Merge branch 'main' into TranslateDocumentRepository

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

@@ -1,36 +1,26 @@
-FROM mariadb:10.5
+FROM mariadb:11.8
 
 ARG BASE_DIR
 
-COPY SQL/0000-00-00-schema.sql /0000-00-00-schema.sql
-COPY SQL/0000-00-01-Modules.sql /0000-00-01-Modules.sql
-COPY SQL/0000-00-02-Permission.sql /0000-00-02-Permission.sql
-COPY SQL/0000-00-03-ConfigTables.sql /0000-00-03-ConfigTables.sql
-COPY SQL/0000-00-04-Help.sql /0000-00-04-Help.sql
-COPY SQL/0000-00-05-ElectrophysiologyTables.sql /0000-00-05-ElectrophysiologyTables.sql
-COPY raisinbread/instruments/instrument_sql/aosi.sql  /aosi.sql
-COPY raisinbread/instruments/instrument_sql/bmi.sql  /bmi.sql
-COPY raisinbread/instruments/instrument_sql/medical_history.sql  /medical_history.sql
-COPY raisinbread/instruments/instrument_sql/mri_parameter_form.sql  /mri_parameter_form.sql
-COPY raisinbread/instruments/instrument_sql/radiology_review.sql  /radiology_review.sql
+COPY SQL/ /sql/
+COPY raisinbread/instruments/instrument_sql/ /instruments_sql/
+COPY raisinbread/RB_files/ /RB_files/
 COPY test/test_instrument/testtest.sql /test_instrument.sql
-COPY raisinbread/RB_files/*.sql /RB_files/
 
-RUN echo "Use LorisTest;" | cat - \
-    0000-00-00-schema.sql \
-    0000-00-01-Modules.sql \
-    0000-00-02-Permission.sql \
-    0000-00-03-ConfigTables.sql \
-    0000-00-04-Help.sql \
-    0000-00-05-ElectrophysiologyTables.sql \
-    aosi.sql \
-    bmi.sql \
-    medical_history.sql \
-    mri_parameter_form.sql \
-    radiology_review.sql \
-    test_instrument.sql \
-    RB_files/*.sql > /docker-entrypoint-initdb.d/0000-compiled.sql
+RUN cat /sql/0000-00-00-schema.sql \
+        /sql/0000-00-01-Modules.sql \
+        /sql/0000-00-02-Permission.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 \
+    > /docker-entrypoint-initdb.d/0000-compiled.sql
 
-RUN echo "Use LorisTest;" >> /docker-entrypoint-initdb.d/0001-paths.sql
-RUN echo "UPDATE Config SET Value='${BASE_DIR}/' WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='base');" >> /docker-entrypoint-initdb.d/0001-paths.sql
-RUN echo "GRANT UPDATE,INSERT,SELECT,DELETE,DROP,CREATE TEMPORARY TABLES ON LorisTest.* TO 'SQLTestUser'@'%' IDENTIFIED BY 'TestPassword' WITH GRANT OPTION;" >> /docker-entrypoint-initdb.d/0004-sql-user.sql
+RUN echo "USE LorisTest;" > /docker-entrypoint-initdb.d/0001-paths.sql \
+    && echo "UPDATE Config SET Value='${BASE_DIR}/' WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='base');" >> /docker-entrypoint-initdb.d/0001-paths.sql \
+    && echo "CREATE USER IF NOT EXISTS 'SQLTestUser'@'%' IDENTIFIED BY 'TestPassword';" >> /docker-entrypoint-initdb.d/0001-paths.sql \
+    && echo "GRANT UPDATE, INSERT, SELECT, DELETE, DROP, CREATE TEMPORARY TABLES ON LorisTest.* TO 'SQLTestUser'@'%';" >> /docker-entrypoint-initdb.d/0001-paths.sql \
+    && echo "FLUSH PRIVILEGES;" >> /docker-entrypoint-initdb.d/0001-paths.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 +1,28 @@
-.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
 
