@apollo-annotation/shared 0.3.10 → 0.3.12

package/dist/Changes/AddAssemblyAliasesChange.d.ts

@@ -14,3 +14,4 @@ export declare class AddAssemblyAliasesChange extends AssemblySpecificChange {
     executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<unknown>;
     get notification(): string;
 }
+//# sourceMappingURL=AddAssemblyAliasesChange.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"AddAssemblyAliasesChange.d.ts","sourceRoot":"","sources":["../../src/Changes/AddAssemblyAliasesChange.ts"],"names":[],"mappings":"AAGA,OAAO,EACL,sBAAsB,EACtB,KAAK,MAAM,EACX,KAAK,aAAa,EAClB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,gCAAgC,EACrC,KAAK,eAAe,EACrB,MAAM,2BAA2B,CAAA;AAGlC,MAAM,WAAW,+BACf,SAAQ,gCAAgC;IACxC,QAAQ,EAAE,0BAA0B,CAAA;IACpC,OAAO,EAAE,MAAM,EAAE,CAAA;CAClB;AAED,qBAAa,wBAAyB,SAAQ,sBAAsB;IAClE,QAAQ,6BAAsC;IAC9C,OAAO,EAAE,MAAM,EAAE,CAAA;gBAEL,IAAI,EAAE,+BAA+B,EAAE,OAAO,CAAC,EAAE,aAAa;IAK1E,eAAe,CAAC,eAAe,EAAE,eAAe;IAUhD,UAAU,IAAI,MAAM;IAIpB,MAAM,IAAI,+BAA+B;IAKnC,eAAe,CAAC,OAAO,EAAE,eAAe;IAc9C,kBAAkB,CAAC,QAAQ,EAAE,kBAAkB,GAAG,OAAO,CAAC,OAAO,CAAC;IAKlE,IAAI,YAAY,IAAI,MAAM,CAEzB;CACF"}

package/dist/Changes/AddAssemblyAliasesChange.js

@@ -1,9 +1,9 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AddAssemblyAliasesChange = void 0;
-const common_1 = require("@apollo-annotation/common");
-const util_1 = require("@jbrowse/core/util");
-class AddAssemblyAliasesChange extends common_1.AssemblySpecificChange {
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+import { AssemblySpecificChange, } from '@apollo-annotation/common';
+import { getSession } from '@jbrowse/core/util';
+export class AddAssemblyAliasesChange extends AssemblySpecificChange {
     typeName = 'AddAssemblyAliasesChange';
     aliases;
     constructor(json, options) {
@@ -11,12 +11,11 @@ class AddAssemblyAliasesChange extends common_1.AssemblySpecificChange {
         this.aliases = json.aliases;
     }
     executeOnClient(clientDataStore) {
-        const { assemblyManager } = (0, util_1.getSession)(clientDataStore);
+        const { assemblyManager } = getSession(clientDataStore);
         const assembly = assemblyManager.get(this.assembly);
         if (!assembly) {
             throw new Error(`assembly ${this.assembly} not found`);
         }
-        // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
         assembly.configuration.aliases.set(this.aliases);
         return Promise.resolve();
     }
@@ -46,5 +45,4 @@ class AddAssemblyAliasesChange extends common_1.AssemblySpecificChange {
         return 'Assembly aliases have been added.';
     }
 }
-exports.AddAssemblyAliasesChange = AddAssemblyAliasesChange;
 //# sourceMappingURL=AddAssemblyAliasesChange.js.map

package/dist/Changes/AddAssemblyAliasesChange.js.map

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

@@ -1,5 +1,5 @@
-import { type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
-import { FromFileBaseChange } from './FromFileBaseChange';
+import type { ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
+import { FromFileBaseChange } from './FromFileBaseChange.js';
 export interface SerializedAddAssemblyAndFeaturesFromFileChangeBase extends SerializedAssemblySpecificChange {
     typeName: 'AddAssemblyAndFeaturesFromFileChange';
 }
@@ -9,7 +9,8 @@ export interface AddAssemblyAndFeaturesFromFileChangeDetails {
         fa: string;
     };
     parseOptions?: {
-        bufferSize: number;
+        bufferSize?: number;
+        strict?: boolean;
     };
 }
 export interface SerializedAddAssemblyAndFeaturesFromFileChangeSingle extends SerializedAddAssemblyAndFeaturesFromFileChangeBase, AddAssemblyAndFeaturesFromFileChangeDetails {
@@ -34,3 +35,4 @@ export declare class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseCh
     executeOnClient(_dataStore: ClientDataStore): Promise<void>;
     getInverse(): AddAssemblyAndFeaturesFromFileChange;
 }
+//# sourceMappingURL=AddAssemblyAndFeaturesFromFileChange.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"AddAssemblyAndFeaturesFromFileChange.d.ts","sourceRoot":"","sources":["../../src/Changes/AddAssemblyAndFeaturesFromFileChange.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EACV,aAAa,EACb,eAAe,EACf,kBAAkB,EAClB,gCAAgC,EAChC,eAAe,EAChB,MAAM,2BAA2B,CAAA;AAElC,OAAO,EAAE,kBAAkB,EAAE,MAAM,yBAAyB,CAAA;AAE5D,MAAM,WAAW,kDACf,SAAQ,gCAAgC;IACxC,QAAQ,EAAE,sCAAsC,CAAA;CACjD;AAED,MAAM,WAAW,2CAA2C;IAC1D,YAAY,EAAE,MAAM,CAAA;IACpB,OAAO,EAAE;QAAE,EAAE,EAAE,MAAM,CAAA;KAAE,CAAA;IACvB,YAAY,CAAC,EAAE;QAAE,UAAU,CAAC,EAAE,MAAM,CAAC;QAAC,MAAM,CAAC,EAAE,OAAO,CAAA;KAAE,CAAA;CACzD;AAED,MAAM,WAAW,oDACf,SAAQ,kDAAkD,EACxD,2CAA2C;CAAG;AAElD,MAAM,WAAW,sDACf,SAAQ,kDAAkD;IAC1D,OAAO,EAAE,2CAA2C,EAAE,CAAA;CACvD;AAED,MAAM,MAAM,8CAA8C,GACtD,oDAAoD,GACpD,sDAAsD,CAAA;AAE1D,qBAAa,oCAAqC,SAAQ,kBAAkB;IAC1E,QAAQ,yCAAkD;IAC1D,OAAO,EAAE,2CAA2C,EAAE,CAAA;gBAGpD,IAAI,EAAE,8CAA8C,EACpD,OAAO,CAAC,EAAE,aAAa;IAMzB,IAAI,YAAY,IAAI,MAAM,CAEzB;IAED,MAAM,IAAI,8CAA8C;IASxD;;;;OAIG;IACG,eAAe,CAAC,OAAO,EAAE,eAAe;IAiFxC,kBAAkB,CAAC,QAAQ,EAAE,kBAAkB;IAK/C,eAAe,CAAC,UAAU,EAAE,eAAe;IAEjD,UAAU;CAOX"}

