@gen-epix/ui 1.14.4 → 1.15.0

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 (739) hide show
  1. package/README.md +3 -3
  2. package/dist/index.js +27287 -27948
  3. package/package.json +94 -84
  4. package/src/@types/environment.d.ts +54 -0
  5. package/src/api/api.ts +43576 -0
  6. package/src/api/base.ts +111 -0
  7. package/src/api/common.ts +168 -0
  8. package/src/api/configuration.ts +118 -0
  9. package/src/api/index.ts +20 -0
  10. package/src/assets/icons/CollectionIcon.svg +1 -0
  11. package/src/assets/icons/DnaIcon.svg +1 -0
  12. package/src/assets/icons/VirusIcon.svg +1 -0
  13. package/src/assets/logo/logo-rijksoverheid.svg +42 -0
  14. package/src/assets/logo/logo-rivm.svg +6 -0
  15. package/src/classes/Subject/Subject.ts +26 -0
  16. package/src/classes/Subject/index.ts +1 -0
  17. package/src/classes/TableEventBus/TableEventBus.ts +14 -0
  18. package/src/classes/TableEventBus/index.ts +1 -0
  19. package/src/classes/abstracts/EventBusAbstract/EventBusAbstract.ts +37 -0
  20. package/src/classes/abstracts/EventBusAbstract/index.ts +1 -0
  21. package/src/classes/abstracts/FilterAbstract/FilterAbstract.ts +54 -0
  22. package/src/classes/abstracts/FilterAbstract/index.ts +1 -0
  23. package/src/classes/abstracts/SubscribableAbstract/SubscribableAbstract.ts +20 -0
  24. package/src/classes/abstracts/SubscribableAbstract/index.ts +1 -0
  25. package/src/classes/errors/UploadError.ts +11 -0
  26. package/src/classes/errors/index.ts +1 -0
  27. package/src/classes/filters/BooleanFilter.ts +31 -0
  28. package/src/classes/filters/DateFilter.ts +133 -0
  29. package/src/classes/filters/GeoFilter.ts +60 -0
  30. package/src/classes/filters/MultiSelectFilter.ts +70 -0
  31. package/src/classes/filters/NumberRangeFilter.ts +82 -0
  32. package/src/classes/filters/SelectionFilter.ts +25 -0
  33. package/src/classes/filters/TextFilter.ts +36 -0
  34. package/src/classes/filters/TreeFilter.ts +22 -0
  35. package/src/classes/managers/AuthenticationManager/AuthenticationManager.ts +94 -0
  36. package/src/classes/managers/AuthenticationManager/index.ts +1 -0
  37. package/src/classes/managers/AuthorizationManager/AuthorizationManager.ts +70 -0
  38. package/src/classes/managers/AuthorizationManager/index.ts +1 -0
  39. package/src/classes/managers/BackendVersionManager/BackendVersionManager.ts +23 -0
  40. package/src/classes/managers/BackendVersionManager/index.ts +1 -0
  41. package/src/classes/managers/BreadcrumbManager/BreadcrumbManager.ts +30 -0
  42. package/src/classes/managers/BreadcrumbManager/index.ts +1 -0
  43. package/src/classes/managers/ConfigManager/ConfigManager.ts +31 -0
  44. package/src/classes/managers/ConfigManager/index.ts +1 -0
  45. package/src/classes/managers/DevicePixelRatioManager/DevicePixelRatioManager.ts +27 -0
  46. package/src/classes/managers/DevicePixelRatioManager/index.ts +1 -0
  47. package/src/classes/managers/EmotionCacheManager/EmotionCacheManager.ts +27 -0
  48. package/src/classes/managers/EmotionCacheManager/index.ts +1 -0
  49. package/src/classes/managers/EpiDataManager/EpiDataManager.ts +196 -0
  50. package/src/classes/managers/EpiDataManager/index.ts +1 -0
  51. package/src/classes/managers/EpiEventBusManager/EpiEventBusManager.ts +61 -0
  52. package/src/classes/managers/EpiEventBusManager/index.ts +1 -0
  53. package/src/classes/managers/EpiHighlightingManager/EpiHighlightingManager.ts +32 -0
  54. package/src/classes/managers/EpiHighlightingManager/index.ts +1 -0
  55. package/src/classes/managers/EpiLineListCaseSetMembersManager/EpiListsCaseSetMembersManager.ts +118 -0
  56. package/src/classes/managers/EpiLineListCaseSetMembersManager/index.ts +1 -0
  57. package/src/classes/managers/FeatureFlagsManager/FeatureFlagsManager.ts +30 -0
  58. package/src/classes/managers/FeatureFlagsManager/index.ts +1 -0
  59. package/src/classes/managers/I18nManager/I18nManager.ts +105 -0
  60. package/src/classes/managers/I18nManager/index.ts +1 -0
  61. package/src/classes/managers/InactivityManager/InactivityManager.ts +119 -0
  62. package/src/classes/managers/InactivityManager/index.ts +1 -0
  63. package/src/classes/managers/KeyboardShortcutManager/KeyboardShortcutManager.ts +78 -0
  64. package/src/classes/managers/KeyboardShortcutManager/index.ts +1 -0
  65. package/src/classes/managers/LogManager/LogManager.ts +151 -0
  66. package/src/classes/managers/LogManager/index.ts +1 -0
  67. package/src/classes/managers/NavigationHistoryManager/NavigationHistoryManager.ts +16 -0
  68. package/src/classes/managers/NavigationHistoryManager/index.ts +1 -0
  69. package/src/classes/managers/NotificationManager/NotificationManager.ts +104 -0
  70. package/src/classes/managers/NotificationManager/index.ts +1 -0
  71. package/src/classes/managers/PageEventBusManager/PageEventBusManager.ts +116 -0
  72. package/src/classes/managers/PageEventBusManager/index.ts +1 -0
  73. package/src/classes/managers/QueryClientManager/QueryClientManager.ts +51 -0
  74. package/src/classes/managers/QueryClientManager/index.ts +1 -0
  75. package/src/classes/managers/RouterManager/RouterManager.ts +25 -0
  76. package/src/classes/managers/RouterManager/index.ts +1 -0
  77. package/src/classes/managers/UserSettingsManager/UserSettingsManager.ts +16 -0
  78. package/src/classes/managers/UserSettingsManager/index.ts +1 -0
  79. package/src/classes/managers/WindowManager/WindowManager.test.ts +23 -0
  80. package/src/classes/managers/WindowManager/WindowManager.ts +26 -0
  81. package/src/classes/managers/WindowManager/index.ts +1 -0
  82. package/src/components/app/App/App.tsx +58 -0
  83. package/src/components/app/App/index.ts +1 -0
  84. package/src/components/app/ApplicationBootstrap/ApplicationBootstrap.tsx +223 -0
  85. package/src/components/app/ApplicationBootstrap/index.ts +1 -0
  86. package/src/components/app/RouterRoot/RouterRoot.tsx +187 -0
  87. package/src/components/app/RouterRoot/index.ts +1 -0
  88. package/src/components/epi/EpiAddCasesToEventDialog/EpiAddCasesToEventDialog.tsx +347 -0
  89. package/src/components/epi/EpiAddCasesToEventDialog/EpiAddCasesToEventDialogSuccessNotificationMessage.tsx +38 -0
  90. package/src/components/epi/EpiAddCasesToEventDialog/index.ts +1 -0
  91. package/src/components/epi/EpiBulkEditCaseDialog/EpiBulkEditCaseDialog.tsx +61 -0
  92. package/src/components/epi/EpiBulkEditCaseDialog/index.ts +1 -0
  93. package/src/components/epi/EpiCaseInfoDialog/EpiCaseCaseSetInfo.tsx +137 -0
  94. package/src/components/epi/EpiCaseInfoDialog/EpiCaseContent.tsx +127 -0
