diff --git a/SQL/0000-00-03-ConfigTables.sql b/SQL/0000-00-03-ConfigTables.sql index 3de025fcc3..b022f026b1 100644 --- a/SQL/0000-00-03-ConfigTables.sql +++ b/SQL/0000-00-03-ConfigTables.sql @@ -1,3 +1,18 @@ +-- +-- Table structure for table `ConfigCategories` +-- + +CREATE TABLE `ConfigCategories` ( + `ID` int(11) NOT NULL AUTO_INCREMENT, + `Name` varchar(255) NOT NULL, + `Description` varchar(255) DEFAULT NULL, + `Visible` tinyint(1) DEFAULT '0', + `Label` varchar(255) DEFAULT NULL, + `OrderNumber` int(11) DEFAULT NULL, + PRIMARY KEY (`ID`), + UNIQUE KEY `Name` (`Name`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8; + -- -- Table structure for table `ConfigSettings` -- @@ -10,11 +25,18 @@ CREATE TABLE `ConfigSettings` ( `AllowMultiple` tinyint(1) DEFAULT '0', `DataType` ENUM('text','boolean','email','instrument','textarea','scan_type','date_format','lookup_center','path','web_path', 'log_level') DEFAULT NULL, `Parent` int(11) DEFAULT NULL, + `CategoryID` 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`) + UNIQUE KEY `Name` (`Name`), + KEY `fk_ConfigSettings_CategoryID_idx` (`CategoryID`), + CONSTRAINT `fk_ConfigSettings_CategoryID` + FOREIGN KEY (`CategoryID`) + REFERENCES `ConfigCategories` (`ID`) + ON DELETE SET NULL + ON UPDATE CASCADE ) ENGINE=InnoDB DEFAULT CHARSET=utf8; CREATE TABLE `ConfigI18n` ( @@ -45,162 +67,162 @@ CREATE TABLE `Config` ( -- Filling ConfigSettings table -- -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, Multilingual) SELECT 'title', 'Full descriptive title of the study', 1, 0, 'text', ID, 'Study title', 1, true 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"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'ageMax', 'Maximum candidate age in years', 1, 0, 'text', ID, 'Maximum candidate age', 8 FROM ConfigSettings WHERE Name="study"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'dobFormat', "Format of the Date of Birth", 1, 0, 'date_format', ID, 'DOB Format', 9 FROM ConfigSettings WHERE Name="study"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'dodFormat', 'Format of the Date of Death', 1, 0, 'date_format', ID, 'DOD Format', 10 FROM ConfigSettings WHERE Name="study"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'useProband', "Enable for proband data collection", 1, 0, 'boolean', ID, 'Use proband', 11 FROM ConfigSettings WHERE Name="study"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'useFamilyID', 'Enable if family members are recruited for the study', 1, 0, 'boolean', ID, 'Use family', 12 FROM ConfigSettings WHERE Name="study"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'useExternalID', "Enable if data is used for blind data distribution, or from external data sources", 1, 0, 'boolean', ID, 'Use external ID', 13 FROM ConfigSettings WHERE Name="study"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'useEDC', 'Use EDC (Expected Date of Confinement) for birthdate estimations if the study involves neonatals', 1, 0, 'boolean', ID, 'Use EDC', 14 FROM ConfigSettings WHERE Name="study"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'useScreening', "Enable if there is a Screening stage with its own distinct instruments, administered before the Visit stage", 1, 0, 'boolean', ID, 'Use screening', 15 FROM ConfigSettings WHERE Name="study"; -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 '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 'allowPrenatalTimepoints', 'Determines whether creation of timepoints prior to Date of Birth is allowed', 1, 0, 'boolean', ID, 'Allow Prenatal Timepoints', 23 FROM ConfigSettings WHERE Name="study"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'ImagingUploaderAutoLaunch', "Allows running the ImagingUpload pre-processing scripts", 1, 0, 'boolean', ID, 'ImagingUploader Auto Launch',24 FROM ConfigSettings WHERE Name="study"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'citation_policy', 'Citation Policy for Acknowledgements module', 1, 0, 'textarea', ID, 'Citation Policy', 25 FROM ConfigSettings WHERE Name="study"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'CSPAdditionalHeaders', 'Extensions to the Content-security policy allow only for self-hosted content', 1, 0, 'text', ID, 'Content-Security Extensions', 26 FROM ConfigSettings WHERE Name="study"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'usePwnedPasswordsAPI', 'Whether to query the Have I Been Pwned password API on password changes to prevent the usage of common and breached passwords', 1, 0, 'boolean', ID, 'Enable "Pwned Password" check', 27 FROM ConfigSettings WHERE Name="study"; -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/$project/data/) ', 1, 0, 'text', ID, 'Images', 9 FROM ConfigSettings WHERE Name="paths"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'base', 'The base filesystem path where LORIS is installed', 1, 0, 'text', ID, 'Base', 1 FROM ConfigSettings WHERE Name="paths"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DownloadPath', 'Where files are downloaded', 1, 0, 'text', ID, 'Downloads', 4 FROM ConfigSettings WHERE Name="paths"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'log', 'Path to logs (relative path starting from /var/www/$projectname)', 1, 0, 'text', ID, 'Logs', 2 FROM ConfigSettings WHERE Name="paths"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT '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 '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, Label, OrderNumber) VALUES ('gui', 'Settings related to the overall display of LORIS', 1, 0, 'GUI', 3); -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber, Multilingual) SELECT 'StudyDescription', 'Description of the Study', 1, 0, 'textarea', ID , 'Study Description', 2, true FROM ConfigSettings WHERE Name="gui"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'useEEGBrowserVisualizationComponents', 'Whether to enable the visualization components on the EEG Browser module', 1, 0, 'boolean', ID, 'Enable the EEG Browser components', 4 FROM ConfigSettings WHERE Name="gui"; - - -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('www', 'Web address settings', 1, 0, 'WWW', 4); -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'host', 'Host', 1, 0, 'text', ID, 'Host', 1 FROM ConfigSettings WHERE Name="www"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'issue_tracker_url', 'URL of the prefered issue tracker for this study', 1, 0, 'text', ID, 'Issue tracker URL', 3 FROM ConfigSettings WHERE Name="www"; - - -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, 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); -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'patientIDRegex', 'Regex for masking the Patient ID header field', 1, 0, 'text', ID, 'Patient ID regex', 1 FROM ConfigSettings WHERE Name="imaging_modules"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'patientNameRegex', 'Regex for masking the Patient Name header field', 1, 0, 'text', ID, 'Patient name regex', 2 FROM ConfigSettings WHERE Name="imaging_modules"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'LegoPhantomRegex', 'Regex for identifying a Lego Phantom scan header', 1, 0, 'text', ID, 'Lego phantom regex', 3 FROM ConfigSettings WHERE Name="imaging_modules"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'LivingPhantomRegex', 'Regex to be used on Living Phantom scan header', 1, 0, 'text', ID, 'Living phantom regex', 4 FROM ConfigSettings WHERE Name="imaging_modules"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'showTransferStatus', 'Show transfer status in the DICOM Archive table', 1, 0, 'boolean', ID, 'Show transfer status', 5 FROM ConfigSettings WHERE Name="imaging_modules"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'useAdvancedPermissions', 'Restricts access to data based on both sites and projects and require a special permission to access data not affiliated to a session (SessionID null). Keeping this setting to NO should ensure backwards compatibility (access to all data when module loads)', 1, 0, 'boolean', ID, 'Use Advanced Permissions', 6 FROM ConfigSettings WHERE Name="imaging_modules"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tblScanTypes', 'Scan types from the mri_scan_type table that the project wants to see displayed in Imaging Browser table', 1, 1, 'scan_type', ID, 'Imaging Browser Tabulated Scan Types', 7 FROM ConfigSettings WHERE Name="imaging_modules"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'ImagingBrowserLinkedInstruments', 'Instruments that the users want to see linked from Imaging Browser', 1, 1, 'instrument', ID, 'Imaging Browser Links to Instruments', 8 FROM ConfigSettings WHERE Name="imaging_modules"; - -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('statistics', 'Statistics module settings', 1, 0, 'Statistics', 7); -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'excludedMeasures', 'Instruments to be excluded from Statistics calculations', 1, 1, 'instrument', ID, 'Excluded instruments', 1 FROM ConfigSettings WHERE Name="statistics"; - - -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('mail', 'LORIS email settings for notifications sent to users', 1, 0, 'Email', 8); -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'From', 'Sender email address header (e.g. admin@myproject.loris.ca)', 1, 0, 'email', ID, 'From', 1 FROM ConfigSettings WHERE Name="mail"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'Reply-to', 'Reply-to email address header (e.g. admin@myproject.loris.ca)', 1, 0, 'email', ID, 'Reply-to', 2 FROM ConfigSettings WHERE Name="mail"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'X-MimeOLE', 'X-MimeOLE', 1, 0, 'text', ID, 'X-MimeOLE', 3 FROM ConfigSettings WHERE Name="mail"; - - -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('uploads', 'Settings related to file uploading', 1, 0, 'Uploads', '9'); - -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'FileGroup', 'Determines the group permission for new subdirectories created for uploaded files', 1, 0, 'text', ID, 'File Group for Uploads', 1 FROM ConfigSettings WHERE Name="uploads"; - - -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('APIKeys', 'Specify any API keys required for LORIS', 1, 0, 'API Keys', 10); -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'JWTKey', 'Secret key for signing JWT tokens on this server. This should be unique and never shared with anyone. ', 1, 0, 'text', ID, 'JWT Secret Key', 1 FROM ConfigSettings WHERE Name="APIKeys"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reCAPTCHAPrivate', 'Private Key for Google reCAPTCHA', 1, 0, 'text', ID, 'reCAPTCHA Private Key', 2 FROM ConfigSettings WHERE Name="APIKeys"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reCAPTCHAPublic', 'Public Key for Google reCaptcha', 1, 0, 'text', ID, 'reCAPTCHA Public Key', 3 FROM ConfigSettings WHERE Name="APIKeys"; +INSERT INTO ConfigCategories (Name, Description, Visible, Label, OrderNumber) VALUES ('study', 'Settings related to details of the study', 1, 'Study', 1); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber, Multilingual) SELECT 'title', 'Full descriptive title of the study', 1, 0, 'text', ID, 'Study title', 1, true FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, 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 ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, 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 ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, 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 ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, 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 ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, 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 ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'partner_logos', 'Logos for partners to be displayed in the homepage', 1, 1, 'text', ID, 'Partner Logos', 4 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'startYear', "Start year for study recruitment or data collection", 1, 0, 'text', ID, 'Start year', 5 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'endYear', "End year for study recruitment or data collection", 1, 0, 'text', ID, 'End year', 6 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'ageMin', 'Minimum candidate age in years (0+)', 1, 0, 'text', ID, 'Minimum candidate age', 7 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'ageMax', 'Maximum candidate age in years', 1, 0, 'text', ID, 'Maximum candidate age', 8 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'dobFormat', "Format of the Date of Birth", 1, 0, 'date_format', ID, 'DOB Format', 9 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'dodFormat', 'Format of the Date of Death', 1, 0, 'date_format', ID, 'DOD Format', 10 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'useProband', "Enable for proband data collection", 1, 0, 'boolean', ID, 