@jbrowse/core 2.5.0 → 2.6.0

package/BaseFeatureWidget/SequenceFeatureDetails/ProteinSequence.d.ts

@@ -1,3 +1,4 @@
+import React from 'react';
 import { Feat } from '../util';
 export default function ProteinSequence({ cds, sequence, codonTable, }: {
     cds: Feat[];
@@ -5,4 +6,4 @@ export default function ProteinSequence({ cds, sequence, codonTable, }: {
     codonTable: {
         [key: string]: string;
     };
-}): JSX.Element;
+}): React.JSX.Element;

package/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts

@@ -1,2 +1,3 @@
+import React from 'react';
 import { BaseProps } from './../types';
-export default function SequenceFeatureDetails({ model, feature: prefeature, }: BaseProps): JSX.Element;
+export default function SequenceFeatureDetails({ model, feature: prefeature, }: BaseProps): React.JSX.Element;

package/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js

@@ -56,40 +56,37 @@ function SequenceFeatureDetails({ model, feature: prefeature, }) {
     var _a, _b;
     const { classes } = useStyles();
     const feature = prefeature;
-    const hasCDS = (_a = feature.subfeatures) === null || _a === void 0 ? void 0 : _a.some(sub => sub.type === 'CDS');
-    const hasExon = (_b = feature.subfeatures) === null || _b === void 0 ? void 0 : _b.some(sub => sub.type === 'exon');
     const seqPanelRef = (0, react_1.useRef)(null);
     const [intronBp, setIntronBp] = (0, util_1.useLocalStorage)('intronBp', 10);
     const [upDownBp, setUpDownBp] = (0, util_1.useLocalStorage)('upDownBp', 500);
     const [copied, setCopied] = (0, react_1.useState)(false);
     const [copiedHtml, setCopiedHtml] = (0, react_1.useState)(false);
     const [force, setForce] = (0, react_1.useState)(false);
+    const hasCDS = (_a = feature.subfeatures) === null || _a === void 0 ? void 0 : _a.some(sub => sub.type === 'CDS');
+    const hasExon = (_b = feature.subfeatures) === null || _b === void 0 ? void 0 : _b.some(sub => sub.type === 'exon');
+    const hasExonOrCDS = hasExon || hasCDS;
     const { sequence, error } = (0, hooks_1.useFeatureSequence)(model, prefeature, upDownBp, force);
     const [mode, setMode] = (0, react_1.useState)(hasCDS ? 'cds' : hasExon ? 'cdna' : 'genomic');
     const rest = {
         ...(hasCDS ? { cds: 'CDS' } : {}),
         ...(hasCDS ? { protein: 'Protein' } : {}),
-        ...(hasExon ? { cdna: 'cDNA' } : {}),
-        ...(hasExon
-            ? {
-                gene: `Genomic w/ full introns`,
-            }
-            : {}),
-        ...(hasExon
+        ...(hasExonOrCDS ? { cdna: 'cDNA' } : {}),
+        ...(hasExonOrCDS ? { gene: `Genomic w/ full introns` } : {}),
+        ...(hasExonOrCDS
             ? {
                 gene_updownstream: `Genomic w/ full introns +/- ${upDownBp}bp up+down stream`,
             }
             : {}),
-        ...(hasExon
+        ...(hasExonOrCDS
             ? { gene_collapsed_intron: `Genomic w/ ${intronBp}bp intron` }
             : {}),
-        ...(hasExon
+        ...(hasExonOrCDS
             ? {
                 gene_updownstream_collapsed_intron: `Genomic w/ ${intronBp}bp intron +/- ${upDownBp}bp up+down stream `,
             }
             : {}),
-        ...(!hasExon ? { genomic: 'Genomic' } : {}),
-        ...(!hasExon
+        ...(!hasExonOrCDS ? { genomic: 'Genomic' } : {}),
+        ...(!hasExonOrCDS
             ? {
                 genomic_sequence_updownstream: `Genomic +/- ${upDownBp}bp up+down stream`,
             }

package/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureSettingsDialog.d.ts

