@apollo-annotation/shared 0.3.6 → 0.3.7

package/dist/util.d.ts

@@ -1 +1,3 @@
+import { type Feature } from '@apollo-annotation/schemas';
 export declare function splitStringIntoChunks(input: string, chunkSize: number): string[];
+export declare function getPrintableId(feature: Feature): string;

package/dist/util.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.splitStringIntoChunks = splitStringIntoChunks;
+exports.getPrintableId = getPrintableId;
 function splitStringIntoChunks(input, chunkSize) {
     const chunks = [];
     for (let i = 0; i < input.length; i += chunkSize) {
@@ -9,4 +10,16 @@ function splitStringIntoChunks(input, chunkSize) {
     }
     return chunks;
 }
+function getPrintableId(feature) {
+    const ff = feature;
+    const gff_id = ff.attributes.get('gff_id')?.join(',');
+    if (gff_id) {
+        return `ID=${gff_id} (_id: ${feature._id.toString()})`;
+    }
+    const gff_name = ff.attributes.get('gff_name')?.join(',');
+    if (gff_name) {
+        return `Name=${gff_name} (_id: ${feature._id.toString()})`;
+    }
+    return `_id: ${feature._id.toString()}`;
+}
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -1 +1 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;AAAA,sDAUC;AAVD,SAAgB,qBAAqB,CACnC,KAAa,EACb,SAAiB;IAEjB,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,IAAI,SAAS,EAAE,CAAC;QACjD,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,CAAA;QAC3C,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IACpB,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC"}
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;AAGA,sDAUC;AAED,wCAWC;AAvBD,SAAgB,qBAAqB,CACnC,KAAa,EACb,SAAiB;IAEjB,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,IAAI,SAAS,EAAE,CAAC;QACjD,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,CAAA;QAC3C,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IACpB,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,SAAgB,cAAc,CAAC,OAAgB;IAC7C,MAAM,EAAE,GAAG,OAAuC,CAAA;IAClD,MAAM,MAAM,GAAG,EAAE,CAAC,UAAU,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAA;IACrD,IAAI,MAAM,EAAE,CAAC;QACX,OAAO,MAAM,MAAM,UAAU,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,GAAG,CAAA;IACxD,CAAC;IACD,MAAM,QAAQ,GAAG,EAAE,CAAC,UAAU,CAAC,GAAG,CAAC,UAAU,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAA;IACzD,IAAI,QAAQ,EAAE,CAAC;QACb,OAAO,QAAQ,QAAQ,UAAU,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,GAAG,CAAA;IAC5D,CAAC;IACD,OAAO,QAAQ,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,EAAE,CAAA;AACzC,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/shared",
-  "version": "0.3.6",
+  "version": "0.3.7",
   "main": "./dist/index.js",
   "scripts": {
     "build": "yarn clean && tsc --build",
@@ -10,9 +10,9 @@
     "test:ci": "NODE_V8_COVERAGE=./coverage glob -c \"tsx --test --test-reporter spec --experimental-test-coverage \" \"**/*.test.ts\""
   },
   "dependencies": {
-    "@apollo-annotation/common": "^0.3.6",
-    "@apollo-annotation/mst": "^0.3.6",
-    "@apollo-annotation/schemas": "^0.3.6",
+    "@apollo-annotation/common": "^0.3.7",
+    "@apollo-annotation/mst": "^0.3.7",
+    "@apollo-annotation/schemas": "^0.3.7",
     "@gmod/gff": "1.2.0",
     "@gmod/indexedfasta": "^2.0.4",
     "@jbrowse/core": "^3.0.1",

