@jbrowse/plugin-data-management 1.7.11 → 2.0.0

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.
Files changed (226) hide show
  1. package/dist/AddConnectionWidget/components/AddConnectionWidget.js +115 -162
  2. package/dist/AddConnectionWidget/components/AddConnectionWidget.js.map +1 -0
  3. package/dist/AddConnectionWidget/components/ConfigureConnection.js +33 -32
  4. package/dist/AddConnectionWidget/components/ConfigureConnection.js.map +1 -0
  5. package/dist/AddConnectionWidget/components/ConnectionTypeSelect.js +48 -64
  6. package/dist/AddConnectionWidget/components/ConnectionTypeSelect.js.map +1 -0
  7. package/dist/AddConnectionWidget/index.js +10 -20
  8. package/dist/AddConnectionWidget/index.js.map +1 -0
  9. package/dist/AddConnectionWidget/model.js +7 -15
  10. package/dist/AddConnectionWidget/model.js.map +1 -0
  11. package/dist/AddTrackWidget/components/AddTrackWidget.js +206 -230
  12. package/dist/AddTrackWidget/components/AddTrackWidget.js.map +1 -0
  13. package/dist/AddTrackWidget/components/ConfirmTrack.js +268 -385
  14. package/dist/AddTrackWidget/components/ConfirmTrack.js.map +1 -0
  15. package/dist/AddTrackWidget/components/TrackSourceSelect.js +28 -55
  16. package/dist/AddTrackWidget/components/TrackSourceSelect.js.map +1 -0
  17. package/dist/AddTrackWidget/index.js +10 -20
  18. package/dist/AddTrackWidget/index.js.map +1 -0
  19. package/dist/AddTrackWidget/model.js +150 -174
  20. package/dist/AddTrackWidget/model.js.map +1 -0
  21. package/dist/AssemblyManager/AssemblyAddForm.js +162 -282
  22. package/dist/AssemblyManager/AssemblyAddForm.js.map +1 -0
  23. package/dist/AssemblyManager/AssemblyEditor.js +12 -23
  24. package/dist/AssemblyManager/AssemblyEditor.js.map +1 -0
  25. package/dist/AssemblyManager/AssemblyManager.js +102 -132
  26. package/dist/AssemblyManager/AssemblyManager.js.map +1 -0
  27. package/dist/AssemblyManager/AssemblyTable.d.ts +1 -1
  28. package/dist/AssemblyManager/AssemblyTable.js +60 -84
  29. package/dist/AssemblyManager/AssemblyTable.js.map +1 -0
  30. package/dist/AssemblyManager/index.js +8 -14
  31. package/dist/AssemblyManager/index.js.map +1 -0
  32. package/dist/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.js +49 -50
  33. package/dist/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.js.map +1 -0
  34. package/dist/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.js +28 -44
  35. package/dist/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.js.map +1 -0
  36. package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.d.ts +1 -0
  37. package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js +416 -639
  38. package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js.map +1 -0
  39. package/dist/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.js +45 -74
  40. package/dist/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.js.map +1 -0
  41. package/dist/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js +57 -91
  42. package/dist/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js.map +1 -0
  43. package/dist/HierarchicalTrackSelectorWidget/index.js +10 -20
  44. package/dist/HierarchicalTrackSelectorWidget/index.js.map +1 -0
  45. package/dist/HierarchicalTrackSelectorWidget/model.d.ts +3 -1
  46. package/dist/HierarchicalTrackSelectorWidget/model.js +247 -285
  47. package/dist/HierarchicalTrackSelectorWidget/model.js.map +1 -0
  48. package/dist/PluginStoreWidget/components/CustomPluginForm.js +140 -202
  49. package/dist/PluginStoreWidget/components/CustomPluginForm.js.map +1 -0
  50. package/dist/PluginStoreWidget/components/InstalledPlugin.js +112 -127
  51. package/dist/PluginStoreWidget/components/InstalledPlugin.js.map +1 -0
  52. package/dist/PluginStoreWidget/components/InstalledPluginsList.js +22 -45
  53. package/dist/PluginStoreWidget/components/InstalledPluginsList.js.map +1 -0
  54. package/dist/PluginStoreWidget/components/PluginCard.js +95 -110
  55. package/dist/PluginStoreWidget/components/PluginCard.js.map +1 -0
  56. package/dist/PluginStoreWidget/components/PluginStoreWidget.js +188 -227
  57. package/dist/PluginStoreWidget/components/PluginStoreWidget.js.map +1 -0
  58. package/dist/PluginStoreWidget/index.d.ts +0 -1
  59. package/dist/PluginStoreWidget/index.js +10 -28
  60. package/dist/PluginStoreWidget/index.js.map +1 -0
  61. package/dist/PluginStoreWidget/model.js +21 -26