@@ -1,3 +1,4 @@
+import React from 'react';
 export default function SequenceFeatureSettingsDialog({ handleClose, intronBp: intronBpArg, upDownBp: upDownBpArg, }: {
     handleClose: (arg?: {
         intronBp: number;
@@ -5,4 +6,4 @@ export default function SequenceFeatureSettingsDialog({ handleClose, intronBp: i
     }) => void;
     intronBp: number;
     upDownBp: number;
-}): JSX.Element;
+}): React.JSX.Element;

package/BaseFeatureWidget/SequenceFeatureDetails/SequenceHelpDialog.d.ts

@@ -1,3 +1,4 @@
+import React from 'react';
 export default function HelpDialog({ handleClose, }: {
     handleClose: () => void;
-}): JSX.Element;
+}): React.JSX.Element;

package/BaseFeatureWidget/SequenceFeatureDetails/SequenceHelpDialog.js

@@ -16,7 +16,7 @@ function HelpDialog({ handleClose, }) {
             react_1.default.createElement("ul", null,
                 react_1.default.createElement("li", null, "CDS - shows the stitched together CDS sequences"),
                 react_1.default.createElement("li", null, "Protein - the translated coding sequence, with the \"standard\" genetic code"),
-                react_1.default.createElement("li", null, "cDNA - shows the 'DNA' version of transcript, formed from exons, including non-coding genes"),
+                react_1.default.createElement("li", null, "cDNA - shows the 'copy DNA' of transcript, formed from exon sequences"),
                 react_1.default.createElement("li", null, "Genomic w/ introns +/- Nbp up+down stream - the sequence underlying the entire gene including including introns, with UTR and CDS highlighted")),
             react_1.default.createElement(material_1.Typography, { paragraph: true }, "For other feature types, the options are:"),
             react_1.default.createElement("ul", null,

package/BaseFeatureWidget/SequenceFeatureDetails/hooks.d.ts

@@ -1,8 +1,8 @@
 import { SeqState, ErrorState } from '../util';
 import { SimpleFeatureSerialized } from '../../util';
 export declare function useFeatureSequence(model: {
-    view: {
-        assemblyNames: string[];
+    view?: {
+        assemblyNames?: string[];
     };
 } | undefined, feature: SimpleFeatureSerialized, upDownBp: number, forceLoad: boolean): {
     sequence: SeqState | ErrorState | undefined;

package/BaseFeatureWidget/SequenceFeatureDetails/index.d.ts

@@ -1,2 +1,3 @@
+import React from 'react';
 import { BaseProps } from './../types';
-export default function SequenceFeaturePanel({ model, feature }: BaseProps): JSX.Element | null;
+export default function SequenceFeaturePanel({ model, feature }: BaseProps): React.JSX.Element | null;

package/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts

@@ -1,20 +1,20 @@
 declare namespace _default {
-    const source: string;
-    const type: string;
-    const start: number;
-    const end: number;
-    const strand: number;
-    const phase: number;
-    const refName: string;
-    const id: string;
-    const dbxref: string[];
-    const name: string;
-    const description: string;
-    const gbkey: string;
-    const gene: string;
-    const gene_biotype: string;
-    const gene_synonym: string[];
-    const subfeatures: {
+    let source: string;
+    let type: string;
+    let start: number;
+    let end: number;
+    let strand: number;
+    let phase: number;
+    let refName: string;
+    let id: string;
+    let dbxref: string[];
+    let name: string;
+    let description: string;
+    let gbkey: string;
+    let gene: string;
+    let gene_biotype: string;
+    let gene_synonym: string[];
+    let subfeatures: {
         source: string;
         type: string;
         start: number;
@@ -75,6 +75,6 @@ declare namespace _default {
         uniqueId: string;
         parentId: string;
     }[];
-    const uniqueId: string;
+    let uniqueId: string;
 }
 export default _default;

package/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts

@@ -1,19 +1,19 @@
 declare namespace _default {
-    const source: string;
-    const type: string;
-    const start: number;
-    const end: number;
-    const strand: number;
-    const phase: number;
-    const refName: string;
-    const id: string;
-    const dbxref: string[];
-    const name: string;
-    const description: string;
-    const gbkey: string;
-    const gene: string;
-    const gene_biotype: string;
-    const subfeatures: ({
+    let source: string;
+    let type: string;
+    let start: number;
+    let end: number;
+    let strand: number;
+    let phase: number;
+    let refName: string;
+    let id: string;
+    let dbxref: string[];
+    let name: string;
+    let description: string;
+    let gbkey: string;
+    let gene: string;
+    let gene_biotype: string;
+    let subfeatures: ({
         source: string;
         type: string;
         start: number;
@@ -136,6 +136,6 @@ declare namespace _default {
         parentId: string;
         tag?: undefined;
     })[];
-    const uniqueId: string;
+    let uniqueId: string;
 }
 export default _default;

