@jbrowse/plugin-data-management 2.13.1 → 2.14.0

package/dist/ucsc-trackhub/ucscTrackHub.js

@@ -10,7 +10,6 @@ exports.makeLoc = makeLoc;
 exports.makeLocAlt = makeLocAlt;
 exports.makeLoc2 = makeLoc2;
 exports.generateTracks = generateTracks;
-/* eslint-disable @typescript-eslint/no-explicit-any */
 const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
 const tracks_1 = require("@jbrowse/core/util/tracks");
@@ -62,8 +61,7 @@ function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, })
         do {
             currentTrackName = ((_a = trackDb.data[currentTrackName]) === null || _a === void 0 ? void 0 : _a.data.parent) || '';
             if (currentTrackName) {
-                ;
-                [currentTrackName] = currentTrackName.split(' ');
+                currentTrackName = currentTrackName.split(' ')[0];
                 parentTracks.push(trackDb.data[currentTrackName]);
             }
         } while (currentTrackName);
@@ -93,7 +91,7 @@ function makeTrackConfig({ track, categories, trackDbLoc, trackDb, sequenceAdapt
     const bigDataUrl = track.data.bigDataUrl || '';
     const bigDataIdx = track.data.bigDataIndex || '';
     const isUri = (0, util_1.isUriLocation)(trackDbLoc);
-    let baseTrackType = (trackType === null || trackType === void 0 ? void 0 : trackType.split(' ')[0]) || '';
+    let baseTrackType = trackType.split(' ')[0] || '';
     if (baseTrackType === 'bam' && bigDataUrl.toLowerCase().endsWith('cram')) {
         baseTrackType = 'cram';
     }
@@ -112,8 +110,8 @@ function makeTrackConfig({ track, categories, trackDbLoc, trackDb, sequenceAdapt
                     bamLocation: bigDataLocation,
                     index: {
                         location: isUri
-                            ? makeLocAlt(bigDataIdx, bigDataUrl + '.bai', trackDbLoc)
-                            : makeLoc2(bigDataIdx, bigDataUrl + '.bai'),
+                            ? makeLocAlt(bigDataIdx, `${bigDataUrl}.bai`, trackDbLoc)
+                            : makeLoc2(bigDataIdx, `${bigDataUrl}.bai`),
                     },
                 },
             };
@@ -127,8 +125,8 @@ function makeTrackConfig({ track, categories, trackDbLoc, trackDb, sequenceAdapt
                     type: 'CramAdapter',
                     cramLocation: bigDataLocation,
                     craiLocation: isUri
-                        ? makeLocAlt(bigDataIdx, bigDataUrl + '.crai', trackDbLoc)
-                        : makeLoc2(bigDataIdx, bigDataUrl + '.crai'),
+                        ? makeLocAlt(bigDataIdx, `${bigDataUrl}.crai`, trackDbLoc)
+                        : makeLoc2(bigDataIdx, `${bigDataUrl}.crai`),
                     sequenceAdapter,
                 },
             };
@@ -172,8 +170,8 @@ function makeTrackConfig({ track, categories, trackDbLoc, trackDb, sequenceAdapt
                     vcfGzLocation: bigDataLocation,
                     index: {
                         location: isUri
-                            ? makeLocAlt(bigDataIdx, bigDataUrl + '.tbi', trackDbLoc)
-                            : makeLoc2(bigDataIdx, bigDataUrl + '.tbi'),
+                            ? makeLocAlt(bigDataIdx, `${bigDataUrl}.tbi`, trackDbLoc)
+                            : makeLoc2(bigDataIdx, `${bigDataUrl}.tbi`),
                     },
                 },
             };

package/esm/AddConnectionWidget/components/AddConnectionWidget.js

@@ -44,7 +44,9 @@ const AddConnectionWidget = observer(function ({ model }) {
                         setConnectionId(`${c.name}-${Date.now()}`);
                     } })) : connectionType && configModel ? (React.createElement(ConfigureConnection, { connectionType: connectionType, model: configModel, session: session })) : null,
                 React.createElement("div", { className: classes.actionsContainer },
-                    React.createElement(Button, { disabled: activeStep === 0, onClick: () => setActiveStep(activeStep - 1), className: classes.button }, "Back"),
+                    React.createElement(Button, { disabled: activeStep === 0, onClick: () => {
+                            setActiveStep(activeStep - 1);
+                        }, className: classes.button }, "Back"),
                     React.createElement(Button, { disabled: !((activeStep === 0 && connectionType) ||
                             (activeStep === 1 && configModel)), variant: "contained", color: "primary", onClick: () => {
                             if (activeStep === steps.length - 1) {

