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Retrieving Services
LexEVS provides a number of services which are retrievable through the LexBIGService interface and the LexEvsServiceLocator interface. We list here a small sample including the more commonly used interfaces.
LexBIGService
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HistoryService
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<source lang LexBIGService lbsv = java> <nowiki> LexBIGService lbsv = LexBIGServiceImpl.LexBIGServiceImpl.defaultInstance(); try { HistoryService historSvc = lbsv.getHistoryService(codingScheme);< } catch (LBException e) { e.printStackTrace(); } </nowiki> </source> |
LexBIGServiceManager
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<source lang = java> <nowiki> //LexBIG Service Manager can accept credentials validation to //preserve service security. LexBIGService lbsv = LexBIGServiceImpl.defaultInstance(); try { LexBIGServiceManager svcManager = lbsv.getServiceManager(credentials); } catch (LBException e) { e.printStackTrace(); } </nowiki> </source> |
LexEVSServiceMetaData
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<source lang = java> <nowiki> // User safe service meta data query interface. LexBIGService lbsv = LexBIGServiceImpl.defaultInstance(); try { LexBIGServiceMetadata svcMetaData = lbsv.getServiceMetadata(); } catch (LBException e) { e.printStackTrace(); } </nowiki> </source> |
LexEvsServiceLocator
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SystemResourceService
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<source lang = java> <nowiki> // The system resource service is commonly wrapped in LexBIGServiceManager calls // and as such it prevents unauthorized users from removing coding schemes from the service. SystemResourceService systemResourceService = LexEvsServiceLocator.getInstance().getSystemResourceService(); // must be marked as inactive or pending before delete. systemResourceService.removeCodingSchemeResourceFromSystem( codingSchemeVersionReference.getCodingSchemeURN(), codingSchemeVersionReference.getCodingSchemeVersion()); </nowiki> </source> |
LexEvsIndexOperations
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Some index operations can Some index operations can be accomplished using the interface returned from the LexEvsServiceLocator.
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<source lang = java> <nowiki> boolean isSingleIndex = LexEvsServiceLocator.getInstance().getSystemResourceService().getSystemVariables().getIsSingleIndex(); if(! isSingleIndex) { throw new RuntimeException("Lucene Clean Up can only be executed in Single Index Mode."); } try { List<AbsoluteCodingSchemeVersionReference> expectedList = new ArrayList<AbsoluteCodingSchemeVersionReference>(); for(RegistryEntry entry : LexEvsServiceLocator.getInstance().getRegistry().getAllRegistryEntriesOfType(ResourceType.CODING_SCHEME)) { AbsoluteCodingSchemeVersionReference ref = new AbsoluteCodingSchemeVersionReference(); ref.setCodingSchemeURN(entry.getResourceUri()); ref.setCodingSchemeVersion(entry.getResourceVersion()); expectedList.add(ref); } LexEvsServiceLocator.getInstance().getLexEvsIndexOperations().cleanUp(expectedList, reindexMissing); } catch (Exception e) { throw new RuntimeException(e); } </nowiki> </source> |
EntityIndexService
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Others operations require using the IndexServiceManager to retrieve a more specific index service
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<source lang = java> <nowiki> AbsoluteCodingSchemeVersionReference acsvr = new AbsoluteCodingSchemeVersionReference(); acsvr.setCodingSchemeURN(css.getCodingSchemeURI()); acsvr.setCodingSchemeVersion(css.getRepresentsVersion()); LexEvsServiceLocator.getInstance(). getIndexServiceManager(). getEntityIndexService().dropIndex(acsvr); </nowiki> </source> |
LexBIGService Administration Methods
We've shown how the LexBIGService interface can retrieve other services, but it also provides some user safe administrative functions. These functions provide users with information about the service and overlap general user API functions, since they give users information about how to use the service.