  95. package/src/components/epi/EpiCaseInfoDialog/EpiCaseForm.tsx +111 -0
  96. package/src/components/epi/EpiCaseInfoDialog/EpiCaseInfoDialog.tsx +377 -0
  97. package/src/components/epi/EpiCaseInfoDialog/EpiCaseSharingForm.tsx +140 -0
  98. package/src/components/epi/EpiCaseInfoDialog/EpiCaseSharingInfo.tsx +23 -0
  99. package/src/components/epi/EpiCaseInfoDialog/EpiReadOnlyCaseContent.tsx +89 -0
  100. package/src/components/epi/EpiCaseInfoDialog/index.ts +1 -0
  101. package/src/components/epi/EpiCaseSetInfoDialog/EpiCaseSetContent.tsx +108 -0
  102. package/src/components/epi/EpiCaseSetInfoDialog/EpiCaseSetDescription.tsx +34 -0
  103. package/src/components/epi/EpiCaseSetInfoDialog/EpiCaseSetForm.tsx +151 -0
  104. package/src/components/epi/EpiCaseSetInfoDialog/EpiCaseSetInfoDialog.tsx +389 -0
  105. package/src/components/epi/EpiCaseSetInfoDialog/EpiCaseSetSharingForm.tsx +155 -0
  106. package/src/components/epi/EpiCaseSetInfoDialog/EpiCaseSetSharingInfo.tsx +23 -0
  107. package/src/components/epi/EpiCaseSetInfoDialog/index.ts +1 -0
  108. package/src/components/epi/EpiCaseSummary/EpiCaseSummary.tsx +141 -0
  109. package/src/components/epi/EpiCaseSummary/index.ts +1 -0
  110. package/src/components/epi/EpiCaseTypeInfoDialog/EpiCaseTypeInfoAccessRights.tsx +91 -0
  111. package/src/components/epi/EpiCaseTypeInfoDialog/EpiCaseTypeInfoColAccessRights.tsx +118 -0
  112. package/src/components/epi/EpiCaseTypeInfoDialog/EpiCaseTypeInfoData.tsx +38 -0
  113. package/src/components/epi/EpiCaseTypeInfoDialog/EpiCaseTypeInfoDialog.tsx +39 -0
  114. package/src/components/epi/EpiCaseTypeInfoDialog/EpiCaseTypeInfoDialogContent.tsx +169 -0
  115. package/src/components/epi/EpiCaseTypeInfoDialog/EpiCaseTypeInfoDialogWithLoader.tsx +42 -0
  116. package/src/components/epi/EpiCaseTypeInfoDialog/EpiCaseTypeInfoRegions.tsx +87 -0
  117. package/src/components/epi/EpiCaseTypeInfoDialog/EpiCaseTypeInfoTrees.tsx +73 -0
  118. package/src/components/epi/EpiCaseTypeInfoDialog/EpiCaseTypeInfoValues.tsx +61 -0
  119. package/src/components/epi/EpiCaseTypeInfoDialog/EpiCaseTypeInfoVariableDetails.tsx +151 -0
  120. package/src/components/epi/EpiCaseTypeInfoDialog/index.ts +10 -0
  121. package/src/components/epi/EpiCasesAlreadyInCaseSetWarning/EpiCasesAlreadyInCaseSetWarning.tsx +190 -0
  122. package/src/components/epi/EpiCasesAlreadyInCaseSetWarning/EpiCasesAlreadyInCaseSetWarningCaseSetLink.tsx +62 -0
  123. package/src/components/epi/EpiCasesAlreadyInCaseSetWarning/index.ts +1 -0
  124. package/src/components/epi/EpiCompletCaseTypeLoader/EpiCompletCaseTypeLoader.tsx +87 -0
  125. package/src/components/epi/EpiCompletCaseTypeLoader/index.ts +1 -0
  126. package/src/components/epi/EpiContactDetailsDialog/EpiContactDetailsDialog.tsx +151 -0
  127. package/src/components/epi/EpiContactDetailsDialog/index.ts +1 -0
  128. package/src/components/epi/EpiContextMenu/EpiContextMenu.tsx +155 -0
  129. package/src/components/epi/EpiContextMenu/index.ts +1 -0
  130. package/src/components/epi/EpiCreateEventDialog/EpiCreateEventDialog.tsx +386 -0
  131. package/src/components/epi/EpiCreateEventDialog/EpiCreateEventDialogSuccessNotificationMessage.tsx +30 -0
  132. package/src/components/epi/EpiCreateEventDialog/index.ts +1 -0
  133. package/src/components/epi/EpiCurve/EpiCurve.tsx +525 -0
  134. package/src/components/epi/EpiCurve/index.ts +1 -0
  135. package/src/components/epi/EpiCustomTabPanel/EpiCustomTabPanel.tsx +27 -0
  136. package/src/components/epi/EpiCustomTabPanel/index.ts +1 -0
  137. package/src/components/epi/EpiDashboard/EpiDashboard.tsx +390 -0
  138. package/src/components/epi/EpiDashboard/EpiDashboardDownloadSidebarItem.tsx +154 -0
  139. package/src/components/epi/EpiDashboard/EpiDashboardGeneralSettingsForm.tsx +89 -0
  140. package/src/components/epi/EpiDashboard/EpiDashboardLayoutRenderer.tsx +248 -0
  141. package/src/components/epi/EpiDashboard/EpiDashboardLayoutSettingsForm.tsx +160 -0
  142. package/src/components/epi/EpiDashboard/EpiDashboardSettingsSidebarItem.tsx +93 -0
  143. package/src/components/epi/EpiDashboard/EpiDashboardTreeSettingsForm.tsx +90 -0
  144. package/src/components/epi/EpiDashboard/index.ts +1 -0
  145. package/src/components/epi/EpiDashboardStoreLoader/EpiDashboardStoreLoader.tsx +34 -0
  146. package/src/components/epi/EpiDashboardStoreLoader/EpiDashboardStoreLoaderContent.tsx +73 -0
  147. package/src/components/epi/EpiDashboardStoreLoader/index.ts +2 -0
  148. package/src/components/epi/EpiDashboardStoreLoader/withEpiDashboardStore.tsx +19 -0
  149. package/src/components/epi/EpiDataCollectionAccessInfo/EpiDataCollectionAccessInfo.tsx +88 -0
  150. package/src/components/epi/EpiDataCollectionAccessInfo/index.ts +1 -0
  151. package/src/components/epi/EpiFindSimilarCasesDialog/EpiFindSimilarCasesDialog.tsx +302 -0
  152. package/src/components/epi/EpiFindSimilarCasesDialog/index.ts +1 -0
  153. package/src/components/epi/EpiLegendaItem/EpiLegendaItem.tsx +106 -0
  154. package/src/components/epi/EpiLegendaItem/index.ts +1 -0
  155. package/src/components/epi/EpiLineList/EpiLineList.tsx +492 -0
  156. package/src/components/epi/EpiLineList/EpiLineListPrimaryMenu.tsx +189 -0
  157. package/src/components/epi/EpiLineList/EpiLineListSecondaryMenu.tsx +56 -0
  158. package/src/components/epi/EpiLineList/EpiLineListTitle.tsx +28 -0
  159. package/src/components/epi/EpiLineList/index.ts +1 -0
  160. package/src/components/epi/EpiLineList/useEpiLineListEmitDownloadOptions.tsx +102 -0
  161. package/src/components/epi/EpiMap/EpiMap.tsx +547 -0
  162. package/src/components/epi/EpiMap/index.ts +1 -0
  163. package/src/components/epi/EpiRemoveCasesFromEventDialog/EpiRemoveCasesFromEventDialog.tsx +169 -0
  164. package/src/components/epi/EpiRemoveCasesFromEventDialog/index.ts +1 -0
  165. package/src/components/epi/EpiRemoveFindSimilarCasesResultDialog/EpiRemoveFindSimilarCasesResultDialog.tsx +216 -0
  166. package/src/components/epi/EpiSequenceDownloadDialog/EpiSequenceDownloadDialog.tsx +151 -0
  167. package/src/components/epi/EpiSequenceDownloadDialog/index.ts +1 -0
  168. package/src/components/epi/EpiStratification/EpiStratification.tsx +241 -0
  169. package/src/components/epi/EpiStratification/index.ts +1 -0
  170. package/src/components/epi/EpiTree/EpiTree.tsx +906 -0
  171. package/src/components/epi/EpiTree/index.ts +1 -0
  172. package/src/components/epi/EpiTreeDescription/EpiTreeDescription.tsx +71 -0
  173. package/src/components/epi/EpiTreeDescription/index.ts +1 -0
  174. package/src/components/epi/EpiUpload/EpiUpload.tsx +107 -0
