Merge remote-tracking branch 'aces/main' into 2024_10_15_NDB_BVL_Inst…

…rument_php_warnings

.eslintrc.json

@@ -47,6 +47,7 @@
         "tabWidth": 2,
         "ignoreComments": true
     }],
+    "indent": ["error", 2],
     "no-unexpected-multiline": "off",
     "no-unused-vars": "error",
     "no-useless-escape": "off",
@@ -110,8 +111,9 @@
           }}
         ],
         "jsdoc/require-param-description": "error",
-        "jsdoc/require-returns": "error",
         "jsdoc/require-returns-description": "error",
+        "jsdoc/require-param-type": "off",
+        "jsdoc/require-returns-type": "off",
         "no-undef": "off",
         "@typescript-eslint/ban-ts-comment": "off",
         "@typescript-eslint/no-explicit-any": "off"

SQL/0000-00-00-schema.sql

@@ -341,6 +341,7 @@ CREATE TABLE `test_battery` (
   `CenterID` int(11) default NULL,
   `firstVisit` enum('Y','N') default NULL,
   `instr_order` tinyint(4) default NULL,
+  `DoubleDataEntryEnabled` enum('Y','N') default 'N',
   PRIMARY KEY  (`ID`),
   KEY `age_test` (`AgeMinDays`,`AgeMaxDays`,`Test_name`),
   KEY `FK_test_battery_1` (`Test_name`),
@@ -1528,6 +1529,7 @@ CREATE TABLE `issues` (
   `candID` int(6) DEFAULT NULL,
   `category` varchar(255) DEFAULT NULL,
   `description` longtext DEFAULT NULL,
+  `instrument` int(10) unsigned DEFAULT NULL,
   PRIMARY KEY (`issueID`),
   KEY `fk_issues_1` (`reporter`),
   KEY `fk_issues_2` (`assignee`),
@@ -1536,20 +1538,22 @@ CREATE TABLE `issues` (
   KEY `fk_issues_5` (`centerID`),
   KEY `fk_issues_6` (`lastUpdatedBy`),
   KEY `fk_issues_8` (`category`),
+  KEY `fk_issues_instrument` (`instrument`),
   CONSTRAINT `fk_issues_8` FOREIGN KEY (`category`) REFERENCES `issues_categories` (`categoryName`),
   CONSTRAINT `fk_issues_1` FOREIGN KEY (`reporter`) REFERENCES `users` (`UserID`),
   CONSTRAINT `fk_issues_2` FOREIGN KEY (`assignee`) REFERENCES `users` (`UserID`),
   CONSTRAINT `fk_issues_3` FOREIGN KEY (`candID`) REFERENCES `candidate` (`CandID`),
   CONSTRAINT `fk_issues_4` FOREIGN KEY (`sessionID`) REFERENCES `session` (`ID`),
   CONSTRAINT `fk_issues_5` FOREIGN KEY (`centerID`) REFERENCES `psc` (`CenterID`),
-  CONSTRAINT `fk_issues_6` FOREIGN KEY (`lastUpdatedBy`) REFERENCES `users` (`UserID`)
-) ENGINE=InnoDB  DEFAULT CHARSET=utf8;
+  CONSTRAINT `fk_issues_6` FOREIGN KEY (`lastUpdatedBy`) REFERENCES `users` (`UserID`),
+  CONSTRAINT `fk_issues_instrument` FOREIGN KEY (`instrument`) REFERENCES `test_names` (`ID`) ON DELETE RESTRICT ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 
 CREATE TABLE `issues_history` (
   `issueHistoryID` int(11) unsigned NOT NULL AUTO_INCREMENT,
   `newValue` longtext NOT NULL,
   `dateAdded` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
-  `fieldChanged` enum('assignee','status','comment','sessionID','centerID','title','category','module','lastUpdatedBy','priority','candID', 'description','watching') NOT NULL DEFAULT 'comment',
+  `fieldChanged` enum('assignee','status','comment','sessionID','centerID','title','category','module','lastUpdatedBy','priority','candID', 'description','watching','instrument') NOT NULL DEFAULT 'comment',
   `issueID` int(11) unsigned NOT NULL,
   `addedBy` varchar(255) NOT NULL DEFAULT '',
   PRIMARY KEY (`issueHistoryID`),
@@ -2095,7 +2099,9 @@ CREATE TABLE `data_release` (
  `file_name` varchar(255),
  `version` varchar(255),
  `upload_date` date,
- PRIMARY KEY (`id`)
+ `ProjectID` INT(10) UNSIGNED NULL,
+ PRIMARY KEY (`id`),
+ FOREIGN KEY (ProjectID) REFERENCES Project (ProjectID)
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 
 CREATE TABLE `data_release_permissions` (

