@apollo-annotation/shared 0.1.11

package/src/Changes/StrandChange.ts

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+/* eslint-disable @typescript-eslint/restrict-template-expressions */
+/* eslint-disable @typescript-eslint/require-await */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+import {
+  ChangeOptions,
+  ClientDataStore,
+  FeatureChange,
+  LocalGFF3DataStore,
+  SerializedFeatureChange,
+  ServerDataStore,
+} from '@apollo-annotation/common'
+import { Feature, FeatureDocument } from '@apollo-annotation/schemas'
+
+interface SerializedStrandChangeBase extends SerializedFeatureChange {
+  typeName: 'StrandChange'
+}
+
+interface StrandChangeDetails {
+  featureId: string
+  oldStrand: -1 | 1 | undefined
+  newStrand: -1 | 1 | undefined
+}
+
+interface SerializedStrandChangeSingle
+  extends SerializedStrandChangeBase,
+    StrandChangeDetails {}
+
+interface SerializedStrandChangeMultiple extends SerializedStrandChangeBase {
+  changes: StrandChangeDetails[]
+}
+
+type SerializedStrandChange =
+  | SerializedStrandChangeSingle
+  | SerializedStrandChangeMultiple
+
+export class StrandChange extends FeatureChange {
+  typeName = 'StrandChange' as const
+  changes: StrandChangeDetails[]
+
+  constructor(json: SerializedStrandChange, options?: ChangeOptions) {
+    super(json, options)
+    this.changes = 'changes' in json ? json.changes : [json]
+  }
+
+  toJSON(): SerializedStrandChange {
+    const { assembly, changedIds, changes, typeName } = this
+    if (changes.length === 1) {
+      const [{ featureId, newStrand, oldStrand }] = changes
+      return { typeName, changedIds, assembly, featureId, oldStrand, newStrand }
+    }
+    return { typeName, changedIds, assembly, changes }
+  }
+
+  /**
+   * Applies the required change to database
+   * @param backend - parameters from backend
+   * @returns
+   */
+  async executeOnServer(backend: ServerDataStore) {
+    const { featureModel, session } = backend
+    const { changes, logger } = this
+    const featuresForChanges: {
+      feature: Feature
+      topLevelFeature: FeatureDocument
+    }[] = []
+    // Let's first check that all features are found and those old values match with expected ones. We do this just to be sure that all changes can be done.
+    for (const entry of changes) {
+      const { featureId, oldStrand } = entry
+
+      // Search correct feature
+      const topLevelFeature = await featureModel
+        .findOne({ allIds: featureId })
+        .session(session)
+        .exec()
+
+      if (!topLevelFeature) {
+        const errMsg = `*** ERROR: The following featureId was not found in database ='${featureId}'`
+        logger.error(errMsg)
+        throw new Error(errMsg)
