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// $Id$
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/**
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* Copyright (C) 2013 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.taxeditor.view.derivateSearch;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Map.Entry;
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import java.util.Set;
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import java.util.UUID;
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import org.eclipse.jface.viewers.ColumnLabelProvider;
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import org.eclipse.jface.viewers.TreeNode;
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import org.eclipse.swt.graphics.Image;
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import org.hibernate.LazyInitializationException;
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import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
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import eu.etaxonomy.cdm.api.service.IOccurrenceService;
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import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.format.CdmFormatterFactory;
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import eu.etaxonomy.cdm.format.ICdmFormatter.FormatKey;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DefinedTerm;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.Identifier;
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import eu.etaxonomy.cdm.model.molecular.DnaSample;
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import eu.etaxonomy.cdm.model.molecular.Sequence;
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import eu.etaxonomy.cdm.model.molecular.SingleRead;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
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import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
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import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
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import eu.etaxonomy.taxeditor.model.ImageResources;
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import eu.etaxonomy.taxeditor.store.CdmStore;
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/**
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* Label provider for the views to show {@link SpecimenOrObservationBase}s.<br>
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* <br>
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* <b>Note:</b> If you use this label provider you need to assure that you
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* created a {@link ConversationHolder} resp. have an open session because
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* the labels are generated from various fields of the derivate hierarchy which
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* are lazy loaded and could therefore throw a {@link LazyInitializationException}.<br>
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* Use <b>{@link #setConversation(ConversationHolder)}</b> to assign the session to this provider.
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*/
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public class DerivateLabelProvider extends ColumnLabelProvider {
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private static final String NO_SAMPLE_DESIGNATION = "[no sample designation]";
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private static Set<SingleRead> multiLinkSingleReads;
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private static Map<DerivedUnit, Collection<SpecimenTypeDesignation>> typeDesignations;
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private ConversationHolder conversation;
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private static DefinedTerm photoTerm = null;
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private static DefinedTerm drawingTerm = null;
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private static DefinedTerm specimenScanTerm = null;
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private static DefinedTerm detailImageTerm = null;
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private static DefinedTerm sampleDesignationTerm = null;
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//FIXME: move static term getters to new singleton utility class
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private static void initializeTerms() {
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List<DefinedTerm> preferredTerms = CdmStore.getTermManager().getPreferredTerms(DefinedTerm.class);
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for (DefinedTerm definedTerm : preferredTerms) {
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if(definedTerm.getUuid().equals(UUID.fromString("c5c59c42-f254-471e-96c6-09f459f7c903"))){
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photoTerm = definedTerm;
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}
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else if(definedTerm.getUuid().equals(UUID.fromString("669b0409-4aa4-4695-aae4-a95ed27bad4c"))){
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drawingTerm = definedTerm;
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}
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else if(definedTerm.getUuid().equals(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))){
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specimenScanTerm = definedTerm;
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}
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else if(definedTerm.getUuid().equals(UUID.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))){
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detailImageTerm = definedTerm;
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}
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else if(definedTerm.getUuid().equals(UUID.fromString("fadeba12-1be3-4bc7-9ff5-361b088d86fc"))){
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sampleDesignationTerm = definedTerm;
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}
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}
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}
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public static DefinedTerm getLivingPlantPhotoTerm(){
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if(photoTerm==null){