  175. package/src/components/epi/EpiUpload/EpiUploadCaseResultTable.tsx +383 -0
  176. package/src/components/epi/EpiUpload/EpiUploadCreateCases.tsx +266 -0
  177. package/src/components/epi/EpiUpload/EpiUploadMapColumns.tsx +261 -0
  178. package/src/components/epi/EpiUpload/EpiUploadMapSequences.tsx +332 -0
  179. package/src/components/epi/EpiUpload/EpiUploadNavigation.tsx +52 -0
  180. package/src/components/epi/EpiUpload/EpiUploadSelectFile.tsx +285 -0
  181. package/src/components/epi/EpiUpload/EpiUploadSelectSequenceFiles.tsx +375 -0
  182. package/src/components/epi/EpiUpload/EpiUploadValidate.tsx +199 -0
  183. package/src/components/epi/EpiUpload/EpiUploadValidateNavigation.tsx +34 -0
  184. package/src/components/epi/EpiUpload/index.ts +1 -0
  185. package/src/components/epi/EpiUserRightsDialog/EpiUserRightsDialog.tsx +101 -0
  186. package/src/components/epi/EpiUserRightsDialog/EpiUserRightsDialogCaseAccessPolicy.tsx +160 -0
  187. package/src/components/epi/EpiUserRightsDialog/index.ts +1 -0
  188. package/src/components/epi/EpiWarning/EpiWarning.tsx +39 -0
  189. package/src/components/epi/EpiWarning/index.ts +1 -0
  190. package/src/components/epi/EpiWidget/EpiWidget.tsx +255 -0
  191. package/src/components/epi/EpiWidget/index.ts +1 -0
  192. package/src/components/epi/EpiWidgetHeaderIconButton/EpiWidgetHeaderIconButton.tsx +40 -0
  193. package/src/components/epi/EpiWidgetHeaderIconButton/index.ts +1 -0
  194. package/src/components/epi/EpiWidgetMenu/EpiWidgetMenu.tsx +56 -0
  195. package/src/components/epi/EpiWidgetMenu/index.ts +1 -0
  196. package/src/components/epi/EpiWidgetUnavailable/EpiWidgetUnavailable.tsx +51 -0
  197. package/src/components/epi/EpiWidgetUnavailable/index.ts +1 -0
  198. package/src/components/filters/BooleanFilterField/BooleanFilterField.tsx +26 -0
  199. package/src/components/filters/BooleanFilterField/index.ts +1 -0
  200. package/src/components/filters/DateFilterField/DateFilterField.tsx +23 -0
  201. package/src/components/filters/DateFilterField/index.ts +1 -0
  202. package/src/components/filters/GeoFilterField/GeoFilterField.tsx +32 -0
  203. package/src/components/filters/GeoFilterField/index.ts +1 -0
  204. package/src/components/filters/MultiSelectFilterField/MultiSelectFilterField.tsx +31 -0
  205. package/src/components/filters/MultiSelectFilterField/index.ts +1 -0
  206. package/src/components/filters/NumberRangeFilterField/NumberRangeFilterField.tsx +20 -0
  207. package/src/components/filters/NumberRangeFilterField/index.ts +1 -0
  208. package/src/components/filters/TextFilterField/TextFilterField.tsx +18 -0
  209. package/src/components/filters/TextFilterField/index.ts +1 -0
  210. package/src/components/form/fields/Autocomplete/Autocomplete.tsx +270 -0
  211. package/src/components/form/fields/Autocomplete/index.ts +1 -0
  212. package/src/components/form/fields/CheckboxGroup/CheckboxGroup.tsx +192 -0
  213. package/src/components/form/fields/CheckboxGroup/index.ts +1 -0
  214. package/src/components/form/fields/DatePicker/DatePicker.tsx +167 -0
  215. package/src/components/form/fields/DatePicker/index.ts +1 -0
  216. package/src/components/form/fields/DateRangePicker/DateRangePicker.tsx +359 -0
  217. package/src/components/form/fields/DateRangePicker/index.ts +1 -0
  218. package/src/components/form/fields/NumberField/NumberField.tsx +277 -0
  219. package/src/components/form/fields/NumberField/index.ts +1 -0
  220. package/src/components/form/fields/NumberRangeInput/NumberRangeInput.tsx +297 -0
  221. package/src/components/form/fields/NumberRangeInput/index.ts +1 -0
  222. package/src/components/form/fields/RadioGroup/RadioGroup.tsx +130 -0
  223. package/src/components/form/fields/RadioGroup/index.ts +1 -0
  224. package/src/components/form/fields/RichTextEditor/RichTextEditor.tsx +321 -0
  225. package/src/components/form/fields/RichTextEditor/RichTextEditorContent.tsx +34 -0
  226. package/src/components/form/fields/RichTextEditor/index.ts +2 -0
  227. package/src/components/form/fields/RichTextEditor/useRichTextEditorExtensions.ts +174 -0
  228. package/src/components/form/fields/Select/Select.tsx +219 -0
  229. package/src/components/form/fields/Select/index.ts +1 -0
  230. package/src/components/form/fields/Switch/Switch.tsx +116 -0
  231. package/src/components/form/fields/Switch/index.ts +1 -0
  232. package/src/components/form/fields/TextField/TextField.tsx +170 -0
  233. package/src/components/form/fields/TextField/index.ts +1 -0
  234. package/src/components/form/fields/ToggleButtonGroup/ToggleButtonGroup.tsx +118 -0
  235. package/src/components/form/fields/ToggleButtonGroup/index.ts +1 -0
  236. package/src/components/form/fields/TransferList/TransferList.tsx +360 -0
  237. package/src/components/form/fields/TransferList/index.ts +1 -0
  238. package/src/components/form/fields/UploadButton/UploadButton.tsx +157 -0
  239. package/src/components/form/helpers/FormFieldHelperText/FormFieldHelperText.tsx +68 -0
  240. package/src/components/form/helpers/FormFieldHelperText/index.ts +1 -0
  241. package/src/components/form/helpers/FormFieldLoadingIndicator/FormFieldLoadingIndicator.tsx +22 -0
  242. package/src/components/form/helpers/FormFieldLoadingIndicator/index.ts +1 -0
  243. package/src/components/form/helpers/GenericForm/GenericForm.tsx +187 -0
  244. package/src/components/form/helpers/GenericForm/index.ts +1 -0
  245. package/src/components/ui/ApplicationBar/ApplicationBar.tsx +74 -0
  246. package/src/components/ui/ApplicationBar/ApplicationBarActions.tsx +124 -0
  247. package/src/components/ui/ApplicationBar/ApplicationBarActionsFeedbackItem.tsx +102 -0
  248. package/src/components/ui/ApplicationBar/ApplicationBarActionsInfotem.tsx +60 -0
  249. package/src/components/ui/ApplicationBar/ApplicationBarActionsNotificationsItem.tsx +82 -0
  250. package/src/components/ui/ApplicationBar/ApplicationBarActionsOrganizationSwitcherItem.tsx +58 -0
  251. package/src/components/ui/ApplicationBar/ApplicationBarActionsOutagesItem.tsx +75 -0
  252. package/src/components/ui/ApplicationBar/ApplicationBarActionsUserItem.tsx +60 -0
  253. package/src/components/ui/ApplicationBar/ApplicationBarNavigationMenu.tsx +159 -0
  254. package/src/components/ui/ApplicationBar/InfoMenu.tsx +120 -0
  255. package/src/components/ui/ApplicationBar/UserMenu.tsx +208 -0
  256. package/src/components/ui/ApplicationBar/UserOrganizationAdminMenuItem.tsx +69 -0
  257. package/src/components/ui/ApplicationBar/UserOwnOrganizationMenuItem.tsx +54 -0