'Use proband', 11 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'useFamilyID', 'Enable if family members are recruited for the study', 1, 0, 'boolean', ID, 'Use family', 12 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'useExternalID', "Enable if data is used for blind data distribution, or from external data sources", 1, 0, 'boolean', ID, 'Use external ID', 13 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'useEDC', 'Use EDC (Expected Date of Confinement) for birthdate estimations if the study involves neonatals', 1, 0, 'boolean', ID, 'Use EDC', 14 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'useScreening', "Enable if there is a Screening stage with its own distinct instruments, administered before the Visit stage", 1, 0, 'boolean', ID, 'Use screening', 15 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'useConsent', 'Enable if the study uses the loris architecture for consent', 1, 0, 'boolean', ID, 'Use consent', 16 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, 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 ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, 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 ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'InstrumentResetting', 'Allows resetting of instrument data', 1, 0, 'boolean', ID, 'Instrument Resetting', 20 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'SupplementalSessionStatus', 'Display supplemental session status information on Timepoint List page', 1, 0, 'boolean', ID, 'Use Supplemental Session Status', 21 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'allowPrenatalTimepoints', 'Determines whether creation of timepoints prior to Date of Birth is allowed', 1, 0, 'boolean', ID, 'Allow Prenatal Timepoints', 23 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'ImagingUploaderAutoLaunch', "Allows running the ImagingUpload pre-processing scripts", 1, 0, 'boolean', ID, 'ImagingUploader Auto Launch',24 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'citation_policy', 'Citation Policy for Acknowledgements module', 1, 0, 'textarea', ID, 'Citation Policy', 25 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'CSPAdditionalHeaders', 'Extensions to the Content-security policy allow only for self-hosted content', 1, 0, 'text', ID, 'Content-Security Extensions', 26 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'usePwnedPasswordsAPI', 'Whether to query the Have I Been Pwned password API on password changes to prevent the usage of common and breached passwords', 1, 0, 'boolean', ID, 'Enable "Pwned Password" check', 27 FROM ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, 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 ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, 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 ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, 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 ConfigCategories WHERE Name="study"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'useDoB', 'Use DoB (Date of Birth)', 1, 0, 'boolean', ID, 'Use DoB', 31 FROM ConfigCategories WHERE Name="study"; + +INSERT INTO ConfigCategories (Name, Description, Visible, 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, 'Paths', 2); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'imagePath', 'Path to images for display in Imaging Browser (e.g. /data/$project/data/) ', 1, 0, 'text', ID, 'Images', 9 FROM ConfigCategories WHERE Name="paths"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'base', 'The base filesystem path where LORIS is installed', 1, 0, 'text', ID, 'Base', 1 FROM ConfigCategories WHERE Name="paths"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'DownloadPath', 'Where files are downloaded', 1, 0, 'text', ID, 'Downloads', 4 FROM ConfigCategories WHERE Name="paths"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'log', 'Path to logs (relative path starting from /var/www/$projectname)', 1, 0, 'text', ID, 'Logs', 2 FROM ConfigCategories WHERE Name="paths"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'GenomicDataPath', 'Path to Genomic data files', 1, 0, 'text', ID, 'Genomic Data Path', 8 FROM ConfigCategories WHERE Name="paths"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'mediaPath', 'Path to uploaded media files', 1, 0, 'text', ID, 'Media', 9 FROM ConfigCategories WHERE Name="paths"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'publication_uploads', 'Path to uploaded publications', 1, 0, 'web_path', ID, 'Publications', 10 FROM ConfigCategories WHERE Name="paths"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'publication_deletions', 'Path to deleted publications', 1, 0, 'web_path', ID, 'Deleted Publications', 11 FROM ConfigCategories WHERE Name="paths"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'documentRepositoryPath', 'Path to uploaded document repository files', 1, 0, 'web_path', ID, 'Document Repository Upload Path', 13 FROM ConfigCategories WHERE Name="paths"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'dataReleasePath', 'Path to uploaded data release files', 1, 0, 'web_path', ID, 'Data release Upload Path', 14 FROM ConfigCategories WHERE Name="paths"; + + +INSERT INTO ConfigCategories (Name, Description, Visible, Label, OrderNumber) VALUES ('gui', 'Settings related to the overall display of LORIS', 1, 'GUI', 3); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber, Multilingual) SELECT 'StudyDescription', 'Description of the Study', 1, 0, 'textarea', ID , 'Study Description', 2, true FROM ConfigCategories WHERE Name="gui"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'useEEGBrowserVisualizationComponents', 'Whether to enable the visualization components on the EEG Browser module', 1, 0, 'boolean', ID, 'Enable the EEG Browser components', 4 FROM ConfigCategories WHERE Name="gui"; + + +INSERT INTO ConfigCategories (Name, Description, Visible, Label, OrderNumber) VALUES ('www', 'Web address settings', 1, 'WWW', 4); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'host', 'Host', 1, 0, 'text', ID, 'Host', 1 FROM ConfigCategories WHERE Name="www"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'issue_tracker_url', 'URL of the prefered issue tracker for this study', 1, 0, 'text', ID, 'Issue tracker URL', 3 FROM ConfigCategories WHERE Name="www"; + + +INSERT INTO ConfigCategories (Name, Description, Visible, Label, OrderNumber) VALUES ('dashboard', 'Settings that affect the appearance of the dashboard and its charts', 1, 'Dashboard', 5); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber, Multilingual) SELECT 'projectDescription', 'Description of the study displayed in main dashboard panel', 1, 0, 'textarea', ID, 'Project Description', 1, true FROM ConfigCategories WHERE Name="dashboard"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'recruitmentTarget', 'Target number of participants for the study', 1, 0, 'text', ID, 'Target number of participants', 2 FROM ConfigCategories WHERE Name="dashboard"; + +INSERT INTO ConfigCategories (Name, Description, Visible, Label, OrderNumber) VALUES ('imaging_modules', 'DICOM Archive and Imaging Browser settings', 1, 'Imaging Modules', 6); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'patientIDRegex', 'Regex for masking the Patient ID header field', 1, 0, 'text', ID, 'Patient ID regex', 1 FROM ConfigCategories WHERE Name="imaging_modules"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'patientNameRegex', 'Regex for masking the Patient Name header field', 1, 0, 'text', ID, 'Patient name regex', 2 FROM ConfigCategories WHERE Name="imaging_modules"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'LegoPhantomRegex', 'Regex for identifying a Lego Phantom scan header', 1, 0, 'text', ID, 'Lego phantom regex', 3 FROM ConfigCategories WHERE Name="imaging_modules"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'LivingPhantomRegex', 'Regex to be used on Living Phantom scan header', 1, 0, 'text', ID, 'Living phantom regex', 4 FROM ConfigCategories WHERE Name="imaging_modules"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'showTransferStatus', 'Show transfer status in the DICOM Archive table', 1, 0, 'boolean', ID, 'Show transfer status', 5 FROM ConfigCategories WHERE Name="imaging_modules"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'useAdvancedPermissions', 'Restricts access to data based on both sites and projects and require a special permission to access data not affiliated to a session (SessionID null). Keeping this setting to NO should ensure backwards compatibility (access to all data when module loads)', 1, 0, 'boolean', ID, 'Use Advanced Permissions', 6 FROM ConfigCategories WHERE Name="imaging_modules"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'tblScanTypes', 'Scan types from the mri_scan_type table that the project wants to see displayed in Imaging Browser table', 1, 1, 'scan_type', ID, 'Imaging Browser Tabulated Scan Types', 7 FROM ConfigCategories WHERE Name="imaging_modules"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'ImagingBrowserLinkedInstruments', 'Instruments that the users want to see linked from Imaging Browser', 1, 1, 'instrument', ID, 'Imaging Browser Links to Instruments', 8 FROM ConfigCategories WHERE Name="imaging_modules"; + +INSERT INTO ConfigCategories (Name, Description, Visible, Label, OrderNumber) VALUES ('statistics', 'Statistics module settings', 1, 'Statistics', 7); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'excludedMeasures', 'Instruments to be excluded from Statistics calculations', 1, 1, 'instrument', ID, 'Excluded instruments', 1 FROM ConfigCategories WHERE Name="statistics"; + + +INSERT INTO ConfigCategories (Name, Description, Visible, Label, OrderNumber) VALUES ('mail', 'LORIS email settings for notifications sent to users', 1, 'Email', 8); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'From', 'Sender email address header (e.g. admin@myproject.loris.ca)', 1, 0, 'email', ID, 'From', 1 FROM ConfigCategories WHERE Name="mail"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'Reply-to', 'Reply-to email address header (e.g. admin@myproject.loris.ca)', 1, 0, 'email', ID, 'Reply-to', 2 FROM ConfigCategories WHERE Name="mail"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'X-MimeOLE', 'X-MimeOLE', 1, 0, 'text', ID, 'X-MimeOLE', 3 FROM ConfigCategories WHERE Name="mail"; + + +INSERT INTO ConfigCategories (Name, Description, Visible, Label, OrderNumber) VALUES ('uploads', 'Settings related to file uploading', 1, 'Uploads', '9'); + +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'FileGroup', 'Determines the group permission for new subdirectories created for uploaded files', 1, 0, 'text', ID, 'File Group for Uploads', 1 FROM ConfigCategories WHERE Name="uploads"; + + +INSERT INTO ConfigCategories (Name, Description, Visible, Label, OrderNumber) VALUES ('APIKeys', 'Specify any API keys required for LORIS', 1, 'API Keys', 10); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'JWTKey', 'Secret key for signing JWT tokens on this server. This should be unique and never shared with anyone. ', 1, 0, 'text', ID, 'JWT Secret Key', 1 FROM ConfigCategories WHERE Name="APIKeys"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'reCAPTCHAPrivate', 'Private Key for Google reCAPTCHA', 1, 0, 'text', ID, 'reCAPTCHA Private Key', 2 FROM ConfigCategories WHERE Name="APIKeys"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'reCAPTCHAPublic', 'Public Key for Google reCaptcha', 1, 0, 'text', ID, 'reCAPTCHA Public Key', 3 FROM ConfigCategories WHERE Name="APIKeys"; -- Issue_Tracker attachments for issues. -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"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'IssueTrackerDataPath', 'Path to Issue Tracker data files', 1, 0, 'web_path', ID, 'Issue Tracker Data Path', 8 FROM ConfigCategories 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', 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"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 4 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'horizontalPics', 'Enable generation of horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 5 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'create_nii', 'Enable creation of NIfTI files', 1, 0, 'boolean', ID, 'NIfTI file creation', 6 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'DICOM converter tool to use (dcm2mnc or dcm2niix)', 7 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 8 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'DICOM field (either PatientName or PatientID) to use to get the patient identifiers and the center name of the DICOM study', 1, 0, 'lookup_center', ID, 'Patient identifiers and center name lookup variable', 9 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Enable candidate creation in the imaging