@apollo-annotation/shared 0.3.13 → 1.0.1

package/dist/Changes/{MergeTranscriptsChange.d.ts → MergeAndUndoMergeTranscriptsChanges.d.ts}

@@ -1,7 +1,6 @@
-import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
+import { type ChangeOptions, FeatureChange, type SerializedFeatureChange } from '@apollo-annotation/common';
 import type { AnnotationFeature, AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
 import type { Feature } from '@apollo-annotation/schemas';
-import { UndoMergeTranscriptsChange } from './UndoMergeTranscriptsChange.js';
 interface SerializedMergeTranscriptsChangeBase extends SerializedFeatureChange {
     typeName: 'MergeTranscriptsChange';
 }
@@ -16,20 +15,37 @@ interface SerializedMergeTranscriptsChangeMultiple extends SerializedMergeTransc
     changes: MergeTranscriptsChangeDetails[];
 }
 export type SerializedMergeTranscriptsChange = SerializedMergeTranscriptsChangeSingle | SerializedMergeTranscriptsChangeMultiple;
+interface SerializedUndoMergeTranscriptsChangeBase extends SerializedFeatureChange {
+    typeName: 'UndoMergeTranscriptsChange';
+}
+export interface UndoMergeTranscriptsChangeDetails {
+    transcriptsToRestore: AnnotationFeatureSnapshot[];
+    parentFeatureId: string;
+}
+interface SerializedUndoMergeTranscriptsChangeSingle extends SerializedUndoMergeTranscriptsChangeBase, UndoMergeTranscriptsChangeDetails {
+}
+interface SerializedUndoMergeTranscriptsChangeMultiple extends SerializedUndoMergeTranscriptsChangeBase {
+    changes: UndoMergeTranscriptsChangeDetails[];
+}
+export type SerializedUndoMergeTranscriptsChange = SerializedUndoMergeTranscriptsChangeSingle | SerializedUndoMergeTranscriptsChangeMultiple;
 export declare class MergeTranscriptsChange extends FeatureChange {
     typeName: "MergeTranscriptsChange";
     changes: MergeTranscriptsChangeDetails[];
     constructor(json: SerializedMergeTranscriptsChange, options?: ChangeOptions);
     get notification(): string;
     toJSON(): SerializedMergeTranscriptsChange;
-    executeOnServer(backend: ServerDataStore): Promise<void>;
     mergeTranscriptsOnServer(firstTranscript: Feature, secondTranscript: AnnotationFeatureSnapshot): void;
     mergeFeatureIntoTranscriptOnServer(secondFeatureChild: AnnotationFeatureSnapshot, firstTranscript: Feature): void;
-    executeOnClient(dataStore: ClientDataStore): Promise<void>;
     mergeTranscriptsOnClient(firstTranscript: AnnotationFeature, secondTranscript: AnnotationFeatureSnapshot): void;
     mergeFeatureIntoTranscriptOnClient(secondFeatureChild: AnnotationFeatureSnapshot, firstTranscript: AnnotationFeature): void;
-    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
     getInverse(): UndoMergeTranscriptsChange;
 }
+export declare class UndoMergeTranscriptsChange extends FeatureChange {
+    typeName: "UndoMergeTranscriptsChange";
+    changes: UndoMergeTranscriptsChangeDetails[];
+    constructor(json: SerializedUndoMergeTranscriptsChange, options?: ChangeOptions);
+    toJSON(): SerializedUndoMergeTranscriptsChange;
+    getInverse(): MergeTranscriptsChange;
+}
 export {};
-//# sourceMappingURL=MergeTranscriptsChange.d.ts.map
+//# sourceMappingURL=MergeAndUndoMergeTranscriptsChanges.d.ts.map

