@jbrowse/plugin-spreadsheet-view 2.17.0 → 3.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/LaunchSpreadsheetView/index.d.ts +1 -1
- package/dist/LaunchSpreadsheetView/index.js +1 -3
- package/dist/SpreadsheetView/ImportWizard.d.ts +51 -0
- package/dist/SpreadsheetView/ImportWizard.js +250 -0
- package/dist/SpreadsheetView/SpreadsheetModel.d.ts +78 -0
- package/dist/SpreadsheetView/SpreadsheetModel.js +119 -0
- package/dist/SpreadsheetView/SpreadsheetViewModel.d.ts +299 -0
- package/dist/SpreadsheetView/SpreadsheetViewModel.js +101 -0
- package/dist/SpreadsheetView/components/BreakendMultiLevelOptionDialog.d.ts +1 -0
- package/dist/SpreadsheetView/components/BreakendMultiLevelOptionDialog.js +5 -0
- package/dist/SpreadsheetView/components/BreakendSingleLevelOptionDialog.d.ts +1 -0
- package/dist/SpreadsheetView/components/BreakendSingleLevelOptionDialog.js +5 -0
- package/dist/SpreadsheetView/components/FeatureMenu.d.ts +7 -0
- package/dist/SpreadsheetView/components/FeatureMenu.js +105 -0
- package/dist/SpreadsheetView/components/ImportWizard.d.ts +3 -4
- package/dist/SpreadsheetView/components/ImportWizard.js +25 -68
- package/dist/SpreadsheetView/components/LocationCell.d.ts +7 -0
- package/dist/SpreadsheetView/components/LocationCell.js +29 -0
- package/dist/SpreadsheetView/components/NumberEditor.d.ts +2 -3
- package/dist/SpreadsheetView/components/NumberEditor.js +4 -28
- package/dist/SpreadsheetView/components/SpreadsheetDataGrid.d.ts +5 -0
- package/dist/SpreadsheetView/components/SpreadsheetDataGrid.js +23 -0
- package/dist/SpreadsheetView/components/SpreadsheetView.d.ts +4 -5
- package/dist/SpreadsheetView/components/SpreadsheetView.js +25 -63
- package/dist/SpreadsheetView/components/SpreadsheetViewActual.d.ts +5 -0
- package/dist/SpreadsheetView/components/SpreadsheetViewActual.js +34 -0
- package/dist/SpreadsheetView/components/TrackSelector.d.ts +6 -0
- package/dist/SpreadsheetView/components/TrackSelector.js +27 -0
- package/dist/SpreadsheetView/importAdapters/BedImport.d.ts +26 -17
- package/dist/SpreadsheetView/importAdapters/BedImport.js +53 -139
- package/dist/SpreadsheetView/importAdapters/BedpeImport.d.ts +36 -0
- package/dist/SpreadsheetView/importAdapters/BedpeImport.js +79 -0
- package/dist/SpreadsheetView/importAdapters/STARFusionImport.d.ts +25 -9
- package/dist/SpreadsheetView/importAdapters/STARFusionImport.js +27 -62
- package/dist/SpreadsheetView/importAdapters/VcfImport.d.ts +19 -12
- package/dist/SpreadsheetView/importAdapters/VcfImport.js +53 -98
- package/dist/SpreadsheetView/importAdapters/isNumber.d.ts +1 -0
- package/dist/SpreadsheetView/importAdapters/isNumber.js +14 -0
- package/dist/SpreadsheetView/importAdapters/util.d.ts +2 -0
- package/dist/SpreadsheetView/importAdapters/util.js +22 -0
- package/dist/SpreadsheetView/index.d.ts +2 -2
- package/dist/SpreadsheetView/index.js +19 -9
- package/dist/SpreadsheetView/util.d.ts +7 -0
- package/dist/SpreadsheetView/util.js +13 -0
- package/dist/index.d.ts +1 -1
- package/dist/index.js +1 -3
- package/esm/LaunchSpreadsheetView/index.d.ts +1 -1
- package/esm/LaunchSpreadsheetView/index.js +1 -3
- package/esm/SpreadsheetView/ImportWizard.d.ts +51 -0
- package/esm/SpreadsheetView/ImportWizard.js +214 -0
- package/esm/SpreadsheetView/SpreadsheetModel.d.ts +78 -0
- package/esm/SpreadsheetView/SpreadsheetModel.js +113 -0
- package/esm/SpreadsheetView/SpreadsheetViewModel.d.ts +299 -0
- package/esm/SpreadsheetView/SpreadsheetViewModel.js +95 -0
- package/esm/SpreadsheetView/components/BreakendMultiLevelOptionDialog.d.ts +1 -0
- package/esm/SpreadsheetView/components/BreakendMultiLevelOptionDialog.js +1 -0
- package/esm/SpreadsheetView/components/BreakendSingleLevelOptionDialog.d.ts +1 -0
- package/esm/SpreadsheetView/components/BreakendSingleLevelOptionDialog.js +1 -0
- package/esm/SpreadsheetView/components/FeatureMenu.d.ts +7 -0
- package/esm/SpreadsheetView/components/FeatureMenu.js +66 -0
- package/esm/SpreadsheetView/components/ImportWizard.d.ts +3 -4
- package/esm/SpreadsheetView/components/ImportWizard.js +26 -46
- package/esm/SpreadsheetView/components/LocationCell.d.ts +7 -0
