Loris 16.0 (Release Candidate 2)

Full List of changes since 16.0 Release Candidate 1

Updates and Improvements

• Minor bug fixes including URLs, Mobile UI issues, broken Pagination was fixed
• Data Dictionary description modifications updates
• User Accounts permission assignment fixes
• MRI Violations module bugs
• Survey module fixed
• Data Query Tool fixed in Firefox
• Flags on Behavioural instrument forms fixed
• Training module
• Statistics for Double Data Entry

Notes for existing projects

Pull requests in this release candidate tagged Caveat for Existing Project

• Fixes to Release patch - Menu items for Data Query Tool and Data Dictionary may need to be manually inserted
• MINC toolkit path variable must be manually added to project/config.xml file #1843

Loris 16.0 (Release Candidate 1)

Spring 2016 release of LORIS : Full list of changes

Note that LORIS 16.0 is only supported for PHP 5.6

New Features

• Data release module #1602
• Acknowledgements module #1489
• Notifications and real-time Log Viewer for Imaging Uploader module #1654
• Improved Automated testing on all modules
• Rest API v.0.0.2 and JWT Token authentification #1421
• Content Security Policy added #1481
• Customizable instrument display order #1500
• Enhance support for custom module development #1404
• DQT is now seamlessly integrated as a LORIS module. Queries can be saved as public or private. Queries now support nested And/Or logic. Install process is unchanged.
• Video embedding in Training module
  Genomic Browser:
• new Subject Genomic Profile tab, GWAS tab, Genomic File support and File metadata display #1579
• Refactored tables, Methylation tab
• Genomic File upload management (methylation) #1669

Install process

• Deployment on Heroku now available
• Improved imaging insertion pipeline configuration process
• Database schema split into more modular components #1342

Updates and Improvements

• Data Query Tool Demographic Import script fixed for projects not using consent feature
• React used for faster rendering of page components
• Pretty URLs; Apache mod rewrite now required for writing URLs
• Improved navigation and breadcrumbs #1643
• Cleanup of Imaging Pipeline scripts and Imaging installation process
• Better versioning documentation and testing infrastructure (#1521)
• Improved Help sections within Loris
• Improved database error logging #1448
• More granular permissions for certain modules #1419
• Only subjects with participant_status Active are pushed to DQT #1502
• Config setting override clarified in Configuration module #1603

Notes for Existing Projects

Check all pull requests tagged Caveat for Existing Project

• Note that LORIS 16.0 is only supported for PHP 5.6

Module support changes:

• Create a project/modules/ directory to house any code that overrides existing modules
• Partial override under project/ is disallowed for modules. Modules can be customized either in the main codebase (not recommended), or by copying all files for that module into project/modules/$givenModule/ and modifying files as desired. All files for this module will then be sourced from project/modules/$givenModule/ even if no modification has been made (e.g. the JavaScript may be unaffected). At the next release, merge all code changes on this module from the main codebase.
• Configuration settings: Study Description #1438 and External Links #1367 fields moved to the Configuration module. Update your new Config table setting with the value currently stored in project/config.xml within the given tagsets, and then remove these tag sections from project/config.xml
• Reliability module files must be moved #1409
• Imaging Projects: Note all Loris-MRI 16.0 Release notes, including updating to the Loris-MRI release branch, manual installation of minc toolkit, and a required update to config.xml
• DQT should update seamlessly to new GUI, housed as a module within LORIS. LORIS menu will point to new DQT skin but old DQT interface will still be accessible. Old queries from the DQT should port seamlessly to the new GUI, however new queries using OR logic will not be backwards compatible to old DQT.
• Apache mod rewrite now required for rewriting Pretty URLs
• 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

Significant MySQL updates:

• Imaging: Selected field has moved to files_qcstatus table. Data will not deleted by release upgrade - to clean old records, run Commented lines in MySQL patch line 278. Also update custom queries using Selected field accordingly.
• Genomics: many improvements to MySQL table definitions. Back up and then carefully update tables.

Known Issues / Beta

• For Genomic file upload, Config:GenomicDataPath/genomic_uploader/ must be writable by Apache (www-data)
• Instrument Manager in Beta
• One-click Download disabled

LORIS 15.10.2

This minor release addresses issues in the 15.10.1 release:

• Updated script for loading demographic data in Data Query Tool to handle new Subproject and Project configuration settings (fix)
• Removed third party script loading, introduced in 15.10 (fix)
• Updated embedded BrainBrowser to the recent v2.4.0 release, to correct for an inconsistency in display convention, where images may have appeared flipped (Left-Right) depending on imaging modality or acquisition type, due to mixing neurological/radiological display conventions (fix)
• Fixed bug where BrainBrowser was not correctly displaying 4 dimensional images (fix)
• Updated version number

Full list of changes since 15.10.1
If upgrading from a previous release, please also read Release notes from both 15.10 and 15.10.1 for additional details, caveats, known issues, and instructions for existing projects.

Known Issues

BrainBrowser 2.4.0 issues applicable to LORIS:

• gray scale mapping input file - fix here
• not compatible with mobile devices
• plane de-synchronization

LORIS 15.10.1

This minor release addresses two issues in the 15.10 release:

• Conflict Resolver not recording new data entry conflicts (fix)
• Search keyword filter impacting other unrelated modules (fix)

Full list of changes since 15.10
If upgrading from a previous release, please also read 15.10 Release notes for additional details, caveats, known issues, and instructions for existing projects.

Known Issues

• BrainBrowser viewer (embedded in Imaging Browser module) may flip images (Left-Right) due to mixing neurological/radiological display conventions. This display difference may appear between images acquired within the same scanning session for a given subject, perhaps depending on imaging modality or acquisition type. BrainBrowser's recent v2.4.0 release corrects this inconsistency in the display convention, and will be incorporated in LORIS 16.04.

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';