@jbrowse/core 4.3.0 → 5.0.0-beta.1

package/esm/ReExports/muiComponentNames.js

@@ -0,0 +1,130 @@
+/**
+ * Every MUI component name the host re-exports to plugins.
+ *
+ * Its own module, with **no MUI imports**, because the two things that need it
+ * cannot both reach the other: `MuiReExports.ts` holds the components
+ * themselves, and `list.ts` must stay importable by bundler configs and
+ * esbuild scripts without pulling MUI in behind it (see that file's header).
+ * The names were therefore written out twice — 112 of them — and kept in
+ * agreement by a load-time throw in `modules.ts`.
+ *
+ * Declaring them here instead makes `Entries` a `Record` over this union, so a
+ * name with no component and a component with no name are both compile errors,
+ * and `list.ts` derives its subpaths by mapping. The runtime check in
+ * `modules.ts` stays: it still covers the framework and `@jbrowse/core` entries,
+ * which are not this list.
+ */
+export const MUI_COMPONENT_NAMES = [
+    'Accordion',
+    'AccordionActions',
+    'AccordionDetails',
+    'AccordionSummary',
+    'Alert',
+    'AlertTitle',
+    'Autocomplete',
+    'Avatar',
+    'AvatarGroup',
+    'Backdrop',
+    'Badge',
+    'Box',
+    'Breadcrumbs',
+    'Button',
+    'ButtonGroup',
+    'Card',
+    'CardActions',
+    'CardActionArea',
+    'CardContent',
+    'CardHeader',
+    'CardMedia',
+    'Chip',
+    'CircularProgress',
+    'Collapse',
+    'ClickAwayListener',
+    'Checkbox',
+    'Container',
+    'Dialog',
+    'DialogActions',
+    'DialogTitle',
+    'DialogContent',
+    'DialogContentText',
+    'Divider',
+    'Drawer',
+    'Fab',
+    'Fade',
+    'FilledInput',
+    'FormLabel',
+    'FormControl',
+    'FormControlLabel',
+    'FormHelperText',
+    'FormGroup',
+    'Grid',
+    'Grid2',
+    'Grow',
+    'Icon',
+    'IconButton',
+    'Input',
+    'InputBase',
+    'InputLabel',
+    'InputAdornment',
+    'Link',
+    'LinearProgress',
+    'List',
+    'ListItem',
+    'ListItemAvatar',
+    'ListItemButton',
+    'ListItemSecondaryAction',
+    'ListItemIcon',
+    'ListSubheader',
+    'ListItemText',
+    'Menu',
+    'MenuItem',
+    'MenuList',
+    'Modal',
+    'NativeSelect',
+    'OutlinedInput',
+    'Pagination',
+    'PaginationItem',
+    'Paper',
+    'Popover',
+    'Popper',
+    'Portal',
+    'Radio',
+    'RadioGroup',
+    'Rating',
+    'ScopedCssBaseline',
+    'Select',
+    'Skeleton',
+    'Slider',
+    'Snackbar',
+    'SnackbarContent',
+    'SpeedDial',
+    'SpeedDialAction',
+    'SpeedDialIcon',
+    'Stack',
+    'Step',
+    'StepButton',
+    'StepConnector',
+    'StepLabel',
+    'StepIcon',
+    'Stepper',
+    'SvgIcon',
+    'Switch',
+    'Tab',
+    'Table',
+    'TableBody',
+    'TableCell',
+    'TableContainer',
+    'TableFooter',
+    'TableHead',
+    'TablePagination',
+    'TableRow',
+    'TableSortLabel',
+    'Tabs',
+    'TextField',
+    'TextareaAutosize',
+    'ToggleButton',
+    'ToggleButtonGroup',
+    'Toolbar',
+    'Tooltip',
+    'Typography',
+];

