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Release 16.3 (August 2018) is a minor update to release 16.2 with Oracle support.

Release Notes tranSMART 16.3

Oracle support

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.

Postgres support

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).

transmartApp

Improved error messages

Error messages now include detailed descriptions in production systems. Previous releases only reported “An error has occurred”

Authentication

Fixed an object size issue when using Kerberos authentication

Create User

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.

Summary Statistics

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.

Analyze tab

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.

Grid View

If grid view was turned off it was not possible to clear a selected subset.

Fixed naming of gene expression columns in grid view.

UploadData page

Fixes for loading template files.

Large studies

Fix for studies with more than 1000 concept codes (e.g. categorical values) using an Oracle database.

Data export

Fix for visibility of all datatypes on Data Export tab.

Utility menu

Clicking away from the Utility menu will now close it.

Genome Browser

The genome browser changes the page title. The title is now changed back when leaving the genome browser.

Advanced Workflows

Help pages

Add configuration parameters to provide custom help pages for workflows

Logistic Regression

Swap the X and Y axes

aCGH Survival Analysis

The description of the censoring variable is updated

Heatmaps

The max rows to display button now has a help text available if defined in a configuration parameter:

  • org.transmartproject.helpUrls.hierarchicalClusteringMaxRows
  • org.transmartproject.helpUrls.heatMapMaxRows
  • org.transmartproject.helpUrls.kMeansClusteringMaxRows

Menus

Unused modification items are not displayed

transmart-data

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.

Filter keywords

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.

R downloads

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.

rserve service

Fix rserve service for Ubuntu 14.04

REST API

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

Admin page

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).

Known issues

None.

 

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