Merge branch 'main' into TranslateHelpEditor

Author: SKADE2303

.gitignore

@@ -26,6 +26,7 @@ modules/*/js/.module-cache/
 htdocs/js/components/.module-cache/
 node_modules/
 modules/*/js/*.map
+**/LC_MESSAGES/*.json
 htdocs/js/components/*.map
 npm-debug.log*
 SQL/Archive/autogenerated/reversion/*.sql

CHANGELOG.md

@@ -8,6 +8,40 @@ core section.***
 - ***When possible please provide the number of the pull request(s) containing the 
 changes in the following format: PR #1234***
 
+## LORIS 27.x (Release Date: TBD)
+### Core
+#### Summary
+- Minor release after v27 release
+### Notes For Existing Projects
+
+Upgrading LORIS requires following the upgrade process each major and minor release (bug fix releases can be script) to ensure the schema is up to date.
+
+For upgrading to 27.x from 27:
+- Run the `tools/single_use/27_Publication_Collaborators_Into_New_Entries.php` to move publication collaborators into their own database entries rather than relying on eachother.
+
+## LORIS 27.0 (Release Date: 2025-06-20)
+### Core
+#### Summary
+The LORIS 27 release adds many new features and optimizations detailed below such as:
+- Optimizations for the new dataquery tool which also optimize various components throughout LORIS
+- Improvements to permission handling through different modules
+- A new "Batch Mode" for the issue tracker
+- The CandID in LORIS is now 10 digits instead of 6 to support larger projects
+- Foreign Key references to the `candidate` table are now standardized: `CandidateID` which refers to `candidate`.`ID`
+- Instrument's `flag`.`data` moved to `instrument_data` table
+- LORIS now has the ability to display summary statistics of the LORIS instance (either from an SQL query or a query built with the new data query tool) on the login page.
+- A new redcap module allows to importing of data from redcap into LORIS
+- Various other bug fixes and features detailed below
+
+### Notes For Existing Projects
+
+Upgrading LORIS requires following the upgrade process each major and minor release (bug fix releases can be script) to ensure the schema is up to date.
+
+For upgrading to 27 from 26:
+- Source the `SQL/Release_patches/26.0_To_27.0_upgrade.sql`
+- Run the `tools/update_issues_with_description.php` to back-populate the new issue tracker description column. (The description was previously based on the first comment.)
+
+
 ## LORIS 26.0 (Release Date: 2024-06-13)
 ### Core
 #### Features

