cloudmr-ux 2.0.7 → 3.0.1

package/dist/core/features/data/dataActionCreation.js

@@ -0,0 +1,340 @@
+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;
+    return g = { next: verb(0), "throw": verb(1), "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 axios from "axios";
+import { createAsyncThunk } from "@reduxjs/toolkit";
+import { getEndpoints, getAppConfig } from "../../config/AppConfig";
+import { getFileExtension } from "../../common/utilities/file-transformation/utilities";
+import { is_safe_twix } from "../../common/utilities/file-transformation/anonymize";
+import { AuthenticatedHttpClient } from "../../common/utilities/AuthenticatedRequests";
+export var getUploadedData = createAsyncThunk("GET_UPLOADED_DATA", function () { return __awaiter(void 0, void 0, void 0, function () {
+    var endpoints, config, data, e_1;
+    return __generator(this, function (_a) {
+        switch (_a.label) {
+            case 0:
+                endpoints = getEndpoints();
+                config = getAppConfig();
+                _a.label = 1;
+            case 1:
+                _a.trys.push([1, 3, , 4]);
+                return [4 /*yield*/, AuthenticatedHttpClient.get(endpoints.DATA_API)];
+            case 2:
+                data = (_a.sent()).data;
+                return [2 /*return*/, data];
+            case 3:
+                e_1 = _a.sent();
+                console.log(e_1);
+                return [2 /*return*/, undefined];
+            case 4: return [2 /*return*/];
+        }
+    });
+}); });
+export var renameUploadedData = createAsyncThunk("RENAME_UPLOADED_DATA", function (_a) {
+    var fileId = _a.fileId, newName = _a.newName, is_demo_data = _a.is_demo_data;
+    return __awaiter(void 0, void 0, void 0, function () {
+        var endpoints, payload, response, e_2;
+        return __generator(this, function (_b) {
+            switch (_b.label) {
+                case 0:
+                    endpoints = getEndpoints();
+                    _b.label = 1;
+                case 1:
+                    _b.trys.push([1, 3, , 4]);
+                    payload = {
+                        fileid: fileId,
+                        filename: newName
+                    };
+                    if (is_demo_data !== undefined && is_demo_data !== null) {
+                        payload.is_demo_data = is_demo_data;
+                    }
+                    return [4 /*yield*/, AuthenticatedHttpClient.post(endpoints.DATA_RENAME_API, payload)];
+                case 2:
+                    response = _b.sent();
+                    return [2 /*return*/, response.data];
+                case 3:
+                    e_2 = _b.sent();
+                    throw e_2;
+                case 4: return [2 /*return*/];
+            }
+        });
+    });
+});
+export var deleteUploadedData = createAsyncThunk("DELETE_UPLOADED_DATA", function (_a) {
+    var fileId = _a.fileId;
+    return __awaiter(void 0, void 0, void 0, function () {
+        var endpoints, response, e_3;
+        return __generator(this, function (_b) {
+            switch (_b.label) {
+                case 0:
+                    endpoints = getEndpoints();
+                    _b.label = 1;
+                case 1:
+                    _b.trys.push([1, 3, , 4]);
+                    return [4 /*yield*/, AuthenticatedHttpClient.post("".concat(endpoints.DATA_DELETE_API, "/").concat(fileId))];
+                case 2:
+                    response = _b.sent();
+                    return [2 /*return*/, response.data];
+                case 3:
+                    e_3 = _b.sent();
+                    throw e_3;
+                case 4: return [2 /*return*/];
+            }
+        });
+    });
+});
+export var uploadData = createAsyncThunk("UploadData", function (_a, thunkAPI) {
+    var uploadToken = _a.uploadToken, file = _a.file, fileAlias = _a.fileAlias, onProgress = _a.onProgress, onUploaded = _a.onUploaded, uploadTarget = _a.uploadTarget;
+    return __awaiter(void 0, void 0, void 0, function () {
+        var FILE_CHUNK_SIZE, payload, uploadPartWithRetries_1, initResponse, _b, uploadId, partUrls_1, Key, fileParts, i, part, totalSize_1, totalUploadedParts_1, uploadedParts, endpoints, finalizeResponse, e_4;
+        return __generator(this, function (_c) {
+            switch (_c.label) {
+                case 0:
+                    console.log("start the upload uploadData");
+                    _c.label = 1;
+                case 1:
+                    _c.trys.push([1, 6, , 7]);
+                    FILE_CHUNK_SIZE = 10 * 1024 * 1024;
+                    return [4 /*yield*/, createPayload(uploadToken, file, fileAlias)];
+                case 2:
+                    payload = _c.sent();
+                    console.log("payload created", payload);
+                    if (payload === undefined)
+                        return [2 /*return*/, {
+                                code: 403,
+                                response: "file not found",
+                                file: undefined,
+                                uploadTarget: uploadTarget
+                            }];
+                    if (payload.lambdaFile === undefined)
+                        return [2 /*return*/, {
+                                code: 403,
+                                response: "data not allowed",
+                                file: undefined,
+                                uploadTarget: uploadTarget
+                            }];
+                    // Set upload progress to 0 if progress handler available
+                    if (onProgress)
+                        onProgress(0);
+                    uploadPartWithRetries_1 = function (partUrl, part, cancelTokenSource, index, retries) {
+                        if (retries === void 0) { retries = 2; }
+                        return __awaiter(void 0, void 0, void 0, function () {
+                            var response, error_1, newCancelTokenSource;
+                            return __generator(this, function (_a) {
+                                switch (_a.label) {
+                                    case 0:
+                                        _a.trys.push([0, 2, , 7]);
+                                        return [4 /*yield*/, axios.put(partUrl, part, {
+                                                headers: {
+                                                    "Content-Type": ""
+                                                },
+                                                onUploadProgress: function (progressEvent) {
+                                                    totalUploadedParts_1[index] = progressEvent.loaded;
+                                                    var totalUploaded = totalUploadedParts_1.reduce(function (a, b) { return a + b; }, 0);
+                                                    var totalProgress = totalUploaded / totalSize_1;
+                                                    if (onProgress)
+                                                        onProgress(totalProgress);
+                                                },
+                                                cancelToken: cancelTokenSource.token
+                                            })];
+                                    case 1:
+                                        response = _a.sent();
+                                        console.log(response);
+                                        return [2 /*return*/, response];
+                                    case 2:
+                                        error_1 = _a.sent();
+                                        if (!axios.isCancel(error_1)) return [3 /*break*/, 3];
+                                        console.log("Upload cancelled:", partUrl);
+                                        return [3 /*break*/, 6];
