@apollo-annotation/common 0.3.8 → 0.3.10

package/dist/AssemblySpecificChange.d.ts

@@ -1,3 +1,4 @@
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
 import { Change, type ChangeOptions, type SerializedChange } from './Change';
 export interface SerializedAssemblySpecificChange extends SerializedChange {
     assembly: string;
@@ -6,4 +7,5 @@ export declare function isAssemblySpecificChange(thing: any): thing is AssemblyS
 export declare abstract class AssemblySpecificChange extends Change {
     assembly: string;
     constructor(json: SerializedAssemblySpecificChange, options?: ChangeOptions);
+    getIndexedIds(feature: AnnotationFeatureSnapshot, idsToIndex: string[] | undefined): string[];
 }

package/dist/AssemblySpecificChange.js

@@ -2,7 +2,6 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.AssemblySpecificChange = void 0;
 exports.isAssemblySpecificChange = isAssemblySpecificChange;
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 const Change_1 = require("./Change");
 function isAssemblySpecificChange(
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
@@ -14,6 +13,23 @@ class AssemblySpecificChange extends Change_1.Change {
         super(json, options);
         this.assembly = json.assembly;
     }
+    getIndexedIds(feature, idsToIndex) {
+        var _a;
+        const indexedIds = [];
+        for (const additionalId of idsToIndex !== null && idsToIndex !== void 0 ? idsToIndex : []) {
+            const idValue = (_a = feature.attributes) === null || _a === void 0 ? void 0 : _a[additionalId];
+            if (idValue) {
+                indexedIds.push(idValue[0]);
+            }
+        }
+        if (feature.children) {
+            for (const child of Object.values(feature.children)) {
+                const childIndexedIds = this.getIndexedIds(child, idsToIndex);
+                indexedIds.push(...childIndexedIds);
+            }
+        }
+        return indexedIds;
+    }
 }
 exports.AssemblySpecificChange = AssemblySpecificChange;
 //# sourceMappingURL=AssemblySpecificChange.js.map

package/dist/AssemblySpecificChange.js.map

@@ -1 +1 @@
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+{"version":3,"file":"AssemblySpecificChange.js","sourceRoot":"","sources":["../src/AssemblySpecificChange.ts"],"names":[],"mappings":";;;AAcA,4DAOC;AAlBD,qCAKiB;AAMjB,SAAgB,wBAAwB;AACtC,8DAA8D;AAC9D,KAAU;IAEV,OAAO,CACL,IAAA,iBAAQ,EAAC,KAAK,CAAC,IAAK,KAAgC,CAAC,QAAQ,KAAK,SAAS,CAC5E,CAAA;AACH,CAAC;AAED,MAAsB,sBAAuB,SAAQ,eAAM;IAGzD,YAAY,IAAsC,EAAE,OAAuB;QACzE,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QACpB,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,QAAQ,CAAA;IAC/B,CAAC;IAED,aAAa,CACX,OAAkC,EAClC,UAAgC;;QAEhC,MAAM,UAAU,GAAa,EAAE,CAAA;QAC/B,KAAK,MAAM,YAAY,IAAI,UAAU,aAAV,UAAU,cAAV,UAAU,GAAI,EAAE,EAAE,CAAC;YAC5C,MAAM,OAAO,GAAG,MAAA,OAAO,CAAC,UAAU,0CAAG,YAAY,CAAC,CAAA;YAClD,IAAI,OAAO,EAAE,CAAC;gBACZ,UAAU,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;YAC7B,CAAC;QACH,CAAC;QACD,IAAI,OAAO,CAAC,QAAQ,EAAE,CAAC;YACrB,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,QAAQ,CAAC,EAAE,CAAC;gBACpD,MAAM,eAAe,GAAG,IAAI,CAAC,aAAa,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;gBAC7D,UAAU,CAAC,IAAI,CAAC,GAAG,eAAe,CAAC,CAAA;YACrC,CAAC;QACH,CAAC;QACD,OAAO,UAAU,CAAA;IACnB,CAAC;CACF;AA3BD,wDA2BC"}