Makefile

@@ -65,6 +65,8 @@ testdata:
 locales: 
 	msgfmt -o locale/en/LC_MESSAGES/loris.mo locale/en/LC_MESSAGES/loris.po
 	npx i18next-conv -l en -s locale/en/LC_MESSAGES/loris.po -t locale/en/LC_MESSAGES/loris.json --compatibilityJSON v4
+	msgfmt -o locale/fr/LC_MESSAGES/loris.mo locale/fr/LC_MESSAGES/loris.po
+	npx i18next-conv -l fr -s locale/fr/LC_MESSAGES/loris.po -t locale/fr/LC_MESSAGES/loris.json --compatibilityJSON v4
 	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 --compatibilityJSON v4
 	msgfmt -o locale/hi/LC_MESSAGES/loris.mo locale/hi/LC_MESSAGES/loris.po
@@ -75,6 +77,9 @@ locales:
 	npx i18next-conv -l ja -s modules/new_profile/locale/ja/LC_MESSAGES/new_profile.po -t modules/new_profile/locale/ja/LC_MESSAGES/new_profile.json
 	msgfmt -o modules/new_profile/locale/hi/LC_MESSAGES/new_profile.mo modules/new_profile/locale/hi/LC_MESSAGES/new_profile.po
 	npx i18next-conv -l hi -s modules/new_profile/locale/hi/LC_MESSAGES/new_profile.po -t modules/new_profile/locale/hi/LC_MESSAGES/new_profile.json
+	msgfmt -o modules/new_profile/locale/es/LC_MESSAGES/new_profile.mo modules/new_profile/locale/es/LC_MESSAGES/new_profile.po
+	npx i18next-conv -l es -s modules/new_profile/locale/es/LC_MESSAGES/new_profile.po -t modules/new_profile/locale/es/LC_MESSAGES/new_profile.json --compatibilityJSON v4
+	msgfmt -o modules/new_profile/locale/hi/LC_MESSAGES/new_profile.mo modules/new_profile/locale/hi/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
 	msgfmt -o modules/battery_manager/locale/ja/LC_MESSAGES/battery_manager.mo modules/battery_manager/locale/ja/LC_MESSAGES/battery_manager.po
@@ -86,6 +91,7 @@ locales:
 	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
+	npx i18next-conv -l ja -s modules/candidate_parameters/locale/ja/LC_MESSAGES/candidate_parameters.po -t modules/candidate_parameters/locale/ja/LC_MESSAGES/candidate_parameters.json
 	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
@@ -119,18 +125,24 @@ locales:
 	msgfmt -o modules/help_editor/locale/hi/LC_MESSAGES/help_editor.mo modules/help_editor/locale/hi/LC_MESSAGES/help_editor.po
 	npx i18next-conv -l hi -s modules/help_editor/locale/hi/LC_MESSAGES/help_editor.po -t modules/help_editor/locale/hi/LC_MESSAGES/help_editor.json
 	msgfmt -o modules/imaging_browser/locale/ja/LC_MESSAGES/imaging_browser.mo modules/imaging_browser/locale/ja/LC_MESSAGES/imaging_browser.po
+	npx i18next-conv -l ja -s modules/imaging_browser/locale/ja/LC_MESSAGES/imaging_browser.po -t modules/imaging_browser/locale/ja/LC_MESSAGES/imaging_browser.json --compatibilityJSON v4
 	msgfmt -o modules/imaging_qc/locale/ja/LC_MESSAGES/imaging_qc.mo modules/imaging_qc/locale/ja/LC_MESSAGES/imaging_qc.po
 	msgfmt -o modules/imaging_uploader/locale/ja/LC_MESSAGES/imaging_uploader.mo modules/imaging_uploader/locale/ja/LC_MESSAGES/imaging_uploader.po
 	msgfmt -o modules/instrument_builder/locale/ja/LC_MESSAGES/instrument_builder.mo modules/instrument_builder/locale/ja/LC_MESSAGES/instrument_builder.po
 	msgfmt -o modules/instrument_list/locale/ja/LC_MESSAGES/instrument_list.mo modules/instrument_list/locale/ja/LC_MESSAGES/instrument_list.po
 	msgfmt -o modules/instrument_list/locale/es/LC_MESSAGES/instrument_list.mo modules/instrument_list/locale/es/LC_MESSAGES/instrument_list.po
 	msgfmt -o modules/instrument_manager/locale/ja/LC_MESSAGES/instrument_manager.mo modules/instrument_manager/locale/ja/LC_MESSAGES/instrument_manager.po
 	msgfmt -o modules/instruments/locale/ja/LC_MESSAGES/instruments.mo modules/instruments/locale/ja/LC_MESSAGES/instruments.po
+	msgfmt -o modules/instruments/locale/es/LC_MESSAGES/instruments.mo modules/instruments/locale/es/LC_MESSAGES/instruments.po
 	msgfmt -o modules/issue_tracker/locale/ja/LC_MESSAGES/issue_tracker.mo modules/issue_tracker/locale/ja/LC_MESSAGES/issue_tracker.po
 	msgfmt -o modules/login/locale/ja/LC_MESSAGES/login.mo modules/login/locale/ja/LC_MESSAGES/login.po
 	msgfmt -o modules/media/locale/ja/LC_MESSAGES/media.mo modules/media/locale/ja/LC_MESSAGES/media.po
 	msgfmt -o modules/module_manager/locale/ja/LC_MESSAGES/module_manager.mo modules/module_manager/locale/ja/LC_MESSAGES/module_manager.po
 	msgfmt -o modules/mri_violations/locale/ja/LC_MESSAGES/mri_violations.mo modules/mri_violations/locale/ja/LC_MESSAGES/mri_violations.po
+	msgfmt -o modules/my_preferences/locale/hi/LC_MESSAGES/my_preferences.mo modules/my_preferences/locale/hi/LC_MESSAGES/my_preferences.po
+	npx i18next-conv -l ja -s modules/my_preferences/locale/ja/LC_MESSAGES/my_preferences.po -t modules/my_preferences/locale/ja/LC_MESSAGES/my_preferences.json --compatibilityJSON v4
+	npx i18next-conv -l hi -s modules/my_preferences/locale/hi/LC_MESSAGES/my_preferences.po -t modules/my_preferences/locale/hi/LC_MESSAGES/my_preferences.json --compatibilityJSON v4
+	msgfmt -o modules/my_preferences/locale/ja/LC_MESSAGES/my_preferences.mo modules/my_preferences/locale/ja/LC_MESSAGES/my_preferences.po
 	msgfmt -o modules/next_stage/locale/ja/LC_MESSAGES/next_stage.mo modules/next_stage/locale/ja/LC_MESSAGES/next_stage.po
 	msgfmt -o modules/next_stage/locale/es/LC_MESSAGES/next_stage.mo modules/next_stage/locale/es/LC_MESSAGES/next_stage.po
 	msgfmt -o modules/oidc/locale/ja/LC_MESSAGES/oidc.mo modules/oidc/locale/ja/LC_MESSAGES/oidc.po
@@ -194,3 +206,8 @@ server_processes_manager: modules/server_processes_manager/locale/ja/LC_MESSAGES
 
