Merge develop branch

.commitlintrc.js

@@ -13,6 +13,7 @@ module.exports = {
             (await getProjects(ctx, projectFilter))
                 .forEach(element => {
                     projectNames.add(element);
+                    projectNames.add(element.replaceAll('itmat-', ''));
                 });
             return [
                 2,

.editorconfig

@@ -8,6 +8,9 @@ indent_size = 4
 insert_final_newline = true
 trim_trailing_whitespace = true
 
+[.yml]
+indent_size = 2
+
 [*.md]
 max_line_length = off
 trim_trailing_whitespace = false

.prettierignore

@@ -14,3 +14,4 @@
 *.mjsx
 *.cjs
 *.cjsx
+*.yaml

SECURITY.md

@@ -7,7 +7,7 @@ currently being supported with security updates.
 
 | Version | Supported          |
 | ------- | ------------------ |
-| 2.5.1   | :white_check_mark: |
+| 2.6.0   | :white_check_mark: |
 | < 2     | :x:                |
 
 ## Reporting a Vulnerability

dependabot.yml

@@ -0,0 +1,58 @@
+version: 2
+updates:
+  - package-ecosystem: "npm"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    target-branch: "develop"
+    labels:
+      - "dependencies"
+    groups:
+      nx:
+        patterns:
+          - "nx"
+          - "@nx/*"
+          - "@jscutlery/semver"
+      lint:
+        patterns:
+          - "eslint*"
+          - "@typescript-eslint/*"
+      dev:
+        patterns:
+          - "commitlint"
+          - "@commitlint/*"
+          - "@swc/*"
+          - "@svgr/webpack"
+          - "esbuild*"
+          - "postcss"
+          - "prettier"
+          - "webpack"
+          - "verdaccio"
+          - "typscript"
+      test:
+        patterns:
+          - "jsdom"
+          - "sinon-chrome"
+          - "jest*"
+          - "babel-jest"
+      babel:
+        patterns:
+          - "babel*"
+          - "@babel/*"
+      types:
+        patterns:
+          - "@types/*"
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    target-branch: "develop"
+    labels:
+      - "actions"
+  - package-ecosystem: "docker"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    target-branch: "develop"
+    labels:
+      - "docker"

package.json

@@ -1,6 +1,6 @@
 {
     "name": "itmat-broker",
-    "version": "2.5.1",
+    "version": "2.6.0",
     "private": true,
     "license": "MIT",
     "scripts": {

packages/itmat-cores/src/GraphQLCore/studyCore.ts

@@ -13,11 +13,22 @@ import { buildPipeline, dataStandardization } from '../utils/query';
 import { DBType } from '../database/database';
 import { ObjectStore } from '@itmat-broker/itmat-commons';
 
