@gen3/frontend 0.12.5 → 0.12.6

package/dist/dts/features/CohortBuilder/downloads/actions/addCohortToDataLibrary.js

@@ -0,0 +1,266 @@
+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 { coreStore, downloadJSONDataFromGuppy, EmptyFilterSet, fetchJSONDataFromURL, GEN3_MANIFEST_API, selectCurrentCohortFilters, } from '@gen3/core';
+import { JSONPath } from 'jsonpath-plus';
+export var processFilesForManifest = function (data, path, fieldMapping) {
+    if (path === void 0) { path = ''; }
+    if (fieldMapping === void 0) { fieldMapping = {
+        file_name: 'file_name',
+        file_size: 'file_size',
+        md5sum: 'md5Sum',
+        object_id: 'object_id',
+    }; }
+    return mapDataToMappingDefinition(data, path, fieldMapping);
+};
+export var processFilesForDataLibrary = function (data, path, fieldMapping) {
+    if (path === void 0) { path = '$.*'; }
+    if (fieldMapping === void 0) { fieldMapping = {
+        name: 'name',
+        size: 'size',
+        md5sum: 'md5Sum',
+        guid: 'guid',
+        type: 'type',
+        dataset_id: 'dataset_id',
+    }; }
+    return mapDataToMappingDefinition(data, path, fieldMapping);
+};
+export var mapDataToMappingDefinition = function (manifestData, path, fieldMapping) {
+    if (fieldMapping === void 0) { fieldMapping = {
+        file_name: 'file_name',
+        file_size: 'file_size',
+        md5sum: 'md5Sum',
+        id: 'id',
+        dataset_id: 'dataset_id',
+    }; }
+    var missing = [];
+    var results = manifestData.reduce(function (acc, data) {
+        var root = JSONPath({ path: path, json: data });
+        if ((root === null || root === void 0 ? void 0 : root.length) > 0) {
+            root[0].forEach(function (dataFileItem) {
+                var manifestEntry = Object.keys(fieldMapping).reduce(function (entry, field) {
+                    if (fieldMapping[field] in dataFileItem) {
+                        entry[field] = dataFileItem[fieldMapping[field]];
+                    }
+                    return entry;
+                }, { type: 'GA4GH_DRS' });
+                if (manifestEntry['id'] !== undefined) {
+                    // only add if we have an object_id
+                    acc.push(manifestEntry);
+                }
+                else {
+                    missing.push(manifestEntry);
+                }
+            });
+        }
+        return acc;
+    }, []);
+    if (missing.length > 0) {
+        console.warn("The following files were not added to the manifest because they do not have an object_id: ".concat(JSON.stringify(missing)));
+    }
+    return results;
+};
+/**
+ * Given a flattened list of data items where the with a dataset_id, create an array of datasets
+ * @param data
+ * @param field
+ */
+export var createDatasets = function (data, field) {
+    return data.reduce(function (acc, item, index) {
+        var _a;
+        var _b;
+        // for every item in the data
+        // get it's dataset is and add it to the acc
+        var datasetId = String(item[field]); // get the id of the dataset or cohort
+        var entryExists = acc[datasetId];
+        var fileItem = item;
+        if (entryExists && entryExists.itemType === 'Dataset') {
+            entryExists.members[fileItem.id] = fileItem;
+        }
+        else {
+            acc[datasetId] = {
+                id: datasetId,
+                name: (_b = item === null || item === void 0 ? void 0 : item.name) !== null && _b !== void 0 ? _b : "".concat(datasetId, "-").concat(index),
+                members: (_a = {},
+                    _a[fileItem.id] = fileItem,
+                    _a),
+                itemType: 'Dataset',
+            };
+        }
+        return acc;
+    }, {});
+};
+var REQUIRED_FIELDS = [
+    'datasetIdField',
+    'fileIndex',
+    'cohortIndex',
+    'fileIdField',
+    'fileFields',
+];
+/* TODO: complete this function */
+export var addCohortDataFilesToDataLibraryAsDataset = function (params, done, onError, onAbort, signal, onComplete) { return __awaiter(void 0, void 0, void 0, function () {
+    var cohort, _a, index, cohortIndex, accessibility, _b, datasetIdField, fileIdField, fileFields, libraryDataItemMapping, _c, dataPath, cohortFilters, fileInformationParameters, cohortDatafiles, datasets, err_1, resultErr;
+    var _d;
+    return __generator(this, function (_e) {
+        switch (_e.label) {
+            case 0:
+                cohort = selectCurrentCohortFilters(coreStore.getState());
+                _a = params, index = _a.index, cohortIndex = _a.cohortIndex, accessibility = _a.accessibility, _b = _a.datasetIdField, datasetIdField = _b === void 0 ? 'dataset_id' : _b, fileIdField = _a.fileIdField, fileFields = _a.fileFields, libraryDataItemMapping = _a.libraryDataItemMapping, _c = _a.dataPath, dataPath = _c === void 0 ? '*' : _c;
+                // test if all required fields are present
+                if (REQUIRED_FIELDS.some(function (field) { return !(field in params); })) {
+                    if (onError)
+                        onError(new Error("Missing required fields: ".concat(REQUIRED_FIELDS.join(', '))));
+                    return [2 /*return*/];
+                }
+                cohortFilters = (_d = cohort[cohortIndex]) !== null && _d !== void 0 ? _d : EmptyFilterSet;
+                fileInformationParameters = {
+                    filter: cohortFilters,
+                    type: index,
+                    fields: fileFields,