package/dist/Changes/MergeAndUndoMergeTranscriptsChanges.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"MergeAndUndoMergeTranscriptsChanges.d.ts","sourceRoot":"","sources":["../../src/Changes/MergeAndUndoMergeTranscriptsChanges.ts"],"names":[],"mappings":"AAGA,OAAO,EACL,KAAK,aAAa,EAClB,aAAa,EACb,KAAK,uBAAuB,EAC7B,MAAM,2BAA2B,CAAA;AAClC,OAAO,KAAK,EACV,iBAAiB,EACjB,yBAAyB,EAC1B,MAAM,wBAAwB,CAAA;AAC/B,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,4BAA4B,CAAA;AAMzD,UAAU,oCAAqC,SAAQ,uBAAuB;IAC5E,QAAQ,EAAE,wBAAwB,CAAA;CACnC;AAED,MAAM,WAAW,6BAA6B;IAC5C,eAAe,EAAE,yBAAyB,CAAA;IAC1C,gBAAgB,EAAE,yBAAyB,CAAA;IAC3C,eAAe,EAAE,MAAM,CAAA;CACxB;AAED,UAAU,sCACR,SAAQ,oCAAoC,EAC1C,6BAA6B;CAAG;AAEpC,UAAU,wCACR,SAAQ,oCAAoC;IAC5C,OAAO,EAAE,6BAA6B,EAAE,CAAA;CACzC;AAED,MAAM,MAAM,gCAAgC,GACxC,sCAAsC,GACtC,wCAAwC,CAAA;AAE5C,UAAU,wCACR,SAAQ,uBAAuB;IAC/B,QAAQ,EAAE,4BAA4B,CAAA;CACvC;AAED,MAAM,WAAW,iCAAiC;IAChD,oBAAoB,EAAE,yBAAyB,EAAE,CAAA;IACjD,eAAe,EAAE,MAAM,CAAA;CACxB;AAED,UAAU,0CACR,SAAQ,wCAAwC,EAC9C,iCAAiC;CAAG;AAExC,UAAU,4CACR,SAAQ,wCAAwC;IAChD,OAAO,EAAE,iCAAiC,EAAE,CAAA;CAC7C;AAED,MAAM,MAAM,oCAAoC,GAC5C,0CAA0C,GAC1C,4CAA4C,CAAA;AAEhD,qBAAa,sBAAuB,SAAQ,aAAa;IACvD,QAAQ,2BAAoC;IAC5C,OAAO,EAAE,6BAA6B,EAAE,CAAA;gBAE5B,IAAI,EAAE,gCAAgC,EAAE,OAAO,CAAC,EAAE,aAAa;IAK3E,IAAI,YAAY,WAEf;IAED,MAAM,IAAI,gCAAgC;IAiB1C,wBAAwB,CACtB,eAAe,EAAE,OAAO,EACxB,gBAAgB,EAAE,yBAAyB;IA+B7C,kCAAkC,CAChC,kBAAkB,EAAE,yBAAyB,EAC7C,eAAe,EAAE,OAAO;IA+F1B,wBAAwB,CACtB,eAAe,EAAE,iBAAiB,EAClC,gBAAgB,EAAE,yBAAyB;IA4B7C,kCAAkC,CAChC,kBAAkB,EAAE,yBAAyB,EAC7C,eAAe,EAAE,iBAAiB;IAuEpC,UAAU;CAuBX;AAED,qBAAa,0BAA2B,SAAQ,aAAa;IAC3D,QAAQ,+BAAwC;IAChD,OAAO,EAAE,iCAAiC,EAAE,CAAA;gBAG1C,IAAI,EAAE,oCAAoC,EAC1C,OAAO,CAAC,EAAE,aAAa;IAMzB,MAAM,IAAI,oCAAoC;IAgB9C,UAAU;CAqBX"}

package/dist/Changes/{MergeTranscriptsChange.js → MergeAndUndoMergeTranscriptsChanges.js}