Getting Filter Extensions
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<source lang=java> <nowiki> // LexEVS has no built-in filter extensions. This method call // will only return filters users have created themselves. LexBIGService lbsv = LexBIGServiceImpl.defaultInstance(); Enumeration<? extends ExtensionDescription> extDesc = lbsv.getFilterExtensions().enumerateExtensionDescription(); while(extDesc.hasMoreElements()){ System.out.println(extDesc.nextElement().getName()); } </nowiki> </source> |
Getting Sort Algorithms
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<source lang=java> <nowiki> LexBIGService lbsv = LexBIGServiceImpl.defaultInstance(); Enumeration<? extends SortDescription> sortDesc = lbsv.getSortAlgorithms(null).enumerateSortDescription(); while(sortDesc.hasMoreElements()){ System.out.println(sortDesc.nextElement().getName()); } </nowiki> </source> |
Getting Match Algorithms
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<source lang=java> <nowiki> LexBIGService lbsv = LexBIGServiceImpl.defaultInstance(); Enumeration<? extends ModuleDescription> modDesc = lbsv.getMatchAlgorithms().enumerateModuleDescription(); while(modDesc.hasMoreElements()){ System.out.println(modDesc.nextElement().getName()); } </nowiki> </source> |
Sample Output:
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SpellingErrorTolerantSubStringSearch
StemmedLuceneQuery
literalContains
startsWith
nonLeadingWildcardLiteralSubString
literal
WeightedDoubleMetaphoneLuceneQuery
literalSubString
DoubleMetaphoneLuceneQuery
RegExp
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Getting Generic Extensions
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<source lang=java> <nowiki> LexBIGService lbsv = LexBIGServiceImpl.defaultInstance(); Enumeration<? extends ExtensionDescription> extDesc = lbsv.getGenericExtensions().enumerateExtensionDescription(); while(extDesc.hasMoreElements()){ System.out.println(extDesc.nextElement().getName()); } </nowiki> </source> |
Sample Output:
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SupplementExtension
LexBIGServiceConvenienceMethods
ApproxNumOfConceptsPostProcessor
MappingExtension
SupportedAttributePostProcessor
OntologyFormatAddingPostProcessor
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Getting Service Information on all Schemes
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<source lang=java> <nowiki> LexBIGService lbsv = LexBIGServiceImpl.defaultInstance(); try { CodingSchemeRenderingList schemes = lbsv.getSupportedCodingSchemes(); for (CodingSchemeRendering csr : schemes.getCodingSchemeRendering()) { // Separator ... System.out.println("============================="); CodingSchemeSummary css = csr.getCodingSchemeSummary(); CodingScheme cs = lbsv.resolveCodingScheme(css.getCodingSchemeURI(), Constructors .createCodingSchemeVersionOrTagFromVersion(css.getRepresentsVersion())); System.out.println(ObjectToString.toString(cs, "", 80));} } catch (LBException e) { // TODO Auto-generated catch block e.printStackTrace(); } </nowiki> </source> |
Sample Output Excerpt
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CodingScheme
Name: MDR12_1_TO_CST95
Formal Name: MDR12_1_TO_CST95
URI: urn:oid:CL413321.MDR.CST
Approximate Number of Concepts: 0
Default Language: null
Represents Version: 200909
Local Names:
Array of 1 items:
MDR12_1_TO_CST95
Mappings:
MappingsSupportedAssociations:
Array of 1 items:
SupportedAssociation
Local ID: mapped_to
Content: mapped_to
AssociationEntity CodingScheme: null
AssociationEntity EntityCodeNamespace: null
AssociationEntity EntityCode: null
SupportedCodingSchemes: ...................................................
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Getting Single Coding Scheme Information
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<source lang=java> <nowiki> public void run(){ String codingScheme = "amino-acid.owl"; CodingSchemeVersionOrTag versionOrTag = new CodingSchemeVersionOrTag(); versionOrTag.setVersion("1.2"); LexBIGService lbsv = LexBIGServiceImpl.defaultInstance(); try { CodingScheme cs = lbsv.resolveCodingScheme(codingScheme, versionOrTag ); System.out.println(ObjectToString.toString(cs, "", 80)); } catch (LBException e) { // TODO Auto-generated catch block e.printStackTrace(); } </nowiki> </source> |
Output same as above preceding but for designated coding scheme only.