+%.mo: %.po
+	msgfmt -o $@ $<
+
 # 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 +40,7 @@ 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 +53,7 @@ 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.
@@ -60,6 +65,10 @@ testdata:
 locales: 
 	msgfmt -o locale/ja/LC_MESSAGES/loris.mo locale/ja/LC_MESSAGES/loris.po
 	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
@@ -69,18 +78,32 @@ 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
+	npx i18next-conv -l hi -s modules/datadict/locale/hi/LC_MESSAGES/datadict.po -t modules/datadict/locale/hi/LC_MESSAGES/datadict.json
+	npx i18next-conv -l ja -s modules/datadict/locale/ja/LC_MESSAGES/datadict.po -t modules/datadict/locale/ja/LC_MESSAGES/datadict.json
 	msgfmt -o modules/dataquery/locale/ja/LC_MESSAGES/dataquery.mo modules/dataquery/locale/ja/LC_MESSAGES/dataquery.po
 	msgfmt -o modules/data_release/locale/ja/LC_MESSAGES/data_release.mo modules/data_release/locale/ja/LC_MESSAGES/data_release.po
+	npx i18next-conv -l ja -s modules/data_release/locale/ja/LC_MESSAGES/data_release.po -t modules/data_release/locale/ja/LC_MESSAGES/data_release.json
+	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
 	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/document_repository/locale/hi/LC_MESSAGES/document_repository.mo modules/document_repository/locale/hi/LC_MESSAGES/document_repository.po
 	npx i18next-conv -l hi -s modules/document_repository/locale/hi/LC_MESSAGES/document_repository.po -t modules/document_repository/locale/hi/LC_MESSAGES/document_repository.json
@@ -108,50 +131,58 @@ 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:
+acknowledgements: modules/acknowledgements/locale/ja/LC_MESSAGES/acknowledgements.mo
 	target=acknowledgements npm run compile
 
-data_release: 
+create_timepoint:
+	target=data_release npm run compile
+
+data_release: modules/data_release/locale/hi/LC_MESSAGES/data_release.mo modules/data_release/locale/ja/LC_MESSAGES/data_release.mo
+	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 
+	npx i18next-conv -l ja -s modules/data_release/locale/ja/LC_MESSAGES/data_release.po -t modules/data_release/locale/ja/LC_MESSAGES/data_release.json 
 	target=data_release npm run compile
 
-instrument_manager:
+instrument_manager: modules/instrument_manager/locale/ja/LC_MESSAGES/instrument_manager.mo
 	target=instrument_manager npm run compile
 
-dataquery:
+dataquery: modules/dataquery/locale/ja/LC_MESSAGES/dataquery.mo
+	msgfmt -o modules/dataquery/locale/ja/LC_MESSAGES/dataquery.mo modules/dataquery/locale/ja/LC_MESSAGES/dataquery.po
 	target=dataquery npm run compile
 
-login:
+login: modules/login/locale/ja/LC_MESSAGES/login.mo
 	target=login npm run compile
 
-module_manager:
+module_manager: modules/module_manager/locale/ja/LC_MESSAGES/module_manager.mo
 	target=module_manager npm run compile
 
-mri_violations:
+mri_violations: modules/mri_violations/locale/ja/LC_MESSAGES/mri_violations.mo
 	target=mri_violations npm run compile
 
-issue_tracker:
+issue_tracker: modules/issue_tracker/locale/ja/LC_MESSAGES/issue_tracker.mo
 	target=issue_tracker npm run compile
 
-candidate_list:
-	msgfmt -o modules/candidate_list/locale/ja/LC_MESSAGES/candidate_list.mo modules/candidate_list/locale/ja/LC_MESSAGES/candidate_list.po
+candidate_list: modules/candidate_list/locale/ja/LC_MESSAGES/candidate_list.mo modules/candidate_list/locale/hi/LC_MESSAGES/candidate_list.mo
 	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
+	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:
+candidate_parameters: modules/candidate_parameters/locale/ja/LC_MESSAGES/candidate_parameters.mo
 	target=candidate_parameters npm run compile
 
