@jbrowse/plugin-data-management 4.0.3 → 4.0.4

package/esm/AddTrackWidget/components/ConfirmTrack.js

@@ -1,5 +1,5 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { Suspense, useEffect, useState } from 'react';
+import { Suspense, useEffect } from 'react';
 import { AssemblySelector } from '@jbrowse/core/ui';
 import { getEnv, getSession, isElectron, isSupportedIndexingAdapter, } from '@jbrowse/core/util';
 import { UNKNOWN } from '@jbrowse/core/util/tracks';
@@ -16,17 +16,21 @@ const useStyles = makeStyles()(theme => ({
     spacing: {
         marginBottom: theme.spacing(3),
     },
+    selectorsContainer: {
+        display: 'flex',
+        flexDirection: 'column',
+        gap: 10,
+    },
 }));
 const ConfirmTrack = observer(function ConfirmTrack({ model, }) {
     const { classes } = useStyles();
-    const [check, setCheck] = useState(true);
     const session = getSession(model);
-    const { trackName, unsupported, trackAdapter, trackType, warningMessage, adapterHint, } = model;
+    const { trackName, unsupported, trackAdapter, trackType, warningMessage, adapterHint, textIndexTrack, } = model;
     useEffect(() => {
         if (adapterHint === '' && trackAdapter) {
             model.setAdapterHint(trackAdapter.type);
         }
-    }, [adapterHint, trackAdapter, trackAdapter?.type, model]);
+    }, [adapterHint, trackAdapter, model]);
     if (unsupported) {
         return _jsx(Unsupported, {});
     }
@@ -49,20 +53,15 @@ const ConfirmTrack = observer(function ConfirmTrack({ model, }) {
                     },
                 },
             } })), { model });
-        return (_jsxs("div", { children: [_jsx(StatusMessage, { trackAdapter: trackAdapter, trackType: trackType }), warningMessage ? (_jsx(Typography, { color: "warning", children: warningMessage })) : null, _jsx(TextField, { className: classes.spacing, label: "trackName", helperText: "A name for this track", fullWidth: true, value: trackName, onChange: event => {
+        return (_jsxs("div", { children: [_jsx(StatusMessage, { trackAdapter: trackAdapter, trackType: trackType }), warningMessage ? (_jsx(Typography, { color: "warning", children: warningMessage })) : null, _jsx(TextField, { className: classes.spacing, label: "Track name", helperText: "A name for this track", fullWidth: true, value: trackName, onChange: event => {
                         model.setTrackName(event.target.value);
                     }, slotProps: {
                         htmlInput: {
                             'data-testid': 'trackNameInput',
                         },
-                    } }), _jsxs("div", { style: {
-                        display: 'flex',
-                        flexDirection: 'column',
-                        gap: 10,
-                    }, children: [_jsx(TrackAdapterSelector, { model: model }), _jsx(TrackTypeSelector, { model: model }), _jsx(Suspense, { fallback: null, children: _jsx(Component, { model: model }) })] }), isElectron && supportedForIndexing && (_jsx(FormControl, { children: _jsx(FormControlLabel, { label: "Index track for text searching?", control: _jsx(Checkbox, { checked: check, onChange: e => {
-                                setCheck(e.target.checked);
+                    } }), _jsxs("div", { className: classes.selectorsContainer, children: [_jsx(TrackAdapterSelector, { model: model }), _jsx(TrackTypeSelector, { model: model }), _jsx(Suspense, { fallback: null, children: _jsx(Component, { model: model }) })] }), isElectron && supportedForIndexing && (_jsx(FormControl, { children: _jsx(FormControlLabel, { label: "Index track for text searching?", control: _jsx(Checkbox, { checked: textIndexTrack, onChange: e => {
                                 model.setTextIndexTrack(e.target.checked);
-                            } }) }) })), isElectron && check && supportedForIndexing ? (_jsx(TextIndexingConfig, { model: model })) : null] }));
+                            } }) }) })), isElectron && textIndexTrack && supportedForIndexing ? (_jsx(TextIndexingConfig, { model: model })) : null] }));
     }
 });
 export default ConfirmTrack;