package/esm/AddConnectionWidget/components/ConnectionTypeSelect.js

@@ -13,6 +13,8 @@ const ConnectionTypeSelect = observer(function ConnectionTypeSelect({ connection
     return (React.createElement("form", { autoComplete: "off" }, connectionType ? (React.createElement(TextField, { value: connectionType.name, label: "connectionType", helperText: connectionType.description ? (React.createElement(React.Fragment, null,
             connectionType.description,
             connectionType.url ? (React.createElement(IconButton, { href: connectionType.url, rel: "noopener noreferrer", target: "_blank" },
-                React.createElement(OpenInNewIcon, null))) : null)) : null, select: true, fullWidth: true, onChange: event => setConnectionType(connectionTypeChoices.find(c => c.name === event.target.value)), variant: "outlined" }, connectionTypeChoices.map(c => (React.createElement(MenuItem, { key: c.name, value: c.name }, c.displayName || c.name))))) : null));
+                React.createElement(OpenInNewIcon, null))) : null)) : null, select: true, fullWidth: true, onChange: event => {
+            setConnectionType(connectionTypeChoices.find(c => c.name === event.target.value));
+        }, variant: "outlined" }, connectionTypeChoices.map(c => (React.createElement(MenuItem, { key: c.name, value: c.name }, c.displayName || c.name))))) : null));
 });
 export default ConnectionTypeSelect;

package/esm/AddTrackWidget/components/AddTrackWidget.js

@@ -18,7 +18,9 @@ const AddTrackSelector = observer(function ({ model, }) {
     const Component = ComponentMap[val2];
     return (React.createElement(React.Fragment, null,
         React.createElement(FormControl, null,
-            React.createElement(Select, { value: val2, onChange: event => setVal(event.target.value) }, Object.keys(ComponentMap).map(e => (React.createElement(MenuItem, { key: e, value: e }, e)))),
+            React.createElement(Select, { value: val2, onChange: event => {
+                    setVal(event.target.value);
+                } }, Object.keys(ComponentMap).map(e => (React.createElement(MenuItem, { key: e, value: e }, e)))),
             React.createElement(FormHelperText, null, "Type of add track workflow")),
         React.createElement("br", null),
         React.createElement(Component, { model: model })));

package/esm/AddTrackWidget/components/ConfirmTrack.js

@@ -50,13 +50,13 @@ const ConfirmTrack = observer(function ConfirmTrack({ model, }) {
     const { classes } = useStyles();
     const [check, setCheck] = useState(true);
     const session = getSession(model);
-    const { trackName, trackAdapter, trackType, warningMessage, adapterHint } = model;
+    const { trackName, unsupported, trackAdapter, trackType, warningMessage, adapterHint, } = model;
     useEffect(() => {
         if (adapterHint === '' && trackAdapter) {
             model.setAdapterHint(trackAdapter.type);
         }
     }, [adapterHint, trackAdapter, trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type, model]);
-    if (model.unsupported) {
+    if (unsupported) {
         return (React.createElement(Typography, { className: classes.spacing },
             "This version of JBrowse cannot display data of this type. It is possible, however, that there is a newer version that can display them. You can",
             ' ',
@@ -74,14 +74,18 @@ const ConfirmTrack = observer(function ConfirmTrack({ model, }) {
     if (!(trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type)) {
         return React.createElement(Typography, null, "Could not recognize this data type.");
     }
-    const supportedForIndexing = isSupportedIndexingAdapter(trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type);
+    const supportedForIndexing = isSupportedIndexingAdapter(trackAdapter.type);
     return (React.createElement("div", null,
-        trackAdapter ? (React.createElement(StatusMessage, { trackAdapter: trackAdapter, trackType: trackType })) : null,
+        React.createElement(StatusMessage, { trackAdapter: trackAdapter, trackType: trackType }),
         warningMessage ? (React.createElement(Typography, { style: { color: 'orange' } }, warningMessage)) : null,
-        React.createElement(TextField, { className: classes.spacing, label: "trackName", helperText: "A name for this track", fullWidth: true, value: trackName, onChange: event => model.setTrackName(event.target.value), inputProps: { 'data-testid': 'trackNameInput' } }),
+        React.createElement(TextField, { className: classes.spacing, label: "trackName", helperText: "A name for this track", fullWidth: true, value: trackName, onChange: event => {
+                model.setTrackName(event.target.value);
+            }, inputProps: { 'data-testid': 'trackNameInput' } }),
         React.createElement(TrackAdapterSelector, { model: model }),
         React.createElement(TrackTypeSelector, { model: model }),
-        React.createElement(AssemblySelector, { session: session, helperText: "Select assembly to add track to", selected: model.assembly, onChange: asm => model.setAssembly(asm), TextFieldProps: {
+        React.createElement(AssemblySelector, { session: session, helperText: "Select assembly to add track to", selected: model.assembly, onChange: asm => {
+                model.setAssembly(asm);
+            }, TextFieldProps: {
                 fullWidth: true,
                 SelectProps: {
                     // @ts-expect-error

