promise<unknown>;
-    abstract executeOnLocalGFF3(backend: LocalGFF3DataStore): Promise<unknown>;
-}
-export {};
-//# sourceMappingURL=Operation.d.ts.map

package/dist/Operation.d.ts.map

@@ -1 +0,0 @@
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package/dist/Operation.js

@@ -1,18 +0,0 @@
-export class Operation {
-    logger;
-    constructor(json, options) {
-        this.logger = options?.logger ?? console;
-    }
-    async execute(backend) {
-        const backendType = backend.typeName;
-        if (backendType === 'Server') {
-            const initialResult = this.executeOnServer(backend);
-            return backend.pluginsService.evaluateExtensionPoint(`${this.typeName}-transformResults`, initialResult, { operation: this, backend });
-        }
-        if (backendType === 'LocalGFF3') {
-            return this.executeOnLocalGFF3(backend);
-        }
-        throw new Error(`no operation implementation for backend type '${backendType}'`);
-    }
-}
-//# sourceMappingURL=Operation.js.map

package/dist/Operation.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"Operation.js","sourceRoot":"","sources":["../src/Operation.ts"],"names":[],"mappings":"AA+EA,MAAM,OAAgB,SAAS;IACnB,MAAM,CAAe;IAG/B,YAAY,IAAyB,EAAE,OAA0B;QAC/D,IAAI,CAAC,MAAM,GAAG,OAAO,EAAE,MAAM,IAAI,OAAO,CAAA;IAC1C,CAAC;IAID,KAAK,CAAC,OAAO,CAAC,OAAyB;QACrC,MAAM,WAAW,GAAG,OAAO,CAAC,QAAQ,CAAA;QACpC,IAAI,WAAW,KAAK,QAAQ,EAAE,CAAC;YAC7B,MAAM,aAAa,GAAG,IAAI,CAAC,eAAe,CAAC,OAAO,CAAC,CAAA;YACnD,OAAO,OAAO,CAAC,cAAc,CAAC,sBAAsB,CAClD,GAAG,IAAI,CAAC,QAAQ,mBAAmB,EACnC,aAAa,EACb,EAAE,SAAS,EAAE,IAAI,EAAE,OAAO,EAAE,CAC7B,CAAA;QACH,CAAC;QACD,IAAI,WAAW,KAAK,WAAW,EAAE,CAAC;YAChC,OAAO,IAAI,CAAC,kBAAkB,CAAC,OAAO,CAAC,CAAA;QACzC,CAAC;QACD,MAAM,IAAI,KAAK,CACb,iDAAiD,WAAW,GAAG,CAChE,CAAA;IACH,CAAC;CAIF"}

package/dist/OperationTypeRegistry.d.ts

@@ -1,11 +0,0 @@
-import type { Operation } from './Operation.js';
-type OperationType = new (...args: any[]) => Operation;
-declare class OperationTypeRegistry {
-    operations: Map<string, OperationType>;
-    registerOperation(name: string, operationType: OperationType): void;
-    getOperationType(name: string): OperationType;
-}
-/** global singleton of all known types of operations */
-export declare const operationRegistry: OperationTypeRegistry;
-export {};
-//# sourceMappingURL=OperationTypeRegistry.d.ts.map

package/dist/OperationTypeRegistry.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"OperationTypeRegistry.d.ts","sourceRoot":"","sources":["../src/OperationTypeRegistry.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAA;AAG/C,KAAK,aAAa,GAAG,KAAK,GAAG,IAAI,EAAE,GAAG,EAAE,KAAK,SAAS,CAAA;AAEtD,cAAM,qBAAqB;IACzB,UAAU,6BAAmC;IAE7C,iBAAiB,CAAC,IAAI,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,GAAG,IAAI;IAOnE,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,aAAa;CAO9C;AAED,wDAAwD;AACxD,eAAO,MAAM,iBAAiB,uBAA8B,CAAA"}

package/dist/OperationTypeRegistry.js

@@ -1,19 +0,0 @@
-class OperationTypeRegistry {
-    operations = new Map();
-    registerOperation(name, operationType) {
-        if (this.operations.has(name)) {
-            throw new Error(`operation type "${name}" has already been registered`);
-        }
-        this.operations.set(name, operationType);
-    }
-    getOperationType(name) {
-        const RegisteredOperationType = this.operations.get(name);
-        if (!RegisteredOperationType) {
-            throw new Error(`No operation constructor registered for "${name}"`);
-        }
-        return RegisteredOperationType;
-    }
-}
-/** global singleton of all known types of operations */
-export const operationRegistry = new OperationTypeRegistry();
-//# sourceMappingURL=OperationTypeRegistry.js.map

package/dist/OperationTypeRegistry.js.map

@@ -1 +0,0 @@
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package/src/Operation.ts

