@apollo-annotation/jbrowse-plugin-apollo 0.3.13 → 1.0.0

package/dist/makeDisplayComponent.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"makeDisplayComponent.d.ts","sourceRoot":"","sources":["../src/makeDisplayComponent.tsx"],"names":[],"mappings":"AAWA,OAAO,KAAK,EAAE,mBAAmB,IAAI,oBAAoB,EAAE,MAAM,kCAAkC,CAAA;AAEnG,OAAO,KAAK,EAAE,2BAA2B,IAAI,4BAA4B,EAAE,MAAM,0CAA0C,CAAA;AA6I3H,eAAO,MAAM,4BAA4B,wBAGtC;IACD,KAAK,EAAE,oBAAoB,CAAA;CAC5B,4CAoFC,CAAA;AAEF,eAAO,MAAM,oCAAoC,wBAI5C;IACD,KAAK,EAAE,4BAA4B,CAAA;CACpC,4CAsFF,CAAA"}
+{"version":3,"file":"makeDisplayComponent.d.ts","sourceRoot":"","sources":["../src/makeDisplayComponent.tsx"],"names":[],"mappings":"AAWA,OAAO,KAAK,EAAE,mBAAmB,IAAI,oBAAoB,EAAE,MAAM,kCAAkC,CAAA;AAEnG,OAAO,KAAK,EAAE,2BAA2B,IAAI,4BAA4B,EAAE,MAAM,0CAA0C,CAAA;AAoJ3H,eAAO,MAAM,4BAA4B,wBAGtC;IACD,KAAK,EAAE,oBAAoB,CAAA;CAC5B,4CAoFC,CAAA;AAEF,eAAO,MAAM,oCAAoC,wBAI5C;IACD,KAAK,EAAE,4BAA4B,CAAA;CACpC,4CAsFF,CAAA"}

package/dist/menus/Icons.d.ts

@@ -0,0 +1,3 @@
+import { type SvgIconProps } from '@mui/material';
+export declare function Apollo(props: SvgIconProps): import("react/jsx-runtime").JSX.Element;
+//# sourceMappingURL=Icons.d.ts.map

package/dist/menus/Icons.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"Icons.d.ts","sourceRoot":"","sources":["../../src/menus/Icons.tsx"],"names":[],"mappings":"AAAA,OAAO,EAAW,KAAK,YAAY,EAAE,MAAM,eAAe,CAAA;AAI1D,wBAAgB,MAAM,CAAC,KAAK,EAAE,YAAY,2CA4CzC"}

package/dist/menus/topLevelMenu.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"topLevelMenu.d.ts","sourceRoot":"","sources":["../../src/menus/topLevelMenu.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EACV,mBAAmB,EAEpB,MAAM,oBAAoB,CAAA;AAkB3B,wBAAgB,gBAAgB,CAAC,SAAS,EAAE,mBAAmB,QAsH9D"}
+{"version":3,"file":"topLevelMenu.d.ts","sourceRoot":"","sources":["../../src/menus/topLevelMenu.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EACV,mBAAmB,EAEpB,MAAM,oBAAoB,CAAA;AAS3B,wBAAgB,gBAAgB,CAAC,SAAS,EAAE,mBAAmB,QAuD9D"}

package/dist/session/changeHandlers.d.ts

@@ -0,0 +1,9 @@
+import { type localChanges } from '@apollo-annotation/shared';
+import type { ClientDataStoreModel } from './ClientDataStore';
+type ChangeHandlers = {
+    [K in keyof typeof localChanges]: (dataStore: ClientDataStoreModel, change: InstanceType<(typeof localChanges)[K]>) => Promise<void>;
+};
+export declare function isLocalChange(changeName: string): changeName is keyof typeof localChanges;
+export declare const changeHandlers: ChangeHandlers;
+export {};
+//# sourceMappingURL=changeHandlers.d.ts.map

package/dist/session/changeHandlers.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"changeHandlers.d.ts","sourceRoot":"","sources":["../../src/session/changeHandlers.ts"],"names":[],"mappings":"AACA,OAAO,EAEL,KAAK,YAAY,EAElB,MAAM,2BAA2B,CAAA;AAElC,OAAO,KAAK,EAAE,oBAAoB,EAAE,MAAM,mBAAmB,CAAA;AAE7D,KAAK,cAAc,GAAG;KACnB,CAAC,IAAI,MAAM,OAAO,YAAY,GAAG,CAChC,SAAS,EAAE,oBAAoB,EAC/B,MAAM,EAAE,YAAY,CAAC,CAAC,OAAO,YAAY,CAAC,CAAC,CAAC,CAAC,CAAC,KAC3C,OAAO,CAAC,IAAI,CAAC;CACnB,CAAA;AAED,wBAAgB,aAAa,CAC3B,UAAU,EAAE,MAAM,GACjB,UAAU,IAAI,MAAM,OAAO,YAAY,CAEzC;AAED,eAAO,MAAM,cAAc,EAAE,cA8O5B,CAAA"}