SQL/0000-00-03-ConfigTables.sql

@@ -51,7 +51,6 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType,
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'useConsent', 'Enable if the study uses the loris architecture for consent', 1, 0, 'boolean', ID, 'Use consent', 16 FROM ConfigSettings WHERE Name="study";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'additional_user_info', 'Display additional user profile fields on the User accounts page (e.g. Institution, Position, Country, Address)', 1, 0, 'boolean', ID, 'Additional user information', 17 FROM ConfigSettings WHERE Name="study";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'excluded_instruments', "Instruments to be excluded from the Data Dictionary and download via the Data Query Tool", 1, 1, 'instrument', ID, 'Excluded instruments', 18 FROM ConfigSettings WHERE Name="study";
-INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DoubleDataEntryInstruments', "Instruments for which double data entry should be enabled", 1, 1, 'instrument', ID, 'Double data entry instruments', 19 FROM ConfigSettings WHERE Name="study";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'InstrumentResetting', 'Allows resetting of instrument data', 1, 0, 'boolean', ID, 'Instrument Resetting', 20 FROM ConfigSettings WHERE Name="study";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'SupplementalSessionStatus', 'Display supplemental session status information on Timepoint List page', 1, 0, 'boolean', ID, 'Use Supplemental Session Status', 21 FROM ConfigSettings WHERE Name="study";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'useScanDone', 'Used for identifying timepoints that have (or should have) imaging data', 1, 0, 'boolean', ID, 'Use Scan Done', 22 FROM ConfigSettings WHERE Name="study";
@@ -63,6 +62,7 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType,
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'dateDisplayFormat', 'The date format to use throughout LORIS for displaying date information - formats for date inputs are browser- and locale-dependent.', 1, 0, 'text', ID, 'Date display format', 28 FROM ConfigSettings WHERE Name="study";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'adminContactEmail', 'An email address that users can write to in order to report issues or ask question', 1, 0, 'text', ID, 'Administrator Email', 29 FROM ConfigSettings WHERE Name="study";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'UserMaximumDaysInactive', 'The maximum number of days since last login before making a user inactive', 1, 0, 'text', ID, 'Maximum Days Before Making User Inactive', 30 FROM ConfigSettings WHERE Name="study";
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'useDoB', 'Use DoB (Date of Birth)', 1, 0, 'boolean', ID, 'Use DoB', 31 FROM ConfigSettings WHERE Name="study";
 
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('paths', 'Specify directories where LORIS-related files are stored or created. Take care when editing these fields as changing them incorrectly can cause certain modules to lose functionality.', 1, 0, 'Paths', 2);
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'imagePath', 'Path to images for display in Imaging Browser (e.g. /data/$project/data/) ', 1, 0, 'text', ID, 'Images', 9 FROM ConfigSettings WHERE Name="paths";
@@ -188,6 +188,7 @@ INSERT INTO Config (ConfigID, Value) SELECT ID, "Example Study" FROM ConfigSetti
 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/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";
 INSERT INTO Config (ConfigID, Value) SELECT ID, 8 FROM ConfigSettings WHERE Name="ageMin";
 INSERT INTO Config (ConfigID, Value) SELECT ID, 11 FROM ConfigSettings WHERE Name="ageMax";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "false" FROM ConfigSettings WHERE Name="useFamilyID";

