@gen3/frontend 0.10.54 → 0.10.56

package/dist/dts/features/DataLibrary/selection/tests/SelectionContext.unit.test.js

@@ -0,0 +1,176 @@
+import { dataLibrarySelectionReducer, updateDataLibrarySelection, updateDataLibraryListMemberSelection, clearDataLibrarySelection, removeDataLibrarySelection, } from '../SelectionContext'; // Update this import path as needed
+describe('DataLibrarySelection', function () {
+    var initialState;
+    beforeEach(function () {
+        initialState = {};
+    });
+    test('updateDataLibrarySelection should update the selections state', function () {
+        var _a;
+        var listId = 'list1';
+        var members = {
+            member1: {
+                id: 'member1',
+                objectIds: { obj1: true, obj2: true },
+            },
+        };
+        var action = updateDataLibrarySelection(listId, members);
+        var newState = dataLibrarySelectionReducer(initialState, action);
+        expect(newState).toEqual((_a = {},
+            _a[listId] = members,
+            _a));
+    });
+    test('updateDataLibraryListMemberSelection should update a specific member selection', function () {
+        var _a, _b;
+        var listId = 'list1';
+        var memberId = 'member1';
+        var selection = { obj1: true, obj2: false };
+        var action = updateDataLibraryListMemberSelection(listId, memberId, selection);
+        var newState = dataLibrarySelectionReducer(initialState, action);
+        expect(newState).toEqual((_a = {},
+            _a[listId] = (_b = {},
+                _b[memberId] = {
+                    id: memberId,
+                    objectIds: selection,
+                },
+                _b),
+            _a));
+    });
+    test('clearDataLibrarySelection should reset the selections state', function () {
+        // First, add some selections
+        var populatedState = {
+            list1: {
+                member1: {
+                    id: 'member1',
+                    objectIds: { obj1: true },
+                },
+            },
+        };
+        var action = clearDataLibrarySelection();
+        var newState = dataLibrarySelectionReducer(populatedState, action);
+        expect(newState).toEqual({});
+    });
+    test('removeDataLibrarySelection should remove list when ', function () {
+        var initialStateWithList = {
+            list1: {
+                member1: {
+                    id: 'member1',
+                    objectIds: { obj1: true },
+                },
+            },
+        };
+        var action = removeDataLibrarySelection('list1');
+        var newState = dataLibrarySelectionReducer(initialStateWithList, action);
+        expect(newState).toEqual({});
+    });
+    test('updateDataLibraryListMemberSelection should remove one dataset', function () {
+        var initialStateWithMember = {
+            buJH_tA38h: {
+                DS_211: {
+                    id: 'DS_211',
+                    objectIds: {
+                        'phs000001.v1.p1.c1': true,
+                    },
+                },
+                DS_3: {
+                    id: 'DS_3',
+                    objectIds: {
+                        'ab6623a7-a474-4ffb-ab88-e926764628c4': true,
+                        'b1aeee0f-fdf1-4092-b8cf-f521c6a6f3ea': true,
+                    },
+                },
+                CF_4: {
+                    id: 'CF_4',
+                    objectIds: {
+                        CF_4: true,
+                    },
+                },
+            },
+        };
+        var action = updateDataLibraryListMemberSelection('buJH_tA38h', 'DS_3', {
+            'ab6623a7-a474-4ffb-ab88-e926764628c4': true,
+        });
+        var newState = dataLibrarySelectionReducer(initialStateWithMember, action);
+        expect(newState).toEqual({
+            buJH_tA38h: {
+                DS_211: {
+                    id: 'DS_211',
+                    objectIds: {
+                        'phs000001.v1.p1.c1': true,
+                    },
+                },
+                DS_3: {
+                    id: 'DS_3',
+                    objectIds: {
+                        'ab6623a7-a474-4ffb-ab88-e926764628c4': true,
+                    },
+                },
+                CF_4: {
+                    id: 'CF_4',
+                    objectIds: {
+                        CF_4: true,
+                    },
+                },
+            },
+        });
+    });
+    test('updateDataLibraryListMemberSelection should remove member when empty selection is provided', function () {
+        var initialStateWithMember = {
+            list1: {
+                member1: {
+                    id: 'member1',
+                    objectIds: { obj1: true },
+                },
+            },
+        };
+        var action = updateDataLibraryListMemberSelection('list1', 'member1', {});
+        var newState = dataLibrarySelectionReducer(initialStateWithMember, action);
+        expect(newState).toEqual({});
+    });
+    test('updateDataLibraryListMemberSelection should remove member when empty selection is provided', function () {
+        var initialStateWithMember = {
+            list1: {
+                member1: {
+                    id: 'member1',
+                    objectIds: { obj1: true },
+                },
+                member2: {
+                    id: 'member2',
+                    objectIds: { obj2: true, obj3: true },
+                },
+            },
+        };
+        var action = updateDataLibraryListMemberSelection('list1', 'member1', {});
+        var newState = dataLibrarySelectionReducer(initialStateWithMember, action);
+        expect(newState).toEqual({
+            list1: {
+                member2: {
+                    id: 'member2',
+                    objectIds: {
+                        obj2: true,
+                        obj3: true,
+                    },
+                },
+            },
+        });
+    });
+    test('newState show set list to {} when passed {}', function () {
+        var initialStateWithMember = {
+            list1: {
+                member1: {
+                    id: 'member1',
+                    objectIds: { obj1: true },
+                },
+                member2: {
+                    id: 'member2',
+                    objectIds: { obj2: true, obj3: true },
+                },
+            },
+        };
+        var action = updateDataLibrarySelection('list1', {});
+        var newState = dataLibrarySelectionReducer(initialStateWithMember, action);
+        expect(newState).toEqual({
+            list1: {},
+        });
+    });
+});
+//# sourceMappingURL=SelectionContext.unit.test.js.map