Getting a Coding Scheme's Copyright Content
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<source lang=java> <nowiki> String codingScheme = "amino-acid.owl"; CodingSchemeVersionOrTag versionOrTag = new CodingSchemeVersionOrTag(); versionOrTag.setVersion("1.2"); LexBIGService lbsv = LexBIGServiceImpl.defaultInstance(); try { String cpywrt = lbsv.resolveCodingSchemeCopyright(codingScheme, versionOrTag); System.out.println(cpywrt); } catch (LBException e) { // TODO Auto-generated catch block e.printStackTrace(); } </nowiki> </source> |
Output is unformatted text
LexBIGService Manager Methods
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These methods are generally not end user safe or access information in the system that is administrator specific in context. In general it should not be exposed to the end user.
Setting Coding Scheme Version Tag
Setting the Coding Scheme tag allows the system administrator to provide status tags or designate a preferred version of a given coding scheme for this terminology service.
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<source lang=java> <nowiki> AbsoluteCodingSchemeVersionReference codingSchemeVersion = new AbsoluteCodingSchemeVersionReference(); codingSchemeVersion.setCodingSchemeURN("http://www.co-ode.org/ontologies/amino-acid/2005/10/11 /amino-acid.owl"); codingSchemeVersion.setCodingSchemeVersion("1.0"); LexBIGService lbsv = LexBIGServiceImpl.defaultInstance(); try { LexBIGServiceManager lbsvm = lbsv.getServiceManager(null); // PRODUCTION tagged vocabularies are interpreted by LexEVS // to be the preferred version of the vocabulary. lbsvm.setVersionTag(codingSchemeVersion, "PRODUCTION"); } catch (LBException e) { // TODO Auto-generated catch block e.printStackTrace(); } </nowiki> </source> |
Activate Coding Scheme
The active designation for a coding scheme is required to enable query functionality for the contained entities and their relationships and properties.
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<source lang=java> <nowiki> AbsoluteCodingSchemeVersionReference codingSchemeVersion = new AbsoluteCodingSchemeVersionReference(); codingSchemeVersion.setCodingSchemeURN("http://www.co-ode.org/ontologies/amino-acid/2005/10/1/amino-acid.owl"); codingSchemeVersion.setCodingSchemeVersion("1.0"); LexBIGService lbsv = LexBIGServiceImpl.defaultInstance(); try { LexBIGServiceManager lbsvm = lbsv.getServiceManager(null); lbsvm.activateCodingSchemeVersion(codingSchemeVersion); } catch (LBException e) { // TODO Auto-generated catch block e.printStackTrace(); </nowiki> </source> |
Deactivate Coding Scheme
Allows administrator to restrict access to coding scheme metadata only.
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<sourceAbsoluteCodingSchemeVersionReference codingSchemeVersion lang=java> <nowiki> AbsoluteCodingSchemeVersionReference codingSchemeVersion = new AbsoluteCodingSchemeVersionReference(); codingSchemeVersion.setCodingSchemeURN("http://www.co-ode.org/ontologies/amino-acid/2005/10/1/amino-acid.owl"); codingSchemeVersion.setCodingSchemeVersion("1.0"); LexBIGService lbsv = LexBIGServiceImpl.defaultInstance(); try { LexBIGServiceManager lbsvm = lbsv.getServiceManager(null); lbsvm.deactivateCodingSchemeVersion(codingSchemeVersion, null); } catch (LBException e) { // TODO Auto-generated catch block e.printStackTrace(); </nowiki> </source> |
Remove Coding Scheme
Removes a coding scheme and it's its indexes from a terminology service.
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This is a slow, resource consuming activity when the service is configured for single table mode. |
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<source lang=java> <nowiki> AbsoluteCodingSchemeVersionReference codingSchemeVersion = new AbsoluteCodingSchemeVersionReference(); codingSchemeVersion.setCodingSchemeURN("http://www.co-ode.org/ontologies/amino-acid/2005/10/1 /amino-acid.owl"); codingSchemeVersion.setCodingSchemeVersion("1.0"); LexBIGService lbsv = LexBIGServiceImpl.defaultInstance(); try { LexBIGServiceManager lbsvm = lbsv.getServiceManager(null); lbsvm.removeCodingSchemeVersion(codingSchemeVersion); } catch (LBException e) { // TODO Auto-generated catch block e.printStackTrace(); { </nowiki> </source> |
Remove History Service
Remove a history service from the terminology service.