package/src/Changes/AddAssemblyAliasesChange.ts

@@ -0,0 +1,69 @@
+import {
+  AssemblySpecificChange,
+  type Change,
+  type ChangeOptions,
+  type ClientDataStore,
+  type LocalGFF3DataStore,
+  type SerializedAssemblySpecificChange,
+  type ServerDataStore,
+} from '@apollo-annotation/common'
+import { getSession } from '@jbrowse/core/util'
+
+export interface SerializedAssemblyAliasesChange
+  extends SerializedAssemblySpecificChange {
+  typeName: 'AddAssemblyAliasesChange'
+  aliases: string[]
+}
+
+export class AddAssemblyAliasesChange extends AssemblySpecificChange {
+  typeName = 'AddAssemblyAliasesChange' as const
+  aliases: string[]
+
+  constructor(json: SerializedAssemblyAliasesChange, options?: ChangeOptions) {
+    super(json, options)
+    this.aliases = json.aliases
+  }
+
+  executeOnClient(clientDataStore: ClientDataStore) {
+    const { assemblyManager } = getSession(clientDataStore)
+    const assembly = assemblyManager.get(this.assembly)
+    if (!assembly) {
+      throw new Error(`assembly ${this.assembly} not found`)
+    }
+    // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+    assembly.configuration.aliases.set(this.aliases)
+    return Promise.resolve()
+  }
+
+  getInverse(): Change {
+    throw new Error('Method not implemented.')
+  }
+
+  toJSON(): SerializedAssemblyAliasesChange {
+    const { assembly, aliases, typeName } = this
+    return { assembly, typeName, aliases }
+  }
+
+  async executeOnServer(backend: ServerDataStore) {
+    const { assemblyModel } = backend
+    const { assembly, logger, aliases } = this
+    logger.debug?.(
+      `Updating assembly aliases for assembly: ${assembly}, aliases: ${JSON.stringify(aliases)}`,
+    )
+    const asm = await assemblyModel.findById(assembly)
+    if (!asm) {
+      throw new Error(`Assembly with ID ${assembly} not found`)
+    }
+    asm.aliases = aliases
+    await asm.save()
+  }
+
+  executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<unknown> {
+    throw new Error('Method not implemented.')
+  }
+
+  // eslint-disable-next-line @typescript-eslint/class-literal-property-style
+  get notification(): string {
+    return 'Assembly aliases have been added.'
+  }
+}

package/src/Changes/AddFeatureChange.ts

@@ -1,5 +1,4 @@
 /* eslint-disable @typescript-eslint/restrict-template-expressions */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import {
@@ -46,6 +45,10 @@ export class AddFeatureChange extends FeatureChange {
     super(json, options)
     this.changes = 'changes' in json ? json.changes : [json]
   }
+  // eslint-disable-next-line @typescript-eslint/class-literal-property-style
+  get notification() {
+    return 'Feature added successfully'
+  }
 
   toJSON(): SerializedAddFeatureChange {
     const { assembly, changedIds, changes, typeName } = this
@@ -133,34 +136,7 @@ export class AddFeatureChange extends FeatureChange {
               `Could not find feature with ID "${parentFeatureId}" in feature "${topLevelFeature._id}"`,
             )
           }
-          if (!parentFeature.children) {
-            parentFeature.children = new Map()
-          }
-          if (!parentFeature.attributes?._id) {
-            let { attributes } = parentFeature
-            if (!attributes) {
-              attributes = {}
-            }
-            attributes = {
-              _id: [parentFeature._id.toString()],
-              // eslint-disable-next-line unicorn/prefer-structured-clone
-              ...JSON.parse(JSON.stringify(attributes)),
-            }
-            parentFeature.attributes = attributes
-          }
-          parentFeature.children.set(_id, {
-            allIds: [],
-            ...addedFeature,
-            // eslint-disable-next-line @typescript-eslint/ban-ts-comment
-            // @ts-expect-error
-            _id,
-          })
-          // Child features should be sorted for click and drag of gene glyphs to work properly
-          parentFeature.children = new Map(
-            [...parentFeature.children.entries()].sort(
-              (a, b) => a[1].min - b[1].min,
-            ),
-          )
+          this.addChild(parentFeature, addedFeature)
           const childIds = this.getChildFeatureIds(addedFeature)
           topLevelFeature.allIds.push(_id, ...childIds)
           await topLevelFeature.save()

package/src/Changes/DeleteFeatureChange.ts

@@ -44,6 +44,10 @@ export class DeleteFeatureChange extends FeatureChange {
     super(json, options)
     this.changes = 'changes' in json ? json.changes : [json]
   }
+  // eslint-disable-next-line @typescript-eslint/class-literal-property-style
+  get notification() {
+    return 'Feature deleted successfully'
+  }
 
   toJSON(): SerializedDeleteFeatureChange {
     const { assembly, changedIds, changes, typeName } = this
@@ -92,9 +96,10 @@ export class DeleteFeatureChange extends FeatureChange {
         continue
       }
 