+        // throw new NotFoundException(errMsg)  -- This is causing runtime error because Exception comes from @nestjs/common!!!
+      }
+      logger.debug?.(`*** Feature found: ${JSON.stringify(topLevelFeature)}`)
+
+      const foundFeature = this.getFeatureFromId(topLevelFeature, featureId)
+      if (!foundFeature) {
+        const errMsg = 'ERROR when searching feature by featureId'
+        logger.error(errMsg)
+        throw new Error(errMsg)
+      }
+      logger.debug?.(`*** Found feature: ${JSON.stringify(foundFeature)}`)
+      if (foundFeature.strand !== oldStrand) {
+        const errMsg = `*** ERROR: Feature's current strand "${topLevelFeature.strand}" doesn't match with expected value "${oldStrand}"`
+        logger.error(errMsg)
+        throw new Error(errMsg)
+      }
+      featuresForChanges.push({ feature: foundFeature, topLevelFeature })
+    }
+
+    // Let's update objects.
+    for (const [idx, change] of changes.entries()) {
+      const { newStrand } = change
+      const { feature, topLevelFeature } = featuresForChanges[idx]
+      feature.strand = newStrand
+      if (topLevelFeature._id.equals(feature._id)) {
+        topLevelFeature.markModified('strand') // Mark as modified. Without this save() -method is not updating data in database
+      } else {
+        topLevelFeature.markModified('children') // Mark as modified. Without this save() -method is not updating data in database
+      }
+
+      try {
+        await topLevelFeature.save()
+      } catch (error) {
+        logger.debug?.(`*** FAILED: ${error}`)
+        throw error
+      }
+      logger.debug?.(
+        `*** Object updated in Mongo. New object: ${JSON.stringify(
+          topLevelFeature,
+        )}`,
+      )
+    }
+  }
+
+  async executeOnLocalGFF3(_backend: LocalGFF3DataStore) {
+    throw new Error('executeOnLocalGFF3 not implemented')
+  }
+
+  async executeOnClient(dataStore: ClientDataStore) {
+    if (!dataStore) {
+      throw new Error('No data store')
+    }
+    for (const [idx, changedId] of this.changedIds.entries()) {
+      const feature = dataStore.getFeature(changedId)
+      if (!feature) {
+        throw new Error(`Could not find feature with identifier "${changedId}"`)
+      }
+      feature.setStrand(this.changes[idx].newStrand)
+    }
+  }
+
+  getInverse() {
+    const { assembly, changedIds, changes, logger, typeName } = this
+    const inverseChangedIds = [...changedIds].reverse()
+    const inverseChanges = [...changes].reverse().map((endChange) => ({
+      featureId: endChange.featureId,
+      oldStrand: endChange.newStrand,
+      newStrand: endChange.oldStrand,
+    }))
+    return new StrandChange(
+      {
+        changedIds: inverseChangedIds,
+        typeName,
+        changes: inverseChanges,
+        assembly,
+      },
+      { logger },
+    )
+  }
+}

