Exports contents of the code system using the exporter specified. *

• java.lang.String codeSystemNameOrURI - (Mandatory) Name or URI of the Code System to be exported.
• java.lang.String codeSystemVersion - (Optional) Version of the Code System to be exported.
• java.net.URI exportDestination - (Mandatory) Destination path information for the exported file.
• org.LexGrid.LexBIG.Extensions.Export.Exporter exporter - (Mandatory) exporter to use. Use getSupportedExporterNames to get all the exporters supported by this instance of CTS2.
  For example, 'OBOExport' could be used to export code system contents in OBO format, 'OwlRdfExporter' for code system contents in OWL/RDF format, 'LexGridExport' for Code System in LexGrid XML format, etc.

java.net.URI - URI of destination if successfully exported

*

org.LexGrid.LexBIG.Exceptions.LBException

*

• Step 1: Instantiate CodeSystemExportOperation if it is not done yet:

  ...

  Code Block org.lexevs.cts2.admin.export.CodeSystemExportOperation csExportOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getCodeSystemExportOperation(); Step 2: Populate Exporter object to use: ... Code Block LexBIGService lbs = LexBIGServiceImpl.defaultInstance(); ... org.LexGrid.LexBIG.Impl.exporters.LexGridExport exporter; ... try { ... _ exporter = (org.LexGrid.LexBIG.Impl.exporters.LexGridExport)lbs.getServiceManager(null).getExporter(org.LexGrid.LexBIG.Impl.exporters.LexGridExport.name); ... } catch (LBException e) { ... throw new RuntimeException(e); ... } org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph cng = lbs.getNodeGraph("Automobiles", Constructors.createCodingSchemeVersionOrTagFromVersion("1.0"), null); ... org.LexGrid.LexBIG.LexBIGService.CodedNodeSet cns = lbs.getNodeSet("Automobiles", Constructors.createCodingSchemeVersionOrTagFromVersion("1.0"), null); ... exporter.setCng(cng); ... exporter.setCns(cns); ... exporter.getOptions().getBooleanOption("Async Load").setOptionValue(false); ... exporter.getOptions().getBooleanOption(Option.getNameForType(Option.FAIL_ON_ERROR)).setOptionValue(true); ... exporter.getOptions().getBooleanOption("force").setOptionValue(true); Step 3: Call export method by passing the code system version, export destination and other parameter values: ... Code Block java.net.URI destURI = csExport.exportCodeSystemContent("Automobiles", "1.0", new File("C: ... \\").toURI(), exporter); ... Export Coded Node Set This function resolves the given CodedNodeSet(CNS) and exports the contents in LexGrid XML format. There is a helper method getCodeSystemCodedNodeSet(String codeSystemNameOrURI, String codeSystemVersion) that could be used to get the Coded Node Set object for given Code System Version, and could apply further restrictions (ex: matchingDesignation, Status, Properties, Codes etc). And this Coded Node Set object could be supplied to this export method which resolves it and exports the contents in LexGrid XML format. exportCodedNodeSet(String codeSystemNameOrURI, String codeSystemVersion, CodedNodeSet cns, URI exportDestination, boolean overwrite, boolean stopOnErrors, boolean async) * * * Description: Resolves the given CodedNodeSet(CNS) and exports the contents. * Input: ... java.lang.String codeSystemNameOrURI - (Mandatory) URI of the Code System to be used for resolving the CNS. java.lang.String codeSystemVersion - (Optional) Version of the Code System to be exported. ... org.LexGrid.LexBIG.LexBIGService.CodedNodeSet cns - (Mandatory) Coded Node Set object to be resolved and exported. java.net.URI exportDestination - (Mandatory) Destination path information for the exported file. boolean overwrite - (Optional) True means, any existing file will be overwritten. boolean stopOnErrors - (Optional) True means stop if any export error is detected. False means attempt to export what can be exported if recoverable errors are encountered. boolean async - (Optional) Flag controlling whether export occurs in the calling thread. If true, the export will occur in a separate asynchronous process. If false, this method blocks until the export operation completes or fails. Regardless of setting, the