@jbrowse/core 2.1.7 → 2.2.1

package/BaseFeatureWidget/BaseFeatureDetail.d.ts

@@ -10,8 +10,8 @@ export declare const useStyles: (params: void, styleOverrides?: {
 } | undefined) => {
     classes: Record<"expansionPanelDetails" | "expandIcon" | "field" | "fieldDescription" | "fieldName" | "fieldValue" | "fieldSubvalue", string>;
     theme: import("@mui/material").Theme;
-    css: import("tss-react/types").Css;
-    cx: import("tss-react/types").Cx;
+    css: import("tss-react").Css;
+    cx: import("tss-react").Cx;
 };
 export declare function BaseCard({ children, title, defaultExpanded, }: BaseCardProps): JSX.Element;
 export declare const FieldName: ({ description, name, width, prefix, }: {
@@ -34,6 +34,7 @@ export declare const BaseCoreDetails: (props: BaseProps) => JSX.Element;
 interface AttributeProps {
     attributes: Record<string, any>;
     omit?: string[];
+    omitSingleLevel?: string[];
     formatter?: (val: unknown, key: string) => React.ReactNode;
     descriptions?: Record<string, React.ReactNode>;
     prefix?: string[];

package/BaseFeatureWidget/BaseFeatureDetail.js

@@ -156,35 +156,41 @@ const ArrayValue = ({ name, value, description, prefix = [], }) => {
     }
 };
 const toLocale = (n) => n.toLocaleString('en-US');
-function CoreDetails(props) {
+function Position(props) {
     const { feature } = props;
-    const obj = feature;
-    // eslint-disable-next-line no-underscore-dangle
-    const formattedFeat = { ...obj, ...obj.__jbrowsefmt };
-    const { start, strand, end, refName } = formattedFeat;
+    const strand = feature.strand;
     const strandMap = {
         '-1': '-',
         '0': '',
         '1': '+',
     };
     const str = strandMap[strand] ? `(${strandMap[strand]})` : '';
+    // @ts-ignore
+    const loc = (0, util_1.assembleLocString)(feature);
+    return react_1.default.createElement(react_1.default.Fragment, null, `${loc} ${str}`);
+}
+function CoreDetails(props) {
+    const { feature } = props;
+    const obj = feature;
+    // eslint-disable-next-line no-underscore-dangle
+    const formattedFeat = { ...obj, ...obj.__jbrowsefmt };
+    const { start, end } = formattedFeat;
     const displayedDetails = {
         ...formattedFeat,
         length: toLocale(end - start),
-        position: `${refName}:${toLocale(start + 1)}..${toLocale(end)} ${str}`,
     };
     const coreRenderedDetails = {
-        position: 'Position',
         description: 'Description',
         name: 'Name',
         length: 'Length',
         type: 'Type',
-        assemblyName: 'Assembly name',
     };
-    return (react_1.default.createElement(react_1.default.Fragment, null, Object.entries(coreRenderedDetails)
-        .map(([key, name]) => [name, displayedDetails[key]])
-        .filter(([, value]) => value !== null && value !== undefined)
-        .map(([name, value]) => (react_1.default.createElement(exports.SimpleValue, { key: name, name: name, value: value })))));
+    return (react_1.default.createElement(react_1.default.Fragment, null,
+        react_1.default.createElement(exports.SimpleValue, { name: "Position", value: react_1.default.createElement(Position, { ...props, feature: formattedFeat }) }),
+        Object.entries(coreRenderedDetails)
+            .map(([key, name]) => [name, displayedDetails[key]])
+            .filter(([, value]) => value != null)
+            .map(([name, value]) => (react_1.default.createElement(exports.SimpleValue, { key: name, name: name, value: value })))));
 }
 const BaseCoreDetails = (props) => {
     return (react_1.default.createElement(BaseCard, { ...props, title: "Primary data" },
@@ -229,23 +235,25 @@ const DataGridDetails = ({ value, prefix, name, }) => {
             width: (0, util_1.measureGridWidth)(rows.map(r => r[val])),
         }));
         const rowHeight = 25;
-        const hideFooter = rows.length < 100;
-        const headerHeight = 80;
+        const hideFoot = rows.length < 100;
+        const headHeight = 80;
+        const height = Math.min(rows.length, 100) * rowHeight + headHeight + (hideFoot ? 0 : 50);
         // disableSelection on click helps avoid
         // https://github.com/mui-org/material-ui-x/issues/1197
         return (react_1.default.createElement(react_1.default.Fragment, null,
             react_1.default.createElement(exports.FieldName, { prefix: prefix, name: name }),
             react_1.default.createElement("div", { style: {
-                    height: Math.min(rows.length, 100) * rowHeight +
-                        headerHeight +
-                        (hideFooter ? 0 : 50),
+                    height,
                     width: '100%',
                 } },
-                react_1.default.createElement(x_data_grid_1.DataGrid, { disableSelectionOnClick: true, rowHeight: rowHeight, rows: rows, rowsPerPageOptions: [], hideFooterSelectedRowCount: true, columns: columns, hideFooter: hideFooter }))));
+                react_1.default.createElement(x_data_grid_1.DataGrid, { disableSelectionOnClick: true, rowHeight: rowHeight, rows: rows, hideFooterSelectedRowCount: true, columns: columns, hideFooter: hideFoot }))));
     }
     return null;
 };
