@apollo-annotation/shared 0.3.12 → 1.0.0

package/dist/Changes/MergeExonsChange.d.ts

@@ -1,30 +0,0 @@
-import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
-import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
-import { UndoMergeExonsChange } from './UndoMergeExonsChange.js';
-interface SerializedMergeExonsChangeBase extends SerializedFeatureChange {
-    typeName: 'MergeExonsChange';
-}
-export interface MergeExonsChangeDetails {
-    firstExon: AnnotationFeatureSnapshot;
-    secondExon: AnnotationFeatureSnapshot;
-    parentFeatureId: string;
-}
-interface SerializedMergeExonsChangeSingle extends SerializedMergeExonsChangeBase, MergeExonsChangeDetails {
-}
-interface SerializedMergeExonsChangeMultiple extends SerializedMergeExonsChangeBase {
-    changes: MergeExonsChangeDetails[];
-}
-export type SerializedMergeExonsChange = SerializedMergeExonsChangeSingle | SerializedMergeExonsChangeMultiple;
-export declare class MergeExonsChange extends FeatureChange {
-    typeName: "MergeExonsChange";
-    changes: MergeExonsChangeDetails[];
-    constructor(json: SerializedMergeExonsChange, options?: ChangeOptions);
-    get notification(): string;
-    toJSON(): SerializedMergeExonsChange;
-    executeOnServer(backend: ServerDataStore): Promise<void>;
-    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
-    executeOnClient(dataStore: ClientDataStore): Promise<void>;
-    getInverse(): UndoMergeExonsChange;
-}
-export {};
-//# sourceMappingURL=MergeExonsChange.d.ts.map

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

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

@@ -1,110 +0,0 @@
-/* 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 { attributesToRecords, stringifyAttributes } from '../util.js';
-import { findAndDeleteChildFeature } from './DeleteFeatureChange.js';
-import { UndoMergeExonsChange } from './UndoMergeExonsChange.js';
-export class MergeExonsChange extends FeatureChange {
-    typeName = 'MergeExonsChange';
-    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 'Exons successfully merged';
-    }
-    toJSON() {
-        const { assembly, changedIds, changes, typeName } = this;
-        if (changes.length === 1) {
-            const [{ firstExon, secondExon, parentFeatureId }] = changes;
-            return {
-                typeName,
-                changedIds,
-                assembly,
-                firstExon,
-                secondExon,
-                parentFeatureId,
-            };
-        }
-        return { typeName, changedIds, assembly, changes };
-    }
-    async executeOnServer(backend) {
-        const { featureModel, session } = backend;
-        const { changes, logger } = this;
-        for (const change of changes) {
-            const { firstExon, secondExon } = change;
-            const topLevelFeature = await featureModel
-                .findOne({ allIds: firstExon._id })
-                .session(session)
-                .exec();
-            if (!topLevelFeature) {
-                const errMsg = `*** ERROR: The following featureId was not found in database ='${firstExon._id}'`;
-                logger.error(errMsg);
-                throw new Error(errMsg);
-            }
-            const mergedExon = this.getFeatureFromId(topLevelFeature, firstExon._id);
-            if (!mergedExon) {
-                const errMsg = 'ERROR when searching feature by featureId';
-                logger.error(errMsg);
-                throw new Error(errMsg);
-            }
-            mergedExon.min = Math.min(firstExon.min, secondExon.min);
-            mergedExon.max = Math.max(firstExon.max, secondExon.max);
-            const mergedAttributes = mergedExon.attributes
-                ? JSON.parse(JSON.stringify(mergedExon.attributes))
-                : {};
-            mergedAttributes.merged_with = [
-                stringifyAttributes(attributesToRecords(secondExon.attributes)),
-            ];
-            mergedExon.attributes = mergedAttributes;
-            const deletedIds = findAndDeleteChildFeature(topLevelFeature, secondExon._id, this);
-            deletedIds.push(secondExon._id);
-            topLevelFeature.allIds = topLevelFeature.allIds.filter((id) => !deletedIds.includes(id));
-            await topLevelFeature.save();
-        }
-    }
-    async executeOnLocalGFF3(_backend) {
-        throw new Error('executeOnLocalGFF3 not implemented');
-    }
-    async executeOnClient(dataStore) {
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-        if (!dataStore) {
-            throw new Error('No data store');
-        }
-        for (const change of this.changes) {
-            const { firstExon, secondExon } = change;
-            const mergedExon = dataStore.getFeature(firstExon._id);
-            if (!mergedExon) {
-                throw new Error(`Could not find feature with identifier "${firstExon._id}"`);
-            }
-            mergedExon.setMin(Math.min(firstExon.min, secondExon.min));
-            mergedExon.setMax(Math.max(firstExon.max, secondExon.max));
-            const mrg = mergedExon.attributes.get('merged_with')?.slice() ?? [];
-            const mergedWith = stringifyAttributes(attributesToRecords(secondExon.attributes));
-            if (!mrg.includes(mergedWith)) {
-                mrg.push(mergedWith);
-            }
-            mergedExon.setAttribute('merged_with', mrg);
-            mergedExon.parent?.deleteChild(secondExon._id);
-        }
-    }
-    getInverse() {
-        const { assembly, changedIds, changes, logger } = this;
-        const inverseChangedIds = [...changedIds].reverse();
-        const inverseChanges = [...changes].reverse().map((mergeExonChange) => ({
-            exonsToRestore: [mergeExonChange.firstExon, mergeExonChange.secondExon],
-            parentFeatureId: mergeExonChange.parentFeatureId,
-        }));
-        logger.debug?.(`INVERSE CHANGE '${JSON.stringify(inverseChanges)}'`);
-        return new UndoMergeExonsChange({
-            changedIds: inverseChangedIds,
-            typeName: 'UndoMergeExonsChange',
-            changes: inverseChanges,
-            assembly,
-        }, { logger });
-    }
-}
-//# sourceMappingURL=MergeExonsChange.js.map