  258. package/src/components/ui/ApplicationBar/index.ts +1 -0
  259. package/src/components/ui/ApplicationFooter/ApplicationFooter.tsx +121 -0
  260. package/src/components/ui/ApplicationFooter/ApplicationFooterLink.tsx +48 -0
  261. package/src/components/ui/ApplicationFooter/ApplicationFooterLinkSection.tsx +56 -0
  262. package/src/components/ui/ApplicationFooter/index.ts +1 -0
  263. package/src/components/ui/AuthenticationWrapper/AuthenticationWrapper.tsx +208 -0
  264. package/src/components/ui/AuthenticationWrapper/index.ts +1 -0
  265. package/src/components/ui/AuthorizationWrapper/AuthorizationWrapper.tsx +75 -0
  266. package/src/components/ui/AuthorizationWrapper/index.ts +1 -0
  267. package/src/components/ui/Breadcrumbs/Breadcrumbs.tsx +92 -0
  268. package/src/components/ui/Breadcrumbs/index.ts +1 -0
  269. package/src/components/ui/Confirmation/Confirmation.tsx +10 -0
  270. package/src/components/ui/Confirmation/ConfirmationRender.tsx +81 -0
  271. package/src/components/ui/Confirmation/index.ts +2 -0
  272. package/src/components/ui/ConsentDialog/ConsentDialog.tsx +57 -0
  273. package/src/components/ui/ConsentDialog/index.ts +1 -0
  274. package/src/components/ui/CopyToClipboardButton/CopyToClipboardButton.tsx +94 -0
  275. package/src/components/ui/CopyToClipboardButton/index.ts +1 -0
  276. package/src/components/ui/Dialog/Dialog.tsx +196 -0
  277. package/src/components/ui/Dialog/index.ts +1 -0
  278. package/src/components/ui/FileSelector/FileSelector.tsx +358 -0
  279. package/src/components/ui/FileSelector/index.ts +1 -0
  280. package/src/components/ui/GenericErrorMessage/GenericErrorMessage.tsx +168 -0
  281. package/src/components/ui/GenericErrorMessage/index.ts +1 -0
  282. package/src/components/ui/HomePageTrends/HomePageTrendCard.tsx +132 -0
  283. package/src/components/ui/HomePageTrends/HomePageTrends.tsx +312 -0
  284. package/src/components/ui/HomePageTrends/index.ts +1 -0
  285. package/src/components/ui/LicensesDialog/LicensesDialog.tsx +231 -0
  286. package/src/components/ui/LicensesDialog/index.ts +1 -0
  287. package/src/components/ui/LinearProgressWithLabel/LinearProgressWithLabel.tsx +31 -0
  288. package/src/components/ui/LinearProgressWithLabel/index.ts +1 -0
  289. package/src/components/ui/LoadingIndicator/LoadingIndicator.tsx +11 -0
  290. package/src/components/ui/LoadingIndicator/index.ts +1 -0
  291. package/src/components/ui/MyPermissionsDialog/MyPermissionsDialog.tsx +95 -0
  292. package/src/components/ui/MyPermissionsDialog/index.ts +1 -0
  293. package/src/components/ui/NavLink/NavLink.tsx +47 -0
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  604. package/src/pages/RouterErrorPage/RouterErrorPage.tsx +23 -0
  605. package/src/pages/RouterErrorPage/index.ts +1 -0
  606. package/src/pages/TrendsPage/TrendsPage.tsx +17 -0
  607. package/src/pages/TrendsPage/index.ts +1 -0
  608. package/src/pages/UploadPage/UploadPage.tsx +40 -0
  609. package/src/pages/UploadPage/index.ts +1 -0
  610. package/src/pages/UserAccessCasePoliciesAdminPage/UserAccessCasePoliciesAdminPage.tsx +209 -0
  611. package/src/pages/UserAccessCasePoliciesAdminPage/index.ts +1 -0
  612. package/src/pages/UserEffectiveRightsAdminPage/UserEffectiveRightsAdminPage.tsx +331 -0
  613. package/src/pages/UserEffectiveRightsAdminPage/index.ts +1 -0
  614. package/src/pages/UserEffectiveRightsTesterAdminPage/UserEffectiveRightsTesterAdminPage.tsx +283 -0
  615. package/src/pages/UserEffectiveRightsTesterAdminPage/index.ts +1 -0
  616. package/src/pages/UserInvitationsAdminPage/UserInvitationConsumeDialog.tsx +143 -0
  617. package/src/pages/UserInvitationsAdminPage/UserInvitationShareDialog.tsx +100 -0
  618. package/src/pages/UserInvitationsAdminPage/UserInvitationsAdminPage.tsx +218 -0
  619. package/src/pages/UserInvitationsAdminPage/index.ts +1 -0
  620. package/src/pages/UserShareCasePoliciesAdminPage/UserShareCasePoliciesAdminPage.tsx +183 -0
  621. package/src/pages/UserShareCasePoliciesAdminPage/index.ts +1 -0
  622. package/src/pages/UsersAdminPage/UsersAdminPage.tsx +240 -0
  623. package/src/pages/UsersAdminPage/index.ts +1 -0
  624. package/src/routes/adminRoutes.tsx +801 -0
  625. package/src/routes/index.ts +2 -0
  626. package/src/routes/routes.tsx +235 -0
  627. package/src/setup/index.ts +1 -0
  628. package/src/setup/setup.ts +5 -0
  629. package/src/setup/yup.ts +203 -0
  630. package/src/stores/epiDashboardStore/epiDashboardStore.ts +750 -0
  631. package/src/stores/epiDashboardStore/epiDashboardStoreContext.tsx +6 -0
  632. package/src/stores/epiDashboardStore/index.ts +2 -0
  633. package/src/stores/epiUploadStore/epiUploadStore.ts +351 -0
  634. package/src/stores/epiUploadStore/epiUploadStoreContext.tsx +6 -0
  635. package/src/stores/epiUploadStore/index.ts +2 -0
  636. package/src/stores/oidcStore/index.ts +1 -0
  637. package/src/stores/oidcStore/oidcStore.ts +43 -0
  638. package/src/stores/outagesStore/index.ts +1 -0
  639. package/src/stores/outagesStore/outagesStore.ts +31 -0
  640. package/src/stores/tableStore/TableStoreContext.tsx +6 -0
  641. package/src/stores/tableStore/TableStoreContextProvider.tsx +20 -0
  642. package/src/stores/tableStore/index.ts +4 -0
  643. package/src/stores/tableStore/tableStore.ts +547 -0
  644. package/src/stores/tableStore/useTableStoreContext.tsx +7 -0
  645. package/src/stores/userProfileStore/index.ts +1 -0
  646. package/src/stores/userProfileStore/userProfileStore.ts +112 -0
  647. package/src/test/integration/lib/render.tsx +33 -0
  648. package/src/test/integration/tests/integration-example/HelloWorld.test.tsx +14 -0
  649. package/src/test/integration/tests/integration-example/HelloWorld.tsx +9 -0
  650. package/src/test/setup-browser.ts +3 -0
  651. package/src/test/setup-jsdom.ts +6 -0
  652. package/src/test/setup.ts +9 -0
  653. package/src/utils/AbacUtil/AbacUtil.ts +21 -0
  654. package/src/utils/AbacUtil/index.ts +1 -0
  655. package/src/utils/AxiosUtil/AxiosUtil.test.ts +66 -0
  656. package/src/utils/AxiosUtil/AxiosUtil.ts +47 -0
  657. package/src/utils/AxiosUtil/index.ts +1 -0
  658. package/src/utils/CaseSelectionUtil/CaseSelectionUtil.ts +32 -0
  659. package/src/utils/CaseSelectionUtil/index.ts +1 -0
  660. package/src/utils/CaseSetUtil/CaseSetUtil.ts +13 -0
  661. package/src/utils/CaseSetUtil/index.ts +1 -0
  662. package/src/utils/CaseTypeUtil/CaseTypeUtil.ts +178 -0
  663. package/src/utils/CaseTypeUtil/index.ts +1 -0
  664. package/src/utils/CaseUtil/CaseUtil.ts +401 -0
  665. package/src/utils/CaseUtil/index.ts +1 -0
