@jbrowse/plugin-data-management 1.7.11 → 2.0.0

package/esm/PluginStoreWidget/components/PluginStoreWidget.js

@@ -0,0 +1,106 @@
+import React, { useState, useEffect } from 'react';
+import { observer } from 'mobx-react';
+import { getEnv } from 'mobx-state-tree';
+import { Accordion, AccordionSummary, Button, IconButton, InputAdornment, TextField, Typography, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { getSession, isElectron } from '@jbrowse/core/util';
+// icons
+import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
+import ClearIcon from '@mui/icons-material/Clear';
+import InfoOutlinedIcon from '@mui/icons-material/InfoOutlined';
+// locals
+import InstalledPluginsList from './InstalledPluginsList';
+import PluginCard from './PluginCard';
+import CustomPluginForm from './CustomPluginForm';
+const useStyles = makeStyles()(theme => ({
+    root: {
+        margin: theme.spacing(1),
+    },
+    expandIcon: {
+        color: '#fff',
+    },
+    adminBadge: {
+        margin: '0.5em',
+        borderRadius: 3,
+        // this is the quaternary color in JB2 palette
+        backgroundColor: '#FFB11D',
+        padding: '1em',
+        display: 'flex',
+        alignContent: 'center',
+    },
+    customPluginButton: {
+        margin: '0.5em',
+        display: 'flex',
+        justifyContent: 'center',
+    },
+}));
+function PluginStoreWidget({ model }) {
+    const { classes } = useStyles();
+    const [pluginArray, setPluginArray] = useState();
+    const [error, setError] = useState();
+    const [customPluginFormOpen, setCustomPluginFormOpen] = useState(false);
+    const { adminMode } = getSession(model);
+    const { pluginManager } = getEnv(model);
+    useEffect(() => {
+        const controller = new AbortController();
+        const { signal } = controller;
+        (async () => {
+            try {
+                const response = await fetch('https://jbrowse.org/plugin-store/plugins.json', { signal });
+                if (!response.ok) {
+                    const err = await response.text();
+                    throw new Error(`Failed to fetch plugin data: ${response.status} ${response.statusText} ${err}`);
+                }
+                const array = await response.json();
+                if (!signal.aborted) {
+                    setPluginArray(array.plugins);
+                }
+            }
+            catch (e) {
+                console.error(e);
+                setError(e);
+            }
+        })();
+        return () => {
+            controller.abort();
+        };
+    }, []);
+    return (React.createElement("div", { className: classes.root },
+        adminMode && (React.createElement(React.Fragment, null,
+            !isElectron && (React.createElement("div", { className: classes.adminBadge },
+                React.createElement(InfoOutlinedIcon, { style: { marginRight: '0.3em' } }),
+                React.createElement(Typography, null,
+                    "You are using the ",
+                    React.createElement("code", null, "admin-server"),
+                    ". Any changes you make will be saved to your configuration file. You also have the ability to add custom plugins that are not in the store."))),
+            React.createElement("div", { className: classes.customPluginButton },
+                React.createElement(Button, { variant: "contained", color: "primary", onClick: () => setCustomPluginFormOpen(true) }, "Add custom plugin")),
+            React.createElement(CustomPluginForm, { open: customPluginFormOpen, onClose: () => setCustomPluginFormOpen(false), model: model }))),
+        React.createElement(TextField, { label: "Filter plugins", value: model.filterText, onChange: event => model.setFilterText(event.target.value), fullWidth: true, InputProps: {
+                endAdornment: (React.createElement(InputAdornment, { position: "end" },
+                    React.createElement(IconButton, { color: "secondary", onClick: () => model.clearFilterText() },
+                        React.createElement(ClearIcon, null)))),
+            } }),
+        React.createElement(Accordion, { defaultExpanded: true },
+            React.createElement(AccordionSummary, { expandIcon: React.createElement(ExpandMoreIcon, { className: classes.expandIcon }) },
+                React.createElement(Typography, { variant: "h5" }, "Installed plugins")),
+            React.createElement("div", { style: { margin: '1em' } },
+                React.createElement(InstalledPluginsList, { pluginManager: pluginManager, model: model }))),
+        React.createElement(Accordion, { defaultExpanded: true },
+            React.createElement(AccordionSummary, { expandIcon: React.createElement(ExpandMoreIcon, { className: classes.expandIcon }) },
+                React.createElement(Typography, { variant: "h5" }, "Available plugins")),
+            error ? (React.createElement(Typography, { color: "error" }, `${error}`)) : pluginArray ? (pluginArray
+                .filter(plugin => {
+                // If pugin only has cjsUrl, don't display outside desktop
+                if (!isElectron &&
+                    !(plugin.esmUrl || plugin.url || plugin.umdUrl)) {
+                    return false;
+                }
+                return plugin.name
+                    .toLowerCase()
+                    .includes(model.filterText.toLowerCase());
+            })
+                .map(plugin => (React.createElement(PluginCard, { key: plugin.name, plugin: plugin, model: model, adminMode: !!adminMode })))) : (React.createElement(Typography, null, "Loading...")))));
+}
+export default observer(PluginStoreWidget);
+//# sourceMappingURL=PluginStoreWidget.js.map

