org.molgenis.omx.biobankconnect.utils

Class PhenoToOmxConvertor

java.lang.Object

org.molgenis.omx.biobankconnect.utils.PhenoToOmxConvertor

public class PhenoToOmxConvertor
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
PhenoToOmxConvertor(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)
org.molgenis.omx.biobankconnect.utils.AbstractOmxConvertor.UniqueCategory	copyCategoryContent(org.molgenis.omx.biobankconnect.utils.AbstractOmxConvertor.UniqueCategory category)
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

PhenoToOmxConvertor

public PhenoToOmxConvertor(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

copyCategoryContent

public org.molgenis.omx.biobankconnect.utils.AbstractOmxConvertor.UniqueCategory copyCategoryContent(org.molgenis.omx.biobankconnect.utils.AbstractOmxConvertor.UniqueCategory category)

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)