package/esm/ReExports/publicUtil.d.ts

@@ -0,0 +1 @@
+export { AuthNeededError, BEZIER_CONNECTOR_MAX_REACH_PX, ENCODED_PREFIX, IUPAC_MOTIF_REGEX, IntervalTree, JSON_PREFIX, MAX_ZOOM_RATE_PER_MS, SCROLL_ZOOM_FACTOR_DIVISOR, SHARE_PREFIX, SimpleFeature, UNKNOWN, UNSUPPORTED, UnknownRefNameError, ZOOM_ACTIVE_WINDOW_MS, accumulateScroll, adapterConfigFromSpec, addAdapterGuesser, addAddTrackComponent, addAndShowTrack, addOrReplaceView, addTrackFromWidget, addTrackTypeGuesser, aesDecrypt, aesEncrypt, animationAllowed, applyOrderWithin, applyZoomAccum, assembleLocString, assembleLocStringRaw, avg, b64PadSuffix, bezierConnectorPath, bpSpanPx, bpToPx, bytesForRegions, calculateRedispatchRange, canReplaceView, capitalizeFirst, checkStopToken, checkStopTokenThrottled, clamp, clearFileFromCache, cmpStr, coarseStripHTML, codonTable, compareLocStrings, compareLocs, complement, complementTable, createProgressReporter, createScrollLatch, createSharedSetup, createStatusChannel, createStatusFanOut, createStatusWindow, createStopToken, createStopTokenChecker, createStopTokenRotation, dedupe, defaultCodonTable, defaultStarts, diagonalizeRegions, diffTrackConfig, doesIntersect2, downloadStatus, drawImageOntoCanvasContext, encodeSessionParam, ensureFileHandleReady, expandLooseTrackConfig, featureSpanPx, fetchAndMaybeUnzip, fetchAndMaybeUnzipText, fetchJson, fileToLocation, findFileHandleIds, findParentThat, findParentThatIs, flattenTrackConfigDelta, formatRelativeTime, fromUrlSafeB64, gatherOverlaps, generateCodonTable, generateUnknownTrackConf, generateUnsupportedTrackConf, getAssemblyHost, getBlob, getBlobMap, getBpDisplayStr, getConfAssemblyNames, getContainingDisplay, getContainingTrack, getContainingView, getDialogHost, getEnv, getFileFromCache, getFileHandle, getFileName, getFillProps, getFrame, getNotificationSink, getNumberGrouping, getPaletteHost, getPluginUpdate, getRenderingServices, getRpcHost, getRpcSessionId, getSession, getSessionServices, getStr, getStrokeProps, getTickDisplayStr, getTrackAssemblyNames, getTrackName, getZoomNormalizer, groupBy, guessAdapter, guessTrackConf, guessTrackType, hasFileHandlesInCache, hasSharedArrayBuffer, hashCode, hideTrackGeneric, installedVersionFromUrl, intersection2, isAbortException, isAbstractMenuManager, isActivelyZooming, isAppRootModel, isAuthNeededException, isBlobLocation, isDataCurrent, isDisplayModel, isElectron, isFeature, isFileHandleLocation, isFileSystemAccessSupported, isGzip, isLocalPathLocation, isLooseTrackConfig, isNode, isObject, isPalindromic, isPluginInstalled, isRootModelWithInternetAccounts, isRpcResult, isSelectionContainer, isSessionModel, isSessionServices, isSessionModelWithConfigEditing, isSessionModelWithConnectionEditing, isSessionModelWithConnections, isSessionModelWithWidgets, isSessionWithAddAssembly, isSessionWithAddSessionTrack, isSessionWithAddTracks, isSessionWithPublishTrackConf, isSessionWithDeleteTrackConf, isSessionWithSessionPlugins, isSessionWithSessionTracks, isSessionWithShareURL, isSessionWithViewReplacement, isStopToken, isStopped, isSupportedIndexingAdapter, isTrackModel, isTrackViewModel, isUriLocation, isValidTag, isViewContainer, isViewModel, iupacToRegex, linkify, locStringsToRegions, localStorageGetBoolean, localStorageGetItem, localStorageGetJSON, localStorageGetNumber, localStorageRemoveItem, localStorageSetBoolean, localStorageSetItem, localStorageSetJSON, localStorageSetNumber, makeAbortError, makeIndex, makeIndexType, makeTrackId, markStopTokenStopped, matchTrackId, max, maxFinite, measureGridWidth, measureText, mergeIntervals, mergeTrackConfig, min, minmax, normalizeWheelDelta, notEmpty, objectHash, openFeatureWidget, openPromotableDisplays, parseLocString, parseLocStringOneBased, parseMotifList, pluralize, polarToCartesian, progressLabel, rIC, radToDeg, readSessionFromDynamo, reducePrecision, registerStopTokenBroadcaster, renameRegionIfNeeded, renameRegionsIfNeeded, renderToStaticMarkup, reorder, reorderWithin, resolvePlugin, resolveSelectedIds, restoreFileHandles, restoreFileHandlesFromSnapshot, revcom, reverse, reverseComplementIupac, revlist, saveAs, saveSvgAsImage, selectNamedRegions, setBlobMap, setFileInCache, setNumberGrouping, sha256, sha256Base64, sha256Base64Url, shareEndpoint, shorten, shorten2, showTrackGeneric, springAnimate, statusFraction, statusMessageText, statusProgressLabel, statusReading, stitch, stopStopToken, stopTokenSignal, storeBlobLocation, storeFileHandle, storeFileHandleLocation, stringify, stripAlpha, stripFileExtension, stripTrackIds, sum, svgHtmlToPngBlob, tagRegex, testAdapter, toBase64, toBase64Url, toLocale, toUrlSafeB64, toggleTrackGeneric, truncateMiddle, updateStatus, useDebounce, useLocalStorage, useWidthSetter, verifyPermission, wheelFrameElapsedMs, wheelZoomAccum, withProgress, withStopTokenCheck, withStopTokenSignal, } from '../util/index.ts';

