@jbrowse/plugin-spreadsheet-view 2.17.0 → 2.18.0

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.
Files changed (197) hide show
  1. package/dist/LaunchSpreadsheetView/index.d.ts +1 -1
  2. package/dist/LaunchSpreadsheetView/index.js +1 -3
  3. package/dist/SpreadsheetView/ImportWizard.d.ts +51 -0
  4. package/dist/SpreadsheetView/ImportWizard.js +240 -0
  5. package/dist/SpreadsheetView/SpreadsheetModel.d.ts +79 -0
  6. package/dist/SpreadsheetView/SpreadsheetModel.js +133 -0
  7. package/dist/SpreadsheetView/SpreadsheetViewModel.d.ts +299 -0
  8. package/dist/SpreadsheetView/SpreadsheetViewModel.js +94 -0
  9. package/dist/SpreadsheetView/components/BreakendMultiLevelOptionDialog.d.ts +1 -0
  10. package/dist/SpreadsheetView/components/BreakendMultiLevelOptionDialog.js +5 -0
  11. package/dist/SpreadsheetView/components/BreakendSingleLevelOptionDialog.d.ts +1 -0
  12. package/dist/SpreadsheetView/components/BreakendSingleLevelOptionDialog.js +5 -0
  13. package/dist/SpreadsheetView/components/FeatureMenu.d.ts +8 -0
  14. package/dist/SpreadsheetView/components/FeatureMenu.js +95 -0
  15. package/dist/SpreadsheetView/components/ImportWizard.d.ts +2 -2
  16. package/dist/SpreadsheetView/components/ImportWizard.js +40 -43
  17. package/dist/SpreadsheetView/components/LocationCell.d.ts +8 -0
  18. package/dist/SpreadsheetView/components/LocationCell.js +31 -0
  19. package/dist/SpreadsheetView/components/NumberEditor.d.ts +1 -1
  20. package/dist/SpreadsheetView/components/NumberEditor.js +1 -3
  21. package/dist/SpreadsheetView/components/SpreadsheetDataGrid.d.ts +6 -0
  22. package/dist/SpreadsheetView/components/SpreadsheetDataGrid.js +27 -0
  23. package/dist/SpreadsheetView/components/SpreadsheetView.d.ts +3 -3
  24. package/dist/SpreadsheetView/components/SpreadsheetView.js +23 -44
  25. package/dist/SpreadsheetView/components/TrackSelector.d.ts +7 -0
  26. package/dist/SpreadsheetView/components/TrackSelector.js +49 -0
  27. package/dist/SpreadsheetView/importAdapters/BedImport.d.ts +26 -17
  28. package/dist/SpreadsheetView/importAdapters/BedImport.js +53 -139
  29. package/dist/SpreadsheetView/importAdapters/BedpeImport.d.ts +36 -0
  30. package/dist/SpreadsheetView/importAdapters/BedpeImport.js +79 -0
  31. package/dist/SpreadsheetView/importAdapters/STARFusionImport.d.ts +25 -9
  32. package/dist/SpreadsheetView/importAdapters/STARFusionImport.js +27 -62
  33. package/dist/SpreadsheetView/importAdapters/VcfImport.d.ts +19 -12
  34. package/dist/SpreadsheetView/importAdapters/VcfImport.js +53 -98
  35. package/dist/SpreadsheetView/importAdapters/isNumber.d.ts +1 -0
  36. package/dist/SpreadsheetView/importAdapters/isNumber.js +14 -0
  37. package/dist/SpreadsheetView/importAdapters/util.d.ts +2 -0
  38. package/dist/SpreadsheetView/importAdapters/util.js +22 -0
  39. package/dist/SpreadsheetView/index.d.ts +2 -2
  40. package/dist/SpreadsheetView/index.js +2 -2
  41. package/dist/SpreadsheetView/util.d.ts +7 -0
  42. package/dist/SpreadsheetView/util.js +13 -0
  43. package/dist/index.d.ts +1 -1
  44. package/dist/index.js +1 -3
  45. package/esm/LaunchSpreadsheetView/index.d.ts +1 -1
  46. package/esm/LaunchSpreadsheetView/index.js +1 -3
  47. package/esm/SpreadsheetView/ImportWizard.d.ts +51 -0
  48. package/esm/SpreadsheetView/ImportWizard.js +214 -0
  49. package/esm/SpreadsheetView/SpreadsheetModel.d.ts +79 -0
  50. package/esm/SpreadsheetView/SpreadsheetModel.js +127 -0
  51. package/esm/SpreadsheetView/SpreadsheetViewModel.d.ts +299 -0
  52. package/esm/SpreadsheetView/SpreadsheetViewModel.js +88 -0
  53. package/esm/SpreadsheetView/components/BreakendMultiLevelOptionDialog.d.ts +1 -0
  54. package/esm/SpreadsheetView/components/BreakendMultiLevelOptionDialog.js +1 -0
  55. package/esm/SpreadsheetView/components/BreakendSingleLevelOptionDialog.d.ts +1 -0
  56. package/esm/SpreadsheetView/components/BreakendSingleLevelOptionDialog.js +1 -0
  57. package/esm/SpreadsheetView/components/FeatureMenu.d.ts +8 -0
  58. package/esm/SpreadsheetView/components/FeatureMenu.js +66 -0
  59. package/esm/SpreadsheetView/components/ImportWizard.d.ts +2 -2
  60. package/esm/SpreadsheetView/components/ImportWizard.js +41 -44
  61. package/esm/SpreadsheetView/components/LocationCell.d.ts +8 -0
  62. package/esm/SpreadsheetView/components/LocationCell.js +25 -0
  63. package/esm/SpreadsheetView/components/NumberEditor.d.ts +1 -1
  64. package/esm/SpreadsheetView/components/NumberEditor.js +2 -4