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initializeTerms();
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}
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return photoTerm;
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}
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public static DefinedTerm getArtworkTerm(){
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if(drawingTerm==null){
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initializeTerms();
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}
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return drawingTerm;
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}
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public static DefinedTerm getSpecimenScanTerm(){
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if(specimenScanTerm==null){
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initializeTerms();
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}
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return specimenScanTerm;
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}
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public static DefinedTerm getDetailImageTerm(){
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if(detailImageTerm==null){
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initializeTerms();
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}
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return detailImageTerm;
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}
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public static DefinedTerm getSampleDesignationTerm(){
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if(sampleDesignationTerm==null){
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initializeTerms();
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}
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return sampleDesignationTerm;
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}
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/** {@inheritDoc} */
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@Override
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public String getText(Object element) {
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if(element instanceof TreeNode){
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element = ((TreeNode) element).getValue();
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}
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FormatKey[] formatKeys = {
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FormatKey.GATHERING_COUNTRY, FormatKey.SPACE,
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FormatKey.GATHERING_LOCALITY_TEXT, FormatKey.SPACE,
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FormatKey.GATHERING_DATE, FormatKey.SPACE,
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FormatKey.GATHERING_COLLECTOR, FormatKey.SPACE,
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FormatKey.FIELD_NUMBER, FormatKey.SPACE,
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FormatKey.COLLECTION_CODE, FormatKey.SPACE,
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FormatKey.MOST_SIGNIFICANT_IDENTIFIER, FormatKey.SPACE,
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// FormatKey.KIND_OF_UNIT, FormatKey.SPACE,
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FormatKey.SAMPLE_DESIGNATION, FormatKey.SPACE,
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FormatKey.SINGLE_READ_PRIMER, FormatKey.SPACE,
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FormatKey.SEQUENCE_DNA_MARKER, FormatKey.SPACE,
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FormatKey.AMPLIFICATION_LABEL, FormatKey.SPACE,
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FormatKey.MEDIA_TITLE, FormatKey.SPACE,
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FormatKey.MEDIA_ARTIST, FormatKey.SPACE
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};
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String text = CdmFormatterFactory.format(element, formatKeys);
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if(element instanceof IdentifiableEntity){
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IdentifiableEntity identifiableEntity = (IdentifiableEntity) element;
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if(identifiableEntity.isProtectedTitleCache()){
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text = identifiableEntity.getTitleCache();
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}
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}
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if(CdmUtils.isBlank(text)){
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return "[-]";
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}
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return text;
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}
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/** {@inheritDoc} */
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@Override
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public String getToolTipText(Object element) {
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return getDerivateText(element);
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}
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/**
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* @param conversation the conversation to set
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*/
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public void setConversation(ConversationHolder conversation) {
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this.conversation = conversation;
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}
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public String getDerivateText(Object element){
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return getDerivateText(element, conversation);
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}
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public static String getDerivateText(Object element, ConversationHolder conversation){
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//TODO: use list of strings to assemble labels to avoid adding the separator every time and to allow null values
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TreeNode parentNode = null;