@@ -1,12 +1,9 @@
 /* eslint-disable unicorn/prefer-structured-clone */
-/* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import { FeatureChange, } from '@apollo-annotation/common';
 import { doesIntersect2 } from '@jbrowse/core/util';
 import { getSnapshot } from '@jbrowse/mobx-state-tree';
 import { attributesToRecords, stringifyAttributes } from '../util.js';
-import { findAndDeleteChildFeature } from './DeleteFeatureChange.js';
-import { UndoMergeTranscriptsChange } from './UndoMergeTranscriptsChange.js';
 export class MergeTranscriptsChange extends FeatureChange {
     typeName = 'MergeTranscriptsChange';
     changes;
@@ -33,33 +30,6 @@ export class MergeTranscriptsChange extends FeatureChange {
         }
         return { typeName, changedIds, assembly, changes };
     }
-    async executeOnServer(backend) {
-        const { featureModel, session } = backend;
-        const { changes, logger } = this;
-        for (const change of changes) {
-            const { firstTranscript, secondTranscript } = change;
-            const topLevelFeature = await featureModel
-                .findOne({ allIds: firstTranscript._id })
-                .session(session)
-                .exec();
-            if (!topLevelFeature) {
-                const errMsg = `*** ERROR: The following featureId was not found in database ='${firstTranscript._id}'`;
-                logger.error(errMsg);
-                throw new Error(errMsg);
-            }
-            const mergedTranscript = this.getFeatureFromId(topLevelFeature, firstTranscript._id);
-            if (!mergedTranscript) {
-                const errMsg = 'ERROR when searching feature by featureId';
-                logger.error(errMsg);
-                throw new Error(errMsg);
-            }
-            this.mergeTranscriptsOnServer(mergedTranscript, secondTranscript);
-            const deletedIds = findAndDeleteChildFeature(topLevelFeature, secondTranscript._id, this);
-            deletedIds.push(secondTranscript._id);
-            topLevelFeature.allIds = topLevelFeature.allIds.filter((id) => !deletedIds.includes(id));
-            await topLevelFeature.save();
-        }
-    }
     mergeTranscriptsOnServer(firstTranscript, secondTranscript) {
         firstTranscript.min = Math.min(firstTranscript.min, secondTranscript.min);
         firstTranscript.max = Math.max(firstTranscript.max, secondTranscript.max);
@@ -137,22 +107,6 @@ export class MergeTranscriptsChange extends FeatureChange {
             this.addChild(firstTranscript, secondFeatureChild);
         }
     }
-    /* --------------------------------- */
-    async executeOnClient(dataStore) {
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-        if (!dataStore) {
-            throw new Error('No data store');
-        }
-        for (const [idx, changedId] of this.changedIds.entries()) {
-            const { firstTranscript, secondTranscript } = this.changes[idx];
-            const mergedTranscript = dataStore.getFeature(firstTranscript._id);
-            if (!mergedTranscript) {
-                throw new Error(`Could not find feature with identifier "${changedId}"`);
-            }
-            this.mergeTranscriptsOnClient(mergedTranscript, secondTranscript);
-            mergedTranscript.parent?.deleteChild(secondTranscript._id);
-        }
-    }
     mergeTranscriptsOnClient(firstTranscript, secondTranscript) {
         firstTranscript.setMin(Math.min(firstTranscript.min, secondTranscript.min));
         firstTranscript.setMax(Math.max(firstTranscript.max, secondTranscript.max));
@@ -214,9 +168,6 @@ export class MergeTranscriptsChange extends FeatureChange {
             firstTranscript.addChild(secondFeatureChild);
         }
     }
-    async executeOnLocalGFF3(_backend) {
-        throw new Error('executeOnLocalGFF3 not implemented');
-    }
     getInverse() {
         const { assembly, changedIds, changes, logger } = this;
         const inverseChangedIds = [...changedIds].reverse();
@@ -238,4 +189,43 @@ export class MergeTranscriptsChange extends FeatureChange {
         }, { logger });
     }
 }
-//# sourceMappingURL=MergeTranscriptsChange.js.map
+export class UndoMergeTranscriptsChange extends FeatureChange {
+    typeName = 'UndoMergeTranscriptsChange';
+    changes;
+    constructor(json, options) {
+        super(json, options);
+        this.changes = 'changes' in json ? json.changes : [json];
+    }
+    toJSON() {
+        const { assembly, changedIds, changes, typeName } = this;
+        if (changes.length === 1) {
+            const [{ transcriptsToRestore, parentFeatureId }] = changes;
+            return {
+                typeName,
+                changedIds,
+                assembly,
+                transcriptsToRestore,
+                parentFeatureId,
+            };
+        }
+        return { typeName, changedIds, assembly, changes };
+    }
+    getInverse() {
+        const { assembly, changedIds, changes, logger } = this;
+        const inverseChangedIds = [...changedIds].reverse();
+        const inverseChanges = [...changes]
+            .reverse()
+            .map((undoMergeTranscriptsChange) => ({
+            firstTranscript: undoMergeTranscriptsChange.transcriptsToRestore[0],
+            secondTranscript: undoMergeTranscriptsChange.transcriptsToRestore[1],
+            parentFeatureId: undoMergeTranscriptsChange.parentFeatureId,
+        }));
+        return new MergeTranscriptsChange({
+            changedIds: inverseChangedIds,
+            typeName: 'MergeTranscriptsChange',
+            changes: inverseChanges,
+            assembly,
+        }, { logger });
+    }
+}
+//# sourceMappingURL=MergeAndUndoMergeTranscriptsChanges.js.map