pipeline', 1, 0, 'boolean', ID, 'Enable candidate creation', 10 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createVisit', 'Enable visit creation in the imaging pipeline', 1, 0, 'boolean', ID, 'Enable visit creation', 11 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'default_project', 'Default project used when creating scan candidate or visit', 1, 0, 'text', ID, 'Default project', 12 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'default_cohort', 'Default cohort used when creating scan visit', 1, 0, 'text', ID, 'Default cohort', 13 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'default_bids_vl', 'Default visit label to use when no visit label set in the BIDS dataset', 1, 0, 'text', ID, 'Default visit label for BIDS dataset', 14 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'is_qsub', 'Enable use of batch management in the imaging pipeline', 1, 0, 'boolean', ID, 'Project batch management used', 15 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'use_legacy_dicom_study_importer', 'Use the legacy DICOM study importer instead of the new one', 1, 0, 'boolean', ID, 'Use legacy DICOM study importer', 15 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DTI_volumes', 'Number of volumes in native DTI acquisitions', 1, 0, 'text', ID, 'Number of volumes in native DTI acquisitions', 16 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 't1_scan_type', 'Scan type of native T1 acquisition (as in the mri_scan_type table)', 1, 0, 'text', ID, 'Scan type of native T1 acquisition', 17 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reject_thresh', 'Max number of directions that can be rejected to PASS QC', 1, 0, 'text', ID, 'Max number of DTI rejected directions for passing QC', 18 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'niak_path', 'Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl)', 1, 0, 'text', ID, 'NIAK Path', 19 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'QCed2_step', 'DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)', 1, 0, 'text', ID, 'Secondary QCed dataset', 20 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'excluded_series_description', 'Series description to be excluded from insertion into the database (typically localizers and scouts)', 1, 1, 'text', ID, 'Series description to exclude from imaging insertion', 21 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'ComputeDeepQC', 'Determines whether a call is made from LORIS-MRI to the DeepQC app for automatic QC prediction', 1, 0, 'boolean', ID, 'Compute automatic QC', 22 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MriConfigFile', 'Name of the Perl MRI config file (stored in dicom-archive/.loris_mri/)', 1, 0, 'text', ID, 'Name of the Perl MRI config file', 23 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'EnvironmentFile', 'Name of the environment file that need to be sourced for the imaging pipeline', 1, 0, 'text', ID, 'Name of the environment file', 24 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'compute_snr_modalities', 'Modalities for which the SNR should be computed when running the insertion MRI scripts', 1, 1, 'scan_type', ID, 'Modalities on which SNR should be calculated', 25 FROM ConfigSettings WHERE Name="imaging_pipeline"; -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"; +INSERT INTO ConfigCategories (Name, Description, Visible, Label, OrderNumber) VALUES ('imaging_pipeline', 'Imaging Pipeline settings', 1, 'Imaging Pipeline', 14); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'dataDirBasepath', 'Base Path to the data directory of Loris-MRI', 1, 0, 'text', ID, 'Loris-MRI Data Directory', 1 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'prefix', 'Study prefix or study name', 1, 0, 'text', ID, 'Study Name', 2 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, 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 ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 4 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'horizontalPics', 'Enable generation of horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 5 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'create_nii', 'Enable creation of NIfTI files', 1, 0, 'boolean', ID, 'NIfTI file creation', 6 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'DICOM converter tool to use (dcm2mnc or dcm2niix)', 7 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 8 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'DICOM field (either PatientName or PatientID) to use to get the patient identifiers and the center name of the DICOM study', 1, 0, 'lookup_center', ID, 'Patient identifiers and center name lookup variable', 9 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'createCandidates', 'Enable candidate creation in the imaging pipeline', 1, 0, 'boolean', ID, 'Enable candidate creation', 10 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'createVisit', 'Enable visit creation in the imaging pipeline', 1, 0, 'boolean', ID, 'Enable visit creation', 11 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'default_project', 'Default project used when creating scan candidate or visit', 1, 0, 'text', ID, 'Default project', 12 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'default_cohort', 'Default cohort used when creating scan visit', 1, 0, 'text', ID, 'Default cohort', 13 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'default_bids_vl', 'Default visit label to use when no visit label set in the BIDS dataset', 1, 0, 'text', ID, 'Default visit label for BIDS dataset', 14 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'is_qsub', 'Enable use of batch management in the imaging pipeline', 1, 0, 'boolean', ID, 'Project batch management used', 15 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'use_legacy_dicom_study_importer', 'Use the legacy DICOM study importer instead of the new one', 1, 0, 'boolean', ID, 'Use legacy DICOM study importer', 15 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'DTI_volumes', 'Number of volumes in native DTI acquisitions', 1, 0, 'text', ID, 'Number of volumes in native DTI acquisitions', 16 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 't1_scan_type', 'Scan type of native T1 acquisition (as in the mri_scan_type table)', 1, 0, 'text', ID, 'Scan type of native T1 acquisition', 17 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'reject_thresh', 'Max number of directions that can be rejected to PASS QC', 1, 0, 'text', ID, 'Max number of DTI rejected directions for passing QC', 18 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'niak_path', 'Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl)', 1, 0, 'text', ID, 'NIAK Path', 19 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'QCed2_step', 'DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)', 1, 0, 'text', ID, 'Secondary QCed dataset', 20 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'excluded_series_description', 'Series description to be excluded from insertion into the database (typically localizers and scouts)', 1, 1, 'text', ID, 'Series description to exclude from imaging insertion', 21 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'ComputeDeepQC', 'Determines whether a call is made from LORIS-MRI to the DeepQC app for automatic QC prediction', 1, 0, 'boolean', ID, 'Compute automatic QC', 22 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'MriConfigFile', 'Name of the Perl MRI config file (stored in dicom-archive/.loris_mri/)', 1, 0, 'text', ID, 'Name of the Perl MRI config file', 23 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'EnvironmentFile', 'Name of the environment file that need to be sourced for the imaging pipeline', 1, 0, 'text', ID, 'Name of the environment file', 24 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'compute_snr_modalities', 'Modalities for which the SNR should be computed when running the insertion MRI scripts', 1, 1, 'scan_type', ID, 'Modalities on which SNR should be calculated', 25 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, 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 ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, 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 ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, 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 ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'MRICodePath', 'Path to directory where Loris-MRI (git) code is installed', 1, 0, 'text', ID, 'LORIS-MRI code', 6 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'MRIUploadIncomingPath', 'Path to the upload directory for incoming MRI studies', 1, 0, 'text', ID, 'MRI Incoming Directory', 7 FROM ConfigCategories WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'MINCToolsPath', 'Path to the MINC tools', 1, 0, 'web_path', ID, 'Path to the MINC tools', 12 FROM ConfigCategories 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); -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'bids_dataset_authors', 'Authors for the BIDS dataset', 1, 1, 'text', ID, 'BIDS Dataset Authors', 1 FROM ConfigSettings WHERE Name='minc2bids'; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'bids_acknowledgments_text', 'Acknowledgments to be added in the dataset_description.json file of the BIDS dataset created out of the MINC files', 1, 0, 'text', ID, 'BIDS Dataset Acknowledgments', 2 FROM ConfigSettings WHERE Name='minc2bids'; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'bids_readme_text', 'Content to be added to the README of the BIDS dataset generated out of the MINC files', 1, 0, 'textarea', ID, 'BIDS Dataset README', 3 FROM ConfigSettings WHERE Name='minc2bids'; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'bids_validator_options_to_ignore', 'Options to be ignored for BIDS validation', 1, 1, 'text', ID, 'BIDS Validation options to ignore', 4 FROM ConfigSettings WHERE Name='minc2bids'; - -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('logs', 'Settings related to logging', 1, 0, 'Log Settings', 12); -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'database_log_level', 'Verbosity of database logging', 1, 0, 'log_level', ID, 'Database Log Level', 3 FROM ConfigSettings WHERE Name='logs'; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'request_log_level', 'Verbosity of HTTP request logs', 1, 0, 'log_level', ID, 'HTTP Request Log Level', 3 FROM ConfigSettings WHERE Name='logs'; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'exception_log_level', 'Verbosity of PHP exception logging', 1, 0, 'log_level', ID, 'Exception Log Level', 3 FROM ConfigSettings WHERE Name='logs'; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'profiler_log_level', 'Verbosity of performance profiler logging', 1, 0, 'log_level', ID, 'Profiler Log Level', 3 FROM ConfigSettings WHERE Name='logs'; - -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('aws', 'Settings related to AWS services', 1, 0, 'AWS Settings', 13); -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'AWS_S3_Endpoint', 'Endpoint to use for accessing files stored in S3. Endpoint or region are required for S3 support.', 1, 0, 'text', ID, 'AWS S3 Endpoint', 3 FROM ConfigSettings WHERE Name='aws'; -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"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'EEGChunksPath', 'Path to store the EEG chunks for Visualization', 1, 0, 'text', ID, 'EEG chunks path', 16 FROM ConfigSettings WHERE Name="eeg_pipeline"; +INSERT INTO ConfigCategories (Name, Description, Visible, Label, OrderNumber) VALUES ('minc2bids', 'Settings related to converting MINC to BIDS LORIS-MRI tool script', 1, 'MINC to BIDS Converter Tool Options', 13); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'bids_dataset_authors', 'Authors for the BIDS dataset', 1, 1, 'text', ID, 'BIDS Dataset Authors', 1 FROM ConfigCategories WHERE Name='minc2bids'; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'bids_acknowledgments_text', 'Acknowledgments to be added in the dataset_description.json file of the BIDS dataset created out of the MINC files', 1, 0, 'text', ID, 'BIDS Dataset Acknowledgments', 2 FROM ConfigCategories WHERE Name='minc2bids'; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'bids_readme_text', 'Content to be added to the README of the BIDS dataset generated out of the MINC files', 1, 0, 'textarea', ID, 'BIDS Dataset README', 3 FROM ConfigCategories WHERE Name='minc2bids'; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'bids_validator_options_to_ignore', 'Options to be ignored for BIDS validation', 1, 1, 'text', ID, 'BIDS Validation options to ignore', 4 FROM ConfigCategories WHERE Name='minc2bids'; + +INSERT INTO ConfigCategories (Name, Description, Visible, Label, OrderNumber) VALUES ('logs', 'Settings related to logging', 1, 'Log Settings', 12); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'database_log_level', 