package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js

@@ -1,9 +1,10 @@
-"use strict";
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/require-await */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AddAssemblyAndFeaturesFromFileChange = void 0;
-const FromFileBaseChange_1 = require("./FromFileBaseChange");
-class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange_1.FromFileBaseChange {
+import { FromFileBaseChange } from './FromFileBaseChange.js';
+export class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange {
     typeName = 'AddAssemblyAndFeaturesFromFileChange';
     changes;
     constructor(json, options) {
@@ -61,15 +62,33 @@ class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange_1.FromFile
             // Add refSeqs
             // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
             await this.addRefSeqIntoDb(fileDoc, newAssemblyDoc._id.toString(), backend);
-            const { bufferSize = 10_000 } = parseOptions ?? {};
+            const { bufferSize = 10_000, strict = true } = parseOptions ?? {};
             const featureStream = filesService.parseGFF3(filesService.getFileStream(fileDoc), { bufferSize });
-            // @ts-expect-error type is wrong here
-            // eslint-disable-next-line @typescript-eslint/await-thenable
-            for await (const f of featureStream) {
-                const gff3Feature = f;
-                logger.verbose?.(`ENTRY=${JSON.stringify(gff3Feature)}`);
+            let featureCount = 0;
+            let errorCount = 0;
+            for await (const gff3Feature of featureStream) {
                 // Add new feature into database
-                await this.addFeatureIntoDb(gff3Feature, backend);
+                try {
+                    await this.addFeatureIntoDb(gff3Feature, backend);
+                }
+                catch (error) {
+                    // if the first feature is an error, assume the file isn't valid and throw
+                    if (strict || featureCount === 0) {
+                        throw error;
+                    }
+                    if (errorCount <= 99) {
+                        logger.warn('Error parsing feature');
+                        logger.warn(error);
+                        if (errorCount === 99) {
+                            logger.warn('Reached 100 parsing errors, omitting further warnings from log');
+                        }
+                    }
+                    errorCount++;
+                }
+                featureCount++;
+                if (featureCount % 1000 === 0) {
+                    logger.debug?.(`Processed ${featureCount} features`);
+                }
             }
         }
     }
@@ -83,5 +102,4 @@ class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange_1.FromFile
         return new AddAssemblyAndFeaturesFromFileChange({ typeName, changes, assembly }, { logger });
     }
 }
-exports.AddAssemblyAndFeaturesFromFileChange = AddAssemblyAndFeaturesFromFileChange;
 //# sourceMappingURL=AddAssemblyAndFeaturesFromFileChange.js.map

package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js.map

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

@@ -32,3 +32,4 @@ export declare class AddAssemblyFromExternalChange extends AssemblySpecificChang
     executeOnClient(_dataStore: ClientDataStore): Promise<void>;
     getInverse(): AddAssemblyFromExternalChange;
 }
+//# sourceMappingURL=AddAssemblyFromExternalChange.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"AddAssemblyFromExternalChange.d.ts","sourceRoot":"","sources":["../../src/Changes/AddAssemblyFromExternalChange.ts"],"names":[],"mappings":"AAKA,OAAO,EACL,sBAAsB,EACtB,KAAK,aAAa,EAClB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,gCAAgC,EACrC,KAAK,eAAe,EACrB,MAAM,2BAA2B,CAAA;AAIlC,MAAM,WAAW,2CACf,SAAQ,gCAAgC;IACxC,QAAQ,EAAE,+BAA+B,CAAA;CAC1C;AAED,MAAM,WAAW,oCAAoC;IACnD,YAAY,EAAE,MAAM,CAAA;IACpB,gBAAgB,EAAE;QAAE,EAAE,EAAE,MAAM,CAAC;QAAC,GAAG,EAAE,MAAM,CAAC;QAAC,GAAG,CAAC,EAAE,MAAM,CAAA;KAAE,CAAA;CAC5D;AAED,MAAM,WAAW,6CACf,SAAQ,2CAA2C,EACjD,oCAAoC;CAAG;AAE3C,MAAM,WAAW,+CACf,SAAQ,2CAA2C;IACnD,OAAO,EAAE,oCAAoC,EAAE,CAAA;CAChD;AAED,MAAM,MAAM,uCAAuC,GAC/C,6CAA6C,GAC7C,+CAA+C,CAAA;AAEnD,qBAAa,6BAA8B,SAAQ,sBAAsB;IACvE,QAAQ,kCAA2C;IACnD,OAAO,EAAE,oCAAoC,EAAE,CAAA;gBAG7C,IAAI,EAAE,uCAAuC,EAC7C,OAAO,CAAC,EAAE,aAAa;IAMzB,IAAI,YAAY,IAAI,MAAM,CAEzB;IAED,MAAM,IAAI,uCAAuC;IASjD;;;;OAIG;IACG,eAAe,CAAC,OAAO,EAAE,eAAe;IAiExC,kBAAkB,CAAC,QAAQ,EAAE,kBAAkB;IAK/C,eAAe,CAAC,UAAU,EAAE,eAAe;IAEjD,UAAU;CAOX"}

