org.molgenis.omx.biobankconnect.utils

Class OpalToOmxConvertor

java.lang.Object

org.molgenis.omx.biobankconnect.utils.OpalToOmxConvertor

public class OpalToOmxConvertor
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
Map<String,org.molgenis.omx.biobankconnect.utils.AbstractOmxConvertor.UniqueCategory>	categoryInfo
Map<String,List<org.molgenis.omx.biobankconnect.utils.AbstractOmxConvertor.UniqueCategory>>	featureCategoryLinks
Map<String,List<String>>	protocolFeatureLinks
String	studyName
Map<String,org.molgenis.omx.biobankconnect.utils.AbstractOmxConvertor.UniqueVariable>	variableInfo

Constructor Summary

Constructors

Constructor and Description
OpalToOmxConvertor(String studyName, String filePath)

Method Summary

Methods

Modifier and Type	Method and Description
void	collectCategoryInfo(RepositoryCollection repositoryCollection)
void	collectProtocolInfo(RepositoryCollection repositoryCollection)
void	collectVariableInfo(RepositoryCollection repositoryCollection)
String	createCategoryIdentifier(String categoryName)
String	createFeatureIdentifier(String featureName)
String	createProtocolIdentifier(String protocolTname)
static void	main(String[] args)
void	start(String fileString)
void	writeToPhenoFormat(WritableFactory writer)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

featureCategoryLinks

public Map<String,List<org.molgenis.omx.biobankconnect.utils.AbstractOmxConvertor.UniqueCategory>> featureCategoryLinks

protocolFeatureLinks

public Map<String,List<String>> protocolFeatureLinks

variableInfo

public Map<String,org.molgenis.omx.biobankconnect.utils.AbstractOmxConvertor.UniqueVariable> variableInfo

categoryInfo

public Map<String,org.molgenis.omx.biobankconnect.utils.AbstractOmxConvertor.UniqueCategory> categoryInfo

studyName

public String studyName

Constructor Detail

OpalToOmxConvertor

public OpalToOmxConvertor(String studyName,
                  String filePath)
                   throws IOException,
                          org.apache.poi.openxml4j.exceptions.InvalidFormatException

Throws:

IOException

org.apache.poi.openxml4j.exceptions.InvalidFormatException

Method Detail

collectProtocolInfo

public void collectProtocolInfo(RepositoryCollection repositoryCollection)
                         throws IOException

Throws:

IOException

collectVariableInfo

public void collectVariableInfo(RepositoryCollection repositoryCollection)
                         throws IOException

Throws:

IOException

collectCategoryInfo

public void collectCategoryInfo(RepositoryCollection repositoryCollection)
                         throws IOException

Throws:

IOException

main

public static void main(String[] args)
                 throws IOException,
                        org.apache.poi.openxml4j.exceptions.InvalidFormatException

Parameters:

args -

Throws:

IOException

org.apache.poi.openxml4j.exceptions.InvalidFormatException

start

public void start(String fileString)
           throws IOException,
                  org.apache.poi.openxml4j.exceptions.InvalidFormatException

Throws:

IOException

org.apache.poi.openxml4j.exceptions.InvalidFormatException

writeToPhenoFormat

public void writeToPhenoFormat(WritableFactory writer)
                        throws IOException

Throws:

IOException

createFeatureIdentifier

public String createFeatureIdentifier(String featureName)

createProtocolIdentifier

public String createProtocolIdentifier(String protocolTname)

createCategoryIdentifier

public String createCategoryIdentifier(String categoryName)