package/BaseFeatureWidget/util.js

@@ -24,10 +24,15 @@ function revlist(list, seqlen) {
         .sort((a, b) => a.start - b.start);
 }
 exports.revlist = revlist;
-// calculates UTRs using impliedUTRs logic
 function calculateUTRs(cds, exons) {
-    const firstCds = cds[0];
-    const lastCds = cds[cds.length - 1];
+    // checking length ensures the .at below are valid
+    if (!cds.length) {
+        return [];
+    }
+    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+    const firstCds = cds.at(0);
+    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+    const lastCds = cds.at(-1);
     const firstCdsIdx = exons.findIndex(exon => exon.end >= firstCds.start && exon.start <= firstCds.start);
     const lastCdsIdx = exons.findIndex(exon => exon.end >= lastCds.end && exon.start <= lastCds.end);
     const lastCdsExon = exons[lastCdsIdx];
@@ -45,8 +50,13 @@ function calculateUTRs(cds, exons) {
 exports.calculateUTRs = calculateUTRs;
 // calculates UTRs using impliedUTRs logic, but there are no exon subfeatures
 function calculateUTRs2(cds, parentFeat) {
-    const firstCds = cds[0];
-    const lastCds = cds[cds.length - 1];
+    if (!cds.length) {
+        return [];
+    }
+    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+    const firstCds = cds.at(0);
+    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+    const lastCds = cds.at(-1);
     const fiveUTRs = [{ start: parentFeat.start, end: firstCds.start }].map(elt => ({ ...elt, type: 'five_prime_UTR' }));
     const threeUTRs = [{ start: lastCds.end, end: parentFeat.end }].map(elt => ({
         ...elt,

package/PluginManager.d.ts

@@ -207,9 +207,9 @@ export default class PluginManager {
         '@jbrowse/core/util/mst-reflection': typeof import("./util/mst-reflection");
         '@jbrowse/core/util/rxjs': typeof import("./util/rxjs");
         '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail': {
-            Attributes: (props: any) => JSX.Element;
-            FeatureDetails: (props: any) => JSX.Element;
-            BaseCard: (props: any) => JSX.Element;
+            Attributes: (props: any) => import("react").JSX.Element;
+            FeatureDetails: (props: any) => import("react").JSX.Element;
+            BaseCard: (props: any) => import("react").JSX.Element;
         };
         '@jbrowse/core/data_adapters/BaseAdapter': typeof import("./data_adapters/BaseAdapter");
         mobx: typeof import("mobx");

package/README.md

@@ -1,8 +1,6 @@
 # jbrowse-core
 
 [![NPM version](https://img.shields.io/npm/v/@jbrowse/core.svg?style=flat-square)](https://npmjs.org/package/@jbrowse/core)
-[![Build Status](https://img.shields.io/travis/GMOD/jbrowse-components/main.svg?style=flat-square)](https://travis-ci.org/GMOD/jbrowse-components)
-[![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/jbrowse-components/main.svg?style=flat-square)](https://codecov.io/gh/GMOD/jbrowse-components/branch/main)
 
 Core JBrowse libraries used by most JBrowse plugins.
 

package/ReExports/modules.d.ts

@@ -124,9 +124,9 @@ declare const libs: {
     '@jbrowse/core/util/mst-reflection': typeof coreMstReflection;
     '@jbrowse/core/util/rxjs': typeof rxjs;
     '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail': {
-        Attributes: (props: any) => JSX.Element;
-        FeatureDetails: (props: any) => JSX.Element;
-        BaseCard: (props: any) => JSX.Element;
+        Attributes: (props: any) => React.JSX.Element;
+        FeatureDetails: (props: any) => React.JSX.Element;
+        BaseCard: (props: any) => React.JSX.Element;
     };
     '@jbrowse/core/data_adapters/BaseAdapter': typeof BaseAdapterExports;
     mobx: typeof mobx;

package/ReExports/modules.js

@@ -306,9 +306,6 @@ const DataGridEntries = {
     GridSaveAltIcon: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/x-data-grid'))).then(module => ({
         default: module.GridSaveAltIcon,
     }))),
-    GridScrollArea: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/x-data-grid'))).then(module => ({
-        default: module.GridScrollArea,
-    }))),
     GridSearchIcon: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/x-data-grid'))).then(module => ({
         default: module.GridSearchIcon,
     }))),

