@jbrowse/plugin-spreadsheet-view 2.13.1 → 2.15.0

package/esm/SpreadsheetView/importAdapters/STARFusionImport.js

@@ -30,7 +30,6 @@ export async function parseSTARFusionBuffer(buffer, options) {
     });
     // decorate each row with a feature object in its extendedData
     data.rowSet.rows.forEach((row, rowNumber) => {
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         const featureData = {};
         row.cells.forEach(({ text }, columnNumber) => {
             const column = data.columns[columnNumber];
@@ -52,7 +51,7 @@ export async function parseSTARFusionBuffer(buffer, options) {
             }
             else if (text && numericColumns[column.name]) {
                 // some other column, numeric
-                featureData[column.name] = parseFloat(text);
+                featureData[column.name] = Number.parseFloat(text);
             }
             else {
                 // some other column, text

package/esm/SpreadsheetView/importAdapters/VcfImport.js

@@ -12,7 +12,6 @@ const vcfCoreColumns = [
     { name: 'INFO', type: 'Text' }, // 7
     { name: 'FORMAT', type: 'Text' }, // 8
 ];
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
 function vcfRecordToRow(vcfParser, line, lineNumber) {
     const vcfVariant = vcfParser.parseLine(line);
     const vcfFeature = new VcfFeature({
@@ -65,7 +64,10 @@ export function parseVcfBuffer(buffer, options = {}) {
     for (let i = 0; i < vcfParser.samples.length; i += 1) {
         const oi = vcfCoreColumns.length + i;
         columnDisplayOrder.push(oi);
-        columns[oi] = { name: vcfParser.samples[i], dataType: { type: 'Text' } };
+        columns[oi] = {
+            name: vcfParser.samples[i],
+            dataType: { type: 'Text' },
+        };
     }
     columnDisplayOrder.push(columnDisplayOrder.length);
     columns.unshift({

package/esm/SpreadsheetView/models/ColumnDataTypes/LocEnd.js

@@ -8,7 +8,7 @@ const LocEnd = MakeSpreadsheetColumnType('LocEnd', {
     categoryName: 'Location',
     displayName: 'End',
     compare(cellA, cellB) {
-        return parseFloat(cellA.text) - parseFloat(cellB.text);
+        return Number.parseFloat(cellA.text) - Number.parseFloat(cellB.text);
     },
     FilterModelType,
 });

package/esm/SpreadsheetView/models/ColumnDataTypes/LocStart.js

@@ -8,7 +8,7 @@ const LocStart = MakeSpreadsheetColumnType('LocStart', {
     categoryName: 'Location',
     displayName: 'Start',
     compare(cellA, cellB) {
-        return parseFloat(cellA.text) - parseFloat(cellB.text);
+        return Number.parseFloat(cellA.text) - Number.parseFloat(cellB.text);
     },
     FilterModelType,
 });

package/esm/SpreadsheetView/models/ColumnDataTypes/LocString.js

@@ -75,7 +75,7 @@ const FilterModelType = types
     type: types.literal('LocString'),
     columnNumber: types.integer,
     locString: '',
-    operation: types.optional(types.enumeration(OPERATIONS), OPERATIONS[0]),
+    operation: types.optional(types.string, OPERATIONS[0]),
 })
     .views(self => ({
     get locStringIsInvalid() {
@@ -91,7 +91,6 @@ const FilterModelType = types
     },
     get parsedLocString() {
         const session = getSession(self);
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         const model = getParent(self, 3).spreadsheet;
         const { assemblyName } = model;
         try {
@@ -111,7 +110,6 @@ const FilterModelType = types
                 return true;
             };
         }
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         return function stringPredicate(_sheet, row) {
             const { cellsWithDerived: cells } = row;
             const cell = cells[columnNumber];
@@ -140,14 +138,9 @@ const FilterModelType = types
 }))
     .volatile(() => ({ ReactComponent: FilterReactComponent }));
 // opens a new LGV at the location described in the locString in the cell text
-async function locationLinkClick(
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-spreadsheet, _columnNumber, 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-cell) {
+async function locationLinkClick(spreadsheet, _columnNumber, cell) {
     const session = getSession(spreadsheet);
     const { assemblyName } = spreadsheet;
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const { id } = getParent(spreadsheet);
     const newViewId = `${id}_${assemblyName}`;
     let view = session.views.find(v => v.id === newViewId);
@@ -169,12 +162,11 @@ const DataCellReactComponent = observer(function ({ cell, columnNumber, spreadsh
                 console.error(e);
                 session.notifyError(`${e}`, e);
             }
-        }, title: "open a new linear genome view here", href: "#link" }, cell.text));
+        }, title: "open a new linear genome view here", href: "#" }, cell.text));
 });
 const LocStringColumnType = MakeSpreadsheetColumnType('LocString', {
     categoryName: 'Location',
     displayName: 'Full location',
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     compare(cellA, cellB) {
         return compareLocs(cellA.extendedData, cellB.extendedData);
     },

