Merge branch 'main' into TranslateImagingBrowser

Author: SKADE2303

.github/workflows/loristest.yml

@@ -22,6 +22,7 @@ jobs:
       # (see https://github.com/actions/runner-images/blob/releases/ubuntu22/20230305/images/linux/Ubuntu2204-Readme.md)
       # that updated the list of installed apt packages/apt repositories. That issue may disappear in future Ubuntu images.
         run: |
+          sudo apt-get update 
           sudo apt install -y imagemagick-6-common libmagickcore-6.q16-7t64 libmagickwand-6.q16-7t64 \
              libprotobuf-dev libprotobuf32t64 libprotoc32t64 protobuf-compiler
           cd modules/electrophysiology_browser/jsx/react-series-data-viewer/
@@ -259,7 +260,7 @@ jobs:
         restore-keys: ${{ runner.os }}-composer-
 
     - name: Change PHP Version in Dockerfile
-      run: sed -i "s/8.0/${{ matrix.php }}/g" Dockerfile.test.php8
+      run: sed -i "s/8.3/${{ matrix.php }}/g" Dockerfile.test.php8
 
     - name: Install protoc-gen-js plugin
       run: npm install -g protoc-gen-js
@@ -270,6 +271,7 @@ jobs:
       # (see https://github.com/actions/runner-images/blob/releases/ubuntu22/20230305/images/linux/Ubuntu2204-Readme.md)
       # that updated the list of installed apt packages/apt repositories. That issue may disappear in future Ubuntu images.
       run: |
+        sudo apt-get update
         sudo apt install -y imagemagick-6-common libmagickcore-6.q16-7t64 libmagickwand-6.q16-7t64 \
            libprotobuf-dev libprotobuf32t64 libprotoc32t64 protobuf-compiler gettext
         cd modules/electrophysiology_browser/jsx/react-series-data-viewer/

Dockerfile.test.db

@@ -13,6 +13,7 @@ RUN cat /sql/0000-00-00-schema.sql \
         /sql/0000-00-03-ConfigTables.sql \
         /sql/0000-00-04-Help.sql \
         /sql/0000-00-05-ElectrophysiologyTables.sql \
+        /sql/0000-00-06-BiobankTables.sql \
         /instruments_sql/*.sql \
         /test_instrument.sql \
         /RB_files/*.sql \

Dockerfile.test.php8

@@ -1,11 +1,11 @@
-FROM php:8.1
+FROM php:8.3
 
 # Install necessary packages
 RUN apt-get update && \
-    apt-get install -y mariadb-client libzip-dev
+    apt-get install -y mariadb-client libzip-dev libicu-dev
 
 # Install PHP extensions
-RUN docker-php-ext-install pdo_mysql zip gettext
+RUN docker-php-ext-install pdo_mysql zip gettext intl
 
 # Ensure the logs directory exists
 RUN mkdir -p /app/logs

Dockerfile.test.php8.debug

@@ -1,4 +1,4 @@
-FROM php:8.1
+FROM php:8.3
 
 RUN apt-get update && \
     apt-get install -y mariadb-client libzip-dev

Makefile

@@ -1,23 +1,25 @@
-.PHONY: clean dev all check checkstatic unittests phpdev jslatest testdata fastdev jsdev locales
+.PHONY: clean dev all check checkstatic unittests jslatest testdata locales
 
-all: locales VERSION
-	composer install --no-dev
-	npm ci
+all: node_modules locales VERSION vendor
 	npm run build
 
 # If anything changes, re-generate the VERSION file
 VERSION: .
 	tools/gen-version.sh
 
-phpdev:
+vendor/bin/phan: composer.lock
+	composer install
+
+vendor/bin/phpunit: composer.lock
 	composer install
 
-dev: locales phpdev jsdev fastdev
+vendor: composer.lock
+	composer install --no-dev
 
-jsdev:
+node_modules: package-lock.json
 	npm ci
 
-fastdev: VERSION
+dev: node_modules locales vendor/bin/phan VERSION vendor
 	npm run compile
 
 jslatest: clean
@@ -35,7 +37,7 @@ clean:
 	rm -f modules/*/locale/*/LC_MESSAGES/*.mo
 
 # Perform static analysis checks
-checkstatic: phpdev
+checkstatic: vendor/bin/phan dev
 	npm run lint:php
 	vendor/bin/phan
 	npm run lint:js
@@ -48,7 +50,7 @@ checkstatic: phpdev
 make checklanguage:
 	npx alex --quiet --why --diff
 
-unittests: phpdev
+unittests: vendor/bin/phpunit
 	vendor/bin/phpunit --configuration test/phpunit.xml
 
