au.csiro.ontology.importer.rf1

Class RF1Importer

java.lang.Object

au.csiro.ontology.importer.BaseImporter

au.csiro.ontology.importer.rf1.RF1Importer

All Implemented Interfaces:

IImporter

public class RF1Importer
extends BaseImporter

Transforms the native RF1 files used in SNOMED into the internal representation. Because of the limitations of the RF1 format, this importer does not handle versions.

Author:

Alejandro Metke

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	RF1Importer.RoleValuePair

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 Map<String,Set<String>>	children
protected InputStream	conceptsFile
protected SnomedMetadata	metadata Contains the meta-data necessary to transform the distribution form of SNOMED into a DL model.
protected Map<String,Set<String>>	parents
protected Map<String,String>	primitive
protected List<String>	problems
protected InputStream	relationshipsFile
protected Map<String,List<String[]>>	rels
protected Map<String,Map<String,String>>	roles
protected String	version

Constructor Summary

Constructors

Constructor and Description
RF1Importer(InputStream conceptsFile, InputStream relationshipsFile, String version) Creates a new RF1Importer.

Method Summary

Modifier and Type	Method and Description
void	clear()
VersionRows	extractVersionRows() Processes the raw RF1 files and generates a VersionRows.
SnomedMetadata	getMetadata()
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 Set<Set<RF1Importer.RoleValuePair>>	groupRoles(List<String[]> groups)
protected void	populateChildren(String src, String tgt)
protected void	populateParent(String src, String tgt)
protected void	populateRels(String src, String role, String tgt, String group)
protected void	populateRoleDef(String code, String rightId, String parentRole)
protected void	populateRoles(Set<String> roles, String parentSCTID)
boolean	usesConcreteDomains()

Methods inherited from class java.lang.Object

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

Field Detail

conceptsFile

protected final InputStream conceptsFile

relationshipsFile

protected final InputStream relationshipsFile

version

protected final String version

metadata

protected SnomedMetadata metadata

Contains the meta-data necessary to transform the distribution form of SNOMED into a DL model.

problems

protected final List<String> problems

primitive

protected final Map<String,String> primitive

parents

protected final Map<String,Set<String>> parents

children

protected final Map<String,Set<String>> children

rels

protected final Map<String,List<String[]>> rels

roles

protected final Map<String,Map<String,String>> roles

Constructor Detail

RF1Importer

public RF1Importer(InputStream conceptsFile,
                   InputStream relationshipsFile,
                   String version)

Creates a new RF1Importer.

Parameters:

conceptsFile -

descriptionsFile -

relationshipsFile -

version - The version of this ontology.

Method Detail

getOntologyVersions

public Iterator<Ontology> getOntologyVersions(IProgressMonitor monitor)

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.

populateParent

protected void populateParent(String src,
                              String tgt)

populateChildren

protected void populateChildren(String src,
                                String tgt)

populateRels

protected void populateRels(String src,
                            String role,
                            String tgt,
                            String group)

populateRoles

protected void populateRoles(Set<String> roles,
                             String parentSCTID)

populateRoleDef

protected void populateRoleDef(String code,
                               String rightId,
                               String parentRole)

groupRoles

protected Set<Set<RF1Importer.RoleValuePair>> groupRoles(List<String[]> groups)

clear

public void clear()

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:

usesConcreteDomains

public boolean usesConcreteDomains()

extractVersionRows

public VersionRows extractVersionRows()

Processes the raw RF1 files and generates a VersionRows.

getMetadata

public SnomedMetadata getMetadata()