+enum enumV2DataType {
+    'INT' = 'int',
+    'DEC' = 'dec',
+    'STR' = 'str',
+    'BOOL' = 'bool',
+    'DATE' = 'date',
+    'FILE' = 'file',
+    'JSON' = 'json',
+    'CAT' = 'cat'
+}
+
 export interface CreateFieldInput {
     fieldId: string;
     fieldName: string
     tableName?: string
-    dataType: string;
+    dataType: enumV2DataType;
     possibleValues?: ICategoricalOption[]
     unit?: string
     comments?: string
@@ -28,7 +39,7 @@ export interface EditFieldInput {
     fieldId: string;
     fieldName: string;
     tableName?: string;
-    dataType: string;
+    dataType: enumV2DataType;
     possibleValues?: ICategoricalOption[]
     unit?: string
     comments?: string
@@ -107,28 +118,35 @@ export class StudyCore {
                     return {
                         id: el.id,
                         code: el.code,
-                        description: el.description
+                        description: el.description,
+                        life: {
+                            createdTime: el.life.createdTime,
+                            createdUser: el.life.createdUser,
+                            deletedTime: el.life.deletedTime,
+                            deletedUser: el.life.deletedUser
+                        },
+                        metadata: {}
                     };
                 }) : [],
                 dataType: (() => {
                     if (field.dataType === enumDataTypes.INTEGER) {
-                        return 'int';
+                        return enumV2DataType.INT;
                     } else if (field.dataType === enumDataTypes.DECIMAL) {
-                        return 'dec';
+                        return enumV2DataType.DEC;
                     } else if (field.dataType === enumDataTypes.STRING) {
-                        return 'str';
+                        return enumV2DataType.STR;
                     } else if (field.dataType === enumDataTypes.BOOLEAN) {
-                        return 'bool';
+                        return enumV2DataType.BOOL;
                     } else if (field.dataType === enumDataTypes.DATETIME) {
-                        return 'date';
+                        return enumV2DataType.DATE;
                     } else if (field.dataType === enumDataTypes.FILE) {
-                        return 'file';
+                        return enumV2DataType.FILE;
                     } else if (field.dataType === enumDataTypes.JSON) {
-                        return 'json';
+                        return enumV2DataType.JSON;
                     } else if (field.dataType === enumDataTypes.CATEGORICAL) {
-                        return 'cat';
+                        return enumV2DataType.CAT;
                     } else {
-                        return 'str';
+                        return enumV2DataType.STR;
                     }
                 })(),
                 dateAdded: field.life.createdTime.toString(),
@@ -654,7 +672,7 @@ export class StudyCore {
             error.push(`Data type shouldn't be ${fieldEntry.dataType}: use 'int' for integer, 'dec' for decimal, 'str' for string, 'bool' for boolean, 'date' for datetime, 'file' for FILE, 'json' for json.`);
         }
         // check possiblevalues to be not-empty if datatype is categorical
-        if (fieldEntry.dataType === enumDataTypes.CATEGORICAL) {
+        if (fieldEntry.dataType === enumV2DataType.CAT) {
             if (fieldEntry.possibleValues !== undefined && fieldEntry.possibleValues !== null) {
                 if (fieldEntry.possibleValues.length === 0) {
                     error.push(`${fieldEntry.fieldId}-${fieldEntry.fieldName}: possible values can't be empty if data type is categorical.`);
@@ -672,7 +690,7 @@ export class StudyCore {
             fieldName: fieldEntry.fieldName,
             tableName: null,
             dataType: fieldEntry.dataType,
-            possibleValues: fieldEntry.dataType === enumDataTypes.CATEGORICAL ? fieldEntry.possibleValues : null,
+            possibleValues: fieldEntry.dataType === enumV2DataType.CAT ? fieldEntry.possibleValues : null,
             unit: fieldEntry.unit,
             comments: fieldEntry.comments,
             metadata: {
@@ -808,27 +826,6 @@ export class StudyCore {
         }
         searchField.fieldId = fieldInput.fieldId;
         searchField.fieldName = fieldInput.fieldName;
-        searchField.dataType = (() => {
-            if (fieldInput.dataType === 'int') {
-                return enumDataTypes.INTEGER;
-            } else if (fieldInput.dataType === 'dec') {
-                return enumDataTypes.DECIMAL;
-            } else if (fieldInput.dataType === 'str') {
-                return enumDataTypes.STRING;
-            } else if (fieldInput.dataType === 'bool') {
-                return enumDataTypes.BOOLEAN;
-            } else if (fieldInput.dataType === 'date') {
-                return enumDataTypes.DATETIME;
-            } else if (fieldInput.dataType === 'file') {
-                return enumDataTypes.FILE;
-            } else if (fieldInput.dataType === 'json') {
-                return enumDataTypes.JSON;
-            } else if (fieldInput.dataType === 'cat') {
-                return enumDataTypes.CATEGORICAL;
-            } else {
-                return enumDataTypes.STRING;
-            }
-        })();
         if (fieldInput.tableName) {
             searchField.metadata['tableName'] = fieldInput.tableName;
         }
@@ -845,7 +842,7 @@ export class StudyCore {
             searchField.comments = fieldInput.comments;
         }
 
-        const { error } = await this.validateAndGenerateFieldEntry(searchField, requester);
+        const { error } = await this.validateAndGenerateFieldEntry({ ...this.fieldTypeConverter([searchField])[0], dataType: fieldInput.dataType }, requester);
         if (error.length !== 0) {
             throw new GraphQLError(JSON.stringify(error), { extensions: { code: errorCodes.CLIENT_MALFORMED_INPUT } });
         }

packages/itmat-cores/src/trpcCore/fileCore.ts

@@ -52,7 +52,6 @@ export class TRPCFileCore {
                 );
             }
         }
-
         let fileConfig: ISystemConfig | IStudyConfig | IUserConfig | IDocConfig | ICacheConfig | IDomainConfig | null = null;
         let userRepoRemainingSpace = 0;
         let fileSizeLimit: number;