 # Perform all tests that don't require an install.
@@ -62,6 +64,8 @@ locales:
 	npx i18next-conv -l ja -s locale/ja/LC_MESSAGES/loris.po -t locale/ja/LC_MESSAGES/loris.json
 	msgfmt -o locale/hi/LC_MESSAGES/loris.mo locale/hi/LC_MESSAGES/loris.po
 	npx i18next-conv -l hi -s locale/hi/LC_MESSAGES/loris.po -t locale/hi/LC_MESSAGES/loris.json
+	msgfmt -o locale/es/LC_MESSAGES/loris.mo locale/es/LC_MESSAGES/loris.po
+	npx i18next-conv -l es -s locale/es/LC_MESSAGES/loris.po -t locale/es/LC_MESSAGES/loris.json
 	msgfmt -o modules/new_profile/locale/ja/LC_MESSAGES/new_profile.mo modules/new_profile/locale/ja/LC_MESSAGES/new_profile.po
 	msgfmt -o modules/acknowledgements/locale/ja/LC_MESSAGES/acknowledgements.mo modules/acknowledgements/locale/ja/LC_MESSAGES/acknowledgements.po
 	msgfmt -o modules/api_docs/locale/ja/LC_MESSAGES/api_docs.mo modules/api_docs/locale/ja/LC_MESSAGES/api_docs.po
@@ -71,12 +75,17 @@ locales:
 	msgfmt -o modules/bvl_feedback/locale/ja/LC_MESSAGES/bvl_feedback.mo modules/bvl_feedback/locale/ja/LC_MESSAGES/bvl_feedback.po
 	msgfmt -o modules/candidate_list/locale/ja/LC_MESSAGES/candidate_list.mo modules/candidate_list/locale/ja/LC_MESSAGES/candidate_list.po
 	npx i18next-conv -l ja -s modules/candidate_list/locale/ja/LC_MESSAGES/candidate_list.po -t modules/candidate_list/locale/ja/LC_MESSAGES/candidate_list.json
+	msgfmt -o modules/candidate_list/locale/hi/LC_MESSAGES/candidate_list.mo modules/candidate_list/locale/hi/LC_MESSAGES/candidate_list.po
+	npx i18next-conv -l hi -s modules/candidate_list/locale/hi/LC_MESSAGES/candidate_list.po -t modules/candidate_list/locale/hi/LC_MESSAGES/candidate_list.json
 	msgfmt -o modules/candidate_parameters/locale/ja/LC_MESSAGES/candidate_parameters.mo modules/candidate_parameters/locale/ja/LC_MESSAGES/candidate_parameters.po
 	msgfmt -o modules/candidate_profile/locale/ja/LC_MESSAGES/candidate_profile.mo modules/candidate_profile/locale/ja/LC_MESSAGES/candidate_profile.po
 	msgfmt -o modules/configuration/locale/ja/LC_MESSAGES/configuration.mo modules/configuration/locale/ja/LC_MESSAGES/configuration.po
 	msgfmt -o modules/configuration/locale/ja/LC_MESSAGES/configuration.mo modules/configuration/locale/ja/LC_MESSAGES/configuration.po
 	msgfmt -o modules/conflict_resolver/locale/ja/LC_MESSAGES/conflict_resolver.mo modules/conflict_resolver/locale/ja/LC_MESSAGES/conflict_resolver.po
 	msgfmt -o modules/create_timepoint/locale/ja/LC_MESSAGES/create_timepoint.mo modules/create_timepoint/locale/ja/LC_MESSAGES/create_timepoint.po
+	npx i18next-conv -l ja -s modules/create_timepoint/locale/ja/LC_MESSAGES/create_timepoint.po -t modules/create_timepoint/locale/ja/LC_MESSAGES/create_timepoint.json
+	msgfmt -o modules/create_timepoint/locale/es/LC_MESSAGES/create_timepoint.mo modules/create_timepoint/locale/es/LC_MESSAGES/create_timepoint.po