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

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

@@ -0,0 +1,2 @@
+export { default as stateModelFactory } from "./model";
+export const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/PluginStoreWidget/index.js

@@ -0,0 +1,4 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export { default as stateModelFactory } from './model';
+export const configSchema = ConfigurationSchema('PluginStoreWidget', {});
+//# sourceMappingURL=index.js.map

package/esm/PluginStoreWidget/index.js.map

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

@@ -0,0 +1,13 @@
+import { Instance } from 'mobx-state-tree';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function f(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<"PluginStoreWidget">;
+    filterText: import("mobx-state-tree").IType<string | undefined, string, string>;
+    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+}, {
+    clearFilterText(): void;
+    setFilterText(newText: string): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export declare type PluginStoreStateModel = ReturnType<typeof f>;
+export declare type PluginStoreModel = Instance<PluginStoreStateModel>;

package/esm/PluginStoreWidget/model.js

@@ -0,0 +1,20 @@
+import { types } from 'mobx-state-tree';
+import { ElementId } from '@jbrowse/core/util/types/mst';
+export default function f(pluginManager) {
+    return types
+        .model('PluginStoreModel', {
+        id: ElementId,
+        type: types.literal('PluginStoreWidget'),
+        filterText: '',
+        view: types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
+    })
+        .actions(self => ({
+        clearFilterText() {
+            self.filterText = '';
+        },
+        setFilterText(newText) {
+            self.filterText = newText;
+        },
+    }));
+}
+//# sourceMappingURL=model.js.map

package/esm/PluginStoreWidget/model.js.map

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package/esm/SetDefaultSession/SetDefaultSession.d.ts

@@ -0,0 +1,6 @@
+/// <reference types="react" />
+declare const SetDefaultSession: ({ rootModel, onClose }: {
+    rootModel?: unknown;
+    onClose: () => void;
+}) => JSX.Element | null;
+export default SetDefaultSession;

