@gen3/frontend 0.10.91 → 0.10.92

package/dist/dts/features/CohortDiscovery/queryApi.js

@@ -0,0 +1,498 @@
+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);
+};
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g = Object.create((typeof Iterator === "function" ? Iterator : Object).prototype);
+    return g.next = verb(0), g["throw"] = verb(1), g["return"] = verb(2), typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (g && (g = 0, op[0] && (_ = 0)), _) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
+            }
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
+    }
+};
+import useSWR from 'swr';
+import { Accessibility, buildGetAggregationQuery, processHistogramResponse, } from '@gen3/core';
+import { getCookie } from 'cookies-next';
+export var useGraphQLData = function (url, body) {
+    var _a;
+    // Create a fetcher function that handles the GraphQL POST request
+    var fetcher = function (fetchUrl, fetchBody) { return __awaiter(void 0, void 0, void 0, function () {
+        var headers, accessToken, response;
+        return __generator(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    headers = new Headers({
+                        Accept: 'application/json',
+                        'Content-Type': 'application/json',
+                    });
+                    if (process.env.NODE_ENV === 'development') {
+                        accessToken = getCookie('credentials_token');
+                        if (accessToken) {
+                            headers.set('Authorization', "Bearer ".concat(accessToken));
+                        }
+                    }
+                    return [4 /*yield*/, fetch(fetchUrl, {
+                            method: 'POST',
+                            headers: headers,
+                            body: JSON.stringify(fetchBody),
+                        })];
+                case 1:
+                    response = _a.sent();
+                    if (!response.ok) {
+                        throw new Error("Error ".concat(response.status, ": ").concat(response.statusText));
+                    }
+                    return [4 /*yield*/, response.json()];
+                case 2: return [2 /*return*/, _a.sent()];
+            }
+        });
+    }); };
+    // Use SWR with the fetcher
+    var _b = useSWR([url, body], function (_a) {
+        var fetchUrl = _a[0], fetchBody = _a[1];
+        return fetcher(fetchUrl, fetchBody);
+    }, {
+        revalidateOnFocus: false, // Disable auto revalidation on window focus
+        // Add any other SWR options you need here
+    }), data = _b.data, error = _b.error, isLoading = _b.isLoading, mutate = _b.mutate;
+    // Format error to match your ErrorDetails interface
+    var formattedError = error
+        ? {
+            status: ((_a = error.message.match(/\d+/)) === null || _a === void 0 ? void 0 : _a[0]) || 'Unknown',
+            message: error.message,
+        }
+        : null;
+    console.log('useGraphQLData', data);
+    return {
+        data: data,
+        isLoading: isLoading,
+        isSuccess: !!data && !error,
+        isError: !!error,
+        error: formattedError,
+        mutate: mutate,
+    };
+};
+export var useRoundedAggsQuery = function (_a) {
+    var _b, _c, _d;
+    var type = _a.type, fields = _a.fields, filters = _a.filters, _e = _a.accessibility, accessibility = _e === void 0 ? Accessibility.ALL : _e;
+    var response = useGraphQLData('/api/analysis/cohortDiscovery', buildGetAggregationQuery(type, fields, filters, accessibility, false));
+    console.log('useRoundedAggsQuery', response);
+    return __assign(__assign({}, response), { data: ((_b = response === null || response === void 0 ? void 0 : response.data) === null || _b === void 0 ? void 0 : _b.data)
+            ? processHistogramResponse((_d = (_c = response === null || response === void 0 ? void 0 : response.data.data) === null || _c === void 0 ? void 0 : _c._aggregation[type]) !== null && _d !== void 0 ? _d : {})
+            : undefined });
+};
+// import { cohortDiscoveryApi } from './appApi';
+//
+// import {
+//   Accessibility,
+//   convertFilterSetToGqlFilter,