package/dist/Changes/AddAssemblyFromExternalChange.js

@@ -1,13 +1,11 @@
-"use strict";
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AddAssemblyFromExternalChange = void 0;
 /* eslint-disable @typescript-eslint/require-await */
-const common_1 = require("@apollo-annotation/common");
-const indexedfasta_1 = require("@gmod/indexedfasta");
-const generic_filehandle_1 = require("generic-filehandle");
-class AddAssemblyFromExternalChange extends common_1.AssemblySpecificChange {
+import { AssemblySpecificChange, } from '@apollo-annotation/common';
+import { BgzipIndexedFasta, IndexedFasta } from '@gmod/indexedfasta';
+import { RemoteFile } from 'generic-filehandle2';
+export class AddAssemblyFromExternalChange extends AssemblySpecificChange {
     typeName = 'AddAssemblyFromExternalChange';
     changes;
     constructor(json, options) {
@@ -39,14 +37,14 @@ class AddAssemblyFromExternalChange extends common_1.AssemblySpecificChange {
             const { assemblyName, externalLocation } = change;
             const { fa, fai, gzi } = externalLocation;
             const sequenceAdapter = gzi
-                ? new indexedfasta_1.BgzipIndexedFasta({
-                    fasta: new generic_filehandle_1.RemoteFile(fa, { fetch }),
-                    fai: new generic_filehandle_1.RemoteFile(fai, { fetch }),
-                    gzi: new generic_filehandle_1.RemoteFile(gzi, { fetch }),
+                ? new BgzipIndexedFasta({
+                    fasta: new RemoteFile(fa, { fetch }),
+                    fai: new RemoteFile(fai, { fetch }),
+                    gzi: new RemoteFile(gzi, { fetch }),
                 })
-                : new indexedfasta_1.IndexedFasta({
-                    fasta: new generic_filehandle_1.RemoteFile(fa, { fetch }),
-                    fai: new generic_filehandle_1.RemoteFile(fai, { fetch }),
+                : new IndexedFasta({
+                    fasta: new RemoteFile(fa, { fetch }),
+                    fai: new RemoteFile(fai, { fetch }),
                 });
             const allSequenceSizes = await sequenceAdapter.getSequenceSizes();
             if (!allSequenceSizes) {
@@ -96,5 +94,4 @@ class AddAssemblyFromExternalChange extends common_1.AssemblySpecificChange {
         return new AddAssemblyFromExternalChange({ typeName, changes, assembly }, { logger });
     }
 }
-exports.AddAssemblyFromExternalChange = AddAssemblyFromExternalChange;
 //# sourceMappingURL=AddAssemblyFromExternalChange.js.map

