@jbrowse/plugin-data-management 1.7.11 → 2.0.0

package/esm/HierarchicalTrackSelectorWidget/model.js

@@ -0,0 +1,200 @@
+import { types, getParent } from 'mobx-state-tree';
+import { getConf, readConfObject, } from '@jbrowse/core/configuration';
+import { getSession } from '@jbrowse/core/util';
+import { ElementId } from '@jbrowse/core/util/types/mst';
+function hasAnyOverlap(a1 = [], a2 = []) {
+    return !!a1.find(value => a2.includes(value));
+}
+function passesFilter(filter, config) {
+    const categories = readConfObject(config, 'category');
+    const filterLower = filter.toLowerCase();
+    return (getTrackName(config).toLowerCase().includes(filterLower) ||
+        (categories === null || categories === void 0 ? void 0 : categories.filter(c => c.toLowerCase().includes(filterLower)).length));
+}
+function getTrackName(config) {
+    if (!config.trackId) {
+        throw new Error('not a track');
+    }
+    return (readConfObject(config, 'name') ||
+        `Reference sequence (${readConfObject(getParent(config), 'name')})`);
+}
+export function generateHierarchy(model, trackConfigurations, collapsed) {
+    const hierarchy = { children: [] };
+    const { filterText, view } = model;
+    trackConfigurations
+        .filter(conf => passesFilter(filterText, conf))
+        .forEach(conf => {
+        // copy the categories since this array can be mutated downstream
+        const categories = [...(readConfObject(conf, 'category') || [])];
+        // silly thing where if trackId ends with sessionTrack, then push it to
+        // a category that starts with a space to force sort to the top...
+        // double whammy hackyness
+        if (conf.trackId.endsWith('sessionTrack')) {
+            categories.unshift(' Session tracks');
+        }
+        let currLevel = hierarchy;
+        // find existing category to put track into or create it
+        for (let i = 0; i < categories.length; i++) {
+            const category = categories[i];
+            const ret = currLevel.children.find(c => c.name === category);
+            const id = categories.slice(0, i + 1).join(',');
+            if (!ret) {
+                const n = {
+                    children: [],
+                    name: category,
+                    id,
+                    isOpenByDefault: !collapsed.get(id),
+                };
+                currLevel.children.push(n);
+                currLevel = n;
+            }
+            else {
+                currLevel = ret;
+            }
+        }
+        const tracks = view.tracks;
+        // using splice here tries to group leaf nodes above hierarchical nodes
+        currLevel.children.splice(currLevel.children.findIndex(elt => elt.children.length), 0, {
+            id: conf.trackId,
+            name: getTrackName(conf),
+            conf,
+            checked: !!tracks.find(f => f.configuration === conf),
+            children: [],
+        });
+    });
+    return hierarchy.children;
+}
+export default function stateTreeFactory(pluginManager) {
+    return types
+        .model('HierarchicalTrackSelectorWidget', {
+        id: ElementId,
+        type: types.literal('HierarchicalTrackSelectorWidget'),
+        collapsed: types.map(types.boolean),
+        filterText: '',
+        view: types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
+    })
+        .actions(self => ({
+        setView(view) {
+            self.view = view;
+        },
+        toggleCategory(pathName) {
+            self.collapsed.set(pathName, !self.collapsed.get(pathName));
+        },
+        clearFilterText() {
+            self.filterText = '';
+        },
+        setFilterText(newText) {
+            self.filterText = newText;
+        },
+    }))
+        .views(self => ({
+        getRefSeqTrackConf(assemblyName) {
+            const { assemblyManager } = getSession(self);
+            const assembly = assemblyManager.get(assemblyName);
+            const trackConf = assembly === null || assembly === void 0 ? void 0 : assembly.configuration.sequence;
+            const viewType = pluginManager.getViewType(self.view.type);
+            if (!trackConf) {
+                return undefined;
+            }
+            for (const display of trackConf.displays) {
+                if (viewType.displayTypes.find(d => d.name === display.type)) {