@@ -1,110 +0,0 @@
-/* eslint-disable @typescript-eslint/no-confusing-void-expression */
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
-import type { FileHandle } from 'node:fs/promises'
-
-import type {
-  AssemblyDocument,
-  CheckDocument,
-  FeatureDocument,
-  FileDocument,
-  JBrowseConfigDocument,
-  RefSeqChunkDocument,
-  RefSeqDocument,
-  UserDocument,
-} from '@apollo-annotation/schemas'
-import type { GFF3Feature } from '@gmod/gff'
-import type { LoggerService } from '@nestjs/common'
-import type { GenericFilehandle } from 'generic-filehandle2'
-import type { ClientSession, Model } from 'mongoose'
-
-export interface LocalGFF3DataStore {
-  typeName: 'LocalGFF3'
-  gff3Handle: FileHandle
-}
-
-interface CreateFileDto {
-  readonly _id: string
-  readonly basename: string
-  readonly checksum: string
-  readonly type: 'text/x-gff3' | 'text/x-fasta'
-  readonly user: string
-}
-
-export interface ServerDataStore {
-  typeName: 'Server'
-  featureModel: Model<FeatureDocument>
-  assemblyModel: Model<AssemblyDocument>
-  refSeqModel: Model<RefSeqDocument>
-  refSeqChunkModel: Model<RefSeqChunkDocument>
-  checkModel: Model<CheckDocument>
-  fileModel: Model<FileDocument>
-  userModel: Model<UserDocument>
-  jbrowseConfigModel: Model<JBrowseConfigDocument>
-  session: ClientSession
-  filesService: {
-    getFileStream(file: FileDocument): ReadableStream<Uint8Array>
-    getFileHandle(file: FileDocument): GenericFilehandle
-    parseGFF3(
-      stream: ReadableStream<Uint8Array>,
-      parseOptions?: {
-        bufferSize?: number
-        errorCallback?(errorMessage: string): void
-      },
-    ): ReadableStream<GFF3Feature>
-    create(createFileDto: CreateFileDto): void
-    remove(id: string): void
-  }
-  pluginsService: {
-    evaluateExtensionPoint(
-      extensionPointName: string,
-      extendee: unknown,
-      props?: Record<string, unknown>,
-    ): void
-  }
-  counterService: {
-    getNextSequenceValue(sequenceName: string): Promise<number>
-  }
-  user: string
-}
-export interface SerializedOperation {
-  typeName: string
-}
-
-export type BackendDataStore = ServerDataStore | LocalGFF3DataStore
-
-export interface OperationOptions {
-  logger: LoggerService
-}
-
-export abstract class Operation implements SerializedOperation {
-  protected logger: LoggerService
-  abstract typeName: string
-
-  constructor(json: SerializedOperation, options?: OperationOptions) {
-    this.logger = options?.logger ?? console
-  }
-
-  abstract toJSON(): SerializedOperation
-
-  async execute(backend: BackendDataStore): Promise<unknown> {
-    const backendType = backend.typeName
-    if (backendType === 'Server') {
-      const initialResult = this.executeOnServer(backend)
-      return backend.pluginsService.evaluateExtensionPoint(
-        `${this.typeName}-transformResults`,
-        initialResult,
-        { operation: this, backend },
-      )
-    }
-    if (backendType === 'LocalGFF3') {
-      return this.executeOnLocalGFF3(backend)
-    }
-    throw new Error(
-      `no operation implementation for backend type '${backendType}'`,
-    )
-  }
-
-  abstract executeOnServer(backend: ServerDataStore): Promise<unknown>
-  abstract executeOnLocalGFF3(backend: LocalGFF3DataStore): Promise<unknown>
-}

package/src/OperationTypeRegistry.ts

@@ -1,26 +0,0 @@
-import type { Operation } from './Operation.js'
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-type OperationType = new (...args: any[]) => Operation
-
-class OperationTypeRegistry {
-  operations = new Map<string, OperationType>()
-
-  registerOperation(name: string, operationType: OperationType): void {
-    if (this.operations.has(name)) {
-      throw new Error(`operation type "${name}" has already been registered`)
-    }
-    this.operations.set(name, operationType)
-  }
-
-  getOperationType(name: string): OperationType {
-    const RegisteredOperationType = this.operations.get(name)
-    if (!RegisteredOperationType) {
-      throw new Error(`No operation constructor registered for "${name}"`)
-    }
-    return RegisteredOperationType
-  }
-}
-
-/** global singleton of all known types of operations */
-export const operationRegistry = new OperationTypeRegistry()