package/assemblyManager/assemblyConfigSchema.d.ts

@@ -1,6 +1,7 @@
 import PluginManager from '../PluginManager';
 /**
  * #config BaseAssembly
+ * #category assemblyManagement
  * This corresponds to the assemblies section of the config
  */
 declare function assemblyConfigSchema(pluginManager: PluginManager): import("../configuration/configurationSchema").ConfigurationSchemaType<{
@@ -54,3 +55,4 @@ declare function assemblyConfigSchema(pluginManager: PluginManager): import("../
     };
 }, import("../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name">>;
 export default assemblyConfigSchema;
+export type BaseAssemblyConfigSchema = ReturnType<typeof assemblyConfigSchema>;

package/assemblyManager/assemblyConfigSchema.js

@@ -3,6 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("../configuration");
 /**
  * #config BaseAssembly
+ * #category assemblyManagement
  * This corresponds to the assemblies section of the config
  */
 function assemblyConfigSchema(pluginManager) {

package/assemblyManager/assemblyManager.d.ts

@@ -68,6 +68,118 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
 }, {
+    readonly assemblyNameMap: {
+        [key: string]: ({
+            configuration: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            error: unknown;
+            loaded: boolean;
+            loadingP: Promise<void> | undefined;
+            volatileRegions: import("./assembly").BasicRegion[] | undefined;
+            refNameAliases: {
+                [x: string]: string | undefined;
+            } | undefined;
+            lowerCaseRefNameAliases: {
+                [x: string]: string | undefined;
+            } | undefined;
+            cytobands: import("../util").Feature[] | undefined;
+        } & {
+            readonly initialized: boolean;
+            readonly name: string;
+            readonly regions: import("./assembly").BasicRegion[] | undefined;
+            readonly aliases: string[];
+            readonly displayName: string | undefined;
+            hasName(name: string): boolean;
+            readonly allAliases: string[];
+            readonly allRefNames: string[] | undefined;
+            readonly lowerCaseRefNames: string[] | undefined;
+            readonly allRefNamesWithLowerCase: string[] | undefined;
+            readonly rpcManager: RpcManager;
+            readonly refNameColors: string[];
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            isValidRefName(refName: string): boolean;
+        } & {
+            setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("./assembly").Loading): void;
+            setError(e: unknown): void;
+            setRegions(regions: import("../util").Region[]): void;
+            setRefNameAliases(aliases: {
+                [x: string]: string | undefined;
+            }, lcAliases: {
+                [x: string]: string | undefined;
+            }): void;
+            setCytobands(cytobands: import("../util").Feature[]): void;
+            setLoadingP(p?: Promise<void> | undefined): void;
+            load(): Promise<void>;
+            loadPre(): Promise<void>;
+        } & {
+            getAdapterMapEntry(adapterConf: unknown, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
+            getRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+            getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
+        }, {
+            error: unknown;
+            loaded: boolean;
+            loadingP: Promise<void> | undefined;
+            volatileRegions: import("./assembly").BasicRegion[] | undefined;
+            refNameAliases: {
+                [x: string]: string | undefined;
+            } | undefined;
+            lowerCaseRefNameAliases: {
+                [x: string]: string | undefined;
+            } | undefined;
+            cytobands: import("../util").Feature[] | undefined;
+        } & {
+            readonly initialized: boolean;
+            readonly name: string;
+            readonly regions: import("./assembly").BasicRegion[] | undefined;
+            readonly aliases: string[];
+            readonly displayName: string | undefined;
+            hasName(name: string): boolean;
+            readonly allAliases: string[];
+            readonly allRefNames: string[] | undefined;
+            readonly lowerCaseRefNames: string[] | undefined;
+            readonly allRefNamesWithLowerCase: string[] | undefined;
+            readonly rpcManager: RpcManager;
+            readonly refNameColors: string[];
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            isValidRefName(refName: string): boolean;
+        } & {
+            setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("./assembly").Loading): void;
+            setError(e: unknown): void;
+            setRegions(regions: import("../util").Region[]): void;
+            setRefNameAliases(aliases: {
+                [x: string]: string | undefined;
+            }, lcAliases: {
+                [x: string]: string | undefined;
+            }): void;
+            setCytobands(cytobands: import("../util").Feature[]): void;
+            setLoadingP(p?: Promise<void> | undefined): void;
+            load(): Promise<void>;
+            loadPre(): Promise<void>;
+        } & {
+            getAdapterMapEntry(adapterConf: unknown, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
+            getRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+            getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
+    };
+} & {
     /**
      * #method
      */