-      const deletedIds = this.findAndDeleteChildFeature(
+      const deletedIds = findAndDeleteChildFeature(
         featureDoc,
         deletedFeature._id,
+        this,
       )
       deletedIds.push(deletedFeature._id)
       featureDoc.allIds = featureDoc.allIds.filter(
@@ -115,38 +120,6 @@ export class DeleteFeatureChange extends FeatureChange {
     }
   }
 
-  /**
-   * Delete feature's subfeatures that match an ID and return the IDs of any
-   * sub-subfeatures that were deleted
-   * @param feature -
-   * @param featureIdToDelete -
-   * @returns - list of deleted feature IDs
-   */
-  findAndDeleteChildFeature(
-    feature: Feature,
-    featureIdToDelete: string,
-  ): string[] {
-    if (!feature.children) {
-      throw new Error(`Feature ${feature._id} has no children`)
-    }
-    const { _id, children } = feature
-    const child = children.get(featureIdToDelete)
-    if (child) {
-      const deletedIds = this.getChildFeatureIds(child)
-      children.delete(featureIdToDelete)
-      return deletedIds
-    }
-    for (const [, childFeature] of children) {
-      try {
-        return this.findAndDeleteChildFeature(childFeature, featureIdToDelete)
-      } catch {
-        // pass
-      }
-    }
-
-    throw new Error(`Feature "${featureIdToDelete}" not found in ${_id}`)
-  }
-
   async executeOnLocalGFF3(_backend: LocalGFF3DataStore) {
     throw new Error('executeOnLocalGFF3 not implemented')
   }
@@ -176,9 +149,9 @@ export class DeleteFeatureChange extends FeatureChange {
     const inverseChangedIds = [...changedIds].reverse()
     const inverseChanges = [...changes]
       .reverse()
-      .map((deleteFeatuerChange) => ({
-        addedFeature: deleteFeatuerChange.deletedFeature,
-        parentFeatureId: deleteFeatuerChange.parentFeatureId,
+      .map((deleteFeatureChange) => ({
+        addedFeature: deleteFeatureChange.deletedFeature,
+        parentFeatureId: deleteFeatureChange.parentFeatureId,
       }))
     logger.debug?.(`INVERSE CHANGE '${JSON.stringify(inverseChanges)}'`)
     return new AddFeatureChange(
@@ -193,6 +166,39 @@ export class DeleteFeatureChange extends FeatureChange {
   }
 }
 
+/**
+ * Delete feature's subfeatures that match an ID and return the IDs of any
+ * sub-subfeatures that were deleted
+ * @param feature -
+ * @param featureIdToDelete -
+ * @returns - list of deleted feature IDs
+ */
+export function findAndDeleteChildFeature(
+  feature: Feature,
+  featureIdToDelete: string,
+  change: FeatureChange,
+): string[] {
+  if (!feature.children) {
+    throw new Error(`Feature ${feature._id} has no children`)
+  }
+  const { _id, children } = feature
+  const child = children.get(featureIdToDelete)
+  if (child) {
+    const deletedIds = change.getChildFeatureIds(child)
+    children.delete(featureIdToDelete)
+    return deletedIds
+  }
+  for (const [, childFeature] of children) {
+    try {
+      return findAndDeleteChildFeature(childFeature, featureIdToDelete, change)
+    } catch {
+      // pass
+    }
+  }
+
+  throw new Error(`Feature "${featureIdToDelete}" not found in ${_id}`)
+}
+
 export function isDeleteFeatureChange(
   change: unknown,
 ): change is DeleteFeatureChange {

package/src/Changes/FeatureAttributeChange.ts

@@ -17,7 +17,8 @@ interface SerializedFeatureAttributeChangeBase extends SerializedFeatureChange {
 
 export interface FeatureAttributeChangeDetails {
   featureId: string
-  attributes: Record<string, string[]>
+  oldAttributes: Record<string, string[]>
+  newAttributes: Record<string, string[]>
 }
 
 interface SerializedFeatureAttributeChangeSingle
@@ -45,8 +46,15 @@ export class FeatureAttributeChange extends FeatureChange {
   toJSON(): SerializedFeatureAttributeChange {
     const { assembly, changedIds, changes, typeName } = this
     if (changes.length === 1) {
-      const [{ attributes, featureId }] = changes
-      return { typeName, changedIds, assembly, featureId, attributes }
+      const [{ oldAttributes, newAttributes, featureId }] = changes
+      return {
+        typeName,
+        changedIds,
+        assembly,
+        featureId,
+        oldAttributes,
+        newAttributes,
+      }
     }
     return { typeName, changedIds, assembly, changes }
   }
@@ -94,9 +102,9 @@ export class FeatureAttributeChange extends FeatureChange {
 
