@Override public boolean isModelClassURI(final EIURI uri) { return (eiModelProvider.getEIClass( uri ) != null); }
private EIEntity getEntity(final EIURI eiURI) { if ( eiURI != null ) { final EIClass eiClass = eiModelProvider.getEIClass( eiURI ); if ( eiClass != null ) { return eiClass.getEntity(); } } return EIEntity.NULL_ENTITY; }
@Override public List<EIClass> getClassAndSuperclassesForInstanceUri(final String sessionId, final EIURI instanceUri) throws RepositoryProviderException { authMgr.isValid( sessionId, true ); List<EIURI> types = queryProvider.retrieveTypes( sessionId, instanceUri ); List<EIClass> classes = new ArrayList<EIClass>(); for (EIURI type : types) { if ( eiModelProvider.getEIClass( type ) != null ) { classes.add( eiModelProvider.getEIClass( type ) ); } } return classes; }
@Override public EIClass getClass(final EIURI classId) throws LoggedException { try { return eiModelProvider.getEIClass( classId ); } catch (final Throwable t) { logger.error( "Error in getClass: " + classId, t ); throw new LoggedException(); } }
private void initSearchCategories(final ApplicationContext ctx) { final List<String> searchCategories = SearchCategories.searchCategories(); searchCategoryClasses = new ArrayList<EIClass>(searchCategories.size()); searchCategoryURIs = new HashSet<EIURI>(searchCategories.size()); for (final String uriStr : searchCategories) { final EIURI uri = EIURI.create(uriStr); searchCategoryClasses.add(eiModelProvider.getEIClass(uri)); searchCategoryURIs.add(uri); } }
@Override public List<String> getClassSynonyms(final EIURI uri) throws LoggedException { try { EIClass eiClass = eiModelProvider.getEIClass( uri ); return eiClass.getSynonyms(); } catch (final Throwable t) { logger.error( "Error in getLabels: ", t ); throw new LoggedException(); } }
@Override public List<String> getClassDefinitions(final List<EIURI> classURIs) throws LoggedException { try { List<String> result = new ArrayList<String>(classURIs.size()); for (EIURI uri : classURIs) { EIClass eiClass = eiModelProvider.getEIClass( uri ); if(eiClass != null) { result.add( eiClass.getDefinition() ); } } return result; } catch (final Throwable t) { logger.error( "Error in getClassDefinitions: ", t ); throw new LoggedException(); } }
@Override public List<EIClass> getSubClasses(final EIURI classId) throws LoggedException { EIClass eiClass = eiModelProvider.getEIClass( classId ); if(!eiClass.hasSubClass()) { return Collections.emptyList(); } try { return eiModelProvider.getSubClasses( classId ); } catch (final Throwable t) { logger.error( "Error in getSubClasses: " + classId, t ); throw new LoggedException(); } }
/** * @return */ public String getTypeLabel(EIURI uri) { return getPluralLabel(eiModel.getEIClass( uri ).getEntity().getLabel()); }
/** * Creates a new NCBIDBProvider that executes queries against NCBI. */ public NIFSearchProvider(final EIModelProvider eiModelProvider) { assert eiModelProvider != null; this.eiModelProvider = eiModelProvider; final EIClass mouse = eiModelProvider.getEIClass( ERO.mouse.getEntity().getURI() ); final EIClass rat = eiModelProvider.getEIClass( ERO.rat.getEntity().getURI() ); final EIClass zebrafish = eiModelProvider.getEIClass(ERO.zebrafish.getEntity().getURI()); if(mouse != null) { mapStringToEntity.put( "mouse", mouse.getEntity()); } if(rat != null) { mapStringToEntity.put( "rat", rat.getEntity() ); } if(zebrafish != null) { mapStringToEntity.put( "zebrafish", zebrafish.getEntity() ); } }
public NCBIProbeSearchProvider(final EIModelProvider eiModelProvider) { super( new NCBIProbeProvider(), eiModelProvider); reagentEntity = eiModelProvider.getEIClass( EIURI.create( REAGENT_URI ) ).getEntity(); constructEntity = eiModelProvider.getEIClass( EIURI.create( CONSTRUCT_URI ) ).getEntity(); locationEntity = EIEntity.create( EIURI.create( NCBIConstants.PROBE_URL ), NCBIProbeProvider.NCBI_PROBE_NAME ); }
public NCBIPubMedSearchProvider(final EIModelProvider eiModelProvider) { super( new NCBIPubMedProvider(), eiModelProvider); //docEntity = eiModelProvider.getEIClass( DOCUMENT_URI ).getEntity(); pubEntity = eiModelProvider.getEIClass( PUBLICATION_URI ).getEntity(); locationEntity = EIEntity.create( EIURI.create( NCBIConstants.PUBMED_URL ), NCBIPubMedProvider.NCBI_PUBMED_NAME ); }
EIClass eiClass = eiModelProvider.getEIClass( term.getURI() ); if ( eiClass != null ) { String prefLabel = eiClass.getEntity().getLabel();
public NCBITaxonomySearchProvider(final EIModelProvider eiModelProvider) { super( new NCBITaxonomyProvider(), eiModelProvider ); orgEntity = eiModelProvider.getEIClass( EIURI.create( ORGANISM_URI ) ).getEntity(); locationEntity = EIEntity.create( EIURI.create( NCBIConstants.TAXONOMY_URL ), NCBITaxonomyProvider.NCBI_TAXONOMY_NAME ); }
/** * Checks, with inference, if a given type is of another type. */ protected boolean isType(final EIURI type, final EIURI target) { if ( type == null || target == null ) { return false; } if ( type.equals( target ) ) { return true; } final EIClass eiClass = eiModelProvider.getEIClass( target ); if ( eiClass != null && eiClass.hasSubClass() ) { for (final EIClass sub : eiModelProvider.getSubClasses( target )) { if ( isType( type, sub.getEntity().getURI() ) ) { return true; } } } return false; }
/** * Checks, with inference, if a given type is of another type. */ protected boolean isType(final EIURI type, final EIURI target) { if ( type == null || target == null ) { return false; } if ( type.equals( target ) ) { return true; } final EIClass eiClass = eiModelProvider.getEIClass( target ); if ( eiClass != null && eiClass.hasSubClass() ) { for (final EIClass sub : eiModelProvider.getSubClasses( target )) { if ( isType( type, sub.getEntity().getURI() ) ) { return true; } } } return false; }
.getEIClass(request.getBinding().getType()).getEntity() : null;
@Override public EIInstance getEmptyEIInstance(final String sessionId, final EIURI classUri) throws RepositoryProviderException { authMgr.isValid( sessionId, true ); final EIInstance instance = crudProvider.getEmptyEIInstance( sessionId, classUri ); if ( instance.getInstanceClass() == null || instance.getInstanceClass().equals( EIClass.NULL_CLASS ) ) { instance.setInstanceClass( eiModelProvider.getEIClass( classUri ) ); } // Protocol is an outlier - it is a primary type but its root is Document // Need to set explicitly Protocol as root super type if ( ERO.protocol.getEntity().equals( instance.getInstanceType() ) ) { instance.setRootSuperType( instance.getInstanceClass(), true, false ); } return instance; }