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<source lang=java> <nowiki> String codingScheme = "NCI Thesaurus"; LexBIGService lbsv = LexBIGServiceImpl.defaultInstance(); try { LexBIGServiceManager lbsvm = lbsv.getServiceManager(null); lbsvm.removeHistoryService(codingScheme); } catch (LBException e) { // TODO Auto-generated catch block e.printStackTrace(); } </nowiki> </source> |
Get Load Extensions
Allows a determination of available loaders by an administrator.
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<source lang=java> <nowiki> LexBIGService lbsv = LexBIGServiceImpl.defaultInstance(); try { LexBIGServiceManager lbsvm = lbsv.getServiceManager(null); Enumeration<? extends ExtensionDescription> extDesc = lbsvm.getLoadExtensions().enumerateExtensionDescription(); while(extDesc.hasMoreElements()){ System.out.println(extDesc.nextElement().getName()); } } catch (LBException e) { // TODO Auto-generated catch block e.printStackTrace(); } </nowiki> </source> |
Sample Output:
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NCIMetaHistoryLoader
OBOLoader
HL7Loader
ClaMLLoader
SemNetLoader
MrMap_Loader
MetaDataLoader
RadLexFramesLoader
TextLoader
NCIThesaurusHistoryLoader
OWLLoader
LexGrid_Loader
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Get Specific Loader
Returns a specific loader instance for use in loading the relevant source file.
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<source lang=java> <nowiki> LexBIGService lbs = LexBIGServiceImpl.defaultInstance(); LexBIGServiceManager lbsm = lbs.getServiceManager(null); LexGrid_Loader loader = (LexGrid_Loader) lbsm .getLoader(org.LexGrid.LexBIG.Impl.loaders.LexGridMultiLoaderImpl.name); loader.setCodingSchemeManifestURI(manifest); loader.load(source, false, true); </nowiki> </source> |
Get Extension Registry
Returns an extension registry service for all externally registered plugins to LexEVS. This provides similar functionality to the other registry retrieval, display and use and we won't repeat method examples here.
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<source lang=java> <nowiki> LexBIGServiceManager lbsvm = lbsv.getServiceManager(null); ExtensionRegistry registry = lbsvm.getExtensionRegistry(); </nowiki> </source> |
Get Export Extensions
Returns a list of Export extensions available as administrative functions to allow administrators to export a terminology to a specifically formatted output file.
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<source lang=java> <nowiki> LexBIGService lbsv = LexBIGServiceImpl.defaultInstance(); try { LexBIGServiceManager lbsvm = lbsv.getServiceManager(null); Enumeration<? extends ExtensionDescription> extDesc = lbsvm.getExportExtensions().enumerateExtensionDescription(); while(extDesc.hasMoreElements()){ System.out.println(extDesc.nextElement().getName()); } } catch (LBException e) { // TODO Auto-generated catch block e.printStackTrace(); } </nowiki> </source> |
Sample Output
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LexGridExport
OwlRdfExporter
OBOExport
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Get Exporter
Returns an exporter for a specific output format.
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<source lang=java> <nowiki> LexBIGService lbs = LexBIGServiceImpl.defaultInstance(); LexBIGServiceManager lbsm = lbs.getServiceManager(null); // Find the registered extension handling this type of export ... OwlRdfExporterImpl exporter = (OwlRdfExporterImpl) lbsm.getExporter(OwlRdfExporterImpl.name); // Perform the requested action ... CnsCngPair cngCngPair = FilterParser.parse(lbs, css.getCodingSchemeURI(), css.getRepresentsVersion(), cl); exporter.setCng(cngCngPair.getCng()); exporter.setCns(cngCngPair.getCns()); exporter.export(Constructors.createAbsoluteCodingSchemeVersionReference(css), destination,overwrite,false, true); </nowiki> </source> |
Remove Metadata
Remove external coding scheme metadata.