package/esm/ReExports/publicUtil.js

@@ -0,0 +1,28 @@
+// The published `@jbrowse/core/util` module, listed by name.
+//
+// modules.ts used to serve `import * as coreUtil from '../util/index.ts'`, which
+// made the external ABI a side effect of an internal barrel. The two want
+// opposite things: in-tree code wants util/ reorganized freely, and a published
+// plugin wants the names it linked against to still be there. Coupling them
+// meant moving a file inside util/ silently edited the ABI, and nothing in the
+// diff said so -- that is how `defaultCodonTable`, `iterMap`, `when` and the
+// rest went, each one an `undefined` inside a bundle nobody was going to build
+// again.
+//
+// Re-exporting by name from the barrel splits those jobs without freezing
+// anything. Moving code between modules under util/ is still free, since only
+// the barrel's own line changes. Taking a name *out* of the barrel stops
+// compiling here, and the fix -- deleting the line below -- is an ABI removal
+// that reads as one in review.
+//
+// So: adding a line is how a helper becomes public, and it is a decision rather
+// than a side effect of where the code happens to live. This list is the ABI,
+// which abiBaseline.json is deliberately not: that baseline fails on removals
+// but not additions, so it sat 11 names behind what was actually being served
+// by the time this was written. A list that has to be edited by hand cannot
+// drift that way.
+//
+// The same split is worth making for '@jbrowse/core/ui' (115 pinned names) and
+// '@jbrowse/core/util/tracks' (36), which have the same shape and the same
+// history: BaseTooltip and getParentRenderProps each left this way.
+export { AuthNeededError, BEZIER_CONNECTOR_MAX_REACH_PX, ENCODED_PREFIX, IUPAC_MOTIF_REGEX, IntervalTree, JSON_PREFIX, MAX_ZOOM_RATE_PER_MS, SCROLL_ZOOM_FACTOR_DIVISOR, SHARE_PREFIX, SimpleFeature, UNKNOWN, UNSUPPORTED, UnknownRefNameError, ZOOM_ACTIVE_WINDOW_MS, accumulateScroll, adapterConfigFromSpec, addAdapterGuesser, addAddTrackComponent, addAndShowTrack, addOrReplaceView, addTrackFromWidget, addTrackTypeGuesser, aesDecrypt, aesEncrypt, animationAllowed, applyOrderWithin, applyZoomAccum, assembleLocString, assembleLocStringRaw, avg, b64PadSuffix, bezierConnectorPath, bpSpanPx, bpToPx, bytesForRegions, calculateRedispatchRange, canReplaceView, capitalizeFirst, checkStopToken, checkStopTokenThrottled, clamp, clearFileFromCache, cmpStr, coarseStripHTML, codonTable, compareLocStrings, compareLocs, complement, complementTable, createProgressReporter, createScrollLatch, createSharedSetup, createStatusChannel, createStatusFanOut, createStatusWindow, createStopToken, createStopTokenChecker, createStopTokenRotation, dedupe, defaultCodonTable, defaultStarts, diagonalizeRegions, diffTrackConfig, doesIntersect2, downloadStatus, drawImageOntoCanvasContext, encodeSessionParam, ensureFileHandleReady, expandLooseTrackConfig, featureSpanPx, fetchAndMaybeUnzip, fetchAndMaybeUnzipText, fetchJson, fileToLocation, findFileHandleIds, findParentThat, findParentThatIs, flattenTrackConfigDelta, formatRelativeTime, fromUrlSafeB64, gatherOverlaps, generateCodonTable, generateUnknownTrackConf, generateUnsupportedTrackConf, getAssemblyHost, getBlob, getBlobMap, getBpDisplayStr, getConfAssemblyNames, getContainingDisplay, getContainingTrack, getContainingView