+                    accessibility: accessibility,
+                    format: 'json',
+                };
+                _e.label = 1;
+            case 1:
+                _e.trys.push([1, 3, , 4]);
+                return [4 /*yield*/, downloadJSONDataFromGuppy({
+                        parameters: fileInformationParameters,
+                        onAbort: onAbort,
+                        signal: signal,
+                    })];
+            case 2:
+                cohortDatafiles = _e.sent();
+                cohortDatafiles = processFilesForDataLibrary(cohortDatafiles, "$.".concat(dataPath), libraryDataItemMapping);
+                if (cohortDatafiles.length === 0) {
+                    throw new Error('No data found for the current filters');
+                }
+                datasets = createDatasets(cohortDatafiles, datasetIdField);
+                // add/update dataset to the data library
+                if (done)
+                    done(); // clear the notification
+                if (onComplete)
+                    onComplete(datasets);
+                return [3 /*break*/, 4];
+            case 3:
+                err_1 = _e.sent();
+                resultErr = void 0;
+                if (typeof err_1 === 'string')
+                    resultErr = new Error(err_1);
+                if (err_1 instanceof Error)
+                    resultErr = err_1;
+                if (!resultErr)
+                    resultErr = new Error('unknown error in download manifest');
+                if (onError)
+                    onError(resultErr);
+                return [3 /*break*/, 4];
+            case 4: return [2 /*return*/];
+        }
+    });
+}); };
+export var exportCohortToWorkspace = function (params, done, onError, onAbort, signal) { return __awaiter(void 0, void 0, void 0, function () {
+    var cohort, _a, index, cohortIndex, accessibility, metadataIndex, fileFields, manifestFieldMapping, metadataFields, _b, dataPath, cohortFilters, fileQueryParameters, metadataQueryParameters, cohortDatafiles, cohortMetaData, err_2, resultErr;
+    var _c;
+    return __generator(this, function (_d) {
+        switch (_d.label) {
+            case 0:
+                cohort = selectCurrentCohortFilters(coreStore.getState());
+                _a = params, index = _a.index, cohortIndex = _a.cohortIndex, accessibility = _a.accessibility, metadataIndex = _a.metadataIndex, fileFields = _a.fileFields, manifestFieldMapping = _a.manifestFieldMapping, metadataFields = _a.metadataFields, _b = _a.dataPath, dataPath = _b === void 0 ? '' : _b;
+                cohortFilters = (_c = cohort[cohortIndex]) !== null && _c !== void 0 ? _c : EmptyFilterSet;
+                fileQueryParameters = {
+                    filter: cohortFilters,
+                    type: index,
+                    fields: fileFields,
+                    accessibility: accessibility,
+                    format: 'json',
+                };
+                metadataQueryParameters = {
+                    filter: cohortFilters,
+                    type: cohortIndex,
+                    fields: metadataFields,
+                    accessibility: accessibility,
+                    format: 'json',
+                };
+                _d.label = 1;
+            case 1:
+                _d.trys.push([1, 6, , 7]);
+                return [4 /*yield*/, downloadJSONDataFromGuppy({
+                        parameters: fileQueryParameters,
+                        onAbort: onAbort,
+                        signal: signal,
+                    })];
+            case 2:
+                cohortDatafiles = _d.sent();
+                cohortDatafiles = processFilesForManifest(cohortDatafiles, dataPath, manifestFieldMapping);
+                if (cohortDatafiles.length === 0) {
+                    throw new Error('No data found for the current filters');
+                }
+                return [4 /*yield*/, downloadJSONDataFromGuppy({
+                        parameters: metadataQueryParameters,
+                        onAbort: onAbort,
+                        signal: signal,
+                    })];
+            case 3:
+                cohortMetaData = _d.sent();
+                // save files manifest
+                return [4 /*yield*/, fetchJSONDataFromURL("".concat(GEN3_MANIFEST_API, "/"), true, 'POST', JSON.stringify(cohortDatafiles), signal)];
+            case 4:
+                // save files manifest
+                _d.sent();
+                // save the metadata
+                return [4 /*yield*/, fetchJSONDataFromURL("".concat(GEN3_MANIFEST_API, "/metadata"), true, 'POST', JSON.stringify(cohortMetaData), signal)];
+            case 5:
+                // save the metadata
+                _d.sent();
+                if (done)
+                    done();
+                return [3 /*break*/, 7];
+            case 6:
+                err_2 = _d.sent();
+                resultErr = void 0;
+                if (typeof err_2 === 'string')
+                    resultErr = new Error(err_2);
+                if (err_2 instanceof Error)
+                    resultErr = err_2;
+                if (!resultErr)
+                    resultErr = new Error('unknown error in download manifest');
+                if (onError)
+                    onError(resultErr);
+                return [3 /*break*/, 7];
+            case 7: return [2 /*return*/];
+        }
+    });
+}); };
+//# sourceMappingURL=addCohortToDataLibrary.js.map

