IDRT - Integrated Data Repository Toolkit
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The IDRT Import and Mapping Tool (IMT) is a client application designed to run on your local machine. It doesn't need administrator's privileges. It is available for Windows (XP/Vista/7/8) and Linux. Up to 2 GB free disk space are used temporarily.

It requires Java 7 (either runtime or standard edition) to be installed.

Because it operates on the i2b2 database directly rather than using the i2b2 Web Service API, you need a physical connection to that database. This includes network access to the database server (check your firewall when in doubt), a JDBC database driver (for PostgreSQL, it is supplied within the tool) and a database account that was granted the right to write to the required i2b2 project tables. If you used the i2b2 wizard to create a project, you already provided the credentials.

PostgreSQL is by default not accessible from computers other than localhost. That means, if you want to connect to a PostgreSQL database from your local computer using the IMT, and i2b2 and PostgreSQL are running within the VM (or on a server), you need to configure PostgreSQL. First, you need to make PostgreSQL listen on all network interfaces:

In postgresql.conf: listen_addresses = '*'

Second, you need to specify the host that are allowed to connect to PostgreSQL.

In pg_hba.conf: host all all md5 where your IP address is

The location of the configuration files varies depending on your platform. For the IDRT VM it is   /etc/postgresql/9.3/main/.

In cases of problems, download and install DbVisualizer Free, then try to create a database connection with the same values as entered in the IMT. DbVisualizer is also a Java application that uses JDBC for database connection. It allows to ping the server and its (read) permissions on connect.

If problems persist with DbVisualizer, it is most likely an issue outside the scope of the IMT.

Installation and Configuration

Download the zip file suitable for your operating system and extract it into a program folder.

Loading and transforming large amounts of data might require more memory than Java is able to allocate by default. It is recommended to assign additional memory by editing the configuration file IDRT IMT.ini and set:

  1. Initial memory allocation (Default: -Xms512m)
  2. Maximum memory allocation (Default: -Xmx1024m)

to higher values.

Finally, run IDRT IMT.exe (Windows) or IDRT IMT (Linux).