Merge branch 'main' into 2023_12_05_fix_eeg_chunk_gaps

.editorconfig

@@ -17,3 +17,7 @@ indent_size = 2
 
 [*.md]
 trim_trailing_whitespace = false
+
+[*.yml]
+indent_size = 2
+

CHANGELOG.md

@@ -16,6 +16,7 @@ changes in the following format: PR #1234***
 #### Bug Fixes
 - Fix examiner site display (PR #8967)
 - bvl_feedback updates in real-time (PR #8966)
+- DoB and DoD format respected in candidate parameters (PR #9001)
 
 ## LORIS 25.0 (Release Date: ????-??-??)
 ### Core

Makefile

@@ -62,6 +62,9 @@ data_release:
 instrument_manager:
 	target=instrument_manager npm run compile
 
+dataquery:
+	target=dataquery npm run compile
+
 login:
 	target=login npm run compile
 

SQL/0000-00-00-schema.sql

@@ -2278,7 +2278,7 @@ CREATE TABLE `consent` (
 CREATE TABLE `candidate_consent_rel` (
   `CandidateID` int(6) NOT NULL,
   `ConsentID` integer unsigned NOT NULL,
-  `Status` enum('yes','no') DEFAULT NULL,
+  `Status` enum('yes','no', 'not_applicable') DEFAULT NULL,
   `DateGiven` date DEFAULT NULL,
   `DateWithdrawn` date DEFAULT NULL,
   CONSTRAINT `PK_candidate_consent_rel` PRIMARY KEY (`CandidateID`,`ConsentID`),
@@ -2294,7 +2294,7 @@ CREATE TABLE `candidate_consent_history` (
   `PSCID` varchar(255) NOT NULL,
   `ConsentName` varchar(255) NOT NULL,
   `ConsentLabel` varchar(255) NOT NULL,
-  `Status` enum('yes','no') DEFAULT NULL,
+  `Status` enum('yes','no', 'not_applicable') DEFAULT NULL,
   `EntryStaff` varchar(255) DEFAULT NULL,
   CONSTRAINT `PK_candidate_consent_history` PRIMARY KEY (`CandidateConsentHistoryID`)
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
@@ -2319,6 +2319,32 @@ CREATE TABLE `visit_project_cohort_rel` (
     REFERENCES `project_cohort_rel`(`ProjectCohortRelID`) ON DELETE CASCADE ON UPDATE CASCADE
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4;
 
+-- Diagnosis Evolution
+CREATE TABLE `diagnosis_evolution` (
+  `DxEvolutionID` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `Name` varchar(255) DEFAULT NULL,
+  `ProjectID` int(10) unsigned NOT NULL,
+  `visitLabel` varchar(255) DEFAULT NULL,
+  `instrumentName` varchar(255) DEFAULT NULL,
+  `sourceField` varchar(255) DEFAULT NULL,
+  `orderNumber` int(10) unsigned DEFAULT NULL,
+  CONSTRAINT `PK_diagnosis_evolution` PRIMARY KEY (`DxEvolutionID`),
+  CONSTRAINT `UK_diagnosis_evolution_Name` UNIQUE KEY `Name` (`Name`),
+  CONSTRAINT `FK_diagnosis_evolution_ProjectID` FOREIGN KEY (`ProjectID`) REFERENCES `Project` (`ProjectID`) ON DELETE RESTRICT ON UPDATE CASCADE,
+  CONSTRAINT `FK_diagnosis_evolution_instrumentName` FOREIGN KEY (`instrumentName`) REFERENCES `test_names` (`Test_name`) ON DELETE RESTRICT ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+CREATE TABLE `candidate_diagnosis_evolution_rel` (
+  `CandID` int(6) NOT NULL,
+  `DxEvolutionID` int(10) unsigned NOT NULL,
+  `Diagnosis` text DEFAULT NULL,
+  `Confirmed` enum('Y', 'N') DEFAULT NULL,
+  `LastUpdate` datetime NOT NULL DEFAULT NOW() ON UPDATE NOW(),
+  CONSTRAINT `PK_candidate_diagnosis_evolution_rel` PRIMARY KEY (`CandID`, `DxEvolutionID`),
+  CONSTRAINT `FK_candidate_diagnosis_evolution_rel_CandID` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`) ON DELETE RESTRICT ON UPDATE RESTRICT,
+  CONSTRAINT `FK_candidate_diagnosis_evolution_rel_DxEvolutionID` FOREIGN KEY (`DxEvolutionID`) REFERENCES `diagnosis_evolution` (`DxEvolutionID`) ON DELETE RESTRICT ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
 -- Publication Status
 CREATE TABLE `publication_status` (
   `PublicationStatusID` int(2) unsigned NOT NULL AUTO_INCREMENT,