package/dist/util/annotationFeatureUtils.d.ts

@@ -1,7 +1,8 @@
-import type { AnnotationFeature } from '@apollo-annotation/mst';
+import type { AnnotationFeature, AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
 export declare function getFeatureName(feature: AnnotationFeature): string;
 export declare function getFeatureId(feature: AnnotationFeature): string;
 export declare function getFeatureNameOrId(feature: AnnotationFeature): string;
 export declare function getStrand(strand: number | undefined): "" | "Forward" | "Reverse";
 export declare function getRelatedFeatures(feature: AnnotationFeature, bp: number, includeSiblings?: boolean): AnnotationFeature[];
+export declare function removeSkippedAttributes(feature: AnnotationFeatureSnapshot, skippedAttributes: Set<string>): void;
 //# sourceMappingURL=annotationFeatureUtils.d.ts.map

package/dist/util/annotationFeatureUtils.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"annotationFeatureUtils.d.ts","sourceRoot":"","sources":["../../src/util/annotationFeatureUtils.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,wBAAwB,CAAA;AAE/D,wBAAgB,cAAc,CAAC,OAAO,EAAE,iBAAiB,UAOxD;AAED,wBAAgB,YAAY,CAAC,OAAO,EAAE,iBAAiB,UAmBtD;AAED,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,iBAAiB,UAU5D;AAED,wBAAgB,SAAS,CAAC,MAAM,EAAE,MAAM,GAAG,SAAS,8BAQnD;AAuBD,wBAAgB,kBAAkB,CAChC,OAAO,EAAE,iBAAiB,EAC1B,EAAE,EAAE,MAAM,EACV,eAAe,UAAQ,GACtB,iBAAiB,EAAE,CAgCrB"}
+{"version":3,"file":"annotationFeatureUtils.d.ts","sourceRoot":"","sources":["../../src/util/annotationFeatureUtils.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EACV,iBAAiB,EACjB,yBAAyB,EAC1B,MAAM,wBAAwB,CAAA;AAE/B,wBAAgB,cAAc,CAAC,OAAO,EAAE,iBAAiB,UAOxD;AAED,wBAAgB,YAAY,CAAC,OAAO,EAAE,iBAAiB,UAmBtD;AAED,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,iBAAiB,UAU5D;AAED,wBAAgB,SAAS,CAAC,MAAM,EAAE,MAAM,GAAG,SAAS,8BAQnD;AAuBD,wBAAgB,kBAAkB,CAChC,OAAO,EAAE,iBAAiB,EAC1B,EAAE,EAAE,MAAM,EACV,eAAe,UAAQ,GACtB,iBAAiB,EAAE,CAgCrB;AAED,wBAAgB,uBAAuB,CACrC,OAAO,EAAE,yBAAyB,EAClC,iBAAiB,EAAE,GAAG,CAAC,MAAM,CAAC,QAqB/B"}