package/esm/SpreadsheetView/models/ColumnDataTypes/Number.js

@@ -46,21 +46,19 @@ const useStyles = makeStyles()({
     },
 });
 // React component for the column filter control
-const FilterReactComponent = observer(
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-({ filterModel }) => {
+const FilterReactComponent = observer(({ filterModel }) => {
     const { classes } = useStyles();
     const operationChoices = OPERATIONS;
     return (React.createElement(React.Fragment, null,
         React.createElement(Select, { value: filterModel.operation, onChange: e => filterModel.setOperation(String(e.target.value)) }, operationChoices.map(name => (React.createElement(MenuItem, { key: name, value: name }, name)))),
         ' ',
         React.createElement(TextField, { label: "number", placeholder: "123", type: "number", error: filterModel.firstNumberIsInvalid, defaultValue: filterModel.firstNumber, onChange: evt => {
-                filterModel.setFirstNumber(parseFloat(evt.target.value));
+                filterModel.setFirstNumber(Number.parseFloat(evt.target.value));
             }, className: classes.textFilterControl }),
         filterModel.operation !== 'between' &&
             filterModel.operation !== 'not between' ? null : (React.createElement(React.Fragment, null,
             ' and ',
-            React.createElement(TextField, { label: "number", placeholder: "456", type: "number", error: filterModel.secondNumberIsInvalid, defaultValue: filterModel.secondNumber, onChange: evt => filterModel.setSecondNumber(parseFloat(evt.target.value)), className: classes.textFilterControl })))));
+            React.createElement(TextField, { label: "number", placeholder: "456", type: "number", error: filterModel.secondNumberIsInvalid, defaultValue: filterModel.secondNumber, onChange: evt => filterModel.setSecondNumber(Number.parseFloat(evt.target.value)), className: classes.textFilterControl })))));
 });
 // MST model for the column filter control
 const FilterModelType = types
@@ -80,14 +78,13 @@ const FilterModelType = types
             };
         }
         const { firstNumber, secondNumber, operation, columnNumber } = self; // avoid closing over self
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         return function stringPredicate(_sheet, row) {
             const { cellsWithDerived } = row;
             const cell = cellsWithDerived[columnNumber];
             if (!(cell === null || cell === void 0 ? void 0 : cell.text)) {
                 return false;
             }
-            const parsedCellText = parseFloat(cell.text);
+            const parsedCellText = Number.parseFloat(cell.text);
             if (typeof parsedCellText !== 'number') {
                 return false;
             }
@@ -115,7 +112,7 @@ const FilterModelType = types
     .volatile(() => ({ ReactComponent: FilterReactComponent }));
 const NumberColumn = MakeSpreadsheetColumnType('Number', {
     compare(cellA, cellB) {
-        return parseFloat(cellA.text) - parseFloat(cellB.text);
+        return Number.parseFloat(cellA.text) - Number.parseFloat(cellB.text);
     },
     FilterModelType,
 });

package/esm/SpreadsheetView/models/ColumnDataTypes/Text.js

@@ -56,9 +56,7 @@ const useStyles = makeStyles()({
     },
 });
 // React component for the column filter control
-const FilterReactComponent = observer(
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-({ filterModel }) => {
+const FilterReactComponent = observer(({ filterModel }) => {
     const { classes } = useStyles();
     const operationChoices = getEnumerationValues(getSubType(getPropertyType(getPropertyMembers(filterModel), 'operation')));
     return (React.createElement(React.Fragment, null,
@@ -90,7 +88,6 @@ const ColumnTextFilter = types
             };
         }
         const s = stringToFind.toLowerCase(); // case insensitive match
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         return function stringPredicate(_sheet, row) {
             const { cellsWithDerived } = row;
             const cell = cellsWithDerived[columnNumber];