SQL/0000-00-02-Permission.sql

@@ -131,7 +131,8 @@ INSERT INTO `permissions` VALUES
     (60,'behavioural_quality_control_view','Flagged Behavioural Entries',(SELECT ID FROM modules WHERE Name='behavioural_qc'),'View','2'),
     (61,'api_docs','API documentation',(SELECT ID FROM modules WHERE Name='api_docs'),'View','2'),
     (62,'electrophysiology_browser_edit_annotations','Annotations',(SELECT ID FROM modules WHERE Name='electrophysiology_browser'),'Create/Edit','2'),
-    (63,'monitor_eeg_uploads','Monitor EEG uploads',(SELECT ID FROM modules WHERE Name='electrophysiology_uploader'),NULL,'2');
+    (63,'monitor_eeg_uploads','Monitor EEG uploads',(SELECT ID FROM modules WHERE Name='electrophysiology_uploader'),NULL,'2'),
+    (64,'dataquery_admin','Admin dataquery queries',(SELECT ID FROM modules WHERE Name='dataquery'),NULL,'2');
 
 INSERT INTO `user_perm_rel` (userID, permID)
   SELECT u.ID, p.permID

SQL/0000-00-03-ConfigTables.sql

@@ -69,17 +69,12 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType,
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'base', 'The base filesystem path where LORIS is installed', 1, 0, 'text', ID, 'Base', 1 FROM ConfigSettings WHERE Name="paths";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DownloadPath', 'Where files are downloaded', 1, 0, 'text', ID, 'Downloads', 4 FROM ConfigSettings WHERE Name="paths";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'log', 'Path to logs (relative path starting from /var/www/$projectname)', 1, 0, 'text', ID, 'Logs', 2 FROM ConfigSettings WHERE Name="paths";
-INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MRICodePath', 'Path to directory where Loris-MRI (git) code is installed', 1, 0, 'text', ID, 'LORIS-MRI code', 6 FROM ConfigSettings WHERE Name="paths";
-INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MRIUploadIncomingPath', 'Path to the upload directory for incoming MRI studies', 1, 0, 'text', ID, 'MRI Incoming Directory', 7 FROM ConfigSettings WHERE Name="paths";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'GenomicDataPath', 'Path to Genomic data files', 1, 0, 'text', ID, 'Genomic Data Path', 8 FROM ConfigSettings WHERE Name="paths";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mediaPath', 'Path to uploaded media files', 1, 0, 'text', ID, 'Media', 9 FROM ConfigSettings WHERE Name="paths";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'publication_uploads', 'Path to uploaded publications', 1, 0, 'web_path', ID, 'Publications', 10 FROM ConfigSettings WHERE Name="paths";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'publication_deletions', 'Path to deleted publications', 1, 0, 'web_path', ID, 'Deleted Publications', 11 FROM ConfigSettings WHERE Name="paths";
-INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MINCToolsPath', 'Path to the MINC tools', 1, 0, 'web_path', ID, 'Path to the MINC tools', 12 FROM ConfigSettings WHERE Name="paths";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'documentRepositoryPath', 'Path to uploaded document repository files', 1, 0, 'web_path', ID, 'Document Repository Upload Path', 13 FROM ConfigSettings WHERE Name="paths";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'dataReleasePath', 'Path to uploaded data release files', 1, 0, 'web_path', ID, 'Data release Upload Path', 14 FROM ConfigSettings WHERE Name="paths";
-INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'EEGUploadIncomingPath', 'Path to the upload directory for incoming EEG studies', 1, 0, 'text', ID, 'EEG Incoming Directory', 7 FROM ConfigSettings WHERE Name="paths";
-
 
 
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('gui', 'Settings related to the overall display of LORIS', 1, 0, 'GUI', 3);
@@ -130,7 +125,7 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType,
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'IssueTrackerDataPath', 'Path to Issue Tracker data files', 1, 0, 'web_path', ID, 'Issue Tracker Data Path', 8 FROM ConfigSettings WHERE Name="paths";
 
