@jbrowse/plugin-config 2.13.1 → 2.14.0

package/dist/ConfigurationEditorWidget/components/BooleanEditor.js

@@ -8,7 +8,9 @@ const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
 const BooleanEditor = (0, mobx_react_1.observer)(function ({ slot, }) {
     return (react_1.default.createElement(material_1.FormControl, null,
-        react_1.default.createElement(material_1.FormControlLabel, { label: slot.name, control: react_1.default.createElement(material_1.Checkbox, { checked: slot.value, onChange: evt => slot.set(evt.target.checked) }) }),
+        react_1.default.createElement(material_1.FormControlLabel, { label: slot.name, control: react_1.default.createElement(material_1.Checkbox, { checked: slot.value, onChange: evt => {
+                    slot.set(evt.target.checked);
+                } }) }),
         react_1.default.createElement(material_1.FormHelperText, null, slot.description)));
 });
 exports.default = BooleanEditor;

package/dist/ConfigurationEditorWidget/components/CallbackEditor.js

@@ -85,7 +85,9 @@ const CallbackEditor = (0, mobx_react_1.observer)(function ({ slot, }) {
     return (react_1.default.createElement(react_1.default.Fragment, null,
         error ? react_1.default.createElement("p", { className: classes.error }, `${error}`) : null,
         react_1.default.createElement("div", { className: classes.callbackContainer },
-            react_1.default.createElement(material_1.TextField, { multiline: true, className: classes.callbackEditor, value: code.startsWith('jexl:') ? code.split('jexl:')[1] : code, onChange: event => setCode(event.target.value), style: { background: error ? '#fdd' : undefined }, InputProps: {
+            react_1.default.createElement(material_1.TextField, { multiline: true, className: classes.callbackEditor, value: code.startsWith('jexl:') ? code.split('jexl:')[1] : code, onChange: event => {
+                    setCode(event.target.value);
+                }, style: { background: error ? '#fdd' : undefined }, InputProps: {
                     classes: {
                         input: classes.textAreaFont,
                     },

package/dist/ConfigurationEditorWidget/components/ColorEditor.js

@@ -35,15 +35,23 @@ const ColorSlot = (props) => {
     const { value = '#000', label = '', TextFieldProps = {}, onChange } = props;
     const [displayed, setDisplayed] = (0, react_1.useState)(false);
     return (react_1.default.createElement("div", { style: { display: 'flex' } },
-        react_1.default.createElement(material_1.TextField, { value: value, label: label, onClick: () => setDisplayed(!displayed), onChange: event => onChange(event.target.value), ...TextFieldProps }),
+        react_1.default.createElement(material_1.TextField, { value: value, label: label, onClick: () => {
+                setDisplayed(!displayed);
+            }, onChange: event => {
+                onChange(event.target.value);
+            }, ...TextFieldProps }),
         react_1.default.createElement("div", { style: { marginTop: 10 } },
             react_1.default.createElement(react_1.default.Suspense, { fallback: null },
-                react_1.default.createElement(ColorPicker_1.default, { color: value, onChange: event => onChange(event) })))));
+                react_1.default.createElement(ColorPicker_1.default, { color: value, onChange: event => {
+                        onChange(event);
+                    } })))));
 };
 exports.ColorSlot = ColorSlot;
 const ColorEditor = (0, mobx_react_1.observer)(function (props) {
     const { slot } = props;
-    return (react_1.default.createElement(exports.ColorSlot, { label: slot.name, value: slot.value, onChange: color => slot.set(color), TextFieldProps: {
+    return (react_1.default.createElement(exports.ColorSlot, { label: slot.name, value: slot.value, onChange: color => {
+            slot.set(color);
+        }, TextFieldProps: {
             helperText: slot.description,
             fullWidth: true,
         } }));

package/dist/ConfigurationEditorWidget/components/ConfigurationEditor.js

@@ -16,25 +16,22 @@ const ExpandMore_1 = __importDefault(require("@mui/icons-material/ExpandMore"));
 // locals
 const SlotEditor_1 = __importDefault(require("./SlotEditor"));
 const TypeSelector_1 = __importDefault(require("./TypeSelector"));
-const useStyles = (0, mui_1.makeStyles)()(theme => {
-    var _a;
-    return ({
-        icon: {
-            color: ((_a = theme.palette.tertiary) === null || _a === void 0 ? void 0 : _a.contrastText) || '#fff',
-        },
-        expansionPanelDetails: {
-            display: 'block',
-            padding: theme.spacing(1),
-        },
-        accordion: {
-            border: `1px solid ${theme.palette.text.primary}`,
-        },
-        noOverflow: {
-            width: '100%',
-            overflowX: 'auto',
-        },
-    });
-});
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    icon: {
+        color: theme.palette.tertiary.contrastText || '#fff',
+    },
+    expansionPanelDetails: {
+        display: 'block',
+        padding: theme.spacing(1),
+    },
+    accordion: {
+        border: `1px solid ${theme.palette.text.primary}`,
+    },
+    noOverflow: {
+        width: '100%',
+        overflowX: 'auto',
+    },
+}));
 const Member = (0, mobx_react_1.observer)(function (props) {
     const { classes } = useStyles();
     const { slotName, slotSchema, schema, slot = schema[slotName], path = [], } = props;
@@ -75,16 +72,17 @@ const Schema = (0, mobx_react_1.observer)(function ({ schema, path = [], }) {
 });
 const ConfigurationEditor = (0, mobx_react_1.observer)(function ({ model, }) {
     const { classes } = useStyles();
-    // key forces a re-render, otherwise the same field can end up being used
-    // for different tracks since only the backing model changes for example
-    // see pr #804
+    // key forces a re-render, otherwise the same field can end up being used for
+    // different tracks since only the backing model changes for example see pr
+    // #804
     const { target } = model;
-    const key = target && (0, configuration_1.readConfObject)(target, 'trackId');
-    const name = target && (0, configuration_1.readConfObject)(target, 'name');
+    const key = (0, configuration_1.readConfObject)(target, 'trackId');
+    const name = (0, configuration_1.readConfObject)(target, 'name');
     return (react_1.default.createElement(material_1.Accordion, { key: key, defaultExpanded: true, className: classes.accordion },
         react_1.default.createElement(material_1.AccordionSummary, { expandIcon: react_1.default.createElement(ExpandMore_1.default, { className: classes.icon }) },
             react_1.default.createElement(material_1.Typography, null,
                 react_1.default.createElement(SanitizedHTML_1.default, { html: name !== null && name !== void 0 ? name : 'Configuration' }))),
-        react_1.default.createElement(material_1.AccordionDetails, { className: classes.expansionPanelDetails, "data-testid": "configEditor" }, !target ? 'no target set' : react_1.default.createElement(Schema, { schema: target }))));
+        react_1.default.createElement(material_1.AccordionDetails, { className: classes.expansionPanelDetails, "data-testid": "configEditor" },
+            react_1.default.createElement(Schema, { schema: target }))));
 });
 exports.default = ConfigurationEditor;