package/dist/Changes/AddAssemblyFromExternalChange.js.map

@@ -1 +1 @@
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+{"version":3,"file":"AddAssemblyFromExternalChange.js","sourceRoot":"","sources":["../../src/Changes/AddAssemblyFromExternalChange.ts"],"names":[],"mappings":"AAAA,+DAA+D;AAC/D,4DAA4D;AAC5D,gEAAgE;AAEhE,qDAAqD;AACrD,OAAO,EACL,sBAAsB,GAMvB,MAAM,2BAA2B,CAAA;AAClC,OAAO,EAAE,iBAAiB,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAA;AACpE,OAAO,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAA;AAyBhD,MAAM,OAAO,6BAA8B,SAAQ,sBAAsB;IACvE,QAAQ,GAAG,+BAAwC,CAAA;IACnD,OAAO,CAAwC;IAE/C,YACE,IAA6C,EAC7C,OAAuB;QAEvB,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QACpB,IAAI,CAAC,OAAO,GAAG,SAAS,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IAC1D,CAAC;IAED,IAAI,YAAY;QACd,OAAO,aAAa,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,YAAY,2DAA2D,CAAA;IAC7G,CAAC;IAED,MAAM;QACJ,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QAC5C,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACzB,MAAM,CAAC,EAAE,YAAY,EAAE,gBAAgB,EAAE,CAAC,GAAG,OAAO,CAAA;YACpD,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,YAAY,EAAE,gBAAgB,EAAE,CAAA;QAC/D,CAAC;QACD,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,OAAO,EAAE,CAAA;IACxC,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,eAAe,CAAC,OAAwB;QAC5C,MAAM,EAAE,aAAa,EAAE,UAAU,EAAE,WAAW,EAAE,IAAI,EAAE,GAAG,OAAO,CAAA;QAChE,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QAC1C,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAC,GAAG,CAAA;QAClC,MAAM,eAAe,GAAG,UAAU,IAAI,MAAM,CAAC,UAAU,CAAC,CAAA;QAExD,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,EAAE,YAAY,EAAE,gBAAgB,EAAE,GAAG,MAAM,CAAA;YACjD,MAAM,EAAE,EAAE,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,gBAAgB,CAAA;YACzC,MAAM,eAAe,GAAG,GAAG;gBACzB,CAAC,CAAC,IAAI,iBAAiB,CAAC;oBACpB,KAAK,EAAE,IAAI,UAAU,CAAC,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC;oBACpC,GAAG,EAAE,IAAI,UAAU,CAAC,GAAG,EAAE,EAAE,KAAK,EAAE,CAAC;oBACnC,GAAG,EAAE,IAAI,UAAU,CAAC,GAAG,EAAE,EAAE,KAAK,EAAE,CAAC;iBACpC,CAAC;gBACJ,CAAC,CAAC,IAAI,YAAY,CAAC;oBACf,KAAK,EAAE,IAAI,UAAU,CAAC,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC;oBACpC,GAAG,EAAE,IAAI,UAAU,CAAC,GAAG,EAAE,EAAE,KAAK,EAAE,CAAC;iBACpC,CAAC,CAAA;YACN,MAAM,gBAAgB,GAAG,MAAM,eAAe,CAAC,gBAAgB,EAAE,CAAA;YAEjE,IAAI,CAAC,gBAAgB,EAAE,CAAC;gBACtB,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;YACrE,CAAC;YAED,MAAM,WAAW,GAAG,MAAM,aAAa;iBACpC,OAAO,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC;iBAC/B,IAAI,EAAE,CAAA;YACT,IAAI,WAAW,EAAE,CAAC;gBAChB,MAAM,IAAI,KAAK,CAAC,aAAa,YAAY,kBAAkB,CAAC,CAAA;YAC9D,CAAC;YACD,MAAM,SAAS,GAAG,MAAM,UAAU,CAAC,IAAI,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,CAAA;YACjE,MAAM,MAAM,GAAG,SAAS,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;YACtE,MAAM,CAAC,cAAc,CAAC,GAAG,MAAM,aAAa,CAAC,MAAM,CAAC;gBAClD;oBACE,GAAG,EAAE,QAAQ;oBACb,IAAI,EAAE,YAAY;oBAClB,IAAI;oBACJ,MAAM,EAAE,CAAC,CAAC;oBACV,gBAAgB;oBAChB,MAAM;iBACP;aACF,CAAC,CAAA;YACF,MAAM,CAAC,KAAK,EAAE,CACZ,uBAAuB,YAAY,aAAa,cAAc,CAAC,GAAG,GAAG,CACtE,CAAA;YAED,KAAK,MAAM,YAAY,IAAI,gBAAgB,EAAE,CAAC;gBAC5C,MAAM,CAAC,YAAY,CAAC,GAAG,MAAM,WAAW,CAAC,MAAM,CAAC;oBAC9C;wBACE,IAAI,EAAE,YAAY;wBAClB,QAAQ,EAAE,cAAc,CAAC,GAAG;wBAC5B,MAAM,EAAE,gBAAgB,CAAC,YAAY,CAAC;wBACtC,GAAG,CAAC,eAAe,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,eAAe,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC;wBAC5D,IAAI;wBACJ,MAAM,EAAE,CAAC,CAAC;qBACX;iBACF,CAAC,CAAA;gBACF,MAAM,CAAC,KAAK,EAAE,CACZ,qBAAqB,YAAY,aAAa,YAAY,CAAC,GAAG,GAAG,CAClE,CAAA;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,KAAK,CAAC,kBAAkB,CAAC,QAA4B;QACnD,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAA;IACvD,CAAC;IAED,gEAAgE;IAChE,KAAK,CAAC,eAAe,CAAC,UAA2B,IAAG,CAAC;IAErD,UAAU;QACR,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QACpD,OAAO,IAAI,6BAA6B,CACtC,EAAE,QAAQ,EAAE,OAAO,EAAE,QAAQ,EAAE,EAC/B,EAAE,MAAM,EAAE,CACX,CAAA;IACH,CAAC;CACF"}

package/dist/Changes/AddAssemblyFromFileChange.d.ts

@@ -1,5 +1,5 @@
-import { type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
-import { FromFileBaseChange } from './FromFileBaseChange';
+import type { ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
+import { FromFileBaseChange } from './FromFileBaseChange.js';
 export interface SerializedAddAssemblyFromFileChangeBase extends SerializedAssemblySpecificChange {
     typeName: 'AddAssemblyFromFileChange';
 }
@@ -41,3 +41,4 @@ export declare class AddAssemblyFromFileChange extends FromFileBaseChange {
     executeOnClient(_dataStore: ClientDataStore): Promise<void>;
     getInverse(): AddAssemblyFromFileChange;
 }
+//# sourceMappingURL=AddAssemblyFromFileChange.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"AddAssemblyFromFileChange.d.ts","sourceRoot":"","sources":["../../src/Changes/AddAssemblyFromFileChange.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EACV,aAAa,EACb,eAAe,EACf,kBAAkB,EAClB,gCAAgC,EAChC,eAAe,EAChB,MAAM,2BAA2B,CAAA;AAGlC,OAAO,EAAE,kBAAkB,EAAE,MAAM,yBAAyB,CAAA;AAE5D,MAAM,WAAW,uCACf,SAAQ,gCAAgC;IACxC,QAAQ,EAAE,2BAA2B,CAAA;CACtC;AAED,MAAM,WAAW,gCAAgC;IAC/C,YAAY,EAAE,MAAM,CAAA;IACpB,OAAO,EAAE;QAAE,EAAE,EAAE,MAAM,CAAA;KAAE,GAAG;QAAE,EAAE,EAAE,MAAM,CAAC;QAAC,GAAG,EAAE,MAAM,CAAC;QAAC,GAAG,EAAE,MAAM,CAAA;KAAE,CAAA;CACnE;AAED,MAAM,WAAW,yCACf,SAAQ,uCAAuC,EAC7C,gCAAgC;CAAG;AAEvC,MAAM,WAAW,2CACf,SAAQ,uCAAuC;IAC/C,OAAO,EAAE,gCAAgC,EAAE,CAAA;CAC5C;AAED,MAAM,MAAM,mCAAmC,GAC3C,yCAAyC,GACzC,2CAA2C,CAAA;AAE/C,qBAAa,yBAA0B,SAAQ,kBAAkB;IAC/D,QAAQ,8BAAuC;IAC/C,OAAO,EAAE,gCAAgC,EAAE,CAAA;gBAGzC,IAAI,EAAE,mCAAmC,EACzC,OAAO,CAAC,EAAE,aAAa;IAMzB,IAAI,YAAY,IAAI,MAAM,CAEzB;IAED,MAAM,IAAI,mCAAmC;IAS7C;;;;OAIG;IACG,eAAe,CAAC,OAAO,EAAE,eAAe;IAUxC,sBAAsB,CAC1B,OAAO,EAAE,eAAe,EACxB,YAAY,EAAE,MAAM,EACpB,OAAO,EAAE;QAAE,EAAE,EAAE,MAAM,CAAC;QAAC,GAAG,EAAE,MAAM,CAAC;QAAC,GAAG,EAAE,MAAM,CAAA;KAAE;IAoF7C,oBAAoB,CACxB,OAAO,EAAE,eAAe,EACxB,YAAY,EAAE,MAAM,EACpB,MAAM,EAAE,MAAM;IA0CV,kBAAkB,CAAC,QAAQ,EAAE,kBAAkB;IAK/C,eAAe,CAAC,UAAU,EAAE,eAAe;IAEjD,UAAU;CAOX"}

