LORIS 15.10

Fall 2015 release of LORIS : Full list of changes

Install process

• Install script enables setup when MySQL is hosted on a different machine than Loris
• For Mac install, see Mac Readme guidelines last updated for 15.04
• Apache configurations include setting AllowOverride All to accommodate Rewrite rules
• Smarty 3 is installed by Composer and does not require prior installation (since 15.04)
• new Wiki page on running the install script

Improvements and Documentation

• Re-designed Behavioural Feedback and Data Team Helper modules
• Subprojects and Projects can be created and managed via the front-end Configuration module. Recruitment targets can now be set at the Subproject level.
• One-click Data View Download to CSV format file in Access Profiles page (Candidate List)
• In User Accounts, when changing a user's permission settings, there is a new option to send a notification email to other site supervisors/coordinators (personnel selected from a list)
• MRI Header information now included in Excel dumps
• Direct links from Behavioural pages to Imaging datasets
• Dockerfile added
• API support
• Version file

Notes for Existing Projects

Note all Caveats for existing projects, update your admin user account with all new/available permissions, and apply the Release patch

• Imaging projects also see Loris-MRI Release Notes for Existing Projects for 15.10
• HTML will be displayed in console box upon first loading your upgraded Loris. Refresh your browser and/or delete the smarty/templates_c/ directory content to resolve.
• Subprojects (cohorts) and Projects are now managed in the front-end Configuration module. Run the import_projects.php script (located in modules/configuration/tools/) to migrate your subproject and projects settings from project/config.xml into the Config table. Then manually clean your config.xml file.
• Several Imaging Feedback categories have changed
• Apache configuration should enable Rewrite rules by setting AllowOverride All
  • Ubuntu apache config file: /etc/apache2/sites-available/$projectname.conf
  • CentOS apache config file: /etc/httpd/conf.d/apache-site.conf

Known Issues / Caveats

• Conflict Resolver does not record new data entry conflicts. Run the tools/detect_conflicts.php script on a frequent basis (e.g. by cronjob) to detect and report new conflicts. (Fix for 16.04)
• Beta features: Imaging Uploader AutoLaunch and Server Processes Manager module may require schema and code modifications
• Statistics module queries and calculations should be customized per project
• Form Rules in the Instrument Builder are in beta
• Data Querying Tool data import scripts should be adapted if Consent feature is not used
• Projects started before October 2014 who are missing the 'edit_final_radiological_review' permission should run:

INSERT INTO permissions (code, description, categoryID) VALUES ('edit_final_radiological_review','Can edit final radiological reviews','2');

• Document Repository is missing from the Tools menu. To display this menu item, run:

SELECT m.ID, p.PermID FROM permissions p CROSS JOIN LorisMenu m WHERE p.code='document_repository_view' AND m.Label='Document Repository';

LORIS 15.10 (Release Candidate 5)

• Fixed bug where non-study sites were appearing in the statistics module

LORIS 15.10 (Release Candidate 4)

• Fixed bug with validation errors not showing up in imaging_uploader
• Fixed bug where page links were not showing up in imaging_uploader

LORIS 15.10 (Release Candidate 3)

• Fixed various bugs in mri violations module
• Fixed issue with certification module not restricting data entry in instruments
• Removed an inefficient query from the statistics module which could cause large datasets to timeout.

LORIS 15.10 (Release Candidate 2)

• Fixed Dashboard loading problem where Project tag was enabled
• Fixed menu template for Survey Accounts

LORIS 15.10 (Release Candidate 1)

Fall 2015 release of LORIS : Full list of changes

Install process

• Install script enables setup when MySQL is hosted on a different machine than Loris
• For Mac install, see Mac Readme guidelines last updated for 15.04
• Apache configurations include setting AllowOverride All to accommodate Rewrite rules
• Smarty 3 is installed by Composer and does not require prior installation (since 15.04)
• new Wiki page on running the install script

Improvements and Documentation

• Re-designed Behavioural Feedback and Data Team Helper modules
• Subprojects and Projects can be created and managed via the front-end Configuration module. Recruitment targets can now be set at the Subproject level.
• One-click Data View Download to CSV format file in Access Profiles page (Candidate List)
• In User Accounts, when changing a user's permission settings, there is a new option to send a notification email to other site supervisors/coordinators (personnel selected from a list)
• MRI Header information now included in Excel dumps
• Direct links from Behavioural pages to Imaging datasets
• Dockerfile added
• API support
• Version file

