synapse-react-client 3.1.28 → 3.1.30

package/dist/utils/functions/sqlFunctions.js

@@ -4,6 +4,12 @@ exports.resultToJson = exports.parseEntityIdAndVersionFromSqlStatement = exports
 var RegularExpressions_1 = require("../functions/RegularExpressions");
 var QueryFilter_1 = require("../synapseTypes/Table/QueryFilter");
 var WITHOUT_SYN_PREFIX = 3;
+function removePrefixIfSynId(value) {
+    if (value.match(RegularExpressions_1.SYNAPSE_ENTITY_ID_REGEX)) {
+        return value.substring(WITHOUT_SYN_PREFIX);
+    }
+    return value;
+}
 /**
  * Given the search params, return a set of QueryFilters to narrow the the query to view just related data. May return null if a QueryFilter should not be added.
  * @param sql
@@ -12,7 +18,7 @@ var WITHOUT_SYN_PREFIX = 3;
  * @returns
  */
 var generateQueryFilterFromSearchParams = function (searchParams, operator) {
-    if (operator === void 0) { operator = 'LIKE'; }
+    if (operator === void 0) { operator = QueryFilter_1.ColumnSingleValueFilterOperator.LIKE; }
     if (!searchParams) {
         return;
     }
@@ -25,43 +31,60 @@ var generateQueryFilterFromSearchParams = function (searchParams, operator) {
     return Object.keys(searchParams)
         .filter(function (key) { return !isQueryWrapperKey(key); })
         .map(function (key) {
-        if (operator === 'HAS') {
-            var filter = {
-                concreteType: 'org.sagebionetworks.repo.model.table.ColumnMultiValueFunctionQueryFilter',
-                columnName: key,
-                function: QueryFilter_1.ColumnMultiValueFunction.HAS,
-                values: searchParams[key].split(','),
-            };
-            return filter;
-        }
-        else if (operator === 'LIKE') {
-            var value = searchParams[key];
-            if (value.match(RegularExpressions_1.SYNAPSE_ENTITY_ID_REGEX)) {
+        switch (operator) {
+            case QueryFilter_1.ColumnSingleValueFilterOperator.EQUAL: {
+                var filter = {
+                    concreteType: 'org.sagebionetworks.repo.model.table.ColumnSingleValueQueryFilter',
+                    columnName: key,
+                    operator: operator,
+                    values: [searchParams[key]],
+                };
+                return filter;
+            }
+            case QueryFilter_1.ColumnSingleValueFilterOperator.IN: {
+                var filter = {
+                    concreteType: 'org.sagebionetworks.repo.model.table.ColumnSingleValueQueryFilter',
+                    columnName: key,
+                    operator: operator,
+                    values: searchParams[key].split(','),
+                };
+                return filter;
+            }
+            case QueryFilter_1.ColumnMultiValueFunction.HAS: {
+                var filter = {
+                    concreteType: 'org.sagebionetworks.repo.model.table.ColumnMultiValueFunctionQueryFilter',
+                    columnName: key,
+                    function: operator,
+                    values: searchParams[key].split(','),
+                };
+                return filter;
+            }
+            case QueryFilter_1.ColumnSingleValueFilterOperator.LIKE: {
                 // If we use a LIKE statement with a synId the backend will look for a string with the first three
                 // characters being 'syn', however, it stores synIds without 'syn', so the query will fail
                 // The backend usually parses 'syn' out, but not with the LIKE clause since its expecting a regex, so we
                 // parse this out. This will cause a bug if something matches the synId regex but is in free text.
-                value = value.substring(WITHOUT_SYN_PREFIX);
+                var filter = {
+                    concreteType: 'org.sagebionetworks.repo.model.table.ColumnSingleValueQueryFilter',
+                    columnName: key,
+                    operator: operator,
+                    // Add wildcards around the value
+                    values: ["%".concat(removePrefixIfSynId(searchParams[key]), "%")],
+                };
+                return filter;
+            }
+            case QueryFilter_1.ColumnMultiValueFunction.HAS_LIKE: {
+                var filter = {
+                    concreteType: 'org.sagebionetworks.repo.model.table.ColumnMultiValueFunctionQueryFilter',
+                    columnName: key,
+                    function: operator,
+                    values: searchParams[key].split(',').map(function (param) {
+                        // Remove synId prefix for the same reasons as in the LIKE case
+                        return "%".concat(removePrefixIfSynId(param), "%");
+                    }),
+                };
+                return filter;
             }
-            var filter = {
-                concreteType: 'org.sagebionetworks.repo.model.table.ColumnSingleValueQueryFilter',
-                columnName: key,
-                operator: QueryFilter_1.ColumnSingleValueFilterOperator.LIKE,
-                // Add wildcards around the value
-                values: ["%".concat(value, "%")],
-            };
-            return filter;
-        }
-        else {
-            // operator is '='
-            // The backend doesn't have an '=' operator for query filters, but we can just use LIKE without wildcards.
-            var filter = {
-                concreteType: 'org.sagebionetworks.repo.model.table.ColumnSingleValueQueryFilter',
-                columnName: key,
-                operator: QueryFilter_1.ColumnSingleValueFilterOperator.LIKE,
-                values: [searchParams[key]],
-            };
-            return filter;
         }
     });
 };