package/dist/Changes/AddAssemblyFromFileChange.js

@@ -1,9 +1,6 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AddAssemblyFromFileChange = void 0;
-const indexedfasta_1 = require("@gmod/indexedfasta");
-const FromFileBaseChange_1 = require("./FromFileBaseChange");
-class AddAssemblyFromFileChange extends FromFileBaseChange_1.FromFileBaseChange {
+import { BgzipIndexedFasta } from '@gmod/indexedfasta';
+import { FromFileBaseChange } from './FromFileBaseChange.js';
+export class AddAssemblyFromFileChange extends FromFileBaseChange {
     typeName = 'AddAssemblyFromFileChange';
     changes;
     constructor(json, options) {
@@ -62,7 +59,7 @@ class AddAssemblyFromFileChange extends FromFileBaseChange_1.FromFileBaseChange
         const fasta = filesService.getFileHandle(faDoc);
         const fai = filesService.getFileHandle(faiDoc);
         const gzi = filesService.getFileHandle(gziDoc);
-        const sequenceAdapter = new indexedfasta_1.BgzipIndexedFasta({ fasta, fai, gzi });
+        const sequenceAdapter = new BgzipIndexedFasta({ fasta, fai, gzi });
         const allSequenceSizes = await sequenceAdapter.getSequenceSizes();
         await Promise.all([fasta.close(), fai.close(), gzi.close()]);
         const assemblyDoc = await assemblyModel
@@ -142,5 +139,4 @@ class AddAssemblyFromFileChange extends FromFileBaseChange_1.FromFileBaseChange
         return new AddAssemblyFromFileChange({ typeName, changes, assembly }, { logger });
     }
 }
-exports.AddAssemblyFromFileChange = AddAssemblyFromFileChange;
 //# sourceMappingURL=AddAssemblyFromFileChange.js.map

package/dist/Changes/AddAssemblyFromFileChange.js.map

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

@@ -1,6 +1,6 @@
 import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
-import { DeleteFeatureChange } from './DeleteFeatureChange';
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import { DeleteFeatureChange } from './DeleteFeatureChange.js';
 interface SerializedAddFeatureChangeBase extends SerializedFeatureChange {
     typeName: 'AddFeatureChange';
 }
@@ -34,3 +34,4 @@ export declare class AddFeatureChange extends FeatureChange {
 }
 export declare function isAddFeatureChange(change: unknown): change is AddFeatureChange;
 export {};
+//# sourceMappingURL=AddFeatureChange.d.ts.map

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

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

@@ -1,13 +1,10 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AddFeatureChange = void 0;
-exports.isAddFeatureChange = isAddFeatureChange;
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/restrict-template-expressions */
 /* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
-const common_1 = require("@apollo-annotation/common");
-const DeleteFeatureChange_1 = require("./DeleteFeatureChange");
-class AddFeatureChange extends common_1.FeatureChange {
+import { FeatureChange, } from '@apollo-annotation/common';
+import { DeleteFeatureChange } from './DeleteFeatureChange.js';
+export class AddFeatureChange extends FeatureChange {
     typeName = 'AddFeatureChange';
     changes;
     constructor(json, options) {
@@ -79,6 +76,7 @@ class AddFeatureChange extends common_1.FeatureChange {
                 featureCnt++;
             }
             else {
+                const indexedIds = this.getIndexedIds(addedFeature, idsToIndex);
                 // Adding new child feature
                 if (parentFeatureId) {
                     const topLevelFeature = await featureModel
@@ -95,12 +93,15 @@ class AddFeatureChange extends common_1.FeatureChange {
                     this.addChild(parentFeature, addedFeature);
                     const childIds = this.getChildFeatureIds(addedFeature);
                     topLevelFeature.allIds.push(_id, ...childIds);
+                    if (indexedIds.length > 0 && !topLevelFeature.indexedIds) {
+                        topLevelFeature.indexedIds = [];
+                    }
+                    topLevelFeature.indexedIds?.push(...indexedIds);
                     await topLevelFeature.save();
                 }
                 else {
                     const childIds = this.getChildFeatureIds(addedFeature);
                     const allIdsV2 = [_id, ...childIds];
-                    const indexedIds = this.getIndexedIds(addedFeature, idsToIndex);
                     const [newFeatureDoc] = await featureModel.create([{ allIds: allIdsV2, indexedIds, status: 0, ...addedFeature }], { session });
                     logger.verbose?.(`Added docId "${newFeatureDoc._id}"`);
                 }
@@ -154,7 +155,7 @@ class AddFeatureChange extends common_1.FeatureChange {
             deletedFeature: addFeatureChange.addedFeature,
             parentFeatureId: addFeatureChange.parentFeatureId,
         }));
-        return new DeleteFeatureChange_1.DeleteFeatureChange({
+        return new DeleteFeatureChange({
             changedIds: inverseChangedIds,
             typeName: 'DeleteFeatureChange',
             changes: inverseChanges,
@@ -162,8 +163,7 @@ class AddFeatureChange extends common_1.FeatureChange {
         }, { logger });
     }
 }
-exports.AddFeatureChange = AddFeatureChange;
-function isAddFeatureChange(change) {
+export function isAddFeatureChange(change) {
     return change.typeName === 'AddFeatureChange';
 }
 //# sourceMappingURL=AddFeatureChange.js.map