 conflict_resolver:
 	target=conflict_resolver npm run compile
+
+my_preferences: modules/my_preferences/locale/ja/LC_MESSAGES/my_preferences.mo modules/my_preferences/locale/hi/LC_MESSAGES/my_preferences.mo
+	npx i18next-conv -l ja -s modules/my_preferences/locale/ja/LC_MESSAGES/my_preferences.po -t modules/my_preferences/locale/ja/LC_MESSAGES/my_preferences.json --compatibilityJSON v4
+	npx i18next-conv -l hi -s modules/my_preferences/locale/hi/LC_MESSAGES/my_preferences.po -t modules/my_preferences/locale/hi/LC_MESSAGES/my_preferences.json --compatibilityJSON v4
+	target=my_preferences npm run compile

SQL/0000-00-00-schema.sql

@@ -105,6 +105,7 @@ CREATE TABLE `users` (
   `Active` enum('Y','N') NOT NULL default 'Y',
   `Password_hash` varchar(255) default NULL,
   `PasswordChangeRequired` tinyint(1) NOT NULL default 0,
+  `TOTPSecret` binary(64) DEFAULT NULL,
   `Pending_approval` enum('Y','N') default 'Y',
   `Doc_Repo_Notifications` enum('Y','N') default 'N',
   `language_preference` integer unsigned default NULL,
@@ -293,13 +294,12 @@ CREATE TABLE `flag` (
   `ID` int(10) unsigned NOT NULL auto_increment,
   `SessionID` int(10) unsigned NOT NULL,
   `TestID` int(10) unsigned NOT NULL,
-  `CommentID` varchar(255) NOT NULL default '',
+  `CommentID` varchar(255) NOT NULL,
   `Data_entry` enum('In Progress','Complete') default NULL,
   `Required_elements_completed` enum('Y','N') NOT NULL default 'N',
   `Administration` enum('None','Partial','All') default NULL,
   `Validity` enum('Questionable','Invalid','Valid') default NULL,
   `Exclusion` enum('Fail','Pass') default NULL,
-  `UserID` varchar(255) default NULL,
   `Testdate` timestamp NOT NULL default CURRENT_TIMESTAMP on update CURRENT_TIMESTAMP,
   `DataID` int(10) unsigned default NULL,
   PRIMARY KEY  (`CommentID`),
@@ -309,12 +309,29 @@ CREATE TABLE `flag` (
   KEY `flag_Data_entry` (`Data_entry`),
   KEY `flag_Validity` (`Validity`),
   KEY `flag_Administration` (`Administration`),
-  KEY `flag_UserID` (`UserID`),
   CONSTRAINT `FK_flag_1` FOREIGN KEY (`SessionID`) REFERENCES `session` (`ID`) ON DELETE CASCADE ON UPDATE CASCADE,
   CONSTRAINT `FK_flag_3` FOREIGN KEY (`DataID`) REFERENCES `instrument_data` (`ID`),
   CONSTRAINT `FK_ibfk_1` FOREIGN KEY (`TestID`) REFERENCES `test_names` (`ID`)
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 
+CREATE TABLE `flag_editors` (
+  `userID` int(10) unsigned NOT NULL,
+  `CommentID` VARCHAR(255) NOT NULL,
+  `editDate` timestamp NOT NULL default CURRENT_TIMESTAMP on update CURRENT_TIMESTAMP,
+  PRIMARY KEY  (`userID`,`CommentID`),
+  KEY `FK_flag_editors_2` (`CommentID`),
+  CONSTRAINT `FK_flag_editors_2`
+  FOREIGN KEY (`CommentID`)
+    REFERENCES `flag` (`CommentID`)
+    ON DELETE CASCADE
+    ON UPDATE CASCADE,
+  CONSTRAINT `FK_flag_editors_1`
+  FOREIGN KEY (`userID`)
+    REFERENCES `users` (`ID`)
+    ON DELETE CASCADE
+    ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
 CREATE TABLE `history` (
   `id` int(11) NOT NULL auto_increment,
   `tbl` varchar(255) NOT NULL default '',
@@ -1204,10 +1221,12 @@ INSERT INTO notification_modules (module_name, operation_type, as_admin, templat
   ('document_repository', 'edit', 'N', 'notifier_document_repository_edit.tpl', 'Document Repository: Document Edited'),
   ('publication', 'submission', 'N', 'notifier_publication_submission.tpl', 'Publication: Submission Received'),
   ('publication', 'review', 'N', 'notifier_publication_review.tpl', 'Publication: Proposal has been reviewed'),
-  ('publication', 'edit', 'N', 'notifier_publication_edit.tpl', 'Publication: Proposal has been edited');
+  ('publication', 'edit', 'N', 'notifier_publication_edit.tpl', 'Publication: Proposal has been edited'),
+  ('issue_tracker', 'create/edit', 'N', 'issue_change.tpl', 'Issue Tracker: All issues created or edited');
 