package/dist/Changes/MergeExonsChange.js.map

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

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package/dist/Changes/MergeTranscriptsChange.js.map

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

@@ -1,34 +0,0 @@
-import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
-import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
-import { UndoSplitExonChange } from './UndoSplitExonChange.js';
-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;
-export declare class SplitExonChange extends FeatureChange {
-    typeName: "SplitExonChange";
-    changes: SplitExonChangeDetails[];
-    constructor(json: SerializedSplitExonChange, options?: ChangeOptions);
-    get notification(): string;
-    toJSON(): SerializedSplitExonChange;
-    executeOnServer(backend: ServerDataStore): Promise<void>;
-    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
-    executeOnClient(dataStore: ClientDataStore): Promise<void>;
-    getInverse(): UndoSplitExonChange;
-    makeSplitExons(exonToBeSplit: AnnotationFeatureSnapshot, upstreamCut: number, downstreamCut: number, leftExonId: string, rightExonId: string): AnnotationFeatureSnapshot[];
-}
-export {};
-//# sourceMappingURL=SplitExonChange.d.ts.map

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

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

@@ -1,138 +0,0 @@
-/* eslint-disable @typescript-eslint/require-await */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
-import { FeatureChange, } from '@apollo-annotation/common';
-import { findAndDeleteChildFeature } from './DeleteFeatureChange.js';
-import { UndoSplitExonChange } from './UndoSplitExonChange.js';
-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 };
-    }
-    async executeOnServer(backend) {
-        const { featureModel, session } = backend;
-        const { changes, logger } = this;
-        for (const change of changes) {
-            const { exonToBeSplit, parentFeatureId, upstreamCut, downstreamCut, leftExonId, rightExonId, } = change;
-            const topLevelFeature = await featureModel
-                .findOne({ allIds: exonToBeSplit._id })
-                .session(session)
-                .exec();
-            if (!topLevelFeature) {
-                const errMsg = `*** ERROR: The following featureId was not found in database ='${exonToBeSplit._id}'`;
-                logger.error(errMsg);
-                throw new Error(errMsg);
-            }
-            const tx = this.getFeatureFromId(topLevelFeature, parentFeatureId);
-            if (!tx?.children) {
-                throw new Error('ERROR: There should be at least one child (i.e. the exon to be split)');
-            }
-            const [leftExon, rightExon] = this.makeSplitExons(exonToBeSplit, upstreamCut, downstreamCut, leftExonId, rightExonId);
-            tx.children.set(leftExon._id, {
-                allIds: [],
-                ...leftExon,
-                // eslint-disable-next-line @typescript-eslint/ban-ts-comment
-                // @ts-expect-error
-                _id: leftExon._id,
-            });
-            tx.children.set(rightExon._id, {
-                allIds: [],
-                ...rightExon,
-                // eslint-disable-next-line @typescript-eslint/ban-ts-comment
-                // @ts-expect-error
-                _id: rightExon._id,
-            });
