IDRT - Integrated Data Repository Toolkit
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IDRT Import and Mapping Tool (IDRT IMT)

When you first start the IMT, you will see a window similar to the screen dump below. Most windows within the IMT don't contain entries. IMT is an Eclipse-based application, so we will stick to their terminology, calling these windows "views".

Image Added

Info

The different Views views of the Software are explained here.

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Server

Info

A Target software are explained in detail in a separate wiki page.

First, you will have to define at least one staging server. A staging server is a connection to a database that hosts one or more i2b2 projects. As the name suggests, it will be the destination for data imports and other modifications.

When you add a staging server, you have to provide a number of parameters. Server configurations can be modified later and even exported/imported for backup.

If you click on a staging server, the IMT will show all i2b2 projects that the database account can read. i2b2 projects correspond to at least one database or schema and start with a leading string "I2B2".

Reference

Menu File

Exits the program.

Menu Server

Info

A Staging Server is an i2b2-Database-Server , that is used to upload data to.
A Source Datasource Server is any Database-Server , that is used to extract data from.

Name

Description

Add Staging I2B2Server...

Creates a new Staging Server.

Edit Staging I2B2Server...

Edits the selected Staging ServerStaging Server.

Delete Staging I2B2Server

Deletes the Deletes the selected Staging ServerStaging Server.

New Datasource ServerDatasource Server...

Creates a new Datasource ServerDatasource Server.

Edit Datasource ServerDatasource Server...

Edits the selected Datasource Server.

Delete Datasource Server Datasource Server

Deletes the Deletes the selected Datasource ServerDatasource Server.

Import Staging I2B2Server...

Lets Let's you import a previously exported Staging ServerStaging Server.

Export Staging I2B2Server...

Lets Let's you export the selected Staging ServerStaging Server.

Target i2b2

Here you can create a new Instance of a Target i2b2. You have to load the Ontology first.

Info

It's a good idea to backup staging servers regularly. Additionally, export/import is useful for copying the configuration to another instance of the IMT.

Menu Options

Name

Description

Default

Target Folder Name:

The Root root i2b2 folder name , where your Data gets data get imported to.

Patientdata

PIDGen URL

The URL , where your TMF PIDGenerator PID generator is running (rarely used).

 

Export Log Location

The Location location where the Log log is stored after exporting it, e.g. /home/idrt/IDRTworkspace/logs/export.log

 

Syso Log

Activates extended Loggin logging

Unchecked

Syso Log Location

The Location location where the Syso Log sys log is stored.

 

Filter Projects

Filters i2b2 projects to exclude e.g. i2b2pm, i2b2hive, etc

Checked

Hide Temporary/Secondary Tables

Only for Oracle: Hides hides temporary/secondary tables.

Unchecked

Show Total Number of Patients

Shows the c_totalnum in the Mapping Editor

Checked

Guess-Rows

The number of rows the CSV Importer importer should check to guess the datatypes of the columns.

50

   
Note

In some cases, specifying a Syso Log Location results in an empty and non-responding import browser view after restart. Closing the import browser view and reopening the view in the view menu solves the problem.

Menu Views

Show View

Here you find all IDRT Views. If you have closed a View, you can restore it here.

...

Name

Description

PerspectiveExpert

Shows all available Views (default).

PerspectiveSimple

Shows only important Views.

Menu Help

Name

Description

Documentation

Links to this wiki.

Report A Bug

Links to the IDRT GitHub.

About

Shows the About Texttext.

Install New Software...

Opens a Window window where you can install new RCP Pluginsplugins.

Update Software...

Updates the software.