-// arr = ['a','b'], obj = {a:{b:'hello}}, returns hello (with special addition to grab description also)
+// pick using a path from an object, similar to _.get from lodash with special logic
+// for Descriptions from e.g. VCF headers
+// @param arr  example ['a','b'], obj = {a:{b:'hello}}
+// @returns hello (with special addition to grab description also)
 function accessNested(arr, obj = {}) {
     arr.forEach(elt => {
         if (obj) {
@@ -259,13 +267,11 @@ function accessNested(arr, obj = {}) {
             : undefined;
 }
 function generateMaxWidth(array, prefix) {
-    // @ts-ignore
     const arr = [];
-    array.forEach((key, value) => {
+    array.forEach(key => {
         const val = [...prefix, key[0]].join('.');
         arr.push((0, util_1.measureText)(val, 12));
     });
-    // @ts-ignore
     return Math.ceil(Math.max(...arr)) + 10;
 }
 function UriAttribute({ value, prefix, name, }) {
@@ -283,8 +289,8 @@ function UriAttribute({ value, prefix, name, }) {
         react_1.default.createElement(exports.BasicValue, { value: href })));
 }
 function Attributes(props) {
-    const { attributes, omit = [], descriptions, formatter = val => val, hideUris, prefix = [], } = props;
-    const omits = [...omit, ...globalOmit];
+    const { attributes, omit = [], omitSingleLevel = [], descriptions, formatter = val => val, hideUris, prefix = [], } = props;
+    const omits = [...omit, ...globalOmit, ...omitSingleLevel];
     const { __jbrowsefmt, ...rest } = attributes;
     const formattedAttributes = { ...rest, ...__jbrowsefmt };
     const maxLabelWidth = generateMaxWidth(Object.entries(formattedAttributes).filter(([k, v]) => v !== undefined && !omits.includes(k)), prefix);
@@ -298,7 +304,8 @@ function Attributes(props) {
             return value.length > 1 && value.every(val => (0, is_object_1.default)(val)) ? (react_1.default.createElement(DataGridDetails, { key: key, name: key, prefix: prefix, value: value })) : (react_1.default.createElement(ArrayValue, { key: key, name: key, value: value, description: description, prefix: prefix }));
         }
         else if ((0, is_object_1.default)(value)) {
-            return (0, util_1.isUriLocation)(value) ? (hideUris ? null : (react_1.default.createElement(UriAttribute, { key: key, name: key, prefix: prefix, value: value }))) : (react_1.default.createElement(Attributes, { ...props, omit: omits, key: key, attributes: value, descriptions: descriptions, prefix: [...prefix, key] }));
+            const { omitSingleLevel, ...rest } = props;
+            return (0, util_1.isUriLocation)(value) ? (hideUris ? null : (react_1.default.createElement(UriAttribute, { key: key, name: key, prefix: prefix, value: value }))) : (react_1.default.createElement(Attributes, { ...rest, key: key, attributes: value, descriptions: descriptions, prefix: [...prefix, key] }));
         }
         else {
             return (react_1.default.createElement(exports.SimpleValue, { key: key, name: key, value: formatter(value, key), description: description, prefix: prefix, width: Math.min(maxLabelWidth, MAX_FIELD_NAME_WIDTH) }));
@@ -323,15 +330,23 @@ function generateTitle(name, id, type) {
 const FeatureDetails = (props) => {
     const { omit = [], model, feature, depth = 0 } = props;
     const { name = '', id = '', type = '', subfeatures } = feature;
-    const { pluginManager } = (0, util_1.getEnv)(model);
+    const pm = (0, util_1.getEnv)(model).pluginManager;
     const session = (0, util_1.getSession)(model);
-    const ExtraPanel = pluginManager === null || pluginManager === void 0 ? void 0 : pluginManager.evaluateExtensionPoint('Core-extraFeaturePanel', null, { session, feature, model });
+    const ExtraPanel = pm.evaluateExtensionPoint('Core-extraFeaturePanel', null, {
+        session,
+        feature,
+        model,
+    });
     return (react_1.default.createElement(BaseCard, { title: generateTitle(name, id, type) },
         react_1.default.createElement(material_1.Typography, null, "Core details"),
         react_1.default.createElement(CoreDetails, { ...props }),
+        feature.mate ? (react_1.default.createElement(react_1.default.Fragment, null,
+            react_1.default.createElement(material_1.Divider, null),
+            react_1.default.createElement(material_1.Typography, null, "Mate details"),
+            react_1.default.createElement(CoreDetails, { ...props, feature: feature.mate }))) : null,
         react_1.default.createElement(material_1.Divider, null),
         react_1.default.createElement(material_1.Typography, null, "Attributes"),
-        react_1.default.createElement(Attributes, { attributes: feature, ...props, omit: [...omit, ...coreDetails] }),
+        react_1.default.createElement(Attributes, { attributes: feature, ...props, omit: omit, omitSingleLevel: coreDetails }),
         react_1.default.createElement(react_error_boundary_1.ErrorBoundary, { FallbackComponent: ({ error }) => react_1.default.createElement(ui_1.ErrorMessage, { error: error }) },
             react_1.default.createElement(SequenceFeatureDetails_1.default, { ...props })),
         ExtraPanel ? (react_1.default.createElement(react_1.default.Fragment, null,

