LORIS Release v16.1.0

This release incorporates 148 backwards compatible small changes and features on top of
LORIS 16.0. There are minor bug fixes but no significant changes from release candidate 1.

Projects currently using LORIS 16.0.x should apply the patch SQL/16.0_To_16.1_upgrade.sql in order to upgrade. Projects using older versions should first apply SQL patches to upgrade to LORIS 16.0.

For a full list of changes see here.

Features:

• Added new Media module to track non-instrument specific candidate media such as videos or instrument scans
• Added Signal-to-Noise Ratio to imaging browser for some modalities (T1, T2, Flair, PD.) (requires updating imaging pipeline)
• Module authors may now implement getCSSDependencies() to customize CSS that gets included on each page
• Unused accounts now get automatically disabled after 1 year of inactivity

Notable bug fixes and clean up:

• Improved many queries in the statistics module
• Improved compatibility with MySQL 5.7+
• Various other bug fixes

Known Issues:

• If you upload the documents with the same filename to multiple categories in the document repository, the document in the second category uploaded will overwrite the document from the first.

LORIS Release 16.1 (Release Candidate 1)

This release incorporates 148 backwards compatible small changes and features on top of
LORIS 16.0.

Projects currently using LORIS 16.0.x should apply the patch SQL/16.0_To_16.1_upgrade.sql in order to upgrade. Projects using older versions should first apply SQL patches to upgrade to LORIS 16.0.

For a full list of changes see here

Features:

• Added new Media module to track non-instrument specific candidate media such as videos or instrument scans
• Added Signal-to-Noise Ratio to imaging browser for some modalities (T1, T2, Flair, PD.) (requires updating imaging pipeline)
• Module authors may now implement getCSSDependencies() to customize CSS that gets included on each page
• Unused accounts now get automatically disabled after 1 year of inactivity

Notable bug fixes and clean up:

• Improved many queries in the statistics module
• Improved compatibility with MySQL 5.7+
• Various other bug fixes

LORIS Release v16.0.2

This release addresses a critical bug fixes from v16.0.1. Anyone on v16.0.0 should update the code to this release with no other changes.

Bug Fixes

• This release fixes a regression in v16.0.1 where users who had the data_entry permission without the access_all_sites permission would receive an SQL error on the dashboard upon logging in.

LORIS Release v16.0.1

This release addresses various minor bug fixes in v16.0.0. Anyone on v16.0.0 should be able to update the code to this release with no other changes.

Please note all 16.* release notes below -- particularly important for Existing projects.

Bug fixes

• Fixed a bug where you couldn't sort on the first column in some tables
• Fixed the scoring algorithm in the sample BMI instrument
• The dashboard statistics now exclude DCC and cancelled candidates
• Fixed a bug where you couldn't search for '0' for a DCCID or PSCID
• Removed a button that didn't do anything in BrainBrowser
• Better instrument search in DQT
• Added "loading" visual feedback in DQT

LORIS Release 16.0.0

Full list of changes

Note that LORIS 16.0 is only supported for PHP 5.6: We recommend installing/upgrading PHP using this (deprecated) PPA repository: ppa:ondrej/php5-5.6

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
• Help Editor now allows inline editing
• Lost password changed to force password reset upon login

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: We recommend installing/upgrading PHP using this (deprecated) PPA repository: ppa:ondrej/php5-5.6

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

• Genomic file upload is in beta and is only for Illumina methylation datasets
• For Genomic file upload, Config:GenomicDataPath/genomic_uploader/ must be writable by Apache (www-data)
• Instrument Manager in Beta

Loris 16.0 (Release Candidate 3)

This release candidate contains minor bug fixes and feature updates:

• Fixed bug where CSS for modules couldn't be overridden
• Help Editor now allows inline editing
• Lost password changed to force password reset upon login
• NRRD download link in imaging browser fixed
• recommended PPA for PHP 5.6 installation/upgrade specified in Ubuntu Readme

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.