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TreeNode node = null;
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Object derivate = element;
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if(element instanceof TreeNode){
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node = (TreeNode) element;
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parentNode = node.getParent();
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//unwrap specimen from TreeNode
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derivate = node.getValue();
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}
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if(conversation!=null){
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conversation.bind();
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}
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final String emptyString = "";
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final String separator = " ";
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String label = emptyString;
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//Field Unit
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if(derivate instanceof FieldUnit){
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FieldUnit fieldUnit = (FieldUnit)derivate;
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if(fieldUnit.getGatheringEvent()!=null){
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GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
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label += gatheringEvent.getCountry()!=null?gatheringEvent.getCountry().getLabel()+separator:emptyString;
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label += gatheringEvent.getLocality()!=null?gatheringEvent.getLocality().getText()+separator:emptyString;
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label += gatheringEvent.getGatheringDate()!=null?gatheringEvent.getGatheringDate()+separator:emptyString;
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label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
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}
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label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber():emptyString;
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}
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//MediaSpecimen
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else if(derivate instanceof MediaSpecimen){
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MediaSpecimen mediaSpecimen = (MediaSpecimen)derivate;
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if(mediaSpecimen.getMediaSpecimen()!=null){
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label += mediaSpecimen.getMediaSpecimen().getTitle()!=null?mediaSpecimen.getMediaSpecimen().getTitle().getText()+separator:"[no motif]";
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label += mediaSpecimen.getMediaSpecimen().getArtist()!=null?mediaSpecimen.getMediaSpecimen().getArtist()+separator:emptyString;
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}
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eu.etaxonomy.cdm.model.occurrence.Collection collection = mediaSpecimen.getCollection();
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if(collection!=null){
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label += collection.getName()!=null?collection.getName()+" ":emptyString;
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label += collection.getCode()!=null?"("+collection.getCode()+")"+separator:emptyString;
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}
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label += mediaSpecimen.getAccessionNumber()!=null?mediaSpecimen.getAccessionNumber()+separator:emptyString;
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label += mediaSpecimen.getBarcode()!=null?mediaSpecimen.getBarcode()+separator:emptyString;
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}
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//TissueSample + DnaSample
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else if(derivate instanceof DnaSample){
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DnaSample dnaSample = (DnaSample)derivate;
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if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.DnaSample){
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Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
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if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
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label += currentSampleDesignation.getIdentifier()+separator;
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}
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else{
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label += NO_SAMPLE_DESIGNATION+separator;
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}
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}
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else if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.TissueSample){
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if(dnaSample.getKindOfUnit()!=null){
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label += dnaSample.getKindOfUnit()+separator;
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}
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Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
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if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
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label += currentSampleDesignation.getIdentifier()+separator;
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}
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else{
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label += NO_SAMPLE_DESIGNATION+separator;
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}
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}
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}
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//DerivedUnit + TissueSample
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else if(derivate instanceof DerivedUnit){
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DerivedUnit derivedUnit = (DerivedUnit)derivate;
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if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