getStatus and getLog calls are used to fetch results. ... * * Output: ... java.net.URI - URI of destination if successfully exported ... * * Exception: ... org.LexGrid.LexBIG.Exceptions.LBException ... * * Sample Call: Step 1: Instantiate CodeSystemExportOperation if it is not done yet: ... Code Block org.lexevs.cts2.admin.export.CodeSystemExportOperation csExportOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getCodeSystemExportOperation(); Step 2: Populate Coded Node Set object to export and apply restrictions: ... Code Block CodedNodeSet cns = csExport.getCodeSystemCodedNodeSet("Automobiles", "1.0"); ... cns.restrictToMatchingDesignations("Ford", null, MatchAlgorithms.LuceneQuery.name(), null); Step 3: Call export method by passing the coded node set object , export destination and other parameter values: ... Code Block ''java.net.URI destURI = csExport.exportCodedNodeSet("Automobiles", "1.0", cns, new File("c: ... \\").toURI(), true, true, true); ... Export Coded Node Graph This function resolves the given CodedNodeGraph(CNG) and exports the contents in LexGrid XML format. There is a helper method getCodeSystemCodedNodeGraph(String codeSystemNameOrURI, String codeSystemVersion) that could be used to get the Coded Node Graph object for given Code System Version, and could apply further restrictions (ex: associations, SourceCodes, TargetCodes, etc). And this Coded Node Graph object could be supplied to this export method which resolves it and exports the contents in LexGrid XML format. exportCodedNodeGraph(String codeSystemNameOrURI, String codeSystemVersion, CodedNodeGraph cng, URI exportDestination, boolean overwrite, boolean stopOnErrors, boolean async) * * * Description: Resolves the given CodedNodeGraph(CNG) and exports the contents. * Input: ... java.lang.String codeSystemNameOrURI - (Mandatory) URI of the Code System to be used for resolving the CNS. java.lang.String codeSystemVersion - (Optional) Version of the Code System to be exported. ''org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph cng - (Mandatory) Coded Node Graph object to be resolved and exported. java.net.URI exportDestination - (Mandatory) Destination path information for the exported file. boolean overwrite - (Optional) True means, any existing file will be overwritten. boolean stopOnErrors - (Optional) True means stop if any export error is detected. False means attempt to export what can be exported if recoverable errors are encountered. boolean async - (Optional) Flag controlling whether export occurs in the calling thread. If true, the export will occur in a separate asynchronous process. If false, this method blocks until the export operation completes or fails. Regardless of setting, the getStatus and getLog calls are used to fetch results. ... * * Output: ... java.net.URI - URI of destination if successfully exported ... * * Exception: ... org.LexGrid.LexBIG.Exceptions.LBException ... * * Sample Call: Step 1: Instantiate CodeSystemExportOperation if it is not done yet: ... Code Block org.lexevs.cts2.admin.export.CodeSystemExportOperation csExportOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getCodeSystemExportOperation(); Step 2: Populate Coded Node Graph object to export and apply restrictions: ... Code Block CodedNodeGraph cng = csExport.getCodeSystemCodedNodeGraph("Automobiles", "1.0"); ... cng.restrictToAssociations(Constructors.createNameAndValueList("uses"), null); Step 3: Call export method by passing the coded node graph object , export destination and other parameter values: ... Code Block ''java.net.URI destURI = csExport.exportCodedNodeGraph("Automobiles", "1.0", cng, new File("c: ... \\").toURI(), true, true, true); ... Value Set Exporter org.lexevs.cts2.admin.export.ValueSetExportOperation is the main interface which can be used to export Value Set Definition or Value Set Resolution (Expanded Value Set). This interface can be accessed using main LexEVSCTS2 interface, like: org.lexevs.cts2.admin.export.ValueSetExportOperation vsExportOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getValueSetExportOperation(); There are three different