cds discontinuous start/end location change

packages/apollo-mst/src/AnnotationFeature.ts

@@ -113,6 +113,15 @@ export const AnnotationFeature = types
         self.start = start
       }
     },
+    setCDSDiscontinuousLocationStart(start: number, index: number) {
+      const dl = self.discontinuousLocations
+      if (dl && dl.length > 0 && dl[index].start !== start) {
+        dl[index].start = start
+        if (index === 0) {
+          self.start = start
+        }
+      }
+    },
     setEnd(end: number) {
       if (end < self.start) {
         throw new Error(`End "${end}" is less than start "${self.start}"`)
@@ -121,6 +130,15 @@ export const AnnotationFeature = types
         self.end = end
       }
     },
+    setCDSDiscontinuousLocationEnd(end: number, index: number) {
+      const dl = self.discontinuousLocations
+      if (dl && dl.length > 0 && dl[index].end !== end) {
+        dl[index].end = end
+        if (index === 0) {
+          self.end = end
+        }
+      }
+    },
     setStrand(strand?: 1 | -1) {
       self.strand = strand
     },

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

@@ -0,0 +1,158 @@
+import {
+  ChangeOptions,
+  ClientDataStore,
+  FeatureChange,
+  LocalGFF3DataStore,
+  SerializedFeatureChange,
+  ServerDataStore,
+} from 'apollo-common'
+
+interface SerializedDiscontinuousLocationChangeBase
+  extends SerializedFeatureChange {
+  typeName: 'DiscontinuousLocationChange'
+}
+
+interface DiscontinuousLocationChangeDetails {
+  featureId: string
+  start?: {
+    newStart: number
+    index: number // discontinuous location index
+  }
+  end?: {
+    newEnd: number
+    index: number // discontinuous location index
+  }
+}
+
+interface SerializedDiscontinuousLocationChangeSingle
+  extends SerializedDiscontinuousLocationChangeBase,
+    DiscontinuousLocationChangeDetails {}
+
+interface SerializedDiscontinuousLocationChangeMultiple
+  extends SerializedDiscontinuousLocationChangeBase {
+  changes: DiscontinuousLocationChangeDetails[]
+}
+
+type SerializedDiscontinuousLocationChange =
+  | SerializedDiscontinuousLocationChangeSingle
+  | SerializedDiscontinuousLocationChangeMultiple
+
+export class DiscontinuousLocationChange extends FeatureChange {
+  typeName = 'DiscontinuousLocationChange' as const
+  changes: DiscontinuousLocationChangeDetails[]
+
+  constructor(
+    json: SerializedDiscontinuousLocationChange,
+    options?: ChangeOptions,
+  ) {
+    super(json, options)
+    this.changes = 'changes' in json ? json.changes : [json]
+  }
+
+  toJSON(): SerializedDiscontinuousLocationChange {
+    const { assembly, changedIds, changes, typeName } = this
+    if (changes.length === 1) {
+      const [{ end, featureId, start }] = changes
+      return { typeName, changedIds, assembly, featureId, start, end }
+    }
+    return { typeName, changedIds, assembly, changes }
+  }
+
+  async executeOnServer(backend: ServerDataStore) {
+    const { featureModel, session } = backend
+    const { changes, logger } = this
+    for (const change of changes) {
+      const { end, featureId, start } = change
+      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)
+      }
+
+      const cdsFeature = this.getFeatureFromId(topLevelFeature, featureId)
+      if (!cdsFeature?.discontinuousLocations) {
+        const errMsg = 'ERROR when searching feature by featureId'
+        logger.error(errMsg)
+        throw new Error(errMsg)
+      }
+
+      let locChanged
+      if (start) {
+        cdsFeature.discontinuousLocations[start.index].start = start.newStart
+        if (start.index === 0) {
+          cdsFeature.start = start.newStart
+        }
+        locChanged = true
+      }
+
+      if (end) {
+        cdsFeature.discontinuousLocations[end.index].end = end.newEnd
+        if (end.index === 0) {
+          cdsFeature.end = end.newEnd
+        }
+        locChanged = true
+      }
+
+      if (locChanged) {
+        try {
+          // Mark as modified. Without this save() -method is not updating data in database
+          topLevelFeature.markModified('children')
+          await topLevelFeature.save()
+        } catch (error) {
+          logger.debug?.(`*** FAILED: ${error}`)
+          throw error
+        }
+      }
+    }
+  }
+
+  async executeOnLocalGFF3(_backend: LocalGFF3DataStore) {
+    throw new Error('executeOnLocalGFF3 not implemented')
+  }
+
+  async executeOnClient(dataStore: ClientDataStore) {
+    if (!dataStore) {
+      throw new Error('No data store')
+    }
+    for (const [idx, changedId] of this.changedIds.entries()) {
+      const feature = dataStore.getFeature(changedId)
+      if (!feature) {
+        throw new Error(`Could not find feature with identifier "${changedId}"`)
+      }
+      const change = this.changes[idx]
+      const { end, start } = change
+
+      if (start) {
+        feature.setCDSDiscontinuousLocationStart(start.newStart, start.index)
+      }
+
+      if (end) {
+        feature.setCDSDiscontinuousLocationEnd(end.newEnd, end.index)
+      }
+    }
+  }
+
+  getInverse() {
+    const { assembly, changedIds, changes, logger, typeName } = this
+    const inverseChangedIds = [...changedIds].reverse()
+    const inverseChanges = [...changes].reverse().map((c) => ({
+      featureId: c.featureId,
+      start: c.start,
+      end: c.end,
+    }))
+    return new DiscontinuousLocationChange(
+      {
+        changedIds: inverseChangedIds,
+        typeName,
+        changes: inverseChanges,
+        assembly,
+      },
+      { logger },
+    )
+  }
+}

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

@@ -6,6 +6,7 @@ import { AddFeaturesFromFileChange } from './AddFeaturesFromFileChange'
 import { DeleteAssemblyChange } from './DeleteAssemblyChange'
 import { DeleteFeatureChange } from './DeleteFeatureChange'
 import { DeleteUserChange } from './DeleteUserChange'
+import { DiscontinuousLocationChange } from './DiscontinuousLocationChange'
 import { FeatureAttributeChange } from './FeatureAttributeChange'
 import { LocationEndChange } from './LocationEndChange'
 import { LocationStartChange } from './LocationStartChange'
@@ -24,6 +25,7 @@ export const changes = {
   DeleteUserChange,
   LocationEndChange,
   LocationStartChange,
+  DiscontinuousLocationChange,
   TypeChange,
   UserChange,
 }
@@ -39,5 +41,6 @@ export * from './DeleteUserChange'
 export * from './FeatureAttributeChange'
 export * from './LocationEndChange'
 export * from './LocationStartChange'
+export * from './DiscontinuousLocationChange'
 export * from './TypeChange'
 export * from './UserChange'