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When you first start the IMT, you will see a window similar to the screendump 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".
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First, you will have to define at least one target staging server. A target 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 target staging server, you have to provide a number of parameters. Server configurations can be modified later and even exported/imported for backup.
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Target server, once they are created, appear in "Staging I2B2 Server". |
If you click on a target 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
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A Target Staging Server is an i2b2-Database-Server , that is used to upload data to. |
Name | Description |
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Add Staging I2B2Server... | Creates a new Staging Server. |
Edit Staging I2B2Server... | Edits the selected Staging Server. |
Delete Staging I2B2Server | Deletes the selected Staging Server. |
New Datasource Server... | Creates a new Datasource Server. |
Edit Datasource Server... | Edits the selected Datasource Server. |
Delete Datasource Server | Deletes the selected Datasource Server. |
Import Staging I2B2Server... | Lets Let's you import a previously exported Staging Server. |
Export Staging I2B2Server... | Lets Let's you export the selected Staging Server. |
Target i2b2
Here you can create a new Instance of a Target i2b2. You have to load the Ontology first.
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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 |
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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). |
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Export Log Location | The Location location where the Log log is stored after exporting it, e.g. /home/idrt/IDRTworkspace/logs/export.log |
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Syso Log | Activates extended Loggin logging | Unchecked |
Syso Log Location | The Location location where the Syso Log sys log is stored. |
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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 |
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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.
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Name | Description |
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PerspectiveExpert | Shows all available Views (default). |
PerspectiveSimple | Shows only important Views. |
Menu Help
Name | Description |
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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. |