+	npx i18next-conv -l es -s modules/create_timepoint/locale/es/LC_MESSAGES/create_timepoint.po -t modules/create_timepoint/locale/es/LC_MESSAGES/create_timepoint.json
 	msgfmt -o modules/dashboard/locale/ja/LC_MESSAGES/dashboard.mo modules/dashboard/locale/ja/LC_MESSAGES/dashboard.po
 	msgfmt -o modules/datadict/locale/ja/LC_MESSAGES/datadict.mo modules/datadict/locale/ja/LC_MESSAGES/datadict.po
 	msgfmt -o modules/datadict/locale/hi/LC_MESSAGES/datadict.mo modules/datadict/locale/hi/LC_MESSAGES/datadict.po
@@ -89,6 +98,9 @@ locales:
 	npx i18next-conv -l hi -s modules/data_release/locale/hi/LC_MESSAGES/data_release.po -t modules/data_release/locale/hi/LC_MESSAGES/data_release.json
 	msgfmt -o modules/dicom_archive/locale/ja/LC_MESSAGES/dicom_archive.mo modules/dicom_archive/locale/ja/LC_MESSAGES/dicom_archive.po
 	msgfmt -o modules/dictionary/locale/ja/LC_MESSAGES/dictionary.mo modules/dictionary/locale/ja/LC_MESSAGES/dictionary.po
+	npx i18next-conv -l ja -s modules/dictionary/locale/ja/LC_MESSAGES/dictionary.po -t modules/dictionary/locale/ja/LC_MESSAGES/dictionary.json
+	msgfmt -o modules/dictionary/locale/hi/LC_MESSAGES/dictionary.mo modules/dictionary/locale/hi/LC_MESSAGES/dictionary.po
+	npx i18next-conv -l hi -s modules/dictionary/locale/hi/LC_MESSAGES/dictionary.po -t modules/dictionary/locale/hi/LC_MESSAGES/dictionary.json
 	msgfmt -o modules/document_repository/locale/ja/LC_MESSAGES/document_repository.mo modules/document_repository/locale/ja/LC_MESSAGES/document_repository.po
 	msgfmt -o modules/dqt/locale/ja/LC_MESSAGES/dqt.mo modules/dqt/locale/ja/LC_MESSAGES/dqt.po
 	msgfmt -o modules/electrophysiology_browser/locale/ja/LC_MESSAGES/electrophysiology_browser.mo modules/electrophysiology_browser/locale/ja/LC_MESSAGES/electrophysiology_browser.po
@@ -116,14 +128,19 @@ locales:
 	msgfmt -o modules/schedule_module/locale/ja/LC_MESSAGES/schedule_module.mo modules/schedule_module/locale/ja/LC_MESSAGES/schedule_module.po
 	msgfmt -o modules/server_processes_manager/locale/ja/LC_MESSAGES/server_processes_manager.mo modules/server_processes_manager/locale/ja/LC_MESSAGES/server_processes_manager.po
 	msgfmt -o modules/statistics/locale/ja/LC_MESSAGES/statistics.mo modules/statistics/locale/ja/LC_MESSAGES/statistics.po
+	npx i18next-conv -l ja -s modules/statistics/locale/ja/LC_MESSAGES/statistics.po -t modules/statistics/locale/ja/LC_MESSAGES/statistics.json
 	msgfmt -o modules/survey_accounts/locale/ja/LC_MESSAGES/survey_accounts.mo modules/survey_accounts/locale/ja/LC_MESSAGES/survey_accounts.po
 	msgfmt -o modules/timepoint_list/locale/ja/LC_MESSAGES/timepoint_list.mo modules/timepoint_list/locale/ja/LC_MESSAGES/timepoint_list.po
+	msgfmt -o modules/timepoint_list/locale/es/LC_MESSAGES/timepoint_list.mo modules/timepoint_list/locale/es/LC_MESSAGES/timepoint_list.po
 	msgfmt -o modules/user_accounts/locale/ja/LC_MESSAGES/user_accounts.mo modules/user_accounts/locale/ja/LC_MESSAGES/user_accounts.po
 