packages/itmat-cores/src/utils/query.ts

@@ -136,7 +136,7 @@ export function standardize(study: IStudy, fields: IField[], data: IGroupedData,
         }
         for (const subjectId of Object.keys(data)) {
             for (const visitId of Object.keys(data[subjectId])) {
-                if (data[subjectId][visitId][field.fieldId] === null) {
+                if (data[subjectId][visitId][field.fieldId] === null || data[subjectId][visitId][field.fieldId] === undefined) {
                     continue;
                 }
                 const dataClip: Record<string, unknown> = {};

packages/itmat-docker/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@itmat-broker/itmat-setup",
-    "version": "2.5.1",
+    "version": "2.6.0",
     "description": "ITMAT Broker",
     "keywords": [
         "itmat",
@@ -17,7 +17,7 @@
     "dependencies": {
         "bcrypt": "5.1.1",
         "compression": "1.7.4",
-        "express": "4.18.2",
+        "express": "4.19.2",
         "express-rate-limit": "7.1.2",
         "isobject": "4.0.0",
         "minio": "7.1.3",

packages/itmat-interface/test/GraphQLTests/file.test.ts

@@ -497,8 +497,6 @@ if (global.hasMinio) {
                     createdFile = res.body.data.uploadFile;
                     if (!createdFile)
                         throw 'Test file could not be retreived.';
-
-
                 });
 
                 afterEach(async () => {

packages/itmat-interface/test/trpcTests/user.test.ts

@@ -18,6 +18,17 @@ import { IOrganisation, enumUserTypes } from '@itmat-broker/itmat-types';
 import { encodeQueryParams } from './helper';
 import { errorCodes } from '@itmat-broker/itmat-cores';
 
+jest.mock('nodemailer', () => {
+    const { TEST_SMTP_CRED, TEST_SMTP_USERNAME } = process.env;
+    if (!TEST_SMTP_CRED || !TEST_SMTP_USERNAME || !config?.nodemailer?.auth?.pass || !config?.nodemailer?.auth?.user)
+        return {
+            createTransport: jest.fn().mockImplementation(() => ({
+                sendMail: jest.fn()
+            }))
+        };
+    return jest.requireActual('nodemailer');
+});
+
 if (global.hasMinio) {
     let app: Express;
     let mongodb: MongoMemoryServer;
@@ -104,9 +115,6 @@ if (global.hasMinio) {
 
     describe('tRPC User APIs', () => {
         test('Create a user', async () => {
-            if (process.env.SKIP_EMAIL_TEST) {
-                return;
-            }
             const response = await admin.post('/trpc/user.createUser')
                 .send({
                     username: 'test',
@@ -121,7 +129,7 @@ if (global.hasMinio) {
             expect(response.body.result.data.username).toBe('test');
             const user = await db.collections.users_collection.findOne({ username: 'test' });
             expect(user).toBeDefined();
-            expect(userProfile.id).toBe(response.body.result.data.id);
+            expect(user.id).toBe(response.body.result.data.id);
         });
         test('Create a user (invalid email format)', async () => {
             const response = await admin.post('/trpc/user.createUser')

packages/itmat-types/src/types/index.ts

@@ -16,7 +16,7 @@ import * as Config from './config';
 import * as ZodSchema from './zod';
 import * as Utils from './utils';
 import * as Drive from './drive';
-import * as Permission  from './permission';
+import * as Permission from './permission';
 
 export * from './field';
 export * from './file';

packages/itmat-ui-react/src/components/datasetDetail/tabContent/files/fileTab.tsx

@@ -638,7 +638,7 @@ const EditableCell: FunctionComponent<EditableCellProps> = ({
                         })
                     ]}
                 >
-                    <RangePicker id={`period_${record.uuid}`} allowClear={false} ref={rangeRef} defaultValue={[record.startDate ?? null, record.endDate ?? null]} disabledDate={(currentDate) => {
+                    <RangePicker id={`period_${record.uuid}`} allowClear={false} ref={rangeRef} defaultValue={[record.startDate ? dayjs(record.startDate) : null, record.endDate ?? null]} disabledDate={(currentDate) => {
                         return dayjs().isBefore(currentDate);
                     }} onCalendarChange={(dates) => {
                         if (dates === null)