@platforma-sdk/ui-vue 1.42.53 → 1.43.0

package/.turbo/turbo-type-check.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/_work/platforma/platforma/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-sdk/ui-vue@1.42.53 type-check /home/runner/_work/platforma/platforma/sdk/ui-vue
+> @platforma-sdk/ui-vue@1.43.0 type-check /home/runner/_work/platforma/platforma/sdk/ui-vue
 > ts-builder types --target browser-lib
 
 ↳ vue-tsc.js --noEmit --project ./tsconfig.json

package/CHANGELOG.md

@@ -1,5 +1,19 @@
 # @platforma-sdk/ui-vue
 
+## 1.43.0
+
+### Minor Changes
+
+- d60cc17: Added support for markup highlighting with multiple sequence columns, added initial support for phylogenetic trees, revamped the MSA data generation and layout
+
+### Patch Changes
+
+- Updated dependencies [d60cc17]
+- Updated dependencies [d60cc17]
+  - @milaboratories/biowasm-tools@2.0.0
+  - @platforma-sdk/model@1.43.0
+  - @milaboratories/uikit@2.4.14
+
 ## 1.42.53
 
 ### Patch Changes

package/dist/AgGridVue/useAgGridOptions.js

@@ -41,7 +41,6 @@ import N from "../components/PlAgCellStatusTag/PlAgCellStatusTag.vue.js";
 
 
 import "../components/PlMultiSequenceAlignment/data.js";
-import "@milaboratories/biowasm-tools";
 import "canonicalize";
 import "../composition/fileContent.js";
 import "d3-format";
@@ -197,7 +196,7 @@ class R {
   }
 }
 o = new WeakMap();
-function pt(r) {
+function ut(r) {
   const t = C(), e = y(() => {
     var u;
     const s = {
@@ -251,6 +250,6 @@ function pt(r) {
   }, { deep: !0, immediate: !0 }), { gridOptions: a, gridApi: t };
 }
 export {
-  pt as useAgGridOptions
+  ut as useAgGridOptions
 };
 //# sourceMappingURL=useAgGridOptions.js.map