-            // Child features should be sorted for click and drag of gene glyphs to work properly
-            tx.children = new Map([...tx.children.entries()].sort((a, b) => a[1].min - b[1].min));
-            const deletedIds = findAndDeleteChildFeature(topLevelFeature, exonToBeSplit._id, this);
-            deletedIds.push(exonToBeSplit._id);
-            topLevelFeature.allIds = topLevelFeature.allIds.filter((id) => !deletedIds.includes(id));
-            topLevelFeature.allIds.push(leftExon._id, rightExon._id);
-            await topLevelFeature.save();
-        }
-    }
-    async executeOnLocalGFF3(_backend) {
-        throw new Error('executeOnLocalGFF3 not implemented');
-    }
-    async executeOnClient(dataStore) {
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-        if (!dataStore) {
-            throw new Error('No data store');
-        }
-        for (const [idx] of this.changedIds.entries()) {
-            const { exonToBeSplit, parentFeatureId, upstreamCut, downstreamCut, leftExonId, rightExonId, } = this.changes[idx];
-            if (!parentFeatureId) {
-                throw new Error('TODO: Split exon without parent');
-            }
-            const [leftExon, rightExon] = this.makeSplitExons(exonToBeSplit, upstreamCut, downstreamCut, leftExonId, rightExonId);
-            const parentFeature = dataStore.getFeature(parentFeatureId);
-            if (!parentFeature) {
-                throw new Error(`Could not find parent feature "${parentFeatureId}"`);
-            }
-            parentFeature.addChild(leftExon);
-            parentFeature.addChild(rightExon);
-            if (dataStore.getFeature(exonToBeSplit._id)) {
-                dataStore.deleteFeature(exonToBeSplit._id);
-            }
-        }
-    }
-    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];
-    }
-}
-//# sourceMappingURL=SplitExonChange.js.map

package/dist/Changes/SplitExonChange.js.map

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package/dist/Changes/UndoMergeExonsChange.d.ts

@@ -1,28 +0,0 @@
-import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
-import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
-import { MergeExonsChange } from './MergeExonsChange.js';
-interface SerializedUndoMergeExonsChangeBase extends SerializedFeatureChange {
-    typeName: 'UndoMergeExonsChange';
-}
-export interface UndoMergeExonsChangeDetails {
-    exonsToRestore: AnnotationFeatureSnapshot[];
-    parentFeatureId: string;
-}
-interface SerializedUndoMergeExonsChangeSingle extends SerializedUndoMergeExonsChangeBase, UndoMergeExonsChangeDetails {
-}
-interface SerializedUndoMergeExonsChangeMultiple extends SerializedUndoMergeExonsChangeBase {
-    changes: UndoMergeExonsChangeDetails[];
-}
-export type SerializedUndoMergeExonsChange = SerializedUndoMergeExonsChangeSingle | SerializedUndoMergeExonsChangeMultiple;
-export declare class UndoMergeExonsChange extends FeatureChange {
-    typeName: "UndoMergeExonsChange";
-    changes: UndoMergeExonsChangeDetails[];
-    constructor(json: SerializedUndoMergeExonsChange, options?: ChangeOptions);
-    toJSON(): SerializedUndoMergeExonsChange;
-    executeOnServer(backend: ServerDataStore): Promise<void>;
-    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
-    executeOnClient(dataStore: ClientDataStore): Promise<void>;
-    getInverse(): MergeExonsChange;
-}
-export {};
-//# sourceMappingURL=UndoMergeExonsChange.d.ts.map