package/esm/AddTrackWidget/components/PasteConfigWorkflow.js

@@ -35,7 +35,7 @@ const PasteConfigAddTrackWorkflow = observer(function PasteConfigAddTrackWorkflo
                                     session.addTrackConf(c);
                                 }
                                 for (const c of confs) {
-                                    model.view.showTrack(c.trackId);
+                                    model.view?.showTrack?.(c.trackId);
                                 }
                                 model.clearData();
                             });

package/esm/AddTrackWidget/components/TextIndexingConfig.js

@@ -17,54 +17,46 @@ const useStyles = makeStyles()(theme => ({
 }));
 const TextIndexingConfig = observer(function TextIndexingConfig({ model, }) {
     const { classes } = useStyles();
-    const [value1, setValue1] = useState('');
-    const [value2, setValue2] = useState('');
+    const [attributeInput, setAttributeInput] = useState('');
+    const [excludeInput, setExcludeInput] = useState('');
     const [attributes, setAttributes] = useState(['Name', 'ID']);
     const [exclude, setExclude] = useState(['CDS', 'exon']);
     const sections = [
         {
             label: 'Indexing attributes',
             values: attributes,
+            setValues: setAttributes,
+            inputValue: attributeInput,
+            setInputValue: setAttributeInput,
         },
         {
             label: 'Feature types to exclude',
             values: exclude,
+            setValues: setExclude,
+            inputValue: excludeInput,
+            setInputValue: setExcludeInput,
         },
     ];
     useEffect(() => {
         model.setTextIndexingConf({ attributes, exclude });
     }, [model, attributes, exclude]);
-    return (_jsxs(Paper, { className: classes.paper, children: [_jsx(InputLabel, { children: "Indexing configuration" }), sections.map((section, index) => (_jsx(Card, { raised: true, className: classes.card, children: _jsxs(CardContent, { children: [_jsx(InputLabel, { children: section.label }), _jsxs(List, { disablePadding: true, children: [section.values.map((val, idx) => (_jsx(ListItem, { disableGutters: true, children: _jsx(TextField, { value: val, slotProps: {
+    return (_jsxs(Paper, { className: classes.paper, children: [_jsx(InputLabel, { children: "Indexing configuration" }), sections.map(section => (_jsx(Card, { raised: true, className: classes.card, children: _jsxs(CardContent, { children: [_jsx(InputLabel, { children: section.label }), _jsxs(List, { disablePadding: true, children: [section.values.map((val, idx) => (_jsx(ListItem, { disableGutters: true, children: _jsx(TextField, { value: val, slotProps: {
                                             input: {
                                                 endAdornment: (_jsx(InputAdornment, { position: "end", children: _jsx(IconButton, { onClick: () => {
-                                                            const newAttr = section.values.filter((_, i) => i !== idx);
-                                                            if (index === 0) {
-                                                                setAttributes(newAttr);
-                                                            }
-                                                            else {
-                                                                setExclude(newAttr);
-                                                            }
+                                                            section.setValues(section.values.filter((_, i) => i !== idx));
                                                         }, children: _jsx(DeleteIcon, {}) }) })),
                                             },
-                                        } }) }, `${val}-${idx}`))), _jsx(ListItem, { disableGutters: true, children: _jsx(TextField, { value: index === 0 ? value1 : value2, placeholder: "add new", onChange: event => {
-                                            if (index === 0) {
-                                                setValue1(event.target.value);
-                                            }
-                                            else {
-                                                setValue2(event.target.value);
-                                            }
+                                        } }) }, `${val}-${idx}`))), _jsx(ListItem, { disableGutters: true, children: _jsx(TextField, { value: section.inputValue, placeholder: "add new", onChange: event => {
+                                            section.setInputValue(event.target.value);
                                         }, slotProps: {
                                             input: {
                                                 endAdornment: (_jsx(InputAdornment, { position: "end", children: _jsx(IconButton, { onClick: () => {
-                                                            if (index === 0) {
-                                                                setAttributes([...attributes, value1]);
-                                                                setValue1('');
-                                                            }
-                                                            else {
-                                                                setExclude([...exclude, value2]);
-                                                                setValue2('');
-                                                            }
-                                                        }, disabled: index === 0 ? value1 === '' : value2 === '', "data-testid": "stringArrayAdd-Feat", children: _jsx(AddIcon, {}) }) })),
+                                                            section.setValues([
+                                                                ...section.values,
+                                                                section.inputValue,
+                                                            ]);
+                                                            section.setInputValue('');
+                                                        }, disabled: section.inputValue === '', "data-testid": "stringArrayAdd-Feat", children: _jsx(AddIcon, {}) }) })),
                                             },
                                         } }) })] })] }) }, section.label)))] }));
 });