'Verbosity of database logging', 1, 0, 'log_level', ID, 'Database Log Level', 3 FROM ConfigCategories WHERE Name='logs'; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'request_log_level', 'Verbosity of HTTP request logs', 1, 0, 'log_level', ID, 'HTTP Request Log Level', 3 FROM ConfigCategories WHERE Name='logs'; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'exception_log_level', 'Verbosity of PHP exception logging', 1, 0, 'log_level', ID, 'Exception Log Level', 3 FROM ConfigCategories WHERE Name='logs'; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'profiler_log_level', 'Verbosity of performance profiler logging', 1, 0, 'log_level', ID, 'Profiler Log Level', 3 FROM ConfigCategories WHERE Name='logs'; + +INSERT INTO ConfigCategories (Name, Description, Visible, Label, OrderNumber) VALUES ('aws', 'Settings related to AWS services', 1, 'AWS Settings', 13); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'AWS_S3_Endpoint', 'Endpoint to use for accessing files stored in S3. Endpoint or region are required for S3 support.', 1, 0, 'text', ID, 'AWS S3 Endpoint', 3 FROM ConfigCategories WHERE Name='aws'; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, 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 ConfigCategories WHERE Name='aws'; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, 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 ConfigCategories WHERE Name='aws'; + +INSERT INTO ConfigCategories (Name, Description, Visible, Label, OrderNumber) VALUES ('eeg_pipeline', 'EEG Pipeline settings', 1, 'EEG Pipeline', 15); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'EEGS3DataPath', 'EEG S3 data path for assembly data', 1, 0, 'text', ID, 'EEG S3 data path', 15 FROM ConfigCategories WHERE Name = 'eeg_pipeline'; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'EEGUploadIncomingPath', 'Path to the upload directory for incoming EEG studies', 1, 0, 'text', ID, 'EEG Incoming Directory', 7 FROM ConfigCategories WHERE Name="eeg_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'EEGChunksPath', 'Path to store the EEG chunks for Visualization', 1, 0, 'text', ID, 'EEG chunks path', 16 FROM ConfigCategories WHERE Name="eeg_pipeline"; -- REDCap settings -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('redcap', 'Settings related to REDCap interoperability', 1, 0, 'REDCap', 16); -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'redcap_issue_assignee', 'REDCap main issue assignee in issue tracker', 1, 0, 'text', parent_config.ID, 'Main issue assignee', 1 FROM ConfigSettings parent_config LEFT JOIN ConfigSettings child_config ON (parent_config.ID = child_config.Parent) WHERE parent_config.Name = 'redcap'; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'redcap_importable_instrument', 'REDCap instrument names from which data should be imported in LORIS', 1, 1, 'text', parent_config.ID, 'Importable instrument names', 2 FROM ConfigSettings parent_config LEFT JOIN ConfigSettings child_config ON (parent_config.ID = child_config.Parent) WHERE parent_config.Name = 'redcap'; +INSERT INTO ConfigCategories (Name, Description, Visible, Label, OrderNumber) VALUES ('redcap', 'Settings related to REDCap interoperability', 1, 'REDCap', 16); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'redcap_issue_assignee', 'REDCap main issue assignee in issue tracker', 1, 0, 'text', ID, 'Main issue assignee', 1 FROM ConfigCategories WHERE Name = 'redcap'; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, CategoryID, Label, OrderNumber) SELECT 'redcap_importable_instrument', 'REDCap instrument names from which data should be imported in LORIS', 1, 1, 'text', ID, 'Importable instrument names', 2 FROM ConfigCategories WHERE Name = 'redcap'; -- -- Filling Config table with default values diff --git a/SQL/9999-99-99-drop_tables.sql b/SQL/9999-99-99-drop_tables.sql index 516d08b870..9b1a042062 100644 --- a/SQL/9999-99-99-drop_tables.sql +++ b/SQL/9999-99-99-drop_tables.sql @@ -93,6 +93,7 @@ DROP TABLE IF EXISTS `help`; DROP TABLE IF EXISTS `ConfigI18n`; DROP TABLE IF EXISTS `Config`; DROP TABLE IF EXISTS `ConfigSettings`; +DROP TABLE IF EXISTS `ConfigCategories`; DROP TABLE IF EXISTS `menu_categories`; -- issues must be deleted before `modules` table diff --git a/SQL/New_patches/2026-05-31_config-categories.sql b/SQL/New_patches/2026-05-31_config-categories.sql new file mode 100644 index 0000000000..e0304c3daa --- /dev/null +++ b/SQL/New_patches/2026-05-31_config-categories.sql @@ -0,0 +1,36 @@ +CREATE TABLE `ConfigCategories` ( + `ID` int(11) NOT NULL AUTO_INCREMENT, + `Name` varchar(255) NOT NULL, + `Description` varchar(255) DEFAULT NULL, + `Visible` tinyint(1) DEFAULT '0', + `Label` varchar(255) DEFAULT NULL, + `OrderNumber` int(11) DEFAULT NULL, + PRIMARY KEY (`ID`), + UNIQUE KEY `Name` (`Name`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8; + +INSERT INTO ConfigCategories (Name, Description, Visible, Label, OrderNumber) +SELECT Name, Description, Visible, Label, OrderNumber +FROM ConfigSettings +WHERE Parent IS NULL AND DataType IS NULL; + +ALTER TABLE ConfigSettings + ADD COLUMN CategoryID int(11) DEFAULT NULL AFTER Parent; + +UPDATE ConfigSettings child +JOIN ConfigSettings category_setting ON child.Parent=category_setting.ID +JOIN ConfigCategories category ON category.Name=category_setting.Name +SET child.CategoryID=category.ID, + child.Parent=NULL +WHERE category_setting.Parent IS NULL AND category_setting.DataType IS NULL; + +DELETE FROM ConfigSettings +WHERE Parent IS NULL AND DataType IS NULL; + +ALTER TABLE ConfigSettings + ADD KEY `fk_ConfigSettings_CategoryID_idx` (`CategoryID`), + ADD CONSTRAINT `fk_ConfigSettings_CategoryID` + FOREIGN KEY (`CategoryID`) + REFERENCES `ConfigCategories` (`ID`) + ON DELETE SET NULL + ON UPDATE CASCADE; diff --git a/modules/configuration/ajax/process.php b/modules/configuration/ajax/process.php index 015db82631..2b131c8e49 100644 --- a/modules/configuration/ajax/process.php +++ b/modules/configuration/ajax/process.php @@ -228,7 +228,6 @@ function getPathIDs(string $table): array */ $query = "SELECT c.ID FROM Config c " . "LEFT JOIN ConfigSettings cs ON (c.ConfigID = cs.ID) " - . "JOIN ConfigSettings csp ON (cs.Parent = csp.ID) " . "WHERE cs.DataType = 'web_path';"; break; case 'ConfigSettings': @@ -268,4 +267,3 @@ function validPath($value) } return true; } - diff --git a/modules/configuration/css/configuration.css b/modules/configuration/css/configuration.css index 6d99b3ea75..868d4155b9 100644 --- a/modules/configuration/css/configuration.css +++ b/modules/configuration/css/configuration.css @@ -9,6 +9,65 @@ margin-top: -3px; } +.configuration-tree-node { + border-left: 1px solid #ddd; + margin-bottom: 10px; + padding-left: 12px; +} + +.configuration-tree-header { + background: #f8f8f8; + border: 1px solid #ddd; + border-radius: 4px; + padding: 10px 12px; + text-align: left; + width: 100%; +} + +.configuration-tree-header:hover, +.configuration-tree-header:focus { + background: #f2f7fc; +} + +.configuration-tree-icon { + color: #31708f; + margin-right: 6px; +} + +.configuration-tree-icon-expanded { + display: none; +} + +.configuration-tree-header[aria-expanded="true"] .configuration-tree-icon-collapsed { + display: none; +} + +.configuration-tree-header[aria-expanded="true"] .configuration-tree-icon-expanded { + display: inline-block; +} + +.configuration-tree-label { + font-weight: 600; +} + +.configuration-tree-name { + color: grey; + font-size: 11px; + margin-left: 8px; +} + +.configuration-tree-description { + color: #555; + display: block; + margin-left: 23px; + margin-top: 4px; +} + +.configuration-tree-children { + margin-left: 18px; + padding-top: 12px; +} + .submit-area { margin-top: 30px; } @@ -16,4 +75,4 @@ .btn-container { display: flex; justify-content: center; -} \ No newline at end of file +} diff --git a/modules/configuration/php/configuration.class.inc b/modules/configuration/php/configuration.class.inc index f37ab85c9e..f09b15df98 100644 --- a/modules/configuration/php/configuration.class.inc +++ b/modules/configuration/php/configuration.class.inc @@ -108,8 +108,8 @@ class Configuration extends \NDB_Form $parentConfigItems = $DB->pselect( "SELECT Label, Name - FROM ConfigSettings - WHERE Parent IS NULL AND Visible=1 ORDER BY OrderNumber", + FROM ConfigCategories + WHERE Visible=1 ORDER BY OrderNumber", [] ); @@ -135,77 +135,160 @@ class Configuration extends \NDB_Form $DB = $this->loris->getDatabaseConnection(); $lang = \User::singleton()->getLanguageCode(); - // Get the names and meta-information for the config settings in the database - $configs = iterator_to_array( + $categories = iterator_to_array( $DB->pselect( - "SELECT * FROM ConfigSettings WHERE Visible=1 ORDER BY OrderNumber", + "SELECT ID, Name, Description, Visible, 0 AS AllowMultiple, + NULL AS DataType, NULL AS Parent, Label, OrderNumber, + 0 AS Multilingual + FROM ConfigCategories + WHERE Visible=1 + ORDER BY OrderNumber", [] ) ); - // Convert the labels and descriptions to the appropriate language - foreach ($configs as &$setting) { - $setting['Label'] = dgettext('ConfigSettings', $setting['Label']); - $setting['Description'] = dgettext( + foreach ($categories as &$category) { + $category['Label'] = dgettext( + 'ConfigSettings', + $category['Label'] + ); + $category['Description'] = dgettext( 'ConfigSettings', - $setting['Description'] + $category['Description'] ); } + unset($category); + + $configs = iterator_to_array( + $DB->pselect( + "SELECT * + FROM ConfigSettings + WHERE Visible=1 + ORDER BY CategoryID, Parent, OrderNumber, ID", + [] + ) + ); - // Check whether any setting is overwritten in the config.xml - // Add this info to the array so form entries can be disabled in front end - // Update the value for the setting to the value from the config.xml - foreach ($configs as &$setting) { - try { - $setting['Disabled'] = 'Yes'; - if ($setting['Parent'] != null) { - $valueFromXML = $config->getSettingFromXML($setting['Name']); - if (!is_array($valueFromXML)) { - $setting['Value'][0] = $valueFromXML; - } else { - $setting['Value'] = $valueFromXML; - } - } - } catch (\ConfigurationException $e) { - $setting['Disabled'] = 'No'; + $childrenByParent = []; + $settingsByCategory = []; + foreach ($configs as $setting) { + $setting = $this->_formatConfigSetting( + $setting, + $config, + $DB, + $lang + ); + if ($setting['Parent'] !== null) { + $childrenByParent[strval($setting['Parent'])][] = $setting; + continue; + } + + if ($setting['CategoryID'] !== null) { + $settingsByCategory[intval($setting['CategoryID'])][] = $setting; } } - // Now check for config settings from the database for the fields not - // overridden in the config.xml - foreach ($configs as &$setting) { - if ($setting['Disabled'] == 'No') { - $value = $DB->pselect( - "SELECT ID, Value FROM Config WHERE ConfigID=:ID", - ['ID' => $setting['ID']] + foreach ($categories as &$category) { + $category['Disabled'] = 'No'; + $category['Value'] = []; + $category['Children'] = []; + $categorySettings = $settingsByCategory[intval($category['ID'])] + ?? []; + foreach ($categorySettings as $setting) { + $setting['Children'] = $this->_buildConfigSettingTree( + $childrenByParent, + intval($setting['ID']) ); - if ($value) { - foreach ($value as $subvalue) { - if ($setting['Multilingual']) { - $setting['Value'][$subvalue['ID']] - = $config->getMultilingualSetting( - $lang, - $setting['Name'] - ); - } else { - $setting['Value'][$subvalue['ID']] = $subvalue['Value']; - } - } - } + $category['Children'][] = $setting; } } + unset($category); + + return $categories; + } + + /** + * Add value and override metadata to a config setting row. + * + * @param array $setting The config setting row + * @param \NDB_Config $config Runtime configuration object + * @param \Database $DB Database handle + * @param string $lang Current language code + * + * @return array + */ + private function _formatConfigSetting( + array $setting, + \NDB_Config $config, + \Database $DB, + string $lang + ) : array { + $setting['Label'] = dgettext('ConfigSettings', $setting['Label']); + $setting['Description'] = dgettext( + 'ConfigSettings', + $setting['Description'] + ); + $setting['Children'] = []; + $setting['Value'] = []; + + if ($setting['DataType'] === null) { + $setting['Disabled'] = 'No'; + return $setting; + } - // build a tree from configs array - $tree = []; - foreach ($configs as &$node) { - $node['Children'] = []; - $tree[intval($node['ID'])] = &$node; + try { + $setting['Disabled'] = 'Yes'; + $valueFromXML = $config->getSettingFromXML($setting['Name']); + if (!is_array($valueFromXML)) { + $setting['Value'][0] = $valueFromXML; + } else { + $setting['Value'] = $valueFromXML; + } + return $setting; + } catch (\ConfigurationException $e) { + $setting['Disabled'] = 'No'; } - foreach ($configs as &$node) { - $tree[$node['Parent'] ?? '']['Children'][] = &$node; + + $values = $DB->pselect( + "SELECT ID, Value FROM Config WHERE ConfigID=:ID", + ['ID' => $setting['ID']] + ); + foreach ($values as $subvalue) { + if ($setting['Multilingual']) { + $setting['Value'][$subvalue['ID']] + = $config->getMultilingualSetting( + $lang, + $setting['Name'] + ); + } else { + $setting['Value'][$subvalue['ID']] = $subvalue['Value']; + } } - return $configs; + return $setting; + } + + /** + * Build a recursive config setting tree from settings grouped by parent. + * + * @param array $childrenByParent Config settings grouped by parent ID + * @param int $parentID Parent ID to build from + * + * @return array + */ + private function _buildConfigSettingTree( + array $childrenByParent, + int $parentID + ) : array { + $settings = []; + foreach ($childrenByParent[strval($parentID)] ?? [] as $setting) { + $setting['Children'] = $this->_buildConfigSettingTree( + $childrenByParent, + intval($setting['ID']) + ); + $settings[] = $setting; + } + return $settings; } /** diff --git a/modules/configuration/templates/form_configuration.tpl b/modules/configuration/templates/form_configuration.tpl index a745e7d3c1..9073d7e418 100644 --- a/modules/configuration/templates/form_configuration.tpl +++ b/modules/configuration/templates/form_configuration.tpl @@ -70,16 +70,40 @@ {function name=printConfigItem} +{assign var=hasChildren value=isset($node['Children']) && $node['Children']} +{assign var=hasInput value=$node['DataType'] ne ''} +{if $hasChildren && !$hasInput} +
