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Add click and drag to gene glyphs (#269)
* click and drag gene glyphs * click and drag canonical gene glyph * ImplicitExonGeneGlyph changes * canonical gene glyph without execute * changes * cds discontinuous start/end location change * change * Fix import of discontinuousLocations features * Draw locations in discontinuousLocations features * Add discontinuous locations to grid editor --------- Co-authored-by: Garrett Stevens <[email protected]>
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packages/apollo-shared/src/Changes/DiscontinuousLocationEndChange.ts
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,175 @@ | ||
| import { | ||
| ChangeOptions, | ||
| ClientDataStore, | ||
| FeatureChange, | ||
| LocalGFF3DataStore, | ||
| SerializedFeatureChange, | ||
| ServerDataStore, | ||
| } from 'apollo-common' | ||
|
|
||
| interface SerializedDiscontinuousLocationEndChangeBase | ||
| extends SerializedFeatureChange { | ||
| typeName: 'DiscontinuousLocationEndChange' | ||
| } | ||
|
|
||
| interface DiscontinuousLocationEndChangeDetails { | ||
| featureId: string | ||
| oldEnd: number | ||
| newEnd: number | ||
| index: number | ||
| } | ||
|
|
||
| interface SerializedDiscontinuousLocationEndChangeSingle | ||
| extends SerializedDiscontinuousLocationEndChangeBase, | ||
| DiscontinuousLocationEndChangeDetails {} | ||
|
|
||
| interface SerializedDiscontinuousLocationEndChangeMultiple | ||
| extends SerializedDiscontinuousLocationEndChangeBase { | ||
| changes: DiscontinuousLocationEndChangeDetails[] | ||
| } | ||
|
|
||
| type SerializedDiscontinuousLocationEndChange = | ||
| | SerializedDiscontinuousLocationEndChangeSingle | ||
| | SerializedDiscontinuousLocationEndChangeMultiple | ||
|
|
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| export class DiscontinuousLocationEndChange extends FeatureChange { | ||
| typeName = 'DiscontinuousLocationEndChange' as const | ||
| changes: DiscontinuousLocationEndChangeDetails[] | ||
|
|
||
| constructor( | ||
| json: SerializedDiscontinuousLocationEndChange, | ||
| options?: ChangeOptions, | ||
| ) { | ||
| super(json, options) | ||
| this.changes = 'changes' in json ? json.changes : [json] | ||
| } | ||
|
|
||
| toJSON(): SerializedDiscontinuousLocationEndChange { | ||
| const { assembly, changedIds, changes, typeName } = this | ||
| if (changes.length === 1) { | ||
| const [{ featureId, index, newEnd, oldEnd }] = changes | ||
| return { | ||
| typeName, | ||
| changedIds, | ||
| assembly, | ||
| featureId, | ||
| oldEnd, | ||
| newEnd, | ||
| index, | ||
| } | ||
| } | ||
| return { typeName, changedIds, assembly, changes } | ||
| } | ||
|
|
||
| async executeOnServer(backend: ServerDataStore) { | ||
| const { featureModel, session } = backend | ||
| const { changes, logger } = this | ||
| for (const change of changes) { | ||
| const { featureId, index, newEnd, oldEnd: expectedOldEnd } = 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 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(feature)}`) | ||
| if ( | ||
| !feature.discontinuousLocations || | ||
| feature.discontinuousLocations.length === 0 | ||
| ) { | ||
| const errMsg = | ||
| 'Must use "LocationEndChange" to change a feature end that does not have discontinuous locations' | ||
| logger.error(errMsg) | ||
| throw new Error(errMsg) | ||
| } | ||
| const oldEnd = feature.discontinuousLocations[index].end | ||
| if (oldEnd !== expectedOldEnd) { | ||
| const errMsg = `Location's current end value ${oldEnd} doesn't match with expected value ${expectedOldEnd}` | ||
| logger.error(errMsg) | ||
| throw new Error(errMsg) | ||
| } | ||
| const { start } = feature.discontinuousLocations[index] | ||
| if (newEnd <= start) { | ||
| const errMsg = `location end (${newEnd}) can't be smaller than location start (${start})` | ||
| logger.error(errMsg) | ||
| throw new Error(errMsg) | ||
| } | ||
| const nextLocation = feature.discontinuousLocations[index + 1] | ||
| if (nextLocation && newEnd >= nextLocation.start) { | ||
| const errMsg = `Location end (${newEnd}) can't be larger than the next location's start (${nextLocation.start})` | ||
| logger.error(errMsg) | ||
| throw new Error(errMsg) | ||
| } | ||
| feature.discontinuousLocations[index].end = newEnd | ||
| if (index === feature.discontinuousLocations.length - 1) { | ||
| feature.end = newEnd | ||
| } | ||
|
|
||
| try { | ||
| topLevelFeature.markModified('discontinuousLocations') | ||
| 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 { index, newEnd } = this.changes[idx] | ||
| feature.setCDSDiscontinuousLocationEnd(newEnd, index) | ||
| } | ||
| } | ||
|
|
||
| getInverse() { | ||
| const { assembly, changedIds, changes, logger, typeName } = this | ||
| const inverseChangedIds = [...changedIds].reverse() | ||
| const inverseChanges = [...changes].reverse().map((change) => ({ | ||
| featureId: change.featureId, | ||
| oldEnd: change.newEnd, | ||
| newEnd: change.oldEnd, | ||
| index: change.index, | ||
| })) | ||
| return new DiscontinuousLocationEndChange( | ||
| { | ||
| changedIds: inverseChangedIds, | ||
| typeName, | ||
| changes: inverseChanges, | ||
| assembly, | ||
| }, | ||
| { logger }, | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| export function isDiscontinuousLocationEndChange( | ||
| change: unknown, | ||
| ): change is DiscontinuousLocationEndChange { | ||
| return ( | ||
| (change as DiscontinuousLocationEndChange).typeName === | ||
| 'DiscontinuousLocationEndChange' | ||
| ) | ||
| } |
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