 
 acknowledgements:
 	target=acknowledgements npm run compile
 
+create_timepoint:
+	target=data_release npm run compile
+
 data_release:
 	msgfmt -o modules/data_release/locale/hi/LC_MESSAGES/data_release.mo modules/data_release/locale/hi/LC_MESSAGES/data_release.po
 	npx i18next-conv -l hi -s modules/data_release/locale/hi/LC_MESSAGES/data_release.po -t modules/data_release/locale/hi/LC_MESSAGES/data_release.json 
@@ -135,6 +152,7 @@ instrument_manager:
 	target=instrument_manager npm run compile
 
 dataquery:
+	msgfmt -o modules/dataquery/locale/ja/LC_MESSAGES/dataquery.mo modules/dataquery/locale/ja/LC_MESSAGES/dataquery.po
 	target=dataquery npm run compile
 
 login:
@@ -152,6 +170,8 @@ issue_tracker:
 candidate_list:
 	msgfmt -o modules/candidate_list/locale/ja/LC_MESSAGES/candidate_list.mo modules/candidate_list/locale/ja/LC_MESSAGES/candidate_list.po
 	npx i18next-conv -l ja -s modules/candidate_list/locale/ja/LC_MESSAGES/candidate_list.po -t modules/candidate_list/locale/ja/LC_MESSAGES/candidate_list.json
+	msgfmt -o modules/candidate_list/locale/hi/LC_MESSAGES/candidate_list.mo modules/candidate_list/locale/hi/LC_MESSAGES/candidate_list.po
+	npx i18next-conv -l hi -s modules/candidate_list/locale/hi/LC_MESSAGES/candidate_list.po -t modules/candidate_list/locale/hi/LC_MESSAGES/candidate_list.json
 	target=candidate_list npm run compile
 
 candidate_parameters:

SQL/0000-00-00-schema.sql

@@ -51,7 +51,7 @@ CREATE TABLE `psc` (
   `Phone2` varchar(12) DEFAULT NULL,
   `Contact1` varchar(150) DEFAULT NULL,
   `Contact2` varchar(150) DEFAULT NULL,
-  `Alias` char(3) NOT NULL DEFAULT '',
+  `Alias` char(4) NOT NULL DEFAULT '',
   `MRI_alias` varchar(4) NOT NULL DEFAULT '',
   `Account` varchar(8) DEFAULT NULL,
   `Study_site` enum('N','Y') DEFAULT 'Y',

SQL/0000-00-03-ConfigTables.sql

@@ -12,10 +12,21 @@ CREATE TABLE `ConfigSettings` (
     `Parent` int(11) DEFAULT NULL,
     `Label` varchar(255) DEFAULT NULL,
     `OrderNumber` int(11) DEFAULT NULL,
+    `Multilingual` boolean DEFAULT false,
     PRIMARY KEY (`ID`),
     UNIQUE KEY `Name` (`Name`)
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 
+CREATE TABLE `ConfigI18n` (
+  `Value` text NOT NULL,
+  `ConfigID` int(11) DEFAULT NULL,
+  `LanguageID` int(10) unsigned DEFAULT NULL,
+  KEY `ConfigID` (`ConfigID`),
+  KEY `LanguageID` (`LanguageID`),
+  CONSTRAINT `ConfigI18n_ibfk_1` FOREIGN KEY (`ConfigID`) REFERENCES `ConfigSettings` (`ID`),
+  CONSTRAINT `ConfigI18n_ibfk_2` FOREIGN KEY (`LanguageID`) REFERENCES `language` (`language_id`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci;
+
 
 CREATE TABLE `Config` (
   `ID` int(11) NOT NULL AUTO_INCREMENT,
@@ -88,7 +99,7 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType,
 
 
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('dashboard', 'Settings that affect the appearance of the dashboard and its charts', 1, 0, 'Dashboard', 5);
-INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'projectDescription', 'Description of the study displayed in main dashboard panel', 1, 0, 'textarea', ID, 'Project Description', 1 FROM ConfigSettings WHERE Name="dashboard";
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber, Multilingual) SELECT 'projectDescription', 'Description of the study displayed in main dashboard panel', 1, 0, 'textarea', ID, 'Project Description', 1, true FROM ConfigSettings WHERE Name="dashboard";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'recruitmentTarget', 'Target number of participants for the study', 1, 0, 'text', ID, 'Target number of participants', 2 FROM ConfigSettings WHERE Name="dashboard";
 
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('imaging_modules', 'DICOM Archive and Imaging Browser settings', 1, 0, 'Imaging Modules', 6);