package/dist/ConfigurationEditorWidget/components/HeadingComponent.js

@@ -13,7 +13,7 @@ const HeadingComponent = (0, mobx_react_1.observer)(function ({ model, }) {
         }
         if ((0, mobx_state_tree_1.isStateTreeNode)(model.target)) {
             const type = (0, mobx_state_tree_1.getType)(model.target);
-            if (type === null || type === void 0 ? void 0 : type.name) {
+            if (type.name) {
                 return `${type.name.replace('ConfigurationSchema', '')} settings`;
             }
         }

package/dist/ConfigurationEditorWidget/components/JsonEditor.js

@@ -70,7 +70,9 @@ const JsonEditor = (0, mobx_react_1.observer)(function JsonEditor({ slot, }) {
         error ? react_1.default.createElement("p", { className: classes.error }, `${error}`) : null,
         react_1.default.createElement("div", { className: classes.callbackContainer },
             react_1.default.createElement(material_1.InputLabel, { shrink: true, htmlFor: "json-editor" }, slot.name),
-            react_1.default.createElement(material_1.TextField, { id: "json-editor", className: classes.callbackEditor, value: contents, helperText: slot.description, multiline: true, onChange: event => setContents(event.target.value), style: { background: error ? '#fdd' : undefined }, InputProps: {
+            react_1.default.createElement(material_1.TextField, { id: "json-editor", className: classes.callbackEditor, value: contents, helperText: slot.description, multiline: true, onChange: event => {
+                    setContents(event.target.value);
+                }, style: { background: error ? '#fdd' : undefined }, InputProps: {
                     classes: {
                         input: classes.textAreaFont,
                     },

package/dist/ConfigurationEditorWidget/components/NumberEditor.js

@@ -41,6 +41,8 @@ const NumberEditor = (0, mobx_react_1.observer)(function ({ slot, }) {
             slot.set(num);
         }
     }, [slot, val]);
-    return (react_1.default.createElement(ConfigurationTextField_1.default, { label: slot.name, helperText: slot.description, value: val, type: "number", onChange: evt => setVal(evt.target.value) }));
+    return (react_1.default.createElement(ConfigurationTextField_1.default, { label: slot.name, helperText: slot.description, value: val, type: "number", onChange: evt => {
+            setVal(evt.target.value);
+        } }));
 });
 exports.default = NumberEditor;

package/dist/ConfigurationEditorWidget/components/NumberMapEditor.js

@@ -45,15 +45,21 @@ const NumberMapEditor = (0, mobx_react_1.observer)(function ({ slot, }) {
     return (react_1.default.createElement(react_1.default.Fragment, null,
         react_1.default.createElement(material_1.InputLabel, null, slot.name),
         [...slot.value].map(([key, val]) => (react_1.default.createElement(material_1.Card, { raised: true, key: key, className: classes.card },
-            react_1.default.createElement(material_1.CardHeader, { title: key, action: react_1.default.createElement(material_1.IconButton, { onClick: () => slot.remove(key) },
+            react_1.default.createElement(material_1.CardHeader, { title: key, action: react_1.default.createElement(material_1.IconButton, { onClick: () => {
+                        slot.remove(key);
+                    } },
                     react_1.default.createElement(Delete_1.default, null)) }),
             react_1.default.createElement(material_1.CardContent, null,
                 react_1.default.createElement(NumberEditor_1.default, { slot: {
                         value: val,
-                        set: (val) => slot.add(key, val),
+                        set: (val) => {
+                            slot.add(key, val);
+                        },
                     } }))))),
         react_1.default.createElement(material_1.Card, { raised: true, className: classes.card },
-            react_1.default.createElement(material_1.CardHeader, { disableTypography: true, title: react_1.default.createElement(material_1.TextField, { fullWidth: true, value: value, placeholder: "add new", onChange: event => setValue(event.target.value), InputProps: {
+            react_1.default.createElement(material_1.CardHeader, { disableTypography: true, title: react_1.default.createElement(material_1.TextField, { fullWidth: true, value: value, placeholder: "add new", onChange: event => {
+                        setValue(event.target.value);
+                    }, InputProps: {
                         endAdornment: (react_1.default.createElement(material_1.InputAdornment, { position: "end" },
                             react_1.default.createElement(material_1.IconButton, { disabled: value === '', onClick: () => {
                                     slot.add(value, 0);

package/dist/ConfigurationEditorWidget/components/SlotEditor.js

@@ -47,10 +47,14 @@ const NumberEditor_1 = __importDefault(require("./NumberEditor"));
 const BooleanEditor_1 = __importDefault(require("./BooleanEditor"));
 const useSlotEditorStyles_1 = require("./useSlotEditorStyles");
 const StringEditor = (0, mobx_react_1.observer)(function ({ slot, }) {
-    return (react_1.default.createElement(ConfigurationTextField_1.default, { label: slot.name, helperText: slot.description, value: slot.value, onChange: evt => slot.set(evt.target.value) }));
+    return (react_1.default.createElement(ConfigurationTextField_1.default, { label: slot.name, helperText: slot.description, value: slot.value, onChange: evt => {
+            slot.set(evt.target.value);
+        } }));
 });
 const TextEditor = (0, mobx_react_1.observer)(function ({ slot, }) {
-    return (react_1.default.createElement(material_1.TextField, { label: slot.name, helperText: slot.description, multiline: true, value: slot.value, onChange: evt => slot.set(evt.target.value) }));
+    return (react_1.default.createElement(material_1.TextField, { label: slot.name, helperText: slot.description, multiline: true, value: slot.value, onChange: evt => {
+            slot.set(evt.target.value);
+        } }));
 });
 // checked checkbox, looks like a styled (x)
 const SvgCheckbox = () => (react_1.default.createElement(material_1.SvgIcon, null,
@@ -63,16 +67,24 @@ const IntegerEditor = (0, mobx_react_1.observer)(function ({ slot, }) {
             slot.set(num);
         }
     }, [slot, val]);
-    return (react_1.default.createElement(ConfigurationTextField_1.default, { label: slot.name, helperText: slot.description, value: val, type: "number", onChange: evt => setVal(evt.target.value) }));
+    return (react_1.default.createElement(ConfigurationTextField_1.default, { label: slot.name, helperText: slot.description, value: val, type: "number", onChange: evt => {
+            setVal(evt.target.value);
+        } }));
 });
 const StringEnumEditor = (0, mobx_react_1.observer)(function ({ slot, slotSchema, }) {
     const p = (0, mobx_state_tree_1.getPropertyMembers)((0, mst_reflection_1.getSubType)(slotSchema));
     const choices = (0, mst_reflection_1.getUnionSubTypes)((0, mst_reflection_1.getUnionSubTypes)((0, mst_reflection_1.getSubType)(p.properties.value))[1]).map(t => t.value);
-    return (react_1.default.createElement(ConfigurationTextField_1.default, { value: slot.value, label: slot.name, select: true, helperText: slot.description, onChange: evt => slot.set(evt.target.value) }, choices.map(str => (react_1.default.createElement(material_1.MenuItem, { key: str, value: str }, str)))));
+    return (react_1.default.createElement(ConfigurationTextField_1.default, { value: slot.value, label: slot.name, select: true, helperText: slot.description, onChange: evt => {
+            slot.set(evt.target.value);
+        } }, choices.map(str => (react_1.default.createElement(material_1.MenuItem, { key: str, value: str }, str)))));
 });
 const FileSelectorWrapper = (0, mobx_react_1.observer)(function ({ slot, }) {
     var _a;
-    return (react_1.default.createElement(ui_1.FileSelector, { location: slot.value, setLocation: location => slot.set(location), name: slot.name, description: slot.description, rootModel: (_a = (0, util_1.getEnv)(slot).pluginManager) === null || _a === void 0 ? void 0 : _a.rootModel }));
+    return (react_1.default.createElement(ui_1.FileSelector, { location: slot.value, setLocation: location => {
+            slot.set(location);
+        }, name: slot.name, description: slot.description, 
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+        rootModel: (_a = (0, util_1.getEnv)(slot).pluginManager) === null || _a === void 0 ? void 0 : _a.rootModel }));
 });
 const valueComponents = {
     string: StringEditor,