  666. package/src/utils/DashboardUtil/DashboardUtil.ts +46 -0
  667. package/src/utils/DashboardUtil/index.ts +1 -0
  668. package/src/utils/DataHookUtil/DataHookUtil.ts +137 -0
  669. package/src/utils/DataHookUtil/index.ts +1 -0
  670. package/src/utils/DataSetUtil/DataSetUtil.ts +70 -0
  671. package/src/utils/DataSetUtil/index.ts +1 -0
  672. package/src/utils/DataUtil/DataUtil.ts +84 -0
  673. package/src/utils/DataUtil/index.ts +1 -0
  674. package/src/utils/DownloadUtil/DownloadUtil.ts +237 -0
  675. package/src/utils/DownloadUtil/index.ts +1 -0
  676. package/src/utils/EffectiveRightsUtil/EffectiveRightsUtil.ts +142 -0
  677. package/src/utils/EffectiveRightsUtil/index.ts +1 -0
  678. package/src/utils/EpiCurveUtil/EpiCurveUtil.ts +180 -0
  679. package/src/utils/EpiCurveUtil/index.ts +1 -0
  680. package/src/utils/EpiFilterUtil/EpiFilterUtil.ts +232 -0
  681. package/src/utils/EpiFilterUtil/index.ts +1 -0
  682. package/src/utils/EpiLineListUtil/EpiLineListUtil.ts +15 -0
  683. package/src/utils/EpiLineListUtil/index.ts +1 -0
  684. package/src/utils/EpiMapUtil/EpiMapUtil.test.ts +54 -0
  685. package/src/utils/EpiMapUtil/EpiMapUtil.ts +80 -0
  686. package/src/utils/EpiMapUtil/index.ts +1 -0
  687. package/src/utils/EpiTreeUtil/EpiTreeUtil.test.ts +2467 -0
  688. package/src/utils/EpiTreeUtil/EpiTreeUtil.ts +1055 -0
  689. package/src/utils/EpiTreeUtil/index.ts +1 -0
  690. package/src/utils/EpiUploadUtil/EpiUploadUtil.ts +857 -0
  691. package/src/utils/EpiUploadUtil/index.ts +1 -0
  692. package/src/utils/FileUtil/FileUtil.ts +22 -0
  693. package/src/utils/FileUtil/index.ts +1 -0
  694. package/src/utils/FormUtil/FormUtil.test.ts +36 -0
  695. package/src/utils/FormUtil/FormUtil.ts +63 -0
  696. package/src/utils/FormUtil/index.ts +1 -0
  697. package/src/utils/MenuDataUtil/MenuDataUtil.ts +54 -0
  698. package/src/utils/MenuDataUtil/index.ts +1 -0
  699. package/src/utils/NewickUtil/NewickUtil.test.ts +187 -0
  700. package/src/utils/NewickUtil/NewickUtil.ts +69 -0
  701. package/src/utils/NewickUtil/index.ts +1 -0
  702. package/src/utils/NotificationUtil/NotificationUtil.ts +28 -0
  703. package/src/utils/NotificationUtil/index.ts +1 -0
  704. package/src/utils/NumberUtil/NumberUtil.test.ts +113 -0
  705. package/src/utils/NumberUtil/NumberUtil.ts +67 -0
  706. package/src/utils/NumberUtil/index.ts +1 -0
  707. package/src/utils/ObjectUtil/ObjectUtil.test.ts +43 -0
  708. package/src/utils/ObjectUtil/ObjectUtil.ts +28 -0
  709. package/src/utils/ObjectUtil/index.ts +1 -0
  710. package/src/utils/OutageUtil/OutageUtil.test.ts +108 -0
  711. package/src/utils/OutageUtil/OutageUtil.ts +81 -0
  712. package/src/utils/OutageUtil/index.ts +1 -0
  713. package/src/utils/QueryUtil/QueryUtil.test.ts +42 -0
  714. package/src/utils/QueryUtil/QueryUtil.ts +105 -0
  715. package/src/utils/QueryUtil/index.ts +1 -0
  716. package/src/utils/StringUtil/StringUtil.test.ts +61 -0
  717. package/src/utils/StringUtil/StringUtil.ts +91 -0
  718. package/src/utils/StringUtil/index.ts +1 -0
  719. package/src/utils/TableUtil/TableUtil.ts +665 -0
  720. package/src/utils/TableUtil/index.ts +1 -0
  721. package/src/utils/TestIdUtil/TestIdUtil.test.ts +12 -0
  722. package/src/utils/TestIdUtil/TestIdUtil.ts +13 -0
  723. package/src/utils/TestIdUtil/index.ts +1 -0
  724. package/src/utils/TimeUtil/TimeUtil.ts +38 -0
  725. package/src/utils/TimeUtil/index.ts +1 -0
  726. package/src/utils/UserManagerUtil/UserManagerUtil.test.ts +41 -0
  727. package/src/utils/UserManagerUtil/UserManagerUtil.ts +39 -0
  728. package/src/utils/UserManagerUtil/index.ts +1 -0
  729. package/src/utils/ValidationUtil/ValidationUtil.test.ts +61 -0
  730. package/src/utils/ValidationUtil/ValidationUtil.ts +56 -0
  731. package/src/utils/ValidationUtil/index.ts +1 -0
  732. package/dist/environment.d.ts +0 -54
  733. package/dist/index.d.ts +0 -16074
  734. /package/{dist → src/@types}/mui.d.ts +0 -0
  735. /package/{dist → src/@types}/ui.d.ts +0 -0
  736. /package/{dist → src/@types}/vite-env.d.ts +0 -0
  737. /package/{dist → src/@types}/yup.d.ts +0 -0
  738. /package/{dist → src}/locale/en.json +0 -0
  739. /package/{dist → src}/locale/nl.json +0 -0
@@ -0,0 +1 @@
1
+ export * from './EpiUploadUtil';
@@ -0,0 +1,22 @@
1
+ import { FileCompression } from '../../api';
2
+
3
+ export class FileUtil {
4
+ public static getReadableFileSize(sizeInBytes: number): string {
5
+ if (sizeInBytes < 1024) {
6
+ return `${sizeInBytes} B`;
7
+ } else if (sizeInBytes < 1024 * 1024) {
8
+ return `${(sizeInBytes / 1024).toFixed(2)} KB`;
9
+ } else if (sizeInBytes < 1024 * 1024 * 1024) {
10
+ return `${(sizeInBytes / (1024 * 1024)).toFixed(2)} MB`;
11
+ }
12
+ return `${(sizeInBytes / (1024 * 1024 * 1024)).toFixed(2)} GB`;
13
+ }
14
+
15
+ public static getFileCompressionFromFileName(fileName: string): FileCompression {
16
+ const lowerFileName = fileName.toLowerCase();
17
+ if (lowerFileName.endsWith('.gz') || lowerFileName.endsWith('.gzip')) {
18
+ return FileCompression.GZIP;
19
+ }
20
+ return FileCompression.NONE;
21
+ }
22
+ }
@@ -0,0 +1 @@
1
+ export * from './FileUtil';
@@ -0,0 +1,36 @@
1
+ import {
2
+ describe,
3
+ it,
4
+ expect,
5
+ } from 'vitest';
6
+ import type {
7
+ FieldErrorsImpl,
8
+ DeepRequired,
9
+ } from 'react-hook-form';
10
+
11
+ import { FormUtil } from './FormUtil';
12
+
13
+ describe('FormUtil', () => {
14
+ describe('getFieldErrorMessage', () => {
15
+ it('should return the error message for the given field name', () => {
16
+ const fieldErrors: Partial<FieldErrorsImpl<DeepRequired<{ name: string }>>> = {
17
+ name: { message: 'Name is required', type: 'required' },
18
+ };
19
+
20
+ const errorMessage = FormUtil.getFieldErrorMessage(fieldErrors, 'name');
21
+ expect(errorMessage).toBe('Name is required');
22
+ });
23
+
24
+ it('should return null if there is no error message for the given field name', () => {
25
+ const fieldErrors: Partial<FieldErrorsImpl<DeepRequired<{ name: string }>>> = {};
26
+
27
+ const errorMessage = FormUtil.getFieldErrorMessage(fieldErrors, 'name');
28
+ expect(errorMessage).toBeNull();
29
+ });
30
+
31
+ it('should return null if the fieldErrors object is undefined', () => {
32
+ const errorMessage = FormUtil.getFieldErrorMessage(undefined, 'name');
33
+ expect(errorMessage).toBeNull();
34
+ });
35
+ });
36
+ });
@@ -0,0 +1,63 @@
1
+ import type {
2
+ FieldValues,
3
+ FieldErrorsImpl,
4
+ DeepRequired,
5
+ } from 'react-hook-form';
6
+ import {
7
+ parseISO,
8
+ isValid,
9
+ } from 'date-fns';
10
+ import type { TFunction } from 'i18next';