package/esm/AddTrackWidget/components/TrackSourceSelect.js

@@ -15,6 +15,6 @@ const useStyles = makeStyles()(theme => ({
 const TrackSourceSelect = observer(function TrackSourceSelect({ model, }) {
     const { classes } = useStyles();
     const rootModel = getRoot(model);
-    return (_jsxs(Paper, { className: classes.paper, children: [_jsx(FileSelector, { name: "Main file", description: "", location: model.trackData, setLocation: model.setTrackData, setName: model.setTrackName, rootModel: rootModel }), _jsx("div", { className: classes.spacer }), _jsx(FileSelector, { name: "Index file", description: "(Optional) The URL of the index file is automatically inferred from the URL of the main file if it is not supplied.", location: model.indexTrackData, setLocation: model.setIndexTrackData, setName: model.setTrackName, rootModel: rootModel })] }));
+    return (_jsxs(Paper, { className: classes.paper, children: [_jsx(FileSelector, { name: "Main file", description: "", location: model.trackData, setLocation: model.setTrackData, setName: model.setTrackName, rootModel: rootModel }), _jsx("div", { className: classes.spacer }), _jsx(FileSelector, { name: "Index file", description: "(Optional) The URL of the index file is automatically inferred from the URL of the main file if it is not supplied.", location: model.indexTrackData, setLocation: model.setIndexTrackData, rootModel: rootModel })] }));
 });
 export default TrackSourceSelect;

package/esm/AddTrackWidget/components/doSubmit.js

@@ -37,7 +37,7 @@ export function doSubmit({ model }) {
             isSupportedIndexingAdapter(trackAdapter.type)) {
             doTextIndexTrack({
                 model,
-                trackId,
+                trackId: String(trackId),
             });
         }
         model.clearData();

package/esm/AddTrackWidget/model.d.ts

@@ -10,7 +10,6 @@ export default function f(pluginManager: PluginManager): import("@jbrowse/mobx-s
     type: import("@jbrowse/mobx-state-tree").ISimpleType<"AddTrackWidget">;
     view: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
 }, {
-    trackSource: string;
     trackData: FileLocation | undefined;
     indexTrackData: FileLocation | undefined;
     altAssemblyName: string;
@@ -19,11 +18,10 @@ export default function f(pluginManager: PluginManager): import("@jbrowse/mobx-s
     adapterHint: string;
     textIndexTrack: boolean;
     textIndexingConf: IndexingAttr | undefined;
-    mixinData: {};
+    mixinData: Record<string, unknown>;
 } & {
     setMixinData(arg: Record<string, unknown>): void;
     setAdapterHint(obj: string): void;
-    setTrackSource(str: string): void;
     setTextIndexingConf(conf: IndexingAttr): void;
     setTextIndexTrack(flag: boolean): void;
     setTrackData(obj: FileLocation): void;
@@ -39,20 +37,16 @@ export default function f(pluginManager: PluginManager): import("@jbrowse/mobx-s
     readonly isRelativeTrackUrl: boolean;
     readonly isRelativeIndexUrl: boolean;
     readonly isRelativeUrl: boolean;
-    readonly trackHttp: any;
-    readonly indexHttp: any;
-    readonly wrongProtocol: any;
+    readonly trackHttp: boolean | undefined;
+    readonly indexHttp: boolean | undefined;
+    readonly wrongProtocol: boolean | undefined;
     readonly unsupported: boolean;
     readonly assembly: any;
     readonly trackAdapterType: string | undefined;
     readonly trackType: string;
 } & {
     getTrackConfig(timestamp: number): {
-        trackId: string;
-        type: string;
-        name: string;
-        assemblyNames: any[];
-        adapter: import("@jbrowse/core/util").AdapterConfig;
+        [x: string]: any;
     } | undefined;
     readonly warningMessage: "" | "Warning: JBrowse cannot access files using the ftp protocol" | "Warning: one or more of your files do not provide the protocol e.g.\n          https://, please provide an absolute URL unless you are sure a\n          relative URL is intended." | "Warning: You entered a http:// resources but we cannot access HTTP\n          resources from JBrowse when it is running on https. Please use an\n          https URL for your track, or access the JBrowse app from the http\n          protocol";
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;