package/esm/AddTrackWidget/components/DefaultAddTrackWorkflow.js

@@ -30,7 +30,6 @@ const steps = ['Enter track data', 'Confirm track type'];
 const DefaultAddTrackWorkflow = observer(function ({ model, }) {
     const [activeStep, setActiveStep] = useState(0);
     const { classes } = useStyles();
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const { jobsManager } = getRoot(model);
     const session = getSession(model);
     const { assembly, trackAdapter, trackData, trackName, trackType, textIndexTrack, textIndexingConf, } = model;
@@ -53,7 +52,7 @@ const DefaultAddTrackWorkflow = observer(function ({ model, }) {
         }
         const trackId = [
             `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
-            `${session.adminMode ? '' : '-sessionTrack'}`,
+            session.adminMode ? '' : '-sessionTrack',
         ].join('');
         const assemblyInstance = session.assemblyManager.get(assembly);
         if (!isSessionWithAddTracks(session)) {
@@ -79,7 +78,7 @@ const DefaultAddTrackWorkflow = observer(function ({ model, }) {
                     attributes: ['Name', 'ID'],
                     exclude: ['CDS', 'exon'],
                 };
-                const indexName = trackName + '-index';
+                const indexName = `${trackName}-index`;
                 const newEntry = {
                     indexingParams: {
                         ...attr,

package/esm/AddTrackWidget/components/PasteConfigWorkflow.js

@@ -20,7 +20,9 @@ const PasteConfigAddTrackWorkflow = observer(function ({ model, }) {
     const [error, setError] = useState();
     return (React.createElement("div", null,
         error ? React.createElement(ErrorMessage, { error: error }) : null,
-        React.createElement(TextField, { multiline: true, rows: 10, value: val, onChange: event => setVal(event.target.value), placeholder: 'Paste track config or array of track configs in JSON format', variant: "outlined", className: classes.textbox }),
+        React.createElement(TextField, { multiline: true, rows: 10, value: val, onChange: event => {
+                setVal(event.target.value);
+            }, placeholder: 'Paste track config or array of track configs in JSON format', variant: "outlined", className: classes.textbox }),
         React.createElement(Button, { variant: "contained", className: classes.submit, onClick: () => {
                 try {
                     setError(undefined);
@@ -29,7 +31,9 @@ const PasteConfigAddTrackWorkflow = observer(function ({ model, }) {
                     const confs = Array.isArray(conf) ? conf : [conf];
                     if (isSessionWithAddTracks(session) &&
                         isSessionModelWithWidgets(session)) {
-                        confs.forEach(c => session.addTrackConf(c));
+                        confs.forEach(c => {
+                            session.addTrackConf(c);
+                        });
                         confs.forEach(c => model.view.showTrack(c.trackId));
                         model.clearData();
                         session.hideWidget(model);

package/esm/AddTrackWidget/components/TextIndexingConfig.js

@@ -40,22 +40,30 @@ const TextIndexingConfig = observer(function ({ model, }) {
             React.createElement(CardContent, null,
                 React.createElement(InputLabel, null, section.label),
                 React.createElement(List, { disablePadding: true },
-                    section.values.map((val, idx) => (React.createElement(ListItem, { key: idx, disableGutters: true },
+                    section.values.map((val, idx) => (
+                    /* biome-ignore lint/suspicious/noArrayIndexKey: */
+                    React.createElement(ListItem, { key: `${val}-${idx}`, disableGutters: true },
                         React.createElement(TextField, { value: val, InputProps: {
                                 endAdornment: (React.createElement(InputAdornment, { position: "end" },
                                     React.createElement(IconButton, { onClick: () => {
                                             const newAttr = section.values.filter((_, i) => i !== idx);
-                                            index === 0
-                                                ? setAttributes(newAttr)
-                                                : setExclude(newAttr);
+                                            if (index === 0) {
+                                                setAttributes(newAttr);
+                                            }
+                                            else {
+                                                setExclude(newAttr);
+                                            }
                                         } },
                                         React.createElement(DeleteIcon, null)))),
                             } })))),
                     React.createElement(ListItem, { disableGutters: true },
                         React.createElement(TextField, { value: index === 0 ? value1 : value2, placeholder: "add new", onChange: event => {
-                                index === 0
-                                    ? setValue1(event.target.value)
-                                    : setValue2(event.target.value);
+                                if (index === 0) {
+                                    setValue1(event.target.value);
+                                }
+                                else {
+                                    setValue2(event.target.value);
+                                }
                             }, InputProps: {
                                 endAdornment: (React.createElement(InputAdornment, { position: "end" },
                                     React.createElement(IconButton, { onClick: () => {
@@ -67,7 +75,7 @@ const TextIndexingConfig = observer(function ({ model, }) {
                                                 setExclude([...exclude, value2]);
                                                 setValue2('');
                                             }
-                                        }, disabled: index === 0 ? value1 === '' : value2 === '', "data-testid": `stringArrayAdd-Feat` },
+                                        }, disabled: index === 0 ? value1 === '' : value2 === '', "data-testid": "stringArrayAdd-Feat" },
                                         React.createElement(AddIcon, null)))),
                             } })))))))));
 });