package/assemblyManager/assemblyManager.js

@@ -22,12 +22,23 @@ function assemblyManagerFactory(conf, pm) {
          */
         assemblies: mobx_state_tree_1.types.array((0, assembly_1.default)(conf, pm)),
     })
+        .views(self => ({
+        get assemblyNameMap() {
+            const obj = {};
+            for (const assembly of self.assemblies) {
+                for (const name of assembly.allAliases) {
+                    obj[name] = assembly;
+                }
+            }
+            return obj;
+        },
+    }))
         .views(self => ({
         /**
          * #method
          */
         get(asmName) {
-            return self.assemblies.find(asm => asm.hasName(asmName));
+            return self.assemblyNameMap[asmName];
         },
         /**
          * #getter

package/assemblyManager/index.d.ts

@@ -1,2 +1,3 @@
 export { default } from './assemblyManager';
 export { default as assemblyConfigSchemaFactory } from './assemblyConfigSchema';
+export type { BaseAssemblyConfigSchema } from './assemblyConfigSchema';

package/configuration/index.d.ts

@@ -1,3 +1,3 @@
 export { ConfigurationSchema, ConfigurationReference, } from './configurationSchema';
-export type { AnyConfigurationSchemaType, AnyConfigurationModel, AnyConfigurationSlot, AnyConfigurationSlotType, } from './types';
+export type { AnyConfigurationSchemaType, AnyConfigurationModel, AnyConfigurationSlot, AnyConfigurationSlotType, AnyConfiguration, } from './types';
 export * from './util';

package/configuration/types.d.ts

@@ -1,4 +1,4 @@
-import type { IStateTreeNode, Instance } from 'mobx-state-tree';
+import type { IStateTreeNode, Instance, SnapshotOut } from 'mobx-state-tree';
 import type { ConfigurationSchemaType, ConfigurationSchemaOptions } from './configurationSchema';
 import type ConfigSlot from './configurationSlot';
 export type GetOptions<SCHEMA> = SCHEMA extends ConfigurationSchemaType<any, infer OPTIONS> ? OPTIONS : never;
@@ -10,4 +10,6 @@ export type AnyConfigurationSchemaType = ConfigurationSchemaType<any, any>;
 export type AnyConfigurationModel = Instance<AnyConfigurationSchemaType>;
 export type AnyConfigurationSlotType = ReturnType<typeof ConfigSlot>;
 export type AnyConfigurationSlot = Instance<AnyConfigurationSlotType>;
+/** any configuration model, or snapshot thereof */
+export type AnyConfiguration = AnyConfigurationModel | SnapshotOut<AnyConfigurationModel>;
 export type ConfigurationModel<SCHEMA extends AnyConfigurationSchemaType> = Instance<SCHEMA>;

package/data_adapters/BaseAdapter/BaseAdapter.js

@@ -33,5 +33,5 @@ class BaseAdapter {
         return (0, configuration_1.readConfObject)(this.config, arg);
     }
 }
-BaseAdapter.capabilities = [];
 exports.BaseAdapter = BaseAdapter;
+BaseAdapter.capabilities = [];

package/data_adapters/BaseAdapter/index.d.ts

@@ -11,5 +11,5 @@ export type { BaseTextSearchAdapter } from './BaseTextSearchAdapter';
 export type { BaseRefNameAliasAdapter } from './BaseRefNameAliasAdapter';
 export type { RegionsAdapter } from './RegionsAdapter';
 export interface AnyAdapter {
-    new (config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager | undefined): AnyDataAdapter;
+    new (config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager): AnyDataAdapter;
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.5.0",
+  "version": "2.6.0",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -74,5 +74,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
+  "gitHead": "9962c94711dd3386dcb76c16f3646937d9c4751a"
 }

