@apollo-annotation/shared 0.3.10 → 0.3.11

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/shared",
-  "version": "0.3.10",
+  "version": "0.3.11",
   "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": "^0.3.10",
-    "@apollo-annotation/mst": "^0.3.10",
-    "@apollo-annotation/schemas": "^0.3.10",
+    "@apollo-annotation/common": "^0.3.11",
+    "@apollo-annotation/mst": "^0.3.11",
+    "@apollo-annotation/schemas": "^0.3.11",
     "@gmod/gff": "^2.0.0",
     "@gmod/indexedfasta": "^2.0.4",
     "@jbrowse/core": "^3.6.5",

package/src/Changes/AddFeatureChange.ts

@@ -123,6 +123,7 @@ export class AddFeatureChange extends FeatureChange {
         )
         featureCnt++
       } else {
+        const indexedIds = this.getIndexedIds(addedFeature, idsToIndex)
         // Adding new child feature
         if (parentFeatureId) {
           const topLevelFeature = await featureModel
@@ -146,11 +147,14 @@ export class AddFeatureChange extends FeatureChange {
           this.addChild(parentFeature, addedFeature)
           const childIds = this.getChildFeatureIds(addedFeature)
           topLevelFeature.allIds.push(_id, ...childIds)
+          if (indexedIds.length > 0 && !topLevelFeature.indexedIds) {
+            topLevelFeature.indexedIds = []
+          }
+          topLevelFeature.indexedIds?.push(...indexedIds)
           await topLevelFeature.save()
         } else {
           const childIds = this.getChildFeatureIds(addedFeature)
           const allIdsV2 = [_id, ...childIds]
-          const indexedIds = this.getIndexedIds(addedFeature, idsToIndex)
           const [newFeatureDoc] = await featureModel.create(
             [{ allIds: allIdsV2, indexedIds, status: 0, ...addedFeature }],
             { session },

package/src/Changes/DeleteFeatureChange.ts

@@ -67,6 +67,12 @@ export class DeleteFeatureChange extends FeatureChange {
     const { featureModel, session } = backend
     const { changes, logger } = this
 
+    const { INDEXED_IDS } = process.env
+    let idsToIndex: string[] | undefined
+    if (INDEXED_IDS) {
+      idsToIndex = INDEXED_IDS.split(',')
+    }
+
     // Loop the changes
     for (const change of changes) {
       const { deletedFeature, parentFeatureId } = change
@@ -105,6 +111,18 @@ export class DeleteFeatureChange extends FeatureChange {
       featureDoc.allIds = featureDoc.allIds.filter(
         (id) => !deletedIds.includes(id),
       )
+      const indexedIds = this.getIndexedIds(featureDoc, idsToIndex)
+      if (featureDoc.indexedIds) {
+        if (indexedIds.length > 0) {
+          featureDoc.indexedIds = indexedIds
+        } else {
+          delete featureDoc.indexedIds
+        }
+      } else {
+        if (indexedIds.length > 0) {
+          featureDoc.indexedIds = indexedIds
+        }
+      }
       // Save updated document in Mongo
       featureDoc.markModified('children') // Mark as modified. Without this save() -method is not updating data in database
       try {

package/src/Changes/FeatureAttributeChange.ts

@@ -100,11 +100,24 @@ export class FeatureAttributeChange extends FeatureChange {
       featuresForChanges.push({ feature: foundFeature, topLevelFeature })
     }
 
+    const { INDEXED_IDS } = process.env
+    let idsToIndex: string[] | undefined
+    if (INDEXED_IDS) {
+      idsToIndex = INDEXED_IDS.split(',')
+    }
     // Let's update objects
     for (const [idx, change] of changes.entries()) {
       const { newAttributes } = change
       const { feature, topLevelFeature } = featuresForChanges[idx]
+      const indexedIdsChanged = idsToIndex?.some(
+        (id) => id in newAttributes || id in (feature?.attributes ?? {}),
+      )
       feature.attributes = newAttributes
+      if (indexedIdsChanged) {
+        const indexedIds = this.getIndexedIds(topLevelFeature, idsToIndex)
+        topLevelFeature.indexedIds = indexedIds
+        topLevelFeature.markModified('indexedIds')
+      }
       if (topLevelFeature._id.equals(feature._id)) {
         topLevelFeature.markModified('attributes') // Mark as modified. Without this save() -method is not updating data in database
       } else {