package/esm/AddTrackWidget/model.js

@@ -1,17 +1,31 @@
-import { getSession } from '@jbrowse/core/util';
+import { getSession, isUriLocation } from '@jbrowse/core/util';
 import { UNSUPPORTED, getFileName, guessAdapter, guessTrackType, } from '@jbrowse/core/util/tracks';
 import { ElementId } from '@jbrowse/core/util/types/mst';
 import { types } from '@jbrowse/mobx-state-tree';
 import deepmerge from 'deepmerge';
-function isAbsoluteUrl(url = '') {
+function getUri(location) {
+    return isUriLocation(location) ? location.uri : undefined;
+}
+function isRelativeUrl(url = '') {
     try {
         new URL(url);
-        return true;
+        return false;
     }
-    catch (error) {
-        return url.startsWith('/');
+    catch {
+        return !url.startsWith('/');
     }
 }
+const defaultVolatileState = {
+    trackData: undefined,
+    indexTrackData: undefined,
+    altAssemblyName: '',
+    altTrackName: '',
+    altTrackType: '',
+    adapterHint: '',
+    textIndexTrack: true,
+    textIndexingConf: undefined,
+    mixinData: {},
+};
 export default function f(pluginManager) {
     return types
         .model('AddTrackModel', {
@@ -19,18 +33,7 @@ export default function f(pluginManager) {
         type: types.literal('AddTrackWidget'),
         view: types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
     })
-        .volatile(() => ({
-        trackSource: 'fromFile',
-        trackData: undefined,
-        indexTrackData: undefined,
-        altAssemblyName: '',
-        altTrackName: '',
-        altTrackType: '',
-        adapterHint: '',
-        textIndexTrack: true,
-        textIndexingConf: undefined,
-        mixinData: {},
-    }))
+        .volatile(() => ({ ...defaultVolatileState }))
         .actions(self => ({
         setMixinData(arg) {
             self.mixinData = arg;
@@ -38,9 +41,6 @@ export default function f(pluginManager) {
         setAdapterHint(obj) {
             self.adapterHint = obj;
         },
-        setTrackSource(str) {
-            self.trackSource = str;
-        },
         setTextIndexingConf(conf) {
             self.textIndexingConf = conf;
         },
@@ -53,6 +53,7 @@ export default function f(pluginManager) {
         },
         setIndexTrackData(obj) {
             self.indexTrackData = obj;
+            self.adapterHint = '';
         },
         setAssembly(str) {
             self.altAssemblyName = str;
@@ -64,15 +65,15 @@ export default function f(pluginManager) {
             self.altTrackType = str;
         },
         clearData() {
-            self.trackSource = '';
-            self.altTrackName = '';
-            self.altTrackType = '';
-            self.altAssemblyName = '';
-            self.adapterHint = '';
-            self.indexTrackData = undefined;
-            self.trackData = undefined;
-            self.textIndexingConf = undefined;
-            self.textIndexTrack = true;
+            self.altTrackName = defaultVolatileState.altTrackName;
+            self.altTrackType = defaultVolatileState.altTrackType;
+            self.altAssemblyName = defaultVolatileState.altAssemblyName;
+            self.adapterHint = defaultVolatileState.adapterHint;
+            self.indexTrackData = defaultVolatileState.indexTrackData;
+            self.trackData = defaultVolatileState.trackData;
+            self.textIndexingConf = defaultVolatileState.textIndexingConf;
+            self.textIndexTrack = defaultVolatileState.textIndexTrack;
+            self.mixinData = {};
         },
     }))
         .views(self => ({
@@ -87,25 +88,26 @@ export default function f(pluginManager) {
                 (self.trackData ? getFileName(self.trackData) : ''));
         },
         get isFtp() {
-            const { trackData: track, indexTrackData: index } = self;
-            return !!((index?.uri?.startsWith('ftp://') || track?.uri?.startsWith('ftp://')));
+            const trackUri = getUri(self.trackData);
+            const indexUri = getUri(self.indexTrackData);
+            return !!(indexUri?.startsWith('ftp://') || trackUri?.startsWith('ftp://'));
         },
         get isRelativeTrackUrl() {
-            const uri = self.trackData?.uri;
-            return uri ? !isAbsoluteUrl(uri) : false;
+            const uri = getUri(self.trackData);
+            return uri ? isRelativeUrl(uri) : false;
         },
         get isRelativeIndexUrl() {
-            const uri = self.indexTrackData?.uri;
-            return uri ? !isAbsoluteUrl(uri) : false;
+            const uri = getUri(self.indexTrackData);
+            return uri ? isRelativeUrl(uri) : false;
         },
         get isRelativeUrl() {
             return this.isRelativeIndexUrl || this.isRelativeTrackUrl;
         },
         get trackHttp() {
-            return self.trackData?.uri?.startsWith('http://');
+            return getUri(self.trackData)?.startsWith('http://');
         },
         get indexHttp() {
-            return self.indexTrackData?.uri?.startsWith('http://');
+            return getUri(self.indexTrackData)?.startsWith('http://');
         },
         get wrongProtocol() {
             return (window.location.protocol === 'https:' &&
@@ -115,7 +117,7 @@ export default function f(pluginManager) {
             return this.trackAdapter?.type === UNSUPPORTED;
         },
         get assembly() {
-            return self.altAssemblyName || self.view.assemblyNames?.[0];
+            return self.altAssemblyName || self.view?.assemblyNames?.[0];
         },
         get trackAdapterType() {
             return this.trackAdapter?.type;