package/dist/util/glyphUtils.d.ts

@@ -4,17 +4,18 @@ import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 import type { LinearApolloDisplayMouseEvents } from '../LinearApolloDisplay/stateModel/mouseEvents';
 import type { LinearApolloSixFrameDisplayMouseEvents } from '../LinearApolloSixFrameDisplay/stateModel/mouseEvents';
 import type { ApolloSessionModel } from '../session';
-import type { MousePositionWithFeature } from '.';
 type NavLocation = Parameters<LinearGenomeViewModel['navTo']>[0];
 export declare function selectFeatureAndOpenWidget(stateModel: LinearApolloDisplayMouseEvents | LinearApolloSixFrameDisplayMouseEvents, feature: AnnotationFeature): void;
+export declare function isGeneFeature(feature: AnnotationFeature, session: ApolloSessionModel): boolean;
 export declare function isTranscriptFeature(feature: AnnotationFeature, session: ApolloSessionModel): boolean;
 export declare function isExonFeature(feature: AnnotationFeature, session: ApolloSessionModel): boolean;
 export declare function isCDSFeature(feature: AnnotationFeature, session: ApolloSessionModel): boolean;
+export declare function looksLikeGene(feature: AnnotationFeature, session: ApolloSessionModel): boolean;
 export interface AdjacentExons {
     upstream: AnnotationFeature | undefined;
     downstream: AnnotationFeature | undefined;
 }
-export declare function getAdjacentExons(currentExon: AnnotationFeature, display: LinearApolloDisplayMouseEvents | LinearApolloSixFrameDisplayMouseEvents, mousePosition: MousePositionWithFeature, session: ApolloSessionModel): AdjacentExons;
+export declare function getAdjacentExons(currentExon: AnnotationFeature, display: LinearApolloDisplayMouseEvents | LinearApolloSixFrameDisplayMouseEvents): AdjacentExons;
 export declare function getStreamIcon(strand: 1 | -1 | undefined, isUpstream: boolean, isFlipped: boolean | undefined): import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
     muiName: string;
 };
@@ -24,7 +25,6 @@ export declare function getOverlappingEdge(feature: AnnotationFeature, x: number
     edge: 'min' | 'max';
 } | undefined;
 export declare function isSelectedFeature(feature: AnnotationFeature, selectedFeature: AnnotationFeature | undefined): boolean;
-export declare function containsSelectedFeature(feature: AnnotationFeature, selectedFeature: AnnotationFeature | undefined): boolean;
 export declare function getContextMenuItemsForFeature(display: LinearApolloSixFrameDisplayMouseEvents | LinearApolloDisplayMouseEvents, sourceFeature: AnnotationFeature): MenuItem[];
 export declare function navToFeatureCenter(feature: AnnotationFeature, paddingPct: number, refSeqLength: number): NavLocation;
 export {};