+                    return trackConf;
+                }
+            }
+        },
+    }))
+        .views(self => ({
+        trackConfigurations(assemblyName) {
+            if (!self.view) {
+                return [];
+            }
+            const { tracks, assemblyManager } = getSession(self);
+            const assembly = assemblyManager.get(assemblyName);
+            if (!assembly) {
+                return [];
+            }
+            const refseq = self.getRefSeqTrackConf(assemblyName);
+            // filter out tracks that don't match the current assembly (check all
+            // assembly aliases) and display types
+            return (refseq ? [refseq] : []).concat([
+                ...tracks
+                    .filter(c => {
+                    const trackConfAssemblies = readConfObject(c, 'assemblyNames');
+                    const { allAliases } = assembly;
+                    return hasAnyOverlap(allAliases, trackConfAssemblies);
+                })
+                    .filter(c => {
+                    const { displayTypes } = pluginManager.getViewType(self.view.type);
+                    const compatibleDisplays = displayTypes.map(d => d.name);
+                    const trackDisplays = c.displays.map((d) => d.type);
+                    return hasAnyOverlap(compatibleDisplays, trackDisplays);
+                }),
+            ]);
+        },
+        get assemblyNames() {
+            var _a;
+            return ((_a = self.view) === null || _a === void 0 ? void 0 : _a.assemblyNames) || [];
+        },
+        connectionTrackConfigurations(assemblyName, connection) {
+            if (!self.view) {
+                return [];
+            }
+            const trackConfigurations = connection.tracks;
+            const { assemblyManager } = getSession(self);
+            const assembly = assemblyManager.get(assemblyName);
+            if (!(assembly && assembly.initialized)) {
+                return [];
+            }
+            // filter out tracks that don't match the current display types
+            return trackConfigurations
+                .filter(c => {
+                const trackConfAssemblies = readConfObject(c, 'assemblyNames');
+                const { allAliases } = assembly;
+                return hasAnyOverlap(allAliases, trackConfAssemblies);
+            })
+                .filter(c => {
+                const { displayTypes } = pluginManager.getViewType(self.view.type);
+                const compatibleDisplays = displayTypes.map(d => d.name);
+                const trackDisplays = c.displays.map((d) => d.type);
+                return hasAnyOverlap(compatibleDisplays, trackDisplays);
+            });
+        },
+    }))
+        .views(self => ({
+        hierarchy(assemblyName) {
+            const hier = generateHierarchy(
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            self, self.trackConfigurations(assemblyName), self.collapsed);
+            const session = getSession(self);
+            const { connections, connectionInstances } = session;
+            const conns = (connectionInstances === null || connectionInstances === void 0 ? void 0 : connectionInstances.filter(c => {
+                const names = getConf(c, 'assemblyNames');
+                return names.length === 0 ? true : names.includes(assemblyName);
+            }).map((conn, index) => {
+                const c = connections[index];
+                return {
+                    id: c.connectionId,
+                    name: readConfObject(c, 'name'),
+                    children: this.connectionHierarchy(assemblyName, conn),
+                    state: {
+                        expanded: true,
+                    },
+                };
+            })) || [];
+            return {
+                name: 'Root',
+                id: 'Root',
+                children: [
+                    { name: 'Tracks', id: 'Tracks', children: hier },
+                    ...conns,
+                ],
+            };
+        },
+        connectionHierarchy(assemblyName, connection) {
+            return generateHierarchy(
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            self, self.connectionTrackConfigurations(assemblyName, connection), self.collapsed);
+        },
+    }));
+}
+//# sourceMappingURL=model.js.map