package/dist/Changes/AddFeatureChange.js.map

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package/dist/Changes/AddFeaturesFromFileChange.d.ts

@@ -1,5 +1,5 @@
-import { type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
-import { FromFileBaseChange } from './FromFileBaseChange';
+import type { ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
+import { FromFileBaseChange } from './FromFileBaseChange.js';
 export interface SerializedAddFeaturesFromFileChangeBase extends SerializedAssemblySpecificChange {
     typeName: 'AddFeaturesFromFileChange';
     deleteExistingFeatures?: boolean;
@@ -7,7 +7,8 @@ export interface SerializedAddFeaturesFromFileChangeBase extends SerializedAssem
 export interface AddFeaturesFromFileChangeDetails {
     fileId: string;
     parseOptions?: {
-        bufferSize: number;
+        bufferSize?: number;
+        strict?: boolean;
     };
 }
 export interface SerializedAddFeaturesFromFileChangeSingle extends SerializedAddFeaturesFromFileChangeBase, AddFeaturesFromFileChangeDetails {
@@ -33,3 +34,4 @@ export declare class AddFeaturesFromFileChange extends FromFileBaseChange {
     executeOnClient(_dataStore: ClientDataStore): Promise<void>;
     getInverse(): AddFeaturesFromFileChange;
 }
+//# sourceMappingURL=AddFeaturesFromFileChange.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"AddFeaturesFromFileChange.d.ts","sourceRoot":"","sources":["../../src/Changes/AddFeaturesFromFileChange.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EACV,aAAa,EACb,eAAe,EACf,kBAAkB,EAClB,gCAAgC,EAChC,eAAe,EAChB,MAAM,2BAA2B,CAAA;AAElC,OAAO,EAAE,kBAAkB,EAAE,MAAM,yBAAyB,CAAA;AAE5D,MAAM,WAAW,uCACf,SAAQ,gCAAgC;IACxC,QAAQ,EAAE,2BAA2B,CAAA;IACrC,sBAAsB,CAAC,EAAE,OAAO,CAAA;CACjC;AAED,MAAM,WAAW,gCAAgC;IAC/C,MAAM,EAAE,MAAM,CAAA;IACd,YAAY,CAAC,EAAE;QAAE,UAAU,CAAC,EAAE,MAAM,CAAC;QAAC,MAAM,CAAC,EAAE,OAAO,CAAA;KAAE,CAAA;CACzD;AAED,MAAM,WAAW,yCACf,SAAQ,uCAAuC,EAC7C,gCAAgC;CAAG;AAEvC,MAAM,WAAW,2CACf,SAAQ,uCAAuC;IAC/C,OAAO,EAAE,gCAAgC,EAAE,CAAA;CAC5C;AAED,MAAM,MAAM,mCAAmC,GAC3C,yCAAyC,GACzC,2CAA2C,CAAA;AAE/C,qBAAa,yBAA0B,SAAQ,kBAAkB;IAC/D,QAAQ,8BAAuC;IAC/C,OAAO,EAAE,gCAAgC,EAAE,CAAA;IAC3C,sBAAsB,UAAQ;gBAG5B,IAAI,EAAE,mCAAmC,EACzC,OAAO,CAAC,EAAE,aAAa;IAQzB,IAAI,YAAY,IAAI,MAAM,CAEzB;IAED,MAAM,IAAI,mCAAmC;IAS7C;;;;OAIG;IACG,eAAe,CAAC,OAAO,EAAE,eAAe;IAgExC,kBAAkB,CAAC,QAAQ,EAAE,kBAAkB;IAK/C,eAAe,CAAC,UAAU,EAAE,eAAe;IAEjD,UAAU;CAOX"}

