merge develop

README.md

@@ -1,3 +1,7 @@
+[![Total alerts](https://img.shields.io/lgtm/alerts/g/dsi-icl/itmat-broker.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/dsi-icl/itmat-broker/alerts/)
+[![Language grade: JavaScript](https://img.shields.io/lgtm/grade/javascript/g/dsi-icl/itmat-broker.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/dsi-icl/itmat-broker/context:javascript)
+![Build status](https://github.com/dsi-icl/itmat-broker/workflows/Test%20and%20Build%20CI/badge.svg)
+
 #Develop branch
 
 To deploy the app, some programs need to be installed:
@@ -17,17 +21,6 @@ Or [convert a standalone to a replica set](https://docs.mongodb.com/manual/tutor
 
 MinIO is required for high-performance object storage. Refer [this to install MinIO](https://docs.min.io/docs/minio-quickstart-guide.html)
 
-### - Initalise the database for the app:
-
-Go to `packages/itmat-interface/src/databaseSetup` to initialise the database using the script `collectionsAndIndexes.ts`.
-
-This script needs to be editted to run the `setupDatabase` function:
-`setupDatabase(mongostr, databaseName).then(() => {});;`
-
-Where `mongostr` and `databaseName` are mongodb connection string and database name for the app, respectively.
-
-
-To start the app, run the following commands at root folder (you will have to have `yarn` installed):
 
 ## 1. Install dependencies and build
 ```bash

package.json

@@ -14,7 +14,8 @@
         "lint": "lerna run --no-bail --stream lint",
         "lint:fix": "lerna run --no-bail --stream lint:fix",
         "clean": "lerna run clean",
-        "publish": "lerna run tsc && lerna publish"
+        "publish": "lerna run tsc && lerna publish",
+        "test:unit": "lerna run --no-bail --concurrency 1 --stream --scope itmat-interface test"
     },
     "workspaces": {
         "packages": [
@@ -33,30 +34,30 @@
         ]
     },
     "devDependencies": {
-        "@types/jest": "26.0.3",
-        "@typescript-eslint/eslint-plugin": "3.4.0",
-        "@typescript-eslint/parser": "3.4.0",
+        "@types/jest": "26.0.5",
+        "@typescript-eslint/eslint-plugin": "3.7.0",
+        "@typescript-eslint/parser": "3.7.0",
         "babel-eslint": "10.1.0",
-        "eslint": "7.3.1",
+        "eslint": "7.5.0",
         "eslint-config-react-app": "5.2.1",
         "eslint-plugin-cypress": "2.11.1",
-        "eslint-plugin-flowtype": "5.1.3",
-        "eslint-plugin-jest": "23.17.1",
+        "eslint-plugin-flowtype": "5.2.0",
         "eslint-plugin-import": "2.22.0",
-        "eslint-plugin-jsx-a11y": "6.2.3",
-        "eslint-plugin-react": "7.20.0",
-        "eslint-plugin-react-hooks": "4.0.5",
+        "eslint-plugin-jest": "23.18.0",
+        "eslint-plugin-jsx-a11y": "6.3.1",
+        "eslint-plugin-react": "7.20.3",
+        "eslint-plugin-react-hooks": "4.0.8",
         "husky": "4.2.5",
         "start-server-and-test": "1.11.0",
         "jest-environment-node": "26.1.0",
         "lerna": "3.22.1",
-        "typescript": "3.9.6"
+        "typescript": "3.9.7"
     },
     "resolutions": {
         "**/**/fs-capacitor": "^6.0.0",
         "**/graphql-upload": "^11.0.0",
-        "**/graphql": "14.5.3",
-        "**/moment": "2.26.0"
+        "**/graphql": "14.7.0",
+        "**/moment": "2.27.0"
     },
     "eslintConfig": {