package/dist/dts/features/DataLibrary/selection/tests/SelectionContext.unit.test.js.map

@@ -0,0 +1 @@
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package/dist/dts/features/DataLibrary/selection/tests/utils.unit.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=utils.unit.test.d.ts.map

package/dist/dts/features/DataLibrary/selection/tests/utils.unit.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"utils.unit.test.d.ts","sourceRoot":"","sources":["../../../../../../src/features/DataLibrary/selection/tests/utils.unit.test.ts"],"names":[],"mappings":""}

package/dist/dts/features/DataLibrary/selection/tests/utils.unit.test.js

@@ -0,0 +1,79 @@
+import { getSelectionPaths } from '../utils';
+describe('getSelectionPaths', function () {
+    it('should return an array of paths based on the state of the data library', function () {
+        var state = {
+            list1: {
+                member1: {
+                    id: 'member1',
+                    objectIds: {},
+                },
+            },
+            list2: {
+                member2: {
+                    id: 'member2',
+                    objectIds: { objectId2: true },
+                },
+            },
+        };
+        var result = getSelectionPaths(state);
+        expect(result).toEqual([
+            {
+                listId: 'list1',
+                memberId: 'member1',
+            },
+            {
+                listId: 'list2',
+                memberId: 'member2',
+                objectId: 'objectId2',
+            },
+        ]);
+    });
+    it('should return an empty array for empty selection state', function () {
+        var state = {};
+        var result = getSelectionPaths(state);
+        expect(result).toEqual([]);
+    });
+});
+describe('getSelectionPaths', function () {
+    var sampleState = {
+        list1: {
+            member1: {
+                id: 'member1',
+                objectIds: { obj1: true, obj2: false },
+            },
+            member2: {
+                id: 'member2',
+                objectIds: {},
+            },
+        },
+        list2: {
+            member3: {
+                id: 'member3',
+                objectIds: { obj3: true, obj4: true, obj5: false },
+            },
+        },
+        list3: {
+            member4: {
+                id: 'member4',
+                objectIds: { obj6: false, obj7: false },
+            },
+        },
+    };
+    it('should correctly generate SelectionPaths', function () {
+        var expected = [
+            { listId: 'list1', memberId: 'member1', objectId: 'obj1' },
+            { listId: 'list1', memberId: 'member2' },
+            { listId: 'list2', memberId: 'member3', objectId: 'obj3' },
+            { listId: 'list2', memberId: 'member3', objectId: 'obj4' },
+        ];
+        var result = getSelectionPaths(sampleState);
+        expect(result).toEqual(expected);
+        expect(result.length).toBe(4);
+        // Additional specific checks
+        expect(result.filter(function (path) { return path.listId === 'list1'; }).length).toBe(2);
+        expect(result.filter(function (path) { return path.listId === 'list2'; }).length).toBe(2);
+        expect(result.filter(function (path) { return path.listId === 'list3'; }).length).toBe(0);
+        expect(result.filter(function (path) { return path.objectId === undefined; }).length).toBe(1);
+    });
+});
+//# sourceMappingURL=utils.unit.test.js.map