package/esm/AddTrackWidget/components/TrackAdapterSelector.js

@@ -27,7 +27,9 @@ const TrackAdapterSelector = observer(({ model }) => {
     const { classes } = useStyles();
     const { trackAdapter } = model;
     const { pluginManager } = getEnv(model);
-    return (React.createElement(TextField, { className: classes.spacing, value: (trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) !== 'UNKNOWN' ? trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type : '', label: "Adapter type", variant: "outlined", helperText: "Select an adapter type", select: true, fullWidth: true, onChange: event => model.setAdapterHint(event.target.value), SelectProps: {
+    return (React.createElement(TextField, { className: classes.spacing, value: (trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) !== 'UNKNOWN' ? trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type : '', label: "Adapter type", variant: "outlined", helperText: "Select an adapter type", select: true, fullWidth: true, onChange: event => {
+            model.setAdapterHint(event.target.value);
+        }, SelectProps: {
             // @ts-expect-error
             SelectDisplayProps: { 'data-testid': 'adapterTypeSelect' },
         } }, Object.entries(categorizeAdapters(pluginManager

package/esm/AddTrackWidget/components/TrackTypeSelector.js

@@ -13,7 +13,9 @@ const TrackTypeSelector = observer(({ model }) => {
     const { pluginManager } = getEnv(model);
     const { trackType } = model;
     const trackTypes = pluginManager.getTrackElements();
-    return (React.createElement(TextField, { className: classes.spacing, value: trackType, variant: "outlined", label: "Track type", helperText: "Select track type", select: true, fullWidth: true, onChange: event => model.setTrackType(event.target.value), SelectProps: {
+    return (React.createElement(TextField, { className: classes.spacing, value: trackType, variant: "outlined", label: "Track type", helperText: "Select track type", select: true, fullWidth: true, onChange: event => {
+            model.setTrackType(event.target.value);
+        }, SelectProps: {
             // @ts-expect-error
             SelectDisplayProps: { 'data-testid': 'trackTypeSelect' },
         } }, trackTypes.map(({ name, displayName }) => (React.createElement(MenuItem, { key: name, value: name }, displayName)))));

package/esm/AddTrackWidget/model.js

@@ -215,7 +215,7 @@ export default function f(pluginManager) {
          */
         get warningMessage() {
             if (self.isFtp) {
-                return `Warning: JBrowse cannot access files using the ftp protocol`;
+                return 'Warning: JBrowse cannot access files using the ftp protocol';
             }
             else if (self.isRelativeUrl) {
                 return `Warning: one or more of your files do not provide the protocol e.g.

package/esm/AssemblyManager/AssemblyAddForm.d.ts

@@ -1,6 +1,7 @@
 import React from 'react';
+import { AbstractRootModel } from '@jbrowse/core/util/types';
 declare const AssemblyAddForm: ({ rootModel, setFormOpen, }: {
-    rootModel: any;
-    setFormOpen: Function;
+    rootModel: AbstractRootModel;
+    setFormOpen: (arg: boolean) => void;
 }) => React.JSX.Element;
 export default AssemblyAddForm;