  65. package/esm/SpreadsheetView/components/SpreadsheetDataGrid.d.ts +6 -0
  66. package/esm/SpreadsheetView/components/SpreadsheetDataGrid.js +22 -0
  67. package/esm/SpreadsheetView/components/SpreadsheetView.d.ts +3 -3
  68. package/esm/SpreadsheetView/components/SpreadsheetView.js +24 -45
  69. package/esm/SpreadsheetView/components/TrackSelector.d.ts +7 -0
  70. package/esm/SpreadsheetView/components/TrackSelector.js +24 -0
  71. package/esm/SpreadsheetView/importAdapters/BedImport.d.ts +26 -17
  72. package/esm/SpreadsheetView/importAdapters/BedImport.js +53 -137
  73. package/esm/SpreadsheetView/importAdapters/BedpeImport.d.ts +36 -0
  74. package/esm/SpreadsheetView/importAdapters/BedpeImport.js +76 -0
  75. package/esm/SpreadsheetView/importAdapters/STARFusionImport.d.ts +25 -9
  76. package/esm/SpreadsheetView/importAdapters/STARFusionImport.js +27 -62
  77. package/esm/SpreadsheetView/importAdapters/VcfImport.d.ts +19 -12
  78. package/esm/SpreadsheetView/importAdapters/VcfImport.js +53 -97
  79. package/esm/SpreadsheetView/importAdapters/isNumber.d.ts +1 -0
  80. package/esm/SpreadsheetView/importAdapters/isNumber.js +11 -0
  81. package/esm/SpreadsheetView/importAdapters/util.d.ts +2 -0
  82. package/esm/SpreadsheetView/importAdapters/util.js +18 -0
  83. package/esm/SpreadsheetView/index.d.ts +2 -2
  84. package/esm/SpreadsheetView/index.js +2 -2
  85. package/esm/SpreadsheetView/util.d.ts +7 -0
  86. package/esm/SpreadsheetView/util.js +10 -0
  87. package/esm/index.d.ts +1 -1
  88. package/esm/index.js +1 -3
  89. package/package.json +6 -6
  90. package/dist/SpreadsheetView/components/CellData.d.ts +0 -9
  91. package/dist/SpreadsheetView/components/CellData.js +0 -14
  92. package/dist/SpreadsheetView/components/ColumnFilterControls.d.ts +0 -3
  93. package/dist/SpreadsheetView/components/ColumnFilterControls.js +0 -58
  94. package/dist/SpreadsheetView/components/ColumnMenu.d.ts +0 -16
  95. package/dist/SpreadsheetView/components/ColumnMenu.js +0 -140
  96. package/dist/SpreadsheetView/components/DataRow.d.ts +0 -12
  97. package/dist/SpreadsheetView/components/DataRow.js +0 -81
  98. package/dist/SpreadsheetView/components/DataTable.d.ts +0 -10
  99. package/dist/SpreadsheetView/components/DataTable.js +0 -42
  100. package/dist/SpreadsheetView/components/DataTableHeader.d.ts +0 -6
  101. package/dist/SpreadsheetView/components/DataTableHeader.js +0 -104
  102. package/dist/SpreadsheetView/components/GlobalFilterControls.d.ts +0 -5
  103. package/dist/SpreadsheetView/components/GlobalFilterControls.js +0 -68
  104. package/dist/SpreadsheetView/components/RowCountMessage.d.ts +0 -6
  105. package/dist/SpreadsheetView/components/RowCountMessage.js +0 -33
  106. package/dist/SpreadsheetView/components/RowMenu.d.ts +0 -9
  107. package/dist/SpreadsheetView/components/RowMenu.js +0 -39
  108. package/dist/SpreadsheetView/components/SortIndicator.d.ts +0 -6
  109. package/dist/SpreadsheetView/components/SortIndicator.js +0 -27
  110. package/dist/SpreadsheetView/components/Spreadsheet.d.ts +0 -11
  111. package/dist/SpreadsheetView/components/Spreadsheet.js +0 -25
  112. package/dist/SpreadsheetView/components/StatusBar.d.ts +0 -11
  113. package/dist/SpreadsheetView/components/StatusBar.js +0 -44
  114. package/dist/SpreadsheetView/importAdapters/ImportUtils.d.ts +0 -42
  115. package/dist/SpreadsheetView/importAdapters/ImportUtils.js +0 -123
  116. package/dist/SpreadsheetView/models/ColumnDataTypes/LocEnd.d.ts +0 -12
  117. package/dist/SpreadsheetView/models/ColumnDataTypes/LocEnd.js +0 -20
  118. package/dist/SpreadsheetView/models/ColumnDataTypes/LocRef.d.ts +0 -12
  119. package/dist/SpreadsheetView/models/ColumnDataTypes/LocRef.js +0 -20
  120. package/dist/SpreadsheetView/models/ColumnDataTypes/LocStart.d.ts +0 -12
  121. package/dist/SpreadsheetView/models/ColumnDataTypes/LocStart.js +0 -20
  122. package/dist/SpreadsheetView/models/ColumnDataTypes/LocString.d.ts +0 -13
  123. package/dist/SpreadsheetView/models/ColumnDataTypes/LocString.js +0 -183
  124. package/dist/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.d.ts +0 -19
  125. package/dist/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.js +0 -23
  126. package/dist/SpreadsheetView/models/ColumnDataTypes/Number.d.ts +0 -30
  127. package/dist/SpreadsheetView/models/ColumnDataTypes/Number.js +0 -126
  128. package/dist/SpreadsheetView/models/ColumnDataTypes/Text.d.ts +0 -28
  129. package/dist/SpreadsheetView/models/ColumnDataTypes/Text.js +0 -129