package/dist/ConfigurationEditorWidget/components/StringArrayEditor.d.ts

@@ -3,9 +3,9 @@ declare const StringArrayEditor: ({ slot, }: {
     slot: {
         name: string;
         value: string[];
-        setAtIndex: Function;
-        removeAtIndex: Function;
-        add: Function;
+        setAtIndex: (arg: number, arg2: string) => void;
+        removeAtIndex: (arg: number) => void;
+        add: (arg: string) => void;
         description: string;
     };
 }) => React.JSX.Element;

package/dist/ConfigurationEditorWidget/components/StringArrayEditor.js

@@ -37,14 +37,20 @@ const StringArrayEditor = (0, mobx_react_1.observer)(function ({ slot, }) {
     return (react_1.default.createElement(react_1.default.Fragment, null,
         slot.name ? react_1.default.createElement(material_1.InputLabel, null, slot.name) : null,
         react_1.default.createElement(material_1.List, { disablePadding: true },
-            slot.value.map((val, idx) => (react_1.default.createElement(material_1.ListItem, { key: idx, disableGutters: true },
-                react_1.default.createElement(material_1.TextField, { value: val, onChange: evt => slot.setAtIndex(idx, evt.target.value), InputProps: {
+            slot.value.map((val, idx) => (react_1.default.createElement(material_1.ListItem, { key: `${JSON.stringify(val)}-${idx}`, disableGutters: true },
+                react_1.default.createElement(material_1.TextField, { value: val, onChange: evt => {
+                        slot.setAtIndex(idx, evt.target.value);
+                    }, InputProps: {
                         endAdornment: (react_1.default.createElement(material_1.InputAdornment, { position: "end" },
-                            react_1.default.createElement(material_1.IconButton, { onClick: () => slot.removeAtIndex(idx) },
+                            react_1.default.createElement(material_1.IconButton, { onClick: () => {
+                                    slot.removeAtIndex(idx);
+                                } },
                                 react_1.default.createElement(Delete_1.default, null)))),
                     } })))),
             addNew ? (react_1.default.createElement(material_1.ListItem, { disableGutters: true },
-                react_1.default.createElement(material_1.TextField, { value: value, placeholder: "add new", onChange: event => setValue(event.target.value), InputProps: {
+                react_1.default.createElement(material_1.TextField, { value: value, placeholder: "add new", onChange: event => {
+                        setValue(event.target.value);
+                    }, InputProps: {
                         endAdornment: (react_1.default.createElement(material_1.InputAdornment, { position: "end" },
                             react_1.default.createElement(react_1.default.Fragment, null,
                                 react_1.default.createElement(material_1.Button, { color: "primary", variant: "contained", style: { margin: 2 }, "data-testid": `stringArrayAdd-${slot.name}`, onClick: () => {
@@ -57,7 +63,9 @@ const StringArrayEditor = (0, mobx_react_1.observer)(function ({ slot, }) {
                                         setValue('');
                                     } }, "Cancel")))),
                     } }))) : null,
-            react_1.default.createElement(material_1.Button, { color: "primary", variant: "contained", style: { margin: 4 }, disabled: addNew, onClick: () => setAddNew(true) }, "Add item")),
+            react_1.default.createElement(material_1.Button, { color: "primary", variant: "contained", style: { margin: 4 }, disabled: addNew, onClick: () => {
+                    setAddNew(true);
+                } }, "Add item")),
         react_1.default.createElement(material_1.FormHelperText, null, slot.description)));
 });
 exports.default = StringArrayEditor;

package/dist/ConfigurationEditorWidget/components/StringArrayMapEditor.js

@@ -46,19 +46,29 @@ const StringArrayMapEditor = (0, mobx_react_1.observer)(function ({ slot, }) {
     return (react_1.default.createElement(react_1.default.Fragment, null,
         react_1.default.createElement(material_1.InputLabel, null, slot.name),
         [...slot.value].map(([key, val]) => (react_1.default.createElement(material_1.Card, { raised: true, key: key, className: classes.card },
-            react_1.default.createElement(material_1.CardHeader, { title: key, action: react_1.default.createElement(material_1.IconButton, { onClick: () => slot.remove(key) },
+            react_1.default.createElement(material_1.CardHeader, { title: key, action: react_1.default.createElement(material_1.IconButton, { onClick: () => {
+                        slot.remove(key);
+                    } },
                     react_1.default.createElement(Delete_1.default, null)) }),
             react_1.default.createElement(material_1.CardContent, null,
                 react_1.default.createElement(StringArrayEditor_1.default, { slot: {
                         name: slot.name,
                         value: val,
                         description: `Values associated with entry ${key}`,
-                        setAtIndex: (idx, val) => slot.setAtKeyIndex(key, idx, val),
-                        removeAtIndex: (idx) => slot.removeAtKeyIndex(key, idx),
-                        add: (val) => slot.addToKey(key, val),
+                        setAtIndex: (idx, val) => {
+                            slot.setAtKeyIndex(key, idx, val);
+                        },
+                        removeAtIndex: (idx) => {
+                            slot.removeAtKeyIndex(key, idx);
+                        },
+                        add: (val) => {
+                            slot.addToKey(key, val);
+                        },
                     } }))))),
         react_1.default.createElement(material_1.Card, { raised: true, className: classes.card },
-            react_1.default.createElement(material_1.CardHeader, { disableTypography: true, title: react_1.default.createElement(material_1.TextField, { fullWidth: true, value: value, placeholder: "add new", onChange: event => setValue(event.target.value), InputProps: {
+            react_1.default.createElement(material_1.CardHeader, { disableTypography: true, title: react_1.default.createElement(material_1.TextField, { fullWidth: true, value: value, placeholder: "add new", onChange: event => {
+                        setValue(event.target.value);
+                    }, InputProps: {
                         endAdornment: (react_1.default.createElement(material_1.InputAdornment, { position: "end" },
                             react_1.default.createElement(material_1.IconButton, { disabled: value === '', onClick: () => {
                                     slot.add(value, []);