package/dist/Changes/AddFeaturesFromFileChange.js

@@ -1,8 +1,5 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AddFeaturesFromFileChange = void 0;
-const FromFileBaseChange_1 = require("./FromFileBaseChange");
-class AddFeaturesFromFileChange extends FromFileBaseChange_1.FromFileBaseChange {
+import { FromFileBaseChange } from './FromFileBaseChange.js';
+export class AddFeaturesFromFileChange extends FromFileBaseChange {
     typeName = 'AddFeaturesFromFileChange';
     changes;
     deleteExistingFeatures = false;
@@ -46,17 +43,34 @@ class AddFeaturesFromFileChange extends FromFileBaseChange_1.FromFileBaseChange
                 throw new Error(`File "${fileId}" not found in Mongo`);
             }
             logger.debug?.(`FileId "${fileId}", checksum "${fileDoc.checksum}"`);
+            let errorCount = 0;
+            // eslint-disable-next-line unicorn/consistent-function-scoping
+            const errorLogger = (error) => {
+                if (errorCount <= 99) {
+                    logger.warn('Error parsing or adding feature');
+                    logger.warn(error);
+                    if (errorCount === 99) {
+                        logger.warn('Reached 100 feature errors, omitting further warnings from log');
+                    }
+                }
+                errorCount++;
+            };
             // Read data from compressed file and parse the content
-            const { bufferSize = 10_000 } = parseOptions ?? {};
-            const featureStream = filesService.parseGFF3(filesService.getFileStream(fileDoc), { bufferSize });
+            const { bufferSize = 10_000, strict = true } = parseOptions ?? {};
+            const featureStream = filesService.parseGFF3(filesService.getFileStream(fileDoc), { bufferSize, errorCallback: strict ? undefined : errorLogger });
             let featureCount = 0;
-            // @ts-expect-error type is wrong here
-            // eslint-disable-next-line @typescript-eslint/await-thenable
-            for await (const f of featureStream) {
-                const gff3Feature = f;
+            for await (const gff3Feature of featureStream) {
                 // Add new feature into database
-                // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
-                await this.addFeatureIntoDb(gff3Feature, backend);
+                try {
+                    await this.addFeatureIntoDb(gff3Feature, backend);
+                }
+                catch (error) {
+                    // if the first feature is an error, assume the file isn't valid and throw
+                    if (strict || featureCount === 0) {
+                        throw error;
+                    }
+                    errorLogger(error);
+                }
                 featureCount++;
                 if (featureCount % 1000 === 0) {
                     logger.debug?.(`Processed ${featureCount} features`);
@@ -75,5 +89,4 @@ class AddFeaturesFromFileChange extends FromFileBaseChange_1.FromFileBaseChange
         return new AddFeaturesFromFileChange({ typeName, changes, assembly }, { logger });
     }
 }
-exports.AddFeaturesFromFileChange = AddFeaturesFromFileChange;
 //# sourceMappingURL=AddFeaturesFromFileChange.js.map

package/dist/Changes/AddFeaturesFromFileChange.js.map

@@ -1 +1 @@
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+{"version":3,"file":"AddFeaturesFromFileChange.js","sourceRoot":"","sources":["../../src/Changes/AddFeaturesFromFileChange.ts"],"names":[],"mappings":"AASA,OAAO,EAAE,kBAAkB,EAAE,MAAM,yBAAyB,CAAA;AA0B5D,MAAM,OAAO,yBAA0B,SAAQ,kBAAkB;IAC/D,QAAQ,GAAG,2BAAoC,CAAA;IAC/C,OAAO,CAAoC;IAC3C,sBAAsB,GAAG,KAAK,CAAA;IAE9B,YACE,IAAyC,EACzC,OAAuB;QAEvB,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QACpB,IAAI,CAAC,sBAAsB,GAAG,IAAI,CAAC,sBAAsB,IAAI,KAAK,CAAA;QAClE,IAAI,CAAC,OAAO,GAAG,SAAS,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IAC1D,CAAC;IAED,2EAA2E;IAC3E,IAAI,YAAY;QACd,OAAO,iEAAiE,CAAA;IAC1E,CAAC;IAED,MAAM;QACJ,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,sBAAsB,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QACpE,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACzB,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC,GAAG,OAAO,CAAA;YAC5B,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,EAAE,sBAAsB,EAAE,CAAA;QAC/D,CAAC;QACD,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,OAAO,EAAE,sBAAsB,EAAE,CAAA;IAChE,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,eAAe,CAAC,OAAwB;QAC5C,MAAM,EAAE,SAAS,EAAE,YAAY,EAAE,GAAG,OAAO,CAAA;QAC3C,MAAM,EAAE,OAAO,EAAE,sBAAsB,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QAExD,IAAI,sBAAsB,EAAE,CAAC;YAC3B,MAAM,IAAI,CAAC,sBAAsB,CAAC,OAAO,CAAC,CAAA;QAC5C,CAAC;QAED,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,CAAA;YAEvC,MAAM,EAAE,kBAAkB,EAAE,GAAG,OAAO,CAAC,GAAG,CAAA;YAC1C,IAAI,CAAC,kBAAkB,EAAE,CAAC;gBACxB,MAAM,IAAI,KAAK,CAAC,0CAA0C,CAAC,CAAA;YAC7D,CAAC;YACD,oBAAoB;YACpB,MAAM,OAAO,GAAG,MAAM,SAAS,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,CAAA;YACvD,IAAI,CAAC,OAAO,EAAE,CAAC;gBACb,MAAM,IAAI,KAAK,CAAC,SAAS,MAAM,sBAAsB,CAAC,CAAA;YACxD,CAAC;YACD,MAAM,CAAC,KAAK,EAAE,CAAC,WAAW,MAAM,gBAAgB,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAA;YAEpE,IAAI,UAAU,GAAG,CAAC,CAAA;YAClB,+DAA+D;YAC/D,MAAM,WAAW,GAAG,CAAC,KAAc,EAAE,EAAE;gBACrC,IAAI,UAAU,IAAI,EAAE,EAAE,CAAC;oBACrB,MAAM,CAAC,IAAI,CAAC,iCAAiC,CAAC,CAAA;oBAC9C,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;oBAClB,IAAI,UAAU,KAAK,EAAE,EAAE,CAAC;wBACtB,MAAM,CAAC,IAAI,CACT,gEAAgE,CACjE,CAAA;oBACH,CAAC;gBACH,CAAC;gBACD,UAAU,EAAE,CAAA;YACd,CAAC,CAAA;YAED,uDAAuD;YACvD,MAAM,EAAE,UAAU,GAAG,MAAM,EAAE,MAAM,GAAG,IAAI,EAAE,GAAG,YAAY,IAAI,EAAE,CAAA;YACjE,MAAM,aAAa,GAAG,YAAY,CAAC,SAAS,CAC1C,YAAY,CAAC,aAAa,CAAC,OAAO,CAAC,EACnC,EAAE,UAAU,EAAE,aAAa,EAAE,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,WAAW,EAAE,CAChE,CAAA;YACD,IAAI,YAAY,GAAG,CAAC,CAAA;YACpB,IAAI,KAAK,EAAE,MAAM,WAAW,IAAI,aAAa,EAAE,CAAC;gBAC9C,gCAAgC;gBAChC,IAAI,CAAC;oBACH,MAAM,IAAI,CAAC,gBAAgB,CAAC,WAAW,EAAE,OAAO,CAAC,CAAA;gBACnD,CAAC;gBAAC,OAAO,KAAK,EAAE,CAAC;oBACf,0EAA0E;oBAC1E,IAAI,MAAM,IAAI,YAAY,KAAK,CAAC,EAAE,CAAC;wBACjC,MAAM,KAAK,CAAA;oBACb,CAAC;oBACD,WAAW,CAAC,KAAK,CAAC,CAAA;gBACpB,CAAC;gBACD,YAAY,EAAE,CAAA;gBACd,IAAI,YAAY,GAAG,IAAI,KAAK,CAAC,EAAE,CAAC;oBAC9B,MAAM,CAAC,KAAK,EAAE,CAAC,aAAa,YAAY,WAAW,CAAC,CAAA;gBACtD,CAAC;YACH,CAAC;QACH,CAAC;QACD,MAAM,CAAC,KAAK,EAAE,CAAC,mCAAmC,CAAC,CAAA;IACrD,CAAC;IAED,KAAK,CAAC,kBAAkB,CAAC,QAA4B;QACnD,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAA;IACvD,CAAC;IAED,gEAAgE;IAChE,KAAK,CAAC,eAAe,CAAC,UAA2B,IAAG,CAAC;IAErD,UAAU;QACR,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QACpD,OAAO,IAAI,yBAAyB,CAClC,EAAE,QAAQ,EAAE,OAAO,EAAE,QAAQ,EAAE,EAC/B,EAAE,MAAM,EAAE,CACX,CAAA;IACH,CAAC;CACF"}