, getDialogHost, getEnv, getFileFromCache, getFileHandle, getFileName, getFillProps, getFrame, getNotificationSink, getNumberGrouping, getPaletteHost, getPluginUpdate, getRenderingServices, getRpcHost, getRpcSessionId, getSession, getSessionServices, getStr, getStrokeProps, getTickDisplayStr, getTrackAssemblyNames, getTrackName, getZoomNormalizer, groupBy, guessAdapter, guessTrackConf, guessTrackType, hasFileHandlesInCache, hasSharedArrayBuffer, hashCode, hideTrackGeneric, installedVersionFromUrl, intersection2, isAbortException, isAbstractMenuManager, isActivelyZooming, isAppRootModel, isAuthNeededException, isBlobLocation, isDataCurrent, isDisplayModel, isElectron, isFeature, isFileHandleLocation, isFileSystemAccessSupported, isGzip, isLocalPathLocation, isLooseTrackConfig, isNode, isObject, isPalindromic, isPluginInstalled, isRootModelWithInternetAccounts, isRpcResult, isSelectionContainer, isSessionModel, isSessionServices, isSessionModelWithConfigEditing, isSessionModelWithConnectionEditing, isSessionModelWithConnections, isSessionModelWithWidgets, isSessionWithAddAssembly, isSessionWithAddSessionTrack, isSessionWithAddTracks, isSessionWithPublishTrackConf, isSessionWithDeleteTrackConf, isSessionWithSessionPlugins, isSessionWithSessionTracks, isSessionWithShareURL, isSessionWithViewReplacement, isStopToken, isStopped, isSupportedIndexingAdapter, isTrackModel, isTrackViewModel, isUriLocation, isValidTag, isViewContainer, isViewModel, iupacToRegex, linkify, locStringsToRegions, localStorageGetBoolean, localStorageGetItem, localStorageGetJSON, localStorageGetNumber, localStorageRemoveItem, localStorageSetBoolean, localStorageSetItem, localStorageSetJSON, localStorageSetNumber, makeAbortError, makeIndex, makeIndexType, makeTrackId, markStopTokenStopped, matchTrackId, max, maxFinite, measureGridWidth, measureText, mergeIntervals, mergeTrackConfig, min, minmax, normalizeWheelDelta, notEmpty, objectHash, openFeatureWidget, openPromotableDisplays, parseLocString, parseLocStringOneBased, parseMotifList, pluralize, polarToCartesian, progressLabel, rIC, radToDeg, readSessionFromDynamo, reducePrecision, registerStopTokenBroadcaster, renameRegionIfNeeded, renameRegionsIfNeeded, renderToStaticMarkup, reorder, reorderWithin, resolvePlugin, resolveSelectedIds, restoreFileHandles, restoreFileHandlesFromSnapshot, revcom, reverse, reverseComplementIupac, revlist, saveAs, saveSvgAsImage, selectNamedRegions, setBlobMap, setFileInCache, setNumberGrouping, sha256, sha256Base64, sha256Base64Url, shareEndpoint, shorten, shorten2, showTrackGeneric, springAnimate, statusFraction, statusMessageText, statusProgressLabel, statusReading, stitch, stopStopToken, stopTokenSignal, storeBlobLocation, storeFileHandle, storeFileHandleLocation, stringify, stripAlpha, stripFileExtension, stripTrackIds, sum, svgHtmlToPngBlob, tagRegex, testAdapter, toBase64, toBase64Url, toLocale, toUrlSafeB64, toggleTrackGeneric, truncateMiddle, updateStatus, useDebounce, useLocalStorage, useWidthSetter, verifyPermission, wheelFrameElapsedMs, wheelZoomAccum, withProgress, withStopTokenCheck, withStopTokenSignal, } from '../util/index.js';

package/esm/ReExports/registry.d.ts

@@ -0,0 +1,2 @@
+export declare function setReExportRegistry(libs: Record<string, unknown>): void;
+export declare function getReExportRegistry(): Record<string, unknown>;