SQL/0000-00-06-BiobankTables.sql

@@ -378,18 +378,27 @@ CREATE TABLE `biobank_container_shipment_rel` (
 
 -- Insert units, processes, container status and shipment status
 INSERT INTO `biobank_unit` VALUES (1,'mL'),(2,'µL');
-INSERT INTO `biobank_specimen_attribute_datatype` VALUES (1, 'text'),(2, 'number'),(3, 'date'),(4, 'time'),(5, 'boolean');
-INSERT INTO `biobank_specimen_protocol` VALUES (1, 'Blood Collection', 1, 1), (2, 'Blood Preparation', 2, 1), (3, 'Serum Collection', 1, 2);
-INSERT INTO `biobank_specimen_type` VALUES (1,'Blood',0),(2,'Serum', 1);
-INSERT INTO `biobank_specimen_type_unit_rel` VALUES (1, 1), (2, 2);
-INSERT INTO `biobank_specimen_type_parent` VALUES (2, 1);
-INSERT INTO `biobank_container_dimension` VALUES (1, 1, 1, 1, 1, 0, 0), (2, 10, 1, 10, 0, 1, 0), (3, 1, 0, 5, 0, 1, 0);
-INSERT INTO `biobank_container_capacity` VALUES (1, 1, 1);
-INSERT INTO `biobank_container_type` VALUES (1, 'Brand', 'Product Number 1', 'Vial', 1, 1, 1), (2, 'Brand', 'Product Number 2', 'Matrix Box', 0, null, 2), (3, 'Brand', 'Product Number 3', 'Rack', 0, null, 3);
-INSERT INTO `biobank_specimen_type_container_type_rel` VALUES (1, 1), (2, 1);
-INSERT INTO `biobank_specimen_process` VALUES (2,'Analysis'),(1,'Collection'),(3,'Preparation');
-INSERT INTO `biobank_container_status` VALUES (1,'Available'),(4,'Discarded'),(3,'Dispensed');
+INSERT INTO `biobank_specimen_attribute_datatype` VALUES (1,'text'),(2,'number'),(3,'date'),(4,'time'),(5,'boolean');
+INSERT INTO `biobank_specimen_process` VALUES (1,'Collection'),(2,'Analysis'),(3,'Preparation');
+INSERT INTO `biobank_container_status` VALUES (1,'Available'),(3,'Dispensed'),(4,'Discarded');
 INSERT INTO `shipment_status` VALUES (1,'cancelled'),(2,'created'),(3,'received'),(4,'returned'),(5,'shipped');
+INSERT INTO `biobank_specimen_type` VALUES (1,'Blood',0),(2,'Serum',1);
+INSERT INTO `biobank_container_dimension`
+VALUES (1,1,1,1,1,0,0),
+       (2,10,1,10,0,1,0),
+       (3,1,0,5,0,1,0);
+INSERT INTO `biobank_container_capacity` VALUES (1,1,1);
+INSERT INTO `biobank_container_type`
+VALUES (1,'Brand','Product Number 1','Vial',1,1,1),
+       (2,'Brand','Product Number 2','Matrix Box',0,NULL,2),
+       (3,'Brand','Product Number 3','Rack',0,NULL,3);
+INSERT INTO `biobank_specimen_protocol`
+VALUES (1,'Blood Collection',1,1),
+       (2,'Blood Preparation',2,1),
+       (3,'Serum Collection',1,2);
+INSERT INTO `biobank_specimen_type_unit_rel` VALUES (1,1),(2,2);
+INSERT INTO `biobank_specimen_type_parent` VALUES (2,1);
+INSERT INTO `biobank_specimen_type_container_type_rel` VALUES (1,1),(2,1);
 
 -- Insert ConfigSettings for label printing endpoint
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('biobank', 'Settings related to the biobank module', 1, 0, 'Biobank', 16);

SQL/New_patches/2025-09-03-multilingualconfig.sql

@@ -0,0 +1,16 @@
+ALTER table ConfigSettings ADD COLUMN Multilingual boolean DEFAULT false;
+UPDATE ConfigSettings SET Multilingual=true WHERE Name='projectDescription';
+
+CREATE TABLE `ConfigI18n` (
+  `Value` text NOT NULL,
+  `ConfigID` int(11) DEFAULT NULL,
+  `LanguageID` int(10) unsigned DEFAULT NULL,
+  KEY `ConfigID` (`ConfigID`),
+  KEY `LanguageID` (`LanguageID`),
+  CONSTRAINT `ConfigI18n_ibfk_1` FOREIGN KEY (`ConfigID`) REFERENCES `ConfigSettings` (`ID`),
+  CONSTRAINT `ConfigI18n_ibfk_2` FOREIGN KEY (`LanguageID`) REFERENCES `language` (`language_id`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci;
+
+-- Sample translation of projectDescription for testing. We do not have a
+-- foreign key value in the 'language' table to add it to RB.
+-- INSERT INTO ConfigI18n VALUES ('このデータベースは、様々な場所で収集された画像データと行動データの両方をオンラインで保存するための仕組みを提供します。このフレームワークには、このプロセスを可能な限り効率的かつシンプルにするためのツールがいくつか用意されています。データベースに関する詳細な情報については、右上のヘルプアイコンをクリックしてください。それ以外の場合は、DCCまでお気軽にお問い合わせください。私たちは、データ収集を楽しいものにすることを目指しています。', 48, 2)

SQL/New_patches/2025-09-09_Issue_Tracker_notification_description.sql

@@ -0,0 +1,3 @@
+UPDATE notification_modules 
+	SET Description='Issue Tracker: All issues created or edited' 
+	WHERE module_name='issue_tracker' AND operation_type='create/edit';