package/esm/HierarchicalTrackSelectorWidget/model.js.map

@@ -0,0 +1 @@
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package/esm/PluginStoreWidget/components/CustomPluginForm.d.ts

@@ -0,0 +1,9 @@
+/// <reference types="react" />
+import { PluginStoreModel } from '../model';
+declare function CustomPluginForm({ open, onClose, model, }: {
+    open: boolean;
+    onClose(): void;
+    model: PluginStoreModel;
+}): JSX.Element;
+declare const _default: typeof CustomPluginForm;
+export default _default;

package/esm/PluginStoreWidget/components/CustomPluginForm.js

@@ -0,0 +1,109 @@
+import React, { useState } from 'react';
+import { observer } from 'mobx-react';
+import { getRoot } from 'mobx-state-tree';
+import { Button, Collapse, Dialog, DialogActions, DialogTitle, DialogContent, DialogContentText, TextField, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+// icons
+import IconButton from '@mui/material/IconButton';
+import CloseIcon from '@mui/icons-material/Close';
+import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
+const useStyles = makeStyles()(theme => ({
+    closeButton: {
+        position: 'absolute',
+        right: theme.spacing(1),
+        top: theme.spacing(1),
+    },
+    dialogContent: {
+        display: 'flex',
+        flexDirection: 'column',
+    },
+    expand: {
+        transform: 'rotate(0deg)',
+        marginLeft: 'auto',
+        transition: theme.transitions.create('transform', {
+            duration: theme.transitions.duration.shortest,
+        }),
+    },
+    expandOpen: {
+        transform: 'rotate(180deg)',
+    },
+}));
+function CustomPluginForm({ open, onClose, model, }) {
+    const { classes, cx } = useStyles();
+    const [umdPluginName, setUMDPluginName] = useState('');
+    const [umdPluginUrl, setUMDPluginUrl] = useState('');
+    const [esmPluginUrl, setESMPluginUrl] = useState('');
+    const [cjsPluginUrl, setCJSPluginUrl] = useState('');
+    const [advancedOptionsOpen, setAdvancedOptionsOpen] = useState(false);
+    function handleChange(event) {
+        const { name, value } = event.target;
+        if (name === 'umdName') {
+            setUMDPluginName(value);
+        }
+        if (name === 'umdUrl') {
+            setUMDPluginUrl(value);
+        }
+        if (name === 'esmUrl') {
+            setESMPluginUrl(value);
+        }
+        if (name === 'cjsUrl') {
+            setCJSPluginUrl(value);
+        }
+    }
+    function handleOpenAdvancedOptions() {
+        setAdvancedOptionsOpen(!advancedOptionsOpen);
+    }
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    const { jbrowse } = getRoot(model);
+    const ready = Boolean((umdPluginName && umdPluginUrl) || esmPluginUrl || cjsPluginUrl);
+    function handleSubmit() {
+        if (!ready) {
+            return;
+        }
+        const pluginDefinition = {};
+        if (umdPluginName && umdPluginUrl) {
+            pluginDefinition.name = umdPluginName;
+            pluginDefinition.umdUrl = umdPluginUrl;
+        }
+        if (esmPluginUrl) {
+            pluginDefinition.esmUrl = esmPluginUrl;
+        }
+        if (cjsPluginUrl) {
+            pluginDefinition.cjsUrl = cjsPluginUrl;
+        }
+        jbrowse.addPlugin(pluginDefinition);
+    }
+    function handleClose() {
+        setUMDPluginName('');
+        setUMDPluginUrl('');
+        setESMPluginUrl('');
+        setCJSPluginUrl('');
+        onClose();
+    }
+    return (React.createElement(Dialog, { open: open, onClose: handleClose },
+        React.createElement(DialogTitle, null,
+            "Add custom plugin",
+            React.createElement(IconButton, { size: "medium", className: classes.closeButton, onClick: () => onClose() },
+                React.createElement(CloseIcon, null))),
+        React.createElement("form", { onSubmit: handleSubmit },
+            React.createElement(DialogContent, { className: classes.dialogContent },
+                React.createElement(DialogContentText, null, "Enter the name of the plugin and its URL. The name should match what is defined in the plugin's build."),
+                React.createElement(TextField, { id: "umd-name-input", name: "umdName", label: "Plugin name", variant: "outlined", value: umdPluginName, onChange: handleChange }),
+                React.createElement(TextField, { id: "umd-url-input", name: "umdUrl", label: "Plugin URL", variant: "outlined", value: umdPluginUrl, onChange: handleChange }),
+                React.createElement(DialogContentText, { onClick: handleOpenAdvancedOptions },
+                    React.createElement(IconButton, { className: cx(classes.expand, {
+                            [classes.expandOpen]: advancedOptionsOpen,
+                        }), "aria-expanded": advancedOptionsOpen, "aria-label": "show more" },
+                        React.createElement(ExpandMoreIcon, null)),
+                    "Advanced options"),
+                React.createElement(Collapse, { in: advancedOptionsOpen },
+                    React.createElement("div", { className: classes.dialogContent },
+                        React.createElement(DialogContentText, null, "The above fields assume that the plugin is built in UMD format. If your plugin is in another format, or you have additional builds you want to add (such as a CJS build for using NodeJS APIs in desktop), you can enter the URLs for those builds below."),
+                        React.createElement(TextField, { id: "esm-url-input", name: "esmUrl", label: "ESM build URL", variant: "outlined", value: esmPluginUrl, onChange: handleChange }),
+                        React.createElement(TextField, { id: "cjs-url-input", name: "cjsUrl", label: "CJS build URL", variant: "outlined", value: cjsPluginUrl, onChange: handleChange })))),
+            React.createElement(DialogActions, null,
+                React.createElement(Button, { variant: "contained", onClick: handleClose }, "Cancel"),
+                React.createElement(Button, { variant: "contained", color: "primary", onClick: handleSubmit, disabled: !ready }, "Submit")))));
+}
+export default observer(CustomPluginForm);
+//# sourceMappingURL=CustomPluginForm.js.map