+ +
+
+ {foreach $node['Children'] as $child} + {call name=printConfigItem node=$child} + {/foreach} +
+
+
+{else}
{if $sandbox}
{$node['Name']}
{/if}
- {if isset($node['Children']) && $node['Children']} - Child nodes go here - {call name=printConfigItem node=$node['Children']} - {else} + {if $hasInput} {call name=printForm node=$node} {/if} {if $node['AllowMultiple'] == 1} @@ -87,8 +111,16 @@ {dgettext('configuration', 'Add field')} {/if} + {if $hasChildren} +
+ {foreach $node['Children'] as $child} + {call name=printConfigItem node=$child} + {/foreach} +
+ {/if}
+{/if} {/function} {function name=printForm} diff --git a/php/libraries/NDB_Config.class.inc b/php/libraries/NDB_Config.class.inc index 772bcd2716..f1fd702fb3 100644 --- a/php/libraries/NDB_Config.class.inc +++ b/php/libraries/NDB_Config.class.inc @@ -292,13 +292,27 @@ class NDB_Config if ($id === null) { $configSetting = $db->pselect( "SELECT cs.ID as ParentID, child.ID as ChildID, - cs.AllowMultiple, child.Name + cs.AllowMultiple, child.Name, 0 AS IsCategory FROM ConfigSettings cs LEFT JOIN ConfigSettings child ON (child.Parent=cs.ID) WHERE cs.Name=:nm", ["nm" => $name] ); + if (count($configSetting) === 0) { + $configSetting = $db->pselect( + "SELECT cc.ID as ParentID, child.ID as ChildID, + 0 AS AllowMultiple, child.Name, 1 AS IsCategory + FROM ConfigCategories cc + LEFT JOIN ConfigSettings child ON ( + child.CategoryID=cc.ID + AND child.Parent IS NULL + ) + WHERE cc.Name=:nm", + ["nm" => $name] + ); + } + if (count($configSetting) === 0) { throw new ConfigurationException( "Config setting $name does not exist in database" @@ -307,7 +321,7 @@ class NDB_Config } else { $configSetting = $db->pselect( "SELECT cs.ID as ParentID, child.ID as ChildID, - cs.AllowMultiple, child.Name + cs.AllowMultiple, child.Name, 0 AS IsCategory FROM ConfigSettings cs LEFT JOIN ConfigSettings child ON (child.Parent=cs.ID) WHERE cs.ID=:nm", @@ -320,13 +334,19 @@ class NDB_Config // If multiple rows are returned, it means that there are children // for this element, so we need to build the tree to be consistent // with what would have come from the config.xml. + $firstConfigSetting = null; if (count($configSetting) === 1) { + $firstConfigSetting = $configSetting->getFirstRow(); + } + if ($firstConfigSetting !== null + && $firstConfigSetting['ChildID'] === null + && intval($firstConfigSetting['IsCategory'] ?? 0) === 0 + ) { // Trying to get a single value from the database. - $configSetting = $configSetting->getFirstRow(); - if ($configSetting['AllowMultiple'] == '0') { + if ($firstConfigSetting['AllowMultiple'] == '0') { $val = $db->pselectOne( "SELECT Value FROM Config WHERE ConfigID=:CID", - ['CID' => $configSetting['ParentID']] + ['CID' => $firstConfigSetting['ParentID']] ); if (empty($val)) { return null; @@ -337,7 +357,7 @@ class NDB_Config // as ie. $config->getSetting("DoubleDataEntryInstruments") $val = $db->pselect( "SELECT Value FROM Config WHERE ConfigID=:CID", - ['CID' => $configSetting['ParentID']] + ['CID' => $firstConfigSetting['ParentID']] ); $ret = []; foreach ($val as $item) { @@ -345,10 +365,13 @@ class NDB_Config } return $ret; } - } else if (count($configSetting) > 1) { + } else if (count($configSetting) >= 1) { // This was a parent element, so construct the children. $tree = []; foreach ($configSetting as $childSetting) { + if ($childSetting['ChildID'] === null) { + continue; + } $childName = $childSetting['Name']; $childID = $childSetting['ChildID']; $childValue = $this->getSettingFromDB( @@ -621,4 +644,3 @@ class NDB_Config } } - diff --git a/raisinbread/RB_files/RB_ConfigCategories.sql b/raisinbread/RB_files/RB_ConfigCategories.sql new file mode 100644 index 0000000000..b0899a50d7 --- /dev/null +++ b/raisinbread/RB_files/RB_ConfigCategories.sql @@ -0,0 +1,21 @@ +/*M!999999\- enable the sandbox mode */ +SET FOREIGN_KEY_CHECKS=0; +TRUNCATE TABLE `ConfigCategories`; +LOCK TABLES `ConfigCategories` WRITE; +INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (1,'study','Settings related to details of the study',1,'Study',1); +INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (26,'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,'Paths',2); +INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (39,'gui','Settings related to the overall display of LORIS',1,'GUI',3); +INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (43,'www','Web address settings',1,'WWW',4); +INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (45,'eeg_pipeline','EEG Pipeline settings',1,'EEG Pipeline',15); +INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (47,'dashboard','Settings that affect the appearance of the dashboard and its charts',1,'Dashboard',5); +INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (50,'imaging_modules','DICOM Archive and Imaging Browser settings',1,'Imaging Modules',6); +INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (57,'statistics','Statistics module settings',1,'Statistics',7); +INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (59,'mail','LORIS email settings for notifications sent to users',1,'Email',8); +INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (63,'uploads','Settings related to file uploading',1,'Uploads',9); +INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (65,'APIKeys','Specify any API keys required for LORIS',1,'API Keys',10); +INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (69,'imaging_pipeline','Imaging Pipeline settings',1,'Imaging Pipeline',14); +INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (111,'logs','Settings related to logging',1,'Log Settings',12); +INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (115,'minc2bids','Settings related to converting MINC to BIDS LORIS-MRI tool script',1,'MINC to BIDS Converter Tool Options',13); +INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (121,'aws','Settings related to AWS services',1,'AWS Settings',13); +INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (135,'biobank','Settings related to the biobank module',1,'Biobank',14); +UNLOCK TABLES; diff --git a/raisinbread/RB_files/RB_ConfigSettings.sql b/raisinbread/RB_files/RB_ConfigSettings.sql index a032d388f4..ffee0c3a8d 100644 --- a/raisinbread/RB_files/RB_ConfigSettings.sql +++ b/raisinbread/RB_files/RB_ConfigSettings.sql @@ -1,134 +1,118 @@ SET FOREIGN_KEY_CHECKS=0; TRUNCATE TABLE `ConfigSettings`; LOCK TABLES `ConfigSettings` WRITE; -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (1,'study','Settings related to details of the study',1,0,NULL,NULL,'Study',1,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (2,'additional_user_info','Display additional user profile fields on the User accounts page (e.g. Institution, Position, Country, Address)',1,0,'boolean',1,'Additional user information',15,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (3,'title','Full descriptive title of the study',1,0,'text',1,'Study title',1,1); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (4,'studylogo','Filename containing logo of the study. File should be located under the htdocs/images/ folder',1,0,'text',1,'Study logo',2,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (5,'useEDC','Use EDC (Expected Date of Confinement) for birthdate estimations if the study involves neonatals',1,0,'boolean',1,'Use EDC',12,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (6,'ageMin','Minimum candidate age in years (0+)',1,0,'text',1,'Minimum candidate age',7,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (7,'ageMax','Maximum candidate age in years',1,0,'text',1,'Maximum candidate age',8,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (9,'useFamilyID','Enable if family members are recruited for the study',1,0,'boolean',1,'Use family',11,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (10,'startYear','Start year for study recruitment or data collection',1,0,'text',1,'Start year',5,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (11,'endYear','End year for study recruitment or data collection',1,0,'text',1,'End year',6,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (12,'dobFormat','Format of the Date of Birth',1,0,'date_format',1,'DOB Format',9,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (13,'useExternalID','Enable if data is used for blind data distribution, or from external data sources',1,0,'boolean',1,'Use external ID',12,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (14,'useProband','Enable for proband data collection',1,0,'boolean',1,'Use proband',11,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (16,'useScreening','Enable if there is a Screening stage with its own distinct instruments, administered before the Visit stage',1,0,'boolean',1,'Use screening',14,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (17,'excluded_instruments','Instruments to be excluded from the Data Dictionary and download via the Data Query Tool',1,1,'instrument',1,'Excluded instruments',16,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (19,'InstrumentResetting','Allows resetting of instrument data',1,0,'boolean',1,'Instrument Resetting',18,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (20,'SupplementalSessionStatus','Display supplemental session status information on Timepoint List page',1,0,'boolean',1,'Use Supplemental Session Status',19,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (22,'allowPrenatalTimepoints','Determines whether creation of timepoints prior to Date of Birth is allowed',1,0,'boolean',1,'Allow Prenatal Timepoints',21,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (23,'ImagingUploaderAutoLaunch','Allows running the ImagingUpload pre-processing scripts',1,0,'boolean',1,'ImagingUploader Auto Launch',22,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (24,'citation_policy','Citation Policy for Acknowledgements module',1,0,'textarea',1,'Citation Policy',23,1); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (25,'CSPAdditionalHeaders','Extensions to the Content-security policy allow only for self-hosted content',1,0,'text',1,'Content-Security Extensions',24,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (26,'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,NULL,NULL,'Paths',2,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (27,'imagePath','Path to images for display in Imaging Browser (e.g. /data/$project/data/) ',1,0,'web_path',26,'Images',9,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (28,'base','The base filesystem path where LORIS is installed',1,0,'web_path',26,'Base',1,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (33,'log','Path to logs (relative path starting from /var/www/$projectname)',1,0,'path',26,'Logs',2,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (34,'IncomingPath','Path for imaging data transferred to the project server (e.g. /data/incoming/$project/)',1,0,'web_path',26,'Incoming data',7,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (35,'MRICodePath','Path to directory where Loris-MRI (git) code is installed',1,0,'path',69,'LORIS-MRI code',6,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (36,'MRIUploadIncomingPath','Path to the upload directory for incoming MRI studies',1,0,'web_path',69,'MRI Incoming Directory',7,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (37,'GenomicDataPath','Path to Genomic data