package/dist/utils/functions/sqlFunctions.js.map

@@ -1 +1 @@
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package/dist/utils/hooks/SynapseAPI/entity/useExportToCavatica.d.ts

@@ -0,0 +1,2 @@
+import { QueryBundleRequest, SelectColumn } from '../../../synapseTypes';
+export declare function useExportToCavatica(queryBundleRequest: QueryBundleRequest, selectColumns?: SelectColumn[]): () => Promise<void>;

package/dist/utils/hooks/SynapseAPI/entity/useExportToCavatica.js

@@ -0,0 +1,55 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.useExportToCavatica = void 0;
+var tslib_1 = require("tslib");
+var __1 = require("../../..");
+var ToastMessage_1 = require("../../../../containers/ToastMessage");
+var sqlFunctions_1 = require("../../../functions/sqlFunctions");
+var SynapseContext_1 = require("../../../SynapseContext");
+function useExportToCavatica(queryBundleRequest, selectColumns) {
+    var _this = this;
+    var accessToken = (0, SynapseContext_1.useSynapseContext)().accessToken;
+    var separator = ',';
+    var writeHeader = true;
+    var includeRowIdAndRowVersion = false;
+    var originalSql = queryBundleRequest.query.sql;
+    return function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        var selectColumnsList, sql, downloadFromTableRequest, result, presignedURL, cavaticaURL, _err_1;
+        return tslib_1.__generator(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    _a.trys.push([0, 3, , 4]);
+                    selectColumnsList = selectColumns === null || selectColumns === void 0 ? void 0 : selectColumns.map(function (col) { return col.name; }).join(',');
+                    sql = "SELECT CONCAT('drs://repo-prod.prod.sagebase.org/syn', id, '.', currentVersion) AS drs_uri, name as file_name, ".concat(selectColumnsList, " FROM ").concat(originalSql.slice(originalSql.toLowerCase().indexOf('from') + 'from'.length + 1));
+                    downloadFromTableRequest = {
+                        sql: sql,
+                        entityId: (0, sqlFunctions_1.parseEntityIdFromSqlStatement)(sql),
+                        selectedFacets: queryBundleRequest.query.selectedFacets,
+                        concreteType: 'org.sagebionetworks.repo.model.table.DownloadFromTableRequest',
+                        writeHeader: writeHeader,
+                        includeRowIdAndRowVersion: includeRowIdAndRowVersion,
+                        csvTableDescriptor: { separator: separator },
+                        additionalFilters: queryBundleRequest.query.additionalFilters,
+                    };
+                    return [4 /*yield*/, __1.SynapseClient.getDownloadFromTableRequest(downloadFromTableRequest, accessToken)];
+                case 1:
+                    result = _a.sent();
+                    return [4 /*yield*/, __1.SynapseClient.getFileHandleByIdURL(result.resultsFileHandleId, accessToken)
+                        // Send this presigned URL to the Cavatica landing page where it can be processed
+                    ];
+                case 2:
+                    presignedURL = _a.sent();
+                    cavaticaURL = "https://cavatica.sbgenomics.com/import-redirect/drs/csv/?URL=".concat(encodeURIComponent(presignedURL));
+                    window.open(cavaticaURL, '_blank');
+                    return [3 /*break*/, 4];
+                case 3:
+                    _err_1 = _a.sent();
+                    (0, ToastMessage_1.displayToast)(_err_1.reason, 'danger');
+                    return [3 /*break*/, 4];
+                case 4: return [2 /*return*/];
+            }
+        });
+    }); };
+}
+exports.useExportToCavatica = useExportToCavatica;
+//# sourceMappingURL=useExportToCavatica.js.map

package/dist/utils/hooks/SynapseAPI/entity/useExportToCavatica.js.map

@@ -0,0 +1 @@
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package/dist/utils/hooks/SynapseAPI/forum/useForum.d.ts

