= 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:
{{{#!yaml
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