package/esm/SetDefaultSession/SetDefaultSession.js

@@ -0,0 +1,34 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+import { Dialog, DialogTitle, DialogContent, DialogActions, Button, Typography, } from '@mui/material';
+function canSetDefaultSession(obj) {
+    return typeof obj === 'object' && !!obj && 'jbrowse' in obj;
+}
+const SetDefaultSession = observer(({ rootModel, onClose }) => {
+    if (!rootModel) {
+        return null;
+    }
+    if (!canSetDefaultSession(rootModel)) {
+        console.error('Incorrect rootmodel');
+        return null;
+    }
+    const { jbrowse, session } = rootModel;
+    return (React.createElement(Dialog, { open: true, onClose: onClose },
+        React.createElement(DialogTitle, null, "Set default session"),
+        React.createElement(DialogContent, null,
+            React.createElement(Typography, null, "Select \"Set current session as default\" to make your current session saved to the config file. You can also hit \"Clear default session\", which would remove the default session from the config.")),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { variant: "contained", onClick: () => {
+                    jbrowse.setDefaultSessionConf({
+                        name: `New session`,
+                    });
+                    onClose();
+                } }, "Clear default session"),
+            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => onClose() }, "Cancel"),
+            React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
+                    jbrowse.setDefaultSessionConf(session);
+                    onClose();
+                } }, "Set current session as default"))));
+});
+export default SetDefaultSession;
+//# sourceMappingURL=SetDefaultSession.js.map

package/esm/SetDefaultSession/SetDefaultSession.js.map

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package/esm/SetDefaultSession/index.d.ts

@@ -0,0 +1 @@
+export { default } from './SetDefaultSession';

package/esm/SetDefaultSession/index.js

@@ -0,0 +1,2 @@
+export { default } from './SetDefaultSession';
+//# sourceMappingURL=index.js.map

package/esm/SetDefaultSession/index.js.map

@@ -0,0 +1 @@
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package/esm/index.d.ts

@@ -0,0 +1,27 @@
+/// <reference types="react" />
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const SetDefaultSession: import("react").LazyExoticComponent<({ rootModel, onClose }: {
+    rootModel?: unknown;
+    onClose: () => void;
+}) => JSX.Element | null>;
+declare const AssemblyManager: import("react").LazyExoticComponent<({ rootModel, onClose, }: {
+    rootModel: any;
+    onClose: (arg: boolean) => void;
+}) => JSX.Element>;
+export default class extends Plugin {
+    name: string;
+    exports: {
+        AssemblyManager: import("react").LazyExoticComponent<({ rootModel, onClose, }: {
+            rootModel: any;
+            onClose: (arg: boolean) => void;
+        }) => JSX.Element>;
+        SetDefaultSession: import("react").LazyExoticComponent<({ rootModel, onClose }: {
+            rootModel?: unknown;
+            onClose: () => void;
+        }) => JSX.Element | null>;
+    };
+    install(pluginManager: PluginManager): void;
+    configure(pluginManager: PluginManager): void;
+}
+export { AssemblyManager, SetDefaultSession };