package/dist/dts/features/CohortBuilder/downloads/actions/addCohortToDataLibrary.js.map

@@ -0,0 +1 @@
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package/dist/dts/features/CohortBuilder/downloads/actions/downloadManifest.d.ts

@@ -15,5 +15,5 @@ export interface DownloadToManifestParams extends Record<string, any> {
     referenceIdFieldInResourceIndex?: string;
     fileFields?: string[];
 }
-export declare const downloadToManifestAction: (params: Record<string, any>, done?: () => void, onError?: (error: Error) => void, onAbort?: () => void, signal?: AbortSignal, dataFormat?: string) => Promise<void>;
+export declare const downloadToManifestAction: (params: Record<string, any>, done?: () => void, onError?: (error: Error) => void, onAbort?: () => void, signal?: AbortSignal) => Promise<void>;
 //# sourceMappingURL=downloadManifest.d.ts.map

package/dist/dts/features/CohortBuilder/downloads/actions/downloadManifest.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"downloadManifest.d.ts","sourceRoot":"","sources":["../../../../../../src/features/CohortBuilder/downloads/actions/downloadManifest.ts"],"names":[],"mappings":"AAAA,OAAO,EAML,UAAU,EACX,MAAM,YAAY,CAAC;AAKpB;;;;;;;GAOG;AACH,eAAO,MAAM,eAAe,GAC1B,MAAM,UAAU,EAAE,EAClB,iBAAiB,MAAM,EACvB,gBAAgB,MAAM,EAAE,iBAQzB,CAAC;AAEF,MAAM,WAAW,wBAAyB,SAAQ,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC;IACnE,iBAAiB,EAAE,MAAM,CAAC;IAC1B,eAAe,EAAE,MAAM,CAAC;IACxB,2BAA2B,CAAC,EAAE,MAAM,CAAC;IACrC,+BAA+B,CAAC,EAAE,MAAM,CAAC;IACzC,UAAU,CAAC,EAAE,MAAM,EAAE,CAAC;CACvB;AAED,eAAO,MAAM,wBAAwB,GACnC,QAAQ,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,EAC3B,OAAO,MAAM,IAAI,EACjB,UAAU,CAAC,KAAK,EAAE,KAAK,KAAK,IAAI,EAChC,UAAU,MAAM,IAAI,EACpB,SAAS,WAAW,EACpB,aAAa,MAAM,KAClB,OAAO,CAAC,IAAI,CA8Hd,CAAC"}
+{"version":3,"file":"downloadManifest.d.ts","sourceRoot":"","sources":["../../../../../../src/features/CohortBuilder/downloads/actions/downloadManifest.ts"],"names":[],"mappings":"AAAA,OAAO,EAML,UAAU,EACX,MAAM,YAAY,CAAC;AAKpB;;;;;;;GAOG;AACH,eAAO,MAAM,eAAe,GAC1B,MAAM,UAAU,EAAE,EAClB,iBAAiB,MAAM,EACvB,gBAAgB,MAAM,EAAE,iBAQzB,CAAC;AAEF,MAAM,WAAW,wBAAyB,SAAQ,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC;IACnE,iBAAiB,EAAE,MAAM,CAAC;IAC1B,eAAe,EAAE,MAAM,CAAC;IACxB,2BAA2B,CAAC,EAAE,MAAM,CAAC;IACrC,+BAA+B,CAAC,EAAE,MAAM,CAAC;IACzC,UAAU,CAAC,EAAE,MAAM,EAAE,CAAC;CACvB;AAED,eAAO,MAAM,wBAAwB,GACnC,QAAQ,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,EAC3B,OAAO,MAAM,IAAI,EACjB,UAAU,CAAC,KAAK,EAAE,KAAK,KAAK,IAAI,EAChC,UAAU,MAAM,IAAI,EACpB,SAAS,WAAW,KACnB,OAAO,CAAC,IAAI,CA+Hd,CAAC"}

