@jbrowse/plugin-spreadsheet-view 2.17.0 → 2.18.0

package/dist/SpreadsheetView/importAdapters/STARFusionImport.d.ts

@@ -1,9 +1,25 @@
-import { ParseOptions } from './ImportUtils';
-import type { Buffer } from 'buffer';
-export declare function parseSTARFusionBuffer(buffer: Buffer, options: ParseOptions): Promise<{
-    rowSet: import("./ImportUtils").RowSet;
-    columnDisplayOrder: number[];
-    hasColumnNames: boolean;
-    columns: import("./ImportUtils").Column[];
-    assemblyName: string | undefined;
-}>;
+export declare function parseSTARFusionBuffer(buffer: Uint8Array): {
+    columns: {
+        name: string;
+    }[];
+    rowSet: {
+        rows: {
+            cellData: {
+                [k: string]: string | number;
+            };
+            feature: {
+                mate: {
+                    refName: string | undefined;
+                    start: number;
+                    end: number;
+                    strand: number | undefined;
+                };
+                refName: string | undefined;
+                start: number;
+                end: number;
+                strand: number | undefined;
+                uniqueId: string;
+            };
+        }[];
+    };
+};

package/dist/SpreadsheetView/importAdapters/STARFusionImport.js

@@ -1,70 +1,35 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseSTARFusionBuffer = parseSTARFusionBuffer;
-const ImportUtils_1 = require("./ImportUtils");
+const isNumber_1 = require("./isNumber");
+const util_1 = require("./util");
 function parseSTARFusionBreakpointString(str) {
     const fields = str.split(':');
-    const refName = fields[0];
-    const pos = Number.parseInt(fields[1], 10);
-    const strand = fields[2] === '-' ? -1 : 1;
-    return { refName, pos, strand };
+    return {
+        refName: fields[0],
+        start: +fields[1],
+        end: +fields[1] + 1,
+        strand: (0, util_1.parseStrand)(fields[2]),
+    };
 }
-const numericColumns = {
-    SpanningFragCount: true,
-    FFPM: true,
-    LeftBreakEntropy: true,
-    RightBreakEntropy: true,
-    JunctionReadCount: true,
-};
-async function parseSTARFusionBuffer(buffer, options) {
-    const data = await (0, ImportUtils_1.parseTsvBuffer)(buffer, {
-        hasColumnNameLine: true,
-        columnNameLineNumber: 1,
-        selectedAssemblyName: options.selectedAssemblyName,
-        isValidRefName: () => false,
-    });
-    // remove the # in #FusionName
-    data.columns[0].name = data.columns[0].name.replace('#', '');
-    // set some columns to be numeric
-    data.columns.forEach(col => {
-        if (numericColumns[col.name]) {
-            col.dataType = { type: 'Number' };
-        }
-    });
-    // decorate each row with a feature object in its extendedData
-    data.rowSet.rows.forEach((row, rowNumber) => {
-        const featureData = {};
-        row.cells.forEach(({ text }, columnNumber) => {
-            const column = data.columns[columnNumber];
-            if (column.name === 'LeftBreakpoint' && text) {
-                const { refName, pos, strand } = parseSTARFusionBreakpointString(text);
-                featureData.refName = refName;
-                featureData.start = pos;
-                featureData.end = pos;
-                featureData.strand = strand;
-            }
-            else if (column.name === 'RightBreakpoint' && text) {
-                const { refName, pos, strand } = parseSTARFusionBreakpointString(text);
-                featureData.mate = {
-                    refName,
-                    start: pos,
-                    end: pos,
-                    strand,
+function parseSTARFusionBuffer(buffer) {
+    const lines = (0, util_1.bufferToLines)(buffer);
+    const columns = lines[0].slice(1).split('\t');
+    return {
+        columns: columns.map(c => ({ name: c })),
+        rowSet: {
+            rows: lines.slice(1).map((line, rowNumber) => {
+                const cols = line.split('\t');
+                const row = Object.fromEntries(columns.map((h, i) => [h, (0, isNumber_1.isNumber)(cols[i]) ? +cols[i] : cols[i]]));
+                return {
+                    cellData: row,
+                    feature: {
+                        uniqueId: `sf-${rowNumber}`,
+                        ...parseSTARFusionBreakpointString(row.LeftBreakpoint),
+                        mate: parseSTARFusionBreakpointString(row.RightBreakpoint),
+                    },
                 };
-            }
-            else if (text && numericColumns[column.name]) {
-                // some other column, numeric
-                featureData[column.name] = Number.parseFloat(text);
-            }
-            else {
-                // some other column, text
-                featureData[column.name] = text;
-            }
-        });
-        featureData.uniqueId = `sf-${rowNumber + 1}`;
-        row.extendedData = {
-            feature: featureData,
-        };
-    });
-    return data;
+            }),
+        },
+    };
 }