package/BaseFeatureWidget/SequenceBox.js

@@ -29,21 +29,17 @@ function GeneProtein({ cds, sequence, codonTable, }) {
 }
 exports.GeneProtein = GeneProtein;
 function GenecDNA({ utr, cds, exons, sequence, upstream, downstream, includeIntrons, collapseIntron, intronBp, }) {
-    const chunks = cds.length
-        ? [...cds, ...utr].sort((a, b) => a.start - b.start)
-        : exons;
+    const chunks = (cds.length ? [...cds, ...utr].sort((a, b) => a.start - b.start) : exons).filter(f => f.start !== f.end);
     return (react_1.default.createElement(react_1.default.Fragment, null,
         upstream ? (react_1.default.createElement("span", { style: { background: updownstreamColor } }, upstream)) : null,
-        chunks
-            .filter(f => f.start !== f.end)
-            .map((chunk, index) => {
+        chunks.map((chunk, idx) => {
             var _a;
-            const intron = sequence.slice(chunk.end, (_a = chunks[index + 1]) === null || _a === void 0 ? void 0 : _a.start);
+            const intron = sequence.slice(chunk.end, (_a = chunks[idx + 1]) === null || _a === void 0 ? void 0 : _a.start);
             return (react_1.default.createElement(react_1.default.Fragment, { key: JSON.stringify(chunk) },
                 react_1.default.createElement("span", { style: {
                         background: chunk.type === 'CDS' ? cdsColor : utrColor,
                     } }, sequence.slice(chunk.start, chunk.end)),
-                includeIntrons && index < chunks.length - 1 ? (react_1.default.createElement("span", { style: { background: intronColor } }, collapseIntron && intron.length > intronBp * 2
+                includeIntrons && idx < chunks.length - 1 ? (react_1.default.createElement("span", { style: { background: intronColor } }, collapseIntron && intron.length > intronBp * 2
                     ? `${intron.slice(0, intronBp)}...${intron.slice(-intronBp)}`
                     : intron)) : null));
         }),