- package/esm/SpreadsheetView/components/LocationCell.js +23 -0
- package/esm/SpreadsheetView/components/NumberEditor.d.ts +2 -3
- package/esm/SpreadsheetView/components/NumberEditor.js +4 -5
- package/esm/SpreadsheetView/components/SpreadsheetDataGrid.d.ts +5 -0
- package/esm/SpreadsheetView/components/SpreadsheetDataGrid.js +21 -0
- package/esm/SpreadsheetView/components/SpreadsheetView.d.ts +4 -5
- package/esm/SpreadsheetView/components/SpreadsheetView.js +8 -56
- package/esm/SpreadsheetView/components/SpreadsheetViewActual.d.ts +5 -0
- package/esm/SpreadsheetView/components/SpreadsheetViewActual.js +29 -0
- package/esm/SpreadsheetView/components/TrackSelector.d.ts +6 -0
- package/esm/SpreadsheetView/components/TrackSelector.js +25 -0
- package/esm/SpreadsheetView/importAdapters/BedImport.d.ts +26 -17
- package/esm/SpreadsheetView/importAdapters/BedImport.js +53 -137
- package/esm/SpreadsheetView/importAdapters/BedpeImport.d.ts +36 -0
- package/esm/SpreadsheetView/importAdapters/BedpeImport.js +76 -0
- package/esm/SpreadsheetView/importAdapters/STARFusionImport.d.ts +25 -9
- package/esm/SpreadsheetView/importAdapters/STARFusionImport.js +27 -62
- package/esm/SpreadsheetView/importAdapters/VcfImport.d.ts +19 -12
- package/esm/SpreadsheetView/importAdapters/VcfImport.js +53 -97
- package/esm/SpreadsheetView/importAdapters/isNumber.d.ts +1 -0
- package/esm/SpreadsheetView/importAdapters/isNumber.js +11 -0
- package/esm/SpreadsheetView/importAdapters/util.d.ts +2 -0
- package/esm/SpreadsheetView/importAdapters/util.js +18 -0
- package/esm/SpreadsheetView/index.d.ts +2 -2
- package/esm/SpreadsheetView/index.js +2 -2
- package/esm/SpreadsheetView/util.d.ts +7 -0
- package/esm/SpreadsheetView/util.js +10 -0
- package/esm/index.d.ts +1 -1
- package/esm/index.js +1 -3
- package/package.json +7 -7
- package/dist/SpreadsheetView/components/CellData.d.ts +0 -9
- package/dist/SpreadsheetView/components/CellData.js +0 -14
- package/dist/SpreadsheetView/components/ColumnFilterControls.d.ts +0 -3
- package/dist/SpreadsheetView/components/ColumnFilterControls.js +0 -58
- package/dist/SpreadsheetView/components/ColumnMenu.d.ts +0 -16
- package/dist/SpreadsheetView/components/ColumnMenu.js +0 -140
- package/dist/SpreadsheetView/components/DataRow.d.ts +0 -12
- package/dist/SpreadsheetView/components/DataRow.js +0 -81
- package/dist/SpreadsheetView/components/DataTable.d.ts +0 -10
- package/dist/SpreadsheetView/components/DataTable.js +0 -42
- package/dist/SpreadsheetView/components/DataTableHeader.d.ts +0 -6
- package/dist/SpreadsheetView/components/DataTableHeader.js +0 -104
- package/dist/SpreadsheetView/components/GlobalFilterControls.d.ts +0 -5
- package/dist/SpreadsheetView/components/GlobalFilterControls.js +0 -68
- package/dist/SpreadsheetView/components/RowCountMessage.d.ts +0 -6
- package/dist/SpreadsheetView/components/RowCountMessage.js +0 -33
- package/dist/SpreadsheetView/components/RowMenu.d.ts +0 -9
- package/dist/SpreadsheetView/components/RowMenu.js +0 -39
- package/dist/SpreadsheetView/components/SortIndicator.d.ts +0 -6
- package/dist/SpreadsheetView/components/SortIndicator.js +0 -27
- package/dist/SpreadsheetView/components/Spreadsheet.d.ts +0 -11
- package/dist/SpreadsheetView/components/Spreadsheet.js +0 -25
- package/dist/SpreadsheetView/components/StatusBar.d.ts +0 -11
- package/dist/SpreadsheetView/components/StatusBar.js +0 -44
- package/dist/SpreadsheetView/importAdapters/ImportUtils.d.ts +0 -42
- package/dist/SpreadsheetView/importAdapters/ImportUtils.js +0 -123
- package/dist/SpreadsheetView/models/ColumnDataTypes/LocEnd.d.ts +0 -12
- package/dist/SpreadsheetView/models/ColumnDataTypes/LocEnd.js +0 -20
- package/dist/SpreadsheetView/models/ColumnDataTypes/LocRef.d.ts +0 -12
- package/dist/SpreadsheetView/models/ColumnDataTypes/LocRef.js +0 -20
- package/dist/SpreadsheetView/models/ColumnDataTypes/LocStart.d.ts +0 -12
- package/dist/SpreadsheetView/models/ColumnDataTypes/LocStart.js +0 -20
- package/dist/SpreadsheetView/models/ColumnDataTypes/LocString.d.ts +0 -13
- package/dist/SpreadsheetView/models/ColumnDataTypes/LocString.js +0 -183