@@ -0,0 +1,7 @@
+import { UseInfiniteQueryOptions, UseQueryOptions } from 'react-query';
+import { SynapseClientError } from '../../../SynapseClientError';
+import { PaginatedResults } from '../../../synapseTypes';
+import { DiscussionFilter, DiscussionThreadBundle, DiscussionThreadOrder } from '../../../synapseTypes/DiscussionBundle';
+import { PaginatedIds } from '../../../synapseTypes/PaginatedIds';
+export declare function useGetModerators(forumId: string, options?: UseQueryOptions<PaginatedIds, SynapseClientError>): import("react-query").UseQueryResult<PaginatedIds, SynapseClientError>;
+export declare function useGetForumInfinite(forumId: string, limit: number, sort: DiscussionThreadOrder, ascending: boolean, filter?: DiscussionFilter, options?: UseInfiniteQueryOptions<PaginatedResults<DiscussionThreadBundle>, SynapseClientError>): import("react-query").UseInfiniteQueryResult<PaginatedResults<DiscussionThreadBundle>, SynapseClientError>;

package/dist/utils/hooks/SynapseAPI/forum/useForum.js

@@ -0,0 +1,31 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.useGetForumInfinite = exports.useGetModerators = void 0;
+var tslib_1 = require("tslib");
+var react_query_1 = require("react-query");
+var __1 = require("../../..");
+var SynapseContext_1 = require("../../../SynapseContext");
+function useGetModerators(forumId, options) {
+    var _a = (0, SynapseContext_1.useSynapseContext)(), accessToken = _a.accessToken, keyFactory = _a.keyFactory;
+    return (0, react_query_1.useQuery)(keyFactory.getForumModeratorsQueryKey(forumId), function () { return __1.SynapseClient.getModerators(accessToken, forumId); }, options);
+}
+exports.useGetModerators = useGetModerators;
+function useGetForumInfinite(forumId, limit, sort, ascending, filter, options) {
+    var _this = this;
+    var _a = (0, SynapseContext_1.useSynapseContext)(), accessToken = _a.accessToken, keyFactory = _a.keyFactory;
+    return (0, react_query_1.useInfiniteQuery)(keyFactory.getForumThreadsQueryKey(forumId, limit, sort, ascending, filter), function (context) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
+            return [2 /*return*/, __1.SynapseClient.getForumThread(accessToken, forumId, context.pageParam, limit, sort, ascending, filter)];
+        });
+    }); }, tslib_1.__assign(tslib_1.__assign({}, options), { getNextPageParam: function (lastPage, pages) {
+            var numberOfFetchedResults = pages.flatMap(function (page) { return page.results; }).length;
+            if (lastPage.totalNumberOfResults > numberOfFetchedResults) {
+                return numberOfFetchedResults;
+            }
+            else {
+                return undefined;
+            }
+        } }));
+}
+exports.useGetForumInfinite = useGetForumInfinite;
+//# sourceMappingURL=useForum.js.map

package/dist/utils/hooks/SynapseAPI/forum/useForum.js.map

@@ -0,0 +1 @@
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package/dist/utils/hooks/SynapseAPI/forum/useReply.d.ts

@@ -0,0 +1,10 @@
+import { UseInfiniteQueryOptions, UseMutationOptions, UseQueryOptions } from 'react-query';
+import { SynapseClientError } from '../../../SynapseClientError';
+import { CreateDiscussionReply, DiscussionFilter, DiscussionReplyBundle, DiscussionReplyOrder, UpdateDiscussionReply } from '../../../synapseTypes/DiscussionBundle';
+import { PaginatedResults } from '../../../synapseTypes';
+import { Match } from '../../../synapseTypes/DiscussionSearch';
+export declare function useGetRepliesInfinite(threadId: string, ascending: boolean, limit: number, sort?: DiscussionReplyOrder, filter?: DiscussionFilter, options?: UseInfiniteQueryOptions<PaginatedResults<DiscussionReplyBundle>, SynapseClientError>): import("react-query").UseInfiniteQueryResult<PaginatedResults<DiscussionReplyBundle>, SynapseClientError>;
+export declare function useGetReply(reply: DiscussionReplyBundle, options?: UseQueryOptions<string, SynapseClientError>): import("react-query").UseQueryResult<string, SynapseClientError>;
+export declare function usePostReply(options?: UseMutationOptions<DiscussionReplyBundle, SynapseClientError, CreateDiscussionReply>): import("react-query").UseMutationResult<DiscussionReplyBundle, SynapseClientError, CreateDiscussionReply, unknown>;
+export declare function usePutReply(options?: UseMutationOptions<DiscussionReplyBundle, SynapseClientError, UpdateDiscussionReply>): import("react-query").UseMutationResult<DiscussionReplyBundle, SynapseClientError, UpdateDiscussionReply, unknown>;
+export declare function useDeleteReply(options?: UseMutationOptions<void, SynapseClientError, Match>): import("react-query").UseMutationResult<void, SynapseClientError, Match, unknown>;