  62. package/dist/PluginStoreWidget/model.js.map +1 -0
  63. package/dist/SetDefaultSession/SetDefaultSession.js +34 -58
  64. package/dist/SetDefaultSession/SetDefaultSession.js.map +1 -0
  65. package/dist/SetDefaultSession/index.js +8 -14
  66. package/dist/SetDefaultSession/index.js.map +1 -0
  67. package/dist/index.js +109 -147
  68. package/dist/index.js.map +1 -0
  69. package/dist/ucsc-trackhub/configSchema.js +18 -28
  70. package/dist/ucsc-trackhub/configSchema.js.map +1 -0
  71. package/dist/ucsc-trackhub/index.js +10 -22
  72. package/dist/ucsc-trackhub/index.js.map +1 -0
  73. package/dist/ucsc-trackhub/model.js +150 -128
  74. package/dist/ucsc-trackhub/model.js.map +1 -0
  75. package/dist/ucsc-trackhub/ucscAssemblies.js +3 -9
  76. package/dist/ucsc-trackhub/ucscAssemblies.js.map +1 -0
  77. package/dist/ucsc-trackhub/ucscTrackHub.js +458 -491
  78. package/dist/ucsc-trackhub/ucscTrackHub.js.map +1 -0
  79. package/esm/AddConnectionWidget/components/AddConnectionWidget.d.ts +9 -0
  80. package/esm/AddConnectionWidget/components/AddConnectionWidget.js +86 -0
  81. package/esm/AddConnectionWidget/components/AddConnectionWidget.js.map +1 -0
  82. package/esm/AddConnectionWidget/components/ConfigureConnection.d.ts +2 -0
  83. package/esm/AddConnectionWidget/components/ConfigureConnection.js +11 -0
  84. package/esm/AddConnectionWidget/components/ConfigureConnection.js.map +1 -0
  85. package/esm/AddConnectionWidget/components/ConnectionTypeSelect.d.ts +8 -0
  86. package/esm/AddConnectionWidget/components/ConnectionTypeSelect.js +24 -0
  87. package/esm/AddConnectionWidget/components/ConnectionTypeSelect.js.map +1 -0
  88. package/esm/AddConnectionWidget/index.d.ts +2 -0
  89. package/esm/AddConnectionWidget/index.js +4 -0
  90. package/esm/AddConnectionWidget/index.js.map +1 -0
  91. package/esm/AddConnectionWidget/model.d.ts +5 -0
  92. package/esm/AddConnectionWidget/model.js +7 -0
  93. package/esm/AddConnectionWidget/model.js.map +1 -0
  94. package/esm/AddTrackWidget/components/AddTrackWidget.d.ts +7 -0
  95. package/esm/AddTrackWidget/components/AddTrackWidget.js +139 -0
  96. package/esm/AddTrackWidget/components/AddTrackWidget.js.map +1 -0
  97. package/esm/AddTrackWidget/components/ConfirmTrack.d.ts +7 -0
  98. package/esm/AddTrackWidget/components/ConfirmTrack.js +247 -0
  99. package/esm/AddTrackWidget/components/ConfirmTrack.js.map +1 -0
  100. package/esm/AddTrackWidget/components/TrackSourceSelect.d.ts +7 -0
  101. package/esm/AddTrackWidget/components/TrackSourceSelect.js +27 -0
  102. package/esm/AddTrackWidget/components/TrackSourceSelect.js.map +1 -0
  103. package/esm/AddTrackWidget/index.d.ts +2 -0
  104. package/esm/AddTrackWidget/index.js +4 -0
  105. package/esm/AddTrackWidget/index.js.map +1 -0
  106. package/esm/AddTrackWidget/model.d.ts +51 -0
  107. package/esm/AddTrackWidget/model.js +154 -0
  108. package/esm/AddTrackWidget/model.js.map +1 -0
  109. package/esm/AssemblyManager/AssemblyAddForm.d.ts +6 -0
  110. package/esm/AssemblyManager/AssemblyAddForm.js +132 -0
  111. package/esm/AssemblyManager/AssemblyAddForm.js.map +1 -0
  112. package/esm/AssemblyManager/AssemblyEditor.d.ts +5 -0
  113. package/esm/AssemblyManager/AssemblyEditor.js +8 -0
  114. package/esm/AssemblyManager/AssemblyEditor.js.map +1 -0
  115. package/esm/AssemblyManager/AssemblyManager.d.ts +6 -0
  116. package/esm/AssemblyManager/AssemblyManager.js +69 -0
  117. package/esm/AssemblyManager/AssemblyManager.js.map +1 -0
  118. package/esm/AssemblyManager/AssemblyTable.d.ts +13 -0
  119. package/esm/AssemblyManager/AssemblyTable.js +62 -0
  120. package/esm/AssemblyManager/AssemblyTable.js.map +1 -0
  121. package/esm/AssemblyManager/index.d.ts +1 -0
  122. package/esm/AssemblyManager/index.js +2 -0
  123. package/esm/AssemblyManager/index.js.map +1 -0
  124. package/esm/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.d.ts +13 -0
  125. package/esm/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.js +26 -0
  126. package/esm/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.js.map +1 -0
  127. package/esm/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.d.ts +13 -0
  128. package/esm/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.js +24 -0
  129. package/esm/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.js.map +1 -0
  130. package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.d.ts +11 -0