package/dist/dts/features/CohortBuilder/downloads/actions/downloadManifest.js

@@ -73,13 +73,13 @@ export var processManifest = function (data, resourceIdField, manifestFields) {
         return hasAllFields && item[resourceIdField] !== undefined;
     });
 };
-export var downloadToManifestAction = function (params, done, onError, onAbort, signal, dataFormat) { return __awaiter(void 0, void 0, void 0, function () {
-    var referenceIdFieldInDataIndex, referenceIdFieldInResourceIndex, resourceIndexType, resourceIdField, fileFields, manifestFields, manifestFilename, cohortFilterParams, resultManifest, str, blob, err_1, resultErr, refIDList, refIdsFilter, resultManifest, bytes, blob, err_2;
+export var downloadToManifestAction = function (params, done, onError, onAbort, signal) { return __awaiter(void 0, void 0, void 0, function () {
+    var referenceIdFieldInDataIndex, referenceIdFieldInResourceIndex, resourceIndexType, resourceIdField, fileFields, dataFormat, manifestFields, manifestFilename, cohortFilterParams, resultManifest, str, blob, err_1, resultErr, refIDList, refIdsFilter, resultManifest, bytes, blob, err_2;
     var _a;
     return __generator(this, function (_b) {
         switch (_b.label) {
             case 0:
-                referenceIdFieldInDataIndex = params.referenceIdFieldInDataIndex, referenceIdFieldInResourceIndex = params.referenceIdFieldInResourceIndex, resourceIndexType = params.resourceIndexType, resourceIdField = params.resourceIdField, fileFields = params.fileFields;
+                referenceIdFieldInDataIndex = params.referenceIdFieldInDataIndex, referenceIdFieldInResourceIndex = params.referenceIdFieldInResourceIndex, resourceIndexType = params.resourceIndexType, resourceIdField = params.resourceIdField, fileFields = params.fileFields, dataFormat = params.dataFormat;
                 manifestFields = fileFields !== null && fileFields !== void 0 ? fileFields : DEFAULT_FILE_FIELDS;
                 manifestFilename = (_a = params === null || params === void 0 ? void 0 : params.filename) !== null && _a !== void 0 ? _a : "".concat(params.type, "_manifest.json");
                 cohortFilterParams = {

package/dist/dts/features/CohortBuilder/downloads/actions/downloadManifest.js.map

@@ -1 +1 @@
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package/dist/dts/features/CohortBuilder/downloads/actions/extractDataSelectionFromCohort.d.ts

@@ -0,0 +1,22 @@
+import { Accessibility, DatasetOrCohort, FilterSet, JSONObject } from '@gen3/core';
+interface ExtractDataSelectionFromCohortParams {
+    index: string;
+    accessibility?: Accessibility;
+    fileFields: string[];
+    datasetIdField: string;
+    libraryDataItemMapping?: Record<string, string>;
+    dataPath?: string;
+    cohortFilters: FilterSet;
+}
+export interface ExtractDataSelectionFromCohortResult {
+    ok: boolean;
+    datasets: DatasetOrCohort;
+    error?: {
+        kind: 'abort' | 'invalid-args' | 'network' | 'unknown';
+        message: string;
+    };
+}
+export declare function extractDataSelectionFromCohort({ cohortFilters, index, accessibility, fileFields, libraryDataItemMapping, datasetIdField, dataPath, }: ExtractDataSelectionFromCohortParams): Promise<ExtractDataSelectionFromCohortResult>;
+export declare function extractDataSelectionFromCohortQuery(data: JSONObject[], libraryDataItemMapping?: Record<string, string>, datasetIdField?: string, dataPath?: string): ExtractDataSelectionFromCohortResult;
+export {};
+//# sourceMappingURL=extractDataSelectionFromCohort.d.ts.map

package/dist/dts/features/CohortBuilder/downloads/actions/extractDataSelectionFromCohort.d.ts.map

@@ -0,0 +1 @@
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package/dist/dts/features/CohortBuilder/downloads/actions/extractDataSelectionFromCohort.js

