@apollo-annotation/shared 0.1.17 → 0.1.19

package/src/Changes/LocationEndChange.ts

@@ -30,7 +30,7 @@ interface SerializedLocationEndChangeMultiple
   changes: LocationEndChangeDetails[]
 }
 
-type SerializedLocationEndChange =
+export type SerializedLocationEndChange =
   | SerializedLocationEndChangeSingle
   | SerializedLocationEndChangeMultiple
 
@@ -80,7 +80,9 @@ export class LocationEndChange extends FeatureChange {
         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)}`)
+      logger.debug?.(
+        `*** TOP level feature found: ${JSON.stringify(topLevelFeature)}`,
+      )
 
       const foundFeature = this.getFeatureFromId(topLevelFeature, featureId)
       if (!foundFeature) {
@@ -89,28 +91,33 @@ export class LocationEndChange extends FeatureChange {
         throw new Error(errMsg)
       }
       logger.debug?.(`*** Found feature: ${JSON.stringify(foundFeature)}`)
-      if (
-        foundFeature.discontinuousLocations &&
-        foundFeature.discontinuousLocations.length > 0
-      ) {
-        const errMsg =
-          'Must use "DiscontinuousLocationEndChange" to change a feature end that has discontinuous locations'
-        logger.error(errMsg)
-        throw new Error(errMsg)
-      }
-      if (foundFeature.end !== oldEnd) {
-        const errMsg = `*** ERROR: Feature's current end value ${foundFeature.end} doesn't match with expected value ${oldEnd}`
-        logger.error(errMsg)
-        throw new Error(errMsg)
+      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
+            }
+          }
+        }
       }
-      featuresForChanges.push({ feature: foundFeature, topLevelFeature })
     }
 
     // Let's update objects.
     for (const [idx, change] of changes.entries()) {
       const { newEnd } = change
       const { feature, topLevelFeature } = featuresForChanges[idx]
-      feature.end = newEnd
+      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 {
@@ -144,7 +151,7 @@ export class LocationEndChange extends FeatureChange {
       if (!feature) {
         throw new Error(`Could not find feature with identifier "${changedId}"`)
       }
-      feature.setEnd(this.changes[idx].newEnd)
+      feature.setMax(this.changes[idx].newEnd)
     }
   }
 

package/src/Changes/LocationStartChange.ts

@@ -30,7 +30,7 @@ interface SerializedLocationStartChangeMultiple
   changes: LocationStartChangeDetails[]
 }
 
-type SerializedLocationStartChange =
+export type SerializedLocationStartChange =
   | SerializedLocationStartChangeSingle
   | SerializedLocationStartChangeMultiple
 
@@ -80,7 +80,9 @@ export class LocationStartChange extends FeatureChange {
         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)}`)
+      logger.debug?.(
+        `*** TOP level feature found: ${JSON.stringify(topLevelFeature)}`,
+      )
 
       const foundFeature = this.getFeatureFromId(topLevelFeature, featureId)
       if (!foundFeature) {
@@ -89,28 +91,33 @@ export class LocationStartChange extends FeatureChange {
         throw new Error(errMsg)
       }
       logger.debug?.(`*** Found feature: ${JSON.stringify(foundFeature)}`)
-      if (
-        foundFeature.discontinuousLocations &&
-        foundFeature.discontinuousLocations.length > 0
-      ) {
-        const errMsg =
-          'Must use "DiscontinuousLocationStartChange" to change a feature start that has discontinuous locations'
-        logger.error(errMsg)
-        throw new Error(errMsg)
-      }
-      if (foundFeature.start !== oldStart) {
-        const errMsg = `*** ERROR: Feature's current start value ${foundFeature.start} doesn't match with expected value ${oldStart}`
-        logger.error(errMsg)
-        throw new Error(errMsg)
+      if (foundFeature.min === oldStart) {
+        featuresForChanges.push({ feature: foundFeature, topLevelFeature })
+      } else {
+        if (foundFeature.children) {
+          for (const [, childFeature] of foundFeature.children) {
+            if (childFeature.min === oldStart) {
+              logger.debug?.(
+                `*** UPDATE CHILD FEATURE ID= ${featureId}, CHILD: ${JSON.stringify(
+                  childFeature,
+                )}`,
+              )
+              featuresForChanges.push({
+                feature: childFeature,
+                topLevelFeature,
+              })
+              break
+            }
+          }
+        }
       }
-      featuresForChanges.push({ feature: foundFeature, topLevelFeature })
     }
 
     // Let's update objects.
     for (const [idx, change] of changes.entries()) {
       const { newStart } = change
       const { feature, topLevelFeature } = featuresForChanges[idx]
-      feature.start = newStart
+      feature.min = newStart
       if (topLevelFeature._id.equals(feature._id)) {
         topLevelFeature.markModified('start') // Mark as modified. Without this save() -method is not updating data in database
       } else {
@@ -144,7 +151,7 @@ export class LocationStartChange extends FeatureChange {
       if (!feature) {
         throw new Error(`Could not find feature with identifier "${changedId}"`)
       }
-      feature.setStart(this.changes[idx].newStart)
+      feature.setMin(this.changes[idx].newStart)
     }
   }
 

package/src/Changes/TypeChange.ts

@@ -29,7 +29,7 @@ interface SerializedTypeChangeMultiple extends SerializedTypeChangeBase {
   changes: TypeChangeDetails[]
 }
 
-type SerializedTypeChange =
+export type SerializedTypeChange =
   | SerializedTypeChangeSingle
   | SerializedTypeChangeMultiple
 

package/src/Changes/index.ts

@@ -3,12 +3,12 @@ import { AddAssemblyFromExternalChange } from './AddAssemblyFromExternalChange'
 import { AddAssemblyFromFileChange } from './AddAssemblyFromFileChange'
 import { AddFeatureChange } from './AddFeatureChange'
 import { AddFeaturesFromFileChange } from './AddFeaturesFromFileChange'
+import { AddRefSeqAliasesChange } from './AddRefSeqAliasesChange'
 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 { ImportJBrowseConfigChange } from './ImportJBrowseConfigChange'
 import { LocationEndChange } from './LocationEndChange'
 import { LocationStartChange } from './LocationStartChange'
 import { StrandChange } from './StrandChange'
@@ -24,14 +24,14 @@ export const changes = {
   DeleteAssemblyChange,
   DeleteFeatureChange,
   DeleteUserChange,
-  DiscontinuousLocationEndChange,
-  DiscontinuousLocationStartChange,
   FeatureAttributeChange,
+  ImportJBrowseConfigChange,
   LocationEndChange,
   LocationStartChange,
   StrandChange,
   TypeChange,
   UserChange,
+  AddRefSeqAliasesChange,
 }
 
 export * from './AddAssemblyAndFeaturesFromFileChange'
@@ -42,11 +42,11 @@ export * from './AddFeaturesFromFileChange'
 export * from './DeleteAssemblyChange'
 export * from './DeleteFeatureChange'
 export * from './DeleteUserChange'
-export * from './DiscontinuousLocationEndChange'
-export * from './DiscontinuousLocationStartChange'
 export * from './FeatureAttributeChange'
+export * from './ImportJBrowseConfigChange'
 export * from './LocationEndChange'
 export * from './LocationStartChange'
 export * from './StrandChange'
 export * from './TypeChange'
 export * from './UserChange'
+export * from './AddRefSeqAliasesChange'