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LORIS Release 16.0.0
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@driusan driusan released this 08 Jun 20:13
· 28 commits to 16.04-dev since this release
16.0.0
670dcda

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
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