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

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

@@ -1,100 +0,0 @@
-/* eslint-disable @typescript-eslint/require-await */
-import { FeatureChange, } from '@apollo-annotation/common';
-import { MergeExonsChange } from './MergeExonsChange.js';
-export class UndoMergeExonsChange extends FeatureChange {
-    typeName = 'UndoMergeExonsChange';
-    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 [{ exonsToRestore, parentFeatureId }] = changes;
-            return {
-                typeName,
-                changedIds,
-                assembly,
-                exonsToRestore,
-                parentFeatureId,
-            };
-        }
-        return { typeName, changedIds, assembly, changes };
-    }
-    async executeOnServer(backend) {
-        const { featureModel, session } = backend;
-        const { changes } = this;
-        for (const change of changes) {
-            const { exonsToRestore, parentFeatureId } = change;
-            if (exonsToRestore.length !== 2) {
-                throw new Error(`Expected exactly two exons to restore. Got :${exonsToRestore.length}`);
-            }
-            const topLevelFeature = await featureModel
-                .findOne({ allIds: parentFeatureId })
-                .session(session)
-                .exec();
-            if (!topLevelFeature) {
-                throw new Error(`Could not find feature with ID "${parentFeatureId}"`);
-            }
-            const parentFeature = this.getFeatureFromId(topLevelFeature, parentFeatureId);
-            if (!parentFeature) {
-                throw new Error(`Could not find feature with ID "${parentFeatureId}" in feature "${topLevelFeature._id.toString()}"`);
-            }
-            if (!parentFeature.children) {
-                parentFeature.children = new Map();
-            }
-            for (const exon of exonsToRestore) {
-                this.addChild(parentFeature, exon);
-                const childIds = this.getChildFeatureIds(exon);
-                topLevelFeature.allIds.push(exon._id, ...childIds);
-            }
-            await topLevelFeature.save();
-        }
-    }
-    async executeOnLocalGFF3(_backend) {
-        throw new Error('executeOnLocalGFF3 not implemented');
-    }
-    async executeOnClient(dataStore) {
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-        if (!dataStore) {
-            throw new Error('No data store');
-        }
-        const { changes } = this;
-        for (const change of changes) {
-            const { exonsToRestore, parentFeatureId } = change;
-            if (!parentFeatureId) {
-                throw new Error('Parent ID is missing');
-            }
-            const parentFeature = dataStore.getFeature(parentFeatureId);
-            if (!parentFeature) {
-                throw new Error(`Could not find parent feature "${parentFeatureId}"`);
-            }
-            // create an ID for the parent feature if it does not have one
-            if (!parentFeature.attributes.get('_id')) {
-                parentFeature.setAttribute('_id', [parentFeature._id]);
-            }
-            for (const exon of exonsToRestore) {
-                parentFeature.addChild(exon);
-            }
-        }
-    }
-    getInverse() {
-        const { assembly, changedIds, changes, logger } = this;
-        const inverseChangedIds = [...changedIds].reverse();
-        const inverseChanges = [...changes]
-            .reverse()
-            .map((undoMergeExonsChange) => ({
-            firstExon: undoMergeExonsChange.exonsToRestore[0],
-            secondExon: undoMergeExonsChange.exonsToRestore[1],
-            parentFeatureId: undoMergeExonsChange.parentFeatureId,
-        }));
-        return new MergeExonsChange({
-            changedIds: inverseChangedIds,
-            typeName: 'MergeExonsChange',
-            changes: inverseChanges,
-            assembly,
-        }, { logger });
-    }
-}
-//# sourceMappingURL=UndoMergeExonsChange.js.map

package/dist/Changes/UndoMergeExonsChange.js.map

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package/dist/Changes/UndoMergeTranscriptsChange.d.ts

@@ -1,28 +0,0 @@
-import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
-import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
-import { MergeTranscriptsChange } from './MergeTranscriptsChange.js';
-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 UndoMergeTranscriptsChange extends FeatureChange {
-    typeName: "UndoMergeTranscriptsChange";
-    changes: UndoMergeTranscriptsChangeDetails[];
-    constructor(json: SerializedUndoMergeTranscriptsChange, options?: ChangeOptions);
-    toJSON(): SerializedUndoMergeTranscriptsChange;
-    executeOnServer(backend: ServerDataStore): Promise<void>;
-    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
-    executeOnClient(dataStore: ClientDataStore): Promise<void>;
-    getInverse(): MergeTranscriptsChange;
-}
-export {};
-//# sourceMappingURL=UndoMergeTranscriptsChange.d.ts.map

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

@@ -1 +0,0 @@
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