 INSERT INTO notification_modules_services_rel SELECT nm.id, ns.id FROM notification_modules nm JOIN notification_services ns WHERE nm.module_name='document_repository' AND ns.service='email_text';
 INSERT INTO notification_modules_services_rel SELECT nm.id, ns.id FROM notification_modules nm JOIN notification_services ns WHERE nm.module_name='publication' AND ns.service='email_text';
+INSERT INTO notification_modules_services_rel SELECT nm.id, ns.id FROM notification_modules nm JOIN notification_services ns WHERE nm.module_name='issue_tracker' AND ns.service='email_text';
 
 -- Transfer Document repository notifications to new system
 INSERT INTO users_notifications_rel SELECT u.ID, nm.id, ns.id FROM users u JOIN notification_modules nm JOIN notification_services ns WHERE nm.module_name='document_repository' AND ns.service='email_text' AND u.Doc_Repo_Notifications='Y';
@@ -2453,7 +2472,6 @@ CREATE TABLE `publication_collaborator` (
 CREATE TABLE `publication` (
     `PublicationID` int(10) unsigned NOT NULL AUTO_INCREMENT,
     `PublicationStatusID` int(2) unsigned NOT NULL default 1,
-    `LeadInvestigatorID` int(10) unsigned NOT NULL,
     `UserID` int(10) unsigned NOT NULL,
     `RatedBy` int(10) unsigned,
     `DateProposed` date NOT NULL,
@@ -2467,12 +2485,13 @@ CREATE TABLE `publication` (
     `link` varchar(255) DEFAULT NULL,
     `publishingStatus` enum('In Progress','Published') DEFAULT NULL,
     `project` int(10) unsigned DEFAULT NULL,
+    `LeadInvestigator` VARCHAR(255) DEFAULT NULL,
+    `LeadInvestigatorEmail` VARCHAR(255) DEFAULT NULL,
     CONSTRAINT `FK_publication_project` FOREIGN KEY (project) REFERENCES Project(ProjectID),
     CONSTRAINT `PK_publication` PRIMARY KEY(`PublicationID`),
     CONSTRAINT `FK_publication_UserID` FOREIGN KEY(`UserID`) REFERENCES `users` (`ID`),
     CONSTRAINT `FK_publication_RatedBy` FOREIGN KEY(`RatedBy`) REFERENCES `users` (`ID`),
     CONSTRAINT `FK_publication_PublicationStatusID` FOREIGN KEY(`PublicationStatusID`) REFERENCES `publication_status` (`PublicationStatusID`),
-    CONSTRAINT `FK_publication_LeadInvestigatorID` FOREIGN KEY(`LeadInvestigatorID`) REFERENCES `publication_collaborator` (`PublicationCollaboratorID`),
     CONSTRAINT `UK_publication_Title` UNIQUE (`Title`)
 ) ENGINE=InnoDB DEFAULT CHARSET='utf8';
 