  131. package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js +326 -0
  132. package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js.map +1 -0
  133. package/esm/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.d.ts +10 -0
  134. package/esm/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.js +45 -0
  135. package/esm/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.js.map +1 -0
  136. package/esm/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.d.ts +11 -0
  137. package/esm/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js +57 -0
  138. package/esm/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js.map +1 -0
  139. package/esm/HierarchicalTrackSelectorWidget/index.d.ts +2 -0
  140. package/esm/HierarchicalTrackSelectorWidget/index.js +4 -0
  141. package/esm/HierarchicalTrackSelectorWidget/index.js.map +1 -0
  142. package/esm/HierarchicalTrackSelectorWidget/model.d.ts +61 -0
  143. package/esm/HierarchicalTrackSelectorWidget/model.js +200 -0
  144. package/esm/HierarchicalTrackSelectorWidget/model.js.map +1 -0
  145. package/esm/PluginStoreWidget/components/CustomPluginForm.d.ts +9 -0
  146. package/esm/PluginStoreWidget/components/CustomPluginForm.js +109 -0
  147. package/esm/PluginStoreWidget/components/CustomPluginForm.js.map +1 -0
  148. package/esm/PluginStoreWidget/components/InstalledPlugin.d.ts +11 -0
  149. package/esm/PluginStoreWidget/components/InstalledPlugin.js +77 -0
  150. package/esm/PluginStoreWidget/components/InstalledPlugin.js.map +1 -0
  151. package/esm/PluginStoreWidget/components/InstalledPluginsList.d.ts +9 -0
  152. package/esm/PluginStoreWidget/components/InstalledPluginsList.js +16 -0
  153. package/esm/PluginStoreWidget/components/InstalledPluginsList.js.map +1 -0
  154. package/esm/PluginStoreWidget/components/PluginCard.d.ts +10 -0
  155. package/esm/PluginStoreWidget/components/PluginCard.js +61 -0
  156. package/esm/PluginStoreWidget/components/PluginCard.js.map +1 -0
  157. package/esm/PluginStoreWidget/components/PluginStoreWidget.d.ts +7 -0
  158. package/esm/PluginStoreWidget/components/PluginStoreWidget.js +106 -0
  159. package/esm/PluginStoreWidget/components/PluginStoreWidget.js.map +1 -0
  160. package/esm/PluginStoreWidget/index.d.ts +2 -0
  161. package/esm/PluginStoreWidget/index.js +4 -0
  162. package/esm/PluginStoreWidget/index.js.map +1 -0
  163. package/esm/PluginStoreWidget/model.d.ts +13 -0
  164. package/esm/PluginStoreWidget/model.js +20 -0
  165. package/esm/PluginStoreWidget/model.js.map +1 -0
  166. package/esm/SetDefaultSession/SetDefaultSession.d.ts +6 -0
  167. package/esm/SetDefaultSession/SetDefaultSession.js +34 -0
  168. package/esm/SetDefaultSession/SetDefaultSession.js.map +1 -0
  169. package/esm/SetDefaultSession/index.d.ts +1 -0
  170. package/esm/SetDefaultSession/index.js +2 -0
  171. package/esm/SetDefaultSession/index.js.map +1 -0
  172. package/esm/index.d.ts +27 -0
  173. package/esm/index.js +70 -0
  174. package/esm/index.js.map +1 -0
  175. package/esm/ucsc-trackhub/configSchema.d.ts +2 -0
  176. package/esm/ucsc-trackhub/configSchema.js +18 -0
  177. package/esm/ucsc-trackhub/configSchema.js.map +1 -0
  178. package/esm/ucsc-trackhub/index.d.ts +2 -0
  179. package/esm/ucsc-trackhub/index.js +3 -0
  180. package/esm/ucsc-trackhub/index.js.map +1 -0
  181. package/esm/ucsc-trackhub/model.d.ts +15 -0
  182. package/esm/ucsc-trackhub/model.js +82 -0
  183. package/esm/ucsc-trackhub/model.js.map +1 -0
  184. package/esm/ucsc-trackhub/ucscAssemblies.d.ts +2 -0
  185. package/esm/ucsc-trackhub/ucscAssemblies.js +201 -0
  186. package/esm/ucsc-trackhub/ucscAssemblies.js.map +1 -0
  187. package/esm/ucsc-trackhub/ucscTrackHub.d.ts +6 -0
  188. package/esm/ucsc-trackhub/ucscTrackHub.js +348 -0
  189. package/esm/ucsc-trackhub/ucscTrackHub.js.map +1 -0
  190. package/package.json +19 -11
  191. package/src/AddConnectionWidget/components/AddConnectionWidget.js +14 -10
  192. package/src/AddConnectionWidget/components/ConnectionTypeSelect.tsx +2 -4
  193. package/src/AddConnectionWidget/components/__snapshots__/AddConnectionWidget.test.js.snap +63 -67
  194. package/src/AddTrackWidget/components/AddTrackWidget.test.js +4 -4
  195. package/src/AddTrackWidget/components/AddTrackWidget.tsx +5 -5
  196. package/src/AddTrackWidget/components/ConfirmTrack.tsx +22 -22
  197. package/src/AddTrackWidget/components/TrackSourceSelect.tsx +9 -5
