i2b2 Mapped Importer

Java program to take input from various sources and load it into i2b2.

Sources

The aim is to allow any type of source to be used that comes in a per patient format. For example, a CSV file with a row per patient, an XML file with a node per patient, a set of XML files with one per patient, or a database query with a row per patient.

Multiple rows (etc) can be supplied for a single patient.

Outputs

The data can be outputted as either an i2b2 PDO XML file or loaded directlt into an i2b2 database.

Settings

The source and output used is defined is a YAML file. By default this file is called settings.yaml in the application root directory, but the setings file path can be defined using the -s=xxx or --settingsFilePath=xxx command line arguments.

The settings that can be defined are dataSource and output. Both settings have a field called type that defines the class used to as a source or output processor. The further fields are specific for the type specified.

Here is an example settings file:

output:
 type: uk.org.briccs.onyxmappedexport2pdo.output.mssql.MsSqlOutput
 server: Server Name
 instance: Instance Name
 database: Database Name
 username: Username
 password: Password
dataSource:
 type: uk.org.briccs.onyxmappedexport2pdo.onyx.OnyxDataSourceSet
 export_directory: data

Mapping