package/dist/Changes/MergeAndUndoMergeTranscriptsChanges.js.map

@@ -0,0 +1 @@
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package/dist/Changes/SplitAndUndoSplitExonChanges.d.ts

@@ -0,0 +1,55 @@
+import { type ChangeOptions, FeatureChange, type SerializedFeatureChange } from '@apollo-annotation/common';
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+interface SerializedSplitExonChangeBase extends SerializedFeatureChange {
+    typeName: 'SplitExonChange';
+}
+export interface SplitExonChangeDetails {
+    exonToBeSplit: AnnotationFeatureSnapshot;
+    parentFeatureId: string;
+    upstreamCut: number;
+    downstreamCut: number;
+    leftExonId: string;
+    rightExonId: string;
+}
+interface SerializedSplitExonChangeSingle extends SerializedSplitExonChangeBase, SplitExonChangeDetails {
+}
+interface SerializedSplitExonChangeMultiple extends SerializedSplitExonChangeBase {
+    changes: SplitExonChangeDetails[];
+}
+export type SerializedSplitExonChange = SerializedSplitExonChangeSingle | SerializedSplitExonChangeMultiple;
+interface SerializedUndoSplitExonChangeBase extends SerializedFeatureChange {
+    typeName: 'UndoSplitExonChange';
+}
+export interface UndoSplitExonChangeDetails {
+    exonToRestore: AnnotationFeatureSnapshot;
+    parentFeatureId: string;
+    idsToDelete: string[];
+    upstreamCut: number;
+    downstreamCut: number;
+    leftExonId: string;
+    rightExonId: string;
+}
+interface SerializedUndoSplitExonChangeSingle extends SerializedUndoSplitExonChangeBase, UndoSplitExonChangeDetails {
+}
+interface SerializedUndoSplitExonChangeMultiple extends SerializedUndoSplitExonChangeBase {
+    changes: UndoSplitExonChangeDetails[];
+}
+export type SerializedUndoSplitExonChange = SerializedUndoSplitExonChangeSingle | SerializedUndoSplitExonChangeMultiple;
+export declare class SplitExonChange extends FeatureChange {
+    typeName: "SplitExonChange";
+    changes: SplitExonChangeDetails[];
+    constructor(json: SerializedSplitExonChange, options?: ChangeOptions);
+    get notification(): string;
+    toJSON(): SerializedSplitExonChange;
+    getInverse(): UndoSplitExonChange;
+    makeSplitExons(exonToBeSplit: AnnotationFeatureSnapshot, upstreamCut: number, downstreamCut: number, leftExonId: string, rightExonId: string): [AnnotationFeatureSnapshot, AnnotationFeatureSnapshot];
+}
+export declare class UndoSplitExonChange extends FeatureChange {
+    typeName: "UndoSplitExonChange";
+    changes: UndoSplitExonChangeDetails[];
+    constructor(json: SerializedUndoSplitExonChange, options?: ChangeOptions);
+    toJSON(): SerializedUndoSplitExonChange;
+    getInverse(): SplitExonChange;
+}
+export {};
+//# sourceMappingURL=SplitAndUndoSplitExonChanges.d.ts.map