files',1,0,'web_path',26,'Genomic Data Path',8,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (38,'mediaPath','Path to uploaded media files',1,0,'web_path',26,'Media',9,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (39,'gui','Settings related to the overall display of LORIS',1,0,NULL,NULL,'GUI',3,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (42,'StudyDescription','Description of the Study',1,0,'textarea',39,'Study Description',2,1); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (43,'www','Web address settings',1,0,NULL,NULL,'WWW',4,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (44,'host','Host',1,0,'text',43,'Host',1,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (45,'eeg_pipeline','EEG Pipeline settings',1,0,NULL,NULL,'EEG Pipeline',15,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (46,'mantis_url','Bug tracker URL',0,0,'text',43,'Bug tracker URL',3,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (47,'dashboard','Settings that affect the appearance of the dashboard and its charts',1,0,NULL,NULL,'Dashboard',5,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (48,'projectDescription','Description of the study displayed in main dashboard panel',1,0,'textarea',47,'Project Description',1,1); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (49,'recruitmentTarget','Target number of participants for the study',1,0,'text',47,'Target number of participants',2,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (50,'imaging_modules','DICOM Archive and Imaging Browser settings',1,0,NULL,NULL,'Imaging Modules',6,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (51,'patientIDRegex','Regex for masking the Patient ID header field',1,0,'text',50,'Patient ID regex',1,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (52,'patientNameRegex','Regex for masking the Patient Name header field',1,0,'text',50,'Patient name regex',2,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (53,'LegoPhantomRegex','Regex for identifying a Lego Phantom scan header',1,0,'text',50,'Lego phantom regex',3,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (54,'LivingPhantomRegex','Regex to be used on Living Phantom scan header',1,0,'text',50,'Living phantom regex',4,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (55,'showTransferStatus','Show transfer status in the DICOM Archive table',1,0,'boolean',50,'Show transfer status',5,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (56,'tblScanTypes','Scan types from the mri_scan_type table that the project wants to see displayed in Imaging Browser table',1,1,'scan_type',50,'Imaging Browser Tabulated Scan Types',6,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (57,'statistics','Statistics module settings',1,0,NULL,NULL,'Statistics',7,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (58,'excludedMeasures','Instruments to be excluded from Statistics calculations',1,1,'instrument',57,'Excluded instruments',1,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (59,'mail','LORIS email settings for notifications sent to users',1,0,NULL,NULL,'Email',8,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (60,'From','Sender email address header (e.g. admin@myproject.loris.ca)',1,0,'email',59,'From',1,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (61,'Reply-to','Reply-to email address header (e.g. admin@myproject.loris.ca)',1,0,'email',59,'Reply-to',2,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (62,'X-MimeOLE','X-MimeOLE',1,0,'text',59,'X-MimeOLE',3,1); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (63,'uploads','Settings related to file uploading',1,0,NULL,NULL,'Uploads',9,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (64,'FileGroup','Determines the group permission for new subdirectories created for uploaded files',1,0,'text',63,'File Group for Uploads',1,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (65,'APIKeys','Specify any API keys required for LORIS',1,0,NULL,NULL,'API Keys',10,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (66,'JWTKey','Secret key for signing JWT tokens on this server. This should be unique and never shared with anyone. ',1,0,'text',65,'JWT Secret Key',1,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (67,'reCAPTCHAPrivate','Private Key for Google reCAPTCHA',1,0,'text',65,'reCAPTCHA Private Key',2,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (68,'reCAPTCHAPublic','Public Key for Google reCaptcha',1,0,'text',65,'reCAPTCHA Public Key',3,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (69,'imaging_pipeline','Imaging Pipeline settings',1,0,NULL,NULL,'Imaging Pipeline',14,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (70,'dataDirBasepath','Base Path to the data directory of Loris-MRI',1,0,'web_path',69,'Loris-MRI Data Directory',1,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (71,'prefix','Study prefix or study name',1,0,'text',69,'Study Name',2,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (72,'mail_user','User to be notified during imaging pipeline execution',1,0,'text',69,'User to notify when executing the pipeline',3,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (73,'get_dicom_info','Full path to get_dicom_info.pl',1,0,'path',69,'Full path to get_dicom_info.pl script',4,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (74,'horizontalPics','Enable generation of horizontal pictures',1,0,'boolean',69,'Horizontal pictures creation',5,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (75,'create_nii','Enable creation of NIfTI files',1,0,'boolean',69,'NIfTI file creation',6,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (76,'converter','If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it',1,0,'text',69,'DICOM converter tool to use (dcm2mnc or dcm2niix)',7,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (77,'tarchiveLibraryDir','Location of storing the library of used tarchives. If this is not set, they will not be moved',1,0,'path',69,'Path to Tarchives',8,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (78,'lookupCenterNameUsing','DICOM field (either PatientName or PatientID) to use to get the patient identifiers and the center name of the DICOM study',1,0,'lookup_center',69,'Patient identifiers and center name lookup variable',9,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (79,'createCandidates','Enable candidate creation in the imaging pipeline',1,0,'boolean',69,'Enable candidate creation',10,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (80,'is_qsub','Enable use of batch management in the imaging pipeline',1,0,'boolean',69,'Project batch management used',15,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (81,'use_legacy_dicom_study_importer','Use the legacy DICOM study importer instead of the new one',1,0,'boolean',69,'Use legacy DICOM study importer',15,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (82,'DTI_volumes','Number of volumes in native DTI acquisitions',1,0,'text',69,'Number of volumes in native DTI acquisitions',16,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (83,'t1_scan_type','Scan type of native T1 acquisition (as in the mri_scan_type table)',1,0,'text',69,'Scan type of native T1 acquisition',17,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (84,'reject_thresh','Max number of directions that can be rejected to PASS QC',1,0,'text',69,'Max number of DTI rejected directions for passing QC',18,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (85,'niak_path','Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl)',1,0,'path',69,'NIAK Path',19,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (86,'QCed2_step','DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)',1,0,'text',69,'Secondary QCed dataset',20,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (87,'issue_tracker_url','URL of the preferred issue tracker for this study',1,0,'text',43,'Issue Tracker URL',3,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (88,'excluded_series_description','Series description to be excluded from insertion into the database (typically localizers and scouts)',1,1,'text',69,'Series description to exclude from imaging insertion',21,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (89,'useConsent','Enable if the study uses the loris architecture for consent',1,0,'boolean',1,'Use consent',15,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (90,'ComputeDeepQC','Determines whether a call is made from LORIS-MRI to the DeepQC app for automatic QC prediction',1,0,'boolean',69,'Compute automatic QC',22,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (91,'ImagingBrowserLinkedInstruments','Instruments that the users want to see linked from Imaging Browser',1,1,'instrument',50,'Imaging Browser Links to Instruments',7,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (92,'MriConfigFile','Name of the Perl MRI config file (stored in dicom-archive/.loris_mri/)',1,0,'text',69,'Name of the Perl MRI config file',23,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (93,'default_bids_vl','Default visit label to use when no visit label set in the BIDS dataset',1,0,'text',69,'Default visit label for BIDS dataset',14,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (94,'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',69,'Scan type to use as a reference for defacing (typically a T1W image)',26,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (95,'modalities_to_deface','Modalities for which defacing should be run and defaced image inserted in the database',1,1,'scan_type',69,'Modalities on which to run the defacing pipeline',27,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (96,'compute_snr_modalities','Modalities for which the SNR should be computed when running the insertion MRI scripts',1,1,'scan_type',69,'Modalities on which SNR should be calculated',25,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (97,'publication_uploads','Path to uploaded publications',1,0,'web_path',26,'Publications',11,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (98,'publication_deletions','Path to deleted publications',1,0,'web_path',26,'Deleted Publications',11,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (99,'usePwnedPasswordsAPI','Whether to query the Have I Been Pwned password API on password changes to prevent the usage of common and breached passwords',1,0,'boolean',1,'Enable \"Pwned Password\" check',22,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (100,'EnvironmentFile','Name of the environment file that need to be sourced for the imaging pipeline',1,0,'text',69,'Name of the environment file',24,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (101,'MINCToolsPath','Path to the MINC tools',1,0,'web_path',69,'Path to the MINC tools',12,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (102,'documentRepositoryPath','Path to uploaded document repository files',1,0,'text',26,'Document Repository Upload Path',13,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (103,'dataReleasePath','Path to uploaded data release files',1,0,'text',26,'Data Release Upload Path',14,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (104,'dodFormat','Format of the Date of Death',1,0,'date_format',1,'DOD Format',10,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (105,'dateDisplayFormat','The date format to use throughout LORIS for displaying date information - formats for date inputs are browser- and locale-dependent.',1,0,'text',1,'Date display format',27,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (106,'IssueTrackerDataPath','Path to Issue Tracker data files',1,0,'web_path',26,'Issue Tracker Data Path',8,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (107,'adminContactEmail','An email address that users can write to in order to report issues or ask question',1,0,'text',1,'Administrator Email',28,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (111,'logs','Settings related to logging',1,0,NULL,NULL,'Log Settings',12,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (112,'database_log_level','Verbosity of database logging',1,0,'log_level',111,'Database Log Level',3,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (113,'request_log_level','Verbosity of HTTP request logs',1,0,'log_level',111,'HTTP Request Log Level',3,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (114,'exception_log_level','Verbosity of PHP exception logging',1,0,'log_level',111,'PHP Exception Log Level',3,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (115,'minc2bids','Settings related to converting MINC to BIDS LORIS-MRI tool script',1,0,NULL,NULL,'MINC to BIDS Converter Tool Options',13,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (116,'bids_dataset_authors','Authors for the BIDS dataset',1,1,'text',115,'BIDS Dataset Authors',1,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (117,'bids_acknowledgments_text','Acknowledgments