edu.emory.cci.aiw.i2b2etl.dest.metadata

Class Metadata

java.lang.Object

edu.emory.cci.aiw.i2b2etl.dest.metadata.Metadata

public final class Metadata
extends Object

Maintains the concepts for the data being loaded into i2b2. The init() method must be called after constructing an instance of this method before using any other methods.

Method Summary

Modifier and Type	Method and Description
void	addModifierRoot(Concept concept)
ProviderDimension	addProvider(ProviderDimension providerDimension)
void	addToIdCache(Concept concept)
String[]	extractDerived()
Concept[]	getAllRoots()
Concept	getConceptRoot()
Data	getDataSection()
FolderSpec[]	getFolderSpecs()
ConceptId	getFromConceptIdCache(List<Object> key)
Concept	getFromIdCache(ConceptId conceptId)
Concept	getFromIdCache(String propId, String propertyName, org.protempa.proposition.value.Value value)
org.arp.javautil.sql.ConnectionSpec	getMetaConnectionSpec() Returns connection information for the i2b2 metadata schema.
Concept[]	getModifierRoots()
org.protempa.PropositionDefinition[]	getPhenotypeDefinitions()
Settings	getSettings()
String	getSourceSystemCode() Returns the source system code used for concepts created by this query results handler.
Concept	newConcept(ConceptId conceptId, String conceptCodePrefix, String sourceSystemCode)
void	putInConceptIdCache(List<Object> key, ConceptId conceptId)

Methods inherited from class java.lang.Object

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

Method Detail

getMetaConnectionSpec

public org.arp.javautil.sql.ConnectionSpec getMetaConnectionSpec()

Returns connection information for the i2b2 metadata schema.

Returns:

connection information for the i2b2 metadata schema, or null if no metadata schema connection information was provided in the destination configuration.

getSettings

public Settings getSettings()

getDataSection

public Data getDataSection()

getConceptRoot

public Concept getConceptRoot()

addModifierRoot

public void addModifierRoot(Concept concept)

getModifierRoots

public Concept[] getModifierRoots()

getAllRoots

public Concept[] getAllRoots()

getPhenotypeDefinitions

public org.protempa.PropositionDefinition[] getPhenotypeDefinitions()

getSourceSystemCode

public String getSourceSystemCode()

Returns the source system code used for concepts created by this query results handler.

Returns:

a String, maximum 50 characters. Guaranteed not null.

getFolderSpecs

public FolderSpec[] getFolderSpecs()

addProvider

public ProviderDimension addProvider(ProviderDimension providerDimension)
                              throws InvalidConceptCodeException,
                                     SQLException

Throws:

InvalidConceptCodeException

SQLException

getFromIdCache

public Concept getFromIdCache(ConceptId conceptId)

getFromIdCache

public Concept getFromIdCache(String propId,
                              String propertyName,
                              org.protempa.proposition.value.Value value)

addToIdCache

public void addToIdCache(Concept concept)

putInConceptIdCache

public void putInConceptIdCache(List<Object> key,
                                ConceptId conceptId)

getFromConceptIdCache

public ConceptId getFromConceptIdCache(List<Object> key)

extractDerived

public String[] extractDerived()
                        throws org.protempa.KnowledgeSourceReadException

Throws:

org.protempa.KnowledgeSourceReadException

newConcept

public Concept newConcept(ConceptId conceptId,
                          String conceptCodePrefix,
                          String sourceSystemCode)
                   throws OntologyBuildException

Throws:

OntologyBuildException