package/dist/Changes/SplitAndUndoSplitExonChanges.d.ts.map

@@ -0,0 +1 @@
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package/dist/Changes/SplitAndUndoSplitExonChanges.js

@@ -0,0 +1,115 @@
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+import { FeatureChange, } from '@apollo-annotation/common';
+export class SplitExonChange extends FeatureChange {
+    typeName = 'SplitExonChange';
+    changes;
+    constructor(json, options) {
+        super(json, options);
+        this.changes = 'changes' in json ? json.changes : [json];
+    }
+    // eslint-disable-next-line @typescript-eslint/class-literal-property-style
+    get notification() {
+        return 'Exon successfully split';
+    }
+    toJSON() {
+        const { assembly, changedIds, changes, typeName } = this;
+        if (changes.length === 1) {
+            const [{ exonToBeSplit, parentFeatureId, upstreamCut, downstreamCut, leftExonId, rightExonId, },] = changes;
+            return {
+                typeName,
+                changedIds,
+                assembly,
+                exonToBeSplit,
+                parentFeatureId,
+                upstreamCut,
+                downstreamCut,
+                leftExonId,
+                rightExonId,
+            };
+        }
+        return { typeName, changedIds, assembly, changes };
+    }
+    getInverse() {
+        const { assembly, changedIds, changes, logger } = this;
+        const inverseChangedIds = [...changedIds].reverse();
+        const inverseChanges = [...changes].reverse().map((splitExonChange) => ({
+            exonToRestore: splitExonChange.exonToBeSplit,
+            parentFeatureId: splitExonChange.parentFeatureId,
+            idsToDelete: [splitExonChange.leftExonId, splitExonChange.rightExonId],
+            upstreamCut: splitExonChange.upstreamCut,
+            downstreamCut: splitExonChange.downstreamCut,
+            leftExonId: splitExonChange.leftExonId,
+            rightExonId: splitExonChange.rightExonId,
+        }));
+        logger.debug?.(`INVERSE CHANGE '${JSON.stringify(inverseChanges)}'`);
+        return new UndoSplitExonChange({
+            changedIds: inverseChangedIds,
+            typeName: 'UndoSplitExonChange',
+            changes: inverseChanges,
+            assembly,
+        }, { logger });
+    }
+    makeSplitExons(exonToBeSplit, upstreamCut, downstreamCut, leftExonId, rightExonId) {
+        // eslint-disable-next-line unicorn/prefer-structured-clone
+        const exon = JSON.parse(JSON.stringify(exonToBeSplit));
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
+        delete exon.attributes._id;
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
+        delete exon.attributes.gff_id;
+        const leftExon = structuredClone(exon);
+        leftExon._id = leftExonId;
+        leftExon.max = upstreamCut;
+        const rightExon = structuredClone(exon);
+        rightExon.min = downstreamCut;
+        rightExon._id = rightExonId;
+        return [leftExon, rightExon];
+    }
+}
+export class UndoSplitExonChange extends FeatureChange {
+    typeName = 'UndoSplitExonChange';
+    changes;
+    constructor(json, options) {
+        super(json, options);
+        this.changes = 'changes' in json ? json.changes : [json];
+    }
+    toJSON() {
+        const { assembly, changedIds, changes, typeName } = this;
+        if (changes.length === 1) {
+            const [{ exonToRestore, parentFeatureId, idsToDelete, upstreamCut, downstreamCut, leftExonId, rightExonId, },] = changes;
+            return {
+                typeName,
+                changedIds,
+                assembly,
+                exonToRestore,
+                parentFeatureId,
+                idsToDelete,
+                upstreamCut,
+                downstreamCut,
+                leftExonId,
+                rightExonId,
+            };
+        }
+        return { typeName, changedIds, assembly, changes };
+    }
+    getInverse() {
+        const { assembly, changedIds, changes, logger } = this;
+        const inverseChangedIds = [...changedIds].reverse();
+        const inverseChanges = [...changes]
+            .reverse()
+            .map((undoSplitExonChange) => ({
+            parentFeatureId: undoSplitExonChange.parentFeatureId,
+            exonToBeSplit: undoSplitExonChange.exonToRestore,
+            upstreamCut: undoSplitExonChange.upstreamCut,
+            downstreamCut: undoSplitExonChange.downstreamCut,
+            leftExonId: undoSplitExonChange.leftExonId,
+            rightExonId: undoSplitExonChange.rightExonId,
+        }));
+        return new SplitExonChange({
+            changedIds: inverseChangedIds,
+            typeName: 'SplitExonChange',
+            changes: inverseChanges,
+            assembly,
+        }, { logger });
+    }
+}
+//# sourceMappingURL=SplitAndUndoSplitExonChanges.js.map

