ADDITIONAL_IDS -> INDEXED_IDS

Author: garrettjstevens

packages/apollo-collaboration-server/src/app.module.ts

@@ -57,7 +57,7 @@ const validationSchema = Joi.object({
   DESCRIPTION: Joi.string(),
   FEATURE_TYPE_ONTOLOGY_LOCATION: Joi.string(),
   PLUGIN_LOCATION: Joi.string(),
-  ADDITIONAL_IDS: Joi.string().default('gff_id'),
+  INDEXED_IDS: Joi.string().default('gff_id'),
   ALLOW_ROOT_USER: Joi.boolean().default(false),
   ROOT_USER_PASSWORD: Joi.string(),
   ROOT_USER_PASSWORD_FILE: Joi.string(),

packages/apollo-common/src/AssemblySpecificChange.ts

@@ -31,18 +31,18 @@ export abstract class AssemblySpecificChange extends Change {
 
   getIndexedIds(
     feature: AnnotationFeatureSnapshot,
-    additionalIds: string[] | undefined,
+    idsToIndex: string[] | undefined,
   ): string[] {
     const indexedIds: string[] = []
-    for (const additionalId of additionalIds ?? []) {
+    for (const additionalId of idsToIndex ?? []) {
       const idValue = feature.attributes?.[additionalId]
       if (idValue) {
         indexedIds.push(idValue[0])
       }
     }
     if (feature.children) {
       for (const child of Object.values(feature.children)) {
-        const childIndexedIds = this.getIndexedIds(child, additionalIds)
+        const childIndexedIds = this.getIndexedIds(child, idsToIndex)
         indexedIds.push(...childIndexedIds)
       }
     }

packages/apollo-shared/src/Changes/AddFeatureChange.ts

@@ -89,10 +89,10 @@ export class AddFeatureChange extends FeatureChange {
     let featureCnt = 0
     logger.debug?.(`changes: ${JSON.stringify(changes)}`)
 
-    const { ADDITIONAL_IDS } = process.env
-    let additionalIds: string[] | undefined
-    if (ADDITIONAL_IDS) {
-      additionalIds = ADDITIONAL_IDS.split(',')
+    const { INDEXED_IDS } = process.env
+    let idsToIndex: string[] | undefined
+    if (INDEXED_IDS) {
+      idsToIndex = INDEXED_IDS.split(',')
     }
 
     // Loop the changes
@@ -112,7 +112,7 @@ export class AddFeatureChange extends FeatureChange {
 
       // CopyFeature is called from CopyFeature.tsx
       if (copyFeature) {
-        const indexedIds = this.getIndexedIds(addedFeature, additionalIds)
+        const indexedIds = this.getIndexedIds(addedFeature, idsToIndex)
         // Add into Mongo
         const [newFeatureDoc] = await featureModel.create(
           [{ ...addedFeature, allIds, indexedIds, status: -1, user }],
@@ -150,7 +150,7 @@ export class AddFeatureChange extends FeatureChange {
         } else {
           const childIds = this.getChildFeatureIds(addedFeature)
           const allIdsV2 = [_id, ...childIds]
-          const indexedIds = this.getIndexedIds(addedFeature, additionalIds)
+          const indexedIds = this.getIndexedIds(addedFeature, idsToIndex)
           const [newFeatureDoc] = await featureModel.create(
             [{ allIds: allIdsV2, indexedIds, status: 0, ...addedFeature }],
             { session },

packages/apollo-shared/src/Changes/FromFileBaseChange.ts

@@ -184,10 +184,10 @@ export abstract class FromFileBaseChange extends AssemblySpecificChange {
   }
 
   async addFeatureIntoDb(gff3Feature: GFF3Feature, backend: ServerDataStore) {
-    const { ADDITIONAL_IDS } = process.env
-    let additionalIds: string[] | undefined
-    if (ADDITIONAL_IDS) {
-      additionalIds = ADDITIONAL_IDS.split(',')
+    const { INDEXED_IDS } = process.env
+    let idsToIndex: string[] | undefined
+    if (INDEXED_IDS) {
+      idsToIndex = INDEXED_IDS.split(',')
     }
     const { assembly, refSeqCache } = this
     const { featureModel, refSeqModel, user } = backend
@@ -214,7 +214,7 @@ export abstract class FromFileBaseChange extends AssemblySpecificChange {
     }
     const newFeature = gff3ToAnnotationFeature(gff3Feature, refSeqDoc._id)
     const allIds = this.getAllIds(newFeature)
-    const indexedIds = this.getIndexedIds(newFeature, additionalIds)
+    const indexedIds = this.getIndexedIds(newFeature, idsToIndex)
 
     // Add into Mongo
     // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction

packages/website/docs/02-installation/04-configuration-options.md

@@ -64,10 +64,10 @@ MICROSOFT_CLIENT_SECRET=client_secret_here
 # Defaults to relative URL 'sequence_ontology.json'
 # FEATURE_TYPE_ONTOLOGY_LOCATION=sequence_ontology.json
 
-# Comma-separated list of additional attributes in features to treat as ids
+# Comma-separated list of attributes in features to treat as ids
 # These will be added to feature documents' "indexedIds"
 # Defaults to gff_id
-# ADDITIONAL_IDS=gff_id,gene_id,transcript_id,exon_id
+# INDEXED_IDS=gff_id,gene_id,transcript_id,exon_id
 
 # Application port, defaults to 3999
 # PORT=3999