 -- Loris-MRI/Imaging Pipeline options from the $profile (commonly "prod") file
-INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('imaging_pipeline', 'Imaging Pipeline settings', 1, 0, 'Imaging Pipeline', 12);
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('imaging_pipeline', 'Imaging Pipeline settings', 1, 0, 'Imaging Pipeline', 14);
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'dataDirBasepath', 'Base Path to the data directory of Loris-MRI', 1, 0, 'text', ID, 'Loris-MRI Data Directory', 1 FROM ConfigSettings WHERE Name="imaging_pipeline";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'prefix', 'Study prefix or study name', 1, 0, 'text', ID, 'Study Name', 2 FROM ConfigSettings WHERE Name="imaging_pipeline";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mail_user', 'User to be notified during imaging pipeline execution', 1, 0, 'text', ID, 'User to notify when executing the pipeline', 3 FROM ConfigSettings WHERE Name="imaging_pipeline";
@@ -159,6 +154,9 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType,
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reference_scan_type_for_defacing', 'Scan type to use as a reference for registration when defacing anatomical images (typically a T1W image)', 1, 0, 'scan_type', ID, 'Scan type to use as a reference for defacing (typically a T1W image)', 26 FROM ConfigSettings WHERE Name="imaging_pipeline";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'modalities_to_deface', 'Modalities for which defacing should be run and defaced image inserted in the database', 1, 1, 'scan_type', ID, 'Modalities on which to run the defacing pipeline', 27 FROM ConfigSettings WHERE Name="imaging_pipeline";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MriPythonConfigFile', 'Name of the Python MRI config file (stored in dicom-archive/.loris_mri/)', 1, 0, 'text', ID, 'Name of the Python MRI config file', 28 FROM ConfigSettings WHERE Name="imaging_pipeline";
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MRICodePath', 'Path to directory where Loris-MRI (git) code is installed', 1, 0, 'text', ID, 'LORIS-MRI code', 6 FROM ConfigSettings WHERE Name="imaging_pipeline";
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MRIUploadIncomingPath', 'Path to the upload directory for incoming MRI studies', 1, 0, 'text', ID, 'MRI Incoming Directory', 7 FROM ConfigSettings WHERE Name="imaging_pipeline";
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MINCToolsPath', 'Path to the MINC tools', 1, 0, 'web_path', ID, 'Path to the MINC tools', 12 FROM ConfigSettings WHERE Name="imaging_pipeline";
 
 -- MINC to BIDS converter settings
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('minc2bids', 'Settings related to converting MINC to BIDS LORIS-MRI tool script', 1, 0,  'MINC to BIDS Converter Tool Options', 13);
@@ -177,6 +175,10 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType,
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'AWS_S3_Region', 'AWS Region to use for accessing files stored in S3. Endpoint or region are required for S3 support.', 1, 0, 'text', ID, 'AWS S3 Region', 3 FROM ConfigSettings WHERE Name='aws';
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'AWS_S3_Default_Bucket', 'Default bucket for LORIS to use for accessing files in S3.', 1, 0, 'text', ID, 'AWS S3 Default Bucket', 3 FROM ConfigSettings WHERE Name='aws';
 
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('eeg_pipeline', 'EEG Pipeline settings', 1, 0, 'EEG Pipeline', 15);
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'EEGS3DataPath', 'EEG S3 data path for assembly data', 1, 0, 'text', ID, 'EEG S3 data path', 15 FROM ConfigSettings WHERE Name = 'eeg_pipeline';
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'EEGUploadIncomingPath', 'Path to the upload directory for incoming EEG studies', 1, 0, 'text', ID, 'EEG Incoming Directory', 7 FROM ConfigSettings WHERE Name="eeg_pipeline";
+
 --
 -- Filling Config table with default values
 --

SQL/0000-00-05-ElectrophysiologyTables.sql

@@ -485,7 +485,7 @@ CREATE TABLE `physiological_annotation_rel` (
 CREATE TABLE `electrophysiology_uploader` (
     `UploadID` int(10) unsigned NOT NULL AUTO_INCREMENT,
     `UploadedBy` varchar(255) NOT NULL,
-    `UploadDate` DateTime NOT NULL,
+    `UploadDate` DateTime NOT NULL DEFAULT CURRENT_TIMESTAMP,
     `UploadLocation` varchar(255) NOT NULL,
     `Status` enum('Not Started', 'Extracted', 'Failed Extraction', 'In Progress', 'Complete', 'Failed', 'Archived') DEFAULT 'Not Started',
     `SessionID` int(10) unsigned,