@@ -0,0 +1,134 @@
+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 { Accessibility, downloadJSONDataFromGuppy, } from '@gen3/core';
+import { createDatasets, processFilesForDataLibrary, } from './addCohortToDataLibrary';
+var toErrorMessage = function (err) {
+    if (err instanceof Error)
+        return err.message || 'Unknown error';
+    if (typeof err === 'string')
+        return err;
+    try {
+        return JSON.stringify(err);
+    }
+    catch (_a) {
+        return 'Unknown error';
+    }
+};
+/**
+ * Accepts either:
+ * - a JSONPath fragment like "*" or "data.items"
+ * - a full JSONPath like "$.*" or "$.data.items"
+ * and normalizes to a valid JSONPath string.
+ */
+var normalizeJsonPath = function (dataPath) {
+    var trimmed = (dataPath !== null && dataPath !== void 0 ? dataPath : '').trim();
+    if (!trimmed)
+        return '$.*';
+    if (trimmed.startsWith('$'))
+        return trimmed;
+    if (trimmed.startsWith('.'))
+        return "$".concat(trimmed);
+    return "$.".concat(trimmed);
+};
+export function extractDataSelectionFromCohort(_a) {
+    return __awaiter(this, arguments, void 0, function (_b) {
+        var fileInformationParameters, raw, err_1, message, kind;
+        var cohortFilters = _b.cohortFilters, index = _b.index, _c = _b.accessibility, accessibility = _c === void 0 ? Accessibility.ALL : _c, fileFields = _b.fileFields, libraryDataItemMapping = _b.libraryDataItemMapping, _d = _b.datasetIdField, datasetIdField = _d === void 0 ? 'dataset_id' : _d, _e = _b.dataPath, dataPath = _e === void 0 ? '*' : _e;
+        return __generator(this, function (_f) {
+            switch (_f.label) {
+                case 0:
+                    if (!index || !Array.isArray(fileFields) || fileFields.length === 0) {
+                        return [2 /*return*/, {
+                                ok: false,
+                                datasets: {},
+                                error: {
+                                    kind: 'invalid-args',
+                                    message: 'Missing required parameters: fileIndex and non-empty fileFields.',
+                                },
+                            }];
+                    }
+                    fileInformationParameters = {
+                        filter: cohortFilters,
+                        type: index,
+                        fields: fileFields,
+                        accessibility: accessibility,
+                        format: 'json',
+                    };
+                    _f.label = 1;
+                case 1:
+                    _f.trys.push([1, 3, , 4]);
+                    return [4 /*yield*/, downloadJSONDataFromGuppy({
+                            parameters: fileInformationParameters,
+                        })];
+                case 2:
+                    raw = (_f.sent());
+                    return [2 /*return*/, extractDataSelectionFromCohortQuery(raw, libraryDataItemMapping, datasetIdField, dataPath)];
+                case 3:
+                    err_1 = _f.sent();
+                    message = toErrorMessage(err_1);
+                    kind = message.toLowerCase().includes('abort') ? 'abort' : 'unknown';
+                    return [2 /*return*/, {
+                            ok: false,
+                            datasets: {},
+                            error: { kind: kind, message: message },
+                        }];
+                case 4: return [2 /*return*/];
+            }
+        });
+    });
+}
+export function extractDataSelectionFromCohortQuery(data, libraryDataItemMapping, datasetIdField, dataPath) {
+    if (libraryDataItemMapping === void 0) { libraryDataItemMapping = {}; }
+    if (datasetIdField === void 0) { datasetIdField = 'dataset_id'; }
+    if (dataPath === void 0) { dataPath = '*'; }
+    try {
+        var path = normalizeJsonPath(dataPath);
+        var files = processFilesForDataLibrary(data, path, libraryDataItemMapping);
+        var datasets = createDatasets(files, datasetIdField);
+        return { ok: true, datasets: datasets };
+    }
+    catch (err) {
+        var message = toErrorMessage(err);
+        var kind = message.toLowerCase().includes('abort') ? 'abort' : 'unknown';
+        return {
+            ok: false,
+            datasets: {},
+            error: { kind: kind, message: message },
+        };
+    }
+}
+//# sourceMappingURL=extractDataSelectionFromCohort.js.map

package/dist/dts/features/CohortBuilder/downloads/actions/extractDataSelectionFromCohort.js.map

@@ -0,0 +1 @@
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package/dist/dts/features/CohortBuilder/downloads/actions/registeredActions.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"registeredActions.d.ts","sourceRoot":"","sources":["../../../../../../src/features/CohortBuilder/downloads/actions/registeredActions.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,4BAA4B,EAE7B,MAAM,aAAa,CAAC;AAMrB,UAAU,wBAAwB;IAChC,QAAQ,CAAC,MAAM,EAAE,4BAA4B,CAAC;IAC9C,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC;CACpC;AAID,eAAO,MAAM,gBAAgB,EAAE,4BAO9B,CAAC;AAEF,eAAO,MAAM,oBAAoB,GAC/B,YAAY,MAAM,EAClB,YAAY,wBAAwB,SAGrC,CAAC;AAEF,eAAO,MAAM,gBAAgB,GAC3B,aAAa,MAAM,KAClB,wBAAwB,GAAG,SAW7B,CAAC;AAEF,eAAO,MAAM,4BAA4B,YAiBxC,CAAC"}
+{"version":3,"file":"registeredActions.d.ts","sourceRoot":"","sources":["../../../../../../src/features/CohortBuilder/downloads/actions/registeredActions.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,4BAA4B,EAAE,MAAM,aAAa,CAAC;AAU3D,UAAU,wBAAwB;IAChC,QAAQ,CAAC,MAAM,EAAE,4BAA4B,CAAC;IAC9C,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC;CACpC;AAID,eAAO,MAAM,gBAAgB,EAAE,4BAO9B,CAAC;AAEF,eAAO,MAAM,oBAAoB,GAC/B,YAAY,MAAM,EAClB,YAAY,wBAAwB,SAGrC,CAAC;AAEF,eAAO,MAAM,gBAAgB,GAC3B,aAAa,MAAM,KAClB,wBAAwB,GAAG,SAW7B,CAAC;AAEF,eAAO,MAAM,4BAA4B,YAyBxC,CAAC"}