package/esm/PluginStoreWidget/components/CustomPluginForm.js.map

@@ -0,0 +1 @@
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package/esm/PluginStoreWidget/components/InstalledPlugin.d.ts

@@ -0,0 +1,11 @@
+/// <reference types="react" />
+import PluginManager from '@jbrowse/core/PluginManager';
+import { BasePlugin } from '@jbrowse/core/util/types';
+import { PluginStoreModel } from '../model';
+declare function InstalledPlugin({ plugin, model, pluginManager, }: {
+    plugin: BasePlugin;
+    model: PluginStoreModel;
+    pluginManager: PluginManager;
+}): JSX.Element;
+declare const _default: typeof InstalledPlugin;
+export default _default;

package/esm/PluginStoreWidget/components/InstalledPlugin.js

@@ -0,0 +1,77 @@
+import React, { useState } from 'react';
+import { observer } from 'mobx-react';
+import { getParent } from 'mobx-state-tree';
+import { Button, Dialog, DialogTitle, DialogActions, DialogContent, IconButton, ListItem, Tooltip, Typography, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import CloseIcon from '@mui/icons-material/Close';
+import LockIcon from '@mui/icons-material/Lock';
+import { getSession } from '@jbrowse/core/util';
+import { isSessionWithSessionPlugins, } from '@jbrowse/core/util/types';
+const useStyles = makeStyles()(() => ({
+    closeDialog: {
+        position: 'absolute',
+        right: 0,
+        top: 0,
+    },
+    dialogContainer: {
+        margin: 15,
+    },
+    lockedPluginTooltip: {
+        marginRight: '0.5rem',
+    },
+}));
+function LockedPlugin() {
+    const { classes } = useStyles();
+    return (React.createElement(Tooltip, { className: classes.lockedPluginTooltip, title: "This plugin was installed by an administrator, you cannot remove it." },
+        React.createElement(LockIcon, null)));
+}
+function PluginDialog({ onClose, plugin, }) {
+    const { classes } = useStyles();
+    return (React.createElement(Dialog, { open: true, onClose: () => onClose() },
+        React.createElement(DialogTitle, null,
+            React.createElement(IconButton, { className: classes.closeDialog, "aria-label": "close-dialog", onClick: () => onClose() },
+                React.createElement(CloseIcon, null))),
+        React.createElement(DialogContent, null,
+            React.createElement(Typography, null,
+                "Please confirm that you want to remove ",
+                plugin,
+                ". Note: if any resources in this session still use this plugin, it may cause your session to crash"),
+            React.createElement(DialogActions, null,
+                React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
+                        // avoid showing runtime plugin warning
+                        window.setTimeout(() => {
+                            onClose(plugin);
+                        }, 500);
+                    } }, "Confirm"),
+                React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
+                        onClose();
+                    } }, "Cancel")))));
+}
+function InstalledPlugin({ plugin, model, pluginManager, }) {
+    const [dialogPlugin, setDialogPlugin] = useState();
+    const session = getSession(model);
+    const { sessionPlugins } = session;