  198. package/src/AddTrackWidget/components/__snapshots__/AddTrackWidget.test.js.snap +76 -95
  199. package/src/AssemblyManager/AssemblyAddForm.tsx +5 -11
  200. package/src/AssemblyManager/AssemblyManager.tsx +8 -8
  201. package/src/AssemblyManager/AssemblyTable.tsx +10 -10
  202. package/src/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.tsx +1 -1
  203. package/src/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.tsx +1 -1
  204. package/src/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.test.js +1 -1
  205. package/src/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.tsx +15 -13
  206. package/src/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.tsx +6 -6
  207. package/src/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.tsx +7 -7
  208. package/src/HierarchicalTrackSelectorWidget/components/__snapshots__/HierarchicalTrackSelector.test.js.snap +122 -115
  209. package/src/PluginStoreWidget/components/CustomPluginForm.tsx +11 -14
  210. package/src/PluginStoreWidget/components/InstalledPlugin.tsx +9 -8
  211. package/src/PluginStoreWidget/components/InstalledPluginsList.tsx +1 -1
  212. package/src/PluginStoreWidget/components/PluginCard.tsx +10 -11
  213. package/src/PluginStoreWidget/components/PluginStoreWidget.tsx +9 -9
  214. package/src/PluginStoreWidget/components/__snapshots__/PluginStoreWidget.test.js.snap +267 -217
  215. package/src/PluginStoreWidget/index.js +0 -1
  216. package/src/SetDefaultSession/SetDefaultSession.tsx +1 -1
  217. package/dist/AddConnectionWidget/components/AddConnectionWidget.test.js +0 -279
  218. package/dist/AddTrackWidget/components/AddTrackWidget.test.js +0 -218
  219. package/dist/AddTrackWidget/index.test.js +0 -292
  220. package/dist/AssemblyManager/AssemblyManager.test.js +0 -113
  221. package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.test.js +0 -191
  222. package/dist/HierarchicalTrackSelectorWidget/model.test.js +0 -28
  223. package/dist/PluginStoreWidget/components/PluginStoreWidget.test.js +0 -201
  224. package/dist/PluginStoreWidget/model.test.js +0 -17
  225. package/dist/SetDefaultSession/SetDefaultSession.test.js +0 -75
  226. package/dist/index.test.js +0 -56
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+ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
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-
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- var _FileSelector = _interopRequireDefault(require("@jbrowse/core/ui/FileSelector"));
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-
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-
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+ if (!m) return o;
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+ var i = m.call(o), r, ar = [], e;
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+ while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
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+ }
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+ catch (error) { e = { error: error }; }
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+ finally {
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+ if (r && !r.done && (m = i["return"])) m.call(i);
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+ }
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+ finally { if (e) throw e.error; }
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+ }
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+ var __importDefault = (this && this.__importDefault) || function (mod) {
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+ var react_1 = __importStar(require("react"));
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+ var FileSelector_1 = __importDefault(require("@jbrowse/core/ui/FileSelector"));
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+ var material_1 = require("@mui/material");
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+ var mui_1 = require("tss-react/mui");
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- overflow: 'hidden',
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+ overflow: 'hidden',
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+ padding: theme.spacing(0, 3),
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- margin: "".concat(theme.spacing(1), "px auto"),
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+ margin: "".concat(theme.spacing(1), "px auto"),