+                                    case 3:
+                                        if (!(retries > 0)) return [3 /*break*/, 5];
+                                        console.log("Retrying upload for part: ".concat(partUrl, ", attempts remaining: ").concat(retries));
+                                        cancelTokenSource.cancel("Cancelling the current request before retry.");
+                                        newCancelTokenSource = axios.CancelToken.source();
+                                        return [4 /*yield*/, uploadPartWithRetries_1(partUrl, part, newCancelTokenSource, index, retries - 1)];
+                                    case 4: return [2 /*return*/, _a.sent()];
+                                    case 5: throw error_1;
+                                    case 6: return [3 /*break*/, 7];
+                                    case 7: return [2 /*return*/];
+                                }
+                            });
+                        });
+                    };
+                    console.log(payload);
+                    console.log("Uploading to destination", payload.destination);
+                    return [4 /*yield*/, AuthenticatedHttpClient.post(payload.destination, payload.lambdaFile, payload.config)];
+                case 3:
+                    initResponse = _c.sent();
+                    console.log(initResponse);
+                    _b = initResponse.data, uploadId = _b.uploadId, partUrls_1 = _b.partUrls, Key = _b.Key;
+                    fileParts = [];
+                    for (i = 0; i < file.size; i += FILE_CHUNK_SIZE) {
+                        part = file.slice(i, i + FILE_CHUNK_SIZE);
+                        fileParts.push(part);
+                        console.log(part);
+                    }
+                    totalSize_1 = payload.file.size;
+                    totalUploadedParts_1 = new Array(fileParts.length).fill(0);
+                    return [4 /*yield*/, Promise.all(fileParts.map(function (part, index) { return __awaiter(void 0, void 0, void 0, function () {
+                            var partUrl, cancelTokenSource, partResponse, etag;
+                            return __generator(this, function (_a) {
+                                switch (_a.label) {
+                                    case 0:
+                                        partUrl = partUrls_1[index];
+                                        cancelTokenSource = axios.CancelToken.source();
+                                        return [4 /*yield*/, uploadPartWithRetries_1(partUrl, part, cancelTokenSource, index)];
+                                    case 1:
+                                        partResponse = _a.sent();
+                                        etag = partResponse === null || partResponse === void 0 ? void 0 : partResponse.headers["etag"];
+                                        console.log(partResponse);
+                                        console.log(partResponse === null || partResponse === void 0 ? void 0 : partResponse.headers);
+                                        console.log(etag);
+                                        return [2 /*return*/, {
+                                                partNumber: index + 1,
+                                                etag: etag.replace(/"/g, "")
+                                            }];
+                                }
+                            });
+                        }); }))];
+                case 4:
+                    uploadedParts = _c.sent();
+                    endpoints = getEndpoints();
+                    return [4 /*yield*/, AuthenticatedHttpClient.post(endpoints.DATA_UPLOAD_FINALIZE, {
+                            uploadId: uploadId,
+                            parts: uploadedParts,
+                            Key: Key
+                        }, payload.config)];
+                case 5:
+                    finalizeResponse = _c.sent();
+                    console.log(finalizeResponse);
+                    console.log("all uploads completed");
+                    console.log("------", onUploaded);
+                    if (onUploaded)
+                        onUploaded(initResponse, file);
+                    console.log("uploaded");
+                    // Refresh uploaded data
+                    thunkAPI.dispatch(getUploadedData());
+                    console.log("refreshed");
+                    return [2 /*return*/, {
+                            code: 200,
+                            response: initResponse.data.response,
+                            file: payload.lambdaFile,
+                            uploadTarget: uploadTarget
+                        }];
+                case 6:
+                    e_4 = _c.sent();
+                    console.log("Following error encountered during uploading:");
+                    console.error(e_4);
+                    return [2 /*return*/, {
+                            code: 500,
+                            response: e_4.response,
+                            file: undefined,
+                            uploadTarget: uploadTarget
+                        }];
+                case 7: return [2 /*return*/];
+            }
+        });
+    });
+});
+var ALLOWED_EXTENSIONS = [
+    "nii",
+    "nii.gz",
+    "mha",
+    "mhd",
+    "mrd",
+    "npx",
+    "npy",
+    "pkl",
+    "mat",
+    "dat",
+    "h5",
+    "png",
+    "jpg",
+    "jpeg",
+];
+var createPayload = function (uploadToken, file, fileAlias) { return __awaiter(void 0, void 0, void 0, function () {
+    var fileExtension, lowerExt, fileType, isSafe, lambdaFile, UploadHeaders, endpoints;
+    return __generator(this, function (_a) {
+        switch (_a.label) {
+            case 0:
+                if (!file)
+                    return [2 /*return*/, undefined];
+                fileExtension = getFileExtension(file.name);
+                lowerExt = fileExtension.toLowerCase();
+                fileType = file.type || "application/octet-stream";
+                // Validate extension
+                if (!ALLOWED_EXTENSIONS.includes(lowerExt)) {
+                    alert("This file type \".".concat(fileExtension, "\" is not allowed."));
+                    return [2 /*return*/, { lambdaFile: undefined, file: undefined }];
+                }
+                if (!(lowerExt === "dat")) return [3 /*break*/, 2];
+                console.log("checking for PHI data");
+                return [4 /*yield*/, is_safe_twix(file)];
+            case 1:
+                isSafe = _a.sent();
+                if (!isSafe) {
+                    alert("This file contains PHI data. Please anonymize the file before uploading");
+                    return [2 /*return*/, undefined];
+                }
+                _a.label = 2;
+            case 2:
+                lambdaFile = {
+                    filename: fileAlias,
+                    filetype: fileType,
+                    filesize: "".concat(file.size),
+                    filemd5: "",
+                    file: {
+                        name: file.name,
+                        lastModified: file.lastModified,
+                        size: file.size,
+                        type: file.type
+                    }
+                };
+                UploadHeaders = {
+                    headers: {
+                        "Content-Type": "application/json",
+                        "X-Api-Key": uploadToken
+                    }
+                };
+                endpoints = getEndpoints();
+                return [2 /*return*/, {
+                        destination: endpoints.DATA_UPLOAD_INIT,
+                        lambdaFile: lambdaFile,
+                        file: file,
+                        config: UploadHeaders
+                    }];
+        }
+    });
+}); };

