i2b2 - Mapped Importer Data Sources

Below are the settings for the specific Data Sources for the i2b2 Mapped Importer

MsSqlDataSourceSet

Settings

• type: uk.org.briccs.i2b2mappedimport.input.sql.MsSqlDataSourceSet
• Server: The name of the SQL Server
• instance: The name of the SQL Server instance
• database: The name of the SQL Server database
• username: The username required to log on
• password: The password for the above user
• query: The query used to extract the patient data

The query should return a row for each patient, and contain a patient identifier.

Mapping Source

The source attribute list for mappings should contain one item: the name of the field from the query.

MySqlDataSourceSet

Settings

• type: uk.org.briccs.i2b2mappedimport.input.sql.MySqlDataSourceSet
• Server: The name of the SQL Server
• database: The name of the SQL Server database
• username: The username required to log on
• password: The password for the above user
• query: The query used to extract the patient data

The query should return a row for each patient, and contain a patient identifier.

Mapping Source

The source attribute list for mappings should contain one item: the name of the field from the query.

CsvDataSourceSet

Settings

• type: uk.org.briccs.i2b2mappedimport.input.csv.CsvDataSourceSet
• filename: The filename of the CSV file
• field_separator: (Optional) The character that separates fields in a record. The default is a comma.
• quote_character: (optional) The character used to surround string values. Use of the quote character around strings is optional, but strings cannot then include field or row separator characters. The default is a double quote.
• has_headers: (optional) Whether to use the first row of the CSV file as the column headers. The default if false.

Mapping Source

The source attribute list for mappings should contain one item, which identifies the field within the CSV.

If headers are not specified, fields are identified by column number starting from "1". Column numbers should be specified in the mapping file enclosed within double-quotes. For example:

    source:
     - "1"

If headers are specified, fields should be identified by the column header text with leading and trailing spaces removed.

OnyxDataSourceSet

Settings

• type: uk.org.briccs.i2b2mappedimport.onyx.OnyxDataSourceSet
• export_directory: The directory where the exported questionnaires are stored

This is a data source written to import questionnaire data exported from the Onyx questionnaire tool.

The tool exports a set of questionnaires into a series of sub-directories, each directory containing the results for all patients for one questionnaire. Each questionnaire folder contains a file called Entities.xml that maps patients to numbered XML files within the same directory (for example 00000001.xml).

Mapping Source

The source attribute list for mappings should contain two items. The first is the name of the questionnaire folder, the second is the name of the variable element within the patient's numbered XML file.