Release 16.3 (August 2018) is a minor update to release 16.2 with Oracle support.
Release Notes tranSMART 16.3
The previous release was not fully tested on Oracle. Release 16.3 has been tested on an Amazon AWS instance running Ubuntu 14 and an Oracle 12.1 Enterprise Edition Docker instance as the database server.
Release 16.2 did not run on Postgres 9.6. The Postgres library has been updated to the latest version and tested on a Postgres 9.6 server.
Ubuntu 16 support
Changes have been made to support installation on Ubuntu 16.04 and Ubuntu 14.04.
Automated install scripts have versions for both with only limited divergence.
Targets in transmart-data are updated as appropriate (for example, a different PHP version is available in Ubuntu 16).
Improved error messages
Error messages now include detailed descriptions in production systems. Previous releases only reported “An error has occurred”
Fixed an object size issue when using Kerberos authentication
Creating a new user failed when first used as a sequence value was incorrectly set. This is fixed in transmart-data for creating a new database, and by a simple SQL statement for existing release 16.2 installations.
Browse delete program/study configurable
New configuration parameters ui.browse.delete.allowprogram and ui.browse.delete.allowstudy display a Delete button for programs and studies for admin users in the Browse tab. The default behaviour is unchanged – to delete a program or study using SQL as described on the Wiki.
Added a custom help page URL if defined as org.transmartproject.helpUrls.summaryStatistics
The pie chart legend is now sorted by category (this was broken n 16.2).
Updated to a later version of the jFreeChart library.
Fixed some issues with drag-and-drop by removing bold markup on nodes.
Across Trials studies are only visible if the user is authorized to access the study.
If grid view was turned off it was not possible to clear a selected subset.
Fixed naming of gene expression columns in grid view.
Fixes for loading template files.
Fix for studies with more than 1000 concept codes (e.g. categorical values) using an Oracle database.
Fix for visibility of all datatypes on Data Export tab.
Clicking away from the Utility menu will now close it.
The genome browser changes the page title. The title is now changed back when leaving the genome browser.
Add configuration parameters to provide custom help pages for workflows
Swap the X and Y axes
aCGH Survival Analysis
The description of the censoring variable is updated
The max rows to display button now has a help text available if defined in a configuration parameter:
Unused modification items are not displayed
Missing rows for disease and therapeutic domain
Some disease and therapeutic domain concepts were missing from the initial biomart.bio_data_uid table. A simple SQL statement can update these for a 16.2 database.
Some keyword categories were missing from the Browse/Analyse tab filters: country, species and filetype. Simple SQL statements can update these for a 16.2 database.
The default provider for R packages is no longer available. An alternative provider is now used when installing through transmart-data
R package QDNAseq version
Version updated. Only one version is available for download.
Fix rserve service for Ubuntu 14.04
Fix a “wrong home page” error when running transmartApp from a war file.
New curated datasets
Over 100 curated GEO studies have been added to the i2b2-tranSMART Foundation server.
Details of the available studies are on the Wiki: https://wiki.transmartfoundation.org/display/transmartwiki/Curated+Data+Repository
A new “Configuration status” page is added.
All known configuration parameters are listed, in groups, with current or default values and descriptions.
Any unknown configuration variables appear in an “Unknown” section at the end. These may be typos in the configuration file or parameters not recognized when the release was built (if so, please let us know so we can add a description for the next release).