@jbrowse/plugin-linear-genome-view 1.7.11 → 2.1.0

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js

@@ -0,0 +1,541 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import React from 'react';
+import { Button, Typography } from '@mui/material';
+import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models';
+import { getConf } from '@jbrowse/core/configuration';
+import { isAbortException, getContainingView, getContainingTrack, getSession, getViewParams, isSelectionContainer, isSessionModelWithWidgets, } from '@jbrowse/core/util';
+import CompositeMap from '@jbrowse/core/util/compositeMap';
+import { isFeature } from '@jbrowse/core/util/simpleFeature';
+import { getParentRenderProps, getRpcSessionId, } from '@jbrowse/core/util/tracks';
+import { autorun } from 'mobx';
+import { addDisposer, isAlive, types } from 'mobx-state-tree';
+// icons
+import MenuOpenIcon from '@mui/icons-material/MenuOpen';
+import { Tooltip } from '../components/BaseLinearDisplay';
+import BlockState, { renderBlockData } from './serverSideRenderedBlock';
+// stabilize clipid under test for snapshot
+function getId(id, index) {
+    const isJest = typeof jest === 'undefined';
+    return `clip-${isJest ? id : 'jest'}-${index}`;
+}
+function getDisplayStr(totalBytes) {
+    let displayBp;
+    if (Math.floor(totalBytes / 1000000) > 0) {
+        displayBp = `${parseFloat((totalBytes / 1000000).toPrecision(3))} Mb`;
+    }
+    else if (Math.floor(totalBytes / 1000) > 0) {
+        displayBp = `${parseFloat((totalBytes / 1000).toPrecision(3))} Kb`;
+    }
+    else {
+        displayBp = `${Math.floor(totalBytes)} bytes`;
+    }
+    return displayBp;
+}
+const minDisplayHeight = 20;
+const defaultDisplayHeight = 100;
+export const BaseLinearDisplay = types
+    .compose('BaseLinearDisplay', BaseDisplay, types.model({
+    height: types.optional(types.refinement('displayHeight', types.number, n => n >= minDisplayHeight), defaultDisplayHeight),
+    blockState: types.map(BlockState),
+    userBpPerPxLimit: types.maybe(types.number),
+    userByteSizeLimit: types.maybe(types.number),
+}))
+    .volatile(() => ({
+    currBpPerPx: 0,
+    message: '',
+    featureIdUnderMouse: undefined,
+    contextMenuFeature: undefined,
+    scrollTop: 0,
+    estimatedRegionStatsP: undefined,
+    estimatedRegionStats: undefined,
+}))
+    .views(self => ({
+    get blockType() {
+        return 'staticBlocks';
+    },
+    get blockDefinitions() {
+        const { blockType } = this;
+        const view = getContainingView(self);
+        if (!view.initialized) {
+            throw new Error('view not initialized yet');
+        }
+        return view[blockType];
+    },
+}))
+    .views(self => ({
+    /**
+     * how many milliseconds to wait for the display to
+     * "settle" before re-rendering a block
+     */
+    get renderDelay() {
+        return 50;
+    },
+    get TooltipComponent() {
+        return Tooltip;
+    },
+    /**
+     * returns a string feature ID if the globally-selected object
+     * is probably a feature
+     */
+    get selectedFeatureId() {
+        if (isAlive(self)) {
+            const { selection } = getSession(self);
+            // does it quack like a feature?