package/dist/SpreadsheetView/importAdapters/VcfImport.d.ts

@@ -1,13 +1,20 @@
-import { RowSet, Column, ParseOptions } from './ImportUtils';
-import type { Buffer } from 'buffer';
-export declare function parseVcfBuffer(buffer: Buffer, options?: ParseOptions): {
-    rowSet: RowSet;
-    columnDisplayOrder: number[];
-    hasColumnNames: boolean;
-    columns: Column[];
-    assemblyName: string | undefined;
-};
-export declare function splitVcfFileHeaderAndBody(wholeFile: string): {
-    header: string;
-    body: string;
+export declare function parseVcfBuffer(buffer: Uint8Array): {
+    columns: {
+        name: string;
+    }[];
+    rowSet: {
+        rows: {
+            cellData: {
+                CHROM: string | undefined;
+                POS: number;
+                ID: string | undefined;
+                REF: string | undefined;
+                ALT: string | undefined;
+                QUAL: string | number | undefined;
+                FILTER: string | undefined;
+                FORMAT: string | undefined;
+            };
+            feature: any;
+        }[];
+    };
 };

package/dist/SpreadsheetView/importAdapters/VcfImport.js

@@ -4,108 +4,63 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseVcfBuffer = parseVcfBuffer;
-exports.splitVcfFileHeaderAndBody = splitVcfFileHeaderAndBody;
 const vcf_1 = __importDefault(require("@gmod/vcf"));
 const plugin_variants_1 = require("@jbrowse/plugin-variants");
-const ImportUtils_1 = require("./ImportUtils");
-const vcfCoreColumns = [
-    { name: 'CHROM', type: 'Text' }, // 0
-    { name: 'POS', type: 'Number' }, // 1
-    { name: 'ID', type: 'Text' }, // 2
-    { name: 'REF', type: 'Text' }, // 3
-    { name: 'ALT', type: 'Text' }, // 4
-    { name: 'QUAL', type: 'Number' }, // 5
-    { name: 'FILTER', type: 'Text' }, // 6
-    { name: 'INFO', type: 'Text' }, // 7
-    { name: 'FORMAT', type: 'Text' }, // 8
-];
-function vcfRecordToRow(vcfParser, line, lineNumber) {
-    const vcfVariant = vcfParser.parseLine(line);
-    const vcfFeature = new plugin_variants_1.VcfFeature({
-        variant: vcfVariant,
-        parser: vcfParser,
-        id: `vcf-${lineNumber}`,
-    });
-    const data = line.split('\t').map(d => (d === '.' ? '' : d));
-    // no format column, add blank
-    if (data.length === 8) {
-        data.push('');
-    }
-    const row = {
-        id: String(lineNumber + 1),
-        extendedData: { vcfFeature: vcfFeature.toJSON() },
-        cells: data.map((text, columnNumber) => {
-            return {
-                columnNumber,
-                text,
-            };
-        }),
-    };
-    return row;
-}
-function parseVcfBuffer(buffer, options = {}) {
-    const { selectedAssemblyName } = options;
-    let { header, body } = splitVcfFileHeaderAndBody((0, ImportUtils_1.bufferToString)(buffer));
-    const rows = [];
+const isNumber_1 = require("./isNumber");
+const util_1 = require("./util");
+function parseVcfBuffer(buffer) {
+    const lines = (0, util_1.bufferToLines)(buffer);
+    const header = lines.filter(l => l.startsWith('#')).join('\n');
+    const body = lines.filter(l => !l.startsWith('#'));
     const vcfParser = new vcf_1.default({ header });
-    header = ''; // garbage collect
-    body.split(/\n|\r\n|\r/).forEach((line, lineNumber) => {
-        if (/\S/.test(line)) {
-            rows.push(vcfRecordToRow(vcfParser, line, lineNumber));
-        }
-    });
-    body = ''; // garbage collect
-    const rowSet = {
-        isLoaded: true,
-        rows,
-    };
-    const columnDisplayOrder = [];
-    const columns = [];
-    for (let i = 0; i < vcfCoreColumns.length; i += 1) {
-        columnDisplayOrder.push(i);
-        columns[i] = {
-            name: vcfCoreColumns[i].name,
-            dataType: { type: vcfCoreColumns[i].type },
-        };
-    }
-    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' },
-        };
-    }
-    columnDisplayOrder.push(columnDisplayOrder.length);
-    columns.unshift({
-        name: 'Location',
-        dataType: { type: 'LocString' },
-        isDerived: true,
-        derivationFunctionText: `jexl:{text:row.extendedData.vcfFeature.refName+':'\n
-    +row.extendedData.vcfFeature.start+'..'+row.extendedData.vcfFeature.end, extendedData:\n
-    {refName:row.extendedData.vcfFeature.refName,start:row.extendedData.vcfFeature.start,end:row.extendedData.vcfFeature.end}}`,
-    });
-    return {
-        rowSet,
-        columnDisplayOrder,
-        hasColumnNames: true,
-        columns,
-        assemblyName: selectedAssemblyName,
-    };
-}
-function splitVcfFileHeaderAndBody(wholeFile) {
-    // split into header and the rest of the file
-    let headerEndIndex = 0;
-    let prevChar;
-    for (; headerEndIndex < wholeFile.length; headerEndIndex += 1) {
-        const c = wholeFile[headerEndIndex];
-        if (prevChar === '\n' && c !== '#') {
-            break;
-        }
-        prevChar = c;
+    const keys = new Set();
+    const rows = [];
+    let i = 0;
+    for (const line of body) {
+        const [CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, ...rest] = line.split('\t');
+        const ret = Object.fromEntries((INFO === null || INFO === void 0 ? void 0 : INFO.split(';').map(f => f.trim()).map(e => {
+            const [key, val = 'true'] = e.split('=');
+            const k = `INFO.${key.trim()}`;
+            keys.add(k);
+            const v = val.trim();
+            return [k, (0, isNumber_1.isNumber)(v) ? +v : v];
+        })) || []);
+        rows.push({
+            cellData: {
+                CHROM,
+                POS: +POS,
+                ID,
+                REF,
+                ALT,
+                QUAL: (0, isNumber_1.isNumber)(QUAL) ? +QUAL : QUAL,
+                FILTER,
+                FORMAT,
+                ...ret,
+                ...Object.fromEntries(vcfParser.samples.map((s, idx) => [s, rest[idx]])),
+            },
+            feature: new plugin_variants_1.VcfFeature({
+                parser: vcfParser,
+                variant: vcfParser.parseLine(line),
+                id: `vcf-${i}`,
+            }).toJSON(),
+        });
+        i++;
     }
     return {
-        header: wholeFile.slice(0, Math.max(0, headerEndIndex)),
-        body: wholeFile.slice(headerEndIndex),
+        columns: [
+            'CHROM',
+            'POS',
+            'ID',
+            'REF',
+            'ALT',
+            'QUAL',
+            'FILTER',
+            ...keys,
+            'FORMAT',
+            ...vcfParser.samples,
+        ].map(c => ({ name: c })),
+        rowSet: {
+            rows,
+        },
     };
 }