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package/dist/dts/features/DataLibrary/selection/types.d.ts

@@ -0,0 +1,31 @@
+import { CohortItem } from '@gen3/core';
+import { FileItemWithParentDatasetNameAndID } from '../types';
+type RuleOperator = 'equals' | 'not' | 'includes' | 'excludes' | 'greater' | 'less';
+type GroupOperator = 'count';
+type RuleValue = string | number | boolean;
+type ValidField<T> = keyof T;
+type CommonFields = ValidField<CohortItem> & ValidField<FileItemWithParentDatasetNameAndID>;
+export interface ItemRule {
+    field: CommonFields;
+    operator: RuleOperator;
+    value: RuleValue;
+    errorMessage: string;
+}
+export interface GroupRule extends Omit<ItemRule, 'operator'> {
+    operator: GroupOperator;
+    total: RuleValue;
+}
+export interface DataLibraryActionConfig {
+    id: string;
+    label: string;
+    rightIcon?: string;
+    leftIcon?: string;
+    buttonLabel: string;
+    actionFunction: string;
+    parameters?: Record<string, unknown>;
+    itemRules?: ItemRule[];
+    groupRules?: GroupRule[];
+}
+export type DataLibraryActionsConfig = ReadonlyArray<DataLibraryActionConfig>;
+export {};
+//# sourceMappingURL=types.d.ts.map

package/dist/dts/features/DataLibrary/selection/types.d.ts.map

@@ -0,0 +1 @@
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package/dist/dts/features/DataLibrary/selection/types.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=types.js.map

package/dist/dts/features/DataLibrary/selection/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../../../src/features/DataLibrary/selection/types.ts"],"names":[],"mappings":""}

package/dist/dts/features/DataLibrary/selection/utils.d.ts

@@ -0,0 +1,15 @@
+import { DataLibrarySelectionState } from './SelectionContext';
+import { CohortItem, DataLibrary } from '@gen3/core';
+import { FileItemWithParentDatasetNameAndID } from '../types';
+export declare const getDataLibraryItem: (dataLibrary: DataLibrary, listId: string, dataId: string, fileId?: string) => FileItemWithParentDatasetNameAndID | (CohortItem & {
+    datasetId: string;
+    datasetName: string;
+}) | undefined;
+export interface SelectionPath {
+    listId: string;
+    memberId: string;
+    objectId?: string;
+}
+export declare const getSelectionPaths: (selections: DataLibrarySelectionState) => SelectionPath[];
+export declare const getSelectedItemsFromDataLibrary: (selections: DataLibrarySelectionState, dataLibrary: DataLibrary) => (CohortItem | FileItemWithParentDatasetNameAndID)[];
+//# sourceMappingURL=utils.d.ts.map

package/dist/dts/features/DataLibrary/selection/utils.d.ts.map

@@ -0,0 +1 @@
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package/dist/dts/features/DataLibrary/selection/utils.js