package/dist/AgGridVue/useAgGridOptions.js.map

@@ -1 +1 @@
-{"version":3,"file":"useAgGridOptions.js","sources":["../../src/AgGridVue/useAgGridOptions.ts"],"sourcesContent":["/* eslint-disable @typescript-eslint/no-explicit-any */\nimport type { ColGroupDef, GridApi, GridOptions, GridReadyEvent, ICellRendererParams, RowSelectionOptions, ValueSetterParams } from 'ag-grid-enterprise';\nimport type { Component } from 'vue';\nimport { computed, shallowRef, watch } from 'vue';\nimport { AgGridTheme } from '../aggrid';\nimport { autoSizeRowNumberColumn, makeRowNumberColDef, PlAgOverlayLoading, type PlAgOverlayLoadingParams } from '../components/PlAgDataTable';\nimport { PlAgOverlayNoRows } from '../components/PlAgDataTable';\nimport { createAgGridColDef, type ColDefExtended } from './createAgGridColDef';\nimport { whenever } from '@vueuse/core';\nimport { PlAgCellFile } from '../components/PlAgCellFile';\nimport { PlAgChartStackedBarCell } from '../components/PlAgChartStackedBarCell';\nimport { PlAgChartHistogramCell } from '../components/PlAgChartHistogramCell';\nimport type { ImportFileHandle } from '@platforma-sdk/model';\nimport type { ImportProgress } from '@platforma-sdk/model';\nimport { PlAgCellStatusTag } from '../components/PlAgCellStatusTag';\ninterface GridOptionsExtended<TData = any> extends Omit<GridOptions<TData>, 'columnDefs' | 'loadingOverlayComponentParams'> {\n  /**\n   * Array of Column / Column Group definitions.\n   */\n  columnDefs?: (ColDefExtended<TData> | ColGroupDef<TData>)[] | null;\n  /**\n   * Show row numbers column\n   */\n  rowNumbersColumn?: boolean;\n  /**\n   * Loading overlay text\n   */\n  loadingText?: string;\n  /**\n   * Not ready overlay (No datasource). Takes priority over \"loading\"\n   */\n  notReady?: boolean;\n  /**\n   * \"No datasource\" by default\n   */\n  notReadyText?: string;\n  /**\n   * Use \"transparent\" to make table headers visible below the loading layer (experimental)\n   */\n  loadingOverlayType?: 'transparent' | undefined;\n  /**\n   * Override standard 'Empty' text for the \"no rows\" overlay\n   */\n  noRowsText?: string;\n  /**\n   * @deprecated Use loading, notReady, loadingText, loadingOverlayType instead\n   */\n  loadingOverlayComponentParams?: never;\n}\n\n// @TODO (super simple builder for now)\nclass Builder<TData> {\n  #options: GridOptionsExtended<TData> = {};\n\n  public options(options: GridOptionsExtended<TData>) {\n    this.#options = Object.assign({}, this.#options, options);\n    return this;\n  }\n\n  private get columnDefs() {\n    return this.#options.columnDefs ?? 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option key\n   * @param value - option value\n   * @returns this\n   */\n  public setOption<K extends keyof GridOptionsExtended<TData>>(key: K, value: GridOptionsExtended<TData>[K]) {\n    this.#options[key] = value;\n    return this;\n  }\n\n  /**\n   * Add an extended column definition\n   * @param def - column definition\n   * @returns this\n   */\n  public column<TValue = any>(def: ColDefExtended<TData, TValue>) {\n    this.#options.columnDefs = [...this.columnDefs, def];\n    return this;\n  }\n\n  /**\n   * Show row numbers column\n   * @param show - show or hide row numbers column\n   * @returns this\n   */\n  public columnRowNumbers(show: boolean = true) {\n    this.#options.rowNumbersColumn = show;\n    return this;\n  }\n\n  /**\n   * Add a file input column\n   * @param def - column definition\n   * @param cb - callback to set params for the file input cell renderer\n   * @returns this\n   */\n  public columnFileInput<TValue = any>(\n    def: ColDefExtended<TData, TValue> & {\n      /**\n       * Allowed file extensions (like ['fastq.gz'])\n       */\n      extensions?: string[];\n      /**\n       * The resolveProgress function is an optional input parameter for the component\n       * that allows tracking the file upload progress in real-time.