methods available to export Value Set: Export Value Set Definition - This method provides capability to export Value Set Definition in LexGrid XML format. This will be helpful if there is a need to import this exported Value Set Definition in different instance of LexEVS. Export Expanded Value Set using custom exporter - This method provides capability to export contents of Value Set using custom exporter. This will be helpful, if you want the contents exported in format other than LexGrid XML. Export Expanded Value Set in LexGrid XML format - This method provides capability to export contents of Value Set using default LexGrid Exporter which exports in LexGrid XML format. Export Value Set Definition This method provides capability to export Value Set Definition in LexGrid XML format. This will be helpful if there is a need to import this exported Value Set Definition in different instance of LexEVS. exportValueSetDefinition(URI valueSetDefinitionURI, String valueSetDefinitionVersion, String xmlFullPathName, boolean overwrite, boolean failOnAllErrors) * * * Description: Export Value Set Definition to LexGrid canonical XML format. * Input: ... java.net.URI valueSetDefinitionURI - (Mandatory) URI of the Value Set Definition to export. java.lang.String valueSetDefinitionVersion - (Optional) Version of the Value Set Definition to be exported. java.lang.String xmlFullPathName - (Mandatory) File location (including file name *.xml) to save the definition. boolean overwrite - (Optional) True means, any existing file will be overwritten. boolean failOnAllErrors - (Optional) True means stop if any export error is detected. False means attempt to export what can be exported if recoverable errors are encountered. ... * * * Output: None * Exception: ... org.LexGrid.LexBIG.Exceptions.LBException ... * * Sample Call: Step 1: Instantiate ValueSetExportOperation if it is not done yet: ... Code Block org.lexevs.cts2.admin.export.ValueSetExportOperation vsExportOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getValueSetExportOperation(); Step 2: Call export method by passing URI of Value Set Definition, output destination and other parameter values: ... Code Block ''vsExport.exportValueSetDefinition(new URI("SRITEST:AUTO:PropertyRefTest1-VSDONLY"), null, new File("c: ... \\TestVSDExport.xml").toURI(), true, true); ... Export Expanded Value Set ... Using Custom Exporter This method provides capability to export contents of Value Set using custom exporter. This will be helpful when there is a requirement to export value set contents in format other than LexGrid XML. There is a helper method getSupportedExporterNames() that could be used to get all the exporters loaded and supported by current LexEVS instance. So, if you have your custom exporter deployed as an extension to LexEVS Exporter, it will be in the list of exporters returned by method getSupportedExporterNames(). exportValueSetContents(URI valueSetDefinitionURI, String valueSetDefinitionVersion, URI exportDestination, String exporter) * * * Description: Exports contents of the Value Set Definition using the exporter specified. * Input: ... java.lang.String valueSetDefinitionURI - (Mandatory) URI of the Value Set Definition to be expanded and exported. java.lang.String valueSetDefinitionVersion - (Optional) Version of the Value Set Definition to be exported. java.net.URI exportDestination - (Mandatory) Destination path information for the exported file. java.lang.String exporter - (Mandatory) Name of the exporter to use. Use getSupportedExporterNames to get all the exporters supported by this instance of CTS2/LexEVS. ... * * Output: ... java.net.URI - URI of destination if successfully exported ... * * Exception: ... org.LexGrid.LexBIG.Exceptions.LBException ... * * Sample Call: Step 1: Instantiate ValueSetExportOperation if it is not done yet: ... Code Block org.lexevs.cts2.admin.export.ValueSetExportOperation vsExportOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getValueSetExportOperation(); Step 2: Call export method by passing the Value Set Definition URI, custom exporter name, output destination and other