- package/dist/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.d.ts +0 -19
- package/dist/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.js +0 -23
- package/dist/SpreadsheetView/models/ColumnDataTypes/Number.d.ts +0 -30
- package/dist/SpreadsheetView/models/ColumnDataTypes/Number.js +0 -126
- package/dist/SpreadsheetView/models/ColumnDataTypes/Text.d.ts +0 -28
- package/dist/SpreadsheetView/models/ColumnDataTypes/Text.js +0 -129
- package/dist/SpreadsheetView/models/ColumnDataTypes/index.d.ts +0 -71
- package/dist/SpreadsheetView/models/ColumnDataTypes/index.js +0 -37
- package/dist/SpreadsheetView/models/FilterControls.d.ts +0 -26
- package/dist/SpreadsheetView/models/FilterControls.js +0 -85
- package/dist/SpreadsheetView/models/ImportWizard.d.ts +0 -31
- package/dist/SpreadsheetView/models/ImportWizard.js +0 -186
- package/dist/SpreadsheetView/models/Row.d.ts +0 -17
- package/dist/SpreadsheetView/models/Row.js +0 -43
- package/dist/SpreadsheetView/models/Spreadsheet.d.ts +0 -260
- package/dist/SpreadsheetView/models/Spreadsheet.js +0 -174
- package/dist/SpreadsheetView/models/SpreadsheetView.d.ts +0 -482
- package/dist/SpreadsheetView/models/SpreadsheetView.js +0 -199
- package/dist/SpreadsheetView/models/StaticRowSet.d.ts +0 -163
- package/dist/SpreadsheetView/models/StaticRowSet.js +0 -56
- package/esm/SpreadsheetView/components/CellData.d.ts +0 -9
- package/esm/SpreadsheetView/components/CellData.js +0 -9
- package/esm/SpreadsheetView/components/ColumnFilterControls.d.ts +0 -3
- package/esm/SpreadsheetView/components/ColumnFilterControls.js +0 -53
- package/esm/SpreadsheetView/components/ColumnMenu.d.ts +0 -16
- package/esm/SpreadsheetView/components/ColumnMenu.js +0 -135
- package/esm/SpreadsheetView/components/DataRow.d.ts +0 -12
- package/esm/SpreadsheetView/components/DataRow.js +0 -76
- package/esm/SpreadsheetView/components/DataTable.d.ts +0 -10
- package/esm/SpreadsheetView/components/DataTable.js +0 -37
- package/esm/SpreadsheetView/components/DataTableHeader.d.ts +0 -6
- package/esm/SpreadsheetView/components/DataTableHeader.js +0 -76
- package/esm/SpreadsheetView/components/GlobalFilterControls.d.ts +0 -5
- package/esm/SpreadsheetView/components/GlobalFilterControls.js +0 -40
- package/esm/SpreadsheetView/components/RowCountMessage.d.ts +0 -6
- package/esm/SpreadsheetView/components/RowCountMessage.js +0 -28
- package/esm/SpreadsheetView/components/RowMenu.d.ts +0 -9
- package/esm/SpreadsheetView/components/RowMenu.js +0 -34
- package/esm/SpreadsheetView/components/SortIndicator.d.ts +0 -6
- package/esm/SpreadsheetView/components/SortIndicator.js +0 -21
- package/esm/SpreadsheetView/components/Spreadsheet.d.ts +0 -11
- package/esm/SpreadsheetView/components/Spreadsheet.js +0 -20
- package/esm/SpreadsheetView/components/StatusBar.d.ts +0 -11
- package/esm/SpreadsheetView/components/StatusBar.js +0 -39
- package/esm/SpreadsheetView/importAdapters/ImportUtils.d.ts +0 -42
- package/esm/SpreadsheetView/importAdapters/ImportUtils.js +0 -95
- package/esm/SpreadsheetView/models/ColumnDataTypes/LocEnd.d.ts +0 -12
- package/esm/SpreadsheetView/models/ColumnDataTypes/LocEnd.js +0 -15
- package/esm/SpreadsheetView/models/ColumnDataTypes/LocRef.d.ts +0 -12
- package/esm/SpreadsheetView/models/ColumnDataTypes/LocRef.js +0 -15
- package/esm/SpreadsheetView/models/ColumnDataTypes/LocStart.d.ts +0 -12
- package/esm/SpreadsheetView/models/ColumnDataTypes/LocStart.js +0 -15
- package/esm/SpreadsheetView/models/ColumnDataTypes/LocString.d.ts +0 -13
- package/esm/SpreadsheetView/models/ColumnDataTypes/LocString.js +0 -178
- package/esm/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.d.ts +0 -19
- package/esm/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.js +0 -20
- package/esm/SpreadsheetView/models/ColumnDataTypes/Number.d.ts +0 -30
- package/esm/SpreadsheetView/models/ColumnDataTypes/Number.js +0 -119
- package/esm/SpreadsheetView/models/ColumnDataTypes/Text.d.ts +0 -28
- package/esm/SpreadsheetView/models/ColumnDataTypes/Text.js +0 -122
- package/esm/SpreadsheetView/models/ColumnDataTypes/index.d.ts +0 -71
- package/esm/SpreadsheetView/models/ColumnDataTypes/index.js +0 -29