package/BaseFeatureWidget/SequenceFeatureDetails.js

@@ -36,6 +36,7 @@ const SequenceHelpDialog_1 = __importDefault(require("./SequenceHelpDialog"));
 const SequencePanel_1 = __importDefault(require("./SequencePanel"));
 const util_1 = require("../util");
 const configuration_1 = require("../configuration");
+const ui_1 = require("../ui");
 // icons
 const Settings_1 = __importDefault(require("@mui/icons-material/Settings"));
 const Help_1 = __importDefault(require("@mui/icons-material/Help"));
@@ -201,7 +202,7 @@ function SequenceFeatureDetails({ model, feature }) {
                 react_1.default.createElement(material_1.IconButton, { onClick: () => setSettingsDlgOpen(true) },
                     react_1.default.createElement(Settings_1.default, null))),
             react_1.default.createElement("br", null),
-            react_1.default.createElement(react_1.default.Fragment, null, error ? (react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`)) : loading ? (react_1.default.createElement(material_1.Typography, null, "Loading gene sequence...")) : sequence ? ('error' in sequence ? (react_1.default.createElement(react_1.default.Fragment, null,
+            react_1.default.createElement(react_1.default.Fragment, null, error ? (react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`)) : loading ? (react_1.default.createElement(ui_1.LoadingEllipses, null)) : sequence ? ('error' in sequence ? (react_1.default.createElement(react_1.default.Fragment, null,
                 react_1.default.createElement(material_1.Typography, { color: "error" }, sequence.error),
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "inherit", onClick: () => setForceLoad({ ...forceLoad, force: true }) }, "Force load"))) : (react_1.default.createElement(SequencePanel_1.default, { ref: seqPanelRef, feature: parentFeature, mode: mode, sequence: sequence, intronBp: intronBp }))) : (react_1.default.createElement(material_1.Typography, null, "No sequence found"))))) : null,
         settingsDlgOpen ? (react_1.default.createElement(SequenceFeatureSettingsDialog_1.default, { handleClose: arg => {

package/Plugin.d.ts

@@ -11,4 +11,4 @@ export default abstract class Plugin {
     configure(_pluginManager: PluginManager): void;
     configurationSchema: AnyConfigurationSchemaType | undefined;
 }
-export declare type PluginConstructor = new (...args: unknown[]) => Plugin;
+export type PluginConstructor = new (...args: unknown[]) => Plugin;

package/PluginLoader.d.ts

@@ -14,7 +14,7 @@ export interface LegacyUMDPluginDefinition {
     url: string;
     name: string;
 }
-declare type UMDPluginDefinition = UMDLocPluginDefinition | UMDUrlPluginDefinition;
+type UMDPluginDefinition = UMDLocPluginDefinition | UMDUrlPluginDefinition;
 export declare function isUMDPluginDefinition(def: PluginDefinition): def is UMDPluginDefinition | LegacyUMDPluginDefinition;
 export interface ESMLocPluginDefinition {
     esmLoc: {
@@ -25,7 +25,7 @@ export interface ESMLocPluginDefinition {
 export interface ESMUrlPluginDefinition {
     esmUrl: string;
 }
-export declare type ESMPluginDefinition = ESMLocPluginDefinition | ESMUrlPluginDefinition;
+export type ESMPluginDefinition = ESMLocPluginDefinition | ESMUrlPluginDefinition;
 export declare function isESMPluginDefinition(def: PluginDefinition): def is ESMPluginDefinition;
 export interface CJSPluginDefinition {
     cjsUrl: string;

