@Override public EIURI deserialize(final JsonElement element, final Type type, final JsonDeserializationContext context) throws JsonParseException { final String strValue = element.getAsString(); if ( NullInstanceString.equals( strValue ) ) { return null; } else { return EIURI.create( strValue ); } } }
private EIEntity rawStringToEntity(final String rawValue) { final String[] value = rawValue.split( SearchRequestTokens.ENTITY_VALUE_DELIMITER_ESC); if ( value.length != 2 ) { log.warning( "Unexpected number of values for object property, search request may not be built as expected. " + "Raw value [" + rawValue + "] Delimiter [" + SearchRequestTokens.ENTITY_VALUE_DELIMITER + "]"); } String valueLabel = value.length < 2 ? null : value[0]; final EIEntity valueEntity = EIEntity.create( EIURI.create( value[1] ), valueLabel ); return valueEntity; }
private TRIBUTARY(final String identifier, final String label) { this.identifier = identifier; this.entity = EIEntity.create( EIURI.create( namespace + identifier ), label) ; }
private EIDT(final String identifier, final String label) { this.identifier = identifier; this.entity = EIEntity.create( EIURI.create( namespace + identifier ), label) ; }
private Vocabulary(final String namespace, final String identifier, final String label) { this.namespace = namespace; this.identifier = identifier; this.entity = EIEntity.create( EIURI.create( namespace + identifier ), label ); }
private EIURI extractEIURI(JsonNode node) { JsonNode idNode = node.get("id"); String id = extractTextNode( idNode ); return EIURI.create( id ); }
private FOAF(final String identifier, final String label) { this.identifier = identifier; this.entity = EIEntity.create( EIURI.create( namespace + identifier ), label) ; }
private ARG(final String identifier, final String label) { this.identifier = identifier; this.entity = EIEntity.create( EIURI.create( namespace + identifier ), label ); }
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); } }
public NCBIMeSHSearchProvider(final EIModelProvider eiModelProvider) { super( new NCBIMeSHProvider(), eiModelProvider ); //diseaseEntity = eiModelProvider.getEIClass( EIURI.create( DISEASE_URI ) ).getEntity(); meshEntity = EIEntity.create( EIURI.create( NCBIConstants.MESH_URL ), "MeSH" ); locationEntity = EIEntity.create( EIURI.create( NCBIConstants.MESH_URL ), NCBIMeSHProvider.NCBI_MESH_NAME ); }
private void cachePreferredLabelPropURIs() { final List<Property> props = ( (JenaEIOntModel)eagleiOntModel ).getPrefLabelProperties(); for (final Property prop : props) { prefLabelProperties.add( EIURI.create( prop.getURI() ) ); } }
@Deprecated public static EIURI getSelectedUri(final ListBox listBox) { final EIURI selectedUri = EIURI.create( listBox.getValue( listBox.getSelectedIndex() ) ); return selectedUri; }
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 ); }
@Override public void addValue(final EIInstance instance, final EIEntity propertyEntity, final String newValue) { if(validateURI(newValue)){ instance.addSameAsValue(EIURI.create(newValue )); } }
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 ); }
private boolean oldValueMissingFromResult(final List<EIInstanceMinimal> fetchedInstances) { // DBW - remove final EIURI oldUri = EIURI.create( oldValue ); for (final EIInstanceMinimal instance : fetchedInstances) { if ( instance.getInstanceURI().equals( oldUri ) ) { return false; } } log.debug( "Old value missing from result: " + oldValue ); return true; }
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 ); }
@Override public void onChange(final ChangeEvent event) { final EIURI selectedUri = EIURI.create( providersList.getValue( providersList.getSelectedIndex() ) ); final EIEntity selectedEntity = providerCache.getResourceProvider( selectedUri ); if ( selectedEntity == null || selectedEntity.equals( EIEntity.NULL_ENTITY ) ) { return; } appState.updateApplicationState( Mode.view, selectedEntity, ResourceProvider.BASE_RESOURCE_CONTAINER, selectedEntity ); } } );
@Override public void onChange(final ChangeEvent event) { final EIURI selectedUri = EIURI.create( providersList.getValue( providersList.getSelectedIndex() ) ); final EIEntity selectedEntity = resourceProviderCache.getResourceProvider( selectedUri ); providersList.setVisible( false ); if ( selectedEntity == null || selectedEntity.equals( EIEntity.NULL_ENTITY ) ) { return; } ApplicationState.getInstance().updateApplicationState( Mode.view, selectedEntity, ResourceProvider.BASE_RESOURCE_CONTAINER, selectedEntity ); } } );
public String attachUserToState() { String userUri = SweetCookies.getUserUri(); if (currentUser == null) { userUri = null; } if (userUri != null) { ApplicationState.getInstance().setUser(EIEntity.create(EIURI.create(userUri), currentUser)); log.debug("User uri " + ApplicationState.getInstance().getUserURI() + "; label " + ApplicationState.getInstance().getUserID()); } return userUri; }