- package/esm/SpreadsheetView/models/FilterControls.d.ts +0 -26
- package/esm/SpreadsheetView/models/FilterControls.js +0 -83
- package/esm/SpreadsheetView/models/ImportWizard.d.ts +0 -31
- package/esm/SpreadsheetView/models/ImportWizard.js +0 -161
- package/esm/SpreadsheetView/models/Row.d.ts +0 -17
- package/esm/SpreadsheetView/models/Row.js +0 -41
- package/esm/SpreadsheetView/models/Spreadsheet.d.ts +0 -260
- package/esm/SpreadsheetView/models/Spreadsheet.js +0 -169
- package/esm/SpreadsheetView/models/SpreadsheetView.d.ts +0 -482
- package/esm/SpreadsheetView/models/SpreadsheetView.js +0 -194
- package/esm/SpreadsheetView/models/StaticRowSet.d.ts +0 -163
- package/esm/SpreadsheetView/models/StaticRowSet.js +0 -51
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export default function SpreadsheetViewF(pluginManager: PluginManager): void;
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export type { SpreadsheetViewModel, SpreadsheetViewStateModel, } from './SpreadsheetViewModel';
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import type { AbstractSessionModel } from '@jbrowse/core/util';
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export declare function locationLinkClick({ assemblyName, session, locString, spreadsheetViewId, }: {
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package/dist/index.d.ts
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export default class SpreadsheetViewPlugin extends Plugin {
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package/dist/index.js
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Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
6
|
const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
|
|
7
7
|
const util_1 = require("@jbrowse/core/util");
|
|
8
|
-
// icons
|
|
9
8
|
const ViewComfy_1 = __importDefault(require("@mui/icons-material/ViewComfy"));
|
|
10
|
-
// locals
|
|
11
|
-
const SpreadsheetView_1 = __importDefault(require("./SpreadsheetView"));
|
|
12
9
|
const LaunchSpreadsheetView_1 = __importDefault(require("./LaunchSpreadsheetView"));
|
|
10
|
+
const SpreadsheetView_1 = __importDefault(require("./SpreadsheetView"));
|
|
13
11
|
class SpreadsheetViewPlugin extends Plugin_1.default {
|
|
14
12
|
constructor() {
|
|
15
13
|
super(...arguments);
|
|
@@ -1,2 +1,2 @@
|
|
|
1
|
-
import PluginManager from '@jbrowse/core/PluginManager';
|
|
1
|
+
import type PluginManager from '@jbrowse/core/PluginManager';
|
|
2
2
|
export default function LaunchSpreadsheetViewF(pluginManager: PluginManager): void;
|
|
@@ -1,7 +1,5 @@
|
|
|
1
1
|
export default function LaunchSpreadsheetViewF(pluginManager) {
|
|
2
|
-
pluginManager.addToExtensionPoint('LaunchView-SpreadsheetView',
|
|
3
|
-
// @ts-expect-error
|
|
4
|
-
async ({ session, assembly, uri, fileType, }) => {
|
|
2
|
+
pluginManager.addToExtensionPoint('LaunchView-SpreadsheetView', async ({ session, assembly, uri, fileType, }) => {
|
|
5
3
|
var _a, _b;
|
|
6
4
|
const view = session.addView('SpreadsheetView');
|
|
7
5
|
const exts = uri.split('.');
|
|
@@ -0,0 +1,51 @@
|
|
|
1
|
+
import type { FileLocation } from '@jbrowse/core/util';
|
|
2
|
+
import type { Instance } from 'mobx-state-tree';
|
|
3
|
+
export default function stateModelFactory(): import("mobx-state-tree").IModelType<{
|
|
4
|
+
fileType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
5
|
+
hasColumnNameLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
6
|
+
columnNameLineNumber: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
7
|
+
selectedAssemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
8
|
+
cachedFileLocation: import("mobx-state-tree").IType<FileLocation | undefined, FileLocation | undefined, FileLocation | undefined>;
|
|
9
|
+
}, {
|
|
10
|
+
fileTypes: string[];
|
|
11
|
+
fileSource: any;
|
|
12
|
+
error: unknown;
|
|
13
|
+
loading: boolean;
|
|
14
|
+
} & {
|
|
15
|
+
readonly isReadyToOpen: any;
|
|
16
|
+
readonly fileName: any;
|
|
17
|
+
readonly requiresUnzip: any;
|
|
18
|
+
isValidRefName(refName: string, assemblyName?: string): boolean;
|
|
19
|
+
tracksForAssembly(selectedAssembly: string): {