package/esm/index.js

@@ -0,0 +1,70 @@
+import { lazy } from 'react';
+import ConnectionType from '@jbrowse/core/pluggableElementTypes/ConnectionType';
+import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType';
+import Plugin from '@jbrowse/core/Plugin';
+import { configSchema as ucscConfigSchema, modelFactory as ucscModelFactory, } from './ucsc-trackhub';
+import { stateModelFactory as AddTrackStateModelFactory, configSchema as AddTrackConfigSchema, } from './AddTrackWidget';
+import { stateModel as AddConnectionStateModel, configSchema as AddConnectionConfigSchema, } from './AddConnectionWidget';
+import { stateModelFactory as HierarchicalTrackSelectorStateModelFactory, configSchema as HierarchicalTrackSelectorConfigSchema, } from './HierarchicalTrackSelectorWidget';
+import { stateModelFactory as PluginStoreStateModelFactory, configSchema as PluginStoreConfigSchema, } from './PluginStoreWidget';
+const SetDefaultSession = lazy(() => import('./SetDefaultSession'));
+const AssemblyManager = lazy(() => import('./AssemblyManager'));
+export default class extends Plugin {
+    constructor() {
+        super(...arguments);
+        this.name = 'DataManagementPlugin';
+        this.exports = {
+            AssemblyManager,
+            SetDefaultSession,
+        };
+    }
+    install(pluginManager) {
+        pluginManager.addConnectionType(() => new ConnectionType({
+            name: 'UCSCTrackHubConnection',
+            configSchema: ucscConfigSchema,
+            stateModel: ucscModelFactory(pluginManager),
+            displayName: 'UCSC Track Hub',
+            description: 'A track or assembly hub in the Track Hub format',
+            url: '//genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Intro',
+        }));
+        pluginManager.addWidgetType(() => {
+            return new WidgetType({
+                name: 'HierarchicalTrackSelectorWidget',
+                heading: 'Available tracks',
+                configSchema: HierarchicalTrackSelectorConfigSchema,
+                stateModel: HierarchicalTrackSelectorStateModelFactory(pluginManager),
+                ReactComponent: lazy(() => import('./HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector')),
+            });
+        });
+        pluginManager.addWidgetType(() => {
+            return new WidgetType({
+                name: 'AddTrackWidget',
+                heading: 'Add a track',
+                configSchema: AddTrackConfigSchema,
+                stateModel: AddTrackStateModelFactory(pluginManager),
+                ReactComponent: lazy(() => import('./AddTrackWidget/components/AddTrackWidget')),
+            });
+        });
+        pluginManager.addWidgetType(() => {
+            return new WidgetType({
+                name: 'AddConnectionWidget',
+                heading: 'Add a connection',
+                configSchema: AddConnectionConfigSchema,
+                stateModel: AddConnectionStateModel,
+                ReactComponent: lazy(() => import('./AddConnectionWidget/components/AddConnectionWidget')),
+            });
+        });
+        pluginManager.addWidgetType(() => {
+            return new WidgetType({
+                name: 'PluginStoreWidget',
+                heading: 'Plugin store',
+                configSchema: PluginStoreConfigSchema,
+                stateModel: PluginStoreStateModelFactory(pluginManager),
+                ReactComponent: lazy(() => import('./PluginStoreWidget/components/PluginStoreWidget')),
+            });
+        });
+    }
+    configure(pluginManager) { }
+}
+export { AssemblyManager, SetDefaultSession };
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -0,0 +1 @@
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package/esm/ucsc-trackhub/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/ucsc-trackhub/configSchema.js

@@ -0,0 +1,18 @@
+import { baseConnectionConfig } from '@jbrowse/core/pluggableElementTypes/models';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('UCSCTrackHubConnection', {
+    hubTxtLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: 'http://mysite.com/path/to/hub.txt',
+            locationType: 'UriLocation',
+        },
+        description: 'location of the hub file (usually called hub.txt)',
+    },
+    assemblyNames: {
+        type: 'stringArray',
+        defaultValue: [],
+        description: 'optional list of genomes to import from this track hub, if empty all genomes will be imported',
+    },
+}, { baseConfiguration: baseConnectionConfig });
+//# sourceMappingURL=configSchema.js.map

package/esm/ucsc-trackhub/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/ucsc-trackhub/index.d.ts

@@ -0,0 +1,2 @@
+export { default as modelFactory } from "./model";
+export { default as configSchema } from "./configSchema";

package/esm/ucsc-trackhub/index.js

@@ -0,0 +1,3 @@
+export { default as modelFactory } from './model';
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/ucsc-trackhub/index.js.map

@@ -0,0 +1 @@
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package/esm/ucsc-trackhub/model.d.ts

@@ -0,0 +1,15 @@
+export default function UCSCTrackHubConnection(pluginManager: any): import("mobx-state-tree").IModelType<{
+    name: import("mobx-state-tree").ISimpleType<string>;
+    tracks: import("mobx-state-tree").IArrayType<any>;
+} & {
+    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    type: import("mobx-state-tree").ISimpleType<"UCSCTrackHubConnection">;
+}, {
+    afterAttach(): void;
+    addTrackConf(trackConf: any): any;
+    addTrackConfs(trackConfs: any): any[];
+    setTrackConfs(trackConfs: any): import("mobx-state-tree").IMSTArray<any> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<any>>;
+    clear(): void;
+} & {
+    connect(): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/ucsc-trackhub/model.js