package/dist/util/glyphUtils.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"glyphUtils.d.ts","sourceRoot":"","sources":["../../src/util/glyphUtils.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EACV,iBAAiB,EACjB,oBAAoB,EACrB,MAAM,wBAAwB,CAAA;AAE/B,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAA;AAMhD,OAAO,KAAK,EAAE,qBAAqB,EAAE,MAAM,oCAAoC,CAAA;AAI/E,OAAO,KAAK,EAAE,8BAA8B,EAAE,MAAM,+CAA+C,CAAA;AACnG,OAAO,KAAK,EAAE,sCAAsC,EAAE,MAAM,uDAAuD,CAAA;AAEnH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAA;AAEpD,OAAO,KAAK,EAAE,wBAAwB,EAAE,MAAM,GAAG,CAAA;AAEjD,KAAK,WAAW,GAAG,UAAU,CAAC,qBAAqB,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AAEhE,wBAAgB,0BAA0B,CACxC,UAAU,EACN,8BAA8B,GAC9B,sCAAsC,EAC1C,OAAO,EAAE,iBAAiB,QAmC3B;AAED,wBAAgB,mBAAmB,CACjC,OAAO,EAAE,iBAAiB,EAC1B,OAAO,EAAE,kBAAkB,GAC1B,OAAO,CAST;AAED,wBAAgB,aAAa,CAC3B,OAAO,EAAE,iBAAiB,EAC1B,OAAO,EAAE,kBAAkB,GAC1B,OAAO,CAMT;AAED,wBAAgB,YAAY,CAC1B,OAAO,EAAE,iBAAiB,EAC1B,OAAO,EAAE,kBAAkB,GAC1B,OAAO,CAMT;AAED,MAAM,WAAW,aAAa;IAC5B,QAAQ,EAAE,iBAAiB,GAAG,SAAS,CAAA;IACvC,UAAU,EAAE,iBAAiB,GAAG,SAAS,CAAA;CAC1C;AAED,wBAAgB,gBAAgB,CAC9B,WAAW,EAAE,iBAAiB,EAC9B,OAAO,EACH,8BAA8B,GAC9B,sCAAsC,EAC1C,aAAa,EAAE,wBAAwB,EACvC,OAAO,EAAE,kBAAkB,GAC1B,aAAa,CAkDf;AAED,wBAAgB,aAAa,CAC3B,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,GAAG,SAAS,EAC1B,UAAU,EAAE,OAAO,EACnB,SAAS,EAAE,OAAO,GAAG,SAAS;;EAsB/B;AAED,wBAAgB,cAAc,CAC5B,OAAO,EAAE,iBAAiB,GAAG,oBAAoB,EACjD,OAAO,EAAE,MAAM,EACf,YAAY,EAAE,MAAM,EACpB,GAAG,EAAE,qBAAqB,GACzB,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,SAAS,CAkB9B;AAED,wBAAgB,kBAAkB,CAChC,OAAO,EAAE,iBAAiB,EAC1B,CAAC,EAAE,MAAM,EACT,MAAM,EAAE,CAAC,MAAM,EAAE,MAAM,CAAC,GACvB;IAAE,OAAO,EAAE,iBAAiB,CAAC;IAAC,IAAI,EAAE,KAAK,GAAG,KAAK,CAAA;CAAE,GAAG,SAAS,CAajE;AAED,wBAAgB,iBAAiB,CAC/B,OAAO,EAAE,iBAAiB,EAC1B,eAAe,EAAE,iBAAiB,GAAG,SAAS,WAG/C;AAED,wBAAgB,uBAAuB,CACrC,OAAO,EAAE,iBAAiB,EAC1B,eAAe,EAAE,iBAAiB,GAAG,SAAS,GAC7C,OAAO,CAQT;AAqBD,wBAAgB,6BAA6B,CAC3C,OAAO,EACH,sCAAsC,GACtC,8BAA8B,EAClC,aAAa,EAAE,iBAAiB,GAC/B,QAAQ,EAAE,CAwGZ;AAED,wBAAgB,kBAAkB,CAChC,OAAO,EAAE,iBAAiB,EAC1B,UAAU,EAAE,MAAM,EAClB,YAAY,EAAE,MAAM,GACnB,WAAW,CAKb"}
+{"version":3,"file":"glyphUtils.d.ts","sourceRoot":"","sources":["../../src/util/glyphUtils.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EACV,iBAAiB,EAEjB,oBAAoB,EACrB,MAAM,wBAAwB,CAAA;AAC/B,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAA;AAKhD,OAAO,KAAK,EAAE,qBAAqB,EAAE,MAAM,oCAAoC,CAAA;AAI/E,OAAO,KAAK,EAAE,8BAA8B,EAAE,MAAM,+CAA+C,CAAA;AACnG,OAAO,KAAK,EAAE,sCAAsC,EAAE,MAAM,uDAAuD,CAAA;AAKnH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAA;AAEpD,KAAK,WAAW,GAAG,UAAU,CAAC,qBAAqB,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AAEhE,wBAAgB,0BAA0B,CACxC,UAAU,EACN,8BAA8B,GAC9B,sCAAsC,EAC1C,OAAO,EAAE,iBAAiB,QAmC3B;AAED,wBAAgB,aAAa,CAC3B,OAAO,EAAE,iBAAiB,EAC1B,OAAO,EAAE,kBAAkB,GAC1B,OAAO,CAST;AAED,wBAAgB,mBAAmB,CACjC,OAAO,EAAE,iBAAiB,EAC1B,OAAO,EAAE,kBAAkB,GAC1B,OAAO,CAST;AAED,wBAAgB,aAAa,CAC3B,OAAO,EAAE,iBAAiB,EAC1B,OAAO,EAAE,kBAAkB,GAC1B,OAAO,CAMT;AAED,wBAAgB,YAAY,CAC1B,OAAO,EAAE,iBAAiB,EAC1B,OAAO,EAAE,kBAAkB,GAC1B,OAAO,CAMT;AAED,wBAAgB,aAAa,CAC3B,OAAO,EAAE,iBAAiB,EAC1B,OAAO,EAAE,kBAAkB,WA0B5B;AAED,MAAM,WAAW,aAAa;IAC5B,QAAQ,EAAE,iBAAiB,GAAG,SAAS,CAAA;IACvC,UAAU,EAAE,iBAAiB,GAAG,SAAS,CAAA;CAC1C;AAED,wBAAgB,gBAAgB,CAC9B,WAAW,EAAE,iBAAiB,EAC9B,OAAO,EACH,8BAA8B,GAC9B,sCAAsC,GACzC,aAAa,CA6Cf;AAED,wBAAgB,aAAa,CAC3B,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,GAAG,SAAS,EAC1B,UAAU,EAAE,OAAO,EACnB,SAAS,EAAE,OAAO,GAAG,SAAS;;EAsB/B;AAED,wBAAgB,cAAc,CAC5B,OAAO,EAAE,iBAAiB,GAAG,oBAAoB,EACjD,OAAO,EAAE,MAAM,EACf,YAAY,EAAE,MAAM,EACpB,GAAG,EAAE,qBAAqB,GACzB,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,SAAS,CAkB9B;AAED,wBAAgB,kBAAkB,CAChC,OAAO,EAAE,iBAAiB,EAC1B,CAAC,EAAE,MAAM,EACT,MAAM,EAAE,CAAC,MAAM,EAAE,MAAM,CAAC,GACvB;IAAE,OAAO,EAAE,iBAAiB,CAAC;IAAC,IAAI,EAAE,KAAK,GAAG,KAAK,CAAA;CAAE,GAAG,SAAS,CAajE;AAED,wBAAgB,iBAAiB,CAC/B,OAAO,EAAE,iBAAiB,EAC1B,eAAe,EAAE,iBAAiB,GAAG,SAAS,WAG/C;AAqBD,wBAAgB,6BAA6B,CAC3C,OAAO,EACH,sCAAsC,GACtC,8BAA8B,EAClC,aAAa,EAAE,iBAAiB,GAC/B,QAAQ,EAAE,CA2HZ;AAED,wBAAgB,kBAAkB,CAChC,OAAO,EAAE,iBAAiB,EAC1B,UAAU,EAAE,MAAM,EAClB,YAAY,EAAE,MAAM,GACnB,WAAW,CAKb"}