package/dist/Changes/SplitAndUndoSplitExonChanges.js.map

@@ -0,0 +1 @@
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package/dist/Changes/StrandChange.d.ts

@@ -1,4 +1,4 @@
-import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
+import { type ChangeOptions, FeatureChange, type SerializedFeatureChange } from '@apollo-annotation/common';
 interface SerializedStrandChangeBase extends SerializedFeatureChange {
     typeName: 'StrandChange';
 }
@@ -18,14 +18,6 @@ export declare class StrandChange extends FeatureChange {
     changes: StrandChangeDetails[];
     constructor(json: SerializedStrandChange, options?: ChangeOptions);
     toJSON(): SerializedStrandChange;
-    /**
-     * Applies the required change to database
-     * @param backend - parameters from backend
-     * @returns
-     */
-    executeOnServer(backend: ServerDataStore): Promise<void>;
-    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
-    executeOnClient(dataStore: ClientDataStore): Promise<void>;
     getInverse(): StrandChange;
 }
 export {};

package/dist/Changes/StrandChange.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"StrandChange.d.ts","sourceRoot":"","sources":["../../src/Changes/StrandChange.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,KAAK,aAAa,EAClB,aAAa,EACb,KAAK,uBAAuB,EAC7B,MAAM,2BAA2B,CAAA;AAElC,UAAU,0BAA2B,SAAQ,uBAAuB;IAClE,QAAQ,EAAE,cAAc,CAAA;CACzB;AAED,UAAU,mBAAmB;IAC3B,SAAS,EAAE,MAAM,CAAA;IACjB,SAAS,EAAE,CAAC,CAAC,GAAG,CAAC,GAAG,SAAS,CAAA;IAC7B,SAAS,EAAE,CAAC,CAAC,GAAG,CAAC,GAAG,SAAS,CAAA;CAC9B;AAED,UAAU,4BACR,SAAQ,0BAA0B,EAChC,mBAAmB;CAAG;AAE1B,UAAU,8BAA+B,SAAQ,0BAA0B;IACzE,OAAO,EAAE,mBAAmB,EAAE,CAAA;CAC/B;AAED,KAAK,sBAAsB,GACvB,4BAA4B,GAC5B,8BAA8B,CAAA;AAElC,qBAAa,YAAa,SAAQ,aAAa;IAC7C,QAAQ,iBAA0B;IAClC,OAAO,EAAE,mBAAmB,EAAE,CAAA;gBAElB,IAAI,EAAE,sBAAsB,EAAE,OAAO,CAAC,EAAE,aAAa;IAKjE,MAAM,IAAI,sBAAsB;IAShC,UAAU;CAkBX"}