package/src/Changes/TypeChange.ts

@@ -0,0 +1,159 @@
+/* eslint-disable @typescript-eslint/restrict-template-expressions */
+/* eslint-disable @typescript-eslint/require-await */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+import {
+  ChangeOptions,
+  ClientDataStore,
+  FeatureChange,
+  LocalGFF3DataStore,
+  SerializedFeatureChange,
+  ServerDataStore,
+} from '@apollo-annotation/common'
+import { Feature, FeatureDocument } from '@apollo-annotation/schemas'
+
+interface SerializedTypeChangeBase extends SerializedFeatureChange {
+  typeName: 'TypeChange'
+}
+
+interface TypeChangeDetails {
+  featureId: string
+  oldType: string
+  newType: string
+}
+
+interface SerializedTypeChangeSingle
+  extends SerializedTypeChangeBase,
+    TypeChangeDetails {}
+
+interface SerializedTypeChangeMultiple extends SerializedTypeChangeBase {
+  changes: TypeChangeDetails[]
+}
+
+type SerializedTypeChange =
+  | SerializedTypeChangeSingle
+  | SerializedTypeChangeMultiple
+
+export class TypeChange extends FeatureChange {
+  typeName = 'TypeChange' as const
+  changes: TypeChangeDetails[]
+
+  constructor(json: SerializedTypeChange, options?: ChangeOptions) {
+    super(json, options)
+    this.changes = 'changes' in json ? json.changes : [json]
+  }
+
+  toJSON(): SerializedTypeChange {
+    const { assembly, changedIds, changes, typeName } = this
+    if (changes.length === 1) {
+      const [{ featureId, newType, oldType }] = changes
+      return { typeName, changedIds, assembly, featureId, oldType, newType }
+    }
+    return { typeName, changedIds, assembly, changes }
+  }
+
+  /**
+   * Applies the required change to database
+   * @param backend - parameters from backend
+   * @returns
+   */
+  async executeOnServer(backend: ServerDataStore) {
+    const { featureModel, session } = backend
+    const { changes, logger } = this
+    const featuresForChanges: {
+      feature: Feature
+      topLevelFeature: FeatureDocument
+    }[] = []
+    // Let's first check that all features are found and those old values match with expected ones. We do this just to be sure that all changes can be done.
+    for (const entry of changes) {
+      const { featureId, oldType } = entry
+
+      // Search correct feature
+      const topLevelFeature = await featureModel
+        .findOne({ allIds: featureId })
+        .session(session)
+        .exec()
+
+      if (!topLevelFeature) {
+        const errMsg = `*** ERROR: The following featureId was not found in database ='${featureId}'`
+        logger.error(errMsg)
+        throw new Error(errMsg)
+        // throw new NotFoundException(errMsg)  -- This is causing runtime error because Exception comes from @nestjs/common!!!
+      }
+      logger.debug?.(`*** Feature found: ${JSON.stringify(topLevelFeature)}`)
+
+      const foundFeature = this.getFeatureFromId(topLevelFeature, featureId)
+      if (!foundFeature) {
+        const errMsg = 'ERROR when searching feature by featureId'
+        logger.error(errMsg)
+        throw new Error(errMsg)
+      }
+      logger.debug?.(`*** Found feature: ${JSON.stringify(foundFeature)}`)
+      if (foundFeature.type !== oldType) {
+        const errMsg = `*** ERROR: Feature's current type "${topLevelFeature.type}" doesn't match with expected value "${oldType}"`
+        logger.error(errMsg)
+        throw new Error(errMsg)
+      }
+      featuresForChanges.push({ feature: foundFeature, topLevelFeature })
+    }
+
+    // Let's update objects.
+    for (const [idx, change] of changes.entries()) {
+      const { newType } = change
+      const { feature, topLevelFeature } = featuresForChanges[idx]
+      feature.type = newType
+      if (topLevelFeature._id.equals(feature._id)) {
+        topLevelFeature.markModified('type') // Mark as modified. Without this save() -method is not updating data in database
+      } else {
+        topLevelFeature.markModified('children') // Mark as modified. Without this save() -method is not updating data in database
+      }
+
+      try {
+        await topLevelFeature.save()
+      } catch (error) {
+        logger.debug?.(`*** FAILED: ${error}`)
+        throw error
+      }
+      logger.debug?.(
+        `*** Object updated in Mongo. New object: ${JSON.stringify(
+          topLevelFeature,
+        )}`,
+      )
+    }
+  }
+
+  async executeOnLocalGFF3(_backend: LocalGFF3DataStore) {
+    throw new Error('executeOnLocalGFF3 not implemented')
+  }
+
+  async executeOnClient(dataStore: ClientDataStore) {
+    if (!dataStore) {
+      throw new Error('No data store')
+    }
+    for (const [idx, changedId] of this.changedIds.entries()) {
+      const feature = dataStore.getFeature(changedId)
+      if (!feature) {
+        throw new Error(`Could not find feature with identifier "${changedId}"`)
+      }
+      feature.setType(this.changes[idx].newType)
+    }
+  }
+
+  getInverse() {
+    const { assembly, changedIds, changes, logger, typeName } = this
+    const inverseChangedIds = [...changedIds].reverse()
+    const inverseChanges = [...changes].reverse().map((endChange) => ({
+      featureId: endChange.featureId,
+      oldType: endChange.newType,
+      newType: endChange.oldType,
+    }))
+    return new TypeChange(
+      {
+        changedIds: inverseChangedIds,
+        typeName,
+        changes: inverseChanges,
+        assembly,
+      },
+      { logger },
+    )
+  }
+}

