au.csiro.ontology.importer.rf2

Class RF2Importer

java.lang.Object

au.csiro.ontology.importer.BaseImporter

au.csiro.ontology.importer.rf2.RF2Importer

All Implemented Interfaces:

IImporter

public class RF2Importer
extends BaseImporter

Imports ontologies specified in RF2 format into the internal representation.

Author:

Alejandro Metke

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	RF2Importer.OntologyBuilder Class that knows how to build an Ontology from a set of RF2 files.
protected class	RF2Importer.RoleValuePair Represents a role-value pair.

Nested classes/interfaces inherited from class au.csiro.ontology.importer.BaseImporter

BaseImporter.ImportEntry, BaseImporter.Module

Field Summary

Fields

Modifier and Type	Field and Description
protected Queue<RF2Input>	inputs Queue with the inputs to process.
protected List<String>	problems List of problems found while importing.

Constructor Summary

Constructors

Constructor and Description
RF2Importer(Collection<Input> inputs) Imports a set of ontologies using the supplied configuration object.
RF2Importer(RF2Input input) Imports an ontology using the supplied configuration object.

Method Summary

Methods

Modifier and Type	Method and Description
protected VersionRows	getBundle(BaseImporter.ImportEntry entry) Returns a VersionRows object for an ImportEntry.
protected Concept	getConcept(String id, Map<String,Concept> ci)
protected NamedFeature	getFeature(String id, Map<String,NamedFeature> fi)
protected Map<String,Set<Version>>	getModuleVersionsToLoad(RF2Input in) Determines which modules and versions should be loaded based on the Inputs object.
protected RF2Importer.OntologyBuilder	getOntologyBuilder(VersionRows vr, String rootModuleId, String rootModuleVersion, Map<String,String> metadata) Hook method for subclasses to override.
Iterator<Ontology>	getOntologyVersions(IProgressMonitor monitor) There are several models used to represent ontologies that have been adopted by different groups.
List<String>	getProblems() Returns a list of problems that happened during the import process.
protected NamedRole	getRole(String id, Map<String,NamedRole> ri)
protected Set<Set<RF2Importer.RoleValuePair>>	groupRoles(List<String[]> groups)
protected void	loadConceptRows(Map<String,String> modMap, Map<String,ConceptRow> conceptMap, InputStream inputStream)
protected IModuleDependencyRefset	loadModuleDependencies(RF2Input input) Loads all the module dependency information from all RF2 inputs into a single IModuleDependencyRefset.
protected <R extends RefsetRow> void	loadReferenceSet(RF2Input input, String refsetFile, Map<String,String> modMap, Map<String,R> refsetMap, au.csiro.ontology.importer.rf2.IRefsetFactory<R> factory)
protected void	loadRelationshipRows(Map<String,String> modMap, Map<String,RelationshipRow> relationshipMap, InputStream inputStream)
protected void	populateCDs(Map<String,List<String[]>> cdMap, String referencedComponentId, String featureId, String operator, String value, String unit) Populates concrete domains information.
protected void	populateChildren(String src, String tgt, Map<String,Set<String>> children)
protected void	populateParent(String src, String tgt, Map<String,Set<String>> parents)
protected void	populateRels(String comp, String src, String role, String tgt, String group, Map<String,List<String[]>> rels)
protected void	populateRoleDef(String code, String rightId, String parentRole, Map<String,Map<String,String>> roles)
protected void	populateRoles(Set<String> roles, String parentSCTID, String rightIdentityIds, Map<String,Set<String>> children, Map<String,Map<String,String>> rolesMap)

Methods inherited from class java.lang.Object

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

Field Detail

problems

protected final List<String> problems

List of problems found while importing.

inputs

protected final Queue<RF2Input> inputs

Queue with the inputs to process.

Constructor Detail

RF2Importer

public RF2Importer(RF2Input input)

Imports an ontology using the supplied configuration object.

Parameters:

input -

RF2Importer

public RF2Importer(Collection<Input> inputs)

Imports a set of ontologies using the supplied configuration object.