package/esm/UCSCTrackHubConnection/doConnect.js

@@ -2,7 +2,7 @@ import { HubFile, SingleFileHub } from '@gmod/ucsc-hub';
 import { getConf } from '@jbrowse/core/configuration';
 import { getEnv, getSession } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
-import { nanoid } from '@jbrowse/core/util/nanoid';
+import { createElementId } from '@jbrowse/core/util/types/mst';
 import { generateTracks } from "./ucscTrackHub.js";
 import { fetchGenomesFile, fetchTrackDbFile, resolve } from "./util.js";
 export async function doConnect(self) {
@@ -34,7 +34,7 @@ export async function doConnect(self) {
                                 }
                                 : {}),
                         },
-                        trackId: `${genomeName}-${nanoid()}`,
+                        trackId: `${genomeName}-${createElementId()}`,
                         adapter: {
                             type: 'TwoBitAdapter',
                             twoBitLocation: {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "4.0.3",
+  "version": "4.0.4",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -24,13 +24,13 @@
     "@jbrowse/mobx-state-tree": "^5.5.0",
     "@mui/icons-material": "^7.3.6",
     "@mui/material": "^7.3.6",
-    "@mui/x-data-grid": "^8.23.0",
+    "@mui/x-data-grid": "^8.25.0",
     "deepmerge": "^4.3.1",
     "mobx": "^6.15.0",
     "mobx-react": "^9.2.1",
-    "@jbrowse/plugin-config": "^4.0.3",
-    "@jbrowse/product-core": "^4.0.3",
-    "@jbrowse/core": "^4.0.3"
+    "@jbrowse/product-core": "^4.0.4",
+    "@jbrowse/core": "^4.0.4",
+    "@jbrowse/plugin-config": "^4.0.4"
   },
   "peerDependencies": {
     "react": ">=18.0.0"