package/src/Changes/UserChange.ts

@@ -0,0 +1,82 @@
+/* eslint-disable @typescript-eslint/require-await */
+import {
+  Change,
+  ChangeOptions,
+  ClientDataStore,
+  LocalGFF3DataStore,
+  SerializedChange,
+  ServerDataStore,
+} from '@apollo-annotation/common'
+
+export interface SerializedUserChangeBase extends SerializedChange {
+  typeName: 'UserChange'
+  userId: string
+}
+
+export interface UserChangeDetails {
+  role: 'admin' | 'user' | 'readOnly'
+}
+
+export interface SerializedUserChangeSingle
+  extends SerializedUserChangeBase,
+    UserChangeDetails {}
+
+export interface SerializedUserChangeMultiple extends SerializedUserChangeBase {
+  changes: UserChangeDetails[]
+}
+
+export type SerializedUserChange =
+  | SerializedUserChangeSingle
+  | SerializedUserChangeMultiple
+
+export class UserChange extends Change {
+  typeName = 'UserChange' as const
+  changes: UserChangeDetails[]
+  userId: string
+
+  constructor(json: SerializedUserChange, options?: ChangeOptions) {
+    super(json, options)
+    this.changes = 'changes' in json ? json.changes : [json]
+    this.userId = json.userId
+  }
+
+  toJSON(): SerializedUserChange {
+    const { changes, typeName, userId } = this
+    if (changes.length === 1) {
+      const [{ role }] = changes
+      return { typeName, userId, role }
+    }
+    return { typeName, userId, changes }
+  }
+
+  async executeOnServer(backend: ServerDataStore) {
+    const { session, userModel } = backend
+    const { changes, logger, userId } = this
+
+    for (const change of changes) {
+      logger.debug?.(`change: ${JSON.stringify(changes)}`)
+      const { role } = change
+      const user = await userModel
+        .findByIdAndUpdate(userId, { role })
+        .session(session)
+        .exec()
+      if (!user) {
+        const errMsg = `*** ERROR: User with id "${userId}" not found`
+        logger.error(errMsg)
+        throw new Error(errMsg)
+      }
+    }
+  }
+
+  async executeOnLocalGFF3(_backend: LocalGFF3DataStore) {
+    throw new Error('executeOnLocalGFF3 not implemented')
+  }
+
+  // eslint-disable-next-line @typescript-eslint/no-empty-function
+  async executeOnClient(_dataStore: ClientDataStore) {}
+
+  getInverse() {
+    const { changes, logger, typeName, userId } = this
+    return new UserChange({ typeName, changes, userId }, { logger })
+  }
+}

package/src/Changes/index.ts

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+import { AddAssemblyAndFeaturesFromFileChange } from './AddAssemblyAndFeaturesFromFileChange'
+import { AddAssemblyFromExternalChange } from './AddAssemblyFromExternalChange'
+import { AddAssemblyFromFileChange } from './AddAssemblyFromFileChange'
+import { AddFeatureChange } from './AddFeatureChange'
+import { AddFeaturesFromFileChange } from './AddFeaturesFromFileChange'
+import { DeleteAssemblyChange } from './DeleteAssemblyChange'
+import { DeleteFeatureChange } from './DeleteFeatureChange'
+import { DeleteUserChange } from './DeleteUserChange'
+import { DiscontinuousLocationEndChange } from './DiscontinuousLocationEndChange'
+import { DiscontinuousLocationStartChange } from './DiscontinuousLocationStartChange'
+import { FeatureAttributeChange } from './FeatureAttributeChange'
+import { LocationEndChange } from './LocationEndChange'
+import { LocationStartChange } from './LocationStartChange'
+import { StrandChange } from './StrandChange'
+import { TypeChange } from './TypeChange'
+import { UserChange } from './UserChange'
+
+export const changes = {
+  AddAssemblyAndFeaturesFromFileChange,
+  AddAssemblyFromFileChange,
+  AddAssemblyFromExternalChange,
+  AddFeatureChange,
+  AddFeaturesFromFileChange,
+  DeleteAssemblyChange,
+  DeleteFeatureChange,
+  DeleteUserChange,
+  DiscontinuousLocationEndChange,
+  DiscontinuousLocationStartChange,
+  FeatureAttributeChange,
+  LocationEndChange,
+  LocationStartChange,
+  StrandChange,
+  TypeChange,
+  UserChange,
+}
+
+export * from './AddAssemblyAndFeaturesFromFileChange'
+export * from './AddAssemblyFromFileChange'
+export * from './AddAssemblyFromExternalChange'
+export * from './AddFeatureChange'
+export * from './AddFeaturesFromFileChange'
+export * from './DeleteAssemblyChange'
+export * from './DeleteFeatureChange'
+export * from './DeleteUserChange'
+export * from './DiscontinuousLocationEndChange'
+export * from './DiscontinuousLocationStartChange'
+export * from './FeatureAttributeChange'
+export * from './LocationEndChange'
+export * from './LocationStartChange'
+export * from './StrandChange'
+export * from './TypeChange'
+export * from './UserChange'