-dashboard:
+dashboard: modules/dashboard/locale/ja/LC_MESSAGES/dashboard.mo
 	target=dashboard npm run compile
 
-publication:
+publication: modules/publication/locale/ja/LC_MESSAGES/publication.mo
 	target=publication npm run compile
 
-server_processes_manager:
+server_processes_manager: modules/server_processes_manager/locale/ja/LC_MESSAGES/server_processes_manager.mo
 	target=server_processes_manager npm run compile
 
 conflict_resolver:

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',
@@ -1426,6 +1426,38 @@ CREATE TABLE `user_account_history` (
   PRIMARY KEY (`ID`)
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 
+
+-- ********************************
+-- tables for policies
+-- ********************************
+
+CREATE TABLE policies (
+    PolicyID INT AUTO_INCREMENT PRIMARY KEY,
+    Name VARCHAR(255) NOT NULL,
+    Version INT NOT NULL,
+    ModuleID INT NOT NULL,
+    PolicyRenewalTime INT DEFAULT 7,
+    PolicyRenewalTimeUnit enum('D','Y','M','H') DEFAULT 'D',
+    Content TEXT NULL,
+    SwalTitle VARCHAR(255) DEFAULT 'Terms of Use',
+    HeaderButton enum('Y','N') DEFAULT 'Y',
+    HeaderButtonText VARCHAR(255) DEFAULT 'Terms of Use',
+    Active enum('Y','N') DEFAULT 'Y',
+    AcceptButtonText VARCHAR(255) DEFAULT 'Accept',
+    DeclineButtonText VARCHAR(255) DEFAULT 'Decline',
+    CreatedAt DATETIME DEFAULT CURRENT_TIMESTAMP,
+    UpdatedAt DATETIME DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP
+);
+
+CREATE TABLE user_policy_decision (
+    ID INT AUTO_INCREMENT PRIMARY KEY,
+    UserID INT NOT NULL,
+    PolicyID INT NOT NULL,
+    Decision enum('Accepted','Declined') NOT NULL,
+    DecisionDate DATETIME DEFAULT CURRENT_TIMESTAMP
+);
+
+
 -- ********************************
 -- user_login_history tables
 -- ********************************

SQL/0000-00-01-Modules.sql

@@ -10,6 +10,7 @@ INSERT INTO modules (Name, Active) VALUES ('acknowledgements', 'Y');
 INSERT INTO modules (Name, Active) VALUES ('api', 'Y');
 INSERT INTO modules (Name, Active) VALUES ('battery_manager', 'Y');
 INSERT INTO modules (Name, Active) VALUES ('behavioural_qc', 'Y');
+INSERT INTO modules (Name, Active) VALUES ('biobank', 'Y');
 INSERT INTO modules (Name, Active) VALUES ('brainbrowser', 'Y');
 INSERT INTO modules (Name, Active) VALUES ('bvl_feedback', 'Y');
 INSERT INTO modules (Name, Active) VALUES ('candidate_list', 'Y');
@@ -55,5 +56,6 @@ INSERT INTO modules (Name, Active) VALUES ('electrophysiology_uploader', 'Y');
 INSERT INTO modules (Name, Active) VALUES ('dataquery', 'Y');
 INSERT INTO modules (Name, Active) VALUES ('schedule_module', 'Y');
 INSERT INTO modules (Name, Active) VALUES ('redcap', 'N');
+INSERT INTO modules (Name, Active) VALUES ('policy_tracker', 'Y');
 
 ALTER TABLE issues ADD CONSTRAINT `fk_issues_7` FOREIGN KEY (`module`) REFERENCES `modules` (`ID`);