     // Let's update objects
     for (const [idx, change] of changes.entries()) {
-      const { attributes } = change
+      const { newAttributes } = change
       const { feature, topLevelFeature } = featuresForChanges[idx]
-      feature.attributes = attributes
+      feature.attributes = newAttributes
       if (topLevelFeature._id.equals(feature._id)) {
         topLevelFeature.markModified('attributes') // Mark as modified. Without this save() -method is not updating data in database
       } else {
@@ -131,7 +139,7 @@ export class FeatureAttributeChange extends FeatureChange {
         throw new Error(`Could not find feature with identifier "${changedId}"`)
       }
       feature.setAttributes(
-        new Map(Object.entries(this.changes[idx].attributes)),
+        new Map(Object.entries(this.changes[idx].newAttributes)),
       )
     }
   }
@@ -141,7 +149,8 @@ export class FeatureAttributeChange extends FeatureChange {
     const inverseChangedIds = [...changedIds].reverse()
     const inverseChanges = [...changes].reverse().map((oneChange) => ({
       featureId: oneChange.featureId,
-      attributes: oneChange.attributes,
+      oldAttributes: oneChange.newAttributes,
+      newAttributes: oneChange.oldAttributes,
     }))
     return new FeatureAttributeChange(
       {

package/src/Changes/ImportJBrowseConfigChange.ts

@@ -26,6 +26,9 @@ interface JBrowseInternetAccount {
 
 export interface JBrowseConfig {
   assemblies?: JBrowseAssembly[]
+  configuration?: {
+    ApolloPlugin?: Record<string, unknown>
+  }
   tracks?: JBrowseTrack[]
   plugins?: JBrowsePlugin[]
   internetAccounts?: JBrowseInternetAccount[]
@@ -39,28 +42,40 @@ export interface SerializedImportJBrowseConfigChange {
 }
 
 export function filterJBrowseConfig(config: JBrowseConfig): JBrowseConfig {
-  const { __v, _id, assemblies, internetAccounts, plugins, tracks, ...rest } =
-    config
-  const filteredAssemblies = assemblies?.filter(
-    (a) => a.sequence.adapter.type !== 'ApolloSequenceAdapter',
-  )
-  const filteredTracks = tracks?.filter((t) => t.type !== 'ApolloTrack')
-  const filteredPlugins = plugins?.filter((p) => p.name !== 'Apollo')
-  const filteredInternetAccounts = internetAccounts?.filter(
-    (i) => i.type !== 'ApolloInternetAccount',
-  )
+  const {
+    __v,
+    _id,
+    assemblies,
+    configuration,
+    internetAccounts,
+    plugins,
+    tracks,
+    ...rest
+  } = config
+  // Need to make sure that configuration.ApolloPlugin.hasRole isn't set
   const filteredConfig = rest as JBrowseConfig
-  if (filteredAssemblies) {
-    filteredConfig.assemblies = filteredAssemblies
+  if (assemblies) {
+    filteredConfig.assemblies = assemblies.filter(
+      (a) => a.sequence.adapter.type !== 'ApolloSequenceAdapter',
+    )
   }
-  if (filteredTracks) {
-    filteredConfig.tracks = filteredTracks
+  if (configuration?.ApolloPlugin?.hasRole) {
+    const { hasRole, ...apolloPluginRest } = configuration.ApolloPlugin
+    filteredConfig.configuration = {
+      ...configuration,
+      ApolloPlugin: apolloPluginRest,
+    }
+  }
+  if (internetAccounts) {
+    filteredConfig.internetAccounts = internetAccounts.filter(
+      (i) => i.type !== 'ApolloInternetAccount',
+    )
   }
-  if (filteredPlugins) {
-    filteredConfig.plugins = filteredPlugins
+  if (plugins) {
+    filteredConfig.plugins = plugins.filter((p) => p.name !== 'Apollo')
   }
-  if (filteredInternetAccounts) {
-    filteredConfig.internetAccounts = filteredInternetAccounts
+  if (tracks) {
+    filteredConfig.trackss = tracks.filter((t) => t.type !== 'ApolloTrack')
   }
   return filteredConfig
 }