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<source lang=java> <nowiki> String urn = "urn:oid:11.00.11.1"; String ver = "1.1"; Enumeration<? extends CodingSchemeRendering> schemes = lbs.getSupportedCodingSchemes() .enumerateCodingSchemeRendering(); while (schemes.hasMoreElements() && css == null) { CodingSchemeSummary summary = schemes.nextElement().getCodingSchemeSummary(); if (urn.equalsIgnoreCase(summary.getCodingSchemeURI()) && ver.equalsIgnoreCase(summary.getRepresentsVersion())) css = summary; } } lbs.getServiceManager(null).removeCodingSchemeVersionMetaData( Constructors.createAbsoluteCodingSchemeVersionReference(css)); </nowiki> </source> |
Register Coding Scheme Supplement
Register a coding scheme as a supplement to another coding scheme.
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<source lang=java> <nowiki> try { try { LexBIGServiceManager lbsvm = lbsv.getServiceManager(null); AbsoluteCodingSchemeVersionReference parentCodingScheme = new AbsoluteCodingSchemeVersionReference(); AbsoluteCodingSchemeVersionReference supplementCodingScheme = new AbsoluteCodingSchemeVersionReference(); String codingSchemeURN = "urn:oid:11.11.0.1.1"; String codingSchemeVersion = "1.0"; String ExtensionCodingSchemeURN = "urn:oid:11.11.0.1.1-extension"; String ExtensionCodingSchemeVersion = "1.0-extension"; parentCodingScheme.setCodingSchemeURN(codingSchemeURN); parentCodingScheme.setCodingSchemeVersion(codingSchemeVersion); supplementCodingScheme.setCodingSchemeURN(ExtensionCodingSchemeURN); supplementCodingScheme.setCodingSchemeVersion(ExtensionCodingSchemeVersion); lbsvm.registerCodingSchemeAsSupplement(parentCodingScheme,supplementCodingScheme); } catch (LBException e) { // TODO Auto-generated catch block e.printStackTrace(); } </nowiki> </source> |
Remove a coding schemes relationship with another as a supplement.
Un-Register Coding Scheme Supplement
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<source lang=java> <nowiki> try { LexBIGServiceManager lbsvm = lbsv.getServiceManager(null); AbsoluteCodingSchemeVersionReference parentCodingScheme = new AbsoluteCodingSchemeVersionReference(); AbsoluteCodingSchemeVersionReference supplementCodingScheme = new AbsoluteCodingSchemeVersionReference(); String codingSchemeURN = "urn:oid:11.11.0.1.1"; String codingSchemeVersion = "1.0"; String ExtensionCodingSchemeURN = "urn:oid:11.11.0.1.1-extension"; String ExtensionCodingSchemeVersion = "1.0-extension"; parentCodingScheme.setCodingSchemeURN(codingSchemeURN); parentCodingScheme.setCodingSchemeVersion(codingSchemeVersion); supplementCodingScheme.setCodingSchemeURN(ExtensionCodingSchemeURN); supplementCodingScheme.setCodingSchemeVersion(ExtensionCodingSchemeVersion); lbsvm.registerCodingSchemeAsSupplement(parentCodingScheme,supplementCodingScheme); } catch (LBException e) { // TODO Auto-generated catch block e.printStackTrace(); } </nowiki> </source> |
LexEVS Authoring Service Management Methods
Currently restricted to the support of Mapping Authoring only.