package/dist/util/index.d.ts

@@ -3,7 +3,6 @@ import type { ApolloSessionModel } from '../session';
 export declare function createFetchErrorMessage(response: Response, additionalText?: string): Promise<string>;
 /** given a session, get our ApolloInternetAccount */
 export declare function getApolloInternetAccount(session: ApolloSessionModel): ApolloInternetAccountModel | undefined;
-export * from './loadAssemblyIntoClient';
 export * from './annotationFeatureUtils';
 export * from './glyphUtils';
 export * from './mouseEventsUtils';

package/dist/util/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/util/index.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,0BAA0B,EAAE,MAAM,gCAAgC,CAAA;AAChF,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAA;AAGpD,wBAAsB,uBAAuB,CAC3C,QAAQ,EAAE,QAAQ,EAClB,cAAc,CAAC,EAAE,MAAM,GACtB,OAAO,CAAC,MAAM,CAAC,CAWjB;AAED,qDAAqD;AACrD,wBAAgB,wBAAwB,CAAC,OAAO,EAAE,kBAAkB,GAG9D,0BAA0B,GAC1B,SAAS,CACd;AAED,cAAc,0BAA0B,CAAA;AACxC,cAAc,0BAA0B,CAAA;AACxC,cAAc,cAAc,CAAA;AAC5B,cAAc,oBAAoB,CAAA"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/util/index.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,0BAA0B,EAAE,MAAM,gCAAgC,CAAA;AAChF,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAA;AAGpD,wBAAsB,uBAAuB,CAC3C,QAAQ,EAAE,QAAQ,EAClB,cAAc,CAAC,EAAE,MAAM,GACtB,OAAO,CAAC,MAAM,CAAC,CAWjB;AAED,qDAAqD;AACrD,wBAAgB,wBAAwB,CAAC,OAAO,EAAE,kBAAkB,GAG9D,0BAA0B,GAC1B,SAAS,CACd;AAED,cAAc,0BAA0B,CAAA;AACxC,cAAc,cAAc,CAAA;AAC5B,cAAc,oBAAoB,CAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/jbrowse-plugin-apollo",
-  "version": "0.3.13",
+  "version": "1.0.0",
   "description": "Apollo plugin for JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -46,9 +46,9 @@
     }
   },
   "dependencies": {
-    "@apollo-annotation/common": "^0.3.13",
-    "@apollo-annotation/mst": "^0.3.13",
-    "@apollo-annotation/shared": "^0.3.13",
+    "@apollo-annotation/common": "^1.0.0",
+    "@apollo-annotation/mst": "^1.0.0",
+    "@apollo-annotation/shared": "^1.0.0",
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
     "@gmod/gff": "^2.1.0",