11
+
12
+ import type { FormFieldDefinition } from '../../models/form';
13
+ import { FORM_FIELD_DEFINITION_TYPE } from '../../models/form';
14
+
15
+ export class FormUtil {
16
+ public static getFieldErrorMessage<TFormFields extends FieldValues>(fieldErrors: Partial<FieldErrorsImpl<DeepRequired<TFormFields>>>, fieldName: string): string {
17
+ const fieldError = fieldErrors?.[fieldName];
18
+ return fieldError?.message as string || null;
19
+ }
20
+
21
+ public static createBooleanOptions(t: TFunction<'translation', undefined>): { label: string; value: boolean }[] {
22
+ return [
23
+ { value: true, label: t`Yes` }, // t`Yes`
24
+ { value: false, label: t`No` }, // t`No`
25
+ ];
26
+ }
27
+
28
+ public static createFormValues<TFormFields extends FieldValues, TData = TFormFields>(formFieldDefinitions: FormFieldDefinition<TFormFields>[], item: TData): TFormFields {
29
+ const itemValues: { [key: string]: unknown } = {};
30
+ formFieldDefinitions.forEach(formFieldDefinition => {
31
+ switch (formFieldDefinition.definition) {
32
+ case FORM_FIELD_DEFINITION_TYPE.TEXTFIELD:
33
+ case FORM_FIELD_DEFINITION_TYPE.RICH_TEXT:
34
+ case FORM_FIELD_DEFINITION_TYPE.BOOLEAN:
35
+ itemValues[formFieldDefinition.name] = item?.[formFieldDefinition.name as unknown as keyof typeof item] ?? '';
36
+ break;
37
+ case FORM_FIELD_DEFINITION_TYPE.TRANSFER_LIST:
38
+ itemValues[formFieldDefinition.name] = item?.[formFieldDefinition.name as unknown as keyof typeof item] ?? [] as TFormFields[keyof TFormFields];
39
+ break;
40
+ case FORM_FIELD_DEFINITION_TYPE.AUTOCOMPLETE:
41
+ case FORM_FIELD_DEFINITION_TYPE.SELECT:
42
+ if (formFieldDefinition.multiple) {
43
+ itemValues[formFieldDefinition.name] = item?.[formFieldDefinition.name as unknown as keyof typeof item] ?? [] as TFormFields[keyof TFormFields];
44
+ } else {
45
+ itemValues[formFieldDefinition.name] = item?.[formFieldDefinition.name as unknown as keyof typeof item] ?? null;
46
+ }
47
+ break;
48
+ case FORM_FIELD_DEFINITION_TYPE.DATE:
49
+ try {
50
+ const dateValue = parseISO(item?.[formFieldDefinition.name as unknown as keyof typeof item] as string);
51
+ itemValues[formFieldDefinition.name] = isValid(dateValue) ? dateValue as TFormFields[keyof TFormFields] : null;
52
+ } catch (_error) {
53
+ itemValues[formFieldDefinition.name] = null;
54
+ }
55
+ break;
56
+ default:
57
+ break;
58
+ }
59
+ });
60
+ return itemValues as unknown as TFormFields;
61
+ }
62
+
63
+ }
@@ -0,0 +1 @@
1
+ export * from './FormUtil';
@@ -0,0 +1,54 @@
1
+ import type { MenuItemData } from '../../models/nestedMenu';
2
+
3
+ export class MenuDataUtil {
4
+
5
+ public static isMenuItemData(value: unknown): value is MenuItemData {
6
+ if (typeof value !== 'object' || value === null) {
7
+ return false;
8
+ }
9
+
10
+ const item = value as Record<string, unknown>;
11
+
12
+ if (item.uid !== undefined && typeof item.uid !== 'string') {
13
+ return false;
14
+ }
15
+
16
+ if (item.label !== undefined && typeof item.label !== 'string') {
17
+ return false;
18
+ }
19
+
20
+ if (item.callback !== undefined && typeof item.callback !== 'function') {
21
+ return false;
22
+ }
23
+
24
+ if (item.items !== undefined && (!Array.isArray(item.items) || !item.items.every(MenuDataUtil.isMenuItemData))) {
25
+ return false;
26
+ }
27
+
28
+ if (item.disabled !== undefined && typeof item.disabled !== 'boolean') {
29
+ return false;
30
+ }
31
+
32
+ if (item.divider !== undefined && typeof item.divider !== 'boolean') {
33
+ return false;
34
+ }
35
+
36
+ if (item.autoCloseDisabled !== undefined && typeof item.autoCloseDisabled !== 'boolean') {
37
+ return false;
38
+ }
39
+
40
+ if (item.active !== undefined && typeof item.active !== 'boolean') {
41
+ return false;
42
+ }
43
+
44
+ if (item.checked !== undefined && !['true', 'false', 'mixed'].includes(item.checked as string)) {
45
+ return false;
46
+ }
47
+
48
+ return true;
49
+ }
50
+
51
+ public static isMenuItemDataArray(value: unknown): value is MenuItemData[] {
52
+ return Array.isArray(value) && value.every(MenuDataUtil.isMenuItemData);
53
+ }
54
+ }
@@ -0,0 +1 @@
1
+ export * from './MenuDataUtil';
@@ -0,0 +1,187 @@
1
+ import {
2
+ describe,
3
+ it,
4
+ expect,
5
+ } from 'vitest';
6
+ import Decimal from 'decimal.js';
7
+
8
+ import type { TreeNode } from '../../models/tree';
9
+
10
+ import { NewickUtil } from './NewickUtil';
11
+
12
+ describe('NewickUtil', () => {
13
+ describe('parseNewick', () => {
14
+ it('should parse a simple Newick string', () => {
15
+ const newick = '(A,B,(C,D));';
16
+ const expectedTree: Partial<TreeNode> = {
17
+ children: [
18
+ {
19
+ name: 'A',
20
+ size: 1,
21
+ maxBranchLength: new Decimal(0),
22
+ subTreeNames: [],
23
+ subTreeLeaveNames: [
24
+ 'A',
25
+ ],
26
+ },
27
+ {
28
+ name: 'B',
29
+ size: 1,
30
+ maxBranchLength: new Decimal(0),
31
+ subTreeNames: [],
32
+ subTreeLeaveNames: [
33
+ 'B',
34
+ ],
35
+ },
36
+ {
37
+ children: [
38
+ {
39
+ name: 'C',
40
+ size: 1,
41
+ maxBranchLength: new Decimal(0),
42
+ subTreeNames: [],
43
+ subTreeLeaveNames: [
44
+ 'C',
45
+ ],
46
+ },
47
+ {
48
+ name: 'D',
49
+ size: 1,
50
+ maxBranchLength: new Decimal(0),
51
+ subTreeNames: [],
52
+ subTreeLeaveNames: [
53
+ 'D',
54
+ ],
55
+ },
56
+ ],
57
+ size: 2,
58
+ subTreeNames: [],
59
+ subTreeLeaveNames: [
60
+ 'C',
61
+ 'D',
62
+ ],
63
+ maxBranchLength: new Decimal(0),
64
+ },
65
+ ],
66
+ size: 4,
67
+ subTreeNames: [],
68
+ subTreeLeaveNames: [
69
+ 'A',
70
+ 'B',
71
+ 'C',
72
+ 'D',
73
+ ],
74
+ name: 'Root',
75
+ branchLength: new Decimal(0),
76
+ maxBranchLength: new Decimal(0),
77
+ };
78
+
79
+ const tree = NewickUtil.parse(newick);
80
+ expect(tree).toEqual(expectedTree);
81
+ });
82
+
83
+ it('should handle branch lengths', () => {
84
+ const newick = '(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);';
85
+ const expectedTree: Partial<TreeNode> = {
86
+ children: [
87
+ {
88
+ name: 'A',
89
+ branchLength: new Decimal('0.1'),
90
+ subTreeNames: [],
91
+ subTreeLeaveNames: [
92
+ 'A',
93
+ ],
94
+ maxBranchLength: new Decimal('0.1'),
95
+ size: 1,
96
+ },
97
+ {
98
+ name: 'B',
99
+ branchLength: new Decimal('0.2'),
100
+ subTreeNames: [],
101
+ subTreeLeaveNames: [
102
+ 'B',
103
+ ],
104
+ maxBranchLength: new Decimal('0.2'),
105
+ size: 1,
106
+ },
107
+ {
108
+ children: [
109
+ {
110
+ name: 'C',
111
+ branchLength: new Decimal('0.3'),
112
+ subTreeNames: [],
113
+ subTreeLeaveNames: [
114
+ 'C',
115
+ ],
116
+ maxBranchLength: new Decimal('0.3'),
117
+ size: 1,
118
+ },
119
+ {
120
+ name: 'D',
121
+ branchLength: new Decimal('0.4'),