package/dist/ConfigurationEditorWidget/model.js

@@ -13,7 +13,6 @@ function stateModelFactory(pluginManager) {
         target: mobx_state_tree_1.types.safeReference(pluginManager.pluggableConfigSchemaType('track')),
     })
         .actions(self => ({
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         setTarget(newTarget) {
             self.target = newTarget;
         },

package/dist/FromConfigAdapter/FromConfigAdapter.js

@@ -11,16 +11,14 @@ const configuration_1 = require("@jbrowse/core/configuration");
 function makeFeatures(fdata) {
     const features = new Map();
     for (const entry of fdata) {
-        if (entry) {
-            const f = new simpleFeature_1.default(entry);
-            const refName = f.get('refName');
-            let bucket = features.get(refName);
-            if (!bucket) {
-                bucket = [];
-                features.set(refName, bucket);
-            }
-            bucket.push(f);
+        const f = new simpleFeature_1.default(entry);
+        const refName = f.get('refName');
+        let bucket = features.get(refName);
+        if (!bucket) {
+            bucket = [];
+            features.set(refName, bucket);
         }
+        bucket.push(f);
     }
     // sort the features on each reference sequence by start coordinate
     for (const refFeatures of features.values()) {
@@ -32,7 +30,7 @@ class FromConfigAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor(conf, getSubAdapter, pluginManager) {
         super(conf, getSubAdapter, pluginManager);
         const feats = (0, configuration_1.readConfObject)(conf, 'features');
-        this.features = makeFeatures(feats || []);
+        this.features = makeFeatures(feats);
     }
     async getRefNames() {
         return [...this.features.keys()];

package/dist/FromConfigRegionsAdapter/FromConfigRegionsAdapter.js

@@ -12,7 +12,7 @@ class FromConfigRegionsAdapter extends BaseAdapter_1.BaseAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
         const f = (0, configuration_1.readConfObject)(config, 'features');
-        this.features = (0, FromConfigAdapter_1.makeFeatures)(f || []);
+        this.features = (0, FromConfigAdapter_1.makeFeatures)(f);
     }
     /**
      * Get refName, start, and end for all features after collapsing any overlaps

package/dist/FromConfigSequenceAdapter/FromConfigSequenceAdapter.d.ts

@@ -13,9 +13,9 @@ export default class FromConfigSequenceAdapter extends FromConfigAdapter impleme
      * Get refName, start, and end for all features after collapsing any overlaps
      */
     getRegions(): Promise<{
-        refName: string;
         start: number;
         end: number;
+        refName: string;
     }[]>;
     /**
      * called to provide a hint that data tied to a certain region

package/dist/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.d.ts

@@ -0,0 +1,9 @@
+import { BaseRefNameAliasAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+export default class NcbiSequenceReportAliasAdapter extends BaseAdapter implements BaseRefNameAliasAdapter {
+    getRefNameAliases(): Promise<{
+        refName: string;
+        aliases: string[];
+        override: any;
+    }[]>;
+    freeResources(): Promise<void>;
+}

package/dist/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.js

@@ -0,0 +1,27 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const io_1 = require("@jbrowse/core/util/io");
+class NcbiSequenceReportAliasAdapter extends BaseAdapter_1.BaseAdapter {
+    async getRefNameAliases() {
+        const loc = this.getConf('location');
+        if (loc.uri === '' || loc.uri === '/path/to/my/sequence_report.tsv') {
+            return [];
+        }
+        const override = this.getConf('useUcscNameOverride');
+        const results = await (0, io_1.openLocation)(loc, this.pluginManager).readFile('utf8');
+        return results
+            .split(/\n|\r\n|\r/)
+            .slice(1)
+            .filter(f => !!f.trim())
+            .map(row => row.split('\t'))
+            .map(cols => ({
+            refName: cols[12],
+            aliases: [cols[9], cols[6]].filter((f) => !!f),
+            override,
+        }))
+            .filter(f => !!f.refName);
+    }
+    async freeResources() { }
+}
+exports.default = NcbiSequenceReportAliasAdapter;

package/dist/NcbiSequenceReportAliasAdapter/configSchema.d.ts

@@ -0,0 +1,18 @@
+declare const NcbiSequenceReportAliasAdapterConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    location: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    useUcscNameOverride: {
+        type: string;
+        defaultValue: boolean;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default NcbiSequenceReportAliasAdapterConfigSchema;

package/dist/NcbiSequenceReportAliasAdapter/configSchema.js

@@ -0,0 +1,26 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+/**
+ * #config NcbiSequenceReportAliasAdapter
+ * can read "sequence_report.tsv" type files from NCBI
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const NcbiSequenceReportAliasAdapterConfigSchema = (0, configuration_1.ConfigurationSchema)('NcbiSequenceReportAliasAdapter', {
+    /**
+     * #slot
+     */
+    location: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my/sequence_report.tsv',
+            locationType: 'UriLocation',
+        },
+    },
+    useUcscNameOverride: {
+        type: 'boolean',
+        defaultValue: true,
+        description: 'forces usage of the UCSC names over the NCBI style names from a FASTA',
+    },
+}, { explicitlyTyped: true });
+exports.default = NcbiSequenceReportAliasAdapterConfigSchema;

package/dist/NcbiSequenceReportAliasAdapter/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function NcbiSequenceReportAliasAdapterF(pluginManager: PluginManager): void;

package/dist/NcbiSequenceReportAliasAdapter/index.js

@@ -0,0 +1,43 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = NcbiSequenceReportAliasAdapterF;
+const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
+const configSchema_1 = __importDefault(require("./configSchema"));
+function NcbiSequenceReportAliasAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => {
+        return new pluggableElementTypes_1.AdapterType({
+            name: 'NcbiSequenceReportAliasAdapter',
+            configSchema: configSchema_1.default,
+            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./NcbiSequenceReportAliasAdapter'))).then(r => r.default),
+            adapterMetadata: {
+                hiddenFromGUI: true,
+            },
+        });
+    });
+}

package/dist/RefNameAliasAdapter/RefNameAliasAdapter.js

@@ -17,7 +17,10 @@ class RefNameAliasAdapter extends BaseAdapter_1.BaseAdapter {
             .map(row => {
             const aliases = row.split('\t');
             const [refName] = aliases.splice(refColumn, 1);
-            return { refName, aliases: aliases.filter(f => !!f.trim()) };
+            return {
+                refName: refName,
+                aliases: aliases.filter(f => !!f.trim()),
+            };
         });
     }
     async freeResources() { }