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//check for type designation
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if(typeDesignations.get(derivedUnit)==null){
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for (SpecimenTypeDesignation specimenTypeDesignation : CdmStore.getService(IOccurrenceService.class).listTypeDesignations(derivedUnit, null, null, null, null)) {
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addTypeDesignation(derivedUnit, specimenTypeDesignation);
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}
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}
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//java.util.Collection<FieldUnit> fieldUnits = CdmStore.getService(IOccurrenceService.class).getFieldUnits(derivedUnit.getUuid());
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//TODO : This is not generic anymore for performance reasons
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Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
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if(originals!=null && originals.size() ==1) {
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SpecimenOrObservationBase specimen = originals.iterator().next();
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if(specimen instanceof FieldUnit) {
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FieldUnit fieldUnit = (FieldUnit)specimen;
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GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
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if(gatheringEvent!=null){
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label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
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}
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label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber()+separator:emptyString;
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}
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}
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eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
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if(collection!=null){
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label += collection.getCode()!=null?"("+collection.getCode()+")"+separator:emptyString;
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}
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String mostSignificantIdentifier = derivedUnit.getMostSignificantIdentifier();
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label += mostSignificantIdentifier!=null?mostSignificantIdentifier+separator:emptyString;
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}
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else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
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//TissueSample should only be created by using it's own class
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//in future using only one class with different SpecimenOrObservationTypes is desired
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// label += derivedUnit.getKindOfUnit() + NO_SAMPLE_DESIGNATION;
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}
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}
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//Sequence
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else if(derivate instanceof Sequence){
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Sequence sequence = (Sequence)derivate;
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Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
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if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
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label += currentSampleDesignation.getIdentifier()+separator;
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}
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else{
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label += NO_SAMPLE_DESIGNATION+separator;
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}
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label += sequence.getDnaMarker()!=null?sequence.getDnaMarker():emptyString;
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}
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//SingleRead
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else if(derivate instanceof SingleRead){
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SingleRead singleRead = (SingleRead)derivate;
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if(parentNode!=null && parentNode.getValue() instanceof Sequence){
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Sequence sequence = (Sequence) parentNode.getValue();
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Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
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if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
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label = currentSampleDesignation.getIdentifier()+separator;
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}
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else{
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label += NO_SAMPLE_DESIGNATION+separator;
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}
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label += singleRead.getPrimer()!=null?singleRead.getPrimer().getLabel()+separator:emptyString;
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if(sequence!=null && sequence.getDnaMarker()!=null){
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label += sequence.getDnaMarker()+separator;
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}
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if(singleRead.getAmplificationResult()!=null && singleRead.getAmplificationResult().getAmplification()!=null){
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label += singleRead.getAmplificationResult().getAmplification().getLabelCache()+separator;
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}
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}
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}
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//SOOB
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else if(derivate instanceof SpecimenOrObservationBase){
