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Revision 5fc450f7

Added by Andreas Müller over 3 years ago

cleanup

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cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/geo/IEditGeoService.java
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 * @author a.kohlbecker
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 * @since 18.06.2009
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 * @author n.hoffmann
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 *
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 */
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public interface IEditGeoService {
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      cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/api/application/CdmIoApplicationController.java
    
  





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import eu.etaxonomy.cdm.persistence.hibernate.HibernateConfiguration;


  		




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public class CdmIoApplicationController extends CdmApplicationController {


  		




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	@SuppressWarnings("unused")


  		




  
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    @SuppressWarnings("unused")


  		




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	private static final Logger logger = Logger.getLogger(CdmIoApplicationController.class);


  		




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                hibernateConfig, omitTermLoading, null);


  		




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    }


  		




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	/**


  		




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	 * @return


  		




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	 */


  		




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	protected static ClassPathResource getClasspathResource() {


  		




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		return new ClassPathResource(DEFAULT_APPLICATION_CONTEXT_RESOURCE);


  		




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	}


  		




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	/**


  		




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	 * Constructor.


  		




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	 * @param applicationContextResource


  		




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	 * @param dataSource


  		




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	 * @param dbSchemaValidation


  		




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	 * @param omitTermLoading


  		




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	 * @param progressMonitor


  		




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	 */


  		




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	protected CdmIoApplicationController(Resource applicationContextResource, ICdmDataSource dataSource,


  		




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	        DbSchemaValidation dbSchemaValidation, HibernateConfiguration hibernateConfig,


  		




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			boolean omitTermLoading, IProgressMonitor progressMonitor) {


  		




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		super(applicationContextResource, dataSource, dbSchemaValidation, hibernateConfig,


  		




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		        omitTermLoading, progressMonitor, null);


  		




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	}


  		




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}


  		












  

    
      cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v512_515/Reference2SourceMover.java
    
  





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    @SuppressWarnings("unused")


  		




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    private static final Logger logger = Logger.getLogger(Reference2SourceMover.class);


  		




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    private static final String stepName = "Move Reference 2 Source";


  		




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    private final String tableName;


  		




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    private final String citationsIdAttr;


  		




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    private final String detailAttr;


  		




  ......




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    private final String sourceType;


  		




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    private final String dtype;


  		




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    public static final Reference2SourceMover NewInstance(List<ISchemaUpdaterStep> stepList, String tableName,


  		




  
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    public static final Reference2SourceMover NewInstance(List<ISchemaUpdaterStep> stepList, String stepName, String tableName,


  		




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            String citationsIdAttr, String detailAttr, String sourceAttr){


  		




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        Reference2SourceMover result = new Reference2SourceMover(stepList, tableName, citationsIdAttr, detailAttr, sourceAttr, null, null);


  		




  
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        Reference2SourceMover result = new Reference2SourceMover(stepList, stepName, tableName, citationsIdAttr, detailAttr, sourceAttr, null, null);


  		




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        return result;


  		




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    }


  		




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    public static final Reference2SourceMover NewInstance(List<ISchemaUpdaterStep> stepList, String tableName,


  		




  
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    public static final Reference2SourceMover NewInstance(List<ISchemaUpdaterStep> stepList, String stepName, String tableName,


  		




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            String citationsIdAttr, String detailAttr, String sourceAttr, String dtype, String sourceType){


  		




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        Reference2SourceMover result = new Reference2SourceMover(stepList, tableName, citationsIdAttr, detailAttr, sourceAttr, sourceType, dtype);


  		




  
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        Reference2SourceMover result = new Reference2SourceMover(stepList, stepName, tableName, citationsIdAttr, detailAttr, sourceAttr, sourceType, dtype);


  		




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        return result;


  		




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    }


  		




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    protected Reference2SourceMover(List<ISchemaUpdaterStep> stepList, String tableName,


  		




  
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    protected Reference2SourceMover(List<ISchemaUpdaterStep> stepList, String stepName, String tableName,


  		




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            String citationsIdAttr, String detailAttr, String sourceAttr, String sourceType, String dtype) {


  		




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        super(stepList, stepName);


  		




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        this.tableName = tableName;


  		




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        this.sourceAttr = sourceAttr;


  		




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        this.sourceType = sourceType == null? "PTS" : sourceType;


  		




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        this.dtype = dtype == null? "DescriptionElementSource" : dtype;


  		




  
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        this.stepName = stepName;


  		




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    }


  		




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    @Override


  		












  

    
      cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v512_515/SchemaUpdater_5151_5152.java
    
  





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        referencedTable = "OriginalSourceBase";


  		




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        ColumnAdder.NewIntegerInstance(stepList, stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL, referencedTable);


  		




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        Reference2SourceMover.NewInstance(stepList, tableName, "referenceForParentChildRelation_id", "microReferenceForParentChildRelation", "source_id");


  		




  
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        stepName = "Move taxon node citation 2 original source";


  		




  
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        Reference2SourceMover.NewInstance(stepList, stepName, tableName, "referenceForParentChildRelation_id", "microReferenceForParentChildRelation", "source_id");


  		




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        //6581


  		




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        stepName = "Add source to Classification";


  		












  

    
      cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v515_518/SchemaUpdater_5152_5180.java
    
  





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        String referenceColumnName = "citation_id";


  		




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        String microReferenceColumnName = "citationMicroReference";


  		




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        String sourceColumnName = "source_id";


  		




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        Reference2SourceMover.NewInstance(stepList, tableName, referenceColumnName, microReferenceColumnName, sourceColumnName);


  		




  
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        Reference2SourceMover.NewInstance(stepList, stepName, tableName, referenceColumnName, microReferenceColumnName, sourceColumnName);