package/PluginManager.d.ts

@@ -26,7 +26,7 @@ declare class PhasedScheduler<PhaseName extends string> {
     add(phase: PhaseName, callback: Function): void;
     run(): void;
 }
-declare type PluggableElementTypeGroup = 'renderer' | 'adapter' | 'display' | 'track' | 'connection' | 'view' | 'widget' | 'rpc method' | 'internet account' | 'text search adapter' | 'add track workflow';
+type PluggableElementTypeGroup = 'renderer' | 'adapter' | 'display' | 'track' | 'connection' | 'view' | 'widget' | 'rpc method' | 'internet account' | 'text search adapter' | 'add track workflow';
 /** internal class that holds the info for a certain element type */
 declare class TypeRecord<ElementClass extends PluggableElementBase> {
     typeName: string;
@@ -48,7 +48,7 @@ declare class TypeRecord<ElementClass extends PluggableElementBase> {
     get(name: string): ElementClass;
     all(): ElementClass[];
 }
-declare type AnyFunction = (...args: any) => any;
+type AnyFunction = (...args: any) => any;
 /**
  * free-form string-to-unknown mapping of metadata related to the instance
  * of this plugin. `isCore` is typically set to `Boolean(true)` if the plugin was
@@ -56,7 +56,7 @@ declare type AnyFunction = (...args: any) => any;
  * Can also use this metadata to stash other things about why the plugin is
  * loaded, such as where it came from, what plugin depends on it, etc.
  */
-export declare type PluginMetadata = Record<string, unknown>;
+export type PluginMetadata = Record<string, unknown>;
 export interface PluginLoadRecord {
     metadata?: PluginMetadata;
     plugin: Plugin;
@@ -223,7 +223,7 @@ export default class PluginManager {
             makeStyles: <Params = void, RuleNameSubsetReferencableInNestedSelectors extends string = never>(params?: {
                 name?: string | Record<string, unknown> | undefined;
                 uniqId?: string | undefined;
-            } | undefined) => <RuleName extends string>(cssObjectByRuleNameOrGetCssObjectByRuleName: Record<RuleName, import("tss-react/types").CSSObject> | ((theme: import("@mui/material").Theme, params: Params, classes: Record<RuleNameSubsetReferencableInNestedSelectors, string>) => Record<RuleNameSubsetReferencableInNestedSelectors | RuleName, import("tss-react/types").CSSObject>)) => (params: Params, styleOverrides?: {
+            } | undefined) => <RuleName extends string>(cssObjectByRuleNameOrGetCssObjectByRuleName: Record<RuleName, import("tss-react").CSSObject> | ((theme: import("@mui/material").Theme, params: Params, classes: Record<RuleNameSubsetReferencableInNestedSelectors, string>) => Record<RuleNameSubsetReferencableInNestedSelectors | RuleName, import("tss-react").CSSObject>)) => (params: Params, styleOverrides?: {
                 props: {
                     classes?: Record<string, string> | undefined;
                 } & Record<string, unknown>;
@@ -231,8 +231,8 @@ export default class PluginManager {
             } | undefined) => {
                 classes: Record<RuleName, string>;
                 theme: import("@mui/material").Theme;
-                css: import("tss-react/types").Css;
-                cx: import("tss-react/types").Cx;
+                css: import("tss-react").Css;
+                cx: import("tss-react").Cx;
             };
         };
         '@material-ui/core': {

package/ReExports/modules.d.ts

@@ -144,7 +144,7 @@ declare const libs: {
         makeStyles: <Params = void, RuleNameSubsetReferencableInNestedSelectors extends string = never>(params?: {
             name?: string | Record<string, unknown> | undefined;
             uniqId?: string | undefined;
-        } | undefined) => <RuleName extends string>(cssObjectByRuleNameOrGetCssObjectByRuleName: Record<RuleName, import("tss-react/types").CSSObject> | ((theme: MUIStyles.Theme, params: Params, classes: Record<RuleNameSubsetReferencableInNestedSelectors, string>) => Record<RuleNameSubsetReferencableInNestedSelectors | RuleName, import("tss-react/types").CSSObject>)) => (params: Params, styleOverrides?: {
+        } | undefined) => <RuleName extends string>(cssObjectByRuleNameOrGetCssObjectByRuleName: Record<RuleName, import("tss-react").CSSObject> | ((theme: MUIStyles.Theme, params: Params, classes: Record<RuleNameSubsetReferencableInNestedSelectors, string>) => Record<RuleNameSubsetReferencableInNestedSelectors | RuleName, import("tss-react").CSSObject>)) => (params: Params, styleOverrides?: {
             props: {
                 classes?: Record<string, string> | undefined;
             } & Record<string, unknown>;
@@ -152,8 +152,8 @@ declare const libs: {
         } | undefined) => {
             classes: Record<RuleName, string>;
             theme: MUIStyles.Theme;
-            css: import("tss-react/types").Css;
-            cx: import("tss-react/types").Cx;
+            css: import("tss-react").Css;
+            cx: import("tss-react").Cx;
         };
     };
     '@material-ui/core': {