package/dist/dts/features/CohortBuilder/downloads/actions/registeredActions.js

@@ -1,5 +1,6 @@
 import { downloadToFileAction } from './downloadToFile';
 import { downloadToManifestAction } from './downloadManifest';
+import { addCohortDataFilesToDataLibraryAsDataset, exportCohortToWorkspace, } from './addCohortToDataLibrary';
 var registeredButtonActions = {};
 export var NullButtonAction = function (_params, done) {
     return new Promise(function (done) {
@@ -38,6 +39,14 @@ export var registerDefaultButtonActions = function () {
         action: downloadToManifestAction,
         args: { format: 'manifest' },
     });
+    registerButtonAction('cohortDataFilesToDataLibrary', {
+        action: addCohortDataFilesToDataLibraryAsDataset,
+        args: { format: 'json' },
+    });
+    registerButtonAction('exportCohortToWorkspace', {
+        action: exportCohortToWorkspace,
+        args: { format: 'json' },
+    });
 };
 registerDefaultButtonActions();
 //# sourceMappingURL=registeredActions.js.map

package/dist/dts/features/CohortBuilder/downloads/actions/registeredActions.js.map

@@ -1 +1 @@
-{"version":3,"file":"registeredActions.js","sourceRoot":"","sources":["../../../../../../src/features/CohortBuilder/downloads/actions/registeredActions.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,oBAAoB,EAAE,MAAM,kBAAkB,CAAC;AACxD,OAAO,EAAE,wBAAwB,EAAE,MAAM,oBAAoB,CAAC;AAS9D,IAAM,uBAAuB,GAA6C,EAAE,CAAC;AAE7E,MAAM,CAAC,IAAM,gBAAgB,GAAiC,UAC5D,OAAO,EACP,IAAI;IAEJ,OAAO,IAAI,OAAO,CAAO,UAAC,IAAI;QAC5B,IAAI,IAAI;YAAE,IAAI,EAAE,CAAC;IACnB,CAAC,CAAC,CAAC;AACL,CAAC,CAAC;AAEF,MAAM,CAAC,IAAM,oBAAoB,GAAG,UAClC,UAAkB,EAClB,UAAoC;IAEpC,uBAAuB,CAAC,UAAU,CAAC,GAAG,UAAU,CAAC;AACnD,CAAC,CAAC;AAEF,MAAM,CAAC,IAAM,gBAAgB,GAAG,UAC9B,UAAmB;IAEnB,IAAI,UAAU,KAAK,SAAS,EAAE,CAAC;QAC7B,OAAO,CAAC,KAAK,CAAC,mCAAmC,CAAC,CAAC;QACnD,OAAO,SAAS,CAAC;IACnB,CAAC;IAED,IAAI,CAAC,CAAC,UAAU,IAAI,uBAAuB,CAAC,EAAE,CAAC;QAC7C,OAAO,CAAC,KAAK,CAAC,sCAAsC,EAAE,UAAU,CAAC,CAAC;QAClE,OAAO,SAAS,CAAC;IACnB,CAAC;IACD,OAAO,uBAAuB,CAAC,UAAU,CAAC,CAAC;AAC7C,CAAC,CAAC;AAEF,MAAM,CAAC,IAAM,4BAA4B,GAAG;IAC1C,oBAAoB,CAAC,WAAW,EAAE;QAChC,MAAM,EAAE,oBAAoB;QAC5B,IAAI,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE;KACzB,CAAC,CAAC;IACH,oBAAoB,CAAC,UAAU,EAAE;QAC/B,MAAM,EAAE,oBAAoB;QAC5B,IAAI,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE;KACxB,CAAC,CAAC;IACH,oBAAoB,CAAC,UAAU,EAAE;QAC/B,MAAM,EAAE,oBAAoB;QAC5B,IAAI,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE;KACxB,CAAC,CAAC;IACH,oBAAoB,CAAC,UAAU,EAAE;QAC/B,MAAM,EAAE,wBAAwB;QAChC,IAAI,EAAE,EAAE,MAAM,EAAE,UAAU,EAAE;KAC7B,CAAC,CAAC;AACL,CAAC,CAAC;AAEF,4BAA4B,EAAE,CAAC"}