         "extends": "./config/eslint.config.js"

packages/itmat-commons/package.json

@@ -21,22 +21,22 @@
     },
     "dependencies": {
         "graphql": "15.0.0",
-        "graphql-tag": "2.10.3",
+        "graphql-tag": "2.10.4",
         "minio": "7.0.16",
         "uuid": "8.1.0"
     },
     "devDependencies": {
-        "@types/express": "4.17.6",
-        "@types/jest": "26.0.3",
+        "@types/express": "4.17.7",
+        "@types/jest": "26.0.5",
         "@types/minio": "7.0.5",
         "@types/mongodb": "3.5.25",
-        "@types/node": "13.13.12",
-        "@types/supertest": "2.0.9",
+        "@types/node": "14.0.23",
+        "@types/supertest": "2.0.10",
         "chalk": "4.1.0",
         "jest": "26.1.0",
         "rimraf": "3.0.2",
-        "ts-jest": "26.1.1",
-        "typescript": "3.9.6"
+        "ts-jest": "26.1.3",
+        "typescript": "3.9.7"
     },
     "eslintConfig": {
         "extends": "./config/eslint.config.js"

packages/itmat-commons/src/graphql/index.ts

@@ -2,6 +2,7 @@ import * as appUsers from './appUsers';
 import * as curation from './curation';
 import * as fields from './fields';
 import * as files from './files';
+import * as log from './log';
 import * as permission from './permission';
 import * as projects from './projects';
 import * as query from './query';
@@ -12,11 +13,11 @@ export * from './appUsers';
 export * from './curation';
 export * from './fields';
 export * from './files';
+export * from './log';
 export * from './permission';
 export * from './projects';
 export * from './query';
 export * from './study';
 export * from './user';
 export * from './subscription';
-
-export const GQLRequests = { ...subscription, ...appUsers, ...curation, ...fields, ...files, ...permission, ...projects, ...query, ...study, ...user };
+export const GQLRequests = { ...subscription, ...appUsers, ...curation, ...fields, ...files, ...log, ...permission, ...projects, ...query, ...study, ...user };

packages/itmat-commons/src/graphql/log.ts

@@ -0,0 +1,29 @@
+import gql from 'graphql-tag';
+
+export const GET_LOGS = gql`
+    query getLogs(
+        $requesterName: String, 
+        $requesterType: USERTYPE,
+        $logType: LOG_TYPE,
+        $actionType: LOG_ACTION,
+        $status: LOG_STATUS 
+    ) {
+        getLogs (
+            requesterName: $requesterName,
+            requesterType: $requesterType,
+            logType: $logType,
+            actionType: $actionType,
+            status: $status
+        ) {
+            id,
+            requesterName,
+            requesterType,
+            logType,
+            actionType,
+            actionData,
+            time,
+            status,
+            error
+        }
+    }
+`;

packages/itmat-commons/src/models/index.ts

@@ -1,6 +1,7 @@
 import * as Field from './field';
 import * as File from './file';
 import * as JobModels from './job';
+import * as Log from './log';
 import * as Query from './query';
 import * as Study from './study';
 import * as UserModels from './user';
@@ -9,8 +10,9 @@ import * as Data from './data';
 export * from './field';
 export * from './file/index';
 export * from './job';
+export * from './log';
 export * from './query';
 export * from './study';
 export * from './user';
 export * from './data';