to be added in the dataset_description.json file of the BIDS dataset created out of the MINC files',1,0,'text',115,'BIDS Dataset Acknowledgments',2,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (118,'bids_readme_text','Content to be added to the README of the BIDS dataset generated out of the MINC files',1,0,'textarea',115,'BIDS Dataset README',3,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (119,'bids_validator_options_to_ignore','Options to be ignored for BIDS validation',1,1,'text',115,'BIDS Validation options to ignore',4,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (120,'MriPythonConfigFile','Name of the Python MRI config file (stored in dicom-archive/.loris_mri/)',1,0,'text',69,'Name of the Python MRI config file',28,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (121,'aws','Settings related to AWS services',1,0,NULL,NULL,'AWS Settings',13,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (122,'AWS_S3_Endpoint','Endpoint to use for accessing files stored in S3. Endpoint or region are required for S3 support.',1,0,'text',121,'AWS S3 Endpoint',3,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (123,'AWS_S3_Region','AWS Region to use for accessing files stored in S3. Endpoint or region are required for S3 support.',1,0,'text',121,'AWS S3 Region',3,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (124,'AWS_S3_Default_Bucket','Default bucket for LORIS to use for accessing files in S3.',1,0,'text',121,'AWS S3 Default Bucket',3,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (125,'useEEGBrowserVisualizationComponents','Whether to enable the visualization components on the EEG Browser module',1,0,'boolean',39,'Enable the EEG Browser components',4,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (126,'createVisit','Enable visit creation in the imaging pipeline',1,0,'boolean',69,'Enable visit creation',11,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (127,'default_project','Default project used when creating scan candidate or visit',1,0,'text',69,'Default project',12,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (128,'default_cohort','Default cohort used when creating scan visit',1,0,'text',69,'Default cohort',13,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (129,'UserMaximumDaysInactive','The maximum number of days since last login before making a user inactive.',1,0,'text',1,'Maximum Days Before Making User Inactive',30,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (130,'DownloadPath','Where files are downloaded',1,0,'text',26,'Downloads',4,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (131,'EEGUploadIncomingPath','Path to the upload directory for incoming EEG studies',1,0,'text',45,'EEG Incoming Directory',15,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (132,'useDoB','Use DoB (Date of Birth)',1,0,'boolean',1,'Use DoB',12,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (133,'EEGS3DataPath','EEG S3 data path for assembly data',1,0,'text',45,'EEG S3 data path',15,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (134,'useAdvancedPermissions','Restricts access to data based on both sites and projects and require a special permission to access data not affiliated to a session (SessionID null). Keeping this setting to NO should ensure backwards compatibility (access to all data when module loads)',1,0,'boolean',50,'Use Advanced Permissions',5,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (135,'biobank','Settings related to the biobank module',1,0,NULL,NULL,'Biobank',14,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (136,'printEndpoint','Endpoint address for label printing logic',1,0,'text',135,'Label Printing Endpoint',1,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (137,'login_logo_left','Path for top left logo on the login page.',1,0,'text',1,'Login Top Left Logo',3,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (138,'login_logo_right','Path for top right logo on the login page.',1,0,'text',1,'Login Top Right Logo',3,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (139,'login_logo_left_link','Optional link to redirect when clicking on top left logo',1,0,'text',1,'Login Top Left Logo Link',4,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (140,'login_logo_right_link','Optional link to redirect when clicking on top right logo',1,0,'text',1,'Login Top Right Logo Link',4,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (141,'partner_logos','Logos for partners to be displayed in the homepage',1,1,'text',1,'Partner Logos',4,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (142,'EEGChunksPath','Path to store the EEG chunks for Visualization',1,0,'text',45,'EEG chunks path',16,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (2,'additional_user_info','Display additional user profile fields on the User accounts page (e.g. Institution, Position, Country, Address)',1,0,'boolean',1,'Additional user information',15,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (3,'title','Full descriptive title of the study',1,0,'text',1,'Study title',1,1); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (4,'studylogo','Filename containing logo of the study. File should be located under the htdocs/images/ folder',1,0,'text',1,'Study logo',2,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (5,'useEDC','Use EDC (Expected Date of Confinement) for birthdate estimations if the study involves neonatals',1,0,'boolean',1,'Use EDC',12,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (6,'ageMin','Minimum candidate age in years (0+)',1,0,'text',1,'Minimum candidate age',7,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (7,'ageMax','Maximum candidate age in years',1,0,'text',1,'Maximum candidate age',8,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (9,'useFamilyID','Enable if family members are recruited for the study',1,0,'boolean',1,'Use family',11,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (10,'startYear','Start year for study recruitment or data collection',1,0,'text',1,'Start year',5,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (11,'endYear','End year for study recruitment or data collection',1,0,'text',1,'End year',6,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (12,'dobFormat','Format of the Date of Birth',1,0,'date_format',1,'DOB Format',9,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (13,'useExternalID','Enable if data is used for blind data distribution, or from external data sources',1,0,'boolean',1,'Use external ID',12,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (14,'useProband','Enable for proband data collection',1,0,'boolean',1,'Use proband',11,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (16,'useScreening','Enable if there is a Screening stage with its own distinct instruments, administered before the Visit stage',1,0,'boolean',1,'Use screening',14,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (17,'excluded_instruments','Instruments to be excluded from the Data Dictionary and download via the Data Query Tool',1,1,'instrument',1,'Excluded instruments',16,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (19,'InstrumentResetting','Allows resetting of instrument data',1,0,'boolean',1,'Instrument Resetting',18,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (20,'SupplementalSessionStatus','Display supplemental session status information on Timepoint List page',1,0,'boolean',1,'Use Supplemental Session Status',19,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (22,'allowPrenatalTimepoints','Determines whether creation of timepoints prior to Date of Birth is allowed',1,0,'boolean',1,'Allow Prenatal Timepoints',21,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (23,'ImagingUploaderAutoLaunch','Allows running the ImagingUpload pre-processing scripts',1,0,'boolean',1,'ImagingUploader Auto Launch',22,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (24,'citation_policy','Citation Policy for Acknowledgements module',1,0,'textarea',1,'Citation Policy',23,1); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (25,'CSPAdditionalHeaders','Extensions to the Content-security policy allow only for self-hosted content',1,0,'text',1,'Content-Security Extensions',24,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (27,'imagePath','Path to images for display in Imaging Browser (e.g. /data/$project/data/) ',1,0,'web_path',26,'Images',9,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (28,'base','The base filesystem path where LORIS is installed',1,0,'web_path',26,'Base',1,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (33,'log','Path to logs (relative path starting from /var/www/$projectname)',1,0,'path',26,'Logs',2,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (34,'IncomingPath','Path for imaging data transferred to the project server (e.g. /data/incoming/$project/)',1,0,'web_path',26,'Incoming data',7,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (35,'MRICodePath','Path to directory where Loris-MRI (git) code is installed',1,0,'path',69,'LORIS-MRI code',6,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (36,'MRIUploadIncomingPath','Path to the upload directory for incoming MRI studies',1,0,'web_path',69,'MRI Incoming Directory',7,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (37,'GenomicDataPath','Path to Genomic data files',1,0,'web_path',26,'Genomic Data Path',8,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (38,'mediaPath','Path to uploaded media files',1,0,'web_path',26,'Media',9,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (42,'StudyDescription','Description of the Study',1,0,'textarea',39,'Study Description',2,1); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (44,'host','Host',1,0,'text',43,'Host',1,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (46,'mantis_url','Bug tracker URL',0,0,'text',43,'Bug tracker URL',3,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (48,'projectDescription','Description of the study displayed in main dashboard panel',1,0,'textarea',47,'Project Description',1,1); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (49,'recruitmentTarget','Target number of participants for the study',1,0,'text',47,'Target number of participants',2,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (51,'patientIDRegex','Regex for masking the Patient ID header field',1,0,'text',50,'Patient ID regex',1,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (52,'patientNameRegex','Regex for masking the Patient Name header field',1,0,'text',50,'Patient name regex',2,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (53,'LegoPhantomRegex','Regex for identifying a Lego Phantom scan header',1,0,'text',50,'Lego phantom regex',3,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (54,'LivingPhantomRegex','Regex to be used on Living Phantom scan header',1,0,'text',50,'Living phantom regex',4,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (55,'showTransferStatus','Show transfer status in the DICOM Archive table',1,0,'boolean',50,'Show transfer status',5,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (56,'tblScanTypes','Scan types from the mri_scan_type table that the project wants to see displayed in Imaging Browser table',1,1,'scan_type',50,'Imaging Browser Tabulated Scan Types',6,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (58,'excludedMeasures','Instruments to be excluded from Statistics calculations',1,1,'instrument',57,'Excluded instruments',1,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (60,'From','Sender email address header (e.g. admin@myproject.loris.ca)',1,0,'email',59,'From',1,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (61,'Reply-to','Reply-to email address header (e.g. admin@myproject.loris.ca)',1,0,'email',59,'Reply-to',2,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (62,'X-MimeOLE','X-MimeOLE',1,0,'text',59,'X-MimeOLE',3,1); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (64,'FileGroup','Determines the group permission for new subdirectories created for uploaded files',1,0,'text',63,'File Group for Uploads',1,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (66,'JWTKey','Secret key for signing JWT tokens on this server. This should be unique and never shared with anyone. ',1,0,'text',65,'JWT Secret Key',1,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (67,'reCAPTCHAPrivate','Private Key for Google reCAPTCHA',1,0,'text',65,'reCAPTCHA Private Key',2,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (68,'reCAPTCHAPublic','Public Key for Google reCaptcha',1,0,'text',65,'reCAPTCHA Public Key',3,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (70,'dataDirBasepath','Base Path to the data directory of Loris-MRI',1,0,'web_path',69,'Loris-MRI Data Directory',1,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (71,'prefix','Study