package/esm/AssemblyManager/AssemblyAddForm.js

@@ -5,35 +5,47 @@ import { FileSelector } from '@jbrowse/core/ui';
 // icons
 import AddIcon from '@mui/icons-material/Add';
 const AdapterSelector = observer(function ({ adapterSelection, setAdapterSelection, adapterTypes, }) {
-    return (React.createElement(TextField, { value: adapterSelection, label: "Type", select: true, helperText: "Type of adapter to use", fullWidth: true, onChange: event => setAdapterSelection(event.target.value) }, adapterTypes.map(str => (React.createElement(MenuItem, { key: str, value: str }, str)))));
+    return (React.createElement(TextField, { value: adapterSelection, label: "Type", select: true, helperText: "Type of adapter to use", fullWidth: true, onChange: event => {
+            setAdapterSelection(event.target.value);
+        } }, adapterTypes.map(str => (React.createElement(MenuItem, { key: str, value: str }, str)))));
 });
-const AdapterInput = observer(({ adapterSelection, fastaLocation, setFastaLocation, faiLocation, setFaiLocation, gziLocation, setGziLocation, twoBitLocation, setTwoBitLocation, chromSizesLocation, setChromSizesLocation, }) => {
+const AdapterInput = observer(function ({ adapterSelection, fastaLocation, faiLocation, gziLocation, twoBitLocation, chromSizesLocation, setFaiLocation, setGziLocation, setTwoBitLocation, setFastaLocation, setChromSizesLocation, }) {
     if (adapterSelection === 'IndexedFastaAdapter' ||
         adapterSelection === 'BgzipFastaAdapter') {
         return (React.createElement(Grid, { container: true, spacing: 2 },
             React.createElement(Grid, { item: true },
-                React.createElement(FileSelector, { name: "fastaLocation", location: fastaLocation, setLocation: loc => setFastaLocation(loc) })),
+                React.createElement(FileSelector, { name: "fastaLocation", location: fastaLocation, setLocation: loc => {
+                        setFastaLocation(loc);
+                    } })),
             React.createElement(Grid, { item: true },
-                React.createElement(FileSelector, { name: "faiLocation", location: faiLocation, setLocation: loc => setFaiLocation(loc) })),
+                React.createElement(FileSelector, { name: "faiLocation", location: faiLocation, setLocation: loc => {
+                        setFaiLocation(loc);
+                    } })),
             adapterSelection === 'BgzipFastaAdapter' ? (React.createElement(Grid, { item: true },
-                React.createElement(FileSelector, { name: "gziLocation", location: gziLocation, setLocation: loc => setGziLocation(loc) }))) : null));
+                React.createElement(FileSelector, { name: "gziLocation", location: gziLocation, setLocation: loc => {
+                        setGziLocation(loc);
+                    } }))) : null));
     }
     if (adapterSelection === 'TwoBitAdapter') {
         return (React.createElement(Grid, { container: true, spacing: 2 },
             React.createElement(Grid, { item: true },
-                React.createElement(FileSelector, { name: "twoBitLocation", location: twoBitLocation, setLocation: loc => setTwoBitLocation(loc) })),
+                React.createElement(FileSelector, { name: "twoBitLocation", location: twoBitLocation, setLocation: loc => {
+                        setTwoBitLocation(loc);
+                    } })),
             React.createElement(Grid, { item: true },
-                React.createElement(FileSelector, { name: "chromSizesLocation (optional, can be added to speed up loading 2bit files with many contigs)", location: chromSizesLocation, setLocation: loc => setChromSizesLocation(loc) }))));
+                React.createElement(FileSelector, { name: "chromSizesLocation (optional, can be added to speed up loading 2bit files with many contigs)", location: chromSizesLocation, setLocation: loc => {
+                        setChromSizesLocation(loc);
+                    } }))));
     }
     return null;
 });
 const blank = { uri: '' };
+const adapterTypes = [
+    'IndexedFastaAdapter',
+    'BgzipFastaAdapter',
+    'TwoBitAdapter',
+];
 const AssemblyAddForm = observer(function ({ rootModel, setFormOpen, }) {
-    const adapterTypes = [
-        'IndexedFastaAdapter',
-        'BgzipFastaAdapter',
-        'TwoBitAdapter',
-    ];
     const [assemblyName, setAssemblyName] = useState('');
     const [assemblyDisplayName, setAssemblyDisplayName] = useState('');
     const [adapterSelection, setAdapterSelection] = useState(adapterTypes[0]);
@@ -43,8 +55,9 @@ const AssemblyAddForm = observer(function ({ rootModel, setFormOpen, }) {
     const [twoBitLocation, setTwoBitLocation] = useState(blank);
     const [chromSizesLocation, setChromSizesLocation] = useState(blank);
     function createAssembly() {
+        var _a, _b;
         if (assemblyName === '') {
-            rootModel.session.notify("Can't create an assembly without a name");
+            (_a = rootModel.session) === null || _a === void 0 ? void 0 : _a.notify("Can't create an assembly without a name");
         }
         else {
             setFormOpen(false);
@@ -89,16 +102,23 @@ const AssemblyAddForm = observer(function ({ rootModel, setFormOpen, }) {
                     },
                 };
             }
+            else {
+                throw new Error(`unknown ${adapterSelection}`);
+            }
             rootModel.jbrowse.addAssemblyConf(newAssembly);
-            rootModel.session.notify(`Successfully added ${assemblyName} assembly to JBrowse 2`, 'success');
+            (_b = rootModel.session) === null || _b === void 0 ? void 0 : _b.notify(`Successfully added ${assemblyName} assembly to JBrowse 2`, 'success');
         }
     }
     return (React.createElement("div", null,
         React.createElement(Paper, null,
-            React.createElement(TextField, { id: "assembly-name", inputProps: { 'data-testid': 'assembly-name' }, label: "Assembly name", helperText: "The assembly name e.g. hg38", variant: "outlined", value: assemblyName, onChange: event => setAssemblyName(event.target.value) }),
-            React.createElement(TextField, { id: "assembly-name", inputProps: { 'data-testid': 'assembly-display-name' }, label: "Assembly display name", helperText: 'A human readable display name for the assembly e.g. "Homo sapiens (hg38)"', variant: "outlined", value: assemblyDisplayName, onChange: event => setAssemblyDisplayName(event.target.value) }),
-            React.createElement(AdapterSelector, { adapterSelection: adapterSelection, setAdapterSelection: setAdapterSelection, adapterTypes: adapterTypes }),
-            React.createElement(AdapterInput, { adapterSelection: adapterSelection, fastaLocation: fastaLocation, setFastaLocation: setFastaLocation, faiLocation: faiLocation, setFaiLocation: setFaiLocation, gziLocation: gziLocation, setGziLocation: setGziLocation, twoBitLocation: twoBitLocation, setTwoBitLocation: setTwoBitLocation, chromSizesLocation: chromSizesLocation, setChromSizesLocation: setChromSizesLocation })),
+            React.createElement(TextField, { id: "assembly-name", inputProps: { 'data-testid': 'assembly-name' }, label: "Assembly name", helperText: "The assembly name e.g. hg38", variant: "outlined", value: assemblyName, onChange: event => {
+                    setAssemblyName(event.target.value);
+                } }),
+            React.createElement(TextField, { id: "assembly-name", inputProps: { 'data-testid': 'assembly-display-name' }, label: "Assembly display name", helperText: 'A human readable display name for the assembly e.g. "Homo sapiens (hg38)"', variant: "outlined", value: assemblyDisplayName, onChange: event => {
+                    setAssemblyDisplayName(event.target.value);
+                } }),
+            React.createElement(AdapterSelector, { adapterSelection: adapterSelection, adapterTypes: adapterTypes, setAdapterSelection: setAdapterSelection }),
+            React.createElement(AdapterInput, { adapterSelection: adapterSelection, fastaLocation: fastaLocation, faiLocation: faiLocation, gziLocation: gziLocation, twoBitLocation: twoBitLocation, chromSizesLocation: chromSizesLocation, setFaiLocation: setFaiLocation, setGziLocation: setGziLocation, setTwoBitLocation: setTwoBitLocation, setFastaLocation: setFastaLocation, setChromSizesLocation: setChromSizesLocation })),
         React.createElement(Button, { variant: "contained", color: "secondary", startIcon: React.createElement(AddIcon, null), onClick: createAssembly }, "Create new assembly")));
 });
 export default AssemblyAddForm;