+            if (isFeature(selection)) {
+                return selection.id();
+            }
+        }
+        return undefined;
+    },
+    /**
+     * if a display-level message should be displayed instead of the blocks,
+     * make this return a react component
+     */
+    get DisplayMessageComponent() {
+        return undefined;
+    },
+}))
+    .views(self => ({
+    /**
+     * a CompositeMap of `featureId -> feature obj` that
+     * just looks in all the block data for that feature
+     */
+    get features() {
+        const featureMaps = [];
+        for (const block of self.blockState.values()) {
+            if (block && block.features) {
+                featureMaps.push(block.features);
+            }
+        }
+        return new CompositeMap(featureMaps);
+    },
+    get featureUnderMouse() {
+        const feat = self.featureIdUnderMouse;
+        return feat ? this.features.get(feat) : undefined;
+    },
+    getFeatureOverlapping(blockKey, x, y) {
+        var _a, _b;
+        return (_b = (_a = self.blockState.get(blockKey)) === null || _a === void 0 ? void 0 : _a.layout) === null || _b === void 0 ? void 0 : _b.getByCoord(x, y);
+    },
+    getFeatureByID(blockKey, id) {
+        var _a, _b;
+        return (_b = (_a = self.blockState.get(blockKey)) === null || _a === void 0 ? void 0 : _a.layout) === null || _b === void 0 ? void 0 : _b.getByID(id);
+    },
+    // if block key is not supplied, can look at all blocks
+    searchFeatureByID(id) {
+        let ret;
+        self.blockState.forEach(block => {
+            var _a;
+            const val = (_a = block === null || block === void 0 ? void 0 : block.layout) === null || _a === void 0 ? void 0 : _a.getByID(id);
+            if (val) {
+                ret = val;
+            }
+        });
+        return ret;
+    },
+    get currentBytesRequested() {
+        var _a;
+        return ((_a = self.estimatedRegionStats) === null || _a === void 0 ? void 0 : _a.bytes) || 0;
+    },
+    get currentFeatureScreenDensity() {
+        var _a;
+        const view = getContainingView(self);
+        return (((_a = self.estimatedRegionStats) === null || _a === void 0 ? void 0 : _a.featureDensity) || 0) * view.bpPerPx;
+    },
+    get maxFeatureScreenDensity() {
+        return getConf(self, 'maxFeatureScreenDensity');
+    },
+    get estimatedStatsReady() {
+        return !!self.estimatedRegionStats;
+    },
+    get maxAllowableBytes() {
+        var _a;
+        return (self.userByteSizeLimit ||
+            ((_a = self.estimatedRegionStats) === null || _a === void 0 ? void 0 : _a.fetchSizeLimit) ||
+            getConf(self, 'fetchSizeLimit'));
+    },
+}))
+    .actions(self => ({
+    // base display reload does nothing, see specialized displays for details
+    setMessage(message) {
+        self.message = message;
+    },
+    afterAttach() {
+        // watch the parent's blocks to update our block state when they change,
+        // then we recreate the blocks on our own model (creating and deleting to
+        // match the parent blocks)
+        const blockWatchDisposer = autorun(() => {
+            const blocksPresent = {};
+            const view = getContainingView(self);
+            if (view.initialized) {
+                self.blockDefinitions.contentBlocks.forEach(block => {
+                    blocksPresent[block.key] = true;
+                    if (!self.blockState.has(block.key)) {
+                        this.addBlock(block.key, block);
+                    }
+                });
+                self.blockState.forEach((_, key) => {
+                    if (!blocksPresent[key]) {
+                        this.deleteBlock(key);
+                    }
+                });
+            }
+        });
+        addDisposer(self, blockWatchDisposer);
+    },
+    estimateRegionsStats(regions, opts) {
+        if (self.estimatedRegionStatsP) {
+            return self.estimatedRegionStatsP;
+        }
+        const { rpcManager } = getSession(self);
+        const { adapterConfig } = self;
+        if (!adapterConfig) {
+            // A track extending the base track might not have an adapter config
+            // e.g. Apollo tracks don't use adapters
+            return Promise.resolve({});
+        }
+        const sessionId = getRpcSessionId(self);
+        const params = {
+            sessionId,
+            regions,
+            adapterConfig,
+            statusCallback: (message) => {
+                if (isAlive(self)) {
+                    this.setMessage(message);
+                }
+            },
+            ...opts,
+        };
+        self.estimatedRegionStatsP = rpcManager
+            .call(sessionId, 'CoreEstimateRegionStats', params)
+            .catch(e => {
+            this.setRegionStatsP(undefined);
+            throw e;