@@ -0,0 +1,82 @@
+import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models';
+import { ConfigurationReference, readConfObject, getConf, } from '@jbrowse/core/configuration';
+import { getSession } from '@jbrowse/core/util';
+import { types } from 'mobx-state-tree';
+import configSchema from './configSchema';
+import { fetchGenomesFile, fetchHubFile, fetchTrackDbFile, generateTracks, } from './ucscTrackHub';
+export default function UCSCTrackHubConnection(pluginManager) {
+    return types.compose('UCSCTrackHubConnection', BaseConnectionModelFactory(pluginManager), types
+        .model({
+        configuration: ConfigurationReference(configSchema),
+        type: types.literal('UCSCTrackHubConnection'),
+    })
+        .actions(self => ({
+        connect() {
+            const connectionName = getConf(self, 'name');
+            const hubFileLocation = getConf(self, 'hubTxtLocation');
+            const session = getSession(self);
+            fetchHubFile(hubFileLocation)
+                .then(hubFile => {
+                const genomesFileLocation = hubFileLocation.uri
+                    ? {
+                        uri: new URL(hubFile.get('genomesFile'), hubFileLocation.uri).href,
+                        locationType: 'UriLocation',
+                    }
+                    : {
+                        localPath: hubFile.get('genomesFile'),
+                        locationType: 'LocalPathLocation',
+                    };
+                return Promise.all([
+                    hubFile,
+                    fetchGenomesFile(genomesFileLocation),
+                ]);
+            })
+                .then(([hubFile, genomesFile]) => {
+                const trackDbData = [];
+                for (const [genomeName, genome] of genomesFile) {
+                    const assemblyNames = getConf(self, 'assemblyNames');
+                    if (assemblyNames.length > 0 &&
+                        !assemblyNames.includes(genomeName)) {
+                        break;
+                    }
+                    const assemblyConf = session.assemblies.find(assembly => readConfObject(assembly, 'name') === genomeName);
+                    if (!assemblyConf) {
+                        throw new Error(`Cannot find assembly for "${genomeName}" from the genomes file for connection "${connectionName}"`);
+                    }
+                    const trackDbFileLocation = hubFileLocation.uri
+                        ? {
+                            uri: new URL(genome.get('trackDb'), new URL(hubFile.get('genomesFile'), hubFileLocation.uri)).href,
+                            locationType: 'UriLocation',
+                        }
+                        : {
+                            localPath: genome.get('trackDb'),
+                            locationType: 'LocalPathLocation',
+                        };
+                    trackDbData.push(Promise.all([
+                        trackDbFileLocation,
+                        fetchTrackDbFile(trackDbFileLocation),
+                        genomeName,
+                        assemblyConf,
+                    ]));
+                }
+                return Promise.all([...trackDbData]);
+            })
+                .then(trackDbData => {
+                for (const [trackDbFileLocation, trackDbFile, genomeName, assemblyConf,] of trackDbData) {
+                    const sequenceAdapter = readConfObject(assemblyConf, [
+                        'sequence',
+                        'adapter',
+                    ]);
+                    const tracks = generateTracks(trackDbFile, trackDbFileLocation, genomeName, sequenceAdapter);
+                    self.addTrackConfs(tracks);
+                }
+            })
+                .catch(error => {
+                console.error(error);
+                session.notify(`There was a problem connecting to the UCSC Track Hub "${self.name}". Please make sure you have entered a valid hub.txt file. The error that was thrown is: "${error}"`, 'error');
+                session.breakConnection(self.configuration);
+            });
+        },
+    })));
+}
+//# sourceMappingURL=model.js.map

package/esm/ucsc-trackhub/model.js.map

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package/esm/ucsc-trackhub/ucscAssemblies.d.ts

@@ -0,0 +1,2 @@
+declare const _default: string[];
+export default _default;