package/esm/AssemblyManager/AssemblyManager.js

@@ -13,16 +13,26 @@ const AssemblyManager = observer(function ({ rootModel, onClose, }) {
     const [isAssemblyBeingEdited, setIsAssemblyBeingEdited] = useState(false);
     const [assemblyBeingEdited, setAssemblyBeingEdited] = useState();
     const showAssemblyTable = !isFormOpen && !isAssemblyBeingEdited;
-    return (React.createElement(Dialog, { open: true, onClose: () => onClose(false), title: "Assembly manager" },
+    return (React.createElement(Dialog, { open: true, onClose: () => {
+            onClose(false);
+        }, title: "Assembly manager" },
         React.createElement(DialogContent, null,
             showAssemblyTable ? (React.createElement(AssemblyTable, { rootModel: rootModel, setIsAssemblyBeingEdited: setIsAssemblyBeingEdited, setAssemblyBeingEdited: setAssemblyBeingEdited })) : null,
             isAssemblyBeingEdited ? (React.createElement(AssemblyEditor, { assembly: assemblyBeingEdited })) : null,
             isFormOpen ? (React.createElement(AssemblyAddForm, { rootModel: rootModel, setFormOpen: setFormOpen })) : null),
         React.createElement(DialogActions, null,
-            isFormOpen ? (React.createElement(Button, { variant: "contained", onClick: () => setFormOpen(false) }, "Back")) : null,
-            isAssemblyBeingEdited ? (React.createElement(Button, { variant: "contained", onClick: () => setIsAssemblyBeingEdited(false) }, "Back")) : null,
+            isFormOpen ? (React.createElement(Button, { variant: "contained", onClick: () => {
+                    setFormOpen(false);
+                } }, "Back")) : null,
+            isAssemblyBeingEdited ? (React.createElement(Button, { variant: "contained", onClick: () => {
+                    setIsAssemblyBeingEdited(false);
+                } }, "Back")) : null,
             showAssemblyTable ? (React.createElement(React.Fragment, null,
-                React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => onClose(false) }, "Close"),
-                React.createElement(Button, { variant: "contained", startIcon: React.createElement(AddIcon, null), onClick: () => setFormOpen(true) }, "Add new assembly"))) : null)));
+                React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
+                        onClose(false);
+                    } }, "Close"),
+                React.createElement(Button, { variant: "contained", startIcon: React.createElement(AddIcon, null), onClick: () => {
+                        setFormOpen(true);
+                    } }, "Add new assembly"))) : null)));
 });
 export default AssemblyManager;

package/esm/AssemblyManager/AssemblyTable.js

@@ -31,7 +31,9 @@ const AssemblyTable = observer(function ({ rootModel, setIsAssemblyBeingEdited,
                                 setAssemblyBeingEdited(assembly);
                             } },
                             React.createElement(CreateIcon, { color: "primary" })),
-                        React.createElement(IconButton, { "data-testid": `${name}-delete`, onClick: () => removeAssembly(name) },
+                        React.createElement(IconButton, { "data-testid": `${name}-delete`, onClick: () => {
+                                removeAssembly(name);
+                            } },
                             React.createElement(DeleteIcon, { color: "error" })))));
             })))));
 });