+//   FilterSet,
+//   isFilterEmpty,
+//   AggregationsData,
+//   RawDataAndTotalCountsParams,
+//   GraphQLQuery,
+// } from '@gen3/core';
+//
+// /*
+//   returns all the fields for a given type
+//   @param type: the type to get fields for
+//   @returns: a list of fields for the given type
+//  */
+//
+// interface AccessibleDataSliceParams {
+//   type: string;
+//   fields: ReadonlyArray<string>;
+//   accessType: Accessibility;
+// }
+//
+// interface QueryAggsParams {
+//   type: string;
+//   fields: ReadonlyArray<string>;
+//   filters: FilterSet;
+//   accessibility?: Accessibility;
+// }
+//
+// interface QueryForSubAggsParams {
+//   type: string;
+//   mainField: string;
+//   numericAggAsText: boolean;
+//   termsFields?: ReadonlyArray<string>;
+//   missingFields?: ReadonlyArray<string>;
+//   gqlFilter?: FilterSet;
+//   accessibility?: Accessibility;
+// }
+//
+// interface QueryCountsParams {
+//   type: string;
+//   filters: FilterSet;
+//   accessibility?: Accessibility;
+// }
+//
+// interface QueryForFileCountSummaryParams {
+//   type: string;
+//   field: string;
+//   filters: FilterSet;
+//   accessibility?: Accessibility;
+// }
+//
+// /**
+//  * The main endpoint used in templating Exploration page queries.
+//  * Includes table, filter and aggregation query types and leverages guppyApi defined in ./gupplApi.ts
+//  * Query templates support filters where applicable
+//  *
+//  * @param endpoints - Defines endpoints used in Exploration page:
+//  * @param getAllFieldsForType - A mapping query that returns all property key names vertex types specified.
+//  *   @see https://github.com/uc-cdis/guppy/blob/master/doc/queries.md#mapping-query
+//  * @param getAccessibleData - An aggregation histogram counts query that filters based on access type
+//  *   @see https://github.com/uc-cdis/guppy/blob/master/doc/queries.md#accessibility-argument-for-regular-tier-access-level
+//  * @param getRawDataAndTotalCounts - Queries both _totalCount for selected vertex types and
+//  * tabular results containing the raw data in the rows of selected vertex types
+//  *   @see https://github.com/uc-cdis/guppy/blob/master/doc/queries.md#1-total-count-aggregation
+//  * @param getAggs - An aggregated histogram counts query which outputs vertex property frequencies
+//  * @param getSubAggs - TODO: not sure what this one does. Looks like nested aggregation
+//  * @param getCounts - Returns total counts of a vertex type
+//  * @returns: A guppy API endpoint for templating queryable data displayed on the exploration page
+//  */
+// const explorerApi = cohortDiscoveryApi.injectEndpoints({
+//   endpoints: (builder) => ({
+//     getAllFieldsForType: builder.query({
+//       query: (type: { type: string }) => ({
+//         query: `{ _mapping ${type} } }`,
+//       }),
+//       transformResponse: (response: Record<string, any>, _meta, params) => {
+//         return response[params.type];
+//       },
+//     }),
+//     getAccessibleData: builder.query({
+//       query: ({ type, fields, accessType }: AccessibleDataSliceParams) => {
+//         const fieldParts = fields.map(
+//           (field) => `${field} { histogram { key count } }`,
+//         );
+//       },
+//     }),
+//     getRawDataAndTotalCounts: builder.query({
+//       query: ({
+//         type,
+//         fields,
+//         filters,
+//         sort,
+//         offset = 0,
+//         size = 20,
+//         accessibility = Accessibility.ALL,
+//         format = undefined,
+//       }: RawDataAndTotalCountsParams) => {
+//         const gqlFilter = convertFilterSetToGqlFilter(filters);
+//         const params = [
+//           ...(sort ? ['$sort: JSON'] : []),
+//           ...(gqlFilter ? ['$filter: JSON'] : []),
+//           ...(format ? ['$format: Format'] : []),
+//         ].join(',');
+//         const queryLine = `query getRawDataAndTotalCounts (${params}) {`;
+//
+//         const dataParams = [
+//           ...(format ? ['format: $format'] : []),
+//           ...(sort ? ['sort: $sort'] : []),
+//           ...(gqlFilter ? ['filter: $filter'] : []),
+//         ].join(',');