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+ padding: theme.spacing(2),
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- select: true,
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- helperText: "Type of adapter to use",
60
- fullWidth: true,
61
- onChange: function onChange(event) {
62
- setAdapterSelection(event.target.value);
78
+ var AdapterInput = (0, mobx_react_1.observer)(function (_a) {
79
+ var adapterSelection = _a.adapterSelection, fastaLocation = _a.fastaLocation, setFastaLocation = _a.setFastaLocation, faiLocation = _a.faiLocation, setFaiLocation = _a.setFaiLocation, gziLocation = _a.gziLocation, setGziLocation = _a.setGziLocation, twoBitLocation = _a.twoBitLocation, setTwoBitLocation = _a.setTwoBitLocation, chromSizesLocation = _a.chromSizesLocation, setChromSizesLocation = _a.setChromSizesLocation;
80
+ if (adapterSelection === 'IndexedFastaAdapter' ||
81
+ adapterSelection === 'BgzipFastaAdapter') {
82
+ return (react_1.default.createElement(material_1.Grid, { container: true, spacing: 2 },
83
+ react_1.default.createElement(material_1.Grid, { item: true },
84
+ react_1.default.createElement(FileSelector_1.default, { name: "fastaLocation", location: fastaLocation, setLocation: function (loc) { return setFastaLocation(loc); } })),
85
+ react_1.default.createElement(material_1.Grid, { item: true },
86
+ react_1.default.createElement(FileSelector_1.default, { name: "faiLocation", location: faiLocation, setLocation: function (loc) { return setFaiLocation(loc); } })),
87
+ adapterSelection === 'BgzipFastaAdapter' ? (react_1.default.createElement(material_1.Grid, { item: true },
88
+ react_1.default.createElement(FileSelector_1.default, { name: "gziLocation", location: gziLocation, setLocation: function (loc) { return setGziLocation(loc); } }))) : null));
63
89
  }
64
- }, adapterTypes.map(function (str) {
65
- return /*#__PURE__*/_react.default.createElement(_core.MenuItem, {
66
- key: str,
67
- value: str
68
- }, str);
69
- }));
70
- });
71
- var AdapterInput = (0, _mobxReact.observer)(function (_ref2) {
72
- var adapterSelection = _ref2.adapterSelection,
73
- fastaLocation = _ref2.fastaLocation,
74
- setFastaLocation = _ref2.setFastaLocation,
75
- faiLocation = _ref2.faiLocation,
76
- setFaiLocation = _ref2.setFaiLocation,
77
- gziLocation = _ref2.gziLocation,
78
- setGziLocation = _ref2.setGziLocation,
79
- twoBitLocation = _ref2.twoBitLocation,
80
- setTwoBitLocation = _ref2.setTwoBitLocation,
81
- chromSizesLocation = _ref2.chromSizesLocation,
82
- setChromSizesLocation = _ref2.setChromSizesLocation;
83
-
84
- if (adapterSelection === 'IndexedFastaAdapter' || adapterSelection === 'BgzipFastaAdapter') {
85
- return /*#__PURE__*/_react.default.createElement(_core.Grid, {
86
- container: true,
87
- spacing: 2
88
- }, /*#__PURE__*/_react.default.createElement(_core.Grid, {
89
- item: true
90
- }, /*#__PURE__*/_react.default.createElement(_FileSelector.default, {
91
- name: "fastaLocation",
92
- location: fastaLocation,
93
- setLocation: function setLocation(loc) {
94
- return setFastaLocation(loc);
95
- }
96
- })), /*#__PURE__*/_react.default.createElement(_core.Grid, {
97
- item: true
98
- }, /*#__PURE__*/_react.default.createElement(_FileSelector.default, {
99
- name: "faiLocation",
100
- location: faiLocation,
101
- setLocation: function setLocation(loc) {
102
- return setFaiLocation(loc);
103
- }
104
- })), adapterSelection === 'BgzipFastaAdapter' ? /*#__PURE__*/_react.default.createElement(_core.Grid, {
105
- item: true
106
- }, /*#__PURE__*/_react.default.createElement(_FileSelector.default, {
107
- name: "gziLocation",
108
- location: gziLocation,
109
- setLocation: function setLocation(loc) {
110
- return setGziLocation(loc);
111
- }
112
- })) : null);
113
- }
114
-
115
- if (adapterSelection === 'TwoBitAdapter') {
116
- return /*#__PURE__*/_react.default.createElement(_core.Grid, {
117
- container: true,
118
- spacing: 2
119
- }, /*#__PURE__*/_react.default.createElement(_core.Grid, {
120
- item: true
121
- }, /*#__PURE__*/_react.default.createElement(_FileSelector.default, {
122
- name: "twoBitLocation",
123
- location: twoBitLocation,
124
- setLocation: function setLocation(loc) {
125
- return setTwoBitLocation(loc);
126
- }
127
- })), /*#__PURE__*/_react.default.createElement(_core.Grid, {
128
- item: true
129
- }, /*#__PURE__*/_react.default.createElement(_FileSelector.default, {