package/dist/utils/hooks/SynapseAPI/forum/useReply.js

@@ -0,0 +1,120 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.useDeleteReply = exports.usePutReply = exports.usePostReply = exports.useGetReply = exports.useGetRepliesInfinite = void 0;
+var tslib_1 = require("tslib");
+var react_query_1 = require("react-query");
+var __1 = require("../../..");
+var SynapseContext_1 = require("../../../SynapseContext");
+function useGetRepliesInfinite(threadId, ascending, limit, sort, filter, options) {
+    var _this = this;
+    var _a = (0, SynapseContext_1.useSynapseContext)(), accessToken = _a.accessToken, keyFactory = _a.keyFactory;
+    return (0, react_query_1.useInfiniteQuery)(keyFactory.getRepliesQueryKey(threadId, ascending, limit, sort, filter), function (context) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
+            return [2 /*return*/, __1.SynapseClient.getReplies(accessToken, threadId, limit, context.pageParam, sort, ascending, filter)];
+        });
+    }); }, tslib_1.__assign(tslib_1.__assign({}, options), { getNextPageParam: function (lastPage, pages) {
+            var numberOfFetchedResults = pages.flatMap(function (page) { return page.results; }).length;
+            if (lastPage.totalNumberOfResults > numberOfFetchedResults) {
+                return numberOfFetchedResults;
+            }
+            else {
+                return undefined;
+            }
+        } }));
+}
+exports.useGetRepliesInfinite = useGetRepliesInfinite;
+function useGetReply(reply, options) {
+    var _this = this;
+    var _a = (0, SynapseContext_1.useSynapseContext)(), accessToken = _a.accessToken, keyFactory = _a.keyFactory;
+    var queryFn = function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        var messageUrl, data;
+        return tslib_1.__generator(this, function (_a) {
+            switch (_a.label) {
+                case 0: return [4 /*yield*/, __1.SynapseClient.getReplyMessageUrl(reply.messageKey, accessToken)];
+                case 1:
+                    messageUrl = _a.sent();
+                    return [4 /*yield*/, fetch(messageUrl.messageUrl, {
+                            method: 'GET',
+                            headers: {
+                                Accept: '*/*',
+                                'Access-Control-Request-Headers': 'authorization',
+                                'Content-Type': 'text/plain; charset=utf-8',
+                            },
+                        })];
+                case 2:
+                    data = _a.sent();
+                    return [2 /*return*/, data.text()];
+            }
+        });
+    }); };
+    return (0, react_query_1.useQuery)(keyFactory.getReplyQueryKey(reply.threadId, reply.id, reply.messageKey), queryFn, options);
+}
+exports.useGetReply = useGetReply;
+function usePostReply(options) {
+    var _this = this;
+    var queryClient = (0, react_query_1.useQueryClient)();
+    var _a = (0, SynapseContext_1.useSynapseContext)(), accessToken = _a.accessToken, keyFactory = _a.keyFactory;
+    return (0, react_query_1.useMutation)(function (request) {
+        return __1.SynapseClient.postReply(request, accessToken);
+    }, tslib_1.__assign(tslib_1.__assign({}, options), { onSuccess: function (newReply, variables, ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            return tslib_1.__generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, queryClient.invalidateQueries(keyFactory.getAllRepliesQueryKey(newReply.threadId))];
+                    case 1:
+                        _a.sent();
+                        if (!(options === null || options === void 0 ? void 0 : options.onSuccess)) return [3 /*break*/, 3];
+                        return [4 /*yield*/, options.onSuccess(newReply, variables, ctx)];
+                    case 2:
+                        _a.sent();
+                        _a.label = 3;
+                    case 3: return [2 /*return*/];
+                }
+            });
+        }); } }));
+}
+exports.usePostReply = usePostReply;
+function usePutReply(options) {
+    var _this = this;
+    var queryClient = (0, react_query_1.useQueryClient)();
+    var _a = (0, SynapseContext_1.useSynapseContext)(), accessToken = _a.accessToken, keyFactory = _a.keyFactory;
+    return (0, react_query_1.useMutation)(function (request) {
+        return __1.SynapseClient.putReply(request, accessToken);
+    }, tslib_1.__assign(tslib_1.__assign({}, options), { onSuccess: function (newReply, variables, ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            return tslib_1.__generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, queryClient.invalidateQueries(keyFactory.getAllRepliesQueryKey(newReply.threadId))];
+                    case 1:
+                        _a.sent();
+                        if (!(options === null || options === void 0 ? void 0 : options.onSuccess)) return [3 /*break*/, 3];
+                        return [4 /*yield*/, options.onSuccess(newReply, variables, ctx)];
+                    case 2:
+                        _a.sent();
+                        _a.label = 3;
+                    case 3: return [2 /*return*/];
+                }
+            });
+        }); } }));
+}
+exports.usePutReply = usePutReply;
+function useDeleteReply(options) {
+    var _this = this;
+    var queryClient = (0, react_query_1.useQueryClient)();
+    var _a = (0, SynapseContext_1.useSynapseContext)(), accessToken = _a.accessToken, keyFactory = _a.keyFactory;
+    return (0, react_query_1.useMutation)(function (match) { return __1.SynapseClient.deleteReply(accessToken, match.replyId); }, tslib_1.__assign(tslib_1.__assign({}, options), { onSuccess: function (updatedReply, variables, ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            return tslib_1.__generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, queryClient.invalidateQueries(keyFactory.getAllRepliesQueryKey(variables.threadId))];
+                    case 1:
+                        _a.sent();
+                        if (!(options === null || options === void 0 ? void 0 : options.onSuccess)) return [3 /*break*/, 3];
+                        return [4 /*yield*/, options.onSuccess(updatedReply, variables, ctx)];
+                    case 2:
+                        _a.sent();
+                        _a.label = 3;
+                    case 3: return [2 /*return*/];
+                }
+            });
+        }); } }));
+}
+exports.useDeleteReply = useDeleteReply;
+//# sourceMappingURL=useReply.js.map