package/dist/index.js

@@ -34,6 +34,7 @@ const FromConfigRegionsAdapter_1 = __importDefault(require("./FromConfigRegionsA
 const FromConfigSequenceAdapter_1 = __importDefault(require("./FromConfigSequenceAdapter"));
 const RefNameAliasAdapter_1 = __importDefault(require("./RefNameAliasAdapter"));
 const ConfigurationEditorWidget_1 = __importDefault(require("./ConfigurationEditorWidget"));
+const NcbiSequenceReportAliasAdapter_1 = __importDefault(require("./NcbiSequenceReportAliasAdapter"));
 const LazyConfigurationEditorComponent = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./ConfigurationEditorWidget/components/ConfigurationEditor'))));
 exports.ConfigurationEditor = LazyConfigurationEditorComponent;
 class ConfigurationPlugin extends Plugin_1.default {
@@ -47,6 +48,7 @@ class ConfigurationPlugin extends Plugin_1.default {
         (0, FromConfigSequenceAdapter_1.default)(pluginManager);
         (0, RefNameAliasAdapter_1.default)(pluginManager);
         (0, ConfigurationEditorWidget_1.default)(pluginManager);
+        (0, NcbiSequenceReportAliasAdapter_1.default)(pluginManager);
     }
 }
 exports.default = ConfigurationPlugin;

package/esm/ConfigurationEditorWidget/components/BooleanEditor.js

@@ -3,7 +3,9 @@ import { observer } from 'mobx-react';
 import { Checkbox, FormControl, FormControlLabel, FormHelperText, } from '@mui/material';
 const BooleanEditor = observer(function ({ slot, }) {
     return (React.createElement(FormControl, null,
-        React.createElement(FormControlLabel, { label: slot.name, control: React.createElement(Checkbox, { checked: slot.value, onChange: evt => slot.set(evt.target.checked) }) }),
+        React.createElement(FormControlLabel, { label: slot.name, control: React.createElement(Checkbox, { checked: slot.value, onChange: evt => {
+                    slot.set(evt.target.checked);
+                } }) }),
         React.createElement(FormHelperText, null, slot.description)));
 });
 export default BooleanEditor;

package/esm/ConfigurationEditorWidget/components/CallbackEditor.js

@@ -57,7 +57,9 @@ const CallbackEditor = observer(function ({ slot, }) {
     return (React.createElement(React.Fragment, null,
         error ? React.createElement("p", { className: classes.error }, `${error}`) : null,
         React.createElement("div", { className: classes.callbackContainer },
-            React.createElement(TextField, { multiline: true, className: classes.callbackEditor, value: code.startsWith('jexl:') ? code.split('jexl:')[1] : code, onChange: event => setCode(event.target.value), style: { background: error ? '#fdd' : undefined }, InputProps: {
+            React.createElement(TextField, { multiline: true, className: classes.callbackEditor, value: code.startsWith('jexl:') ? code.split('jexl:')[1] : code, onChange: event => {
+                    setCode(event.target.value);
+                }, style: { background: error ? '#fdd' : undefined }, InputProps: {
                     classes: {
                         input: classes.textAreaFont,
                     },

package/esm/ConfigurationEditorWidget/components/ColorEditor.js

@@ -6,14 +6,22 @@ export const ColorSlot = (props) => {
     const { value = '#000', label = '', TextFieldProps = {}, onChange } = props;
     const [displayed, setDisplayed] = useState(false);
     return (React.createElement("div", { style: { display: 'flex' } },
-        React.createElement(TextField, { value: value, label: label, onClick: () => setDisplayed(!displayed), onChange: event => onChange(event.target.value), ...TextFieldProps }),
+        React.createElement(TextField, { value: value, label: label, onClick: () => {
+                setDisplayed(!displayed);
+            }, onChange: event => {
+                onChange(event.target.value);
+            }, ...TextFieldProps }),
         React.createElement("div", { style: { marginTop: 10 } },
             React.createElement(React.Suspense, { fallback: null },
-                React.createElement(ColorPicker, { color: value, onChange: event => onChange(event) })))));
+                React.createElement(ColorPicker, { color: value, onChange: event => {
+                        onChange(event);
+                    } })))));
 };
 const ColorEditor = observer(function (props) {
     const { slot } = props;
-    return (React.createElement(ColorSlot, { label: slot.name, value: slot.value, onChange: color => slot.set(color), TextFieldProps: {
+    return (React.createElement(ColorSlot, { label: slot.name, value: slot.value, onChange: color => {
+            slot.set(color);
+        }, TextFieldProps: {
             helperText: slot.description,
             fullWidth: true,
         } }));

package/esm/ConfigurationEditorWidget/components/ConfigurationEditor.js

@@ -11,25 +11,22 @@ import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
 // locals
 import SlotEditor from './SlotEditor';
 import TypeSelector from './TypeSelector';
-const useStyles = makeStyles()(theme => {
-    var _a;
-    return ({
-        icon: {
-            color: ((_a = theme.palette.tertiary) === null || _a === void 0 ? void 0 : _a.contrastText) || '#fff',
-        },
-        expansionPanelDetails: {
-            display: 'block',
-            padding: theme.spacing(1),
-        },
-        accordion: {
-            border: `1px solid ${theme.palette.text.primary}`,
-        },
-        noOverflow: {
-            width: '100%',
-            overflowX: 'auto',
-        },
-    });
-});
+const useStyles = makeStyles()(theme => ({
+    icon: {
+        color: theme.palette.tertiary.contrastText || '#fff',
+    },
+    expansionPanelDetails: {
+        display: 'block',
+        padding: theme.spacing(1),
+    },
+    accordion: {
+        border: `1px solid ${theme.palette.text.primary}`,
+    },
+    noOverflow: {
+        width: '100%',
+        overflowX: 'auto',
+    },
+}));
 const Member = observer(function (props) {
     const { classes } = useStyles();
     const { slotName, slotSchema, schema, slot = schema[slotName], path = [], } = props;
@@ -70,16 +67,17 @@ const Schema = observer(function ({ schema, path = [], }) {
 });
 const ConfigurationEditor = observer(function ({ model, }) {
     const { classes } = useStyles();
-    // key forces a re-render, otherwise the same field can end up being used
-    // for different tracks since only the backing model changes for example
-    // see pr #804
+    // key forces a re-render, otherwise the same field can end up being used for
+    // different tracks since only the backing model changes for example see pr
+    // #804
     const { target } = model;
-    const key = target && readConfObject(target, 'trackId');
-    const name = target && readConfObject(target, 'name');
+    const key = readConfObject(target, 'trackId');
+    const name = readConfObject(target, 'name');
     return (React.createElement(Accordion, { key: key, defaultExpanded: true, className: classes.accordion },
         React.createElement(AccordionSummary, { expandIcon: React.createElement(ExpandMoreIcon, { className: classes.icon }) },
             React.createElement(Typography, null,
                 React.createElement(SanitizedHTML, { html: name !== null && name !== void 0 ? name : 'Configuration' }))),
-        React.createElement(AccordionDetails, { className: classes.expansionPanelDetails, "data-testid": "configEditor" }, !target ? 'no target set' : React.createElement(Schema, { schema: target }))));
+        React.createElement(AccordionDetails, { className: classes.expansionPanelDetails, "data-testid": "configEditor" },
+            React.createElement(Schema, { schema: target }))));
 });
 export default ConfigurationEditor;