\n       * By passing resolveProgress, you can ensure that the component\n       * displays accurate progress values for each file as they upload.\n       * How to use it in AgGrid\n       * cellRendererParams: {\n       *  resolveProgress: (cellData) => {\n       *    const progresses = app.progresses;\n       *    if (!cellData.value.importFileHandle) return undefined;\n       *    else return progresses[cellData.value.importFileHandle];\n       *  }\n       * }\n       */\n      resolveImportProgress?: (cellData: ICellRendererParams<TData, TValue>) => ImportProgress | undefined;\n\n      /**\n       * The resolveFileHandle function is an optional input parameter for the component\n       * that allows tracking the file upload progress in real-time.\n       * By passing resolveFileHandle, you can ensure that the component\n       * displays accurate progress values for each file as they upload.\n       * How to use it in AgGrid\n       * cellRendererParams: {\n       *  resolveFileHandle: (cellData) => {\n       *    return cellData.value.importFileHandle;\n       *  }\n       * }\n       */\n      resolveImportFileHandle?: (cellData: ICellRendererParams<TData, TValue>) => ImportFileHandle | undefined;\n\n      setImportFileHandle?: (d: ValueSetterParams<TData, ImportFileHandle | undefined>) => void;\n    }) {\n    return this.column(Object.assign({\n      cellRenderer: 'PlAgCellFile',\n      headerComponentParams: { type: 'File' },\n      cellStyle: { padding: 0 },\n      valueSetter: (d: ValueSetterParams<TData, ImportFileHandle | undefined>) => {\n        def.setImportFileHandle?.(d);\n        return true;\n      },\n      cellRendererSelector: (cellData: ICellRendererParams<TData, TValue>) => {\n        return {\n          component: 'PlAgCellFile',\n          params: {\n            extensions: def.extensions,\n            value: def.resolveImportFileHandle?.(cellData),\n            resolveProgress: () => {\n              return def.resolveImportProgress?.(cellData);\n            },\n          },\n        };\n      },\n    }, def));\n  }\n\n  public build() {\n    return this.#options;\n  }\n}\n\n// Simple helper to use like column<string> in grid options literal\ntype ColumnFunc<TData> = <TValue>(def: ColDefExtended<TData, TValue>) => ColDefExtended<TData, TValue>;\n\n/**\n * Returns a set of Ag Grid options along with a reference to the Ag Grid API.\n * (This is a fast prototype)\n *\n * @example\n * ```ts\n * const { gridOptions, gridApi } = useAgGridOptions(() => ({\n *   // custom grid options here\n * }));\n *\n * // Usage in a template (v-bind is required!)\n * <template>\n *   <AgGridVue :style=\"{ height: '100%' }\" v-bind=\"gridOptions\" />\n * </template>\n * ```\n */\nexport function useAgGridOptions<TData>(\n  factory: (context: { builder: Builder<TData>; column: ColumnFunc<TData> }) => Builder<TData> | GridOptionsExtended<TData>,\n) {\n  const gridApi = shallowRef<GridApi>();\n\n  const extOptions = computed<GridOptionsExtended>(() => {\n    const def: GridOptionsExtended<TData> = {\n      theme: AgGridTheme,\n      loadingOverlayComponent: PlAgOverlayLoading,\n      noRowsOverlayComponent: PlAgOverlayNoRows,\n      onGridReady: (e: GridReadyEvent) => {\n        gridApi.value = e.api;\n        autoSizeRowNumberColumn(e.api); // @TODO\n      },\n    };\n\n    const column = <TValue>(def: ColDefExtended<TData, TValue>) => {\n      return def;\n    };\n\n    const result = factory({ builder: new Builder(), column });\n\n    const options = Object.assign({}, def, result instanceof Builder ? result.build() : result);\n\n    if (options.rowNumbersColumn) {\n      options.columnDefs = [makeRowNumberColDef(), ...(options.columnDefs ?? 