130
- name: "chromSizesLocation (optional, can be added to speed up loading 2bit files with many contigs)",
131
- location: chromSizesLocation,
132
- setLocation: function setLocation(loc) {
133
- return setChromSizesLocation(loc);
134
- }
135
- })));
136
- }
137
-
138
- return null;
90
+ if (adapterSelection === 'TwoBitAdapter') {
91
+ return (react_1.default.createElement(material_1.Grid, { container: true, spacing: 2 },
92
+ react_1.default.createElement(material_1.Grid, { item: true },
93
+ react_1.default.createElement(FileSelector_1.default, { name: "twoBitLocation", location: twoBitLocation, setLocation: function (loc) { return setTwoBitLocation(loc); } })),
94
+ react_1.default.createElement(material_1.Grid, { item: true },
95
+ react_1.default.createElement(FileSelector_1.default, { name: "chromSizesLocation (optional, can be added to speed up loading 2bit files with many contigs)", location: chromSizesLocation, setLocation: function (loc) { return setChromSizesLocation(loc); } }))));
96
+ }
97
+ return null;
139
98
  });
140
- var blank = {
141
- uri: ''
142
- };
143
- var AssemblyAddForm = (0, _mobxReact.observer)(function (_ref3) {
144
- var rootModel = _ref3.rootModel,
145
- setFormOpen = _ref3.setFormOpen;
146
- var classes = useStyles();
147
- var adapterTypes = ['IndexedFastaAdapter', 'BgzipFastaAdapter', 'TwoBitAdapter'];
148
-
149
- var _useState = (0, _react.useState)(''),
150
- _useState2 = (0, _slicedToArray2.default)(_useState, 2),
151
- assemblyName = _useState2[0],
152
- setAssemblyName = _useState2[1];
153
-
154
- var _useState3 = (0, _react.useState)(''),
155
- _useState4 = (0, _slicedToArray2.default)(_useState3, 2),
156
- assemblyDisplayName = _useState4[0],
157
- setAssemblyDisplayName = _useState4[1];
158
-
159
- var _useState5 = (0, _react.useState)(adapterTypes[0]),
160
- _useState6 = (0, _slicedToArray2.default)(_useState5, 2),
161
- adapterSelection = _useState6[0],
162
- setAdapterSelection = _useState6[1];
163
-
164
- var _useState7 = (0, _react.useState)(blank),
165
- _useState8 = (0, _slicedToArray2.default)(_useState7, 2),
166
- fastaLocation = _useState8[0],
167
- setFastaLocation = _useState8[1];
168
-
169
- var _useState9 = (0, _react.useState)(blank),
170
- _useState10 = (0, _slicedToArray2.default)(_useState9, 2),
171
- faiLocation = _useState10[0],
172
- setFaiLocation = _useState10[1];
173
-
174
- var _useState11 = (0, _react.useState)(blank),
175
- _useState12 = (0, _slicedToArray2.default)(_useState11, 2),
176
- gziLocation = _useState12[0],
177
- setGziLocation = _useState12[1];
178
-
179
- var _useState13 = (0, _react.useState)(blank),
180
- _useState14 = (0, _slicedToArray2.default)(_useState13, 2),
181
- twoBitLocation = _useState14[0],
182
- setTwoBitLocation = _useState14[1];
183
-
184
- var _useState15 = (0, _react.useState)(blank),
185
- _useState16 = (0, _slicedToArray2.default)(_useState15, 2),
186
- chromSizesLocation = _useState16[0],
187
- setChromSizesLocation = _useState16[1];
188
-
189
- function createAssembly() {
190
- if (assemblyName === '') {
191
- rootModel.session.notify("Can't create an assembly without a name");
192
- } else {
193
- setFormOpen(false);
194
- var newAssembly;
195
-
196
- if (adapterSelection === 'IndexedFastaAdapter') {
197
- newAssembly = {
198
- name: assemblyName,
199
- displayName: assemblyDisplayName,
200
- sequence: {
201
- adapter: {
202
- type: 'IndexedFastaAdapter',
203
- fastaLocation: fastaLocation,
204
- faiLocation: faiLocation
99
+ var blank = { uri: '' };
100
+ var AssemblyAddForm = (0, mobx_react_1.observer)(function (_a) {
101
+ var rootModel = _a.rootModel, setFormOpen = _a.setFormOpen;
102
+ var classes = useStyles().classes;
103
+ var adapterTypes = [
104
+ 'IndexedFastaAdapter',
105
+ 'BgzipFastaAdapter',
106
+ 'TwoBitAdapter',
107
+ ];
108
+ var _b = __read((0, react_1.useState)(''), 2), assemblyName = _b[0], setAssemblyName = _b[1];
109
+ var _c = __read((0, react_1.useState)(''), 2), assemblyDisplayName = _c[0], setAssemblyDisplayName = _c[1];
110
+ var _d = __read((0, react_1.useState)(adapterTypes[0]), 2), adapterSelection = _d[0], setAdapterSelection = _d[1];
111
+ var _e = __read((0, react_1.useState)(blank), 2), fastaLocation = _e[0], setFastaLocation = _e[1];
112
+ var _f = __read((0, react_1.useState)(blank), 2), faiLocation = _f[0], setFaiLocation = _f[1];
113
+ var _g = __read((0, react_1.useState)(blank), 2), gziLocation = _g[0], setGziLocation = _g[1];