SQL/9999-99-99-drop_tables.sql

@@ -7,13 +7,18 @@ DROP TABLE IF EXISTS dataquery_query_names;
 DROP TABLE IF EXISTS dataquery_queries;
 
 -- 0000-00-05-ElectrophysiologyTables.sql
+DROP TABLE IF EXISTS `physiological_event_parameter_category_level`;
+DROP TABLE IF EXISTS `physiological_event_parameter`;
+DROP TABLE IF EXISTS `physiological_event_archive`;
+DROP TABLE IF EXISTS `physiological_event_file`;
 DROP TABLE IF EXISTS `physiological_coord_system_electrode_rel`;
 DROP TABLE IF EXISTS `physiological_coord_system_point_3d_rel`;
 DROP TABLE IF EXISTS `point_3d`;
 DROP TABLE IF EXISTS `physiological_coord_system`;
 DROP TABLE IF EXISTS `physiological_coord_system_unit`;
 DROP TABLE IF EXISTS `physiological_coord_system_name`;
 DROP TABLE IF EXISTS `physiological_coord_system_type`;
+DROP TABLE IF EXISTS `electrophysiology_uploader`;
 DROP TABLE IF EXISTS `physiological_annotation_rel`;
 DROP TABLE IF EXISTS `physiological_annotation_instance`;
 DROP TABLE IF EXISTS `physiological_annotation_parameter`;
@@ -53,6 +58,7 @@ DROP TABLE IF EXISTS `issues`;
 DROP TABLE IF EXISTS `issues_categories`;
 
 -- 0000-00-02-Permission.sql
+DROP TABLE IF EXISTS `testnames_permissions_rel`;
 DROP TABLE IF EXISTS `user_perm_rel`;
 DROP TABLE IF EXISTS `notification_modules_perm_rel`;
 DROP TABLE IF EXISTS `permissions`;

SQL/Archive/25.0/2022-03-03-AddHEDTags.sql

@@ -44,6 +44,7 @@ INSERT INTO physiological_event_file (PhysiologicalFileID, FilePath, FileType)
 UPDATE physiological_task_event te
     SET EventFileID=(SELECT EventFileID FROM physiological_event_file WHERE PhysiologicalFileID=te.PhysiologicalFileID)
 ;
+SET FOREIGN_KEY_CHECKS= 1;
 
 -- Delete FilePath column in `physiological_task_event` table
 ALTER TABLE physiological_task_event

SQL/New_patches/2021-07-28_diagnosis_evolution.sql

@@ -0,0 +1,24 @@
+CREATE TABLE `diagnosis_evolution` (
+  `DxEvolutionID` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `Name` varchar(255) DEFAULT NULL,
+  `ProjectID` int(10) unsigned NOT NULL,
+  `visitLabel` varchar(255) DEFAULT NULL,
+  `instrumentName` varchar(255) DEFAULT NULL,
+  `sourceField` varchar(255) DEFAULT NULL,
+  `orderNumber` int(10) unsigned DEFAULT NULL,
+  CONSTRAINT `PK_diagnosis_evolution` PRIMARY KEY (`DxEvolutionID`),
+  CONSTRAINT `UK_diagnosis_evolution_Name` UNIQUE KEY `Name` (`Name`),
+  CONSTRAINT `FK_diagnosis_evolution_ProjectID` FOREIGN KEY (`ProjectID`) REFERENCES `Project` (`ProjectID`) ON DELETE RESTRICT ON UPDATE CASCADE,
+  CONSTRAINT `FK_diagnosis_evolution_instrumentName` FOREIGN KEY (`instrumentName`) REFERENCES `test_names` (`Test_name`) ON DELETE RESTRICT ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+CREATE TABLE `candidate_diagnosis_evolution_rel` (
+  `CandID` int(6) NOT NULL,
+  `DxEvolutionID` int(10) unsigned NOT NULL,
+  `Diagnosis` text DEFAULT NULL,
+  `Confirmed` enum('Y', 'N') DEFAULT NULL,
+  `LastUpdate` datetime NOT NULL DEFAULT NOW() ON UPDATE NOW(),
+  CONSTRAINT `PK_candidate_diagnosis_evolution_rel` PRIMARY KEY (`CandID`, `DxEvolutionID`),
+  CONSTRAINT `FK_candidate_diagnosis_evolution_rel_CandID` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`) ON DELETE RESTRICT ON UPDATE RESTRICT,
+  CONSTRAINT `FK_candidate_diagnosis_evolution_rel_DxEvolutionID` FOREIGN KEY (`DxEvolutionID`) REFERENCES `diagnosis_evolution` (`DxEvolutionID`) ON DELETE RESTRICT ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;