package/esm/SpreadsheetView/models/ColumnDataTypes/index.js

@@ -2,11 +2,11 @@ import LocString from './LocString';
 import LocRef from './LocRef';
 import LocStart from './LocStart';
 import LocEnd from './LocEnd';
-import { NumberColumn as Number } from './Number';
+import { NumberColumn } from './Number';
 import { TextColumn as Text } from './Text';
 import { types } from 'mobx-state-tree';
 const ColumnTypes = {
-    Number,
+    Number: NumberColumn,
     Text,
     LocString,
     LocRef,

package/esm/SpreadsheetView/models/FilterControls.js

@@ -17,11 +17,10 @@ const RowFullTextFilter = types
         }
         s = s.toLowerCase();
         return function stringPredicate(_sheet, row) {
-            var _a;
             const { cellsWithDerived } = row;
             for (const cell of cellsWithDerived) {
                 // note: case insensitive
-                if ((_a = cell.text) === null || _a === void 0 ? void 0 : _a.toLowerCase().includes(s)) {
+                if (cell.text.toLowerCase().includes(s)) {
                     return true;
                 }
             }
@@ -67,9 +66,7 @@ const model = types
 }))
     .actions(self => ({
     addBlankColumnFilter(columnNumber) {
-        const { dataType } = 
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        getParent(self).spreadsheet.columns[columnNumber];
+        const { dataType } = getParent(self).spreadsheet.columns[columnNumber];
         self.columnFilters.push({
             type: dataType.type,
             columnNumber,

package/esm/SpreadsheetView/models/ImportWizard.js

@@ -40,7 +40,6 @@ const ImportWizard = types
 })
     .volatile(() => ({
     fileTypes,
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     fileSource: undefined,
     error: undefined,
     loading: false,
@@ -54,7 +53,6 @@ const ImportWizard = types
                 self.fileSource.uri));
     },
     get canCancel() {
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         return getParent(self).readyToDisplay;
     },
     get fileName() {
@@ -117,7 +115,6 @@ const ImportWizard = types
     },
     cancelButton() {
         self.error = undefined;
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         getParent(self).setDisplayMode();
     },
     // fetch and parse the file, make a new Spreadsheet model for it,
@@ -133,9 +130,6 @@ const ImportWizard = types
         self.loading = true;
         const type = self.fileType;
         const typeParser = await fileTypeParsers[type]();
-        if (!typeParser) {
-            throw new Error(`cannot open files of type '${self.fileType}'`);
-        }
         const { unzip } = await import('@gmod/bgzf-filehandle');
         const { pluginManager } = getEnv(self);
         const filehandle = openLocation(self.fileSource, pluginManager);
@@ -156,7 +150,6 @@ const ImportWizard = types
                 .then(buffer => typeParser(buffer, self))
                 .then(spreadsheet => {
                 this.setLoaded();
-                // eslint-disable-next-line @typescript-eslint/no-explicit-any
                 getParent(self).displaySpreadsheet(spreadsheet);
             });
         }

package/esm/SpreadsheetView/models/Row.js

@@ -26,10 +26,8 @@ const RowModel = types
 }))
     .views(self => ({
     get cellsWithDerived() {
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         const { columns } = getParent(self, 3);
         let i = 0;
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         return columns.map((column) => {
             if (column.isDerived) {
                 return column.expr.evalSync({

package/esm/SpreadsheetView/models/Spreadsheet.d.ts

@@ -1,5 +1,5 @@
 import { SnapshotIn, Instance } from 'mobx-state-tree';
-import RowModel from './Row';
+import type RowModel from './Row';
 type Row = Instance<typeof RowModel>;
 type RowMenuPosition = {
     anchorEl: Element;

package/esm/SpreadsheetView/models/Spreadsheet.js

@@ -86,7 +86,6 @@ const Spreadsheet = types
      */
     get hideRowSelection() {
         // just delegates to parent
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         return getParent(self).hideRowSelection;
     },
     /**
@@ -148,6 +147,7 @@ const Spreadsheet = types
      * #action
      */
     setSortColumns(newSort) {
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (newSort) {
             // @ts-expect-error
             self.sortColumns = newSort;
@@ -163,7 +163,7 @@ const Spreadsheet = types
      * #action
      */
     unselectAll() {
-        return self.rowSet.unselectAll();
+        self.rowSet.unselectAll();
     },
 }));
 export default Spreadsheet;

package/esm/SpreadsheetView/models/SpreadsheetView.d.ts

@@ -465,10 +465,6 @@ declare const SpreadsheetView: import("mobx-state-tree").IModelType<{
      * #action
      */
     setDisplayMode(): void;
-    /**
-     * #action
-     */
-    closeView(): void;
 } & {
     /**
      * #method