114
+ var _h = __read((0, react_1.useState)(blank), 2), twoBitLocation = _h[0], setTwoBitLocation = _h[1];
115
+ var _j = __read((0, react_1.useState)(blank), 2), chromSizesLocation = _j[0], setChromSizesLocation = _j[1];
116
+ function createAssembly() {
117
+ if (assemblyName === '') {
118
+ rootModel.session.notify("Can't create an assembly without a name");
119
+ }
120
+ else {
121
+ setFormOpen(false);
122
+ var newAssembly = void 0;
123
+ if (adapterSelection === 'IndexedFastaAdapter') {
124
+ newAssembly = {
125
+ name: assemblyName,
126
+ displayName: assemblyDisplayName,
127
+ sequence: {
128
+ adapter: {
129
+ type: 'IndexedFastaAdapter',
130
+ fastaLocation: fastaLocation,
131
+ faiLocation: faiLocation,
132
+ },
133
+ },
134
+ };
205
135
  }
206
- }
207
- };
208
- } else if (adapterSelection === 'BgzipFastaAdapter') {
209
- newAssembly = {
210
- name: assemblyName,
211
- displayName: assemblyDisplayName,
212
- sequence: {
213
- adapter: {
214
- type: 'BgzipFastaAdapter',
215
- fastaLocation: fastaLocation,
216
- faiLocation: faiLocation,
217
- gziLocation: gziLocation
136
+ else if (adapterSelection === 'BgzipFastaAdapter') {
137
+ newAssembly = {
138
+ name: assemblyName,
139
+ displayName: assemblyDisplayName,
140
+ sequence: {
141
+ adapter: {
142
+ type: 'BgzipFastaAdapter',
143
+ fastaLocation: fastaLocation,
144
+ faiLocation: faiLocation,
145
+ gziLocation: gziLocation,
146
+ },
147
+ },
148
+ };
218
149
  }
219
- }
220
- };
221
- } else if (adapterSelection === 'TwoBitAdapter') {
222
- newAssembly = {
223
- name: assemblyName,
224
- displayName: assemblyDisplayName,
225
- sequence: {
226
- adapter: {
227
- type: 'TwoBitAdapter',
228
- twoBitLocation: twoBitLocation,
229
- chromSizesLocation: chromSizesLocation
150
+ else if (adapterSelection === 'TwoBitAdapter') {
151
+ newAssembly = {
152
+ name: assemblyName,
153
+ displayName: assemblyDisplayName,
154
+ sequence: {
155
+ adapter: {
156
+ type: 'TwoBitAdapter',
157
+ twoBitLocation: twoBitLocation,
158
+ chromSizesLocation: chromSizesLocation,
159
+ },
160
+ },
161
+ };
230
162
  }
231
- }
232
- };
233
- }
234
-
235
- rootModel.jbrowse.addAssemblyConf(newAssembly);
236
- rootModel.session.notify("Successfully added ".concat(assemblyName, " assembly to JBrowse 2"), 'success');
237
- }
238
- }
239
-
240
- return /*#__PURE__*/_react.default.createElement("div", {
241
- className: classes.root
242
- }, /*#__PURE__*/_react.default.createElement(_core.Paper, {
243
- className: classes.paper
244
- }, /*#__PURE__*/_react.default.createElement(_core.TextField, {
245
- id: "assembly-name",
246
- inputProps: {
247
- 'data-testid': 'assembly-name'
248
- },
249
- label: "Assembly name",
250
- helperText: "The assembly name e.g. hg38",
251
- variant: "outlined",
252
- value: assemblyName,
253
- onChange: function onChange(event) {
254
- return setAssemblyName(event.target.value);
255
- }
256
- }), /*#__PURE__*/_react.default.createElement(_core.TextField, {
257
- id: "assembly-name",
258
- inputProps: {
259
- 'data-testid': 'assembly-display-name'
260
- },
261
- label: "Assembly display name",
262
- helperText: "A human readable display name for the assembly e.g. \"Homo sapiens (hg38)\"",
263
- variant: "outlined",
264
- value: assemblyDisplayName,
265
- onChange: function onChange(event) {
266
- return setAssemblyDisplayName(event.target.value);
163
+ rootModel.jbrowse.addAssemblyConf(newAssembly);
164
+ rootModel.session.notify("Successfully added ".concat(assemblyName, " assembly to JBrowse 2"), 'success');
165
+ }
267
166
  }
268
- }), /*#__PURE__*/_react.default.createElement(AdapterSelector, {
269
- adapterSelection: adapterSelection,
270
- setAdapterSelection: setAdapterSelection,
271
- adapterTypes: adapterTypes
272
- }), /*#__PURE__*/_react.default.createElement("div", {
273
- className: classes.paperContent
274
- }, /*#__PURE__*/_react.default.createElement(AdapterInput, {
275
- adapterSelection: adapterSelection,
276
- fastaLocation: fastaLocation,
277
- setFastaLocation: setFastaLocation,
278
- faiLocation: faiLocation,
279
- setFaiLocation: setFaiLocation,
280
- gziLocation: gziLocation,
281
- setGziLocation: setGziLocation,
282
- twoBitLocation: twoBitLocation,
283
- setTwoBitLocation: setTwoBitLocation,
284
- chromSizesLocation: chromSizesLocation,
285
- setChromSizesLocation: setChromSizesLocation
286