SQL/New_patches/2023-12-08_useDoB.sql

@@ -0,0 +1,2 @@
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'useDoB', 'Use DoB (Date of Birth)', 1, 0, 'boolean', ID, 'Use DoB', 31 FROM ConfigSettings WHERE Name="study";
+INSERT INTO Config (ConfigID, Value) SELECT ID, "false" FROM ConfigSettings WHERE Name="useDoB";

SQL/New_patches/2024-07-19-issuetracker_AddsInstrumentToIssuesTable.sql

@@ -0,0 +1,11 @@
+ALTER TABLE `issues`
+    ADD `instrument` int(10) unsigned DEFAULT NULL
+    AFTER `description`;
+
+ALTER TABLE `issues`
+    ADD CONSTRAINT `fk_issues_instrument`
+    FOREIGN KEY (`instrument`) REFERENCES `test_names` (`ID`)
+    ON DELETE RESTRICT ON UPDATE CASCADE;
+
+ALTER TABLE `issues_history`
+    MODIFY `fieldChanged` enum('assignee','status','comment','sessionID','centerID','title','category','module','lastUpdatedBy','priority','candID', 'description','watching','instrument') NOT NULL DEFAULT 'comment';

SQL/New_patches/2024-10-02-Data_Release_Project_separation.sql

@@ -0,0 +1,4 @@
+ALTER TABLE data_release
+ADD COLUMN ProjectID INT(10) UNSIGNED NULL DEFAULT NULL,
+ADD CONSTRAINT FK_ProjectID
+FOREIGN KEY (ProjectID) REFERENCES Project (ProjectID);

SQL/New_patches/2024_05_13_Add_DDE_To_Battery.sql

@@ -0,0 +1,9 @@
+ALTER TABLE test_battery ADD COLUMN DoubleDataEntryEnabled enum("Y", "N") DEFAULT "N";
+
+UPDATE test_battery SET DoubleDataEntryEnabled = 'Y' WHERE Test_name IN (
+    SELECT Value from Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = 'DoubleDataEntryInstruments')
+);
+
+DELETE FROM Config WHERE ConfigID IN (SELECT ID FROM ConfigSettings WHERE Name = 'DoubleDataEntryInstruments');
+
+DELETE FROM ConfigSettings WHERE Name = 'DoubleDataEntryInstruments';

docker-compose.yml

@@ -1,4 +1,4 @@
-version: '2'
+version: '3.8'
 services:
   db:
     build:
@@ -13,12 +13,9 @@ services:
       - MYSQL_RANDOM_ROOT_PASSWORD=yes
 
   selenium:
-    image: selenium/standalone-firefox-debug:3.141.59-zirconium
-    volumes:
-      - /dev/shm:/dev/shm
+    image: selenium/standalone-firefox:4.25
     ports:
       - "5900:5900"
-
   web:
     build:
       context: .
@@ -62,58 +59,3 @@ services:
       - selenium
       - web
     entrypoint: /app/test/wait-for-services.sh
-
-  selenium-debug:
-    image: selenium/standalone-firefox-debug:3.141.59-zirconium
-    links:
-      - web-debug:web
-    ports:
-      - "5901:5900"
-
-  web-debug:
-    build:
-      context: .
-      dockerfile: Dockerfile.test.php8.debug
-    volumes:
-      - ./:/app
-      - ./test/test_instrument:/app/project/instruments
-    environment:
-      - LORIS_DB_CONFIG=/app/test/config.xml
-      - XDEBUG_CONFIG=remote_host=${XDEBUG_REMOTE_HOST}
-      - PHP_IDE_CONFIG=serverName=LorisTests
-    depends_on:
-      - db
-    command: php -S 0.0.0.0:8000 -t /app/htdocs /app/htdocs/router.php
-
-  unit-tests-debug:
-    build:
-      context: .
-      dockerfile: Dockerfile.test.php8.debug
-    volumes:
-      - ./:/app
-    working_dir: /app
-    environment:
-      - LORIS_DB_CONFIG=test/config.xml
-      - XDEBUG_CONFIG=remote_host=${XDEBUG_REMOTE_HOST}
-      - PHP_IDE_CONFIG=serverName=LorisTests
-    depends_on:
-      - db
-    entrypoint: /app/test/wait-for-services.sh
-
-  integration-tests-debug:
-    build:
-      context: .
-      dockerfile: Dockerfile.test.php8.debug
-    volumes:
-      - ./:/app
-    working_dir: /app
-    environment:
-      - LORIS_DB_CONFIG=test/config.xml
-      - SELENIUM_REQUIRED=true
-      - XDEBUG_CONFIG=remote_host=${XDEBUG_REMOTE_HOST}
-      - PHP_IDE_CONFIG=serverName=LorisTests
-    links:
-      - db
-      - selenium-debug:selenium
-      - web-debug:web
-    entrypoint: /app/test/wait-for-services.sh