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notReadyText: options.notReadyText,\n        overlayType: options.loadingOverlayType,\n      } satisfies PlAgOverlayLoadingParams,\n    };\n  });\n\n  whenever(() => extOptions.value.rowNumbersColumn, () => {\n    if (gridApi.value) {\n      autoSizeRowNumberColumn(gridApi.value);\n    }\n  });\n\n  watch([\n    () => extOptions.value.notReady,\n    () => extOptions.value.loading,\n  ], ([notReady, loading]) => {\n    const loadingOverlayComponentParams = {\n      notReady,\n      // we probably don't need to update the parameters below\n      notReadyText: extOptions.value.notReadyText,\n      overlayType: extOptions.value.loadingOverlayType,\n      loadingText: extOptions.value.loadingText,\n    } satisfies PlAgOverlayLoadingParams;\n\n    // Hack to apply loadingOverlayComponentParams\n    gridApi.value?.updateGridOptions({\n      loading: !loading,\n      loadingOverlayComponentParams,\n    });\n\n    gridApi.value?.updateGridOptions({\n      loading,\n      loadingOverlayComponentParams,\n    });\n  }, { deep: true, immediate: true });\n\n  return { gridOptions, gridApi 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+{"version":3,"file":"useAgGridOptions.js","sources":["../../src/AgGridVue/useAgGridOptions.ts"],"sourcesContent":["/* eslint-disable @typescript-eslint/no-explicit-any */\nimport type { ColGroupDef, GridApi, GridOptions, GridReadyEvent, ICellRendererParams, RowSelectionOptions, ValueSetterParams } from 'ag-grid-enterprise';\nimport type { Component } from 'vue';\nimport { computed, shallowRef, watch } from 'vue';\nimport { AgGridTheme } from '../aggrid';\nimport { autoSizeRowNumberColumn, makeRowNumberColDef, PlAgOverlayLoading, type PlAgOverlayLoadingParams } from '../components/PlAgDataTable';\nimport { PlAgOverlayNoRows } from '../components/PlAgDataTable';\nimport { createAgGridColDef, type ColDefExtended } from './createAgGridColDef';\nimport { whenever } from '@vueuse/core';\nimport { PlAgCellFile } from '../components/PlAgCellFile';\nimport { PlAgChartStackedBarCell } from '../components/PlAgChartStackedBarCell';\nimport { PlAgChartHistogramCell } from '../components/PlAgChartHistogramCell';\nimport type { ImportFileHandle } from '@platforma-sdk/model';\nimport type { ImportProgress } from '@platforma-sdk/model';\nimport { PlAgCellStatusTag } from '../components/PlAgCellStatusTag';\ninterface GridOptionsExtended<TData = any> extends Omit<GridOptions<TData>, 'columnDefs' | 'loadingOverlayComponentParams'> {\n  /**\n   * Array of Column / Column Group definitions.\n   */\n  columnDefs?: (ColDefExtended<TData> | ColGroupDef<TData>)[] | null;\n  /**\n   * Show row numbers column\n   */\n  rowNumbersColumn?: boolean;\n  /**\n   * Loading overlay text\n   */\n  loadingText?: string;\n  /**\n   * Not ready overlay (No datasource). 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[];\n  }\n\n  /**\n   * Set default column definition\n   * @param def - column definition\n   * @returns this\n   */\n  public setDefaultColDef(def: ColDefExtended<TData>) {\n    this.#options.defaultColDef = def;\n    return this;\n  }\n\n  /**\n   * Show loading overlay\n   * @param loading\n   * @returns this\n   */\n  public setLoading(loading?: boolean) {\n    this.#options.loading = loading;\n    return this;\n  }\n\n  /**\n   * Set loading overlay custom text (default is \"Loading\")\n   * @param loadingText\n   * @returns this\n   */\n  public setLoadingText(loadingText?: string) {\n    this.#options.loadingText = loadingText;\n    return this;\n  }\n\n  /**\n   * Show \"not ready overlay\n   * @param notReady\n   * @returns this\n   */\n  public setNotReady(notReady?: boolean) {\n    this.#options.notReady = notReady;\n    return this;\n  }\n\n  /**\n   * Set loading overlay type\n   * @param type\n   * @returns this\n   */\n  public setLoadingOverlayType(type?: 'transparent') {\n    this.#options.loadingOverlayType = type;\n    return this;\n  }\n\n  /**\n   * Set \"not ready\" text\n   * @param notReadyText\n   * @returns this\n   */\n  public setNotReadyText(notReadyText?: string) {\n    this.#options.notReadyText = notReadyText;\n    return this;\n  }\n\n  /**\n   * Set \"no rows\" text when there are no rows (default is \"Empty\")\n   * @param noRowsText\n   * @returns this\n   */\n  public setNoRowsText(noRowsText?: string) {\n    this.