package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalFab.js

@@ -22,9 +22,13 @@ const HierarchicalFab = observer(function ({ model, }) {
     const hasConnections = isSessionModelWithConnections(session);
     const hasAddTrack = isSessionWithAddTracks(session);
     return hasAddTrack || hasConnections ? (React.createElement(React.Fragment, null,
-        React.createElement(Fab, { color: "secondary", className: classes.fab, onClick: event => setAnchorEl(event.currentTarget) },
+        React.createElement(Fab, { color: "secondary", className: classes.fab, onClick: event => {
+                setAnchorEl(event.currentTarget);
+            } },
             React.createElement(AddIcon, null)),
-        React.createElement(Menu, { anchorEl: anchorEl, open: Boolean(anchorEl), onClose: () => setAnchorEl(null) },
+        React.createElement(Menu, { anchorEl: anchorEl, open: Boolean(anchorEl), onClose: () => {
+                setAnchorEl(null);
+            } },
             hasConnections ? (React.createElement(MenuItem, { onClick: () => {
                     handleFabClose();
                     if (isSessionModelWithWidgets(session)) {

package/esm/HierarchicalTrackSelectorWidget/components/ShoppingCart.js

@@ -11,10 +11,21 @@ const ShoppingCart = observer(function ({ model, }) {
     const session = getSession(model);
     const items = pluginManager.evaluateExtensionPoint('TrackSelector-multiTrackMenuItems', [], { session });
     return selection.length ? (React.createElement(CascadingMenuButton, { menuItems: [
-            { label: 'Clear', onClick: () => model.clearSelection() },
+            {
+                label: 'Clear',
+                onClick: () => {
+                    model.clearSelection();
+                },
+            },
             ...items.map(item => ({
                 ...item,
-                ...('onClick' in item ? { onClick: () => item.onClick(model) } : {}),
+                ...('onClick' in item
+                    ? {
+                        onClick: () => {
+                            item.onClick(model);
+                        },
+                    }
+                    : {}),
             })),
         ] },
         React.createElement(Badge, { badgeContent: selection.length, color: "primary" },

package/esm/HierarchicalTrackSelectorWidget/components/dialogs/CloseConnectionDialog.js

@@ -11,12 +11,12 @@ const CloseConnectionDialog = observer(function CloseConnectionDialog({ modalInf
                 React.createElement(List, null, Object.entries(dereferenceTypeCount).map(([key, value]) => (React.createElement(ListItem, { key: key }, `${value} ${key}`)))))) : null,
             React.createElement(DialogContentText, null, "Are you sure you want to close this connection?")),
         React.createElement(DialogActions, null,
-            React.createElement(Button, { onClick: () => onClose(), color: "primary" }, "Cancel"),
-            React.createElement(Button, { variant: "contained", onClick: modalInfo
-                    ? () => {
-                        safelyBreakConnection === null || safelyBreakConnection === void 0 ? void 0 : safelyBreakConnection();
-                        onClose();
-                    }
-                    : () => { }, color: "primary" }, "OK"))));
+            React.createElement(Button, { onClick: () => {
+                    onClose();
+                }, color: "primary" }, "Cancel"),
+            React.createElement(Button, { variant: "contained", onClick: () => {
+                    safelyBreakConnection === null || safelyBreakConnection === void 0 ? void 0 : safelyBreakConnection();
+                    onClose();
+                }, color: "primary" }, "OK"))));
 });
 export default CloseConnectionDialog;

package/esm/HierarchicalTrackSelectorWidget/components/dialogs/DeleteConnectionDialog.js

@@ -8,12 +8,12 @@ const DeleteConnectionDialog = observer(function DeleteConnectionDialog({ delete
         React.createElement(DialogContent, null,
             React.createElement(DialogContentText, null, "Are you sure you want to delete this connection?")),
         React.createElement(DialogActions, null,
-            React.createElement(Button, { onClick: () => handleClose(), color: "primary" }, "Cancel"),
+            React.createElement(Button, { onClick: () => {
+                    handleClose();
+                }, color: "primary" }, "Cancel"),
             React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
                     var _a;
-                    if (connectionConf) {
-                        (_a = session.deleteConnection) === null || _a === void 0 ? void 0 : _a.call(session, connectionConf);
-                    }
+                    (_a = session.deleteConnection) === null || _a === void 0 ? void 0 : _a.call(session, connectionConf);
                     handleClose();
                 } }, "OK"))));
 });

package/esm/HierarchicalTrackSelectorWidget/components/dialogs/ManageConnectionsDialog.js