+        });
+        return self.estimatedRegionStatsP;
+    },
+    setRegionStatsP(p) {
+        self.estimatedRegionStatsP = p;
+    },
+    setRegionStats(estimatedRegionStats) {
+        self.estimatedRegionStats = estimatedRegionStats;
+    },
+    clearRegionStats() {
+        self.estimatedRegionStatsP = undefined;
+        self.estimatedRegionStats = undefined;
+    },
+    setHeight(displayHeight) {
+        if (displayHeight > minDisplayHeight) {
+            self.height = displayHeight;
+        }
+        else {
+            self.height = minDisplayHeight;
+        }
+        return self.height;
+    },
+    resizeHeight(distance) {
+        const oldHeight = self.height;
+        const newHeight = this.setHeight(self.height + distance);
+        return newHeight - oldHeight;
+    },
+    setScrollTop(scrollTop) {
+        self.scrollTop = scrollTop;
+    },
+    updateStatsLimit(stats) {
+        const view = getContainingView(self);
+        if (stats.bytes) {
+            self.userByteSizeLimit = stats.bytes;
+        }
+        else {
+            self.userBpPerPxLimit = view.bpPerPx;
+        }
+    },
+    addBlock(key, block) {
+        self.blockState.set(key, BlockState.create({
+            key,
+            region: block.toRegion(),
+        }));
+    },
+    setCurrBpPerPx(n) {
+        self.currBpPerPx = n;
+    },
+    deleteBlock(key) {
+        self.blockState.delete(key);
+    },
+    selectFeature(feature) {
+        const session = getSession(self);
+        if (isSessionModelWithWidgets(session)) {
+            const featureWidget = session.addWidget('BaseFeatureWidget', 'baseFeature', {
+                view: getContainingView(self),
+                track: getContainingTrack(self),
+                featureData: feature.toJSON(),
+            });
+            session.showWidget(featureWidget);
+        }
+        if (isSelectionContainer(session)) {
+            session.setSelection(feature);
+        }
+    },
+    clearFeatureSelection() {
+        const session = getSession(self);
+        session.clearSelection();
+    },
+    setFeatureIdUnderMouse(feature) {
+        self.featureIdUnderMouse = feature;
+    },
+    reload() {
+        ;
+        [...self.blockState.values()].map(val => val.doReload());
+    },
+    setContextMenuFeature(feature) {
+        self.contextMenuFeature = feature;
+    },
+}))
+    .views(self => ({
+    // region is too large if:
+    // - stats are ready
+    // - region is greater than 20kb (don't warn when zoomed in less than that)
+    // - and bytes > max allowed bytes || curr density>max density
+    get regionTooLarge() {
+        const view = getContainingView(self);
+        if (!self.estimatedStatsReady || view.dynamicBlocks.totalBp < 20000) {
+            return false;
+        }
+        const bpLimitOrDensity = self.userBpPerPxLimit
+            ? view.bpPerPx > self.userBpPerPxLimit
+            : self.currentFeatureScreenDensity > self.maxFeatureScreenDensity;
+        return (self.currentBytesRequested > self.maxAllowableBytes || bpLimitOrDensity);
+    },
+    // only shows a message of bytes requested is defined, the feature density
+    // based stats don't produce any helpful message besides to zoom in
+    get regionTooLargeReason() {
+        const req = self.currentBytesRequested;
+        const max = self.maxAllowableBytes;
+        return req && req > max
+            ? `Requested too much data (${getDisplayStr(req)})`
+            : '';
+    },
+}))
+    .actions(self => {
+    const { reload: superReload } = self;
+    return {
+        async reload() {
+            self.setError();
+            const aborter = new AbortController();
+            const view = getContainingView(self);
+            // extra check for contentBlocks.length
+            // https://github.com/GMOD/jbrowse-components/issues/2694
+            if (!view.initialized || !view.staticBlocks.contentBlocks.length) {
+                return;
+            }
+            try {
+                self.estimatedRegionStatsP = self.estimateRegionsStats(view.staticBlocks.contentBlocks, { signal: aborter.signal });
+                const estimatedRegionStats = await self.estimatedRegionStatsP;
+                if (isAlive(self)) {
+                    self.setRegionStats(estimatedRegionStats);
+                    superReload();
+                }
+                else {
+                    return;
+                }
+            }
+            catch (e) {
+                console.error(e);
+                self.setError(e);
+            }
+        },
+        afterAttach() {
+            // this autorun performs stats estimation
+            //
+            // the chain of events calls estimateRegionsStats against the data
+            // adapter which by default uses featureDensity, but can also respond