|
|
20
|
+
track: {
|
|
21
|
+
[x: string]: any;
|
|
22
|
+
} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
|
|
23
|
+
setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
|
|
24
|
+
[x: string]: any;
|
|
25
|
+
} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
|
|
26
|
+
setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
|
|
27
|
+
[x: string]: any;
|
|
28
|
+
} & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
|
|
29
|
+
} & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
|
|
30
|
+
} & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
|
|
31
|
+
label: string;
|
|
32
|
+
assemblyNames: any;
|
|
33
|
+
type: string;
|
|
34
|
+
loc: FileLocation;
|
|
35
|
+
}[];
|
|
36
|
+
} & {
|
|
37
|
+
setSelectedAssemblyName(s: string): void;
|
|
38
|
+
setFileSource(newSource: unknown): void;
|
|
39
|
+
setColumnNameLineNumber(newnumber: number): void;
|
|
40
|
+
setFileType(typeName: string): void;
|
|
41
|
+
setError(error: unknown): void;
|
|
42
|
+
setLoading(arg: boolean): void;
|
|
43
|
+
cancelButton(): void;
|
|
44
|
+
setCachedFileHandle(arg: FileLocation): void;
|
|
45
|
+
} & {
|
|
46
|
+
import(assemblyName: string): Promise<void>;
|
|
47
|
+
} & {
|
|
48
|
+
afterAttach(): void;
|
|
49
|
+
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
|
|
50
|
+
export type ImportWizardStateModel = ReturnType<typeof stateModelFactory>;
|
|
51
|
+
export type ImportWizardModel = Instance<ImportWizardStateModel>;
|
|
@@ -0,0 +1,214 @@
|
|
|
1
|
+
import { readConfObject } from '@jbrowse/core/configuration';
|
|
2
|
+
import { getEnv, getSession } from '@jbrowse/core/util';
|
|
3
|
+
import { openLocation } from '@jbrowse/core/util/io';
|
|
4
|
+
import { getTrackName } from '@jbrowse/core/util/tracks';
|
|
5
|
+
import { getParent, types } from 'mobx-state-tree';
|
|
6
|
+
const IMPORT_SIZE_LIMIT = 100000000;
|
|
7
|
+
const fileTypes = ['VCF', 'BED', 'BEDPE', 'STAR-Fusion'];
|
|
8
|
+
const fileTypeParsers = {
|
|
9
|
+
VCF: () => import('./importAdapters/VcfImport').then(r => r.parseVcfBuffer),
|
|
10
|
+
BED: () => import('./importAdapters/BedImport').then(r => r.parseBedBuffer),
|
|
11
|
+
BEDPE: () => import('./importAdapters/BedpeImport').then(r => r.parseBedPEBuffer),
|
|
12
|
+
'STAR-Fusion': () => import('./importAdapters/STARFusionImport').then(r => r.parseSTARFusionBuffer),
|
|
13
|
+
};
|
|
14
|
+
function getType(adapter) {
|
|
15
|
+
if (adapter.vcfLocation || adapter.vcfGzLocation) {
|
|
16
|
+
return 'VCF';
|
|
17
|
+
}
|
|
18
|
+
else if (adapter.bedLocation || adapter.bedGzLocation) {
|
|
19
|
+
return 'BED';
|
|
20
|
+
}
|
|
21
|
+
else if (adapter.bedpeLocation) {
|
|
22
|
+
return 'BEDPE';
|
|
23
|
+
}
|
|
24
|
+
else {
|
|
25
|
+
return undefined;
|
|
26
|
+
}
|
|
27
|
+
}
|
|
28
|
+
function getAdapterLoc(adapter) {
|
|
29
|
+
return (adapter.vcfLocation ||
|
|
30
|
+
adapter.vcfGzLocation ||
|
|
31
|
+
adapter.bedLocation ||
|
|
32
|
+
adapter.bedGzLocation ||
|
|
33
|
+
adapter.bedpeLocation);
|
|
34
|
+
}
|
|
35
|
+
const fileTypesRegexp = new RegExp(`\\.(${fileTypes.join('|')})(\\.gz)?$`, 'i');
|
|
36
|
+
function x() { }
|
|
37
|
+
export default function stateModelFactory() {
|
|
38
|
+
return types
|
|
39
|
+
.model('SpreadsheetImportWizard', {
|
|
40
|
+
fileType: types.optional(types.enumeration(fileTypes), 'VCF'),
|
|
41
|
+
hasColumnNameLine: true,
|
|
42
|
+
columnNameLineNumber: 1,
|
|
43
|
+
selectedAssemblyName: types.maybe(types.string),
|
|
44
|
+
cachedFileLocation: types.frozen(),
|
|
45
|
+
})
|
|
46
|
+
.volatile(() => ({
|
|
47
|
+
fileTypes,
|
|
48
|
+
fileSource: undefined,
|
|
49
|
+
error: undefined,
|
|
50
|
+
loading: false,
|
|
51
|
+
}))
|
|
52
|
+
.views(self => ({
|
|
53
|
+
get isReadyToOpen() {
|
|
54
|
+
return (self.fileSource &&
|
|
55
|
+
(self.fileSource.blobId ||
|
|
56
|
+
self.fileSource.localPath ||
|
|
57
|
+
self.fileSource.uri));
|
|
58
|
+
},
|
|
59
|
+
get fileName() {
|
|
60
|
+
return (self.fileSource.uri ||
|
|
61
|
+
self.fileSource.localPath ||
|
|
62
|
+
(self.fileSource.blobId && self.fileSource.name));
|
|
63
|
+
},
|
|
64
|
+