  130. package/dist/SpreadsheetView/models/ColumnDataTypes/index.d.ts +0 -71
  131. package/dist/SpreadsheetView/models/ColumnDataTypes/index.js +0 -37
  132. package/dist/SpreadsheetView/models/FilterControls.d.ts +0 -26
  133. package/dist/SpreadsheetView/models/FilterControls.js +0 -85
  134. package/dist/SpreadsheetView/models/ImportWizard.d.ts +0 -31
  135. package/dist/SpreadsheetView/models/ImportWizard.js +0 -186
  136. package/dist/SpreadsheetView/models/Row.d.ts +0 -17
  137. package/dist/SpreadsheetView/models/Row.js +0 -43
  138. package/dist/SpreadsheetView/models/Spreadsheet.d.ts +0 -260
  139. package/dist/SpreadsheetView/models/Spreadsheet.js +0 -174
  140. package/dist/SpreadsheetView/models/SpreadsheetView.d.ts +0 -482
  141. package/dist/SpreadsheetView/models/SpreadsheetView.js +0 -199
  142. package/dist/SpreadsheetView/models/StaticRowSet.d.ts +0 -163
  143. package/dist/SpreadsheetView/models/StaticRowSet.js +0 -56
  144. package/esm/SpreadsheetView/components/CellData.d.ts +0 -9
  145. package/esm/SpreadsheetView/components/CellData.js +0 -9
  146. package/esm/SpreadsheetView/components/ColumnFilterControls.d.ts +0 -3
  147. package/esm/SpreadsheetView/components/ColumnFilterControls.js +0 -53
  148. package/esm/SpreadsheetView/components/ColumnMenu.d.ts +0 -16
  149. package/esm/SpreadsheetView/components/ColumnMenu.js +0 -135
  150. package/esm/SpreadsheetView/components/DataRow.d.ts +0 -12
  151. package/esm/SpreadsheetView/components/DataRow.js +0 -76
  152. package/esm/SpreadsheetView/components/DataTable.d.ts +0 -10
  153. package/esm/SpreadsheetView/components/DataTable.js +0 -37
  154. package/esm/SpreadsheetView/components/DataTableHeader.d.ts +0 -6
  155. package/esm/SpreadsheetView/components/DataTableHeader.js +0 -76
  156. package/esm/SpreadsheetView/components/GlobalFilterControls.d.ts +0 -5
  157. package/esm/SpreadsheetView/components/GlobalFilterControls.js +0 -40
  158. package/esm/SpreadsheetView/components/RowCountMessage.d.ts +0 -6
  159. package/esm/SpreadsheetView/components/RowCountMessage.js +0 -28
  160. package/esm/SpreadsheetView/components/RowMenu.d.ts +0 -9
  161. package/esm/SpreadsheetView/components/RowMenu.js +0 -34
  162. package/esm/SpreadsheetView/components/SortIndicator.d.ts +0 -6
  163. package/esm/SpreadsheetView/components/SortIndicator.js +0 -21
  164. package/esm/SpreadsheetView/components/Spreadsheet.d.ts +0 -11
  165. package/esm/SpreadsheetView/components/Spreadsheet.js +0 -20
  166. package/esm/SpreadsheetView/components/StatusBar.d.ts +0 -11
  167. package/esm/SpreadsheetView/components/StatusBar.js +0 -39
  168. package/esm/SpreadsheetView/importAdapters/ImportUtils.d.ts +0 -42
  169. package/esm/SpreadsheetView/importAdapters/ImportUtils.js +0 -95
  170. package/esm/SpreadsheetView/models/ColumnDataTypes/LocEnd.d.ts +0 -12
  171. package/esm/SpreadsheetView/models/ColumnDataTypes/LocEnd.js +0 -15
  172. package/esm/SpreadsheetView/models/ColumnDataTypes/LocRef.d.ts +0 -12
  173. package/esm/SpreadsheetView/models/ColumnDataTypes/LocRef.js +0 -15
  174. package/esm/SpreadsheetView/models/ColumnDataTypes/LocStart.d.ts +0 -12
  175. package/esm/SpreadsheetView/models/ColumnDataTypes/LocStart.js +0 -15
  176. package/esm/SpreadsheetView/models/ColumnDataTypes/LocString.d.ts +0 -13
  177. package/esm/SpreadsheetView/models/ColumnDataTypes/LocString.js +0 -178
  178. package/esm/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.d.ts +0 -19
  179. package/esm/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.js +0 -20
  180. package/esm/SpreadsheetView/models/ColumnDataTypes/Number.d.ts +0 -30
  181. package/esm/SpreadsheetView/models/ColumnDataTypes/Number.js +0 -119
  182. package/esm/SpreadsheetView/models/ColumnDataTypes/Text.d.ts +0 -28
  183. package/esm/SpreadsheetView/models/ColumnDataTypes/Text.js +0 -122
  184. package/esm/SpreadsheetView/models/ColumnDataTypes/index.d.ts +0 -71
  185. package/esm/SpreadsheetView/models/ColumnDataTypes/index.js +0 -29
  186. package/esm/SpreadsheetView/models/FilterControls.d.ts +0 -26
  187. package/esm/SpreadsheetView/models/FilterControls.js +0 -83
  188. package/esm/SpreadsheetView/models/ImportWizard.d.ts +0 -31
  189. package/esm/SpreadsheetView/models/ImportWizard.js +0 -161
  190. package/esm/SpreadsheetView/models/Row.d.ts +0 -17
  191. package/esm/SpreadsheetView/models/Row.js +0 -41
  192. package/esm/SpreadsheetView/models/Spreadsheet.d.ts +0 -260
  193. package/esm/SpreadsheetView/models/Spreadsheet.js +0 -169