package/assemblyManager/assembly.d.ts

@@ -1,7 +1,7 @@
 import { Instance, IAnyType } from 'mobx-state-tree';
 import PluginManager from '../PluginManager';
 import { Region, Feature } from '../util';
-declare type RefNameAliases = Record<string, string>;
+type RefNameAliases = Record<string, string>;
 export interface BaseOptions {
     signal?: AbortSignal;
     sessionId: string;
@@ -17,44 +17,50 @@ export interface BasicRegion {
     refName: string;
     assemblyName: string;
 }
-export default function assemblyFactory(assemblyConfigType: IAnyType, pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
+export interface Loading {
+    adapterRegionsWithAssembly: Region[];
+    refNameAliases: RefNameAliases;
+    lowerCaseRefNameAliases: RefNameAliases;
+    cytobands: Feature[];
+}
+export default function assemblyFactory(assemblyConfigType: IAnyType, pm: PluginManager): import("mobx-state-tree").IModelType<{
     configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
 }, {
-    error: Error | undefined;
-    regions: BasicRegion[] | undefined;
+    error: unknown;
+    loaded: boolean;
+    loadingP: Promise<void> | undefined;
+    volatileRegions: BasicRegion[] | undefined;
     refNameAliases: RefNameAliases | undefined;
     lowerCaseRefNameAliases: RefNameAliases | undefined;
     cytobands: Feature[] | undefined;
 } & {
     readonly initialized: boolean;
     readonly name: string;
+    readonly regions: BasicRegion[] | undefined;
     readonly aliases: string[];
     readonly displayName: string | undefined;
     hasName(name: string): boolean;
     readonly allAliases: string[];
-    readonly refNames: string[] | undefined;
     readonly allRefNames: string[] | undefined;
     readonly lowerCaseRefNames: string[] | undefined;
     readonly allRefNamesWithLowerCase: string[] | undefined;
     readonly rpcManager: any;
     readonly refNameColors: string[];
+} & {
+    readonly refNames: string[] | undefined;
 } & {
     getCanonicalRefName(refName: string): string;
     getRefNameColor(refName: string): string | undefined;
     isValidRefName(refName: string): boolean;
 } & {
-    setLoading(): void;
-    setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
-        adapterRegionsWithAssembly: Region[];
-        refNameAliases: RefNameAliases;
-        lowerCaseRefNameAliases: RefNameAliases;
-        cytobands: Feature[];
-    }): void;
-    setError(e: Error): void;
+    setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: Loading): void;
+    setError(e: unknown): void;
     setRegions(regions: Region[]): void;
-    setRefNameAliases(aliases: RefNameAliases, lowerCase: RefNameAliases): void;
+    setRefNameAliases(aliases: RefNameAliases, lcAliases: RefNameAliases): void;
     setCytobands(cytobands: Feature[]): void;
-    afterAttach(): void;
+    setLoadingP(p?: Promise<void>): void;
+    load(): Promise<void>;
+    loadPre(): Promise<void>;
 } & {
     getAdapterMapEntry(adapterConf: unknown, options: BaseOptions): Promise<RefNameMap>;
     /**
@@ -66,6 +72,6 @@ export default function assemblyFactory(assemblyConfigType: IAnyType, pluginMana
      */
     getReverseRefNameMapForAdapter(adapterConf: unknown, opts: BaseOptions): Promise<RefNameAliases>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare type AssemblyModel = ReturnType<typeof assemblyFactory>;
-export declare type Assembly = Instance<AssemblyModel>;
+export type AssemblyModel = ReturnType<typeof assemblyFactory>;
+export type Assembly = Instance<AssemblyModel>;
 export {};