+    const isSessionPlugin = sessionPlugins === null || sessionPlugins === void 0 ? void 0 : sessionPlugins.some(p => pluginManager.pluginMetadata[plugin.name].url === p.url);
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    const rootModel = getParent(model, 3);
+    const { jbrowse, adminMode } = rootModel;
+    return (React.createElement(React.Fragment, null,
+        dialogPlugin ? (React.createElement(PluginDialog, { plugin: dialogPlugin, onClose: name => {
+                if (name) {
+                    const pluginMetadata = pluginManager.pluginMetadata[plugin.name];
+                    if (adminMode) {
+                        jbrowse.removePlugin(pluginMetadata);
+                    }
+                    else if (isSessionWithSessionPlugins(session)) {
+                        session.removeSessionPlugin(pluginMetadata);
+                    }
+                }
+                setDialogPlugin(undefined);
+            } })) : null,
+        React.createElement(ListItem, { key: plugin.name },
+            adminMode || isSessionPlugin ? (React.createElement(IconButton, { "aria-label": "removePlugin", "data-testid": `removePlugin-${plugin.name}`, onClick: () => setDialogPlugin(plugin.name) },
+                React.createElement(CloseIcon, null))) : (React.createElement(LockedPlugin, null)),
+            React.createElement(Typography, null, plugin.name))));
+}
+export default observer(InstalledPlugin);
+//# sourceMappingURL=InstalledPlugin.js.map

package/esm/PluginStoreWidget/components/InstalledPlugin.js.map

@@ -0,0 +1 @@
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package/esm/PluginStoreWidget/components/InstalledPluginsList.d.ts

@@ -0,0 +1,9 @@
+/// <reference types="react" />
+import PluginManager from '@jbrowse/core/PluginManager';
+import { PluginStoreModel } from '../model';
+declare function InstalledPluginsList({ pluginManager, model, }: {
+    pluginManager: PluginManager;
+    model: PluginStoreModel;
+}): JSX.Element;
+declare const _default: typeof InstalledPluginsList;
+export default _default;

package/esm/PluginStoreWidget/components/InstalledPluginsList.js

@@ -0,0 +1,16 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+import { List, Typography } from '@mui/material';
+import InstalledPlugin from './InstalledPlugin';
+function InstalledPluginsList({ pluginManager, model, }) {
+    const { plugins } = pluginManager;
+    const corePlugins = plugins
+        .filter(p => { var _a; return (_a = pluginManager.pluginMetadata[p.name]) === null || _a === void 0 ? void 0 : _a.isCore; })
+        .map(p => p.name);
+    const externalPlugins = plugins.filter(plugin => !corePlugins.includes(plugin.name));
+    return (React.createElement(List, null, externalPlugins.length ? (externalPlugins
+        .filter(plugin => plugin.name.toLowerCase().includes(model.filterText.toLowerCase()))
+        .map(plugin => (React.createElement(InstalledPlugin, { key: plugin.name, plugin: plugin, model: model, pluginManager: pluginManager })))) : (React.createElement(Typography, null, "No plugins currently installed"))));
+}
+export default observer(InstalledPluginsList);
+//# sourceMappingURL=InstalledPluginsList.js.map

package/esm/PluginStoreWidget/components/InstalledPluginsList.js.map

@@ -0,0 +1 @@
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package/esm/PluginStoreWidget/components/PluginCard.d.ts