package/esm/ReExports/registry.js

@@ -0,0 +1,28 @@
+/**
+ * Where the runtime re-export registry lands once something has actually loaded
+ * a runtime plugin.
+ *
+ * `ReExports/modules.ts` is the ABI external plugins link against, and it
+ * reaches it by spreading `import * as` namespaces of `@jbrowse/core/ui`,
+ * `configuration`, `util` and a dozen more into one object. A namespace spread
+ * *names every export*, so nothing downstream of those barrels can be
+ * tree-shaken — and the module also throws at top level if `libs` and `list.ts`
+ * disagree, so it cannot be dropped either. `PluginManager` used to import it
+ * statically for `jbrequire`, which put the whole surface — most of
+ * `@jbrowse/core/ui` and, behind it, ~400 KB of Material UI — into the eager
+ * first-paint graph of **every** host, including embedded ones that load no
+ * runtime plugin at all. Measured on `products/jbrowse-build-your-own`'s
+ * examples site: 128 fewer eager chunks, 299 KB raw / 126 KB gzipped.
+ *
+ * Nothing can call `jbrequire` before a runtime plugin exists, and the only way
+ * one exists is `PluginLoader.load()`, which is async — so the registry is
+ * imported there and parked here for the synchronous `jbrequire` to find. This
+ * module deliberately imports nothing, so holding the slot costs no graph.
+ */
+let registry = {};
+export function setReExportRegistry(libs) {
+    registry = libs;
+}
+export function getReExportRegistry() {
+    return registry;
+}

package/esm/TextSearch/BaseResults.d.ts

@@ -1,46 +1,45 @@
-import type React from 'react';
-import type { SearchType } from '../data_adapters/BaseAdapter/index.ts';
-import type TextSearchAdapterType from '../pluggableElementTypes/TextSearchAdapterType.ts';
 export interface BaseResultArgs {
+    /** #resultField primary display text, and the fallback for `displayString` */
     label: string;
+    /** #resultField alternate display text; falls back to `label` */
     displayString?: string;
-    renderingComponent?: React.ReactElement;
-    matchedAttribute?: string;
-    matchedObject?: object;
-    textSearchAdapter?: TextSearchAdapterType;
-    relevance?: SearchType;
+    /** #resultField where to navigate, e.g. `chr1:1000..2000`. A hit with neither this nor `results` is treated as a refName */
     locString?: string;
+    /** #resultField a refName to navigate to; `RefSequenceResult` reads it in place of `locString` */
     refName?: string;
+    /** #resultField the track to open or highlight alongside the navigation */
     trackId?: string;
-    score?: number;
+    /** #resultField nested hits, shown as a disambiguation dialog instead of navigating */
     results?: BaseResult[];
+    /**
+     * #resultField this hit matched the query exactly, as the adapter judges it
+     *
+     * Whether this hit matched the query exactly, as the adapter judges it —
+     * which is not something a caller can recompute. Trix calls a hit exact when
+     * *any* indexed attribute equals the query, so searching a feature's ID
+     * matches exactly even though neither the label nor the display string is
+     * the query. Set it and a single unrestricted search answers both "what
+     * matches?" and "what matches precisely?"; leave it unset and an adapter's
+     * results simply never win the exact-first pass.
+     */
+    exact?: boolean;
 }
 export default class BaseResult {
     label: string;
-    renderingComponent?: React.ReactElement;
     displayString?: string;
-    matchedAttribute?: string;
-    matchedObject?: object;
-    textSearchAdapter?: TextSearchAdapterType;
-    relevance?: SearchType;
     trackId?: string;
-    score: number;
     locString?: string;
     results?: BaseResult[];
+    exact?: boolean;
     constructor(args: BaseResultArgs);
     getLabel(): string;
     getDisplayString(): string;
-    getRenderingComponent(): React.ReactElement<unknown, string | React.JSXElementConstructor<any>> | undefined;
     getTrackId(): string | undefined;
-    getScore(): number;
-    updateScore(newScore: number): number;
     getId(): string;
+    isExact(): boolean;
     hasLocation(): boolean;
     getLocation(): string | undefined;
-    getComboResults(): BaseResult[] | undefined;
 }
 export declare class RefSequenceResult extends BaseResult {
-    refName: string;
     constructor(args: BaseResultArgs);
-    getLocation(): string;
 }