#options.noRowsText = noRowsText;\n    return this;\n  }\n\n  /**\n   * Set row selection options\n   * @param rowSelection\n   * @returns this\n   */\n  public setRowSelection(rowSelection?: RowSelectionOptions) {\n    this.#options.rowSelection = rowSelection;\n    return this;\n  }\n\n  /**\n   * Set row data\n   * @param rowData\n   * @returns this\n   */\n  public setRowData(rowData?: TData[]) {\n    this.#options.rowData = rowData;\n    return this;\n  }\n\n  /**\n   * Set components\n   * @param components\n   * @returns this\n   */\n  public setComponents(components?: Record<string, Component>) {\n    this.#options.components = components;\n    return this;\n  }\n\n  /**\n   * Set an option\n   * @param key - option key\n   * @param value - option value\n   * @returns this\n   */\n  public setOption<K extends keyof GridOptionsExtended<TData>>(key: K, value: GridOptionsExtended<TData>[K]) {\n    this.#options[key] = value;\n    return this;\n  }\n\n  /**\n   * Add an extended column definition\n   * @param def - column definition\n   * @returns this\n   */\n  public column<TValue = any>(def: ColDefExtended<TData, TValue>) {\n    this.#options.columnDefs = [...this.columnDefs, def];\n    return this;\n  }\n\n  /**\n   * Show row numbers column\n   * @param show - show or hide row numbers column\n   * @returns this\n   */\n  public columnRowNumbers(show: boolean = true) {\n    this.#options.rowNumbersColumn = show;\n    return this;\n  }\n\n  /**\n   * Add a file input column\n   * @param def - column definition\n   * @param cb - callback to set params for the file input cell renderer\n   * @returns this\n   */\n  public columnFileInput<TValue = any>(\n    def: ColDefExtended<TData, TValue> & {\n      /**\n       * Allowed file extensions (like ['fastq.gz'])\n       */\n      extensions?: string[];\n      /**\n       * The resolveProgress function is an optional input parameter for the component\n       * that allows tracking the file upload progress in real-time.\n       * By passing resolveProgress, you can ensure that the component\n       * displays accurate progress values for each file as they upload.\n       * How to use it in AgGrid\n       * cellRendererParams: {\n       *  resolveProgress: (cellData) => {\n       *    const progresses = app.progresses;\n       *    if (!cellData.value.importFileHandle) return undefined;\n       *    else return progresses[cellData.value.importFileHandle];\n       *  }\n       * }\n       */\n      resolveImportProgress?: (cellData: ICellRendererParams<TData, TValue>) => ImportProgress | undefined;\n\n      /**\n       * The resolveFileHandle function is an optional input parameter for the component\n       * that allows tracking the file upload progress in real-time.\n       * By passing resolveFileHandle, you can ensure that the component\n       * displays accurate progress values for each file as they upload.\n       * How to use it in AgGrid\n       * cellRendererParams: {\n       *  resolveFileHandle: (cellData) => {\n       *    return cellData.value.importFileHandle;\n       *  }\n       * }\n       */\n      resolveImportFileHandle?: (cellData: ICellRendererParams<TData, TValue>) => ImportFileHandle | undefined;\n\n      setImportFileHandle?: (d: ValueSetterParams<TData, ImportFileHandle | undefined>) => void;\n    }) {\n    return this.column(Object.assign({\n      cellRenderer: 'PlAgCellFile',\n      headerComponentParams: { type: 'File' },\n      cellStyle: { padding: 0 },\n      valueSetter: (d: ValueSetterParams<TData, ImportFileHandle | undefined>) => {\n        def.setImportFileHandle?.(d);\n        return true;\n      },\n      cellRendererSelector: (cellData: ICellRendererParams<TData, TValue>) => {\n        return {\n          component: 'PlAgCellFile',\n          params: {\n            extensions: def.extensions,\n            value: def.resolveImportFileHandle?.