package/assemblyManager/assembly.js

@@ -3,8 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const json_stable_stringify_1 = __importDefault(require("json-stable-stringify"));
 const mobx_state_tree_1 = require("mobx-state-tree");
+const json_stable_stringify_1 = __importDefault(require("json-stable-stringify"));
 const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
 // locals
 const configuration_1 = require("../configuration");
@@ -45,7 +45,7 @@ const refNameColors = [
 ];
 async function loadRefNameMap(assembly, adapterConfig, options, signal) {
     const { sessionId } = options;
-    await (0, util_1.when)(() => Boolean(assembly.regions && assembly.refNameAliases), {
+    await (0, util_1.when)(() => !!(assembly.regions && assembly.refNameAliases), {
         signal,
         name: 'when assembly ready',
     });
@@ -81,7 +81,7 @@ function checkRefName(refName) {
 function getAdapterId(adapterConf) {
     return (0, json_stable_stringify_1.default)(adapterConf);
 }
-function assemblyFactory(assemblyConfigType, pluginManager) {
+function assemblyFactory(assemblyConfigType, pm) {
     const adapterLoads = new abortable_promise_cache_1.default({
         cache: new QuickLRU_1.default({ maxSize: 1000 }),
         async fill(args, signal, statusCallback) {
@@ -95,18 +95,27 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
     })
         .volatile(() => ({
         error: undefined,
-        regions: undefined,
+        loaded: false,
+        loadingP: undefined,
+        volatileRegions: undefined,
         refNameAliases: undefined,
         lowerCaseRefNameAliases: undefined,
         cytobands: undefined,
     }))
         .views(self => ({
         get initialized() {
+            // @ts-ignore
+            self.load();
             return !!self.refNameAliases;
         },
         get name() {
             return (0, configuration_1.getConf)(self, 'name');
         },
+        get regions() {
+            // @ts-ignore
+            self.load();
+            return self.volatileRegions;
+        },
         get aliases() {
             return (0, configuration_1.getConf)(self, 'aliases');
         },
@@ -119,10 +128,6 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
         get allAliases() {
             return [this.name, ...this.aliases];
         },
-        get refNames() {
-            var _a;
-            return (_a = self.regions) === null || _a === void 0 ? void 0 : _a.map(region => region.refName);
-        },
         // note: lowerCaseRefNameAliases not included here: this allows the list
         // of refnames to be just the "normal casing", but things like
         // getCanonicalRefName can resolve a lower-case name if needed
@@ -149,6 +154,12 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
             const colors = (0, configuration_1.getConf)(self, 'refNameColors');
             return colors.length === 0 ? refNameColors : colors;
         },
+    }))
+        .views(self => ({
+        get refNames() {
+            var _a;
+            return (_a = self.regions) === null || _a === void 0 ? void 0 : _a.map(region => region.refName);
+        },
     }))
         .views(self => ({
         getCanonicalRefName(refName) {
@@ -158,9 +169,11 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
             return (self.refNameAliases[refName] || self.lowerCaseRefNameAliases[refName]);
         },
         getRefNameColor(refName) {
-            var _a;
-            const idx = (_a = self.refNames) === null || _a === void 0 ? void 0 : _a.findIndex(r => r === refName);
-            if (idx === undefined || idx === -1) {
+            if (!self.refNames) {
+                return undefined;
+            }
+            const idx = self.refNames.findIndex(r => r === refName);
+            if (idx === -1) {
                 return undefined;
             }
             return self.refNameColors[idx % self.refNameColors.length];
@@ -173,8 +186,8 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
         },
     }))
         .actions(self => ({
-        setLoading() { },
         setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }) {
+            self.loaded = true;
             this.setRegions(adapterRegionsWithAssembly);
             this.setRefNameAliases(refNameAliases, lowerCaseRefNameAliases);
             this.setCytobands(cytobands);
@@ -184,21 +197,62 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
             self.error = e;
         },
         setRegions(regions) {
-            self.regions = regions;
+            self.volatileRegions = regions;
         },
-        setRefNameAliases(aliases, lowerCase) {
+        setRefNameAliases(aliases, lcAliases) {
             self.refNameAliases = aliases;
-            self.lowerCaseRefNameAliases = lowerCase;
+            self.lowerCaseRefNameAliases = lcAliases;
         },
         setCytobands(cytobands) {
             self.cytobands = cytobands;
         },
-        afterAttach() {
-            (0, util_1.makeAbortableReaction)(
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            self, 
-            // @ts-ignore
-            makeLoadAssemblyData(pluginManager), loadAssemblyReaction, { name: `${self.name} assembly loading`, fireImmediately: true }, this.setLoading, this.setLoaded, this.setError);