package/dist/core/features/data/dataSlice.d.ts

@@ -0,0 +1,37 @@
+import { PayloadAction } from '@reduxjs/toolkit';
+export interface UploadedFile {
+    id: number;
+    fileName: string;
+    link: string;
+    md5?: string;
+    size: string;
+    status: string;
+    createdAt: string;
+    updatedAt: string;
+    database: string;
+    location: string;
+    renamingPending?: boolean;
+    deletionPending?: boolean;
+    is_demo_data?: boolean;
+}
+interface DataState {
+    files: Array<UploadedFile>;
+    loading: boolean;
+}
+export declare const dataSlice: import("@reduxjs/toolkit").Slice<DataState, {
+    renameData(state: DataState, action: PayloadAction<{
+        index: number;
+        alias: string;
+    }>): void;
+    deleteData(state: DataState, action: PayloadAction<{
+        index: number;
+    }>): void;
+}, "data", "data", import("@reduxjs/toolkit").SliceSelectors<DataState>>;
+export declare const renameData: import("@reduxjs/toolkit").ActionCreatorWithPayload<{
+    index: number;
+    alias: string;
+}, "data/renameData">, deleteData: import("@reduxjs/toolkit").ActionCreatorWithPayload<{
+    index: number;
+}, "data/deleteData">;
+declare const _default: import("redux").Reducer<DataState, import("redux").UnknownAction, DataState>;
+export default _default;