- }))), /*#__PURE__*/_react.default.createElement(_core.Grid, {
287
- container: true,
288
- className: classes.createButton
289
- }, /*#__PURE__*/_react.default.createElement(_core.Grid, {
290
- item: true
291
- }, /*#__PURE__*/_react.default.createElement(_core.Button, {
292
- variant: "contained",
293
- color: "secondary",
294
- startIcon: /*#__PURE__*/_react.default.createElement(_Add.default, null),
295
- onClick: createAssembly
296
- }, "Create new assembly"))));
167
+ return (react_1.default.createElement("div", { className: classes.root },
168
+ react_1.default.createElement(material_1.Paper, { className: classes.paper },
169
+ react_1.default.createElement(material_1.TextField, { id: "assembly-name", inputProps: { 'data-testid': 'assembly-name' }, label: "Assembly name", helperText: "The assembly name e.g. hg38", variant: "outlined", value: assemblyName, onChange: function (event) { return setAssemblyName(event.target.value); } }),
170
+ react_1.default.createElement(material_1.TextField, { id: "assembly-name", inputProps: { 'data-testid': 'assembly-display-name' }, label: "Assembly display name", helperText: 'A human readable display name for the assembly e.g. "Homo sapiens (hg38)"', variant: "outlined", value: assemblyDisplayName, onChange: function (event) { return setAssemblyDisplayName(event.target.value); } }),
171
+ react_1.default.createElement(AdapterSelector, { adapterSelection: adapterSelection, setAdapterSelection: setAdapterSelection, adapterTypes: adapterTypes }),
172
+ react_1.default.createElement("div", { className: classes.paperContent },
173
+ react_1.default.createElement(AdapterInput, { adapterSelection: adapterSelection, fastaLocation: fastaLocation, setFastaLocation: setFastaLocation, faiLocation: faiLocation, setFaiLocation: setFaiLocation, gziLocation: gziLocation, setGziLocation: setGziLocation, twoBitLocation: twoBitLocation, setTwoBitLocation: setTwoBitLocation, chromSizesLocation: chromSizesLocation, setChromSizesLocation: setChromSizesLocation }))),
174
+ react_1.default.createElement(material_1.Grid, { container: true, className: classes.createButton },
175
+ react_1.default.createElement(material_1.Grid, { item: true },
176
+ react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", startIcon: react_1.default.createElement(Add_1.default, null), onClick: createAssembly }, "Create new assembly")))));
297
177
  });
298
- var _default = AssemblyAddForm;
299
- exports.default = _default;
178
+ exports.default = AssemblyAddForm;
179
+ //# sourceMappingURL=AssemblyAddForm.js.map
@@ -0,0 +1 @@
1
+ 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@@ -1,25 +1,14 @@
1
1
  "use strict";
2
-
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
4
-
5
- Object.defineProperty(exports, "__esModule", {
6
- value: true
2
+ var __importDefault = (this && this.__importDefault) || function (mod) {
3
+ return (mod && mod.__esModule) ? mod : { "default": mod };
4
+ };
5
+ Object.defineProperty(exports, "__esModule", { value: true });
6
+ var react_1 = __importDefault(require("react"));
7
+ var mobx_react_1 = require("mobx-react");
8
+ var plugin_config_1 = require("@jbrowse/plugin-config");
9
+ var AssemblyEditor = (0, mobx_react_1.observer)(function (_a) {
10
+ var assembly = _a.assembly;
11
+ return react_1.default.createElement(plugin_config_1.ConfigurationEditor, { model: { target: assembly } });
7
12
  });
8
- exports.default = void 0;
9
-
10
- var _react = _interopRequireDefault(require("react"));
11
-
12
- var _mobxReact = require("mobx-react");
13
-
14
- var _pluginConfig = require("@jbrowse/plugin-config");
15
-
16
- var AssemblyEditor = (0, _mobxReact.observer)(function (_ref) {
17
- var assembly = _ref.assembly;
18
- return /*#__PURE__*/_react.default.createElement(_pluginConfig.ConfigurationEditor, {
19
- model: {
20
- target: assembly
21
- }
22
- });
23
- });
24
- var _default = AssemblyEditor;
25
- exports.default = _default;
13
+ exports.default = AssemblyEditor;
14
+ //# sourceMappingURL=AssemblyEditor.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"AssemblyEditor.js","sourceRoot":"","sources":["../../src/AssemblyManager/AssemblyEditor.tsx"],"names":[],"mappings":";;;;;AAAA,gDAAyB;AACzB,yCAAqC;AACrC,wDAA4D;AAE5D,IAAM,cAAc,GAAG,IAAA,qBAAQ,EAC7B,UAAC,EAKA;QAJC,QAAQ,cAAA;IAKR,OAAO,8BAAC,mCAAmB,IAAC,KAAK,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAI,CAAA;AAC7D,CAAC,CACF,CAAA;AAED,kBAAe,cAAc,CAAA"}