@@ -0,0 +1,10 @@
+/// <reference types="react" />
+import { JBrowsePlugin } from '@jbrowse/core/util/types';
+import { PluginStoreModel } from '../model';
+declare function PluginCard({ plugin, model, adminMode, }: {
+    plugin: JBrowsePlugin;
+    model: PluginStoreModel;
+    adminMode: boolean;
+}): JSX.Element;
+declare const _default: typeof PluginCard;
+export default _default;

package/esm/PluginStoreWidget/components/PluginCard.js

@@ -0,0 +1,61 @@
+import React, { useState } from 'react';
+import { observer } from 'mobx-react';
+import { getEnv, getParent } from 'mobx-state-tree';
+import { getSession } from '@jbrowse/core/util';
+import { isSessionWithSessionPlugins, } from '@jbrowse/core/util/types';
+import { Card, CardActions, CardContent, Button, Link, Typography, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+// icons
+import PersonIcon from '@mui/icons-material/Person';
+import AddIcon from '@mui/icons-material/Add';
+import CheckIcon from '@mui/icons-material/Check';
+const useStyles = makeStyles()(() => ({
+    card: {
+        margin: '1em',
+    },
+    icon: {
+        marginLeft: '0.5em',
+        marginRight: '0.5em',
+    },
+    bold: {
+        fontWeight: 600,
+    },
+    dataField: {
+        display: 'flex',
+        alignItems: 'center',
+        margin: '0.4em 0em',
+    },
+}));
+function PluginCard({ plugin, model, adminMode, }) {
+    const { classes } = useStyles();
+    const session = getSession(model);
+    const { pluginManager } = getEnv(model);
+    const isInstalled = Boolean(pluginManager.runtimePluginDefinitions.find(def => def.url === plugin.url));
+    const [tempDisabled, setTempDisabled] = useState(false);
+    const disableButton = isInstalled || tempDisabled;
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    const rootModel = getParent(model, 3);
+    const { jbrowse } = rootModel;
+    return (React.createElement(Card, { variant: "outlined", key: plugin.name, className: classes.card },
+        React.createElement(CardContent, null,
+            React.createElement("div", { className: classes.dataField },
+                React.createElement(Typography, { variant: "h5" },
+                    React.createElement(Link, { href: `${plugin.location}#readme`, target: "_blank", rel: "noopener" }, plugin.name))),
+            React.createElement("div", { className: classes.dataField },
+                React.createElement(PersonIcon, { style: { marginRight: '0.5em' } }),
+                React.createElement(Typography, null, plugin.authors.join(', '))),
+            React.createElement(Typography, { className: classes.bold }, "Description:"),
+            React.createElement(Typography, null, plugin.description)),
+        React.createElement(CardActions, null,
+            React.createElement(Button, { variant: "contained", color: "primary", disabled: disableButton, startIcon: isInstalled ? React.createElement(CheckIcon, null) : React.createElement(AddIcon, null), onClick: () => {
+                    if (adminMode) {
+                        jbrowse.addPlugin({ name: plugin.name, url: plugin.url });
+                    }
+                    else if (isSessionWithSessionPlugins(session)) {
+                        session.addSessionPlugin(plugin);
+                    }
+                    setTempDisabled(true);
+                } }, isInstalled ? 'Installed' : 'Install'))));
+}
+export default observer(PluginCard);
+//# sourceMappingURL=PluginCard.js.map

package/esm/PluginStoreWidget/components/PluginCard.js.map

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package/esm/PluginStoreWidget/components/PluginStoreWidget.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { PluginStoreModel } from '../model';
+declare function PluginStoreWidget({ model }: {
+    model: PluginStoreModel;
+}): JSX.Element;
+declare const _default: typeof PluginStoreWidget;
+export default _default;