  194. package/esm/SpreadsheetView/models/SpreadsheetView.d.ts +0 -482
  195. package/esm/SpreadsheetView/models/SpreadsheetView.js +0 -194
  196. package/esm/SpreadsheetView/models/StaticRowSet.d.ts +0 -163
  197. package/esm/SpreadsheetView/models/StaticRowSet.js +0 -51
@@ -1,26 +0,0 @@
1
- import { AnyFilterModelType as AnyColumnFilter } from './ColumnDataTypes';
2
- declare const model: import("mobx-state-tree").IModelType<{
3
- rowFullText: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
4
- type: import("mobx-state-tree").ISimpleType<"RowFullText">;
5
- stringToFind: import("mobx-state-tree").IType<string | undefined, string, string>;
6
- }, {
7
- readonly predicate: (_sheet: unknown, row: {
8
- cellsWithDerived: {
9
- text: string;
10
- }[];
11
- }) => boolean;
12
- } & {
13
- setString(s: string): void;
14
- clear(): void;
15
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
16
- columnFilters: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
17
- }, {
18
- readonly filters: any[];
19
- setRowFullTextFilter(stringToFind: string): void;
20
- rowPassesFilters(sheet: unknown, row: unknown): boolean;
21
- } & {
22
- addBlankColumnFilter(columnNumber: number): void;
23
- removeColumnFilter(filter: typeof AnyColumnFilter): boolean;
24
- clearAllFilters(): void;
25
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
26
- export default model;
@@ -1,83 +0,0 @@
1
- import { types, getParent } from 'mobx-state-tree';
2
- import { AnyFilterModelType as AnyColumnFilter } from './ColumnDataTypes';
3
- // filter that finds a simple string in any of the cells of a row
4
- const RowFullTextFilter = types
5
- .model('RowFullTextFilter', {
6
- type: types.literal('RowFullText'),
7
- stringToFind: '',
8
- })
9
- .views(self => ({
10
- // returns a function that tests the given row
11
- get predicate() {
12
- let s = self.stringToFind; // avoid closing over self
13
- if (!s) {
14
- return function alwaysTrue() {
15
- return true;
16
- };
17
- }
18
- s = s.toLowerCase();
19
- return function stringPredicate(_sheet, row) {
20
- const { cellsWithDerived } = row;
21
- for (const cell of cellsWithDerived) {
22
- // note: case insensitive
23
- if (cell.text.toLowerCase().includes(s)) {
24
- return true;
25
- }
26
- }
27
- return false;
28
- };
29
- },
30
- }))
31
- .actions(self => ({
32
- setString(s) {
33
- self.stringToFind = s;
34
- },
35
- clear() {
36
- self.stringToFind = '';
37
- },
38
- }));
39
- const model = types
40
- .model('SpreadsheetFilterControls', {
41
- rowFullText: types.optional(RowFullTextFilter, () => ({
42
- type: 'RowFullText',
43
- stringToFind: '',
44
- })),
45
- columnFilters: types.array(AnyColumnFilter),
46
- })
47
- .views(self => ({
48
- get filters() {
49
- return [self.rowFullText, ...self.columnFilters].filter(f => !!f);
50
- },
51
- setRowFullTextFilter(stringToFind) {
52
- // @ts-expect-error
53
- self.rowFullText = {
54
- type: 'RowFullText',
55
- stringToFind,
56
- };
57
- },
58
- rowPassesFilters(sheet, row) {
59
- for (const filter of this.filters) {
60
- if (!filter.predicate(sheet, row)) {
61
- return false;
62
- }
63
- }
64
- return true;
65
- },
66
- }))
67
- .actions(self => ({
68
- addBlankColumnFilter(columnNumber) {
69
- const { dataType } = getParent(self).spreadsheet.columns[columnNumber];
70
- self.columnFilters.push({
71
- type: dataType.type,
72
- columnNumber,
73
- });
74
- },
75
- removeColumnFilter(filter) {
76
- return self.columnFilters.remove(filter);
77
- },
78
- clearAllFilters() {
79
- self.columnFilters.clear();
80
- self.rowFullText.clear();
81
- },
82
- }));
83
- export default model;
@@ -1,31 +0,0 @@
1
- import { Instance } from 'mobx-state-tree';
2
- declare const ImportWizard: import("mobx-state-tree").IModelType<{
3
- fileType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
4
- hasColumnNameLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
5
- columnNameLineNumber: import("mobx-state-tree").IType<number | undefined, number, number>;
6
- selectedAssemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
7
- }, {
8
- fileTypes: string[];
9
- fileSource: any;
10
- error: unknown;
11
- loading: boolean;
12
- } & {
13
- readonly isReadyToOpen: any;
14
- readonly canCancel: any;
15
- readonly fileName: any;
16
- readonly requiresUnzip: any;
17
- isValidRefName(refName: string, assemblyName?: string): boolean;
18
- } & {
19
- setSelectedAssemblyName(s: string): void;
20
- setFileSource(newSource: unknown): void;
21