Notes for Existing Projects

Note all Caveats for existing projects, update your admin user account with all new/available permissions, and apply the Release patch

• Imaging projects also see Loris-MRI Release Notes for Existing Projects for 15.10
• HTML will be displayed in console box upon first loading your upgraded Loris. Refresh your browser and/or delete the smarty/templates_c/ directory content to resolve.
• Subprojects (cohorts) and Projects are now managed in the front-end Configuration module. Run the import_projects.php script (located in modules/configuration/tools/) to migrate your subproject and projects settings from project/config.xml into the Config table. Then manually clean your config.xml file.
• Several Imaging Feedback categories have changed
• Apache configuration should enable Rewrite rules by setting AllowOverride All
  • Ubuntu apache config file: /etc/apache2/sites-available/$projectname.conf
  • CentOS apache config file: /etc/httpd/conf.d/apache-site.conf

Known Issues / Caveats

• Statistics module queries and calculations should be customized per project
• Form Rules in the Instrument Builder are in beta
• Data Querying Tool data import scripts should be adapted if Consent feature is not used
• Projects started before October 2014 who are missing the 'edit_final_radiological_review' permission should run:

INSERT INTO permissions (code, description, categoryID) VALUES ('edit_final_radiological_review','Can edit final radiological reviews','2');

• Document Repository is missing from the Tools menu. To display this menu item, run:

SELECT m.ID, p.PermID FROM permissions p CROSS JOIN LorisMenu m WHERE p.code='document_repository_view' AND m.Label='Document Repository';

LORIS 15.04

Spring 2015 release of LORIS : Full list of changes

Install process

• CentOS install support added to install script
• Updated Mac install Readme for Yosemite

Improvements and Documentation

• Composer dependency manager
• New project/data directory for project-specific data uploads
• More strict error handling for permissions and configuration settings
• Improved password hashing (with PHP 5.5+)
• Basic unit tests for every module
• New LorisForm class to replace HTML_QuickForm
• New Server Process Manager module for monitoring large data processes
• New Genomic Browser module
• New Training module for examiner certification
• Examiner module re-designed
• New Imaging Uploader module, including phantom handling
• Sample ranges provided for MRI protocol parameter checks
• Statistics module improvements
• Document Repository improvements
• Instrument Manager improvements
• Imaging Browser GUI enhancements

Notes for Existing Projects

Note all Caveats for existing projects, update your admin user account with all new/available permissions, and apply the Release patch

• Install Composer
• Configuration settings found in project/config.xml take precedence over Configuration module settings;
  it is recommended to remove any duplicate/overlapping settings from the config.xml file
• Config settings to be added to project/config.xml: HeaderTable, instrumentPermissions, multiSiteEnabledCenters
• New project/data directory recommended
• Access Profiles page hides Open Profile dialog for users with permission to view candidate data from multiple sites
• Retiring file extension *.super_sql for tables generated from .linst files; all MySQL files now just *.sql
• Please see the LORIS-MRI repository and wiki for details about our new web-based imaging uploader

Known Issues / Caveats

• localhost installations (e.g. on Mac) may encounter partial reduplication in URL path (More info:1173)
• isError() calls should be removed e.g. in php instrument files; error-checking now handled by base classes
• Numeric fields in forms created via the Instrument Builder will store a default value of 0 if not completed or if marked not_answered
• Statistics module queries and calculations should be customized per project
• Rules in the Instrument Builder are in beta
• Data Querying Tool data import scripts should be adapted if Consent feature is not used in Loris
• Projects started since January 2014 without a caveat_options table should run:

CREATE TABLE caveat_options (ID INT, Description varchar(255), PRIMARY KEY (ID));

• Projects started since September 2014 missing the 'mri_upload' permission should run:

INSERT INTO permissions (code, description, categoryID) VALUES ('mri_upload','MRI Uploader','2');

Loris 14.12.1

This minor release addresses bugs found in scripts in the 14.12 release which prevented some scripts from running properly.