+//         const dataTypeLine = `${type} (accessibility: ${accessibility}, offset: ${offset}, first: ${size},
+//         ${dataParams}) {`;
+//
+//         const typeAggsLine = `${type} (${
+//           gqlFilter && 'filter: $filter,'
+//         } accessibility: ${accessibility}) {`;
+//
+//         const processedFields = fields.map((field) =>
+//           rawDataQueryStrForEachField(field),
+//         );
+//
+//         const query = `${queryLine}
+//     ${dataTypeLine}
+//       ${processedFields.join(' ')}
+//             }
+//             _aggregation {
+//               ${typeAggsLine}
+//                 _totalCount
+//               }
+//             }
+//         }`;
+//         const variables = {
+//           ...(sort && { sort }),
+//           ...(gqlFilter && { filter: gqlFilter }),
+//           ...(format && { format }),
+//         };
+//         return { query, variables };
+//       },
+//     }),
+//     getAggs: builder.query<AggregationsData, QueryAggsParams>({
+//       query: ({
+//         type,
+//         fields,
+//         filters,
+//         accessibility = Accessibility.ALL,
+//       }: QueryAggsParams) => {
+//         const queryStart = isFilterEmpty(filters)
+//           ? `
+//               query getAggs {
+//               _aggregation {
+//               ${type} (accessibility: ${accessibility}) {`
+//           : `query getAggs ($filter: JSON) {
+//                _aggregation {
+//                       ${type} (filter: $filter, filterSelf: false, accessibility: ${accessibility}) {`;
+//         const query = `${queryStart}
+//                   ${fields.map((field: string) =>
+//                     histogramQueryStrForEachField(field),
+//                   )}
+//                 }
+//               }
+//             }`;
+//         const queryBody: GraphQLQuery = {
+//           query: query,
+//           variables: { filter: convertFilterSetToGqlFilter(filters) },
+//         };
+//         return queryBody;
+//       },
+//     }),
+//     getAggsNoFilterSelf: builder.query<AggregationsData, QueryAggsParams>({
+//       query: ({
+//         type,
+//         fields,
+//         filters,
+//         accessibility = Accessibility.ALL,
+//       }: QueryAggsParams) => {
+//         const queryStart = isFilterEmpty(filters)
+//           ? `
+//               query getAggs {
+//               _aggregation {
+//               ${type} (accessibility: ${accessibility}) {`
+//           : `query getAggs ($filter: JSON) {
+//                _aggregation {
+//                       ${type} (filter: $filter, filterSelf: true, accessibility: ${accessibility}) {`;
+//         const query = `${queryStart}
+//                   ${fields.map((field: string) =>
+//                     histogramQueryStrForEachField(field),
+//                   )}
+//                 }
+//               }
+//             }`;
+//         const queryBody: GraphQLQuery = {
+//           query: query,
+//           variables: { filter: convertFilterSetToGqlFilter(filters) },
+//         };
+//         return queryBody;
+//       },
+//     }),
+//     getSubAggs: builder.query<AggregationsData, QueryForSubAggsParams>({
+//       query: ({
+//         type,
+//         mainField,
+//         termsFields = undefined,
+//         missingFields = undefined,
+//         numericAggAsText = false,
+//         gqlFilter = undefined,
+//         accessibility = Accessibility.ALL,
+//       }: QueryForSubAggsParams) => {
+//         const nestedAggFields = {
+//           termsFields: termsFields,
+//           missingFields: missingFields,
+//         };
+//
+//         const query = `query getSubAggs ( ${
+//           gqlFilter ?? '$filter: JSON,'
+//         } $nestedAggFields: JSON) {
+//     _aggregation {
+//       ${type} ( ${
+//         gqlFilter ?? 'filter: $filter, filterSelf: false,'
+//       } nestedAggFields: $nestedAggFields, accessibility: ${accessibility}) {
+//         ${nestedHistogramQueryStrForEachField(mainField, numericAggAsText)}
+//       }`;
+//
+//         return {
+//           query: query,
+//           variables: {
+//             ...(gqlFilter && {