Create a Mapping Coding Scheme from Scratch
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<source lang=java> <nowiki> LexEVSAuthoringService authoring = new LexEVSAuthoringServiceImpl(); EntryState entryState = new EntryState(); entryState.setChangeType(ChangeType.NEW); entryState.setContainingRevision("FirstVersionNCItToICD9_12_1_54"); entryState.setRelativeOrder(new Long(1)); //Minimum meta data for the mapping coding scheme should be defined here AbsoluteCodingSchemeVersionReference mappingCodingScheme = new AbsoluteCodingSchemeVersionReference(); mappingCodingScheme.setCodingSchemeURN("urn:oid:11.0011.1.1"); mappingCodingScheme.setCodingSchemeVersion("1.0"); AbsoluteCodingSchemeVersionReference sourceCodingScheme = new AbsoluteCodingSchemeVersionReference(); sourceCodingScheme.setCodingSchemeURN("http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"); sourceCodingScheme.setCodingSchemeVersion("10.10e"); AbsoluteCodingSchemeVersionReference targetCodingScheme = new AbsoluteCodingSchemeVersionReference(); targetCodingScheme.setCodingSchemeURN("urn:oid:2.16.840.1.113883.6.2"); targetCodingScheme.setCodingSchemeVersion("200909"); AssociationSource[] associationSource = new AssociationSource[2]; String associationType = "mapped_to"; String relationsContainerName = "relations"; Date effectiveDate = new Date(); Revision revision = new Revision(); revision.setRevisionId(entryState.getContainingRevision()); boolean loadEntities = false; try { authoring.createAssociationMapping( entryState, mappingCodingScheme, sourceCodingScheme, targetCodingScheme, associationSource, associationType, relationsContainerName, effectiveDate, null, revision, false ); } catch (LBException e) { // TODO Auto-generated catch block e.printStackTrace(); } </nowiki> </source> |
Create a Mapping Coding Scheme with Default Coding Scheme Values
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<source lang=java> <nowiki> authoring.createMappingWithDefaultValues(sources, "NCI Thesaurus", "10.10a", "ICD9", "200909", "mapped_to", false); AbsoluteCodingSchemeVersionReference codingSchemeVersion = new AbsoluteCodingSchemeVersionReference(); codingSchemeVersion .setCodingSchemeURN("http://default.mapping.container"); codingSchemeVersion.setCodingSchemeVersion("1.0"); lbsm.activateCodingSchemeVersion(codingSchemeVersion); </nowiki> </source> |
CTS2 Management Methods
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Insert Entity
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private VersionableEventEntityService service;
private AuthoringService authoringService;
CodingScheme scheme = new CodingScheme();
scheme.setApproxNumConcepts(111l);
scheme.setCodingSchemeName("testName");
scheme.setCodingSchemeURI("uri");
scheme.setRepresentsVersion("v1");
authoringService.loadRevision(scheme, null, null);
CodingScheme cs = codingSchemeservice.getCodingSchemeByUriAndVersion("uri", "v1");
System.out.println(cs);
Entity entity = new Entity();
entity.setEntityCode("c1");
entity.setEntityCodeNamespace("ns");
service.insertEntity("uri", "v1", entity); |
Updating an Existing Entity
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private VersionableEventEntityService service;
private AuthoringService authoringService;
CodingScheme scheme = new CodingScheme();
scheme.setApproxNumConcepts(111l);
scheme.setCodingSchemeName("testName");
scheme.setCodingSchemeURI("uri");
scheme.setRepresentsVersion("v1");
authoringService.loadRevision(scheme, null, null);
CodingScheme cs = codingSchemeservice.getCodingSchemeByUriAndVersion("uri", "v1");
System.out.println(cs);
// Create a new entity
Entity entity = new Entity();
entity.setEntityCode("c1");
entity.setEntityCodeNamespace("ns");
entity.setIsDefined(false);
EntryState entryState = new EntryState();
entryState.setChangeType(ChangeType.MODIFY);
entity.setEntryState(entryState);
EntityDescription ed = new EntityDescription();
ed.setContent("pre-update");
entity.setEntityDescription(ed);
// Insert the new entity
service.insertEntity("uri", "v1", entity);
// Update the entity description
entity.getEntityDescription().setContent("post-update");
try {
// Update the entity
service.updateEntity("uri", "v1", entity);
} catch (Exception e) {
}
Entity modifiedEntity = service.getEntity("uri", "v1", "c1", "ns"); |
CTS2 Management Methods
No further information provided
Pick List and Value Set Managment Methods
No further information provided
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