package/esm/ConfigurationEditorWidget/components/HeadingComponent.js

@@ -8,7 +8,7 @@ const HeadingComponent = observer(function ({ model, }) {
         }
         if (isStateTreeNode(model.target)) {
             const type = getType(model.target);
-            if (type === null || type === void 0 ? void 0 : type.name) {
+            if (type.name) {
                 return `${type.name.replace('ConfigurationSchema', '')} settings`;
             }
         }

package/esm/ConfigurationEditorWidget/components/JsonEditor.js

@@ -45,7 +45,9 @@ const JsonEditor = observer(function JsonEditor({ slot, }) {
         error ? React.createElement("p", { className: classes.error }, `${error}`) : null,
         React.createElement("div", { className: classes.callbackContainer },
             React.createElement(InputLabel, { shrink: true, htmlFor: "json-editor" }, slot.name),
-            React.createElement(TextField, { id: "json-editor", className: classes.callbackEditor, value: contents, helperText: slot.description, multiline: true, onChange: event => setContents(event.target.value), style: { background: error ? '#fdd' : undefined }, InputProps: {
+            React.createElement(TextField, { id: "json-editor", className: classes.callbackEditor, value: contents, helperText: slot.description, multiline: true, onChange: event => {
+                    setContents(event.target.value);
+                }, style: { background: error ? '#fdd' : undefined }, InputProps: {
                     classes: {
                         input: classes.textAreaFont,
                     },

package/esm/ConfigurationEditorWidget/components/NumberEditor.js

@@ -13,6 +13,8 @@ const NumberEditor = observer(function ({ slot, }) {
             slot.set(num);
         }
     }, [slot, val]);
-    return (React.createElement(ConfigurationTextField, { label: slot.name, helperText: slot.description, value: val, type: "number", onChange: evt => setVal(evt.target.value) }));
+    return (React.createElement(ConfigurationTextField, { label: slot.name, helperText: slot.description, value: val, type: "number", onChange: evt => {
+            setVal(evt.target.value);
+        } }));
 });
 export default NumberEditor;

package/esm/ConfigurationEditorWidget/components/NumberMapEditor.js

@@ -17,15 +17,21 @@ const NumberMapEditor = observer(function ({ slot, }) {
     return (React.createElement(React.Fragment, null,
         React.createElement(InputLabel, null, slot.name),
         [...slot.value].map(([key, val]) => (React.createElement(Card, { raised: true, key: key, className: classes.card },
-            React.createElement(CardHeader, { title: key, action: React.createElement(IconButton, { onClick: () => slot.remove(key) },
+            React.createElement(CardHeader, { title: key, action: React.createElement(IconButton, { onClick: () => {
+                        slot.remove(key);
+                    } },
                     React.createElement(DeleteIcon, null)) }),
             React.createElement(CardContent, null,
                 React.createElement(NumberEditor, { slot: {
                         value: val,
-                        set: (val) => slot.add(key, val),
+                        set: (val) => {
+                            slot.add(key, val);
+                        },
                     } }))))),
         React.createElement(Card, { raised: true, className: classes.card },
-            React.createElement(CardHeader, { disableTypography: true, title: React.createElement(TextField, { fullWidth: true, value: value, placeholder: "add new", onChange: event => setValue(event.target.value), InputProps: {
+            React.createElement(CardHeader, { disableTypography: true, title: React.createElement(TextField, { fullWidth: true, value: value, placeholder: "add new", onChange: event => {
+                        setValue(event.target.value);
+                    }, InputProps: {
                         endAdornment: (React.createElement(InputAdornment, { position: "end" },
                             React.createElement(IconButton, { disabled: value === '', onClick: () => {
                                     slot.add(value, 0);

package/esm/ConfigurationEditorWidget/components/SlotEditor.js

@@ -19,10 +19,14 @@ import NumberEditor from './NumberEditor';
 import BooleanEditor from './BooleanEditor';
 import { useSlotEditorStyles } from './useSlotEditorStyles';
 const StringEditor = observer(function ({ slot, }) {
-    return (React.createElement(ConfigurationTextField, { label: slot.name, helperText: slot.description, value: slot.value, onChange: evt => slot.set(evt.target.value) }));
+    return (React.createElement(ConfigurationTextField, { label: slot.name, helperText: slot.description, value: slot.value, onChange: evt => {
+            slot.set(evt.target.value);
+        } }));
 });
 const TextEditor = observer(function ({ slot, }) {
-    return (React.createElement(TextField, { label: slot.name, helperText: slot.description, multiline: true, value: slot.value, onChange: evt => slot.set(evt.target.value) }));
+    return (React.createElement(TextField, { label: slot.name, helperText: slot.description, multiline: true, value: slot.value, onChange: evt => {
+            slot.set(evt.target.value);
+        } }));
 });
 // checked checkbox, looks like a styled (x)
 const SvgCheckbox = () => (React.createElement(SvgIcon, null,
@@ -35,16 +39,24 @@ const IntegerEditor = observer(function ({ slot, }) {
             slot.set(num);
         }
     }, [slot, val]);
-    return (React.createElement(ConfigurationTextField, { label: slot.name, helperText: slot.description, value: val, type: "number", onChange: evt => setVal(evt.target.value) }));
+    return (React.createElement(ConfigurationTextField, { label: slot.name, helperText: slot.description, value: val, type: "number", onChange: evt => {
+            setVal(evt.target.value);
+        } }));
 });
 const StringEnumEditor = observer(function ({ slot, slotSchema, }) {
     const p = getPropertyMembers(getSubType(slotSchema));
     const choices = getUnionSubTypes(getUnionSubTypes(getSubType(p.properties.value))[1]).map(t => t.value);
-    return (React.createElement(ConfigurationTextField, { value: slot.value, label: slot.name, select: true, helperText: slot.description, onChange: evt => slot.set(evt.target.value) }, choices.map(str => (React.createElement(MenuItem, { key: str, value: str }, str)))));
+    return (React.createElement(ConfigurationTextField, { value: slot.value, label: slot.name, select: true, helperText: slot.description, onChange: evt => {
+            slot.set(evt.target.value);
+        } }, choices.map(str => (React.createElement(MenuItem, { key: str, value: str }, str)))));
 });
 const FileSelectorWrapper = observer(function ({ slot, }) {
     var _a;
-    return (React.createElement(FileSelector, { location: slot.value, setLocation: location => slot.set(location), name: slot.name, description: slot.description, rootModel: (_a = getEnv(slot).pluginManager) === null || _a === void 0 ? void 0 : _a.rootModel }));
+    return (React.createElement(FileSelector, { location: slot.value, setLocation: location => {
+            slot.set(location);
+        }, name: slot.name, description: slot.description, 
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+        rootModel: (_a = getEnv(slot).pluginManager) === null || _a === void 0 ? void 0 : _a.rootModel }));
 });
 const valueComponents = {
     string: StringEditor,