+//               filter: convertFilterSetToGqlFilter(gqlFilter),
+//             }),
+//             nestedAggFields: nestedAggFields,
+//           },
+//         };
+//       },
+//     }),
+//     getCounts: builder.query<number, QueryCountsParams>({
+//       query: ({
+//         type,
+//         filters,
+//         accessibility = Accessibility.ALL,
+//       }: QueryCountsParams) => {
+//         const gqlFilters = convertFilterSetToGqlFilter(filters);
+//         const queryLine = `query totalCounts ${
+//           gqlFilters ? '($filter: JSON)' : ''
+//         }{`;
+//         const typeAggsLine = `${type} ${
+//           gqlFilters ? '(filter: $filter, ' : '('
+//         } accessibility: ${accessibility}) {`;
+//
+//         const query = `${queryLine} _aggregation {
+//           ${typeAggsLine}
+//             _totalCount
+//             }
+//            }
+//         }`;
+//         return {
+//           query: query,
+//           variables: {
+//             ...(gqlFilters && {
+//               filter: gqlFilters,
+//             }),
+//           },
+//         };
+//       },
+//     }),
+//     getFieldCountSummary: builder.query<
+//       Record<string, any>,
+//       QueryForFileCountSummaryParams
+//     >({
+//       query: ({
+//         type,
+//         field,
+//         filters,
+//         accessibility = Accessibility.ALL,
+//       }: QueryForFileCountSummaryParams) => {
+//         const gqlFilters = convertFilterSetToGqlFilter(filters);
+//         const query = `query summary ($filter: JSON) {
+//         _aggregation {
+//           ${type} (filter: $filter, accessibility: ${accessibility}) {
+//             ${field} {
+//               histogram {
+//                 sum,
+//               }
+//             }
+//           }
+//         }
+//       }`;
+//         return {
+//           query: query,
+//           variables: {
+//             ...(gqlFilters && {
+//               filter: gqlFilters,
+//             }),
+//           },
+//         };
+//       },
+//     }),
+//     getFieldsForIndex: builder.query({
+//       query: (index: string) => {
+//         return {
+//           query: `{
+//             _mapping { ${index} }
+//           }`,
+//         };
+//       },
+//     }),
+//   }),
+// });
+//
+// // query for aggregate data
+// // convert the function below to typescript
+//
+// const histogramQueryStrForEachField = (field: string): string => {
+//   const splittedFieldArray = field.split('.');
+//   const splittedField = splittedFieldArray.shift();
+//   if (splittedFieldArray.length === 0) {
+//     return `
+//     ${splittedField} {
+//       histogram {
+//         key
+//         count
+//       }
+//     }`;
+//   }
+//   return `
+//   ${splittedField} {
+//     ${histogramQueryStrForEachField(splittedFieldArray.join('.'))}
+//   }`;
+// };
+//
+// const nestedHistogramQueryStrForEachField = (
+//   mainField: string,
+//   numericAggAsText: boolean,
+// ) => `
+//   ${mainField} {
+//     ${numericAggAsText ? 'asTextHistogram' : 'histogram'} {
+//       key
+//       count
+//       missingFields {
+//         field
+//         count
+//       }
+//       termsFields {
+//         field
+//         count
+//         terms {
+//           key
+//           count
+//         }
+//       }
+//     }
+//   }`;
+//
+// export const rawDataQueryStrForEachField = (field: string): string => {
+//   const splitFieldArray = field.split('.');
+//   const splitField = splitFieldArray.shift();
+//   if (splitFieldArray.length === 0) {
+//     return `
+//     ${splitField}
+//     `;
+//   }
+//   return `
+//   ${splitField} {
+//     ${rawDataQueryStrForEachField(splitFieldArray.join('.'))}
+//   }`;
+// };
+//
+// export const {
+//   useGetRawDataAndTotalCountsQuery,
+//   useGetAccessibleDataQuery,
+//   useGetAllFieldsForTypeQuery,
+//   useGetAggsQuery,
+//   useGetAggsNoFilterSelfQuery,
+//   useLazyGetAggsQuery,
+//   useGetSubAggsQuery,
+//   useGetCountsQuery,
+//   useGetFieldCountSummaryQuery,
+//   useGetFieldsForIndexQuery,
+// } = explorerApi;
+//# sourceMappingURL=queryApi.js.map