Bug Fixes

Scripts from tools/ directory affected by this release:

• generate_tables_sql_and_testNames.php
• generate_tables_sql.php
• quickform_parser.php,
• data_dictionary_builder.php
• generic_includes.php (resolves issues with CouchDB import scripts, excelDump, and various others)

Click here for a full list of changes

Loris 14.12

This release is designed to fix minor issues including permissions and cosmetics
Click here for a full list of changes

Improvements and Documentation

• Documentation migration to GitHub wiki for Setup and Developer’s Guide
• Improved Configuration module
• Upgraded version of BrainBrowser
• Document Repository upload/download/delete functionality
• Cleaned up error handling by replacing PEAR errors with PHP exceptions

Beta modules

• MRI upload page times out for large datasets; this does not impact the upload operation. Creates /tmp/ subdirectory which should be cleaned up to conserve space. Parallel uploading not recommended.
• Document Repository GUI improvements with future improvements planned to structural layout
• Data Team Helper for tracking data entry
• Data Integrity Flag module for tracking dataset validation progress
• Examiner Certification tracker for clinical staff
• Examiner Reliability for clinical/psychometric assessments
• Instrument Manager

Notes for Existing Projects

• Many permissions have been renamed and/or made more granular. User permission re-granting may be required for modules such as Imaging Browser, Instrument Builder, Candidate Parameters, and more.
• Document Repository files have moved. From your lorisroot directory (e.g. /var/www/loris/), run (sudo) the following command to move all previously uploaded files to the new location:
  mv htdocs/document_repository/* modules/document_repository/user_uploads
  Run patch SQL/14.12/2014-12-15-DocumentRepositoryDataDir.sql to update paths in document_repository table.
• Statistics sub-modules are now registered via the new StatisticsTabs table
• Developers Guide documentation moved to GitHub wiki
• Old “Data Query GUI” tables, code and directories have been removed. (can be restored using “git revert 0eb4889”)
• Removed two files used only by legacy instruments: RequiredIf.inc RequiredIfGroup.inc Move these files to project/libraries/ if still required by your php instruments.

Known Issues

• A few scripts in the tools/ directory use old calls to create Config and Database objects. These lines should be removed where not required by the script, or else updated to use methods found in the LORIS base classes.

LORIS 14.10

New Features

• Updated Mobile-friendly GUI
• New user-specific dashboard upon login containing customized metrics and notification, and status updates
• New MRI uploader module
• New front-end Configuration module
• Improved inline Help
• New Account Request form, accessible from the login page, for new users. Site coordinators receive dashboard notification and can approve requests for user accounts for their own site.
• New Participant surveys enable instruments/surveys to be completed directly by subjects (e.g. from home)
• New Instrument Builder
• New MRI violations module for tracking imaging pipeline errors
• New “First Visit” battery feature populates specific instruments for the first subject visit regardless of age or visit sequence
• Miscellaneous bug fixes.

Update: Mac Install Readme available, compatible with 14.10

Beta modules

• Data Team Helper for tracking data entry
• Data Integrity Flag module for tracking dataset validation progress
• Examiner Certification tracker for clinical staff
• Examiner Reliability for clinical/psychometric assessments
• Instrument Manager

Notes for existing projects

• Our GitHub “Loris-Trunk” repository has been renamed “Loris”. We recommend re-forking. There should be no impact on SSH keys.
• Schema updates: MySQL patches for this release are stored in SQL/Archive/Pre-14.10/ subdirectory. Be sure to apply patches in order from oldest merged, to most recent.
• Ensure the Loris “admin” superuser has been granted every permission, by running patch SQL/Archive/Pre-14.10/2014-10-17-AdminAllPermissions.sql
• There is now a configuration module for this release of LORIS. For more information, see the Configuration module Readme.
  Be sure to run the script tools/config_to_db.php (after applying MySQL patches)
• Note new tags in config.xml (e.g. sandbox)
• Imaging Browser: Jiv viewer no longer supported (link still present)
• Smarty3 installation required

Known Issues

• In project/config.xml, sandbox tag should be nested inside parent dev tagset (#779)
• Instrument Manager and Data Integrity Flag modules (in Beta) are in the codebase but not in the LorisMenu table by default.