-export { File, JobModels, UserModels, Study, Query, Field, Data };
+export { File, JobModels, Log, UserModels, Study, Query, Field, Data };

packages/itmat-commons/src/models/log.ts

@@ -1,21 +1,74 @@
+import { userTypes } from './user';
+
 export interface ILogEntry {
-    type: LOG_TYPE;
-    subtype?: LOG_SUBTYPE;
-    user?: string;
-    ref: string;
-    content: string;
-    request: string;
-    outcome: string;
+    id: string,
+    requesterName: string,
+    requesterType: userTypes,
+    logType: LOG_TYPE,
+    actionType: LOG_ACTION,
+    actionData: any,
+    time: number,
+    status: LOG_STATUS,
+    errors: string | null
+}
+
+export enum LOG_TYPE {
+    SYSTEM_LOG = 'SYSTEM_LOG',
+    REQUEST_LOG = 'REQUEST_LOG'
 }
 
-enum LOG_TYPE {
-    ERROR = 'ERROR',
-    USER_ACTION = 'USER_ACTION',
-    LOGIN_ATTEMPT = 'LOGIN_ATTEMPT',
-    SYSTEM_LOG = 'SYSTEM_LOG'
+export enum LOG_ACTION {
+    // SYSTEM
+    startSERVER = 'START_SERVER',
+    stopSERVER = 'STOP_SERVER',
+
+    // USER
+    getUsers = 'GET_USERS',
+    EditUser = 'EDIT_USER',
+    DeleteUser = 'DELETE_USER',
+    CreateUser = 'CREATE_USER',
+    login = 'LOGIN_USER',
+    whoAmI = 'WHO_AM_I',
+    logout = 'LOGOUT',
+    requestUsernameOrResetPassword = 'REQUEST_USERNAME_OR_RESET_PASSWORD',
+    resetPassword = 'RESET_PASSWORD',
+
+    // PROJECT
+    getProject = 'GET_PROJECT',
+    // GET_PROJECT_PATIENT_MAPPING = 'GET_PROJECT_PATIENT_MAPPING',
+    editProjectApprovedFields = 'EDIT_PROJECT_APPROVED_FIELDS',
+    editProjectApprovedFiles = 'EDIT_PROJECT_APPROVED_FILES',
+    createProject = 'CREATE_PROJECT',
+    deleteProject = 'DELETE_PROJECT',
+    setDataversionAsCurrent = 'SET_DATAVERSION_AS_CURRENT',
+    subscribeToJobStatusChange = 'SUBSCRIBE_TO_JOB_STATUS',
+
+    // STUDY | DATASET
+    deleteStudy = 'DELETE_STUDY',
+    getStudy = 'GET_STUDY',
+    getStudyFields = 'GET_STUDY_FIELDS',
+    createStudy = 'CREATE_STUDY',
+    createDataCurationJob = 'CREATE_DATA_CREATION_JOB',
+    //createDataCurationJob = 'CREATE_FIELD_CURATION_JOB',
+
+    // STUDY & PROJECT
+    editRole = 'EDIT_ROLE',
+    addRoleToStudyOrProject = 'ADD_NEW_ROLE',
+    removeRole = 'REMOVE_ROLE',
+
+    // FILE
+    uploadFile = 'UPLOAD_FILE',
+    DOWNLOAD_FILE = 'DOWNLOAD_FILE',
+    deleteFile = 'DELETE_FILE',
+
+    //QUERY
+    getQueries = 'GET_QUERY',
+    createQuery = 'CREATE_QUERY',
+    //GET_QUERY_RESULT = 'GET_QUERY_RESULT'
+
 }
 
-enum LOG_SUBTYPE {
-    DATADASE_WRITE = 'DATABASE_WRITE',
-    DATADASE_READ = 'DATABASE_READ'
+export enum LOG_STATUS {
+    SUCCESS = 'SUCCESS',
+    FAIL = 'FAIL'
 }

packages/itmat-commons/src/models/user.ts

@@ -1,6 +1,7 @@
 export enum userTypes {
     ADMIN = 'ADMIN',
-    STANDARD = 'STANDARD'
+    STANDARD = 'STANDARD',
+    SYSTEM = 'SYSTEM'
 }
 
 export interface IUserWithoutToken {

packages/itmat-interface/config/webpack.config.js

@@ -26,7 +26,11 @@ module.exports = {
         express: 'commonjs express',
         mongodb: 'commonjs mongodb',
         // "subscriptions-transport-ws": "commonjs subscriptions-transport-ws",
+<<<<<<< HEAD
         isobject: 'commonjs isobject',
+=======
+        isobject: 'commonjs isobject',
+>>>>>>> develop
         require_optional: 'commonjs require_optional'
     }],
     module: {