@@ -27,12 +27,16 @@ const ManageConnectionsDialog = observer(function ({ session, handleClose, break
                 connections.map(conf => {
                     const name = readConfObject(conf, 'name');
                     return (React.createElement(Typography, { key: `conn-${name}` },
-                        adminMode || (sessionConnections === null || sessionConnections === void 0 ? void 0 : sessionConnections.includes(conf)) ? (React.createElement(IconButton, { onClick: () => breakConnection(conf, true) },
+                        adminMode || (sessionConnections === null || sessionConnections === void 0 ? void 0 : sessionConnections.includes(conf)) ? (React.createElement(IconButton, { onClick: () => {
+                                breakConnection(conf, true);
+                            } },
                             React.createElement(CloseIcon, { color: "error" }))) : (React.createElement(DisabledButton, null)),
                         name));
                 }),
                 !connections.length ? (React.createElement(Typography, null, "No connections found")) : null)),
         React.createElement(DialogActions, null,
-            React.createElement(Button, { onClick: () => handleClose(), variant: "contained", color: "primary" }, "Close"))));
+            React.createElement(Button, { onClick: () => {
+                    handleClose();
+                }, variant: "contained", color: "primary" }, "Close"))));
 });
 export default ManageConnectionsDialog;

package/esm/HierarchicalTrackSelectorWidget/components/dialogs/ToggleConnectionsDialog.js

@@ -35,7 +35,7 @@ const ConnectionRow = observer(function ConnectionRow({ conf, session, breakConn
 });
 const ConnectionList = observer(function ConnectionsList({ session, breakConnection, }) {
     const { classes } = useStyles();
-    return (React.createElement("div", { className: classes.connectionContainer }, !session.connections.length ? (React.createElement(Typography, null, "No connections found")) : (session.connections.map((conf, idx) => (React.createElement("div", { key: conf.name + '_' + idx },
+    return (React.createElement("div", { className: classes.connectionContainer }, !session.connections.length ? (React.createElement(Typography, null, "No connections found")) : (session.connections.map((conf, idx) => (React.createElement("div", { key: `${conf.name}_${idx}` },
         React.createElement(ConnectionRow, { conf: conf, session: session, breakConnection: breakConnection })))))));
 });
 const ToggleConnectionDialog = observer(function ({ session, handleClose, breakConnection, }) {
@@ -44,6 +44,8 @@ const ToggleConnectionDialog = observer(function ({ session, handleClose, breakC
             React.createElement(Typography, null, "Use the checkbox to turn on/off connections"),
             React.createElement(ConnectionList, { session: session, breakConnection: breakConnection })),
         React.createElement(DialogActions, null,
-            React.createElement(Button, { onClick: () => handleClose(), variant: "contained", color: "primary" }, "Close"))));
+            React.createElement(Button, { onClick: () => {
+                    handleClose();
+                }, variant: "contained", color: "primary" }, "Close"))));
 });
 export default ToggleConnectionDialog;

package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetFilter.js

@@ -18,12 +18,16 @@ const useStyles = makeStyles()(theme => ({
 }));
 function ClearButton({ onClick }) {
     return (React.createElement(Tooltip, { title: "Clear selection on this facet filter" },
-        React.createElement(IconButton, { onClick: () => onClick(), size: "small" },
+        React.createElement(IconButton, { onClick: () => {
+                onClick();
+            }, size: "small" },
             React.createElement(ClearIcon, null))));
 }
 function ExpandButton({ visible, onClick, }) {
     return (React.createElement(Tooltip, { title: "Minimize/expand this facet filter" },
-        React.createElement(IconButton, { onClick: () => onClick(), size: "small" }, visible ? React.createElement(MinimizeIcon, null) : React.createElement(AddIcon, null))));
+        React.createElement(IconButton, { onClick: () => {
+                onClick();
+            }, size: "small" }, visible ? React.createElement(MinimizeIcon, null) : React.createElement(AddIcon, null))));
 }
 const FacetFilter = observer(function ({ column, vals, model, }) {
     const { classes } = useStyles();
@@ -34,8 +38,12 @@ const FacetFilter = observer(function ({ column, vals, model, }) {
     return (React.createElement(FormControl, { className: classes.facet, fullWidth: true },
         React.createElement("div", null,
             React.createElement(Typography, { component: "span" }, field),
-            React.createElement(ClearButton, { onClick: () => faceted.setFilter(field, []) }),
-            React.createElement(ExpandButton, { visible: visible, onClick: () => setVisible(!visible) })),
+            React.createElement(ClearButton, { onClick: () => {
+                    faceted.setFilter(field, []);
+                } }),
+            React.createElement(ExpandButton, { visible: visible, onClick: () => {
+                    setVisible(!visible);
+                } })),
         visible ? (React.createElement(Select, { multiple: true, native: true, className: classes.select, value: filters.get(column.field) || [], onChange: event => {
                 faceted.setFilter(column.field, 
                 // @ts-expect-error