package/dist/SpreadsheetView/importAdapters/isNumber.d.ts

@@ -0,0 +1 @@
+export declare function isNumber(num: unknown): num is number;

package/dist/SpreadsheetView/importAdapters/isNumber.js

@@ -0,0 +1,14 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.isNumber = isNumber;
+function isNumber(num) {
+    if (typeof num === 'number') {
+        return num - num === 0;
+    }
+    else if (typeof num === 'string' && num.trim() !== '') {
+        return Number.isFinite(+num);
+    }
+    else {
+        return false;
+    }
+}

package/dist/SpreadsheetView/importAdapters/util.d.ts

@@ -0,0 +1,2 @@
+export declare function parseStrand(strand?: string): 1 | -1 | undefined;
+export declare function bufferToLines(buffer: Uint8Array): string[];

package/dist/SpreadsheetView/importAdapters/util.js

@@ -0,0 +1,22 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.parseStrand = parseStrand;
+exports.bufferToLines = bufferToLines;
+function parseStrand(strand) {
+    if (strand === '+') {
+        return 1;
+    }
+    else if (strand === '-') {
+        return -1;
+    }
+    else {
+        return undefined;
+    }
+}
+function bufferToLines(buffer) {
+    return new TextDecoder('utf8')
+        .decode(buffer)
+        .split(/\n|\r\n|\r/)
+        .map(f => f.trim())
+        .filter(f => !!f);
+}

package/dist/SpreadsheetView/index.d.ts

@@ -1,3 +1,3 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function SpreadsheetViewF(pluginManager: PluginManager): void;
-export { type SpreadsheetViewModel, type SpreadsheetViewStateModel, } from './models/SpreadsheetView';
+export type { SpreadsheetViewModel, SpreadsheetViewStateModel, } from './SpreadsheetViewModel';