package/src/ApolloInternetAccount/model.ts

@@ -19,6 +19,7 @@ import { ConfigurationReference, getConf } from '@jbrowse/core/configuration'
 import { InternetAccount } from '@jbrowse/core/pluggableElementTypes'
 import {
   type AbstractSessionModel,
+  type UriLocation,
   isAbstractMenuManager,
   isElectron,
 } from '@jbrowse/core/util'
@@ -68,8 +69,8 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
     .volatile(() => ({
       role: undefined as Role | undefined,
       controller: new AbortController(),
+      tokenPromise: undefined as Promise<string> | undefined,
     }))
-
     .actions((self) => ({
       setRole() {
         const token = self.retrieveToken()
@@ -78,12 +79,75 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
           return
         }
         const dec = getDecodedToken(token)
-        const { role } = dec
+        const { role, exp } = dec
+        if (exp < Date.now() / 1000) {
+          self.role = undefined
+          self.removeToken()
+          return
+        }
         if (self.role !== role) {
           self.role = role
         }
       },
     }))
+    .actions((self) => {
+      const superGetFetcher = self.getFetcher
+      return {
+        getFetcher(loc?: UriLocation) {
+          const fetcher = superGetFetcher(loc)
+          return async (input: RequestInfo, init?: RequestInit) => {
+            const response = await fetcher(input, init)
+            if (response.status === 403) {
+              self.removeToken()
+              self.setRole()
+              return fetcher(input, init)
+            }
+            return response
+          }
+        },
+      }
+    })
+    .actions((self) => ({
+      removeToken() {
+        sessionStorage.removeItem(self.tokenKey)
+        self.tokenPromise = undefined
+      },
+    }))
+    .actions((self) => ({
+      async getToken(location?: UriLocation): Promise<string> {
+        if (self.tokenPromise) {
+          return self.tokenPromise
+        }
+        let token = location?.internetAccountPreAuthorization?.authInfo?.token
+        if (token) {
+          self.tokenPromise = Promise.resolve(token)
+          return self.tokenPromise
+        }
+        if (inWebWorker) {
+          throw new Error(
+            'Did not get internet account pre-authorization info in worker',
+          )
+        }
+        token = self.retrieveToken()
+        if (token) {
+          self.tokenPromise = Promise.resolve(token)
+          return self.tokenPromise
+        }
+        self.tokenPromise = new Promise((resolve, reject) => {
+          self.getTokenFromUser(
+            (token) => {
+              self.storeToken(token)
+              resolve(token)
+            },
+            (error) => {
+              self.removeToken()
+              reject(error)
+            },
+          )
+        })
+        return self.tokenPromise
+      },
+    }))
     .actions((self) => {
       let listener: (event: MessageEvent) => void
       return {
@@ -253,7 +317,7 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
             )
             throw new Error(errorMessage)
           }
-          const changes = yield response.json()
+          const { changes } = yield response.json()
           const sequence = changes.length > 0 ? changes[0].sequence : 0
           self.setLastChangeSequenceNumber(sequence)
         },
@@ -298,7 +362,7 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
           )
           return
         }
-        const serializedChanges = yield response.json()
+        const { changes: serializedChanges } = yield response.json()
         for (const serializedChange of serializedChanges) {
           const change = Change.fromJSON(serializedChange)
           void changeManager.submit(change, { submitToBackend: false })

package/src/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.ts

@@ -38,9 +38,12 @@ export default class RefNameAliasAdapter
   extends BaseAdapter
   implements BaseRefNameAliasAdapter
 {
-  private refNameAliases: RefNameAliases[] | undefined
+  private refNameAliasesP: Promise<RefNameAliases[]> | undefined
 
   async getRefNameAliases() {
+    if (this.refNameAliasesP) {
+      return this.refNameAliasesP
+    }
     const assemblyId = readConfObject(this.config, 'assemblyId') as string
     if (!isInWebWorker) {
       const dataStore = (
@@ -56,7 +59,7 @@ export default class RefNameAliasAdapter
       const refNameAliases = await backendDriver.getRefNameAliases(assemblyId)
       return refNameAliases
     }
-    const refNameAliases = await new Promise(
+    const refNameAliases = new Promise(
       (
         resolve: (refNameAliases: RefNameAliases[]) => void,
         reject: (reason: Error) => void,
@@ -86,7 +89,7 @@ export default class RefNameAliasAdapter
         })
       },
     )
-    this.refNameAliases = refNameAliases
+    this.refNameAliasesP = refNameAliases
     return refNameAliases
   }
 

package/src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts

@@ -16,7 +16,7 @@ function getMatchedFeature(
   feature: AnnotationFeatureSnapshot,
 ): AnnotationFeatureSnapshot | undefined {
   // @ts-expect-error this actually has a bit more info that a plain snapshot
-  const { children, indexedIds, ...featureWithoutChildren } = feature
+  const { children, indexedIds, allIds, ...featureWithoutChildren } = feature
   const featureString = JSON.stringify(featureWithoutChildren)
   if (featureString.includes(query)) {
     return feature