@@ -0,0 +1,85 @@
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+import { isCohortItem, isFileItem, } from '@gen3/core';
+export var getDataLibraryItem = function (dataLibrary, listId, dataId, fileId) {
+    if (!(listId in dataLibrary))
+        return undefined;
+    if (!(dataId in dataLibrary[listId].items))
+        return undefined;
+    var datasetOrCohort = dataLibrary[listId].items[dataId];
+    var name = datasetOrCohort.name;
+    if (isCohortItem(datasetOrCohort)) {
+        return __assign(__assign({}, datasetOrCohort), { datasetId: dataId, datasetName: name });
+    }
+    else {
+        if (!fileId)
+            return undefined;
+        if (!(fileId in datasetOrCohort.items))
+            return undefined;
+        if (isFileItem(datasetOrCohort.items[fileId])) {
+            return __assign({ datasetName: name, datasetId: dataId }, datasetOrCohort.items[fileId]);
+        }
+        return undefined;
+    }
+};
+export var getSelectionPaths = function (selections) {
+    var paths = [];
+    for (var _i = 0, _a = Object.entries(selections); _i < _a.length; _i++) {
+        var _b = _a[_i], listId = _b[0], listMembers = _b[1];
+        for (var _c = 0, _d = Object.entries(listMembers); _c < _d.length; _c++) {
+            var _e = _d[_c], memberId = _e[0], member = _e[1];
+            if (Object.keys(member.objectIds).length === 0) {
+                // If there are no objectIds, add a path with undefined objectId
+                paths.push({
+                    listId: listId,
+                    memberId: memberId,
+                });
+            }
+            else {
+                for (var _f = 0, _g = Object.entries(member.objectIds); _f < _g.length; _f++) {
+                    var _h = _g[_f], objectId = _h[0], isSelected = _h[1];
+                    if (isSelected) {
+                        paths.push({
+                            listId: listId,
+                            memberId: memberId,
+                            objectId: objectId,
+                        });
+                    }
+                }
+            }
+        }
+    }
+    return paths;
+};
+export var getSelectedItemsFromDataLibrary = function (selections, dataLibrary) {
+    var selectedPaths = getSelectionPaths(selections);
+    var uniqueItems = new Map();
+    selectedPaths.forEach(function (path) {
+        var item = getDataLibraryItem(dataLibrary, path.listId, path.memberId, path.objectId);
+        if (item) {
+            var key = getUniqueItemKey(item);
+            uniqueItems.set(key, item);
+        }
+    });
+    return Array.from(uniqueItems.values());
+};
+var getUniqueItemKey = function (item) {
+    if (isCohortItem(item)) {
+        // For CohortItems
+        return "cohort_".concat(item.datasetId);
+    }
+    else {
+        // For FileItems
+        return "file_".concat(item.datasetId, "_").concat(item.id);
+    }
+};
+//# sourceMappingURL=utils.js.map

package/dist/dts/features/DataLibrary/selection/utils.js.map

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package/dist/dts/features/DataLibrary/tables/AdditionalDataTable.d.ts

@@ -0,0 +1,8 @@
+interface AdditionalDataTableTableProps {
+    data: any;
+    header: string;
+    size?: string;
+}
+declare const AdditionalDataTableTable: ({ data, header, size, }: AdditionalDataTableTableProps) => import("react/jsx-runtime").JSX.Element;
+export default AdditionalDataTableTable;
+//# sourceMappingURL=AdditionalDataTable.d.ts.map