package/dist/Changes/StrandChange.js

@@ -1,6 +1,3 @@
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
-/* eslint-disable @typescript-eslint/require-await */
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { FeatureChange, } from '@apollo-annotation/common';
 export class StrandChange extends FeatureChange {
     typeName = 'StrandChange';
@@ -17,80 +14,6 @@ export class StrandChange extends FeatureChange {
         }
         return { typeName, changedIds, assembly, changes };
     }
-    /**
-     * Applies the required change to database
-     * @param backend - parameters from backend
-     * @returns
-     */
-    async executeOnServer(backend) {
-        const { featureModel, session } = backend;
-        const { changes, logger } = this;
-        const featuresForChanges = [];
-        // Let's first check that all features are found and those old values match with expected ones. We do this just to be sure that all changes can be done.
-        for (const entry of changes) {
-            const { featureId, oldStrand } = entry;
-            // Search correct feature
-            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);
-                // throw new NotFoundException(errMsg)  -- This is causing runtime error because Exception comes from @nestjs/common!!!
-            }
-            logger.debug?.(`*** Feature found: ${JSON.stringify(topLevelFeature)}`);
-            const foundFeature = this.getFeatureFromId(topLevelFeature, featureId);
-            if (!foundFeature) {
-                const errMsg = 'ERROR when searching feature by featureId';
-                logger.error(errMsg);
-                throw new Error(errMsg);
-            }
-            logger.debug?.(`*** Found feature: ${JSON.stringify(foundFeature)}`);
-            if (foundFeature.strand !== oldStrand) {
-                const errMsg = `*** ERROR: Feature's current strand "${topLevelFeature.strand}" doesn't match with expected value "${oldStrand}"`;
-                logger.error(errMsg);
-                throw new Error(errMsg);
-            }
-            featuresForChanges.push({ feature: foundFeature, topLevelFeature });
-        }
-        // Let's update objects.
-        for (const [idx, change] of changes.entries()) {
-            const { newStrand } = change;
-            const { feature, topLevelFeature } = featuresForChanges[idx];
-            feature.strand = newStrand;
-            if (topLevelFeature._id.equals(feature._id)) {
-                topLevelFeature.markModified('strand'); // Mark as modified. Without this save() -method is not updating data in database
-            }
-            else {
-                topLevelFeature.markModified('children'); // Mark as modified. Without this save() -method is not updating data in database
-            }
-            try {
-                await topLevelFeature.save();
-            }
-            catch (error) {
-                logger.debug?.(`*** FAILED: ${error}`);
-                throw error;
-            }
-            logger.debug?.(`*** Object updated in Mongo. New object: ${JSON.stringify(topLevelFeature)}`);
-        }
-    }
-    async executeOnLocalGFF3(_backend) {
-        throw new Error('executeOnLocalGFF3 not implemented');
-    }
-    async executeOnClient(dataStore) {
-        if (!dataStore) {
-            throw new Error('No data store');
-        }
-        for (const [idx, changedId] of this.changedIds.entries()) {
-            const feature = dataStore.getFeature(changedId);
-            if (!feature) {
-                throw new Error(`Could not find feature with identifier "${changedId}"`);
-            }
-            feature.setStrand(this.changes[idx].newStrand);
-        }
-    }
     getInverse() {
         const { assembly, changedIds, changes, logger, typeName } = this;
         const inverseChangedIds = [...changedIds].reverse();

package/dist/Changes/StrandChange.js.map

@@ -1 +1 @@
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package/dist/Changes/TypeChange.d.ts