@@ -2688,4 +2707,4 @@ CREATE TABLE `redcap_notification` (
   `handled_dt` datetime NULL,
   PRIMARY KEY (`id`),
   KEY `i_redcap_notif_received_dt` (`received_dt`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;

SQL/0000-00-03-ConfigTables.sql

@@ -48,6 +48,11 @@ CREATE TABLE `Config` (
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('study', 'Settings related to details of the study', 1, 0, 'Study', 1);
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'title', 'Full descriptive title of the study', 1, 0, 'text', ID, 'Study title', 1 FROM ConfigSettings WHERE Name="study";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'studylogo', 'Filename containing logo of the study. File should be located under the htdocs/images/ folder', 1, 0, 'text', ID, 'Study logo', 2 FROM ConfigSettings WHERE Name="study";
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'login_logo_left', 'Path for top left logo on the login page.', 1, 0, 'text', ID, 'Login Top Left Logo', 3 FROM ConfigSettings WHERE Name="study";
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'login_logo_right', 'Path for top right logo on the login page.', 1, 0, 'text', ID, 'Login Top Right Logo', 3 FROM ConfigSettings WHERE Name="study";
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'login_logo_left_link', 'Optional link to redirect when clicking on top left logo', 1, 0, 'text', ID, 'Login Top Left Logo Link', 4 FROM ConfigSettings WHERE Name="study";
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'login_logo_right_link', 'Optional link to redirect when clicking on top right logo', 1, 0, 'text', ID, 'Login Top Right Logo Link', 4 FROM ConfigSettings WHERE Name="study";
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'partner_logos', 'Logos for partners to be displayed in the homepage', 1, 1, 'text', ID, 'Partner Logos', 4 FROM ConfigSettings WHERE Name="study";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'startYear', "Start year for study recruitment or data collection", 1, 0, 'text', ID, 'Start year', 5 FROM ConfigSettings WHERE Name="study";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'endYear', "End year for study recruitment or data collection", 1, 0, 'text', ID, 'End year', 6 FROM ConfigSettings WHERE Name="study";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'ageMin', 'Minimum candidate age in years (0+)', 1, 0, 'text', ID, 'Minimum candidate age', 7 FROM ConfigSettings WHERE Name="study";
@@ -204,6 +209,10 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType,
 INSERT INTO Config (ConfigID, Value) SELECT ID, 1 FROM ConfigSettings WHERE Name="additional_user_info";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "Example Study" FROM ConfigSettings WHERE Name="title";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "<h3>Example Study Description</h3>\r\n <p>This is a sample description for this study, because it is a new LORIS install that has not yet customized this text.</p>\r\n <p>A LORIS administrator can customize this text in the configuration module, under the configuration option labeled \"Study Description\"</p>\r\n <h3>Useful Links</h3>\r\n <ul>\r\n <li><a href=\"https://github.com/aces/Loris\" >LORIS GitHub Repository</a></li>\r\n <li><a href=\"https://github.com/aces/Loris/wiki/Setup\" >LORIS Setup Guide</a></li>\r\n <li><a href=\"https://www.youtube.com/watch?v=2Syd_BUbl5A\" >A video of a loris on YouTube</a></li>\r\n </ul>" FROM ConfigSettings WHERE Name="StudyDescription";
+INSERT INTO Config (ConfigID, Value) SELECT ID, "/images/LORIS_logo_white.svg" FROM ConfigSettings WHERE Name="login_logo_left";
+INSERT INTO Config (ConfigID, Value) SELECT ID, "/images/github-mark.svg" FROM ConfigSettings WHERE Name="login_logo_right";
+INSERT INTO Config (ConfigID, Value) SELECT ID, "/" FROM ConfigSettings WHERE Name="login_logo_left_link";
+INSERT INTO Config (ConfigID, Value) SELECT ID, "https://github.com/aces/Loris" FROM ConfigSettings WHERE Name="login_logo_right_link";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "images/neurorgb_web.jpg" FROM ConfigSettings WHERE Name="studylogo";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "false" FROM ConfigSettings WHERE Name="useEDC";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "false" FROM ConfigSettings WHERE Name="useDoB";