package/dist/dts/features/DataLibrary/tables/AdditionalDataTable.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"AdditionalDataTable.d.ts","sourceRoot":"","sources":["../../../../../src/features/DataLibrary/tables/AdditionalDataTable.tsx"],"names":[],"mappings":"AAoBA,UAAU,6BAA6B;IACrC,IAAI,EAAE,GAAG,CAAC;IACV,MAAM,EAAE,MAAM,CAAC;IACf,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,QAAA,MAAM,wBAAwB,4BAI3B,6BAA6B,4CAmB/B,CAAC;AAEF,eAAe,wBAAwB,CAAC"}

package/dist/dts/features/DataLibrary/tables/AdditionalDataTable.js

@@ -0,0 +1,36 @@
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { MantineReactTable, useMantineReactTable } from 'mantine-react-table';
+import { commonTableSettings } from './tableSettings';
+import { Text } from '@mantine/core';
+var columns = [
+    {
+        accessorKey: 'name',
+        header: 'Name',
+    },
+    {
+        accessorKey: 'description',
+        header: 'Description',
+    },
+    {
+        accessorKey: 'documentation',
+        header: 'Documentation',
+    },
+];
+var AdditionalDataTableTable = function (_a) {
+    var data = _a.data, header = _a.header, _b = _a.size, size = _b === void 0 ? 'sm' : _b;
+    var table = useMantineReactTable(__assign(__assign({ columns: columns, data: data }, commonTableSettings(size)), { enableRowActions: false, enableRowSelection: false, enableBottomToolbar: data.length > 10, enablePagination: data.length > 10 }));
+    return (_jsxs("div", { className: "flex flex-col w-inherit gap-y-1", children: [_jsx(Text, { fw: 600, fs: "md", c: "secondary.5", tt: "uppercase", children: header }), _jsx(MantineReactTable, { table: table })] }));
+};
+export default AdditionalDataTableTable;
+//# sourceMappingURL=AdditionalDataTable.js.map

package/dist/dts/features/DataLibrary/tables/AdditionalDataTable.js.map

@@ -0,0 +1 @@
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package/dist/dts/features/DataLibrary/tables/DatalistContentsPanel.d.ts

@@ -0,0 +1 @@
+//# sourceMappingURL=DatalistContentsPanel.d.ts.map

package/dist/dts/features/DataLibrary/tables/DatalistContentsPanel.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"DatalistContentsPanel.d.ts","sourceRoot":"","sources":["../../../../../src/features/DataLibrary/tables/DatalistContentsPanel.tsx"],"names":[],"mappings":""}