+{"version":3,"file":"registeredActions.js","sourceRoot":"","sources":["../../../../../../src/features/CohortBuilder/downloads/actions/registeredActions.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,oBAAoB,EAAE,MAAM,kBAAkB,CAAC;AACxD,OAAO,EAAE,wBAAwB,EAAE,MAAM,oBAAoB,CAAC;AAC9D,OAAO,EACL,wCAAwC,EACxC,uBAAuB,GACxB,MAAM,0BAA0B,CAAC;AASlC,IAAM,uBAAuB,GAA6C,EAAE,CAAC;AAE7E,MAAM,CAAC,IAAM,gBAAgB,GAAiC,UAC5D,OAAO,EACP,IAAI;IAEJ,OAAO,IAAI,OAAO,CAAO,UAAC,IAAI;QAC5B,IAAI,IAAI;YAAE,IAAI,EAAE,CAAC;IACnB,CAAC,CAAC,CAAC;AACL,CAAC,CAAC;AAEF,MAAM,CAAC,IAAM,oBAAoB,GAAG,UAClC,UAAkB,EAClB,UAAoC;IAEpC,uBAAuB,CAAC,UAAU,CAAC,GAAG,UAAU,CAAC;AACnD,CAAC,CAAC;AAEF,MAAM,CAAC,IAAM,gBAAgB,GAAG,UAC9B,UAAmB;IAEnB,IAAI,UAAU,KAAK,SAAS,EAAE,CAAC;QAC7B,OAAO,CAAC,KAAK,CAAC,mCAAmC,CAAC,CAAC;QACnD,OAAO,SAAS,CAAC;IACnB,CAAC;IAED,IAAI,CAAC,CAAC,UAAU,IAAI,uBAAuB,CAAC,EAAE,CAAC;QAC7C,OAAO,CAAC,KAAK,CAAC,sCAAsC,EAAE,UAAU,CAAC,CAAC;QAClE,OAAO,SAAS,CAAC;IACnB,CAAC;IACD,OAAO,uBAAuB,CAAC,UAAU,CAAC,CAAC;AAC7C,CAAC,CAAC;AAEF,MAAM,CAAC,IAAM,4BAA4B,GAAG;IAC1C,oBAAoB,CAAC,WAAW,EAAE;QAChC,MAAM,EAAE,oBAAoB;QAC5B,IAAI,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE;KACzB,CAAC,CAAC;IACH,oBAAoB,CAAC,UAAU,EAAE;QAC/B,MAAM,EAAE,oBAAoB;QAC5B,IAAI,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE;KACxB,CAAC,CAAC;IACH,oBAAoB,CAAC,UAAU,EAAE;QAC/B,MAAM,EAAE,oBAAoB;QAC5B,IAAI,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE;KACxB,CAAC,CAAC;IACH,oBAAoB,CAAC,UAAU,EAAE;QAC/B,MAAM,EAAE,wBAAwB;QAChC,IAAI,EAAE,EAAE,MAAM,EAAE,UAAU,EAAE;KAC7B,CAAC,CAAC;IACH,oBAAoB,CAAC,8BAA8B,EAAE;QACnD,MAAM,EAAE,wCAAwC;QAChD,IAAI,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE;KACzB,CAAC,CAAC;IACH,oBAAoB,CAAC,yBAAyB,EAAE;QAC9C,MAAM,EAAE,uBAAuB;QAC/B,IAAI,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE;KACzB,CAAC,CAAC;AACL,CAAC,CAAC;AAEF,4BAA4B,EAAE,CAAC"}

package/dist/dts/features/CohortBuilder/downloads/downloadActionHook.d.ts

@@ -1,8 +1,9 @@
 import { GuppyActionButtonProps } from '../types';
 interface GuppyDownloadActionHookProps extends Pick<GuppyActionButtonProps, 'Modal403' | 'Modal400' | 'done' | 'customErrorMessage' | 'hideNotification' | 'actionFunction' | 'actionArgs'> {
     setIsActive?: (active: boolean) => void;
+    onCompleted?: (args?: unknown) => void;
 }
-declare const useGuppyActionButton: ({ Modal403, Modal400, done, customErrorMessage, hideNotification, actionFunction, actionArgs, setIsActive, }: GuppyDownloadActionHookProps) => {
+declare const useGuppyActionButton: ({ Modal403, Modal400, done, customErrorMessage, hideNotification, actionFunction, actionArgs, setIsActive, onCompleted, }: GuppyDownloadActionHookProps) => {
     handleClick: () => Promise<void>;
     icon: import("react/jsx-runtime").JSX.Element;
     active: boolean;