- toggleHasColumnNameLine(): void;
22
- setColumnNameLineNumber(newnumber: number): void;
23
- setFileType(typeName: string): void;
24
- setError(error: unknown): void;
25
- setLoaded(): void;
26
- cancelButton(): void;
27
- import(assemblyName: string): Promise<void>;
28
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
29
- export type ImportWizardStateModel = typeof ImportWizard;
30
- export type ImportWizardModel = Instance<ImportWizardStateModel>;
31
- export default ImportWizard;
@@ -1,161 +0,0 @@
1
- import { types, getParent } from 'mobx-state-tree';
2
- import { openLocation } from '@jbrowse/core/util/io';
3
- import { getSession, getEnv } from '@jbrowse/core/util';
4
- // 30MB
5
- const IMPORT_SIZE_LIMIT = 30000000;
6
- const fileTypes = ['CSV', 'TSV', 'VCF', 'BED', 'BEDPE', 'STAR-Fusion'];
7
- const fileTypeParsers = {
8
- CSV: () => import('../importAdapters/ImportUtils').then(r => r.parseCsvBuffer),
9
- TSV: () => import('../importAdapters/ImportUtils').then(r => r.parseTsvBuffer),
10
- VCF: () => import('../importAdapters/VcfImport').then(r => r.parseVcfBuffer),
11
- BED: () => import('../importAdapters/BedImport').then(r => r.parseBedBuffer),
12
- BEDPE: () => import('../importAdapters/BedImport').then(r => r.parseBedPEBuffer),
13
- 'STAR-Fusion': () => import('../importAdapters/STARFusionImport').then(r => r.parseSTARFusionBuffer),
14
- };
15
- // regexp used to guess the type of a file or URL from its file extension
16
- const fileTypesRegexp = new RegExp(`\\.(${fileTypes.join('|')})(\\.gz)?$`, 'i');
17
- /**
18
- * #stateModel SpreadsheetImportWizard
19
- * #category view
20
- */
21
- function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
22
- const ImportWizard = types
23
- .model('SpreadsheetImportWizard', {
24
- /**
25
- * #property
26
- */
27
- fileType: types.optional(types.enumeration(fileTypes), 'CSV'),
28
- /**
29
- * #property
30
- */
31
- hasColumnNameLine: true,
32
- /**
33
- * #property
34
- */
35
- columnNameLineNumber: 1,
36
- /**
37
- * #property
38
- */
39
- selectedAssemblyName: types.maybe(types.string),
40
- })
41
- .volatile(() => ({
42
- fileTypes,
43
- fileSource: undefined,
44
- error: undefined,
45
- loading: false,
46
- }))
47
- .views(self => ({
48
- get isReadyToOpen() {
49
- return (!self.error &&
50
- self.fileSource &&
51
- (self.fileSource.blobId ||
52
- self.fileSource.localPath ||
53
- self.fileSource.uri));
54
- },
55
- get canCancel() {
56
- return getParent(self).readyToDisplay;
57
- },
58
- get fileName() {
59
- return (self.fileSource.uri ||
60
- self.fileSource.localPath ||
61
- (self.fileSource.blobId && self.fileSource.name));
62
- },
63
- get requiresUnzip() {
64
- return this.fileName.endsWith('gz');
65
- },
66
- isValidRefName(refName, assemblyName) {
67
- const { assemblyManager } = getSession(self);
68
- if (!assemblyName) {
69
- return false;
70
- }
71
- return assemblyManager.isValidRefName(refName, assemblyName);
72
- },
73
- }))
74
- .actions(self => ({
75
- setSelectedAssemblyName(s) {
76
- self.selectedAssemblyName = s;
77
- },
78
- setFileSource(newSource) {
79
- var _a;
80
- self.fileSource = newSource;
81
- self.error = undefined;
82
- if (self.fileSource) {
83
- // try to autodetect the file type, ignore errors
84
- const name = self.fileName;
85
- if (name) {
86
- const firstMatch = (_a = fileTypesRegexp.exec(name)) === null || _a === void 0 ? void 0 : _a[1];
87
- if (firstMatch) {
88
- self.fileType =
89
- firstMatch === 'tsv' && name.includes('star-fusion')
90
- ? 'STAR-Fusion'
91
- : firstMatch.toUpperCase();
92
- }
93
- }
94
- }
95
- },
96
- toggleHasColumnNameLine() {
97
- self.hasColumnNameLine = !self.hasColumnNameLine;
98
- },
99
- setColumnNameLineNumber(newnumber) {
100
- if (newnumber > 0) {
101
- self.columnNameLineNumber = newnumber;
102
- }
103
- },
104
- setFileType(typeName) {
105
- self.fileType = typeName;
106
- },
107
- setError(error) {
108
- console.error(error);
109
- self.loading = false;
110
- self.error = error;
111
- },
112
- setLoaded() {
113
- self.loading = false;
114
- self.error = undefined;
115
- },
116
- cancelButton() {
117
- self.error = undefined;
118
- getParent(self).setDisplayMode();
119
- },
120
- // fetch and parse the file, make a new Spreadsheet model for it,
121
- // then set the parent to display it
122
- async import(assemblyName) {
123
- if (!self.fileSource) {
124
- return;
125
- }
126
- if (self.loading) {
127
- throw new Error('Cannot import, load already in progress');
128
- }
129