package/src/Changes/LocationEndChange.ts

@@ -60,19 +60,32 @@ export class LocationEndChange extends FeatureChange {
   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.
+    const topLevelFeatures: FeatureDocument[] = []
     for (const change of changes) {
-      const { featureId, oldEnd } = change
-
-      // Search correct feature
-      const topLevelFeature = await featureModel
-        .findOne({ allIds: featureId })
-        .session(session)
-        .exec()
+      const { featureId, oldEnd, newEnd } = change
+
+      // See if we already have top-level feature for this feature
+      let topLevelFeature: FeatureDocument | undefined | null
+      let feature: Feature | undefined | null
+      for (const tlv of topLevelFeatures) {
+        const childFeature = this.getFeatureFromId(tlv, featureId)
+        if (childFeature) {
+          topLevelFeature = tlv
+          feature = childFeature
+          break
+        }
+      }
+      if (!topLevelFeature) {
+        // Don't already have top-level feature, so let's query it
+        topLevelFeature = await featureModel
+          .findOne({ allIds: featureId })
+          .session(session)
+          .exec()
+        if (topLevelFeature) {
+          topLevelFeatures.push(topLevelFeature)
+        }
+      }
 
       if (!topLevelFeature) {
         const errMsg = `*** ERROR: The following featureId was not found in database ='${featureId}'`
@@ -84,57 +97,34 @@ export class LocationEndChange extends FeatureChange {
         `*** TOP level feature found: ${JSON.stringify(topLevelFeature)}`,
       )
 
-      const foundFeature = this.getFeatureFromId(topLevelFeature, featureId)
-      if (!foundFeature) {
+      if (!feature) {
+        feature = this.getFeatureFromId(topLevelFeature, featureId)
+      }
+      if (!feature) {
         const errMsg = 'ERROR when searching feature by featureId'
         logger.error(errMsg)
         throw new Error(errMsg)
       }
-      logger.debug?.(`*** Found feature: ${JSON.stringify(foundFeature)}`)
-      if (foundFeature.max === oldEnd) {
-        featuresForChanges.push({ feature: foundFeature, topLevelFeature })
-      } else {
-        if (foundFeature.children) {
-          for (const [, childFeature] of foundFeature.children) {
-            if (childFeature.max === oldEnd) {
-              logger.debug?.(
-                `*************** UPDATE CHILD FEATURE ID= ${featureId}, CHILD: ${JSON.stringify(
-                  childFeature,
-                )}`,
-              )
-              featuresForChanges.push({
-                feature: childFeature,
-                topLevelFeature,
-              })
-              break
-            }
-          }
-        }
+      logger.debug?.(`*** Found feature: ${JSON.stringify(feature)}`)
+      if (feature.max !== oldEnd) {
+        const errMsg = 'Expected previous max does not match'
+        logger.error(errMsg)
+        throw new Error(errMsg)
       }
-    }
-
-    // Let's update objects.
-    for (const [idx, change] of changes.entries()) {
-      const { newEnd } = change
-      const { feature, topLevelFeature } = featuresForChanges[idx]
       feature.max = newEnd
       if (topLevelFeature._id.equals(feature._id)) {
         topLevelFeature.markModified('end') // 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
       }
-
+    }
+    for (const tlv of topLevelFeatures) {
       try {
-        await topLevelFeature.save()
+        await tlv.save()
       } catch (error) {
         logger.debug?.(`*** FAILED: ${error}`)
         throw error
       }
-      logger.debug?.(
-        `*** Object updated in Mongo. New object: ${JSON.stringify(
-          topLevelFeature,
-        )}`,
-      )
     }
   }
 
@@ -146,12 +136,13 @@ export class LocationEndChange extends FeatureChange {
     if (!dataStore) {
       throw new Error('No data store')
     }
-    for (const [idx, changedId] of this.changedIds.entries()) {
-      const feature = dataStore.getFeature(changedId)
+    for (const change of this.changes) {
+      const { featureId, newEnd } = change
+      const feature = dataStore.getFeature(featureId)
       if (!feature) {
-        throw new Error(`Could not find feature with identifier "${changedId}"`)
+        throw new Error(`Could not find feature with identifier "${featureId}"`)
       }
-      feature.setMax(this.changes[idx].newEnd)
+      feature.setMax(newEnd)
     }
   }