122
+ subTreeNames: [],
123
+ subTreeLeaveNames: [
124
+ 'D',
125
+ ],
126
+ maxBranchLength: new Decimal('0.4'),
127
+ size: 1,
128
+ },
129
+ ],
130
+ size: 2,
131
+ subTreeNames: [
132
+ 'C',
133
+ 'D',
134
+ ],
135
+ subTreeLeaveNames: [
136
+ 'C',
137
+ 'D',
138
+ ],
139
+ branchLength: new Decimal('0.5'),
140
+ maxBranchLength: new Decimal('0.9'),
141
+ name: 'Generated-7225787341756924',
142
+ },
143
+ ],
144
+ size: 4,
145
+ subTreeNames: [
146
+ 'C',
147
+ 'D',
148
+ ],
149
+ subTreeLeaveNames: [
150
+ 'A',
151
+ 'B',
152
+ 'C',
153
+ 'D',
154
+ ],
155
+ name: 'Root',
156
+ branchLength: new Decimal('0'),
157
+ maxBranchLength: new Decimal('0.9'),
158
+ };
159
+ const tree = NewickUtil.parse(newick);
160
+ expect(tree).toEqual(expectedTree);
161
+ });
162
+
163
+ it('should handle a single leaf (no parentheses)', () => {
164
+ const newick = 'A;';
165
+ const expectedTree: Partial<TreeNode> = {
166
+ branchLength: new Decimal(0),
167
+ maxBranchLength: new Decimal(0),
168
+ name: 'Root',
169
+ };
170
+
171
+ const tree = NewickUtil.parse(newick);
172
+ expect(tree).toEqual(expectedTree);
173
+ });
174
+ });
175
+
176
+ describe('getSortedNames', () => {
177
+ it('should return the name for a leaf node', () => {
178
+ const leaf: TreeNode = { name: 'A' };
179
+ expect(NewickUtil.getSortedNames(leaf)).toEqual(['A']);
180
+ });
181
+
182
+ it('should return leaf names in depth-first order for a tree', () => {
183
+ const tree = NewickUtil.parse('(A,B,(C,D));');
184
+ expect(NewickUtil.getSortedNames(tree)).toEqual(['A', 'B', 'C', 'D']);
185
+ });
186
+ });
187
+ });
@@ -0,0 +1,69 @@
1
+ import Decimal from 'decimal.js';
2
+ import sum from 'lodash/sum';
3
+
4
+ import { StringUtil } from '../StringUtil';
5
+ import type { TreeNode } from '../../models/tree';
6
+
7
+ export class NewickUtil {
8
+ public static parse(newick: string): TreeNode {
9
+ const ancestors: Array<Partial<TreeNode>> = [];
10
+ let tree: Partial<TreeNode> = {};
11
+ const tokens = newick.split(/(;|\(|\)|,|:)/).map(x => x.trim()).filter(x => x);
12
+ for (let i = 0; i < tokens.length; i++) {
13
+ const token = tokens[i];
14
+ const subtree: Partial<TreeNode> = {};
15
+ const x = tokens[i - 1];
16
+ switch (token) {
17
+ case '(': // new children
18
+ tree.children = [subtree];
19
+ ancestors.push(tree);
20
+ tree = subtree;
21
+ break;
22
+ case ',': // another branch
23
+ ancestors[ancestors.length - 1].children.push(subtree);
24
+ tree = subtree;
25
+ break;
26
+ case ')': // optional name next
27
+ tree = ancestors.pop();
28
+ tree.children.forEach(child => {
29
+ if (!child.children) {
30
+ child.size = 1;
31
+ child.maxBranchLength = new Decimal(child.branchLength ?? 0);
32
+ child.subTreeLeaveNames = [child.name];
33
+ child.subTreeNames = child.subTreeNames ?? [];
34
+ }
35
+ });
36
+ tree.size = sum(tree.children.map(child => child.size));
37
+ tree.subTreeNames = tree.children.map(child => child.subTreeNames).flat().filter(n => n);
38
+ tree.subTreeLeaveNames = tree.children.map(child => child.subTreeLeaveNames).flat().filter(n => n);
39
+ tree.maxBranchLength = Decimal.max(...tree.children.map(child => child.maxBranchLength));
40
+ break;
41
+ case ':': // optional length next
42
+ break;
43
+ case ';': // end of tree, nothing to do
44
+ break;
45
+ default:
46
+ if (x === ')' || x === '(' || x === ',') {
47
+ tree.name = token;
48
+ } else if (x === ':') {
49
+ tree.branchLength = new Decimal(token);
50
+ tree.subTreeNames = (tree.children ?? []).map(child => [child.name, ...child.subTreeNames]).flat().filter(n => n);
51
+ tree.subTreeLeaveNames = (tree.children ?? []).map(child => child.subTreeLeaveNames).flat().filter(n => n);
52
+ tree.maxBranchLength = tree.branchLength.add(tree.children?.length ? Decimal.max(...tree.children.map(child => child.maxBranchLength)) : 0);
53
+ tree.name = tree.name || `Generated-${StringUtil.createHash(tree.subTreeNames.join(','))}`;
54
+ }
55
+ }
56
+ }
57
+ tree.branchLength = tree.branchLength ?? new Decimal(0);
58
+ tree.maxBranchLength = tree.children?.length ? Decimal.max(...tree.children.map(child => child.maxBranchLength)) : new Decimal(0);
59
+ tree.name = 'Root';
60
+ return tree;
61
+ }
62
+
63
+ public static getSortedNames(node: TreeNode): string[] {
64
+ return [
65
+ ...(node.children ?? []).map(child => NewickUtil.getSortedNames(child)).flat(),
66
+ ...(!node.children ? [node.name] : []),
67
+ ];
68
+ }
69
+ }
@@ -0,0 +1 @@
1
+ export * from './NewickUtil';
@@ -0,0 +1,28 @@
1
+ import { t } from 'i18next';
2
+ import type { ReactElement } from 'react';
3
+
4
+ import { AxiosUtil } from '../AxiosUtil';
5
+
6
+ export class NotificationUtil {
7
+ public static wrapErrorNotificationMessage(message: string | ReactElement, error: unknown): string | ReactElement {
8
+ if (AxiosUtil.isAxiosForbiddenError(error)) {
9
+ message = t('{{message}} - You do not have permission to perform this action.', { message });
10
+ }
11
+ if (AxiosUtil.isAxiosUnauthorizedError(error)) {
12
+ message = t('{{message}} - You are not logged in.', { message });
13
+ }
14
+ if (AxiosUtil.isAxiosNotFoundError(error)) {
15
+ message = t('{{message}} - The item does not exist.', { message });
16
+ }
17
+ if (AxiosUtil.isAxiosBadRequestError(error)) {
18
+ message = t('{{message}} - Bad request. The input data was not correct.', { message });
19
+ }
20
+ if (AxiosUtil.isAxiosConflictError(error)) {
21
+ message = t('{{message}} - Conflict. The request could not be completed due to a conflict with the current state of the resource.', { message });
22
+ }
23
+ if (AxiosUtil.isAxiosInternalServerError(error)) {
24
+ message = t('{{message}} - Internal Server Error. Please try again later.', { message });
25
+ }
26
+ return message;
27
+ }
28
+ }
@@ -0,0 +1 @@
1
+ export * from './NotificationUtil';
@@ -0,0 +1,113 @@
1
+ import {
2
+ describe,
3
+ it,
4
+ expect,
5
+ } from 'vitest';
6
+
7
+ import { NumberUtil } from './NumberUtil';
8
+
9
+ describe('NumberUtil', () => {
10
+ describe('toStringWithPrecision', () => {
11
+ it('should return a string with the correct precision', () => {
12
+ expect(NumberUtil.toStringWithPrecision(123.456, 0.01)).toBe('123.45');
13
+ expect(NumberUtil.toStringWithPrecision(123.4, 0.01)).toBe('123.40');
14
+ expect(NumberUtil.toStringWithPrecision(123, 0.01)).toBe('123.00');
15
+ expect(NumberUtil.toStringWithPrecision(123.456, 0.1)).toBe('123.4');
16
+ expect(NumberUtil.toStringWithPrecision(123.456, 1)).toBe('123');
17
+ });
18
+
19
+ it('should return an empty string if the value is not a number', () => {