parameter values: ... Code Block ''java.net.URI destURI = vsExport.exportValueSetContents(new URI("SRITEST:AUTO:PropertyRefTest1-VSDONLY"), null, new File("c://AutomobilesTestVSD.xml").toURI(), "CustomExporter"); ... Export Expanded Value Set in LexGrid XML ... Format This method provides capability to export contents of Value Set as a Code System using LexGrid Exporter which exports in LexGrid XML format. exportValueSetContents(URI valueSetDefinitionURI, String valueSetDefinitionVersion, URI exportDestination, AbsoluteCodingSchemeVersionReferenceList csVersionList, String csVersionTag, boolean overwrite, boolean failOnAllErrors) * * * Description: Exports contents of Value Set as Code System in LexGrid canonical XML format. * Input: ... java.net.URI valueSetDefinitionURI - (Mandatory) URI of the Value Set Definition to export. java.lang.String valueSetDefinitionVersion - (Optional) Version of the Value Set Definition to be exported. java.net.URI exportDestination - (Mandatory) Location (path to the folder withOUT the file name) to save the definition. org.LexGrid.LexBIG.DataModel.Collections.AbsoluteCodingSchemeVersionReferenceList csVersionList - (Optional) A list of code system URI's and versions to be used. These will be used only if they are present in the service. If absent, the most recent version will be used instead. java.lang.String csVersionTag - (Optional) The tag (e.g "devel", "production", ...) to be used to reconcile code system when more than one is present. boolean overwrite - (Optional) True means, any existing file will be overwritten. boolean failOnAllErrors - (Optional) True means stop if any export error is detected. False means attempt to export what can be exported if recoverable errors are encountered. ... * * Output: ... java.net.URI - URI of destination if successfully exported. ... * * Exception: ... org.LexGrid.LexBIG.Exceptions.LBException ... * * Sample Call: Step 1: Instantiate ValueSetExportOperation if it is not done yet: ... Code Block org.lexevs.cts2.admin.export.ValueSetExportOperation vsExportOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getValueSetExportOperation(); Step 2: Populate the Code System Version Reference List to be used to resolve the Value Set Definition: ... Code Block AbsoluteCodingSchemeVersionReferenceList csVerList = new AbsoluteCodingSchemeVersionReferenceList(); ... csVerList.addAbsoluteCodingSchemeVersionReference(Constructors.createAbsoluteCodingSchemeVersionReference("urn:oid:11.11.0.1", "1.0")); Step 3: Call export method by passing URI of Value Set Definition, output destination and other parameter values: ... Code Block ''vsExport.exportValueSetDefinition(exportValueSetContents(new URI("SRITEST:AUTO:PropertyRefTest1-VSDONLY"), null, new File("c: ... \\TestVSDExport.xml").toURI(), csVerList, null, true, true); ... Association Exporter - Export Association org.lexevs.cts2.admin.export.AssociationExportOperation is the main interface which can be used to export Association(s). This interface can be accessed using main LexEVSCTS2 interface, like:: Code Block org.lexevs.cts2.admin.export.AssociationExportOperation assnExportOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getAssociationExportOperation(); ... Method exportAssociation provides capability to apply filters and export association(s) in LexGrid XML format. exportAssociation(String codeSystemNameOrURI, String codeSystemVersion, CodedNodeGraph cng, URI exportDestination, boolean overwrite, boolean stopOnErrors, boolean async) * * * Description: Export Association(s) in LexGrid canonical XML format. * Input: ... java.lang.String codeSystemNameOrURI - (Mandatory) Name or URI of the Code System that contains the association. java.lang.String codeSystemVersion - (Mandatory) Version of the Code System that contains the association. org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph cng - (Mandatory) Coded Node Graph(CNG) that contains all the filters. This CNG will be resolved and exported. java.net.URI exportDestination - (Mandatory) Directory location (with out file name). The name of the file will be constructed based on the