package/dist/Changes/AddRefSeqAliasesChange.d.ts

@@ -18,3 +18,4 @@ export declare class AddRefSeqAliasesChange extends AssemblySpecificChange {
     executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<unknown>;
     get notification(): string;
 }
+//# sourceMappingURL=AddRefSeqAliasesChange.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"AddRefSeqAliasesChange.d.ts","sourceRoot":"","sources":["../../src/Changes/AddRefSeqAliasesChange.ts"],"names":[],"mappings":"AAGA,OAAO,EACL,sBAAsB,EACtB,KAAK,MAAM,EACX,KAAK,aAAa,EAClB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,gCAAgC,EACrC,KAAK,eAAe,EACrB,MAAM,2BAA2B,CAAA;AAGlC,MAAM,WAAW,uBAAuB;IACtC,OAAO,EAAE,MAAM,CAAA;IACf,OAAO,EAAE,MAAM,EAAE,CAAA;CAClB;AAED,MAAM,WAAW,6BACf,SAAQ,gCAAgC;IACxC,QAAQ,EAAE,wBAAwB,CAAA;IAClC,aAAa,EAAE,uBAAuB,EAAE,CAAA;CACzC;AAED,qBAAa,sBAAuB,SAAQ,sBAAsB;IAChE,QAAQ,2BAAoC;IAC5C,aAAa,EAAE,uBAAuB,EAAE,CAAA;gBAE5B,IAAI,EAAE,6BAA6B,EAAE,OAAO,CAAC,EAAE,aAAa;IAKxE,eAAe,CAAC,eAAe,EAAE,eAAe;IAkBhD,UAAU,IAAI,MAAM;IAIpB,MAAM,IAAI,6BAA6B;IAKjC,eAAe,CAAC,OAAO,EAAE,eAAe;IAe9C,kBAAkB,CAAC,QAAQ,EAAE,kBAAkB,GAAG,OAAO,CAAC,OAAO,CAAC;IAKlE,IAAI,YAAY,IAAI,MAAM,CAEzB;CACF"}

package/dist/Changes/AddRefSeqAliasesChange.js

@@ -1,9 +1,9 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AddRefSeqAliasesChange = void 0;
-const common_1 = require("@apollo-annotation/common");
-const util_1 = require("@jbrowse/core/util");
-class AddRefSeqAliasesChange extends common_1.AssemblySpecificChange {
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+import { AssemblySpecificChange, } from '@apollo-annotation/common';
+import { getSession } from '@jbrowse/core/util';
+export class AddRefSeqAliasesChange extends AssemblySpecificChange {
     typeName = 'AddRefSeqAliasesChange';
     refSeqAliases;
     constructor(json, options) {
@@ -11,7 +11,7 @@ class AddRefSeqAliasesChange extends common_1.AssemblySpecificChange {
         this.refSeqAliases = json.refSeqAliases;
     }
     executeOnClient(clientDataStore) {
-        const { assemblyManager } = (0, util_1.getSession)(clientDataStore);
+        const { assemblyManager } = getSession(clientDataStore);
         const assembly = assemblyManager.get(this.assembly);
         if (!assembly) {
             throw new Error(`assembly ${this.assembly} not found`);
@@ -52,5 +52,4 @@ class AddRefSeqAliasesChange extends common_1.AssemblySpecificChange {
         return 'RefSeq aliases have been added.';
     }
 }
-exports.AddRefSeqAliasesChange = AddRefSeqAliasesChange;
 //# sourceMappingURL=AddRefSeqAliasesChange.js.map

package/dist/Changes/AddRefSeqAliasesChange.js.map

@@ -1 +1 @@
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