package/dist/core/features/data/dataSlice.js

@@ -0,0 +1,87 @@
+var _a;
+import { createSlice } from '@reduxjs/toolkit';
+import { deleteUploadedData, getUploadedData, renameUploadedData } from './dataActionCreation';
+import { convertTimestamp } from '../../common/utilities/CalendarHelper';
+var initialState = {
+    files: [],
+    loading: true
+};
+export var dataSlice = createSlice({
+    name: 'data',
+    initialState: initialState,
+    reducers: {
+        renameData: function (state, action) {
+            state.files[action.payload.index].fileName = action.payload.alias;
+        },
+        deleteData: function (state, action) {
+            state.files.splice(action.payload.index, 1);
+        }
+    },
+    extraReducers: function (builder) { return (builder.addCase(getUploadedData.pending, function (state, action) {
+        state.loading = true;
+    }),
+        builder.addCase(getUploadedData.fulfilled, function (state, action) {
+            var data = [];
+            var payloadData = action.payload;
+            if (payloadData == undefined)
+                return;
+            if (payloadData.length > 0) {
+                payloadData.forEach(function (element) {
+                    data.push({
+                        id: element.id,
+                        fileName: element.filename,
+                        link: element.link,
+                        md5: element.md5,
+                        size: element.size,
+                        status: (element.status == 'notavailable') ? 'not available' : element.status,
+                        createdAt: convertTimestamp(element.created_at),
+                        updatedAt: convertTimestamp(element.updated_at),
+                        database: element.database,
+                        location: element.location,
+                        renamingPending: false,
+                        is_demo_data: element.is_demo_data
+                    });
+                });
+            }
+            state.files = data;
+            state.loading = false;
+        }),
+        builder.addCase(renameUploadedData.pending, function (state, action) {
+            var id = action.meta.arg.fileId;
+            for (var _i = 0, _a = state.files; _i < _a.length; _i++) {
+                var file = _a[_i];
+                if (file.id == id) {
+                    file.renamingPending = true;
+                }
+            }
+        }),
+        builder.addCase(renameUploadedData.fulfilled, function (state, action) {
+            var id = action.meta.arg.fileId;
+            for (var _i = 0, _a = state.files; _i < _a.length; _i++) {
+                var file = _a[_i];
+                if (file.id == id) {
+                    delete file.renamingPending;
+                }
+            }
+        }),
+        builder.addCase(deleteUploadedData.pending, function (state, action) {
+            var id = action.meta.arg.fileId;
+            for (var _i = 0, _a = state.files; _i < _a.length; _i++) {
+                var file = _a[_i];
+                if (file.id == id) {
+                    file.deletionPending = true;
+                }
+            }
+        }),
+        builder.addCase(deleteUploadedData.fulfilled, function (state, action) {
+            var id = action.meta.arg.fileId;
+            for (var _i = 0, _a = state.files; _i < _a.length; _i++) {
+                var file = _a[_i];
+                if (file.id == id) {
+                    delete file.deletionPending;
+                }
+            }
+        })); }
+});
+export var renameData = (_a = dataSlice.actions, _a.renameData), deleteData = _a.deleteData;
+export default dataSlice.reducer;

package/dist/core/features/jobs/jobActionCreation.d.ts

@@ -0,0 +1,35 @@
+import { AxiosResponse } from 'axios';
+import { Job } from "./jobsSlice";
+export declare const getUpstreamJobs: import("@reduxjs/toolkit").AsyncThunk<any, void, import("@reduxjs/toolkit").AsyncThunkConfig>;
+export declare const renameUpstreamJob: import("@reduxjs/toolkit").AsyncThunk<void, {
+    jobReference: Job;
+}, import("@reduxjs/toolkit").AsyncThunkConfig>;
+export declare const deleteUpstreamJob: import("@reduxjs/toolkit").AsyncThunk<void, {
+    jobId: string;
+}, import("@reduxjs/toolkit").AsyncThunkConfig>;
+type uploadJobParameters = {
+    uploadToken: string;
+    file: File;
+    fileAlias: string;
+    onProgress?: (progress: number) => void;
+    uploadTarget?: string;
+    onUploaded?: (res: AxiosResponse, file: File) => void;
+};
+export declare const uploadJob: import("@reduxjs/toolkit").AsyncThunk<{
+    code: number;
+    response: any;
+    file: {
+        filename: string;
+        filetype: string;
+        filesize: string;
+        filemd5: string;
+        file: File;
+    };
+    uploadTarget: string | undefined;
+} | {
+    code: number;
+    response: any;
+    file: undefined;
+    uploadTarget: string | undefined;
+}, uploadJobParameters, import("@reduxjs/toolkit").AsyncThunkConfig>;
+export {};