package/esm/ConfigurationEditorWidget/components/StringArrayEditor.d.ts

@@ -3,9 +3,9 @@ declare const StringArrayEditor: ({ slot, }: {
     slot: {
         name: string;
         value: string[];
-        setAtIndex: Function;
-        removeAtIndex: Function;
-        add: Function;
+        setAtIndex: (arg: number, arg2: string) => void;
+        removeAtIndex: (arg: number) => void;
+        add: (arg: string) => void;
         description: string;
     };
 }) => React.JSX.Element;

package/esm/ConfigurationEditorWidget/components/StringArrayEditor.js

@@ -9,14 +9,20 @@ const StringArrayEditor = observer(function ({ slot, }) {
     return (React.createElement(React.Fragment, null,
         slot.name ? React.createElement(InputLabel, null, slot.name) : null,
         React.createElement(List, { disablePadding: true },
-            slot.value.map((val, idx) => (React.createElement(ListItem, { key: idx, disableGutters: true },
-                React.createElement(TextField, { value: val, onChange: evt => slot.setAtIndex(idx, evt.target.value), InputProps: {
+            slot.value.map((val, idx) => (React.createElement(ListItem, { key: `${JSON.stringify(val)}-${idx}`, disableGutters: true },
+                React.createElement(TextField, { value: val, onChange: evt => {
+                        slot.setAtIndex(idx, evt.target.value);
+                    }, InputProps: {
                         endAdornment: (React.createElement(InputAdornment, { position: "end" },
-                            React.createElement(IconButton, { onClick: () => slot.removeAtIndex(idx) },
+                            React.createElement(IconButton, { onClick: () => {
+                                    slot.removeAtIndex(idx);
+                                } },
                                 React.createElement(DeleteIcon, null)))),
                     } })))),
             addNew ? (React.createElement(ListItem, { disableGutters: true },
-                React.createElement(TextField, { value: value, placeholder: "add new", onChange: event => setValue(event.target.value), InputProps: {
+                React.createElement(TextField, { value: value, placeholder: "add new", onChange: event => {
+                        setValue(event.target.value);
+                    }, InputProps: {
                         endAdornment: (React.createElement(InputAdornment, { position: "end" },
                             React.createElement(React.Fragment, null,
                                 React.createElement(Button, { color: "primary", variant: "contained", style: { margin: 2 }, "data-testid": `stringArrayAdd-${slot.name}`, onClick: () => {
@@ -29,7 +35,9 @@ const StringArrayEditor = observer(function ({ slot, }) {
                                         setValue('');
                                     } }, "Cancel")))),
                     } }))) : null,
-            React.createElement(Button, { color: "primary", variant: "contained", style: { margin: 4 }, disabled: addNew, onClick: () => setAddNew(true) }, "Add item")),
+            React.createElement(Button, { color: "primary", variant: "contained", style: { margin: 4 }, disabled: addNew, onClick: () => {
+                    setAddNew(true);
+                } }, "Add item")),
         React.createElement(FormHelperText, null, slot.description)));
 });
 export default StringArrayEditor;

package/esm/ConfigurationEditorWidget/components/StringArrayMapEditor.js

@@ -18,19 +18,29 @@ const StringArrayMapEditor = observer(function ({ slot, }) {
     return (React.createElement(React.Fragment, null,
         React.createElement(InputLabel, null, slot.name),
         [...slot.value].map(([key, val]) => (React.createElement(Card, { raised: true, key: key, className: classes.card },
-            React.createElement(CardHeader, { title: key, action: React.createElement(IconButton, { onClick: () => slot.remove(key) },
+            React.createElement(CardHeader, { title: key, action: React.createElement(IconButton, { onClick: () => {
+                        slot.remove(key);
+                    } },
                     React.createElement(DeleteIcon, null)) }),
             React.createElement(CardContent, null,
                 React.createElement(StringArrayEditor, { slot: {
                         name: slot.name,
                         value: val,
                         description: `Values associated with entry ${key}`,
-                        setAtIndex: (idx, val) => slot.setAtKeyIndex(key, idx, val),
-                        removeAtIndex: (idx) => slot.removeAtKeyIndex(key, idx),
-                        add: (val) => slot.addToKey(key, val),
+                        setAtIndex: (idx, val) => {
+                            slot.setAtKeyIndex(key, idx, val);
+                        },
+                        removeAtIndex: (idx) => {
+                            slot.removeAtKeyIndex(key, idx);
+                        },
+                        add: (val) => {
+                            slot.addToKey(key, val);
+                        },
                     } }))))),
         React.createElement(Card, { raised: true, className: classes.card },
-            React.createElement(CardHeader, { disableTypography: true, title: React.createElement(TextField, { fullWidth: true, value: value, placeholder: "add new", onChange: event => setValue(event.target.value), InputProps: {
+            React.createElement(CardHeader, { disableTypography: true, title: React.createElement(TextField, { fullWidth: true, value: value, placeholder: "add new", onChange: event => {
+                        setValue(event.target.value);
+                    }, InputProps: {
                         endAdornment: (React.createElement(InputAdornment, { position: "end" },
                             React.createElement(IconButton, { disabled: value === '', onClick: () => {
                                     slot.add(value, []);

package/esm/ConfigurationEditorWidget/model.js

@@ -10,7 +10,6 @@ export default function stateModelFactory(pluginManager) {
         target: types.safeReference(pluginManager.pluggableConfigSchemaType('track')),
     })
         .actions(self => ({
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         setTarget(newTarget) {
             self.target = newTarget;
         },