@@ -60,4 +64,4 @@ module.exports = {
         libraryTarget: NODE_ENV === 'development' ? undefined : 'umd',
         umdNamedDefine: NODE_ENV === 'development' ? undefined : true
     }
-};
+};

packages/itmat-interface/package.json

@@ -20,7 +20,7 @@
         "prepublishOnly": "yarn run build"
     },
     "dependencies": {
-        "apollo-server-express": "2.15.1",
+        "apollo-server-express": "2.16.0",
         "bcrypt": "5.0.0",
         "body-parser": "1.19.0",
         "connect-mongo": "3.2.0",
@@ -43,19 +43,19 @@
     "devDependencies": {
         "@types/bcrypt": "3.0.0",
         "@types/connect-mongo": "3.1.3",
-        "@types/express": "4.17.6",
+        "@types/express": "4.17.7",
         "@types/express-session": "1.17.0",
         "@types/graphql": "14.5.0",
-        "@types/jest": "26.0.3",
+        "@types/jest": "26.0.5",
         "@types/mongodb": "3.5.25",
         "@types/mongodb-memory-server": "2.3.0",
         "@types/multer": "1.4.3",
-        "@types/node": "13.13.12",
+        "@types/node": "14.0.23",
         "@types/node-fetch": "2.5.7",
         "@types/nodemailer": "6.4.0",
-        "@types/passport": "1.0.3",
+        "@types/passport": "1.0.4",
         "@types/passport-local": "1.0.33",
-        "@types/supertest": "2.0.9",
+        "@types/supertest": "2.0.10",
         "@types/uuid": "8.0.0",
         "@types/webpack-env": "1.15.2",
         "chalk": "4.1.0",
@@ -71,17 +71,17 @@
         "rimraf": "3.0.2",
         "start-server-webpack-plugin": "2.2.5",
         "supertest": "4.0.2",
-        "ts-jest": "26.1.1",
-        "ts-loader": "7.0.5",
-        "typescript": "3.9.6",
+        "ts-jest": "26.1.3",
+        "ts-loader": "8.0.1",
+        "typescript": "3.9.7",
         "typescript-eslint-parser": "22.0.0",
         "webpack": "4.43.0",
-        "webpack-cli": "3.3.11"
+        "webpack-cli": "3.3.12"
     },
     "resolutions": {
         "**/**/fs-capacitor": "^6.0.0",
         "**/graphql-upload": "^11.0.0",
-        "**/graphql": "14.5.3"
+        "**/graphql": "14.7.0"
     },
     "eslintConfig": {
         "extends": "./config/eslint.config.js"

packages/itmat-interface/src/graphql/resolvers/index.ts

@@ -8,14 +8,16 @@ import { userResolvers } from './userResolvers';
 import { ApolloError } from 'apollo-server-core';
 import { errorCodes } from '../errors';
 import { IUser } from 'itmat-commons';
+import { logResolvers } from './logResolvers';
 
 const modules = [
     studyResolvers,
     userResolvers,
     queryResolvers,
     permissionResolvers,
     jobResolvers,
-    fileResolvers
+    fileResolvers,
+    logResolvers
 ];
 
 // const loggingDecorator = (reducerFunction: Function) => {
@@ -27,7 +29,7 @@ const modules = [
 
 const bounceNotLoggedInDecorator = (reducerFunction: any) => {
     return async (parent: any, args: any, context: any, info: any) => {
-        const uncheckedFunctionWhitelist = ['login', 'whoAmI', 'requestUsernameOrResetPassword', 'resetPassword', 'createUser'];
+        const uncheckedFunctionWhitelist = ['login', 'whoAmI', 'requestUsernameOrResetPassword', 'resetPassword', 'createUser', 'writeLog'];
         const requester: IUser = context.req.user;
         if (!requester) {
             if (!(uncheckedFunctionWhitelist as any).includes(reducerFunction.name)) {