SQL/New_patches/2023-04-25-FixIssueWrongModuleID.sql

@@ -0,0 +1,8 @@
+-- NOTE: This SQL patch follows up the running of single use tool `tools/single_use/Convert_LorisMenuID_to_ModuleID.php`
+-- that was necessary to upgrade the `issues` table from LORIS version 22 to version 23. The tool forgot
+-- to include an upgrade of the `issues_history` table, which is now tackled by this SQL patch.
+
+-- delete from issues_history any orphaned module IDs
+DELETE FROM issues_history WHERE fieldChanged='module' AND issueID IN (SELECT issueID FROM issues WHERE module IS NULL);
+-- set issues history module ID to correct moduleID, replacing old LorisMenu ID
+UPDATE issues_history ih SET newValue=(SELECT i.module FROM issues i WHERE i.issueID=ih.issueID) WHERE fieldChanged='module';

SQL/New_patches/2023-05-01-imaging-eeg-configs.sql

@@ -0,0 +1,55 @@
+-- Add the EEG Pipeline Config group
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber)
+VALUES ('eeg_pipeline', 'EEG Pipeline settings', 1, 0, 'EEG Pipeline', 15);
+
+-- Add the EEGS3DataPath Config
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber, Parent)
+SELECT 'EEGS3DataPath', 'EEG S3 data path for assembly data', 1, 0, 'EEG S3 data path', 15, ID
+    FROM ConfigSettings
+    WHERE Name = 'eeg_pipeline';
+
+UPDATE
+  ConfigSettings cs1,
+  (
+    SELECT *
+    FROM ConfigSettings
+    WHERE Name = 'eeg_pipeline'
+  ) AS cs2
+SET cs1.Parent = cs2.ID
+WHERE cs1.Name = 'EEGUploadIncomingPath';
+
+-- Add the Imaging Pipeline Config group
+UPDATE ConfigSettings SET OrderNumber = 14 WHERE Name = 'imaging_pipeline';
+
+UPDATE
+  ConfigSettings cs1,
+  (
+    SELECT *
+    FROM ConfigSettings
+    WHERE Name = 'imaging_pipeline'
+  ) AS cs2
+SET cs1.Parent = cs2.ID
+WHERE cs1.Name = 'MRICodePath';
+
+UPDATE
+  ConfigSettings cs1,
+  (
+    SELECT *
+    FROM ConfigSettings
+    WHERE Name = 'imaging_pipeline'
+  ) AS cs2
+SET cs1.Parent = cs2.ID
+WHERE cs1.Name = 'MRIUploadIncomingPath';
+
+UPDATE
+  ConfigSettings cs1,
+  (
+    SELECT *
+    FROM ConfigSettings
+    WHERE Name = 'imaging_pipeline'
+  ) AS cs2
+SET cs1.Parent = cs2.ID
+WHERE cs1.Name = 'MINCToolsPath';
+
+-- Add default value to electrophysiology_uploader UploadDate
+ALTER TABLE `electrophysiology_uploader` MODIFY COLUMN `UploadDate` DateTime NOT NULL DEFAULT CURRENT_TIMESTAMP;

SQL/New_patches/2023-06-06-add_NA_to_consent_status.sql

@@ -0,0 +1,2 @@
+ALTER TABLE candidate_consent_rel MODIFY COLUMN `Status` enum('yes', 'no', 'not_applicable') DEFAULT NULL;
+ALTER TABLE candidate_consent_history MODIFY COLUMN `Status` enum('yes', 'no', 'not_applicable') DEFAULT NULL;

SQL/New_patches/2023-12-02-DQT-AdminPermission.sql

@@ -0,0 +1,6 @@
+INSERT INTO permissions (code, description, moduleID)
+    VALUES (
+      'dataquery_admin',
+      'Dataquery Admin',
+      (SELECT ID FROM modules WHERE Name='dataquery')
+    );