get requiresUnzip() {
|
|
65
|
+
return this.fileName.endsWith('gz');
|
|
66
|
+
},
|
|
67
|
+
isValidRefName(refName, assemblyName) {
|
|
68
|
+
const { assemblyManager } = getSession(self);
|
|
69
|
+
return !assemblyName
|
|
70
|
+
? false
|
|
71
|
+
: assemblyManager.isValidRefName(refName, assemblyName);
|
|
72
|
+
},
|
|
73
|
+
tracksForAssembly(selectedAssembly) {
|
|
74
|
+
const session = getSession(self);
|
|
75
|
+
const { tracks = [], sessionTracks = [] } = session;
|
|
76
|
+
const allTracks = [
|
|
77
|
+
...tracks,
|
|
78
|
+
...sessionTracks,
|
|
79
|
+
];
|
|
80
|
+
return allTracks
|
|
81
|
+
.map(track => {
|
|
82
|
+
const assemblyNames = readConfObject(track, 'assemblyNames');
|
|
83
|
+
const adapter = readConfObject(track, 'adapter');
|
|
84
|
+
const category = readConfObject(track, 'category').join(',');
|
|
85
|
+
const loc = getAdapterLoc(adapter);
|
|
86
|
+
return assemblyNames.includes(selectedAssembly) && loc
|
|
87
|
+
? {
|
|
88
|
+
track,
|
|
89
|
+
label: [
|
|
90
|
+
category ? `[${category}]` : '',
|
|
91
|
+
getTrackName(track, session),
|
|
92
|
+
]
|
|
93
|
+
.filter(f => !!f)
|
|
94
|
+
.join(' '),
|
|
95
|
+
assemblyNames,
|
|
96
|
+
type: getType(adapter) || 'UNKNOWN',
|
|
97
|
+
loc,
|
|
98
|
+
}
|
|
99
|
+
: undefined;
|
|
100
|
+
})
|
|
101
|
+
.filter(f => !!f)
|
|
102
|
+
.sort((a, b) => a.label.localeCompare(b.label));
|
|
103
|
+
},
|
|
104
|
+
}))
|
|
105
|
+
.actions(self => ({
|
|
106
|
+
setSelectedAssemblyName(s) {
|
|
107
|
+
self.selectedAssemblyName = s;
|
|
108
|
+
},
|
|
109
|
+
setFileSource(newSource) {
|
|
110
|
+
var _a;
|
|
111
|
+
self.fileSource = newSource;
|
|
112
|
+
self.error = undefined;
|
|
113
|
+
if (self.fileSource) {
|
|
114
|
+
const name = self.fileName;
|
|
115
|
+
if (name) {
|
|
116
|
+
const firstMatch = (_a = fileTypesRegexp.exec(name)) === null || _a === void 0 ? void 0 : _a[1];
|
|
117
|
+
if (firstMatch) {
|
|
118
|
+
self.fileType =
|
|
119
|
+
firstMatch === 'tsv' && name.includes('star-fusion')
|
|
120
|
+
? 'STAR-Fusion'
|
|
121
|
+
: firstMatch.toUpperCase();
|
|
122
|
+
}
|
|
123
|
+
}
|
|
124
|
+
}
|
|
125
|
+
},
|
|
126
|
+
setColumnNameLineNumber(newnumber) {
|
|
127
|
+
if (newnumber > 0) {
|
|
128
|
+
self.columnNameLineNumber = newnumber;
|
|
129
|
+
}
|
|
130
|
+
},
|
|
131
|
+
setFileType(typeName) {
|
|
132
|
+
self.fileType = typeName;
|
|
133
|
+
},
|
|
134
|
+
setError(error) {
|
|
135
|
+
self.error = error;
|
|
136
|
+
},
|
|
137
|
+
setLoading(arg) {
|
|
138
|
+
self.loading = arg;
|
|
139
|
+
},
|
|
140
|
+
cancelButton() {
|
|
141
|
+
self.error = undefined;
|
|
142
|
+
getParent(self).setDisplayMode();
|
|
143
|
+
},
|
|
144
|
+
setCachedFileHandle(arg) {
|
|
145
|
+
self.cachedFileLocation = arg;
|
|
146
|
+
},
|
|
147
|
+
}))
|
|
148
|
+
.actions(self => ({
|
|
149
|
+
async import(assemblyName) {
|
|
150
|
+
if (!self.fileSource) {
|
|
151
|
+
return;
|
|
152
|
+
}
|
|
153
|
+
self.selectedAssemblyName = assemblyName;
|
|
154
|
+
const type = self.fileType;
|
|
155
|
+
const typeParser = await fileTypeParsers[type]();
|
|
156
|
+
const { fetchAndMaybeUnzip } = await import('@jbrowse/core/util');
|
|
157
|
+
const { pluginManager } = getEnv(self);
|
|
158
|
+
const filehandle = openLocation(self.fileSource, pluginManager);
|
|
159
|
+
self.setLoading(true);
|
|
160
|
+
try {
|
|
161
|
+
const stat = await filehandle.stat();
|
|
162
|
+
if (stat.size > IMPORT_SIZE_LIMIT) {
|
|
163
|
+
self.setError(`File is too big. Tabular files are limited to at most ${(IMPORT_SIZE_LIMIT / 1000).toLocaleString()}kb.`);
|
|
164
|
+
return;
|
|
165
|
+
}
|
|
166
|
+
}
|
|
167
|
+
catch (e) {
|
|
168
|
+
console.warn(e);
|
|
169
|
+
}
|
|
170
|
+
finally {
|
|
171
|
+
self.setLoading(false);
|
|
172
|
+
}
|
|
173
|
+
self.setLoading(true);
|
|
174
|
+
try {
|
|
175
|
+
if (self.fileSource.uri) {
|
|
176
|
+
self.setCachedFileHandle({
|
|
177
|
+
uri: self.fileSource.uri,
|
|
178
|
+
baseUri: self.fileSource.baseUri,
|
|
179
|
+
locationType: 'UriLocation',
|
|
180
|
+
});
|
|
181
|
+
}
|
|
182
|
+
const data = await fetchAndMaybeUnzip(filehandle);
|
|
183
|
+
getParent(self).displaySpreadsheet({