package/pluggableElementTypes/RpcMethodType.d.ts

@@ -2,20 +2,22 @@ import PluginManager from '../PluginManager';
 import PluggableElementBase from './PluggableElementBase';
 import { UriLocation } from '../util/types';
 import { RemoteAbortSignal } from '../rpc/remoteAbortSignals';
+interface SerializedArgs {
+    signal?: RemoteAbortSignal;
+    blobMap?: Record<string, File>;
+}
 export type RpcMethodConstructor = new (pm: PluginManager) => RpcMethodType;
 export default abstract class RpcMethodType extends PluggableElementBase {
     pluginManager: PluginManager;
     constructor(pluginManager: PluginManager);
-    serializeArguments(args: {}, _rpcDriverClassName: string): Promise<{}>;
-    serializeNewAuthArguments(loc: UriLocation): Promise<UriLocation>;
-    deserializeArguments<T extends {
-        signal?: RemoteAbortSignal;
-        blobMap?: Record<string, File>;
-    }>(serializedArgs: T, _rpcDriverClassName: string): Promise<T & {
+    serializeArguments(args: {}, rpcDriverClassName: string): Promise<{}>;
+    serializeNewAuthArguments(loc: UriLocation, rpcDriverClassName: string): Promise<UriLocation>;
+    deserializeArguments<T extends SerializedArgs>(serializedArgs: T, _rpcDriverClassName: string): Promise<T & {
         signal: AbortSignal | undefined;
     }>;
     abstract execute(serializedArgs: unknown, rpcDriverClassName: string): Promise<unknown>;
     serializeReturn(originalReturn: unknown, _args: unknown, _rpcDriverClassName: string): Promise<unknown>;
-    deserializeReturn(serializedReturn: unknown, _args: unknown, _rpcDriver: string): Promise<unknown>;
+    deserializeReturn(serializedReturn: unknown, _args: unknown, _rpcDriverClassName: string): Promise<unknown>;
     private augmentLocationObjects;
 }
+export {};

package/pluggableElementTypes/RpcMethodType.js

@@ -13,19 +13,21 @@ class RpcMethodType extends PluggableElementBase_1.default {
         super({});
         this.pluginManager = pluginManager;
     }
-    async serializeArguments(args, _rpcDriverClassName) {
+    async serializeArguments(args, rpcDriverClassName) {
         const blobMap = (0, tracks_1.getBlobMap)();
-        await this.augmentLocationObjects(args);
+        await this.augmentLocationObjects(args, rpcDriverClassName);
         return { ...args, blobMap };
     }
-    async serializeNewAuthArguments(loc) {
+    async serializeNewAuthArguments(loc, rpcDriverClassName) {
         const rootModel = this.pluginManager.rootModel;
         // args dont need auth or already have auth
         if (!(0, types_1.isAppRootModel)(rootModel) || loc.internetAccountPreAuthorization) {
             return loc;
         }
         const account = rootModel.findAppropriateInternetAccount(loc);
-        if (account) {
+        // mutating loc object is not allowed in MainThreadRpcDriver, and is only
+        // needed for web worker RPC
+        if (account && rpcDriverClassName !== 'MainThreadRpcDriver') {
             loc.internetAccountPreAuthorization =
                 await account.getPreAuthorizationInformation(loc);
         }
@@ -46,7 +48,7 @@ class RpcMethodType extends PluggableElementBase_1.default {
     async serializeReturn(originalReturn, _args, _rpcDriverClassName) {
         return originalReturn;
     }
-    async deserializeReturn(serializedReturn, _args, _rpcDriver) {
+    async deserializeReturn(serializedReturn, _args, _rpcDriverClassName) {
         var _a;
         let r;
         try {
@@ -63,7 +65,7 @@ class RpcMethodType extends PluggableElementBase_1.default {
         }
         return r;
     }
-    async augmentLocationObjects(thing) {
+    async augmentLocationObjects(thing, rpcDriverClassName) {
         const uris = [];
         // using map-obj avoids cycles, seen in circular view svg export
         (0, map_obj_1.default)(thing, val => {
@@ -72,7 +74,7 @@ class RpcMethodType extends PluggableElementBase_1.default {
             }
         });
         for (const uri of uris) {
-            await this.serializeNewAuthArguments(uri);
+            await this.serializeNewAuthArguments(uri, rpcDriverClassName);
         }
         return thing;
     }

package/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts

@@ -12,6 +12,23 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
      * #property
      */
     tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    /**
+     * #property
+     */
+    configuration: import("../../configuration/configurationSchema").ConfigurationSchemaType<{
+        name: {
+            type: string;
+            defaultValue: string;
+            description: string;
+        }; /**
+         * #property
+         */
+        assemblyNames: {
+            type: string;
+            defaultValue: never[];
+            description: string;
+        };
+    }, import("../../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
 }, {
     afterAttach(): void;
     /**
@@ -31,4 +48,5 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
      */
     clear(): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export type BaseConnectionModel = ReturnType<typeof stateModelFactory>;
 export default stateModelFactory;