package/esm/TextSearch/BaseResults.js

@@ -1,27 +1,17 @@
 export default class BaseResult {
     label;
-    renderingComponent;
     displayString;
-    matchedAttribute;
-    matchedObject;
-    textSearchAdapter;
-    relevance;
     trackId;
-    score;
     locString;
     results;
+    exact;
     constructor(args) {
         this.label = args.label;
         this.locString = args.locString;
-        this.renderingComponent = args.renderingComponent;
         this.displayString = args.displayString;
-        this.matchedAttribute = args.matchedAttribute;
-        this.matchedObject = args.matchedObject;
-        this.textSearchAdapter = args.textSearchAdapter;
-        this.relevance = args.relevance;
         this.trackId = args.trackId;
-        this.score = args.score || 1;
-        this.results = args.results || [];
+        this.results = args.results;
+        this.exact = args.exact;
     }
     getLabel() {
         return this.label;
@@ -29,21 +19,14 @@ export default class BaseResult {
     getDisplayString() {
         return this.displayString || this.label;
     }
-    getRenderingComponent() {
-        return this.renderingComponent;
-    }
     getTrackId() {
         return this.trackId;
     }
-    getScore() {
-        return this.score;
-    }
-    updateScore(newScore) {
-        this.score = newScore;
-        return this.score;
-    }
     getId() {
-        return `${this.getLabel()}-${this.getLocation()}-${this.getTrackId()}`;
+        return `${this.label}-${this.locString}-${this.trackId}`;
+    }
+    isExact() {
+        return !!this.exact;
     }
     hasLocation() {
         return !!this.locString;
@@ -51,17 +34,9 @@ export default class BaseResult {
     getLocation() {
         return this.locString;
     }
-    getComboResults() {
-        return this.results;
-    }
 }
 export class RefSequenceResult extends BaseResult {
-    refName;
     constructor(args) {
-        super(args);
-        this.refName = args.refName ?? '';
-    }
-    getLocation() {
-        return this.refName;
+        super({ ...args, locString: args.refName ?? args.locString });
     }
 }

package/esm/TextSearch/TextSearchManager.d.ts

@@ -1,49 +1,29 @@
 import QuickLRU from '../util/QuickLRU/index.ts';
-import type BaseResult from './BaseResults.ts';
 import type PluginManager from '../PluginManager.ts';
 import type { AnyConfigurationModel } from '../configuration/index.ts';
 import type { BaseTextSearchAdapter, BaseTextSearchArgs } from '../data_adapters/BaseAdapter/index.ts';
-export interface SearchScope {
-    includeAggregateIndexes: boolean;
-    assemblyName: string;
-    tracks?: string[];
-}
+import type BaseResult from './BaseResults.ts';
 export default class TextSearchManager {
     pluginManager: PluginManager;
     adapterCache: QuickLRU<string, BaseTextSearchAdapter>;
     constructor(pluginManager: PluginManager);
     clearCache(): void;
-    loadTextSearchAdapters(searchScope: SearchScope): Promise<BaseTextSearchAdapter[]>;
-    relevantAdapters(searchScope: SearchScope): ({
-        [x: string]: any;
-    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("../configuration/types.ts").AnyConfigurationSchemaType>);
+    loadTextSearchAdapters(assemblyName: string): Promise<BaseTextSearchAdapter[]>;
+    relevantAdapters(assemblyName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
+        setSubschema(slotName: string, data: Record<string, unknown>): any;
+        setSlot(slotName: string, value: unknown): void;
     } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("../configuration/types.ts").AnyConfigurationSchemaType>)[];
-    getAdaptersWithAssembly(assemblyName: string, confs: AnyConfigurationModel[]): ({
-        [x: string]: any;
-    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("../configuration/types.ts").AnyConfigurationSchemaType>);
+    getAdaptersWithAssembly(matches: (names: string[] | undefined) => boolean, confs: AnyConfigurationModel[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
+        setSubschema(slotName: string, data: Record<string, unknown>): any;
+        setSlot(slotName: string, value: unknown): void;
     } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("../configuration/types.ts").AnyConfigurationSchemaType>)[];
-    getTrackAdaptersWithAssembly(assemblyName: string, confs: AnyConfigurationModel[]): ({
-        [x: string]: any;
-    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("../configuration/types.ts").AnyConfigurationSchemaType>);
+    getTrackAdaptersWithAssembly(matches: (names: string[] | undefined) => boolean, confs: AnyConfigurationModel[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
+        setSubschema(slotName: string, data: Record<string, unknown>): any;
+        setSlot(slotName: string, value: unknown): void;
     } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("../configuration/types.ts").AnyConfigurationSchemaType>)[];
-    search(args: BaseTextSearchArgs, searchScope: SearchScope, rankFn: (results: BaseResult[]) => BaseResult[]): Promise<BaseResult[]>;
-    search2({ args, searchScope, rankFn, }: {
-        args: BaseTextSearchArgs;
-        searchScope: SearchScope;
-        rankFn: (results: BaseResult[]) => BaseResult[];
-    }): Promise<BaseResult[]>;
-    sortResults2({ results, rankFn, args, }: {
+    search(args: BaseTextSearchArgs, assemblyName: string): Promise<BaseResult[]>;
+    sortResults({ results, args, }: {
         results: BaseResult[];
         args: BaseTextSearchArgs;
-        rankFn: (results: BaseResult[]) => BaseResult[];
-    }): BaseResult[];
+    }): Promise<BaseResult[]>;
 }