|
|
184
|
+
...typeParser(data),
|
|
185
|
+
assemblyName,
|
|
186
|
+
});
|
|
187
|
+
}
|
|
188
|
+
catch (e) {
|
|
189
|
+
console.error(e);
|
|
190
|
+
self.setError(e);
|
|
191
|
+
}
|
|
192
|
+
finally {
|
|
193
|
+
self.setLoading(false);
|
|
194
|
+
}
|
|
195
|
+
},
|
|
196
|
+
}))
|
|
197
|
+
.actions(self => ({
|
|
198
|
+
afterAttach() {
|
|
199
|
+
;
|
|
200
|
+
(async () => {
|
|
201
|
+
try {
|
|
202
|
+
if (self.cachedFileLocation && self.selectedAssemblyName) {
|
|
203
|
+
self.setFileSource(self.cachedFileLocation);
|
|
204
|
+
await self.import(self.selectedAssemblyName);
|
|
205
|
+
}
|
|
206
|
+
}
|
|
207
|
+
catch (e) {
|
|
208
|
+
console.error(e);
|
|
209
|
+
getSession(self).notifyError(`${e}`, e);
|
|
210
|
+
}
|
|
211
|
+
})();
|
|
212
|
+
},
|
|
213
|
+
}));
|
|
214
|
+
}
|
|
@@ -0,0 +1,78 @@
|
|
|
1
|
+
import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
|
|
2
|
+
import type { Instance } from 'mobx-state-tree';
|
|
3
|
+
export interface Row {
|
|
4
|
+
feature?: SimpleFeatureSerialized;
|
|
5
|
+
cellData?: Record<string, unknown>;
|
|
6
|
+
cells?: {
|
|
7
|
+
text: unknown;
|
|
8
|
+
}[];
|
|
9
|
+
}
|
|
10
|
+
export interface RowSet {
|
|
11
|
+
rows: Row[];
|
|
12
|
+
}
|
|
13
|
+
export default function stateModelFactory(): import("mobx-state-tree").IModelType<{
|
|
14
|
+
rowSet: import("mobx-state-tree").IType<RowSet | undefined, RowSet | undefined, RowSet | undefined>;
|
|
15
|
+
columns: import("mobx-state-tree").IType<{
|
|
16
|
+
name: string;
|
|
17
|
+
}[], {
|
|
18
|
+
name: string;
|
|
19
|
+
}[], {
|
|
20
|
+
name: string;
|
|
21
|
+
}[]>;
|
|
22
|
+
assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
23
|
+
visibleColumns: import("mobx-state-tree").IType<Record<string, boolean>, Record<string, boolean>, Record<string, boolean>>;
|
|
24
|
+
}, {
|
|
25
|
+
visibleRowFlags: Record<number, boolean> | undefined;
|
|
26
|
+
} & {
|
|
27
|
+
readonly rows: {
|
|
28
|
+
id: number;
|
|
29
|
+
feature: SimpleFeatureSerialized | undefined;
|
|
30
|
+
}[] | undefined;
|
|
31
|
+
readonly initialized: boolean | undefined;
|
|
32
|
+
} & {
|
|
33
|
+
readonly dataGridColumns: ({
|
|
34
|
+
field: string;
|
|
35
|
+
width: number;
|
|
36
|
+
type: "number" | undefined;
|
|
37
|
+
} | {
|
|
38
|
+
field: string;
|
|
39
|
+
width: number;
|
|
40
|
+
renderCell: ({ row }: import("@mui/x-data-grid").GridRenderCellParams<{
|
|
41
|
+
id: number;
|
|
42
|
+
feature: SimpleFeatureSerialized | undefined;
|
|
43
|
+
}, any, any, import("@mui/x-data-grid").GridTreeNodeWithRender>) => import("react/jsx-runtime").JSX.Element | "N/A";
|
|
44
|
+
type?: undefined;
|
|
45
|
+
valueGetter?: undefined;
|
|
46
|
+
valueFormatter?: undefined;
|
|
47
|
+
} | {
|
|
48
|
+
field: string;
|
|
49
|
+
type: "number";
|
|
50
|
+
width: number;
|
|
51
|
+
valueGetter: (_val: unknown, row: {
|
|
52
|
+
feature?: SimpleFeatureSerialized;
|
|
53
|
+
}) => number | undefined;
|
|
54
|
+
valueFormatter: (arg: never) => string;
|
|
55
|
+
renderCell?: undefined;
|
|
56
|
+
})[] | undefined;
|
|
57
|
+
} & {
|
|
58
|
+
readonly visibleRows: {
|
|
59
|
+
id: number;
|
|
60
|
+
feature: SimpleFeatureSerialized | undefined;
|
|
61
|
+
}[] | undefined;
|
|
62
|
+
} & {
|
|
63
|
+
setVisibleRows(arg?: Record<number, boolean>): void;
|
|
64
|
+
setVisibleColumns(arg: Record<string, boolean>): void;
|
|
65
|
+
}, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
|
|
66
|
+
rowSet: import("mobx-state-tree").IType<RowSet | undefined, RowSet | undefined, RowSet | undefined>;
|
|
67
|
+
columns: import("mobx-state-tree").IType<{
|
|
68
|
+
name: string;
|
|
69
|
+
}[], {
|
|
70
|
+
name: string;
|
|
71
|
+
}[], {
|
|
72
|
+
name: string;
|
|
73
|
+
}[]>;
|
|
74
|
+
assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
75
|
+
visibleColumns: import("mobx-state-tree").IType<Record<string, boolean>, Record<string, boolean>, Record<string, boolean>>;
|
|
76
|
+
}>>, import("mobx-state-tree")._NotCustomized>;
|
|
77
|
+
export type SpreadsheetStateModel = ReturnType<typeof stateModelFactory>;
|
|
78
|
+
export type SpreadsheetModel = Instance<SpreadsheetStateModel>;