package/esm/FromConfigAdapter/FromConfigAdapter.js

@@ -5,16 +5,14 @@ import { readConfObject, } from '@jbrowse/core/configuration';
 export function makeFeatures(fdata) {
     const features = new Map();
     for (const entry of fdata) {
-        if (entry) {
-            const f = new SimpleFeature(entry);
-            const refName = f.get('refName');
-            let bucket = features.get(refName);
-            if (!bucket) {
-                bucket = [];
-                features.set(refName, bucket);
-            }
-            bucket.push(f);
+        const f = new SimpleFeature(entry);
+        const refName = f.get('refName');
+        let bucket = features.get(refName);
+        if (!bucket) {
+            bucket = [];
+            features.set(refName, bucket);
         }
+        bucket.push(f);
     }
     // sort the features on each reference sequence by start coordinate
     for (const refFeatures of features.values()) {
@@ -26,7 +24,7 @@ export default class FromConfigAdapter extends BaseFeatureDataAdapter {
     constructor(conf, getSubAdapter, pluginManager) {
         super(conf, getSubAdapter, pluginManager);
         const feats = readConfObject(conf, 'features');
-        this.features = makeFeatures(feats || []);
+        this.features = makeFeatures(feats);
     }
     async getRefNames() {
         return [...this.features.keys()];

package/esm/FromConfigRegionsAdapter/FromConfigRegionsAdapter.js

@@ -10,7 +10,7 @@ export default class FromConfigRegionsAdapter extends BaseAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
         const f = readConfObject(config, 'features');
-        this.features = makeFeatures(f || []);
+        this.features = makeFeatures(f);
     }
     /**
      * Get refName, start, and end for all features after collapsing any overlaps

package/esm/FromConfigSequenceAdapter/FromConfigSequenceAdapter.d.ts

@@ -13,9 +13,9 @@ export default class FromConfigSequenceAdapter extends FromConfigAdapter impleme
      * Get refName, start, and end for all features after collapsing any overlaps
      */
     getRegions(): Promise<{
-        refName: string;
         start: number;
         end: number;
+        refName: string;
     }[]>;
     /**
      * called to provide a hint that data tied to a certain region

package/esm/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.d.ts

@@ -0,0 +1,9 @@
+import { BaseRefNameAliasAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+export default class NcbiSequenceReportAliasAdapter extends BaseAdapter implements BaseRefNameAliasAdapter {
+    getRefNameAliases(): Promise<{
+        refName: string;
+        aliases: string[];
+        override: any;
+    }[]>;
+    freeResources(): Promise<void>;
+}

package/esm/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.js

@@ -0,0 +1,24 @@
+import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+export default class NcbiSequenceReportAliasAdapter extends BaseAdapter {
+    async getRefNameAliases() {
+        const loc = this.getConf('location');
+        if (loc.uri === '' || loc.uri === '/path/to/my/sequence_report.tsv') {
+            return [];
+        }
+        const override = this.getConf('useUcscNameOverride');
+        const results = await openLocation(loc, this.pluginManager).readFile('utf8');
+        return results
+            .split(/\n|\r\n|\r/)
+            .slice(1)
+            .filter(f => !!f.trim())
+            .map(row => row.split('\t'))
+            .map(cols => ({
+            refName: cols[12],
+            aliases: [cols[9], cols[6]].filter((f) => !!f),
+            override,
+        }))
+            .filter(f => !!f.refName);
+    }
+    async freeResources() { }
+}

package/esm/NcbiSequenceReportAliasAdapter/configSchema.d.ts

@@ -0,0 +1,18 @@
+declare const NcbiSequenceReportAliasAdapterConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    location: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    useUcscNameOverride: {
+        type: string;
+        defaultValue: boolean;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default NcbiSequenceReportAliasAdapterConfigSchema;

package/esm/NcbiSequenceReportAliasAdapter/configSchema.js

@@ -0,0 +1,24 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config NcbiSequenceReportAliasAdapter
+ * can read "sequence_report.tsv" type files from NCBI
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const NcbiSequenceReportAliasAdapterConfigSchema = ConfigurationSchema('NcbiSequenceReportAliasAdapter', {
+    /**
+     * #slot
+     */
+    location: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my/sequence_report.tsv',
+            locationType: 'UriLocation',
+        },
+    },
+    useUcscNameOverride: {
+        type: 'boolean',
+        defaultValue: true,
+        description: 'forces usage of the UCSC names over the NCBI style names from a FASTA',
+    },
+}, { explicitlyTyped: true });
+export default NcbiSequenceReportAliasAdapterConfigSchema;

package/esm/NcbiSequenceReportAliasAdapter/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function NcbiSequenceReportAliasAdapterF(pluginManager: PluginManager): void;

package/esm/NcbiSequenceReportAliasAdapter/index.js

@@ -0,0 +1,14 @@
+import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
+import configSchema from './configSchema';
+export default function NcbiSequenceReportAliasAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => {
+        return new AdapterType({
+            name: 'NcbiSequenceReportAliasAdapter',
+            configSchema,
+            getAdapterClass: () => import('./NcbiSequenceReportAliasAdapter').then(r => r.default),
+            adapterMetadata: {
+                hiddenFromGUI: true,
+            },
+        });
+    });
+}

package/esm/RefNameAliasAdapter/RefNameAliasAdapter.js

@@ -15,7 +15,10 @@ export default class RefNameAliasAdapter extends BaseAdapter {
             .map(row => {
             const aliases = row.split('\t');
             const [refName] = aliases.splice(refColumn, 1);
-            return { refName, aliases: aliases.filter(f => !!f.trim()) };
+            return {
+                refName: refName,
+                aliases: aliases.filter(f => !!f.trim()),
+            };
         });
     }
     async freeResources() { }

package/esm/index.js

@@ -5,6 +5,7 @@ import FromConfigRegionsAdapterF from './FromConfigRegionsAdapter';
 import FromConfigSequenceAdapterF from './FromConfigSequenceAdapter';
 import RefNameAliasAdapterF from './RefNameAliasAdapter';
 import ConfigurationEditorWidgetF from './ConfigurationEditorWidget';
+import NcbiSequenceReportAliasAdapterF from './NcbiSequenceReportAliasAdapter';
 const LazyConfigurationEditorComponent = lazy(() => import('./ConfigurationEditorWidget/components/ConfigurationEditor'));
 export default class ConfigurationPlugin extends Plugin {
     constructor() {
@@ -17,6 +18,7 @@ export default class ConfigurationPlugin extends Plugin {
         FromConfigSequenceAdapterF(pluginManager);
         RefNameAliasAdapterF(pluginManager);
         ConfigurationEditorWidgetF(pluginManager);
+        NcbiSequenceReportAliasAdapterF(pluginManager);
     }
 }
 export { default as JsonEditor } from './ConfigurationEditorWidget/components/JsonEditor';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-config",
-  "version": "2.13.1",
+  "version": "2.14.0",
   "description": "JBrowse 2 config utilities",
   "keywords": [
     "jbrowse",
@@ -24,7 +24,7 @@
   ],
   "scripts": {
     "build": "npm-run-all build:*",
-    "test": "cd ../..; jest plugins/config",
+    "test": "cd ../..; jest --passWithNoTests plugins/config",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
@@ -56,5 +56,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "fcebca71cc1d066654603e1a9accfa6c6d4f764d"
+  "gitHead": "9fb8231d932db40adf0a283081765431756c66ff"
 }