package/esm/TextSearch/TextSearchManager.js

@@ -1,6 +1,26 @@
-import uFuzzy from '@leeoniya/ufuzzy';
-import { readConfObject } from "../configuration/index.js";
-import QuickLRU from "../util/QuickLRU/index.js";
+import { readConfObject } from '../configuration/index.js';
+import QuickLRU from '../util/QuickLRU/index.js';
+import { isAbortException } from '../util/aborting.js';
+import { checkStopToken } from '../util/stopToken.js';
+import { canonicalAssemblyNames } from '../util/tracks.js';
+// A misconfigured or unreachable index (a 404 .ix, a config missing
+// ixFilePath) must not take down search as a whole: the remaining indexes, and
+// the refName results the caller merges in afterwards, are still useful. Log
+// the failures and keep going rather than rejecting. An abort is not a failure
+// — every keystroke supersedes the previous query, so logging those would turn
+// normal typing into console spam.
+async function keepFulfilled(promises, message) {
+    const out = [];
+    for (const settled of await Promise.allSettled(promises)) {
+        if (settled.status === 'fulfilled') {
+            out.push(settled.value);
+        }
+        else if (!isAbortException(settled.reason)) {
+            console.error(message, settled.reason);
+        }
+    }
+    return out;
+}
 export default class TextSearchManager {
     pluginManager;
     adapterCache = new QuickLRU({
@@ -12,8 +32,8 @@ export default class TextSearchManager {
     clearCache() {
         this.adapterCache.clear();
     }
-    loadTextSearchAdapters(searchScope) {
-        return Promise.all(this.relevantAdapters(searchScope).map(async (conf) => {
+    loadTextSearchAdapters(assemblyName) {
+        return keepFulfilled(this.relevantAdapters(assemblyName).map(async (conf) => {
             const adapterId = readConfObject(conf, 'textSearchAdapterId');
             const r = this.adapterCache.get(adapterId);
             if (r) {
@@ -26,55 +46,88 @@ export default class TextSearchManager {
                 this.adapterCache.set(adapterId, adapterInstance);
                 return adapterInstance;
             }
-        }));
+        }), 'failed to load text search adapter');
     }
-    relevantAdapters(searchScope) {
-        const rootModel = this.pluginManager.rootModel;
-        const { aggregateTextSearchAdapters } = rootModel?.jbrowse;
-        const { tracks } = rootModel?.session;
-        const { assemblyName } = searchScope;
+    relevantAdapters(assemblyName) {
+        const { rootModel } = this.pluginManager;
+        // jbrowse is typed as a bare state tree node, so its config slots need a
+        // shape assertion; both it and the session are absent until a session is
+        // loaded, which is before anything can search
+        const { aggregateTextSearchAdapters = [] } = (rootModel?.jbrowse ?? {});
+        // The caller searches an assembly by the name the session knows it by,
+        // while an index names whatever the track it was built from named — so both
+        // sides go through the aliases, as every other "does this belong to this
+        // assembly" test in the app now does. Absent a session there is nothing to
+        // resolve against and the raw name is the best available answer.
+        const assemblyManager = rootModel?.session?.assemblyManager;
+        const canonical = (names) => assemblyManager
+            ? canonicalAssemblyNames(names, assemblyManager)
+            : names.filter(name => !!name);
+        const [wanted] = canonical([assemblyName]);
+        const matches = (names) => !!wanted && !!names && canonical(names).includes(wanted);
         return [
-            ...this.getAdaptersWithAssembly(assemblyName, aggregateTextSearchAdapters),
-            ...this.getTrackAdaptersWithAssembly(assemblyName, tracks),
+            ...this.getAdaptersWithAssembly(matches, aggregateTextSearchAdapters),
+            ...this.getTrackAdaptersWithAssembly(matches, rootModel?.session?.tracks ?? []),
         ];
     }
-    getAdaptersWithAssembly(assemblyName, confs) {
-        return confs.filter(c => readConfObject(c, 'assemblyNames')?.includes(assemblyName));