+            // with a byte size estimate and fetch size limit (data adapter can
+            // define what is too much data)
+            addDisposer(self, autorun(async () => {
+                var _a;
+                try {
+                    const aborter = new AbortController();
+                    const view = getContainingView(self);
+                    // extra check for contentBlocks.length
+                    // https://github.com/GMOD/jbrowse-components/issues/2694
+                    if (!view.initialized ||
+                        !view.staticBlocks.contentBlocks.length) {
+                        return;
+                    }
+                    // don't re-estimate featureDensity even if zoom level changes,
+                    // jbrowse1-style assume it's sort of representative
+                    if (((_a = self.estimatedRegionStats) === null || _a === void 0 ? void 0 : _a.featureDensity) !== undefined) {
+                        self.setCurrBpPerPx(view.bpPerPx);
+                        return;
+                    }
+                    // we estimate stats once at a given zoom level
+                    if (view.bpPerPx === self.currBpPerPx) {
+                        return;
+                    }
+                    self.clearRegionStats();
+                    self.setCurrBpPerPx(view.bpPerPx);
+                    const statsP = self.estimateRegionsStats(view.staticBlocks.contentBlocks, { signal: aborter.signal });
+                    self.setRegionStatsP(statsP);
+                    const estimatedRegionStats = await statsP;
+                    if (isAlive(self)) {
+                        self.setRegionStats(estimatedRegionStats);
+                    }
+                }
+                catch (e) {
+                    if (!isAbortException(e) && isAlive(self)) {
+                        console.error(e);
+                        self.setError(e);
+                    }
+                }
+            }, { delay: 500 }));
+        },
+    };
+})
+    .views(self => ({
+    regionCannotBeRenderedText(_region) {
+        return self.regionTooLarge ? 'Force load to see features' : '';
+    },
+    /**
+     * @param region -
+     * @returns falsy if the region is fine to try rendering. Otherwise,
+     *  return a react node + string of text.
+     *  string of text describes why it cannot be rendered
+     *  react node allows user to force load at current setting
+     */
+    regionCannotBeRendered(_region) {
+        const { regionTooLarge, regionTooLargeReason } = self;
+        if (regionTooLarge) {
+            return (React.createElement(React.Fragment, null,
+                React.createElement(Typography, { component: "span", variant: "body2" },
+                    regionTooLargeReason ? regionTooLargeReason + '. ' : '',
+                    "Zoom in to see features or",
+                    ' '),
+                React.createElement(Button, { "data-testid": "force_reload_button", onClick: () => {
+                        if (!self.estimatedRegionStats) {
+                            console.error('No global stats?');
+                        }
+                        else {
+                            self.updateStatsLimit(self.estimatedRegionStats);
+                            self.reload();
+                        }
+                    }, variant: "outlined" }, "Force Load"),
+                React.createElement(Typography, { component: "span", variant: "body2" }, "(force load may be slow)")));
+        }
+        return undefined;
+    },
+    trackMenuItems() {
+        return [];
+    },
+    contextMenuItems() {
+        return self.contextMenuFeature
+            ? [
+                {
+                    label: 'Open feature details',
+                    icon: MenuOpenIcon,
+                    onClick: () => {
+                        if (self.contextMenuFeature) {
+                            self.selectFeature(self.contextMenuFeature);
+                        }
+                    },
+                },
+            ]
+            : [];
+    },
+    renderProps() {
+        const view = getContainingView(self);
+        return {
+            ...getParentRenderProps(self),
+            notReady: self.currBpPerPx !== view.bpPerPx || !self.estimatedRegionStats,
+            rpcDriverName: self.rpcDriverName,
+            displayModel: self,
+            onFeatureClick(_, featureId) {
+                const f = featureId || self.featureIdUnderMouse;
+                if (!f) {
+                    self.clearFeatureSelection();
+                }
+                else {
+                    const feature = self.features.get(f);
+                    if (feature) {
+                        self.selectFeature(feature);
+                    }
+                }
+            },
+            onClick() {