- self.selectedAssemblyName = assemblyName;
130
- self.loading = true;
131
- const type = self.fileType;
132
- const typeParser = await fileTypeParsers[type]();
133
- const { unzip } = await import('@gmod/bgzf-filehandle');
134
- const { pluginManager } = getEnv(self);
135
- const filehandle = openLocation(self.fileSource, pluginManager);
136
- try {
137
- const stat = await filehandle.stat();
138
- if (stat.size > IMPORT_SIZE_LIMIT) {
139
- throw new Error(`File is too big. Tabular files are limited to at most ${(IMPORT_SIZE_LIMIT / 1000).toLocaleString()}kb.`);
140
- }
141
- }
142
- catch (e) {
143
- // not required for stat to succeed to proceed, but it is helpful
144
- console.warn(e);
145
- }
146
- try {
147
- await filehandle
148
- .readFile()
149
- .then(buffer => (self.requiresUnzip ? unzip(buffer) : buffer))
150
- .then(buffer => typeParser(buffer, self))
151
- .then(spreadsheet => {
152
- this.setLoaded();
153
- getParent(self).displaySpreadsheet(spreadsheet);
154
- });
155
- }
156
- catch (e) {
157
- this.setError(e);
158
- }
159
- },
160
- }));
161
- export default ImportWizard;
@@ -1,17 +0,0 @@
1
- declare const RowModel: import("mobx-state-tree").IModelType<{
2
- id: import("mobx-state-tree").ISimpleType<string>;
3
- cells: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
4
- text: import("mobx-state-tree").ISimpleType<string>;
5
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
6
- }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
7
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
8
- isSelected: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
9
- }, {
10
- toggleSelect(): void;
11
- unSelect(): void;
12
- select(): void;
13
- setExtendedData(data: unknown): void;
14
- } & {
15
- readonly cellsWithDerived: any;
16
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
17
- export default RowModel;
@@ -1,41 +0,0 @@
1
- import { types, getParent } from 'mobx-state-tree';
2
- const CellModel = types.model('SpreadsheetCell', {
3
- text: types.string,
4
- extendedData: types.maybe(types.frozen()),
5
- });
6
- const RowModel = types
7
- .model('SpreadsheetRow', {
8
- id: types.identifier,
9
- cells: types.array(CellModel),
10
- extendedData: types.maybe(types.frozen()),
11
- isSelected: false,
12
- })
13
- .actions(self => ({
14
- toggleSelect() {
15
- self.isSelected = !self.isSelected;
16
- },
17
- unSelect() {
18
- self.isSelected = false;
19
- },
20
- select() {
21
- self.isSelected = true;
22
- },
23
- setExtendedData(data) {
24
- self.extendedData = data;
25
- },
26
- }))
27
- .views(self => ({
28
- get cellsWithDerived() {
29
- const { columns } = getParent(self, 3);
30
- let i = 0;
31
- return columns.map((column) => {
32
- if (column.isDerived) {
33
- return column.expr.evalSync({
34
- row: self,
35
- });
36
- }
37
- return self.cells[i++];
38
- });
39
- },
40
- }));
41
- export default RowModel;
@@ -1,260 +0,0 @@
1
- import { SnapshotIn, Instance } from 'mobx-state-tree';
2
- import type RowModel from './Row';
3
- type Row = Instance<typeof RowModel>;
4
- type RowMenuPosition = {
5
- anchorEl: Element;
6
- rowNumber: string;
7
- } | null;
8
- declare const Spreadsheet: import("mobx-state-tree").IModelType<{
9
- rowSet: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
10
- isLoaded: import("mobx-state-tree").ISimpleType<true>;
11
- rows: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
12
- id: import("mobx-state-tree").ISimpleType<string>;
13
- cells: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
14
- text: import("mobx-state-tree").ISimpleType<string>;
15
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
16
- }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
17
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
18
- isSelected: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
19
- }, {
20
- toggleSelect(): void;
21
- unSelect(): void;
22
- select(): void;
23
- setExtendedData(data: unknown): void;
24
- } & {
25
- readonly cellsWithDerived: any;
26
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
27
- }, {
28
- readonly count: number;
29
- readonly passingFiltersCount: number;
30
- readonly selectedCount: number;
31
- readonly selectedAndPassingFiltersCount: number;
32
- readonly sortedRows: ({
33
- id: string;
34
- cells: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
35
- text: import("mobx-state-tree").ISimpleType<string>;
36
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
37
- }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