+        setLoadingP(p) {
+            self.loadingP = p;
+        },
+        load() {
+            if (!self.loadingP) {
+                self.loadingP = this.loadPre().catch(e => {
+                    this.setLoadingP(undefined);
+                    this.setError(e);
+                });
+            }
+            return self.loadingP;
+        },
+        async loadPre() {
+            var _a, _b;
+            const conf = self.configuration;
+            const refNameAliasesAdapterConf = (_a = conf.refNameAliases) === null || _a === void 0 ? void 0 : _a.adapter;
+            const cytobandAdapterConf = (_b = conf.cytobands) === null || _b === void 0 ? void 0 : _b.adapter;
+            const sequenceAdapterConf = conf.sequence.adapter;
+            const assemblyName = self.name;
+            const regions = await getAssemblyRegions(sequenceAdapterConf, pm);
+            const adapterRegionsWithAssembly = regions.map(r => {
+                checkRefName(r.refName);
+                return { ...r, assemblyName };
+            });
+            const refNameAliases = {};
+            const ret = await getRefNameAliases(refNameAliasesAdapterConf, pm);
+            const cytobands = await getCytobands(cytobandAdapterConf, pm);
+            ret.forEach(({ refName, aliases }) => {
+                aliases.forEach(a => {
+                    checkRefName(a);
+                    refNameAliases[a] = refName;
+                });
+            });
+            // add identity to the refNameAliases list
+            adapterRegionsWithAssembly.forEach(region => {
+                refNameAliases[region.refName] = region.refName;
+            });
+            const lowerCaseRefNameAliases = Object.fromEntries(Object.entries(refNameAliases).map(([key, val]) => [
+                key.toLowerCase(),
+                val,
+            ]));
+            this.setLoaded({
+                adapterRegionsWithAssembly,
+                refNameAliases,
+                lowerCaseRefNameAliases,
+                cytobands,
+            });
         },
     }))
         .views(self => ({
@@ -237,61 +291,6 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
     }));
 }
 exports.default = assemblyFactory;
-function makeLoadAssemblyData(pluginManager) {
-    return (self) => {
-        if (self.configuration) {
-            // use full configuration instead of snapshot of the config, the
-            // rpcManager normally receives a snapshot but we bypass rpcManager here
-            // to avoid spinning up a webworker
-            const { sequence, refNameAliases, cytobands } = self.configuration;
-            const sequenceAdapterConfig = sequence.adapter;
-            const refNameAliasesAdapterConfig = refNameAliases === null || refNameAliases === void 0 ? void 0 : refNameAliases.adapter;
-            const cytobandAdapterConfig = cytobands === null || cytobands === void 0 ? void 0 : cytobands.adapter;
-            return {
-                sequenceAdapterConfig,
-                assemblyName: self.name,
-                refNameAliasesAdapterConfig,
-                cytobandAdapterConfig,
-                pluginManager,
-            };
-        }
-        return undefined;
-    };
-}
-async function loadAssemblyReaction(props, signal) {
-    if (!props) {
-        return;
-    }
-    const { sequenceAdapterConfig, assemblyName, refNameAliasesAdapterConfig, cytobandAdapterConfig, pluginManager, } = props;
-    const adapterRegions = await getAssemblyRegions(sequenceAdapterConfig, pluginManager, signal);
-    const adapterRegionsWithAssembly = adapterRegions.map(adapterRegion => {
-        checkRefName(adapterRegion.refName);
-        return { ...adapterRegion, assemblyName };
-    });
-    const refNameAliases = {};
-    const aliases = await getRefNameAliases(refNameAliasesAdapterConfig, pluginManager, signal);
-    const cytobands = await getCytobands(cytobandAdapterConfig, pluginManager);
-    aliases.forEach(({ refName, aliases }) => {
-        aliases.forEach(alias => {
-            checkRefName(alias);
-            refNameAliases[alias] = refName;
-        });
-    });
-    // add identity to the refNameAliases list
-    adapterRegionsWithAssembly.forEach(region => {
-        refNameAliases[region.refName] = region.refName;
-    });
-    const lowerCaseRefNameAliases = Object.fromEntries(Object.entries(refNameAliases).map(([key, val]) => [
-        key.toLowerCase(),
-        val,
-    ]));
-    return {
-        adapterRegionsWithAssembly,
-        refNameAliases,
-        lowerCaseRefNameAliases,
-        cytobands,
-    };
-}
 async function getRefNameAliases(config, pm, signal) {
     const type = pm.getAdapterType(config.type);
     const CLASS = await type.getAdapterClass();

package/assemblyManager/assemblyConfigSchema.d.ts

@@ -1,3 +1,7 @@
 import PluginManager from '../PluginManager';
-declare const _default: (pluginManager: PluginManager) => import("../configuration").AnyConfigurationSchemaType;
-export default _default;
+/**
+ * #config BaseAssembly
+ * This corresponds to the assemblies section of the config
+ */
+declare function assemblyConfigSchema(pluginManager: PluginManager): import("../configuration").AnyConfigurationSchemaType;
+export default assemblyConfigSchema;