package/dist/dts/features/CohortDiscovery/queryApi.js.map

@@ -0,0 +1 @@
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package/dist/dts/features/CohortDiscovery/tableSettings.d.ts

@@ -0,0 +1,3 @@
+import { MRT_RowData, MRT_TableOptions } from 'mantine-react-table';
+export declare const commonTableSettings: <T extends MRT_RowData = Record<string, any>>(size?: string) => Partial<MRT_TableOptions<T>>;
+//# sourceMappingURL=tableSettings.d.ts.map

package/dist/dts/features/CohortDiscovery/tableSettings.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"tableSettings.d.ts","sourceRoot":"","sources":["../../../../src/features/CohortDiscovery/tableSettings.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,gBAAgB,EAAE,MAAM,qBAAqB,CAAC;AAGpE,eAAO,MAAM,mBAAmB,GAC9B,CAAC,SAAS,WAAW,GAAG,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,EAE3C,OAAM,MAAa,KAClB,OAAO,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAkE7B,CAAC"}

package/dist/dts/features/CohortDiscovery/tableSettings.js

@@ -0,0 +1,68 @@
+import { TableIcons } from '../../components/Tables/TableIcons';
+export var commonTableSettings = function (size) {
+    if (size === void 0) { size = 'sm'; }
+    return {
+        enableColumnResizing: false,
+        icons: TableIcons,
+        enableTopToolbar: false,
+        enableColumnFilters: false,
+        enableColumnActions: false,
+        enableRowActions: true,
+        enableColumnOrdering: false,
+        enableFacetedValues: true,
+        enableGrouping: false,
+        enableColumnPinning: false,
+        enableRowSelection: false,
+        enablePagination: false,
+        enableSelectAll: false,
+        enableExpandAll: false,
+        displayColumnDefOptions: {
+            'mrt-row-select': {
+                size: 5,
+                header: '',
+            },
+            'mrt-row-expand': {
+                size: 5,
+                header: '',
+            },
+            'mrt-row-actions': {
+                header: '',
+            },
+        },
+        initialState: {
+            density: 'xs',
+            columnPinning: {
+                left: ['mrt-row-select', 'mrt-row-expand'],
+                right: ['mrt-row-actions'],
+            },
+        },
+        layoutMode: 'semantic',
+        mantineDetailPanelProps: {
+            style: {
+                boxShadow: '0 -2px 0px 0px var(--table-border-color) inset',
+            },
+        },
+        mantineTableProps: {
+            style: {
+                backgroundColor: 'var(--mantine-color-base-1)',
+                '--mrt-striped-row-background-color': 'var(--mantine-color-base-3)',
+                fontSize: "var(--mantine-font-size-".concat(size, ")"),
+            },
+        },
+        mantineTableHeadCellProps: {
+            style: {
+                backgroundColor: 'var(--mantine-color-table-1)',
+                color: 'var(--mantine-color-table-contrast-1)',
+                textAlign: 'center',
+                fontWeight: 600,
+                fontSize: "var(--mantine-font-size-".concat(size, ")"),
+                textTransform: 'uppercase',
+            },
+        },
+        mantinePaginationProps: {
+            rowsPerPageOptions: ['5', '10', '20', '40', '100'],
+            withEdges: false, //note: changed from `showFirstLastButtons` in v1.0
+        },
+    };
+};
+//# sourceMappingURL=tableSettings.js.map

package/dist/dts/features/CohortDiscovery/tableSettings.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"DataLibrary.d.ts","sourceRoot":"","sources":["../../../../src/features/DataLibrary/DataLibrary.tsx"],"names":[],"mappings":"AAGA,OAAO,EAAE,iBAAiB,EAAE,MAAM,SAAS,CAAC;AAE5C,QAAA,MAAM,WAAW,GAAI,QAAQ,iBAAiB,4CAM7C,CAAC;AAEF,eAAe,WAAW,CAAC"}
+{"version":3,"file":"DataLibrary.d.ts","sourceRoot":"","sources":["../../../../src/features/DataLibrary/DataLibrary.tsx"],"names":[],"mappings":"AAGA,OAAO,EAAE,iBAAiB,EAAE,MAAM,SAAS,CAAC;AAE5C,QAAA,MAAM,WAAW,GAAI,QAAQ,iBAAiB,4CAQ7C,CAAC;AAEF,eAAe,WAAW,CAAC"}

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

@@ -13,6 +13,7 @@ import { jsx as _jsx } from "react/jsx-runtime";
 import { DataLibrarySelectionProvider } from './selection/SelectionContext';
 import DataLibraryLists from './DataLibraryLists';
 var DataLibrary = function (config) {
+    console.log(config);
     return (_jsx(DataLibrarySelectionProvider, { children: _jsx(DataLibraryLists, __assign({}, config)) }));
 };
 export default DataLibrary;

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

@@ -1 +1 @@
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package/dist/dts/features/DataLibrary/DataLibraryLists.d.ts.map

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