package/src/BackendDrivers/BackendDriver.ts

@@ -1,4 +1,4 @@
-import type { Change, ClientDataStore } from '@apollo-annotation/common'
+import type { Change, SerializedChange } from '@apollo-annotation/common'
 import type {
   AnnotationFeatureSnapshot,
   CheckResultSnapshot,
@@ -8,15 +8,41 @@ import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import type { Region } from '@jbrowse/core/util'
 
 import type { SubmitOpts } from '../ChangeManager'
+import type { ClientDataStoreModel } from '../session/ClientDataStore'
 
 export interface RefNameAliases {
   refName: string
   aliases: string[]
-  uniqueId: string
+  uniqueId?: string
+}
+
+export interface ChangeDocument extends SerializedChange {
+  sequence: IDBValidKey
+  user?: string
+  createdAt: string
+  changes?: SerializedChange[]
+}
+
+export interface GetChangesOpts {
+  page?: number
+  pageSize?: number
+  sortField?: string
+  sortOrder?: 'asc' | 'desc'
+  filters?: {
+    user?: string
+    typeName?: string
+    startTime?: string
+    endTime?: string
+  }
+}
+
+export interface GetChangesResult {
+  changes: ChangeDocument[]
+  totalCount: number
 }
 
 export abstract class BackendDriver {
-  constructor(protected clientStore: ClientDataStore) {}
+  constructor(protected clientStore: ClientDataStoreModel) {}
 
   abstract getFeatures(
     region: Region,
@@ -39,4 +65,11 @@ export abstract class BackendDriver {
     term: string,
     assemblies: string[],
   ): Promise<AnnotationFeatureSnapshot[]>
+
+  abstract getChanges(
+    assemblyName: string,
+    opts?: GetChangesOpts,
+  ): Promise<GetChangesResult>
+
+  abstract getCheckResults(assemblyName: string): Promise<CheckResultSnapshot[]>
 }

package/src/BackendDrivers/CollaborationServerDriver.ts

@@ -28,7 +28,12 @@ import type { Socket } from 'socket.io-client'
 import { ChangeManager, type SubmitOpts } from '../ChangeManager'
 import { createFetchErrorMessage } from '../util'
 
-import { BackendDriver, type RefNameAliases } from './BackendDriver'
+import {
+  BackendDriver,
+  type GetChangesOpts,
+  type GetChangesResult,
+  type RefNameAliases,
+} from './BackendDriver'
 
 export interface ApolloRefSeqResponse {
   _id: string
@@ -72,9 +77,7 @@ export class CollaborationServerDriver extends BackendDriver {
   }
 
   async searchFeatures(term: string, assemblies: string[]) {
-    const internetAccount = this.clientStore.getInternetAccount(
-      assemblies[0],
-    ) as ApolloInternetAccount
+    const internetAccount = this.clientStore.getInternetAccount(assemblies[0])
     const { baseURL } = internetAccount
 
     const url = new URL('features/searchFeatures', baseURL)
@@ -114,9 +117,7 @@ export class CollaborationServerDriver extends BackendDriver {
       throw new Error(`Could not find refSeq "${refName}"`)
     }
     const refSeq = refSeqEntry.id
-    const internetAccount = this.clientStore.getInternetAccount(
-      assemblyName,
-    ) as ApolloInternetAccount
+    const internetAccount = this.clientStore.getInternetAccount(assemblyName)
     const { baseURL } = internetAccount
 
     const url = new URL('features/getFeatures', baseURL)
@@ -154,16 +155,16 @@ export class CollaborationServerDriver extends BackendDriver {
     internetAccount: ApolloInternetAccount,
   ) {
     const { socket } = internetAccount
-    const token = internetAccount.retrieveToken()
-    if (!token) {
-      return
-    }
-    const localSessionId = makeUserSessionId(token)
     const channel = `${assembly}-${refSeq}`
-    const changeManager = new ChangeManager(this.clientStore)
 