htdocs/js/advancedMenu.js

@@ -8,17 +8,17 @@ function isElementSet() {
   let set = 0;
   let options = $('.advancedOptions option:selected'); // get all the selected dropdowns for the TR with the ID advancedOptions
   let texts = $('.advancedOptions input[type=text]');
-    // brows through the selected dropdowns
-    // if any of the dropdown is not equal to 'All' then set the variable set to true
+  // brows through the selected dropdowns
+  // if any of the dropdown is not equal to 'All' then set the variable set to true
   options.each(function() {
     let value = $(this).text();
     if (value !== 'All') {
       set = 1;
       return;
     }
   });
-    // browse though the text elements
-    // /if any of the text element is not empty then set the variable set to true
+  // browse though the text elements
+  // /if any of the text element is not empty then set the variable set to true
   texts.each(function() {
     let value = $(this).val();
     if (value !== '') {

htdocs/js/instrument_controlpanel_control.js

@@ -1,3 +1,3 @@
 $(function() {
-    $('[data-toggle="tooltip"]').tooltip();
+  $('[data-toggle="tooltip"]').tooltip();
 });

htdocs/js/invalid_form_scroll.js

@@ -4,35 +4,35 @@
  */
 
 $(document).ready(function bindInvalidFormListeners() {
-    // This will make sure that the flag indicating whether we scrolled
-    // to an invalid element when the form is submitted is reset
+  // This will make sure that the flag indicating whether we scrolled
+  // to an invalid element when the form is submitted is reset
   document.getElementsByName('fire_away')[0].addEventListener(
     'click',
     function() {
       bindInvalidFormListeners.scrollingDone = false;
     }
   );
 
-    // Override default event handler for invalid input elements
-    // This will make sure that the invalid element appears at the top
-    // of the page.
+  // Override default event handler for invalid input elements
+  // This will make sure that the invalid element appears at the top
+  // of the page.
   let elements = document.querySelectorAll('input,select,textarea');
   let navbarHeader = document.getElementsByClassName('navbar-header');
   for (let i = elements.length; i--;) {
     elements[i].addEventListener('invalid', function() {
-            // Only make the uppermost invalid element visible when the
-            // form is submitted
+      // Only make the uppermost invalid element visible when the
+      // form is submitted
       if (!bindInvalidFormListeners.scrollingDone) {
         this.scrollIntoView(true);
-                // scrollingIntoView is not enough: the navigation bar will appear
-                // over the invalid element and hide it.
-                // We have to scroll an additional number of pixels down so that
-                // the elements becomes visible.
+        // scrollingIntoView is not enough: the navigation bar will appear
+        // over the invalid element and hide it.
+        // We have to scroll an additional number of pixels down so that
+        // the elements becomes visible.
         if (navbarHeader) {
           window.scrollBy(0, -$(navbarHeader).height() - 10);
         }
 
-                // Only scroll once
+        // Only scroll once
         bindInvalidFormListeners.scrollingDone = true;
       }
     });

htdocs/js/jquery.fileupload.js

@@ -26,8 +26,8 @@
       $(element).change(function() {
         let filename = $(this).val().split('\\').pop();
         let placeHolder = $(this)
-                          .parent().parent().parent()
-                          .find('.file-caption-name');
+          .parent().parent().parent()
+          .find('.file-caption-name');
         $(placeHolder).html(filename);
       });
     });