@jbrowse/plugin-data-management 1.7.11 → 2.1.0

package/esm/index.d.ts

@@ -0,0 +1,30 @@
+/// <reference types="react" />
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { AddTrackModel } from './AddTrackWidget/model';
+import { HierarchicalTrackSelectorModel } from './HierarchicalTrackSelectorWidget';
+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 };
+export type { HierarchicalTrackSelectorModel, AddTrackModel };

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

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

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

package/esm/ucsc-trackhub/ucscAssemblies.js

@@ -0,0 +1,201 @@
+// These are the assemblies for which there is a sequence file located at
+// http://hgdownload.soe.ucsc.edu/goldenPath/${assemblyName}/bigZips/${assemblyName}.2bit
+// This list was generated by `getUcscAssemblies.js`
+export default `ailMel1
+allMis1
+anoCar1
+anoCar2
+anoGam1
+anoGam3
+apiMel1
+apiMel2
+aplCal1
+aptMan1
+aquChr2
+balAcu1
+bisBis1
+bosTau2
+bosTau3
+bosTau4
+bosTau6
+bosTau7
+bosTau8
+braFlo1
+caeJap1
+caePb1
+caePb2
+caeRem2
+caeRem3
+calJac1
+calJac3
+calMil1
+canFam1
+canFam3
+cavPor3
+cb3
+ce10
+ce11
+ce2
+ce4
+ce6
+cerSim1
+chlSab2
+choHof1
+chrPic1
+ci1
+ci2
+ci3
+criGri1
+criGriChoV1
+danRer10
+danRer11
+danRer3
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+xenTro3
+xenTro7
+xenTro9`.split(/\r?\n/);
+//# sourceMappingURL=ucscAssemblies.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"ucscAssemblies.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/ucscAssemblies.js"],"names":[],"mappings":"AAAA,yEAAyE;AACzE,yFAAyF;AACzF,oDAAoD;AAEpD,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;QAoMP,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA"}

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

@@ -0,0 +1,6 @@
+export function fetchHubFile(hubFileLocation: any): Promise<any>;
+export function fetchGenomesFile(genomesFileLocation: any): Promise<any>;
+export function fetchTrackDbFile(trackDbFileLocation: any): Promise<any>;
+export function generateTracks(trackDb: any, trackDbFileLocation: any, assemblyName: any, sequenceAdapter: any): any[];
+export { ucscAssemblies };
+import ucscAssemblies from "./ucscAssemblies";