prefix or study name',1,0,'text',69,'Study Name',2,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (72,'mail_user','User to be notified during imaging pipeline execution',1,0,'text',69,'User to notify when executing the pipeline',3,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (73,'get_dicom_info','Full path to get_dicom_info.pl',1,0,'path',69,'Full path to get_dicom_info.pl script',4,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (74,'horizontalPics','Enable generation of horizontal pictures',1,0,'boolean',69,'Horizontal pictures creation',5,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (75,'create_nii','Enable creation of NIfTI files',1,0,'boolean',69,'NIfTI file creation',6,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (76,'converter','If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it',1,0,'text',69,'DICOM converter tool to use (dcm2mnc or dcm2niix)',7,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (77,'tarchiveLibraryDir','Location of storing the library of used tarchives. If this is not set, they will not be moved',1,0,'path',69,'Path to Tarchives',8,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (78,'lookupCenterNameUsing','DICOM field (either PatientName or PatientID) to use to get the patient identifiers and the center name of the DICOM study',1,0,'lookup_center',69,'Patient identifiers and center name lookup variable',9,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (79,'createCandidates','Enable candidate creation in the imaging pipeline',1,0,'boolean',69,'Enable candidate creation',10,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (80,'is_qsub','Enable use of batch management in the imaging pipeline',1,0,'boolean',69,'Project batch management used',15,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (81,'use_legacy_dicom_study_importer','Use the legacy DICOM study importer instead of the new one',1,0,'boolean',69,'Use legacy DICOM study importer',15,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (82,'DTI_volumes','Number of volumes in native DTI acquisitions',1,0,'text',69,'Number of volumes in native DTI acquisitions',16,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (83,'t1_scan_type','Scan type of native T1 acquisition (as in the mri_scan_type table)',1,0,'text',69,'Scan type of native T1 acquisition',17,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (84,'reject_thresh','Max number of directions that can be rejected to PASS QC',1,0,'text',69,'Max number of DTI rejected directions for passing QC',18,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (85,'niak_path','Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl)',1,0,'path',69,'NIAK Path',19,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (86,'QCed2_step','DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)',1,0,'text',69,'Secondary QCed dataset',20,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (87,'issue_tracker_url','URL of the preferred issue tracker for this study',1,0,'text',43,'Issue Tracker URL',3,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (88,'excluded_series_description','Series description to be excluded from insertion into the database (typically localizers and scouts)',1,1,'text',69,'Series description to exclude from imaging insertion',21,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (89,'useConsent','Enable if the study uses the loris architecture for consent',1,0,'boolean',1,'Use consent',15,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (90,'ComputeDeepQC','Determines whether a call is made from LORIS-MRI to the DeepQC app for automatic QC prediction',1,0,'boolean',69,'Compute automatic QC',22,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (91,'ImagingBrowserLinkedInstruments','Instruments that the users want to see linked from Imaging Browser',1,1,'instrument',50,'Imaging Browser Links to Instruments',7,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (92,'MriConfigFile','Name of the Perl MRI config file (stored in dicom-archive/.loris_mri/)',1,0,'text',69,'Name of the Perl MRI config file',23,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (93,'default_bids_vl','Default visit label to use when no visit label set in the BIDS dataset',1,0,'text',69,'Default visit label for BIDS dataset',14,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (94,'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',69,'Scan type to use as a reference for defacing (typically a T1W image)',26,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (95,'modalities_to_deface','Modalities for which defacing should be run and defaced image inserted in the database',1,1,'scan_type',69,'Modalities on which to run the defacing pipeline',27,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (96,'compute_snr_modalities','Modalities for which the SNR should be computed when running the insertion MRI scripts',1,1,'scan_type',69,'Modalities on which SNR should be calculated',25,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (97,'publication_uploads','Path to uploaded publications',1,0,'web_path',26,'Publications',11,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (98,'publication_deletions','Path to deleted publications',1,0,'web_path',26,'Deleted Publications',11,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (99,'usePwnedPasswordsAPI','Whether to query the Have I Been Pwned password API on password changes to prevent the usage of common and breached passwords',1,0,'boolean',1,'Enable \"Pwned Password\" check',22,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (100,'EnvironmentFile','Name of the environment file that need to be sourced for the imaging pipeline',1,0,'text',69,'Name of the environment file',24,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (101,'MINCToolsPath','Path to the MINC tools',1,0,'web_path',69,'Path to the MINC tools',12,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (102,'documentRepositoryPath','Path to uploaded document repository files',1,0,'text',26,'Document Repository Upload Path',13,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (103,'dataReleasePath','Path to uploaded data release files',1,0,'text',26,'Data Release Upload Path',14,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (104,'dodFormat','Format of the Date of Death',1,0,'date_format',1,'DOD Format',10,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (105,'dateDisplayFormat','The date format to use throughout LORIS for displaying date information - formats for date inputs are browser- and locale-dependent.',1,0,'text',1,'Date display format',27,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (106,'IssueTrackerDataPath','Path to Issue Tracker data files',1,0,'web_path',26,'Issue Tracker Data Path',8,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (107,'adminContactEmail','An email address that users can write to in order to report issues or ask question',1,0,'text',1,'Administrator Email',28,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (112,'database_log_level','Verbosity of database logging',1,0,'log_level',111,'Database Log Level',3,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (113,'request_log_level','Verbosity of HTTP request logs',1,0,'log_level',111,'HTTP Request Log Level',3,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (114,'exception_log_level','Verbosity of PHP exception logging',1,0,'log_level',111,'PHP Exception Log Level',3,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (116,'bids_dataset_authors','Authors for the BIDS dataset',1,1,'text',115,'BIDS Dataset Authors',1,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (117,'bids_acknowledgments_text','Acknowledgments to be added in the dataset_description.json file of the BIDS dataset created out of the MINC files',1,0,'text',115,'BIDS Dataset Acknowledgments',2,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (118,'bids_readme_text','Content to be added to the README of the BIDS dataset generated out of the MINC files',1,0,'textarea',115,'BIDS Dataset README',3,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (119,'bids_validator_options_to_ignore','Options to be ignored for BIDS validation',1,1,'text',115,'BIDS Validation options to ignore',4,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (120,'MriPythonConfigFile','Name of the Python MRI config file (stored in dicom-archive/.loris_mri/)',1,0,'text',69,'Name of the Python MRI config file',28,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (122,'AWS_S3_Endpoint','Endpoint to use for accessing files stored in S3. Endpoint or region are required for S3 support.',1,0,'text',121,'AWS S3 Endpoint',3,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (123,'AWS_S3_Region','AWS Region to use for accessing files stored in S3. Endpoint or region are required for S3 support.',1,0,'text',121,'AWS S3 Region',3,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (124,'AWS_S3_Default_Bucket','Default bucket for LORIS to use for accessing files in S3.',1,0,'text',121,'AWS S3 Default Bucket',3,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (125,'useEEGBrowserVisualizationComponents','Whether to enable the visualization components on the EEG Browser module',1,0,'boolean',39,'Enable the EEG Browser components',4,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (126,'createVisit','Enable visit creation in the imaging pipeline',1,0,'boolean',69,'Enable visit creation',11,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (127,'default_project','Default project used when creating scan candidate or visit',1,0,'text',69,'Default project',12,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (128,'default_cohort','Default cohort used when creating scan visit',1,0,'text',69,'Default cohort',13,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (129,'UserMaximumDaysInactive','The maximum number of days since last login before making a user inactive.',1,0,'text',1,'Maximum Days Before Making User Inactive',30,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (130,'DownloadPath','Where files are downloaded',1,0,'text',26,'Downloads',4,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (131,'EEGUploadIncomingPath','Path to the upload directory for incoming EEG studies',1,0,'text',45,'EEG Incoming Directory',15,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (132,'useDoB','Use DoB (Date of Birth)',1,0,'boolean',1,'Use DoB',12,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (133,'EEGS3DataPath','EEG S3 data path for assembly data',1,0,'text',45,'EEG S3 data path',15,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (134,'useAdvancedPermissions','Restricts access to data based on both sites and projects and require a special permission to access data not affiliated to a session (SessionID null). Keeping this setting to NO should ensure backwards compatibility (access to all data when module loads)',1,0,'boolean',50,'Use Advanced Permissions',5,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (136,'printEndpoint','Endpoint address for label printing logic',1,0,'text',135,'Label Printing Endpoint',1,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (137,'login_logo_left','Path for top left logo on the login page.',1,0,'text',1,'Login Top Left Logo',3,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (138,'login_logo_right','Path for top right logo on the login page.',1,0,'text',1,'Login Top Right Logo',3,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (139,'login_logo_left_link','Optional link to redirect when clicking on top left logo',1,0,'text',1,'Login Top Left Logo Link',4,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (140,'login_logo_right_link','Optional link to redirect when clicking on top right logo',1,0,'text',1,'Login Top Right Logo Link',4,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (141,'partner_logos','Logos for partners to be displayed in the homepage',1,1,'text',1,'Partner Logos',4,0); +INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `CategoryID`, `Label`, `OrderNumber`, `Multilingual`) VALUES (142,'EEGChunksPath','Path to store the EEG chunks for Visualization',1,0,'text',45,'EEG chunks path',16,0); UNLOCK TABLES; SET FOREIGN_KEY_CHECKS=1; diff --git a/tools/single_use/config_to_db.php b/tools/single_use/config_to_db.php index 003b0d6a74..76b1d8f124 100755 --- a/tools/single_use/config_to_db.php +++ b/tools/single_use/config_to_db.php @@ -50,9 +50,11 @@ function iterate($iterator, $parentKey, $DB) // If the key already exists if (!empty($configID)) { $dbParentKey = $db->pselectone( - "SELECT Name - FROM ConfigSettings - WHERE ID=(SELECT Parent FROM ConfigSettings WHERE Name=:name)", + "SELECT Name + FROM ConfigCategories + WHERE ID=( + SELECT CategoryID FROM ConfigSettings WHERE Name=:name + )", ['name' => $name] ); if ($parentKey==$dbParentKey) {