package/dist/dts/features/DataLibrary/tables/DatalistContentsPanel.js

@@ -0,0 +1,130 @@
+"use strict";
+// import React, { useState } from 'react';
+// import { useDeepCompareEffect, useDeepCompareMemo } from 'use-deep-compare';
+// import { MRT_RowSelectionState, MRT_Updater } from 'mantine-react-table';
+// import { DatalistContents } from '../types';
+// import {
+//   getNumberOfDataSetItemsSelected,
+//   useDataLibrarySelection,
+// } from '../selection/SelectionContext';
+// import { selectAllDatasetMembers } from '../selection/selection';
+// import FilesTable from './FilesTable';
+// import QueryTable from './QueriesTable';
+//
+// /**
+//  *  Component that manages a List items, which are composed of Dataset and/or Cohorts
+//  */
+// const columns = [
+//   {
+//     accessorKey: 'name',
+//     header: 'Name',
+//   },
+//   {
+//     accessorKey: 'id',
+//     header: 'Id',
+//   },
+//   {
+//     accessorKey: 'numFiles',
+//     header: '# Files',
+//   },
+//   {
+//     accessorKey: 'itemType',
+//     header: 'Type',
+//   },
+//   {
+//     accessorKey: 'isAddDataSource',
+//     header: 'Additional Data Sources',
+//   },
+//   {
+//     accessorKey: 'datesetGui',
+//     header: 'Dataset GUI',
+//   },
+// ];
+//
+// export interface ListsTableProps {
+//   listId: string;
+//   contents: DatalistContents;
+//   removeList: (itemId: string) => void;
+// }
+//
+// const DatalistContentsPanel = ({
+//   listId,
+//   contents,
+//   removeList,
+// }: ListsTableProps) => {
+//   // const [rowSelection, setRowSelection] = useState<MRT_RowSelectionState>({});
+//
+//   // const { selections, updateSelections } = useDataLibrarySelection();
+//
+//   console.log('contents', contents);
+//
+//   /**
+//    * Handles the change in row selection.
+//    *
+//    * @param {MRT_Updater<MRT_RowSelectionState>} updater - A function or value
+//    * that provides the new state of row selection. If a function is provided,
+//    * it will be called with the previous selection state.
+//    *
+//    * This function updates the state of selected rows by transforming the
+//    * updater's value. It generates a mapping of selected members for each
+//    * dataset, containing the dataset ID and an object representing the selected
+//    * object IDs. It then updates the selections for a given list and filters
+//    * the values to indicate whether each dataset has any selected objects.
+//    */
+//   // const handleRowSelectionChange = (
+//   //   updater: MRT_Updater<MRT_RowSelectionState>,
+//   // ) => {
+//   //   setRowSelection((prevSelection) => {
+//   //     const value =
+//   //       updater instanceof Function ? updater(prevSelection) : updater;
+//   //
+//   //     const members = selectAllDatasetMembers(Object.keys(value), data);
+//   //     updateSelections(listId, members);
+//   //     return Object.keys(members).reduce(
+//   //       (acc: Record<string, boolean>, key) => {
+//   //         acc[key] = Object.keys(members[key].objectIds).length > 0;
+//   //         return acc;
+//   //       },
+//   //       {},
+//   //     );
+//   //   });
+//   // };
+//
+//   // useDeepCompareEffect(() => {
+//   //   if (!selections[listId]) {
+//   //     // not found in selections, unselect all
+//   //     setRowSelection({});
+//   //     return;
+//   //   }
+//   //
+//   //   const filteredValues = Object.keys(selections[listId]).reduce(
+//   //     (acc: Record<string, boolean>, key) => {
+//   //       const objectIds = selections[listId][key]?.objectIds;
+//   //       if (!objectIds) {
+//   //         console.warn(
+//   //           `Object IDs for key ${key} in list ${listId} are not available`,
+//   //         );
+//   //         return acc;
+//   //       }
+//   //       acc[key] = Object.keys(objectIds).length > 0;
+//   //       return acc;
+//   //     },
+//   //     {},
+//   //   );
+//   //   setRowSelection(filteredValues);
+//   // }, [setRowSelection, selections, listId]);
+//
+//   return (
+//     <div className="flex flex-col w-full gap-y-4 pr-4">
+//       {contents.files.length > 0 && (
+//         <FilesTable header={'Files'} listId={listId} data={contents.files} />
+//       )}
+//       {contents.queries.length > 0 && (
+//         <QueryTable header={'Queries'} data={contents.queries} />
+//       )}
+//     </div>
+//   );
+// };
+//
+// export default DatalistContentsPanel;
+//# sourceMappingURL=DatalistContentsPanel.js.map

package/dist/dts/features/DataLibrary/tables/DatalistContentsPanel.js.map

@@ -0,0 +1 @@
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package/dist/dts/features/DataLibrary/tables/DatasetContentsTable.d.ts

@@ -0,0 +1,10 @@
+import { DatalistMembers } from '../types';
+export interface ListsTableProps {
+    listId: string;
+    data: DatalistMembers;
+    removeList: (itemId: string) => void;
+    size: string;
+}
+declare const DataSetContentsTable: ({ listId, data, removeList, size, }: ListsTableProps) => import("react/jsx-runtime").JSX.Element;
+export default DataSetContentsTable;
+//# sourceMappingURL=DatasetContentsTable.d.ts.map

package/dist/dts/features/DataLibrary/tables/DatasetContentsTable.d.ts.map

@@ -0,0 +1 @@
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