package/dist/Change.d.ts

@@ -7,7 +7,7 @@ export interface ClientDataStore {
     checkResults: Map<string | number, CheckResultI>;
     internetAccounts: AppRootModel['internetAccounts'];
     getInternetAccount(assemblyName?: string, internetAccountId?: string): AppRootModel['internetAccounts'][0];
-    loadFeatures(regions: Region[]): void;
+    loadFeatures(regions: Region[]): Promise<void>;
     loadRefSeq(regions: Region[]): void;
     getFeature(featureId: string): AnnotationFeature | undefined;
     addFeature(assemblyId: string, feature: AnnotationFeatureSnapshot): void;

package/dist/Operation.d.ts

@@ -1,6 +1,6 @@
-import { type ReadStream } from 'node:fs';
 import { type FileHandle } from 'node:fs/promises';
 import { type AssemblyDocument, type CheckDocument, type FeatureDocument, type FileDocument, type JBrowseConfigDocument, type RefSeqChunkDocument, type RefSeqDocument, type UserDocument } from '@apollo-annotation/schemas';
+import { type GFF3Feature } from '@gmod/gff';
 import { type LoggerService } from '@nestjs/common';
 import { type GenericFilehandle } from 'generic-filehandle';
 import { type ClientSession, type Model } from 'mongoose';
@@ -27,9 +27,11 @@ export interface ServerDataStore {
     jbrowseConfigModel: Model<JBrowseConfigDocument>;
     session: ClientSession;
     filesService: {
-        getFileStream(file: FileDocument): ReadStream;
+        getFileStream(file: FileDocument): ReadableStream<Uint8Array>;
         getFileHandle(file: FileDocument): GenericFilehandle;
-        parseGFF3(stream: ReadStream): ReadStream;
+        parseGFF3(stream: ReadableStream<Uint8Array>, parseOptions?: {
+            bufferSize?: number;
+        }): ReadableStream<GFF3Feature>;
         create(createFileDto: CreateFileDto): void;
         remove(id: string): void;
     };

package/dist/Operation.js.map

@@ -1 +1 @@
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+{"version":3,"file":"Operation.js","sourceRoot":"","sources":["../src/Operation.ts"],"names":[],"mappings":";;;AA4EA,MAAsB,SAAS;IAI7B,YAAY,IAAyB,EAAE,OAA0B;;QAC/D,IAAI,CAAC,MAAM,GAAG,MAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,MAAM,mCAAI,OAAO,CAAA;IAC1C,CAAC;IAID,KAAK,CAAC,OAAO,CAAC,OAAyB;QACrC,MAAM,WAAW,GAAG,OAAO,CAAC,QAAQ,CAAA;QACpC,IAAI,WAAW,KAAK,QAAQ,EAAE,CAAC;YAC7B,MAAM,aAAa,GAAG,IAAI,CAAC,eAAe,CAAC,OAAO,CAAC,CAAA;YACnD,OAAO,OAAO,CAAC,cAAc,CAAC,sBAAsB,CAClD,GAAG,IAAI,CAAC,QAAQ,mBAAmB,EACnC,aAAa,EACb,EAAE,SAAS,EAAE,IAAI,EAAE,OAAO,EAAE,CAC7B,CAAA;QACH,CAAC;QACD,IAAI,WAAW,KAAK,WAAW,EAAE,CAAC;YAChC,OAAO,IAAI,CAAC,kBAAkB,CAAC,OAAO,CAAC,CAAA;QACzC,CAAC;QACD,MAAM,IAAI,KAAK,CACb,iDAAiD,WAAW,GAAG,CAChE,CAAA;IACH,CAAC;CAIF;AA9BD,8BA8BC"}