package/dist/SpreadsheetView/index.js

@@ -29,13 +29,13 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SpreadsheetViewF;
 const react_1 = require("react");
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const SpreadsheetView_1 = __importDefault(require("./models/SpreadsheetView"));
+const SpreadsheetViewModel_1 = __importDefault(require("./SpreadsheetViewModel"));
 function SpreadsheetViewF(pluginManager) {
     pluginManager.addViewType(() => {
         return new pluggableElementTypes_1.ViewType({
             name: 'SpreadsheetView',
             displayName: 'Spreadsheet view',
-            stateModel: SpreadsheetView_1.default,
+            stateModel: (0, SpreadsheetViewModel_1.default)(),
             ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SpreadsheetView')))),
         });
     });

package/dist/SpreadsheetView/util.d.ts

@@ -0,0 +1,7 @@
+import type { AbstractSessionModel } from '@jbrowse/core/util';
+export declare function locationLinkClick({ assemblyName, session, locString, spreadsheetViewId, }: {
+    assemblyName: string;
+    session: AbstractSessionModel;
+    locString: string;
+    spreadsheetViewId: string;
+}): Promise<void>;

package/dist/SpreadsheetView/util.js

@@ -0,0 +1,13 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.locationLinkClick = locationLinkClick;
+function locationLinkClick({ assemblyName, session, locString, spreadsheetViewId, }) {
+    const newViewId = `${spreadsheetViewId}_${assemblyName}`;
+    let view = session.views.find(v => v.id === newViewId);
+    if (!view) {
+        view = session.addView('LinearGenomeView', {
+            id: newViewId,
+        });
+    }
+    return view.navToLocString(locString, assemblyName);
+}

package/dist/index.d.ts

@@ -1,5 +1,5 @@
-import PluginManager from '@jbrowse/core/PluginManager';
 import Plugin from '@jbrowse/core/Plugin';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class SpreadsheetViewPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -5,11 +5,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
 const util_1 = require("@jbrowse/core/util");
-// icons
 const ViewComfy_1 = __importDefault(require("@mui/icons-material/ViewComfy"));
-// locals
-const SpreadsheetView_1 = __importDefault(require("./SpreadsheetView"));
 const LaunchSpreadsheetView_1 = __importDefault(require("./LaunchSpreadsheetView"));
+const SpreadsheetView_1 = __importDefault(require("./SpreadsheetView"));
 class SpreadsheetViewPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);

package/esm/LaunchSpreadsheetView/index.d.ts

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

package/esm/LaunchSpreadsheetView/index.js

@@ -1,7 +1,5 @@
 export default function LaunchSpreadsheetViewF(pluginManager) {
-    pluginManager.addToExtensionPoint('LaunchView-SpreadsheetView', 
-    // @ts-expect-error
-    async ({ session, assembly, uri, fileType, }) => {
+    pluginManager.addToExtensionPoint('LaunchView-SpreadsheetView', async ({ session, assembly, uri, fileType, }) => {
         var _a, _b;
         const view = session.addView('SpreadsheetView');
         const exts = uri.split('.');

package/esm/SpreadsheetView/ImportWizard.d.ts

@@ -0,0 +1,51 @@
+import type { FileLocation } from '@jbrowse/core/util';
+import type { Instance } from 'mobx-state-tree';
+export default function stateModelFactory(): import("mobx-state-tree").IModelType<{
+    fileType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    hasColumnNameLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    columnNameLineNumber: import("mobx-state-tree").IType<number | undefined, number, number>;
+    selectedAssemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    cachedFileLocation: import("mobx-state-tree").IType<FileLocation | undefined, FileLocation | undefined, FileLocation | undefined>;
+}, {
+    fileTypes: string[];
+    fileSource: any;
+    error: unknown;
+    loading: boolean;
+} & {
+    readonly isReadyToOpen: any;
+    readonly fileName: any;
+    readonly requiresUnzip: any;
+    isValidRefName(refName: string, assemblyName?: string): boolean;
+    tracksForAssembly(selectedAssembly: string): {
+        track: {
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                    [x: string]: any;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+        label: string;
+        assemblyNames: any;
+        type: string;
+        loc: FileLocation;
+    }[];
+} & {
+    setSelectedAssemblyName(s: string): void;
+    setFileSource(newSource: unknown): void;
+    setColumnNameLineNumber(newnumber: number): void;
+    setFileType(typeName: string): void;
+    setError(error: unknown): void;
+    setLoading(arg: boolean): void;
+    cancelButton(): void;
+    setCachedFileHandle(arg: FileLocation): void;
+} & {
+    import(assemblyName: string): Promise<void>;
+} & {
+    afterAttach(): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export type ImportWizardStateModel = ReturnType<typeof stateModelFactory>;
+export type ImportWizardModel = Instance<ImportWizardStateModel>;