     if (!socket.hasListeners(channel)) {
       socket.on(channel, async (message: ChangeMessage) => {
+        const token = internetAccount.retrieveToken()
+        if (!token) {
+          return
+        }
+        const localSessionId = makeUserSessionId(token)
+        const changeManager = new ChangeManager(this.clientStore)
         // Save server last change sequence into session storage
         internetAccount.setLastChangeSequenceNumber(
           Number(message.changeSequence),
@@ -229,9 +230,7 @@ export class CollaborationServerDriver extends BackendDriver {
     if (clientStoreSequence.length === end - start) {
       return { seq: clientStoreSequence, refSeq }
     }
-    const internetAccount = this.clientStore.getInternetAccount(
-      assemblyName,
-    ) as ApolloInternetAccount
+    const internetAccount = this.clientStore.getInternetAccount(assemblyName)
     const { baseURL } = internetAccount
 
     const url = new URL('sequence', baseURL)
@@ -293,9 +292,7 @@ export class CollaborationServerDriver extends BackendDriver {
     if (!assembly) {
       throw new Error(`Could not find assembly with name "${assemblyName}"`)
     }
-    const internetAccount = this.clientStore.getInternetAccount(
-      assemblyName,
-    ) as ApolloInternetAccount
+    const internetAccount = this.clientStore.getInternetAccount(assemblyName)
     const { baseURL } = internetAccount
     const url = new URL('refSeqs', baseURL)
     const searchParams = new URLSearchParams({ assembly: assemblyName })
@@ -351,9 +348,7 @@ export class CollaborationServerDriver extends BackendDriver {
     if (!assembly) {
       throw new Error(`Could not find assembly with name "${assemblyName}"`)
     }
-    const internetAccount = this.clientStore.getInternetAccount(
-      assemblyName,
-    ) as ApolloInternetAccount
+    const internetAccount = this.clientStore.getInternetAccount(assemblyName)
     const { baseURL } = internetAccount
     const url = new URL('refSeqs', baseURL)
     const searchParams = new URLSearchParams({ assembly: assemblyName })
@@ -402,6 +397,66 @@ export class CollaborationServerDriver extends BackendDriver {
     })
   }
 
+  async getChanges(
+    assemblyName: string,
+    opts: GetChangesOpts = {},
+  ): Promise<GetChangesResult> {
+    const internetAccount = this.clientStore.getInternetAccount(assemblyName)
+    const { baseURL } = internetAccount
+    const url = new URL('changes', baseURL)
+    const params: Record<string, string> = { assembly: assemblyName }
+    if (opts.page !== undefined) {
+      params.page = String(opts.page)
+    }
+    if (opts.pageSize !== undefined) {
+      params.pageSize = String(opts.pageSize)
+    }
+    if (opts.sortField) {
+      params.sortField = opts.sortField
+    }
+    if (opts.sortOrder) {
+      params.sortOrder = opts.sortOrder
+    }
+    if (opts.filters?.user) {
+      params.user = opts.filters.user
+    }
+    if (opts.filters?.typeName) {
+      params.typeName = opts.filters.typeName
+    }
+    if (opts.filters?.startTime) {
+      params.startTime = opts.filters.startTime
+    }
+    if (opts.filters?.endTime) {
+      params.endTime = opts.filters.endTime
+    }
+    url.search = new URLSearchParams(params).toString()
+    const response = await this.fetch(internetAccount, url.toString())
+    if (!response.ok) {
+      const errorMessage = await createFetchErrorMessage(
+        response,
+        'getChanges failed',
+      )
+      throw new Error(errorMessage)
+    }
+    return response.json() as Promise<GetChangesResult>
+  }
+
+  async getCheckResults(assemblyName: string): Promise<CheckResultSnapshot[]> {
+    const internetAccount = this.clientStore.getInternetAccount(assemblyName)
+    const { baseURL } = internetAccount
+    const url = new URL('checks', baseURL)
+    url.search = new URLSearchParams({ assembly: assemblyName }).toString()
+    const response = await this.fetch(internetAccount, url.toString())
+    if (!response.ok) {
+      const errorMessage = await createFetchErrorMessage(
+        response,
+        'getCheckResults failed',
+      )
+      throw new Error(errorMessage)
+    }
+    return response.json() as Promise<CheckResultSnapshot[]>
+  }
+
   async submitChange(
     change: Change | AssemblySpecificChange,
     opts: SubmitOpts = {},
@@ -410,7 +465,7 @@ export class CollaborationServerDriver extends BackendDriver {
     const internetAccount = this.clientStore.getInternetAccount(
       'assembly' in change ? change.assembly : undefined,
       internetAccountId,
-    ) as ApolloInternetAccount
+    )
     const { baseURL } = internetAccount
     const url = new URL('changes', baseURL).href
     const response = await this.fetch(internetAccount, url, {