38
- text: import("mobx-state-tree").ISimpleType<string>;
39
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
40
- }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
41
- extendedData: any;
42
- isSelected: boolean;
43
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
44
- toggleSelect(): void;
45
- unSelect(): void;
46
- select(): void;
47
- setExtendedData(data: unknown): void;
48
- } & {
49
- readonly cellsWithDerived: any;
50
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
51
- id: import("mobx-state-tree").ISimpleType<string>;
52
- cells: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
53
- text: import("mobx-state-tree").ISimpleType<string>;
54
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
55
- }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
56
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
57
- isSelected: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
58
- }, {
59
- toggleSelect(): void;
60
- unSelect(): void;
61
- select(): void;
62
- setExtendedData(data: unknown): void;
63
- } & {
64
- readonly cellsWithDerived: any;
65
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>)[];
66
- readonly selectedRows: ({
67
- id: string;
68
- cells: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
69
- text: import("mobx-state-tree").ISimpleType<string>;
70
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
71
- }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
72
- text: import("mobx-state-tree").ISimpleType<string>;
73
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
74
- }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
75
- extendedData: any;
76
- isSelected: boolean;
77
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
78
- toggleSelect(): void;
79
- unSelect(): void;
80
- select(): void;
81
- setExtendedData(data: unknown): void;
82
- } & {
83
- readonly cellsWithDerived: any;
84
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
85
- id: import("mobx-state-tree").ISimpleType<string>;
86
- cells: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
87
- text: import("mobx-state-tree").ISimpleType<string>;
88
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
89
- }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
90
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
91
- isSelected: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
92
- }, {
93
- toggleSelect(): void;
94
- unSelect(): void;
95
- select(): void;
96
- setExtendedData(data: unknown): void;
97
- } & {
98
- readonly cellsWithDerived: any;
99
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>)[];
100
- readonly selectedFilteredRows: ({
101
- id: string;
102
- cells: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
103
- text: import("mobx-state-tree").ISimpleType<string>;
104
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
105
- }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
106
- text: import("mobx-state-tree").ISimpleType<string>;
107
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
108
- }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
109
- extendedData: any;
110
- isSelected: boolean;
111
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
112
- toggleSelect(): void;
113
- unSelect(): void;
114
- select(): void;
115
- setExtendedData(data: unknown): void;
116
- } & {
117
- readonly cellsWithDerived: any;
118
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
119
- id: import("mobx-state-tree").ISimpleType<string>;
120
- cells: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
121
- text: import("mobx-state-tree").ISimpleType<string>;
122
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
123
- }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
124
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
125
- isSelected: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
126
- }, {
127
- toggleSelect(): void;
128
- unSelect(): void;
129
- select(): void;
130
- setExtendedData(data: unknown): void;
131
- } & {
132
- readonly cellsWithDerived: any;
133
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>)[];
134
- readonly sortedFilteredRows: ({
135
- id: string;
136
- cells: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
137
- text: import("mobx-state-tree").ISimpleType<string>;
138
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
139
- }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
140
- text: import("mobx-state-tree").ISimpleType<string>;
141
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