Parameters:

inputs -

Method Detail

getOntologyVersions

public Iterator<Ontology> getOntologyVersions(IProgressMonitor monitor)
                                       throws ImportException

Description copied from interface: IImporter

There are several models used to represent ontologies that have been adopted by different groups. In this implementation a model based on SNOMED's RF2 format is used because it contains features that are not available in other formats.

An ontology in RF2 maps to a set of interdependent modules. This method returns all the ontologies found in a set of files. Implementations of importers for other file formats can simply return a single ontology.

If the files contain related modules then all of them are returned as a single ontology. This method returns an iterator that allows importing each ontology version.

Parameters:

monitor - A progress monitor.

Returns:

An interator that allows importing one ontology version at a time.

Throws:

ImportException - if a problem occurs when importing the ontologies.

getProblems

public List<String> getProblems()

Description copied from interface: IImporter

Returns a list of problems that happened during the import process. This method should be called after an ImportException is thrown to get a detailed list of problems.

Returns:

loadModuleDependencies

protected IModuleDependencyRefset loadModuleDependencies(RF2Input input)
                                                  throws ImportException

Loads all the module dependency information from all RF2 inputs into a single IModuleDependencyRefset.

Returns:

Throws:

ImportException

getModuleVersionsToLoad

protected Map<String,Set<Version>> getModuleVersionsToLoad(RF2Input in)

Determines which modules and versions should be loaded based on the Inputs object. Returns a Map with the module ids as keys and the set of versions to import as values.

Returns:

populateCDs

protected void populateCDs(Map<String,List<String[]>> cdMap,
               String referencedComponentId,
               String featureId,
               String operator,
               String value,
               String unit)

Populates concrete domains information.

Parameters:

cdMap -

referencedComponentId -

featureId -

operator -

value -

unit -

loadReferenceSet

protected <R extends RefsetRow> void loadReferenceSet(RF2Input input,
                                          String refsetFile,
                                          Map<String,String> modMap,
                                          Map<String,R> refsetMap,
                                          au.csiro.ontology.importer.rf2.IRefsetFactory<R> factory)
                         throws ImportException

Throws:

ImportException

getBundle

protected VersionRows getBundle(BaseImporter.ImportEntry entry)
                         throws ImportException

Returns a VersionRows object for an ImportEntry.

Parameters:

entry -

Returns:

Throws:

ImportException

loadRelationshipRows

protected void loadRelationshipRows(Map<String,String> modMap,
                        Map<String,RelationshipRow> relationshipMap,
                        InputStream inputStream)
                             throws IOException

Throws:

IOException

loadConceptRows

protected void loadConceptRows(Map<String,String> modMap,
                   Map<String,ConceptRow> conceptMap,
                   InputStream inputStream)
                        throws IOException,
                               UnsupportedEncodingException

Throws:

IOException

UnsupportedEncodingException

getConcept

protected Concept getConcept(String id,
                 Map<String,Concept> ci)

getRole

protected NamedRole getRole(String id,
                Map<String,NamedRole> ri)

getFeature

protected NamedFeature getFeature(String id,
                      Map<String,NamedFeature> fi)

populateParent

protected void populateParent(String src,
                  String tgt,
                  Map<String,Set<String>> parents)

populateChildren

protected void populateChildren(String src,
                    String tgt,
                    Map<String,Set<String>> children)

populateRels

protected void populateRels(String comp,
                String src,
                String role,
                String tgt,
                String group,
                Map<String,List<String[]>> rels)

populateRoles

protected void populateRoles(Set<String> roles,
                 String parentSCTID,
                 String rightIdentityIds,
                 Map<String,Set<String>> children,
                 Map<String,Map<String,String>> rolesMap)

populateRoleDef

protected void populateRoleDef(String code,
                   String rightId,
                   String parentRole,
                   Map<String,Map<String,String>> roles)

groupRoles

protected Set<Set<RF2Importer.RoleValuePair>> groupRoles(List<String[]> groups)

getOntologyBuilder

protected RF2Importer.OntologyBuilder getOntologyBuilder(VersionRows vr,
                                             String rootModuleId,
                                             String rootModuleVersion,
                                             Map<String,String> metadata)

Hook method for subclasses to override.

Parameters:

vr -

rootModuleId -

rootModuleVersion -

includeInactiveAxioms -

Returns: