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-commons/src/utils/objStore.ts

@@ -71,6 +71,25 @@ export class ObjectStore {
         return result.etag;
     }
 
+    public async copyObject(sourceBucket: string, sourceUri: string, targetBucket: string, targetUri: string) {
+        if (!this.client) {
+            throw new Error('Connection failed.');
+        }
+
+        const lowerSourceBucket = sourceBucket.toLowerCase();
+        const lowerTargetBucket = targetBucket.toLowerCase();
+
+        // Ensure target bucket exists
+        const bucketExists = await this.client.bucketExists(lowerTargetBucket);
+        if (!bucketExists) {
+            await this.client.makeBucket(lowerTargetBucket, this.config?.bucketRegion ?? '');
+        }
+        // Copy the object
+        const conds = new Minio.CopyConditions();
+        const result = await this.client.copyObject(lowerTargetBucket, targetUri, `/${lowerSourceBucket}/${sourceUri}`, conds);
+        return result.etag;
+    }
+
     public async downloadFile(studyId: string, uri: string): Promise<Readable> {
         if (!this.client) {
             throw new Error('Connection failed.');

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 } });
         }
@@ -1187,7 +1184,7 @@ export class StudyCore {
                             error = `Field ${dataClip.fieldId}: Cannot parse as decimal.`;
                             break;
                         }
-                        if (!/^\d+(.\d+)?$/.test(dataClip.value)) {
+                        if (!/^-?\d+(\.\d+)?$/.test(dataClip.value)) {
                             error = `Field ${dataClip.fieldId}: Cannot parse as decimal.`;
                             break;
                         }

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

@@ -573,7 +573,7 @@ export class TRPCDataCore {
                             error = makeGenericReponse(counter.toString(), false, enumCoreErrors.CLIENT_MALFORMED_INPUT, `Field ${dataClip.fieldId}: Cannot parse as decimal.`);
                             break;
                         }
-                        if (!/^\d+(.\d+)?$/.test(dataClip.value)) {
+                        if (!/^-?\d+(\.\d+)?$/.test(dataClip.value)) {
                             error = makeGenericReponse(counter.toString(), false, enumCoreErrors.CLIENT_MALFORMED_INPUT, `Field ${dataClip.fieldId}: Cannot parse as decimal.`);
                             break;
                         }