package/dist/dts/features/CohortBuilder/downloads/downloadActionHook.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"downloadActionHook.d.ts","sourceRoot":"","sources":["../../../../../src/features/CohortBuilder/downloads/downloadActionHook.tsx"],"names":[],"mappings":"AAEA,OAAO,EAAE,sBAAsB,EAAE,MAAM,UAAU,CAAC;AAalD,UAAU,4BAA6B,SAAQ,IAAI,CACjD,sBAAsB,EACpB,UAAU,GACV,UAAU,GACV,MAAM,GACN,oBAAoB,GACpB,kBAAkB,GAClB,gBAAgB,GAChB,YAAY,CACf;IACC,WAAW,CAAC,EAAE,CAAC,MAAM,EAAE,OAAO,KAAK,IAAI,CAAC;IACxC,WAAW,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,OAAO,KAAK,IAAI,CAAC;CACxC;AAED,QAAA,MAAM,oBAAoB,GAAI,2HAU3B,4BAA4B;;;;CA6G9B,CAAC;AAEF,eAAe,oBAAoB,CAAC"}

package/dist/dts/features/CohortBuilder/downloads/downloadActionHook.js

@@ -48,8 +48,8 @@ var showErrorMessage = function (error) {
     });
 };
 var useGuppyActionButton = function (_a) {
-    var _b = _a.Modal403, Modal403 = _b === void 0 ? Modals.NoAccessModal : _b, _c = _a.Modal400, Modal400 = _c === void 0 ? Modals.GeneralErrorModal : _c, done = _a.done, customErrorMessage = _a.customErrorMessage, _d = _a.hideNotification, hideNotification = _d === void 0 ? false : _d, actionFunction = _a.actionFunction, actionArgs = _a.actionArgs, _e = _a.setIsActive, setIsActive = _e === void 0 ? function (_) { return null; } : _e;
-    var _f = useState(false), active = _f[0], setActive = _f[1];
+    var _b = _a.Modal403, Modal403 = _b === void 0 ? Modals.NoAccessModal : _b, _c = _a.Modal400, Modal400 = _c === void 0 ? Modals.GeneralErrorModal : _c, done = _a.done, customErrorMessage = _a.customErrorMessage, _d = _a.hideNotification, hideNotification = _d === void 0 ? false : _d, actionFunction = _a.actionFunction, actionArgs = _a.actionArgs, _e = _a.setIsActive, setIsActive = _e === void 0 ? function (_) { return null; } : _e, _f = _a.onCompleted, onCompleted = _f === void 0 ? function () { return null; } : _f;
+    var _g = useState(false), active = _g[0], setActive = _g[1];
     var dispatch = useCoreDispatch();
     var handleError = useDeepCompareCallback(function (error) {
         var errorMessage = error.message;
@@ -126,7 +126,7 @@ var useGuppyActionButton = function (_a) {
                                 setIsActive(false);
                             // Clean up notifications...
                             cleanNotifications();
-                        }, controller.signal)];
+                        }, controller.signal, onCompleted)];
                 case 1:
                     _a.sent();
                     return [2 /*return*/];

package/dist/dts/features/CohortBuilder/downloads/downloadActionHook.js.map

@@ -1 +1 @@
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package/dist/dts/features/CohortBuilder/types.d.ts

@@ -94,8 +94,8 @@ export declare enum DownloadFileFormats {
     DATA = "DATA",
     UNDEFINED = "UNDEFINED"
 }
-export type ActionButtonFunction = (done?: () => void, onError?: (error: Error) => void, onAbort?: () => void, signal?: AbortSignal) => Promise<void>;
-export type ActionButtonWithArgsFunction = (params: Record<string, any>, done?: () => void, onError?: (error: Error) => void, onAbort?: () => void, signal?: AbortSignal) => Promise<void>;
+export type ActionButtonFunction = (done?: () => void, onError?: (error: Error) => void, onAbort?: () => void, signal?: AbortSignal, onCompleted?: (data: any) => void) => Promise<void>;
+export type ActionButtonWithArgsFunction = (params: Record<string, any>, done?: () => void, onError?: (error: Error) => void, onAbort?: () => void, signal?: AbortSignal, onCompleted?: (data: any) => void) => Promise<void>;
 export interface DownloadButtonPropsWithAction extends Omit<DownloadButtonProps, 'action' | 'actionArgs'> {
     actionFunction: ActionButtonWithArgsFunction;
     actionArgs: Record<string, any>;