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Version 1.2 Release (August 1, 2014)

(out of date: needs to be updated)

tranSMART Version 1.2 incorporates functionality developed by ConvergeHEALTH, The Hyve, CTMM TraIT, IMI eTRIKS, Pfizer, Sanofi, Takeda and other community members.  A community-based global effort has merged these contributions into a single codebase with support for both PostgreSQL and Oracle.  All future enhancements to the tranSMART platform will be based on version 1.2.

Version 1.2 is an early production release that represents the collaborative effort of several hundred community members.  A PostgreSQL demo instance hosted by BT Global is available at http://75.124.74.64/transmart/Please log in with user=admin for the administrator role and user=guest for the visitor role. The password is the same as the username in both cases.

During August and early September 2014, community-based testing and bug fixing will continue. Technical and user documentation, video tutorials, an Oracle-based demo instance, virtual machines and data set contributions will also be developed.

The Formal Launch of v1.2 will take place during the second week of September 2014.  Launch activities will include presentation and demonstrations of the new functionality.  Please visit www.transmartfoundation.org for more information.

Information on specific functionality, community-based activities, testing, release plan and software releases are available on the tranSMART Version 1.2 wiki space.

Please Contribute

There are two significant ways that you can contribute to tranSMART Version 1.2 –

How to Get Help / How to Report Problems

The best avenue to obtain help is to report your problem as a new topic in the tranSMART Google transmart-discuss group.  Our experienced community of developers, testers and users monitor and offer assistance to questions, issues and problems posed to the discussion group.

How to Obtain and Set Up the Release

The release consists of two parts: a WAR file (which can be built from source) and a test/demo database.

The WAR File

The following instructions assume that you have locally installed Tomcat 7 or a similar container for web applications and Java 7 running.

The release war file can be obtained as a download from the transmart release demo site: here. Click on the transmart.war link to download the war file.

Once you have obtained the war file put it into the webapps directory of the Tomcat. If Tomcat is running, there is no need to shut it down, as it will redeploy the war file when you replace it (or copy it for the first time) into the webapps directory. The URL of the application is http://your-host-and-port/transmart, for example http://localhost:8080/transmart. Please note: the application will not run without that test/demo database or a similar tranSMART database. In addition, the account of the user who is running the tomcat will have to have the configuration file defined). That person is usually you if you are running in a single user environment.

In addition, you can obtain the latest version of the ongoing development, that is pre-release version for 1.2.1, directly from the continuous-integration system:

Setting up the configuration file.

The user running the transmart.war file, that is, the user running tomcat, must have access to a set of the configuration files. These files resides in that users home directory in a folder located at ~/.grails/transmartConfig; they are BuildConfig.groovy (optional), DataSource.groovy, and Config.groovy. They will usually be build by the data install process, see below.

Building from Source

We recommend downloading the war file, but if you wish the build to war file from source, these are the steps:

  1. Install Java 7 and Grails 2.3.7 (https://grails.org/Installation).
  2. Download the source code as a zip file. Browse to https://github.com/transmart/transmartApp/tree/london_hackaton, and click on the Download ZIP button (middle right side of the page). The unzipped directory is transmartApp-london_hackaton.
  3. Set up configuration as described above.
  4. Build the WAR file with this command: grails war. When the command completes successfully it will indicate the location of the war file. Copy that to your tomcat webapps directory. You can also run the application in a stand-alone development mode using the command: grails run-app.

The Test/Demo Database

You will need to have installed either a version of PostgreSQL (http://www.postgresql.org/) or Oracle (http://www.oracle.com/).

These instructions are based on PostgreSQL 9.2. For using the Oracle database, we recommend the Enterprise version of Oracle.

Download either the ZIP file or the Git clone from https://github.com/transmart/transmart-data/tree/london_hackathon. The ZIP file is the easiest. Go to the URL and click on the Download ZIP button (middle right-hand-side of the page). The unzipped file will create a directory transmart-data-london_hackathon. In that directory you will find a file README.md. Follow the instructions in that file. These instructions assume that you are using a Linux Bourne shell (e.g. bash).

The README also described how to set up the configuration files.

Also note, for full functionality you will want to set up SOLR as per the README instructions.

 

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