(cellData),\n            resolveProgress: () => {\n              return def.resolveImportProgress?.(cellData);\n            },\n          },\n        };\n      },\n    }, def));\n  }\n\n  public build() {\n    return this.#options;\n  }\n}\n\n// Simple helper to use like column<string> in grid options literal\ntype ColumnFunc<TData> = <TValue>(def: ColDefExtended<TData, TValue>) => ColDefExtended<TData, TValue>;\n\n/**\n * Returns a set of Ag Grid options along with a reference to the Ag Grid API.\n * (This is a fast prototype)\n *\n * @example\n * ```ts\n * const { gridOptions, gridApi } = useAgGridOptions(() => ({\n *   // custom grid options here\n * }));\n *\n * // Usage in a template (v-bind is required!)\n * <template>\n *   <AgGridVue :style=\"{ height: '100%' }\" v-bind=\"gridOptions\" />\n * </template>\n * ```\n */\nexport function useAgGridOptions<TData>(\n  factory: (context: { builder: Builder<TData>; column: ColumnFunc<TData> }) => Builder<TData> | GridOptionsExtended<TData>,\n) {\n  const gridApi = shallowRef<GridApi>();\n\n  const extOptions = computed<GridOptionsExtended>(() => {\n    const def: GridOptionsExtended<TData> = {\n      theme: AgGridTheme,\n      loadingOverlayComponent: PlAgOverlayLoading,\n      noRowsOverlayComponent: PlAgOverlayNoRows,\n      onGridReady: (e: GridReadyEvent) => {\n        gridApi.value = e.api;\n        autoSizeRowNumberColumn(e.api); // @TODO\n      },\n    };\n\n    const column = <TValue>(def: ColDefExtended<TData, TValue>) => {\n      return def;\n    };\n\n    const result = factory({ builder: new Builder(), column });\n\n    const options = Object.assign({}, def, result instanceof Builder ? result.build() : result);\n\n    if (options.rowNumbersColumn) {\n      options.columnDefs = [makeRowNumberColDef(), ...(options.columnDefs ?? [])];\n    }\n\n    if (options.noRowsText) {\n      options.noRowsOverlayComponentParams = {\n        text: options.noRowsText,\n      };\n    }\n\n    if ('loadingOverlayComponentParams' in options) {\n      console.warn('useAgGridOptions: remove loadingOverlayComponentParams from options, use loading, notReady, loadingText, loadingOverlayType instead');\n    }\n\n    options.loading = options.notReady || options.loading;\n\n    options.columnDefs = options.columnDefs?.map((it) => createAgGridColDef(it));\n\n    // Register all special components\n    options.components = Object.assign({}, options.components ?? {}, {\n      PlAgCellFile,\n      PlAgChartStackedBarCell,\n      PlAgChartHistogramCell,\n      PlAgCellStatusTag,\n    });\n\n    return options;\n  });\n\n  const gridOptions = computed<GridOptions>(() => {\n    const options = extOptions.value;\n\n    return {\n      ...options,\n      loadingOverlayComponentParams: {\n        notReady: options.notReady,\n        notReadyText: options.notReadyText,\n        overlayType: options.loadingOverlayType,\n      } satisfies PlAgOverlayLoadingParams,\n    };\n  });\n\n  whenever(() => extOptions.value.rowNumbersColumn, () => {\n    if (gridApi.value) {\n      autoSizeRowNumberColumn(gridApi.value);\n    }\n  });\n\n  watch([\n    () => extOptions.value.notReady,\n    () => extOptions.value.loading,\n  ], ([notReady, loading]) => {\n    const loadingOverlayComponentParams = {\n      notReady,\n      // we probably don't need to update the parameters below\n      notReadyText: extOptions.value.notReadyText,\n      overlayType: extOptions.value.loadingOverlayType,\n      loadingText: extOptions.value.loadingText,\n    } satisfies PlAgOverlayLoadingParams;\n\n    // Hack to apply loadingOverlayComponentParams\n    gridApi.value?.updateGridOptions({\n      loading: !loading,\n      loadingOverlayComponentParams,\n    });\n\n    gridApi.value?.updateGridOptions({\n      loading,\n      loadingOverlayComponentParams,\n    });\n  }, { deep: true, immediate: true });\n\n  return { gridOptions, gridApi 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