package/esm/SpreadsheetView/models/SpreadsheetView.js

@@ -1,4 +1,4 @@
-import { types, getParent, getEnv, cast, } from 'mobx-state-tree';
+import { types, getEnv, cast } from 'mobx-state-tree';
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models';
 import { readConfObject } from '@jbrowse/core/configuration';
 import { getSession } from '@jbrowse/core/util';
@@ -90,7 +90,8 @@ const model = types
      * #getter
      */
     get outputRows() {
-        if (self.spreadsheet && self.spreadsheet.rowSet.isLoaded) {
+        var _a;
+        if ((_a = self.spreadsheet) === null || _a === void 0 ? void 0 : _a.rowSet.isLoaded) {
             const selected = self.spreadsheet.rowSet.selectedFilteredRows;
             if (selected.length) {
                 return selected;
@@ -107,7 +108,7 @@ const model = types
         const name = (_a = self.spreadsheet) === null || _a === void 0 ? void 0 : _a.assemblyName;
         if (name) {
             const assemblies = getSession(self).assemblies;
-            return assemblies === null || assemblies === void 0 ? void 0 : assemblies.find(asm => readConfObject(asm, 'name') === name);
+            return assemblies.find(asm => readConfObject(asm, 'name') === name);
         }
         return undefined;
     },
@@ -172,13 +173,6 @@ const model = types
             self.mode = 'display';
         }
     },
-    /**
-     * #action
-     */
-    closeView() {
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        getParent(self, 2).removeView(self);
-    },
 }))
     .views(self => ({
     /**
@@ -188,7 +182,9 @@ const model = types
         return [
             {
                 label: 'Return to import form',
-                onClick: () => self.setImportMode(),
+                onClick: () => {
+                    self.setImportMode();
+                },
                 icon: FolderOpenIcon,
             },
         ];

package/esm/SpreadsheetView/models/StaticRowSet.js

@@ -19,7 +19,6 @@ const StaticRowModel = types
         return this.selectedFilteredRows.length;
     },
     get sortedRows() {
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         const parent = getParent(self);
         return [...self.rows].sort(parent.rowSortingComparisonFunction);
     },
@@ -27,18 +26,14 @@ const StaticRowModel = types
         return self.rows.filter(r => r.isSelected);
     },
     get selectedFilteredRows() {
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         const sheet = getParent(self);
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         const view = getParent(sheet);
         const { filterControls } = view;
         return this.selectedRows.filter(row => filterControls.rowPassesFilters(sheet, row));
     },
     // the set of all rows that pass the filters, sorted
     get sortedFilteredRows() {
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         const sheet = getParent(self);
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         const view = getParent(sheet);
         const { filterControls } = view;
         return self.rows
@@ -48,7 +43,9 @@ const StaticRowModel = types
 }))
     .actions(self => ({
     unselectAll() {
-        self.rows.forEach(row => row.unSelect());
+        self.rows.forEach(row => {
+            row.unSelect();
+        });
     },
 }));
 export default StaticRowModel;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-spreadsheet-view",
-  "version": "2.13.1",
+  "version": "2.15.0",
   "description": "JBrowse 2 spreadsheet view",
   "keywords": [
     "jbrowse",
@@ -24,7 +24,7 @@
   ],
   "scripts": {
     "build": "npm-run-all build:*",
-    "test": "cd ../..; jest plugins/spreadsheet-view",
+    "test": "cd ../..; jest --passWithNoTests plugins/spreadsheet-view",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
@@ -38,14 +38,14 @@
   "dependencies": {
     "@gmod/bgzf-filehandle": "^1.4.3",
     "@gmod/vcf": "^5.0.9",
-    "@jbrowse/plugin-variants": "^2.13.1",
-    "@mui/icons-material": "^5.0.1",
+    "@jbrowse/plugin-variants": "^2.15.0",
+    "@mui/icons-material": "^6.0.0",
     "csvtojson": "^2.0.10"
   },
   "peerDependencies": {
     "@jbrowse/core": "^2.0.0",
     "@jbrowse/plugin-linear-genome-view": "^2.0.0",
-    "@mui/material": "^5.0.0",
+    "@mui/material": "^6.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
@@ -60,5 +60,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "fcebca71cc1d066654603e1a9accfa6c6d4f764d"
+  "gitHead": "87eeb1fbf8311dbf88d5e75b5a265f03beffdda8"
 }