20
+ expect(NumberUtil.toStringWithPrecision(NaN, 0.01)).toBe('');
21
+ expect(NumberUtil.toStringWithPrecision(undefined as unknown as number, 0.01)).toBe('');
22
+ expect(NumberUtil.toStringWithPrecision(null as unknown as number, 0.01)).toBe('');
23
+ });
24
+
25
+ it('should handle cases where the base has no decimal part', () => {
26
+ expect(NumberUtil.toStringWithPrecision(123.456, 1)).toBe('123');
27
+ expect(NumberUtil.toStringWithPrecision(123.456, 10)).toBe('123');
28
+ });
29
+ });
30
+
31
+
32
+ describe('parse', () => {
33
+ it('should parse decimal formats with dots', () => {
34
+ expect(NumberUtil.parse('1.0')).toBe(1.0);
35
+ expect(NumberUtil.parse('1.5')).toBe(1.5);
36
+ expect(NumberUtil.parse('0.001')).toBe(0.001);
37
+ });
38
+
39
+ it('should parse decimal formats with commas', () => {
40
+ expect(NumberUtil.parse('1,0')).toBe(1.0);
41
+ expect(NumberUtil.parse('1,5')).toBe(1.5);
42
+ expect(NumberUtil.parse('123,456')).toBe(123.456);
43
+ expect(NumberUtil.parse('0,001')).toBe(0.001);
44
+ });
45
+
46
+ it('should parse thousands separators correctly', () => {
47
+ expect(NumberUtil.parse('1.000')).toBe(1);
48
+ expect(NumberUtil.parse('1,000')).toBe(1);
49
+ expect(NumberUtil.parse('123,456')).toBe(123.456);
50
+ expect(NumberUtil.parse('1.234.567')).toBe(1234567);
51
+ expect(NumberUtil.parse('1,234,567')).toBe(1234567);
52
+ expect(NumberUtil.parse('1,234,567.5')).toBe(1234567.5);
53
+ expect(NumberUtil.parse('1 234.567')).toBe(1234.567);
54
+ expect(NumberUtil.parse('1 234 567')).toBe(1234567);
55
+ expect(NumberUtil.parse('1 234 567.5')).toBe(1234567.5);
56
+ });
57
+
58
+ it('should parse mixed formats with thousands and decimals', () => {
59
+ expect(NumberUtil.parse('1,234.56')).toBe(1234.56);
60
+ expect(NumberUtil.parse('1.234,56')).toBe(1234.56);
61
+ expect(NumberUtil.parse('123,456.789')).toBe(123456.789);
62
+ expect(NumberUtil.parse('123.456,789')).toBe(123456.789);
63
+ expect(NumberUtil.parse('123 456.789')).toBe(123456.789);
64
+ expect(NumberUtil.parse('123 456,789')).toBe(123456.789);
65
+ });
66
+
67
+ it('should parse negative numbers', () => {
68
+ expect(NumberUtil.parse('-1.0')).toBe(-1.0);
69
+ expect(NumberUtil.parse('-1,0')).toBe(-1.0);
70
+ expect(NumberUtil.parse('-123.456')).toBe(-123.456);
71
+ expect(NumberUtil.parse('-1,234.56')).toBe(-1234.56);
72
+ expect(NumberUtil.parse('-1,000')).toBe(-1);
73
+ });
74
+
75
+ it('should parse whole numbers without separators', () => {
76
+ expect(NumberUtil.parse('123')).toBe(123);
77
+ expect(NumberUtil.parse('0')).toBe(0);
78
+ expect(NumberUtil.parse('999')).toBe(999);
79
+ expect(NumberUtil.parse('-456')).toBe(-456);
80
+ });
81
+
82
+ it('should handle whitespace', () => {
83
+ expect(NumberUtil.parse(' 123.45 ')).toBe(123.45);
84
+ expect(NumberUtil.parse(' 1,234.56 ')).toBe(1234.56);
85
+ expect(NumberUtil.parse('\t123\t')).toBe(123);
86
+ });
87
+
88
+ it('should handle edge cases and invalid inputs', () => {
89
+ expect(NumberUtil.parse('')).toBeNaN();
90
+ expect(NumberUtil.parse(' ')).toBeNaN();
91
+ expect(NumberUtil.parse('abc')).toBeNaN();
92
+ expect(NumberUtil.parse('12.34.56.78')).toBe(12345678);
93
+ expect(NumberUtil.parse('1,2,3,4')).toBe(1234);
94
+ });
95
+
96
+ it('should handle type safety', () => {
97
+ expect(NumberUtil.parse(null)).toBeNaN();
98
+ expect(NumberUtil.parse(undefined)).toBeNaN();
99
+ expect(NumberUtil.parse(123)).toBe(123);
100
+ });
101
+
102
+ it('should handle precision edge cases', () => {
103
+ expect(NumberUtil.parse('1.1234')).toBe(1.1234);
104
+ expect(NumberUtil.parse('1,1234')).toBe(1.1234);
105
+ expect(NumberUtil.parse('123.45,67')).toBe(12345.67);
106
+ expect(NumberUtil.parse('0.0')).toBe(0.0);
107
+ expect(NumberUtil.parse('0,0')).toBe(0.0);
108
+ expect(NumberUtil.parse(' ')).toBe(NaN);
109
+ expect(NumberUtil.parse('')).toBe(NaN);
110
+
111
+ });
112
+ });
113
+ });
@@ -0,0 +1,67 @@
1
+ import { number } from 'yup';
2
+
3
+ export class NumberUtil {
4
+ public static get yup() {
5
+ return number().typeError('');
6
+ }
7
+
8
+ public static toStringWithPrecision(value: number, base: number): string {
9
+ if (typeof value !== 'number' || !isFinite(value)) {
10
+ return '';
11
+ }
12
+ const precision = base.toString().split('.')?.[1]?.length ?? 0;
13
+ const splitValue = value.toString().split('.');
14
+
15
+ let stringValue = splitValue[0];
16
+ if (precision > 0) {
17
+ stringValue = `${stringValue}.${(splitValue[1] ?? '').padEnd(precision, '0').slice(0, precision)}`;
18
+ }
19
+ return stringValue;
20
+ }
21
+
22
+
23
+ public static parse(value: string | number): number {
24
+ if (typeof value === 'number') {
25
+ return value;
26
+ }
27
+
28
+ if (typeof value !== 'string' || value.trim() === '') {
29
+ return NaN;
30
+ }
31
+
32
+ let sanitizedValue = value
33
+ .trim()
34
+ .replace(/[^0-9,.-\s]/g, ''); // Remove all except digits, commas, periods, minus signs, and whitespace
35
+
36
+ // if multiple commas or periods exist, assume they are thousands separators and remove them
37
+ const periodMatchesLength = (sanitizedValue.match(/[.]/g) || []).length;
38
+ const commaMatchesLength = (sanitizedValue.match(/[,]/g) || []).length;
39
+ const spaceMatchesLength = (sanitizedValue.match(/[\s]/g) || []).length;
40
+
41
+ if ([periodMatchesLength, commaMatchesLength, spaceMatchesLength].filter(count => count > 1).length > 1) {
42
+ return NaN;
43
+ }
44
+
45
+ if (commaMatchesLength > 1) {
46
+ // Remove all commas if there are multiple, assuming they are thousands separators
47
+ // Note: remaining periods are treated as decimal separators
48
+ return parseFloat(sanitizedValue.replace(/[,\s]/g, ''));
49
+ }
50
+ if (spaceMatchesLength > 1) {
51
+ // Remove all whitespace if there are multiple, assuming they are thousands separators
52
+ sanitizedValue = sanitizedValue.replace(/\s/g, '');
53
+ // Note: remaining commas or periods are treated as decimal separators
54
+ return parseFloat(sanitizedValue.replace(',', '.'));
55
+ }
56
+ if (periodMatchesLength > 1) {
57
+ // Remove all periods if there are multiple, assuming they are thousands separators
58
+ sanitizedValue = sanitizedValue.replace(/[.\s]/g, '').replace(',', '.'); // Replace remaining comma with period for decimal
59
+ return parseFloat(sanitizedValue);
60
+ }
61
+
62
+ sanitizedValue = sanitizedValue.replace(/[,.\s](?=.*[,.\s])/g, '')
63
+ .replace(',', '.'); // Replace remaining comma with period for decimal
64
+
65
+ return parseFloat(sanitizedValue);
66
+ }
67
+ }
@@ -0,0 +1 @@
1
+ export * from './NumberUtil';