Changes between Version 5 and Version 6 of i2b2 Mapped Importer

Timestamp:

10/03/13 15:26:37 (11 years ago)

Author:

Richard Bramley

Comment:

--

i2b2 Mapped Importer

@@ -13 +13 @@
 
 == 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 source and output to 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.
+The settings that can be defined are {{{dataSource}}} and {{{output}}}.  Both settings have a field called {{{type}}} that defines the class to be used as a source or output processor.  The further fields are specific for the {{{type}}} specified.
 
 Here is an example settings file:
@@ -30 +30 @@
  export_directory: data
 }}}
+
+=== Available !DataSources
+
+There are three data sources at present, with others to be written as the need arises. The available ones are:
+
+* !MsSqlDataSourceSet
+* !MySqlDataSourceSet
+* !OnyxDataSourceSet
+
+==== !MsSqlDataSourceSet
+
+Settings
+
+* {{{type}}}: {{{uk.org.briccs.onyxmappedexport2pdo.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.
+
+==== !MySqlDataSourceSet
+
+Settings
+
+* {{{type}}}: {{{uk.org.briccs.onyxmappedexport2pdo.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.
+
+==== !OnyxDataSourceSet
+
+Settings
+
+* {{{type}}}: uk.org.briccs.onyxmappedexport2pdo.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 (see later) 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.
+
 == Mapping
 
@@ -58 +110 @@
 * !DataSourceDateField
 * !YearOnlyDateField
-