Code System Name/URI and the Version. boolean overwrite - (Optional) True means, any existing file will be overwritten. boolean stopOnErrors - (Optional) True means stop if any export error is detected. False means attempt to export what can be exported if recoverable errors are encountered. boolean async - (Optional) Flag controlling whether export occurs in the calling thread. If true, the export will occur in a separate asynchronous process. If false, this method blocks until the export operation completes or fails. Regardless of setting, the getStatus and getLog calls are used to fetch results. ... * * * Output: None * Exception: ... org.LexGrid.LexBIG.Exceptions.LBException ... * * Sample Call: Step 1: Instantiate AssociationExportOperation if it is not done yet: ... Code Block org.lexevs.cts2.admin.export.AssociationExportOperation assnExportOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getAssociationExportOperation(); Step 2: Populate the Coded Node Graph (CNG) and apply filters: ... Code Block org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph cng = LexBIGServiceImpl.defaultInstance().getNodeGraph("urn:oid:cts:1.1.1", "1.0", null); ... _ org.LexGrid.LexBIG.DataModel.Core.NameAndValue nv = new org.LexGrid.LexBIG.DataModel.Core.NameAndValue(); ... _ nv.setName("hasSubtype"); ... _ org.LexGrid.LexBIG.DataModel.Collections.NameAndValueList assocNames = new org.LexGrid.LexBIG.DataModel.Collections.NameAndValueList(); ... _ assocNames.addNameAndValue(nv); ... _ cng.restrictToAssociations(assocNames, null);_ Step 3: Call export method by passing Code System Information, Coded Node Graph, destination path and other parameter values: ... Code Block ''assnExport.exportAssociation("urn:oid:cts:1.1.1", "1.0", cng, new File("c:\\exportedFiles ... \\").toURI(), true, true, true); ... Exporter Mappings ... - OwlRdf Exporter Mapping OwlRdf exporter is based on Jena 2.6.3. It use SDB to build up triple store. The triple store tables are under the same database of LexEvs. LexEvs retrieval api does not support to fetch AssociatedData. It cannot retrieve the association that is from an entity to a data/value. The owl/rdf exporter, based on LexEVS has the limiation of handling the owl:hasValue, owl:maxCardinality, owl:minCardinality, owl:cardinality constraints as well. \ LexGrid Owl/Rdf Comment CodingScheme     codingScheme owl:Ontology   codingScheme.source dc:source a property of owl:ontology codingScheme.copyright dc:right a property of owl:ontology codingScheme.Name rdfs:label a property of owl:ontology codingScheme.URI xmlns a property of owl:ontology codingScheme.representVersion owl:versionInfo a property of owl:ontology codingScheme.formalName dc:title a property of owl:ontology codingScheme.defaultLanguage dc:language a property of owl:ontology codingScheme.approxNumConcpts not mapped   Entity     entity skos:Concept   concept owl:Class   instance entity owl:Thing   associationEntity owl:property owl:objectProperty or owl:datatypeProperty entityCode rdf:ID local name entityCodeNamespace xmlns   isDefined LexRDF:isDefined LexRDF is a namespace generated by Mayo Property   Use reification statement for the property 's property property owl:AnnotationProperty when no type specified   language dc:language   source dc:source   comment skos:note   presentation skos:altLabel, skos:prefLabel According to lg isPrefered definition skos:definition   isPreferred LexRDF:isPreferred   degreeOfFidelity LexRDF:degreeOfFidelity   matchIfNoContext LexRDF:matchIfNoContext   representationForm LexRDF:presentationForm   propertyLink LexRDF:propertyLink   Association     associationPredicate.associationName rdf:id   associationEntity owl:property owl:objectProperty or owl:datatypeProperty associationEntity.forwardName rdf:id if not null associationEntity.isTransitive owl:TransitiveProperty   Scrollbar icons false Accessibility | Contact CBIIT | FOIA | HHS Vulnerability Disclosure | Comment Policy U.S. Department of Health and Human Services | National Institutes of Health | National Cancer Institute | USA.gov NIH ... 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