package/dist/utils/hooks/SynapseAPI/forum/useReply.js.map

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package/dist/utils/hooks/SynapseAPI/forum/useThread.d.ts

@@ -0,0 +1,18 @@
+import { UseQueryOptions, UseMutationOptions } from 'react-query';
+import { CreateDiscussionThread, DiscussionThreadBundle, UpdateThreadMessageRequest, UpdateThreadTitleRequest } from '../../../synapseTypes/DiscussionBundle';
+import { SynapseClientError } from '../../../SynapseClientError';
+export declare function useGetThread(threadId: string): {
+    threadData: DiscussionThreadBundle | undefined;
+    threadBody: string | undefined;
+    togglePin: () => void;
+    isLoading: boolean;
+};
+export declare function useGetThreadBundle(threadId: string, options?: UseQueryOptions<DiscussionThreadBundle, SynapseClientError>): import("react-query").UseQueryResult<DiscussionThreadBundle, SynapseClientError>;
+export declare function useGetThreadBody(threadData?: DiscussionThreadBundle, options?: UseQueryOptions<string, SynapseClientError>): import("react-query").UseQueryResult<string, SynapseClientError>;
+export declare function useUpdateThreadTitle(options?: UseMutationOptions<DiscussionThreadBundle, SynapseClientError, UpdateThreadTitleRequest>): import("react-query").UseMutationResult<DiscussionThreadBundle, SynapseClientError, UpdateThreadTitleRequest, unknown>;
+export declare function useUpdateThreadMessage(options?: UseMutationOptions<DiscussionThreadBundle, SynapseClientError, UpdateThreadMessageRequest>): import("react-query").UseMutationResult<DiscussionThreadBundle, SynapseClientError, UpdateThreadMessageRequest, unknown>;
+export declare function useCreateThread(options?: UseMutationOptions<DiscussionThreadBundle, SynapseClientError, CreateDiscussionThread>): import("react-query").UseMutationResult<DiscussionThreadBundle, SynapseClientError, CreateDiscussionThread, unknown>;
+export declare function useDeleteThread(options?: UseMutationOptions<void, SynapseClientError, DiscussionThreadBundle>): import("react-query").UseMutationResult<void, SynapseClientError, DiscussionThreadBundle, unknown>;
+export declare function useRestoreThread(options?: UseMutationOptions<void, SynapseClientError, DiscussionThreadBundle>): import("react-query").UseMutationResult<void, SynapseClientError, DiscussionThreadBundle, unknown>;
+export declare function usePinThread(options?: UseMutationOptions<void, SynapseClientError, DiscussionThreadBundle>): import("react-query").UseMutationResult<void, SynapseClientError, DiscussionThreadBundle, unknown>;
+export declare function useUnPinThread(options?: UseMutationOptions<void, SynapseClientError, DiscussionThreadBundle>): import("react-query").UseMutationResult<void, SynapseClientError, DiscussionThreadBundle, unknown>;