+                self.clearFeatureSelection();
+            },
+            // similar to click but opens a menu with further options
+            onFeatureContextMenu(_, featureId) {
+                const f = featureId || self.featureIdUnderMouse;
+                if (!f) {
+                    self.clearFeatureSelection();
+                }
+                else {
+                    // feature id under mouse passed to context menu
+                    self.setContextMenuFeature(self.features.get(f));
+                }
+            },
+            onMouseMove(_, featureId) {
+                self.setFeatureIdUnderMouse(featureId);
+            },
+            onMouseLeave(_) {
+                self.setFeatureIdUnderMouse(undefined);
+            },
+            onContextMenu() {
+                self.setContextMenuFeature(undefined);
+                self.clearFeatureSelection();
+            },
+        };
+    },
+}))
+    .actions(self => ({
+    async renderSvg(opts) {
+        const { height, id } = self;
+        const { overrideHeight } = opts;
+        const view = getContainingView(self);
+        const { offsetPx: viewOffsetPx, roundedDynamicBlocks, width } = view;
+        const renderings = await Promise.all(roundedDynamicBlocks.map(block => {
+            const blockState = BlockState.create({
+                key: block.key,
+                region: block,
+            });
+            // regionCannotBeRendered can return jsx so look for plaintext
+            // version, or just get the default if none available
+            const cannotBeRenderedReason = self.regionCannotBeRenderedText(block) ||
+                self.regionCannotBeRendered(block);
+            if (cannotBeRenderedReason) {
+                return {
+                    reactElement: (React.createElement(React.Fragment, null,
+                        React.createElement("rect", { x: 0, y: 0, width: width, height: 20, fill: "#aaa" }),
+                        React.createElement("text", { x: 0, y: 15 }, cannotBeRenderedReason))),
+                };
+            }
+            const { rpcManager, renderArgs, renderProps, rendererType } = renderBlockData(blockState, self);
+            return rendererType.renderInClient(rpcManager, {
+                ...renderArgs,
+                ...renderProps,
+                viewParams: getViewParams(self, true),
+                exportSVG: opts,
+            });
+        }));
+        return (React.createElement(React.Fragment, null, renderings.map((rendering, index) => {
+            const { offsetPx } = roundedDynamicBlocks[index];
+            const offset = offsetPx - viewOffsetPx;
+            const clipid = getId(id, index);
+            return (React.createElement(React.Fragment, { key: `frag-${index}` },
+                React.createElement("defs", null,
+                    React.createElement("clipPath", { id: clipid },
+                        React.createElement("rect", { x: 0, y: 0, width: width, height: overrideHeight || height }))),
+                React.createElement("g", { transform: `translate(${offset} 0)` },
+                    React.createElement("g", { clipPath: `url(#${clipid})` }, React.isValidElement(rendering.reactElement) ? (rendering.reactElement) : (
+                    // eslint-disable-next-line react/no-danger
+                    React.createElement("g", { dangerouslySetInnerHTML: { __html: rendering.html } }))))));
+        })));
+    },
+}))
+    .postProcessSnapshot(self => {
+    // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+    const r = self;
+    const { blockState, ...rest } = r;
+    return rest;
+});
+//# sourceMappingURL=BaseLinearDisplayModel.js.map

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js.map

@@ -0,0 +1 @@
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package/esm/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.d.ts

@@ -0,0 +1 @@
+export declare const baseLinearDisplayConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.js

@@ -0,0 +1,14 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export const baseLinearDisplayConfigSchema = ConfigurationSchema('BaseLinearDisplay', {
+    maxFeatureScreenDensity: {
+        type: 'number',
+        description: 'maximum features per pixel that is displayed in the view, used if byte size estimates not available',
+        defaultValue: 0.3,
+    },
+    fetchSizeLimit: {
+        type: 'number',
+        defaultValue: 1000000,
+        description: "maximum data to attempt to download for a given track, used if adapter doesn't specify one",
+    },
+}, { explicitIdentifier: 'displayId' });
+//# sourceMappingURL=baseLinearDisplayConfigSchema.js.map

package/esm/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.js.map

@@ -0,0 +1 @@
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