142
- }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
143
- extendedData: any;
144
- isSelected: boolean;
145
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
146
- toggleSelect(): void;
147
- unSelect(): void;
148
- select(): void;
149
- setExtendedData(data: unknown): void;
150
- } & {
151
- readonly cellsWithDerived: any;
152
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
153
- id: import("mobx-state-tree").ISimpleType<string>;
154
- cells: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
155
- text: import("mobx-state-tree").ISimpleType<string>;
156
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
157
- }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
158
- extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
159
- isSelected: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
160
- }, {
161
- toggleSelect(): void;
162
- unSelect(): void;
163
- select(): void;
164
- setExtendedData(data: unknown): void;
165
- } & {
166
- readonly cellsWithDerived: any;
167
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>)[];
168
- } & {
169
- unselectAll(): void;
170
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
171
- columns: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
172
- name: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
173
- dataType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IAnyType, [undefined]>;
174
- isDerived: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
175
- derivationFunctionText: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
176
- }, {
177
- readonly expr: any;
178
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
179
- columnDisplayOrder: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<number>>;
180
- hasColumnNames: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
181
- sortColumns: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
182
- columnNumber: import("mobx-state-tree").ISimpleType<number>;
183
- descending: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
184
- }, {
185
- switchDirection(): void;
186
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
187
- assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
188
- }, {
189
- defaultDataType: import("mobx-state-tree").IModelType<{
190
- type: import("mobx-state-tree").ISimpleType<string>;
191
- }, {
192
- DataCellReactComponent: import("react").FC<any> | null;
193
- FilterModelType: any;
194
- displayName: string;
195
- categoryName: string | undefined;
196
- } & {
197
- compare: any;
198
- readonly hasFilter: boolean;
199
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
200
- rowMenuPosition: RowMenuPosition;
201
- isLoaded: boolean;
202
- } & {
203
- /**
204
- * #getter
205
- */
206
- readonly initialized: boolean | undefined;
207
- /**
208
- * #getter
209
- */
210
- readonly hideRowSelection: any;
211
- /**
212
- * #getter
213
- * list of data type names to be made available in the column
214
- * dropdown menu
215
- */
216
- readonly dataTypeChoices: {
217
- typeName: "LocString" | "Text" | "LocRef" | "Number" | "LocStart" | "LocEnd";
218
- displayName: string;
219
- categoryName: string | undefined;
220
- }[];
221
- /**
222
- * #method
223
- */
224
- rowSortingComparisonFunction(rowA: Row, rowB: Row): any;
225
- } & {
226
- afterAttach(): void;
227
- /**
228
- * #action
229
- */
230
- setLoaded(flag: boolean): void;
231
- /**
232
- * #action
233
- */
234
- setRowMenuPosition(newPosition: RowMenuPosition): void;
235
- /**
236
- * #action
237
- */
238
- setSortColumns(newSort: NonNullable<SnapshotIn<import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
239
- columnNumber: import("mobx-state-tree").ISimpleType<number>;
240
- descending: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
241
- }, {
242
- switchDirection(): void;
243
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
244
- columnNumber: import("mobx-state-tree").ISimpleType<number>;
245
- descending: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
246
- }, {
247
- switchDirection(): void;
248
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>>>): void;
249
- /**
250
- * #action
251
- */
252
- setColumnType(columnNumber: number, newTypeName: string): void;
253
- /**
254
- * #action
255
- */
256
- unselectAll(): void;
257
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
258
- export type SpreadsheetStateModel = typeof Spreadsheet;
259
- export type SpreadsheetModel = Instance<SpreadsheetStateModel>;
260
- export default Spreadsheet;