|
|
@@ -0,0 +1,113 @@
|
|
|
1
|
+
import { jsx as _jsx } from "react/jsx-runtime";
|
|
2
|
+
import { assembleLocStringFast, getSession, measureGridWidth, toLocale, } from '@jbrowse/core/util';
|
|
3
|
+
import { types } from 'mobx-state-tree';
|
|
4
|
+
import LocationCell from './components/LocationCell';
|
|
5
|
+
export default function stateModelFactory() {
|
|
6
|
+
return types
|
|
7
|
+
.model('Spreadsheet', {
|
|
8
|
+
rowSet: types.frozen(),
|
|
9
|
+
columns: types.frozen(),
|
|
10
|
+
assemblyName: types.maybe(types.string),
|
|
11
|
+
visibleColumns: types.frozen(),
|
|
12
|
+
})
|
|
13
|
+
.volatile(() => ({
|
|
14
|
+
visibleRowFlags: undefined,
|
|
15
|
+
}))
|
|
16
|
+
.views(self => ({
|
|
17
|
+
get rows() {
|
|
18
|
+
var _a;
|
|
19
|
+
return (_a = self.rowSet) === null || _a === void 0 ? void 0 : _a.rows.map((row, i) => ({
|
|
20
|
+
id: i,
|
|
21
|
+
feature: row.feature,
|
|
22
|
+
...Object.fromEntries(self.columns.map((c, idx) => {
|
|
23
|
+
var _a, _b, _c, _d;
|
|
24
|
+
return [
|
|
25
|
+
c.name,
|
|
26
|
+
(_b = (_a = row.cellData) === null || _a === void 0 ? void 0 : _a[c.name]) !== null && _b !== void 0 ? _b : (_d = (_c = row.cells) === null || _c === void 0 ? void 0 : _c[idx]) === null || _d === void 0 ? void 0 : _d.text,
|
|
27
|
+
];
|
|
28
|
+
})),
|
|
29
|
+
}));
|
|
30
|
+
},
|
|
31
|
+
get initialized() {
|
|
32
|
+
var _a;
|
|
33
|
+
const session = getSession(self);
|
|
34
|
+
const name = self.assemblyName;
|
|
35
|
+
return (self.rowSet &&
|
|
36
|
+
(name ? (_a = session.assemblyManager.get(name)) === null || _a === void 0 ? void 0 : _a.initialized : false));
|
|
37
|
+
},
|
|
38
|
+
}))
|
|
39
|
+
.views(self => ({
|
|
40
|
+
get dataGridColumns() {
|
|
41
|
+
const { rows } = self;
|
|
42
|
+
return rows
|
|
43
|
+
? [
|
|
44
|
+
{
|
|
45
|
+
field: 'Location',
|
|
46
|
+
width: measureGridWidth(rows.map(row => row.feature ? assembleLocStringFast(row.feature) : 0)) + 40,
|
|
47
|
+
renderCell: ({ row }) => {
|
|
48
|
+
const { feature } = row;
|
|
49
|
+
return feature ? (_jsx(LocationCell, { model: self, feature: feature })) : ('N/A');
|
|
50
|
+
},
|
|
51
|
+
},
|
|
52
|
+
{
|
|
53
|
+
field: 'Length',
|
|
54
|
+
type: 'number',
|
|
55
|
+
width: measureGridWidth(rows.map(row => {
|
|
56
|
+
const { feature } = row;
|
|
57
|
+
return feature ? feature.end - feature.start : 0;
|
|
58
|
+
})),
|
|
59
|
+
valueGetter: (_val, row) => {
|
|
60
|
+
const { feature } = row;
|
|
61
|
+
return feature ? feature.end - feature.start : undefined;
|
|
62
|
+
},
|
|
63
|
+
valueFormatter: arg => toLocale(arg),
|
|
64
|
+
},
|
|
65
|
+
...self.columns.map(f => ({
|
|
66
|
+
field: f.name,
|
|
67
|
+
width: measureGridWidth([...rows.map(r => r[f.name]), f.name], { minWidth: 20 }),
|
|
68
|
+
type: typeof rows[0][f.name] === 'number'
|
|
69
|
+
? 'number'
|
|
70
|
+
: undefined,
|
|
71
|
+
})),
|
|
72
|
+
]
|
|
73
|
+
: undefined;
|
|
74
|
+
},
|
|
75
|
+
}))
|
|
76
|
+
.views(self => ({
|
|
77
|
+
get visibleRows() {
|
|
78
|
+
var _a;
|
|
79
|
+
const { visibleRowFlags } = self;
|
|
80
|
+
return visibleRowFlags
|
|
81
|
+
? (_a = self.rows) === null || _a === void 0 ? void 0 : _a.filter((_f, idx) => !!visibleRowFlags[idx])
|
|
82
|
+
: self.rows;
|
|
83
|
+
},
|
|
84
|
+
}))
|
|
85
|
+
.actions(self => ({
|
|
86
|
+
setVisibleRows(arg) {
|
|
87
|
+
self.visibleRowFlags = arg;
|
|
88
|
+
},
|
|
89
|
+
setVisibleColumns(arg) {
|
|
90
|
+
self.visibleColumns = arg;
|
|
91
|
+
},
|
|
92
|
+
}))
|
|
93
|
+
.preProcessSnapshot(snap => {
|
|
94
|
+
return snap
|
|
95
|
+
? {
|
|
96
|
+
...snap,
|
|
97
|
+
columns: snap.columns.filter(f => !f.isDerived),
|
|
98
|
+
rowSet: snap.rowSet
|
|
99
|
+
? {
|
|
100
|
+
...snap.rowSet,
|
|
101
|
+
rows: snap.rowSet.rows.map(r => {
|
|
102
|
+
var _a, _b;
|
|
103
|
+
return ({
|
|
104
|
+
...r,
|
|
105
|
+
feature: (_a = r.feature) !== null && _a !== void 0 ? _a : (_b = r.extendedData) === null || _b === void 0 ? void 0 : _b.vcfFeature,
|
|
106
|
+
});
|
|
107
|
+
}),
|
|
108
|
+
}
|
|
109
|
+
: undefined,
|
|
110
|
+
}
|
|
111
|
+
: snap;
|
|
112
|
+
});
|
|
113
|
+
}
|