@@ -1,4 +1,4 @@
-import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
+import { type ChangeOptions, FeatureChange, type SerializedFeatureChange } from '@apollo-annotation/common';
 interface SerializedTypeChangeBase extends SerializedFeatureChange {
     typeName: 'TypeChange';
 }
@@ -18,14 +18,6 @@ export declare class TypeChange extends FeatureChange {
     changes: TypeChangeDetails[];
     constructor(json: SerializedTypeChange, options?: ChangeOptions);
     toJSON(): SerializedTypeChange;
-    /**
-     * Applies the required change to database
-     * @param backend - parameters from backend
-     * @returns
-     */
-    executeOnServer(backend: ServerDataStore): Promise<void>;
-    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
-    executeOnClient(dataStore: ClientDataStore): Promise<void>;
     getInverse(): TypeChange;
 }
 export {};

package/dist/Changes/TypeChange.d.ts.map

@@ -1 +1 @@
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package/dist/Changes/TypeChange.js

@@ -1,6 +1,3 @@
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
-/* eslint-disable @typescript-eslint/require-await */
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { FeatureChange, } from '@apollo-annotation/common';
 export class TypeChange extends FeatureChange {
     typeName = 'TypeChange';
@@ -17,80 +14,6 @@ export class TypeChange extends FeatureChange {
         }
         return { typeName, changedIds, assembly, changes };
     }
-    /**
-     * Applies the required change to database
-     * @param backend - parameters from backend
-     * @returns
-     */
-    async executeOnServer(backend) {
-        const { featureModel, session } = backend;
-        const { changes, logger } = this;
-        const featuresForChanges = [];
-        // Let's first check that all features are found and those old values match with expected ones. We do this just to be sure that all changes can be done.
-        for (const entry of changes) {
-            const { featureId, oldType } = entry;
-            // Search correct feature
-            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);
-                // throw new NotFoundException(errMsg)  -- This is causing runtime error because Exception comes from @nestjs/common!!!
-            }
-            logger.debug?.(`*** Feature found: ${JSON.stringify(topLevelFeature)}`);
-            const foundFeature = this.getFeatureFromId(topLevelFeature, featureId);
-            if (!foundFeature) {
-                const errMsg = 'ERROR when searching feature by featureId';
-                logger.error(errMsg);
-                throw new Error(errMsg);
-            }
-            logger.debug?.(`*** Found feature: ${JSON.stringify(foundFeature)}`);
-            if (foundFeature.type !== oldType) {
-                const errMsg = `*** ERROR: Feature's current type "${topLevelFeature.type}" doesn't match with expected value "${oldType}"`;
-                logger.error(errMsg);
-                throw new Error(errMsg);
-            }
-            featuresForChanges.push({ feature: foundFeature, topLevelFeature });
-        }
-        // Let's update objects.
-        for (const [idx, change] of changes.entries()) {
-            const { newType } = change;
-            const { feature, topLevelFeature } = featuresForChanges[idx];
-            feature.type = newType;
-            if (topLevelFeature._id.equals(feature._id)) {
-                topLevelFeature.markModified('type'); // Mark as modified. Without this save() -method is not updating data in database
-            }
-            else {
-                topLevelFeature.markModified('children'); // Mark as modified. Without this save() -method is not updating data in database
-            }
-            try {
-                await topLevelFeature.save();
-            }
-            catch (error) {
-                logger.debug?.(`*** FAILED: ${error}`);
-                throw error;
-            }
-            logger.debug?.(`*** Object updated in Mongo. New object: ${JSON.stringify(topLevelFeature)}`);
-        }
-    }
-    async executeOnLocalGFF3(_backend) {
-        throw new Error('executeOnLocalGFF3 not implemented');
-    }
-    async executeOnClient(dataStore) {
-        if (!dataStore) {
-            throw new Error('No data store');
-        }
-        for (const [idx, changedId] of this.changedIds.entries()) {
-            const feature = dataStore.getFeature(changedId);
-            if (!feature) {
-                throw new Error(`Could not find feature with identifier "${changedId}"`);
-            }
-            feature.setType(this.changes[idx].newType);
-        }
-    }
     getInverse() {
         const { assembly, changedIds, changes, logger, typeName } = this;
         const inverseChangedIds = [...changedIds].reverse();