+    getAdaptersWithAssembly(matches, confs) {
+        return confs.filter(c => matches(readConfObject(c, 'assemblyNames')));
     }
-    getTrackAdaptersWithAssembly(assemblyName, confs) {
+    getTrackAdaptersWithAssembly(matches, confs) {
         return confs
-            .filter(conf => readConfObject(conf, [
+            .filter(conf => matches(readConfObject(conf, [
             'textSearching',
             'textSearchAdapter',
             'assemblyNames',
-        ])?.includes(assemblyName))
+        ])))
             .map(conf => conf.textSearching.textSearchAdapter);
     }
-    async search(args, searchScope, rankFn) {
-        return this.search2({ args, searchScope, rankFn });
-    }
-    async search2({ args, searchScope, rankFn, }) {
-        const adapters = await this.loadTextSearchAdapters(searchScope);
-        const results = await Promise.all(adapters.map(a => a.searchIndex(args)));
-        return this.sortResults2({
-            args,
-            results: results.flat(),
-            rankFn,
-        });
+    async search(args, assemblyName) {
+        const adapters = await this.loadTextSearchAdapters(assemblyName);
+        const results = await keepFulfilled(adapters.map(a => a.searchIndex(args)), 'text search adapter failed');
+        // the ranking below is the expensive half — a dynamic import plus a fuzzy
+        // sort over every hit — and a superseded keystroke has no use for it.
+        // Checked here rather than only inside the adapters because keepFulfilled
+        // deliberately drops a failing adapter and carries on, so an abort thrown
+        // by one of them would otherwise still land here as "no results from that
+        // index" and rank the rest
+        checkStopToken(args.stopToken);
+        return await this.sortResults({ args, results: results.flat() });
     }
-    sortResults2({ results, rankFn, args, }) {
+    // Ranks, never filters: the adapters have already decided what matches, and
+    // they match against attributes the display string does not always carry (a
+    // multi-word query hits e.g. the description while the display string is just
+    // the gene name). uFuzzy floats the results whose display string matches the
+    // query to the top and the rest keep their adapter order behind them.
+    //
+    // uFuzzy is imported here rather than at the top of the file so its 26KB stay
+    // out of the startup bundle: TextSearchManager is constructed by BaseRootModel
+    // on every page load, but nothing ranks results until the user searches.
+    async sortResults({ results, args, }) {
+        const { default: uFuzzy } = await import('@leeoniya/ufuzzy');
         const uf = new uFuzzy({});
+        // this code sample relatively unmodified from
+        // https://github.com/leeoniya/uFuzzy?tab=readme-ov-file#example
         const haystack = results.map(r => r.getDisplayString());
         const needle = args.queryString;
+        // false positive, this is not Array.prototype.filter
         const idxs = uf.filter(haystack, needle);
-        const res = [];
-        if (idxs != null && idxs.length > 0) {
+        const ranked = [];
+        const seen = new Set();
+        // idxs can be null when the needle is non-searchable (has no alpha-numeric chars)
+        if (idxs?.length) {
             const info = uf.info(idxs, haystack, needle);
+            // order is a double-indirection array (a re-order of the passed-in idxs)
+            // this allows corresponding info to be grabbed directly by idx, if needed
             const order = uf.sort(info, haystack, needle);
             for (const element of order) {
-                res.push(results[info.idx[element]]);
+                // using info.idx here instead of idxs because uf.info() may have
+                // further reduced the initial idxs based on prefix/suffix rules
+                const idx = info.idx[element];
+                seen.add(idx);
+                ranked.push(results[idx]);
             }
         }
-        return rankFn(res);
+        return [...ranked, ...results.filter((_, i) => !seen.has(i))];
     }
 }