  		




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        //6581


  		




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        //move name relationship reference to source


  		




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        referenceColumnName = "citation_id";


  		




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        microReferenceColumnName = "citationMicroReference";


  		




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        sourceColumnName = "source_id";


  		




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        Reference2SourceMover.NewInstance(stepList, tableName, referenceColumnName, microReferenceColumnName, sourceColumnName);


  		




  
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        Reference2SourceMover.NewInstance(stepList, stepName, tableName, referenceColumnName, microReferenceColumnName, sourceColumnName);


  		




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        //6581


  		




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        //move taxon relationship reference to source


  		




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        referenceColumnName = "citation_id";


  		




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        microReferenceColumnName = "citationMicroReference";


  		




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        sourceColumnName = "source_id";


  		




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        Reference2SourceMover.NewInstance(stepList, tableName, referenceColumnName, microReferenceColumnName, sourceColumnName);


  		




  
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        Reference2SourceMover.NewInstance(stepList, stepName, tableName, referenceColumnName, microReferenceColumnName, sourceColumnName);


  		




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        //6581


  		




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        //move hybrid relationship reference to source


  		




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        referenceColumnName = "citation_id";


  		




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        microReferenceColumnName = "citationMicroReference";


  		




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        sourceColumnName = "source_id";


  		




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        Reference2SourceMover.NewInstance(stepList, tableName, referenceColumnName, microReferenceColumnName, sourceColumnName);


  		




  
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        Reference2SourceMover.NewInstance(stepList, stepName, tableName, referenceColumnName, microReferenceColumnName, sourceColumnName);


  		




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        //6581


  		




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        //move type designation reference to source


  		




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        referenceColumnName = "citation_id";


  		




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        microReferenceColumnName = "citationMicroReference";


  		




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        sourceColumnName = "source_id";


  		




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        Reference2SourceMover.NewInstance(stepList, tableName, referenceColumnName, microReferenceColumnName, sourceColumnName);


  		




  
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        Reference2SourceMover.NewInstance(stepList, stepName, tableName, referenceColumnName, microReferenceColumnName, sourceColumnName);


  		




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        //6581


  		




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        //move nomenclatural reference to nomenclatural source


  		




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        sourceColumnName = "nomenclaturalSource_id";


  		




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        String sourceType = "NOR";


  		




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        String dtype = "NomenclaturalSource";


  		




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        Reference2SourceMover.NewInstance(stepList, tableName, referenceColumnName, microReferenceColumnName, sourceColumnName, dtype, sourceType);


  		




  
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        Reference2SourceMover.NewInstance(stepList, stepName, tableName, referenceColumnName, microReferenceColumnName, sourceColumnName, dtype, sourceType);


  		




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        //9094


  		




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        // update TaxonNode.source from IdentifiableSource to DescriptionElementSource


  		












  

    
      cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dto/TermNodeDto.java
    
  





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//        TermTree termTree = HibernateProxyHelper.deproxy(node.getGraph(), TermTree.class);


  		




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//        tree = TermTreeDto.fromTree(termTree);


  		




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//        treeIndex = node.treeIndex();


  		




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        List<TermNodeDto> children = new ArrayList();


  		




  
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        List<TermNodeDto> children = new ArrayList<>();


  		




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        for (Object o: node.getChildNodes()){


  		




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            if (o instanceof TermNode){


  		




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                TermNode child = (TermNode)o;


  		




  
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                TermNode<?> child = (TermNode<?>)o;


  		




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                if (child != null){


  		




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                    if(child.getTerm().getTermType().equals(TermType.Character)){


  		




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                        children.add(CharacterNodeDto.fromTermNode(child, treeDto));


  		




  
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                        children.add(CharacterNodeDto.fromTermNode((TermNode)child, treeDto));


  		




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                    }else{


  		




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                        children.add(TermNodeDto.fromNode(child, treeDto));


  		




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                    }


  		












  

    
      cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/ICdmRepository.java
    
  





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import org.springframework.transaction.TransactionStatus;


  		




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import eu.etaxonomy.cdm.api.conversation.ConversationHolder;


  		




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import eu.etaxonomy.cdm.api.service.longrunningService.ILongRunningTasksService;


  		




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import eu.etaxonomy.cdm.api.service.IAgentService;


  		




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import eu.etaxonomy.cdm.api.service.IAnnotationService;


  		




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import eu.etaxonomy.cdm.api.service.IClassificationService;


  		




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import eu.etaxonomy.cdm.api.service.ITermTreeService;


  		




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import eu.etaxonomy.cdm.api.service.IUserService;


  		




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import eu.etaxonomy.cdm.api.service.IVocabularyService;


  		




  
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import eu.etaxonomy.cdm.api.service.longrunningService.ILongRunningTasksService;


  		




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import eu.etaxonomy.cdm.api.service.molecular.IAmplificationService;


  		




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import eu.etaxonomy.cdm.api.service.molecular.IPrimerService;


  		




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import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;


  		




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	public Object getBean(String string);


  		




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    public IAnnotationService getAnnotationService();


  		




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	public INameService getNameService();


  		




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	public ConversationHolder NewConversation();


  		




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	public ICollectionService getCollectionService();


  		




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	public ILongRunningTasksService getLongRunningTasksService();


  		




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	/**


  		




  ......




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	public IEntityConstraintViolationService getEntityConstraintViolationService();


  		




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    public IRegistrationService getRegistrationService();


  		




  
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	/**


  		




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	 * @return the configured PermissionEvaluator, usually the


  		




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	 *         {@link CdmPermissionEvaluator}


  		




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	void authenticate(String username, String password);


  		




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    public IRegistrationService getRegistrationService();


  		




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}


  		












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