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SpecimenOrObservationBase<?> specimen = (SpecimenOrObservationBase<?>) derivate;
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SpecimenOrObservationType type = specimen.getRecordBasis();
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return specimen.getTitleCache() + (type!=null?" ["+type.toString()+"]":emptyString);
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}
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337
|
if(label.isEmpty()){
|
|
338
|
label = derivate.toString();
|
|
339
|
}
|
|
340
|
//remove last comma
|
|
341
|
else if(label.endsWith(separator)){
|
|
342
|
label = label.substring(0, label.length()-separator.length());
|
|
343
|
}
|
|
344
|
return label;
|
|
345
|
}
|
|
346
|
|
|
347
|
@Override
|
|
348
|
public Image getImage(Object element) {
|
|
349
|
if(element instanceof TreeNode){
|
|
350
|
element = ((TreeNode) element).getValue();
|
|
351
|
}
|
|
352
|
if(element instanceof CdmBase){
|
|
353
|
CdmBase cdmBase = (CdmBase)element;
|
|
354
|
boolean hasCharacterData = false;
|
|
355
|
if(cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
|
|
356
|
SpecimenOrObservationBase<?> specimen = HibernateProxyHelper.deproxy(cdmBase, SpecimenOrObservationBase.class);
|
|
357
|
if(specimen.hasCharacterData()){
|
|
358
|
hasCharacterData = true;
|
|
359
|
}
|
|
360
|
}
|
|
361
|
if(cdmBase.isInstanceOf(FieldUnit.class)){
|
|
362
|
return hasCharacterData?ImageResources.getImage(ImageResources.FIELD_UNIT_CHARACTER_DATA):ImageResources.getImage(ImageResources.FIELD_UNIT);
|
|
363
|
}
|
|
364
|
else if(cdmBase.isInstanceOf(DerivedUnit.class)){
|
|
365
|
DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(element, DerivedUnit.class);
|
|
366
|
|
|
367
|
if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.FieldUnit){
|
|
368
|
return hasCharacterData?ImageResources.getImage(ImageResources.FIELD_UNIT_CHARACTER_DATA):ImageResources.getImage(ImageResources.FIELD_UNIT);
|
|
369
|
}
|
|
370
|
else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.DnaSample){
|
|
371
|
return hasCharacterData?ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE);
|
|
372
|
}
|
|
373
|
else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
|
|
374
|
return hasCharacterData?ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE);
|
|
375
|
}
|
|
376
|
else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
|
|
377
|
if(typeDesignations.get(derivedUnit)!=null && !typeDesignations.get(derivedUnit).isEmpty()){
|
|
378
|
return ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE_TYPE);
|
|
379
|
}
|
|
380
|
return hasCharacterData?ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE);
|
|
381
|
}
|
|
382
|
else if(derivedUnit.getRecordBasis().isKindOf(SpecimenOrObservationType.Media)){
|
|
383
|
if(derivedUnit.getKindOfUnit()!=null){
|
|
384
|
if(derivedUnit.getKindOfUnit().equals(getArtworkTerm())){
|
|
385
|
return hasCharacterData?ImageResources.getImage(ImageResources.ARTWORK_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.ARTWORK_DERIVATE);
|
|
386
|
}
|
|
387
|
else if(derivedUnit.getKindOfUnit().equals(getLivingPlantPhotoTerm())){
|
|
388
|
return hasCharacterData?ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE);
|
|
389
|
}
|
|
390
|
else if(derivedUnit.getKindOfUnit().equals(getSpecimenScanTerm())){
|
|
391
|
return hasCharacterData?ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE);
|
|
392
|
}
|
|
393
|
else if(derivedUnit.getKindOfUnit().equals(getDetailImageTerm())){
|
|
394
|
return hasCharacterData?ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE);
|
|
395
|
}
|
|
396
|
}
|
|
397
|
}
|
|
398
|
}
|
|
399
|
else if(cdmBase.isInstanceOf(Sequence.class)){
|
|
400
|
return ImageResources.getImage(ImageResources.SEQUENCE_DERIVATE);
|
|
401
|
}
|
|
402
|
|
|
403
|
else if(cdmBase.isInstanceOf(SingleRead.class)){
|
|
404
|
if(multiLinkSingleReads!=null && multiLinkSingleReads.contains(element)){
|
|
405
|
return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE_MULTILINK);
|
|
406
|
}
|
|
407
|
else{
|
|
408
|
return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE);
|
|
409
|
}
|
|
410
|
}
|
|
411
|
}
|
|
412
|
return ImageResources.getImage(ImageResources.DEFAULT_DERIVATIVE);
|
|
413
|
}
|
|
414
|
|
|
415
|
public static Identifier<DnaSample> getCurrentSampleDesignation(CdmBase entity) {
|
|
416
|
if(entity.isInstanceOf(DnaSample.class)){
|
|
417
|
DnaSample dnaSample = HibernateProxyHelper.deproxy(entity, DnaSample.class);
|
|
418
|
for (Identifier<DnaSample> identifier : dnaSample.getIdentifiers()) {
|
|
419
|
if(identifier.getType()!=null && identifier.getType().equals(DerivateLabelProvider.getSampleDesignationTerm())){
|
|
420
|
//first sample designation is the current
|
|
421
|
return identifier;
|
|
422
|
}
|
|
423
|
}
|
|
424
|
}
|
|
425
|
else if(entity.isInstanceOf(Sequence.class)){
|
|
426
|
Sequence sequence = HibernateProxyHelper.deproxy(entity, Sequence.class);
|
|
427
|
if(sequence.getDnaSample()!=null){
|
|
428
|
return getCurrentSampleDesignation(sequence.getDnaSample());
|
|
429
|
}
|
|
430
|
}
|
|
431
|
return null;
|
|
432
|
}
|
|
433
|
|
|
434
|
private static void addTypeDesignation(DerivedUnit derivedUnit, SpecimenTypeDesignation typeDesignation){
|
|
435
|
Collection<SpecimenTypeDesignation> list = typeDesignations.get(derivedUnit);
|
|
436
|
if(list==null){
|
|
437
|
list = new ArrayList<SpecimenTypeDesignation>();
|
|
438
|
}
|
|
439
|
list.add(typeDesignation);
|
|
440
|
typeDesignations.put(derivedUnit, list);
|
|
441
|
}
|
|
442
|
|
|
443
|
public static Set<SingleRead> getMultiLinkSingleReads() {
|
|
444
|
return multiLinkSingleReads;
|
|
445
|
}
|
|
446
|
|
|
447
|
public void updateLabelCache(Collection<SpecimenOrObservationBase<?>> rootElements) {
|
|
448
|
multiLinkSingleReads = new HashSet<SingleRead>();
|
|
449
|
typeDesignations = new HashMap<DerivedUnit, Collection<SpecimenTypeDesignation>>();
|
|
450
|
for(Entry<SingleRead, Collection<Sequence>> entry:CdmStore.getService(ISequenceService.class).getSingleReadSequencesMap().entrySet()){
|
|
451
|
if(entry.getValue().size()>1){
|
|
452
|
multiLinkSingleReads.add(entry.getKey());
|
|
453
|
}
|
|
454
|
}
|
|
455
|
if(rootElements!=null){
|
|
456
|
Collection<DerivedUnit> derivedUnits = new ArrayList<DerivedUnit>();
|
|
457
|
for (SpecimenOrObservationBase specimenOrObservationBase : rootElements) {
|
|
458
|
derivedUnits.addAll(CdmStore.getService(IOccurrenceService.class).getAllChildDerivatives(specimenOrObservationBase.getUuid()));
|
|
459
|
if(specimenOrObservationBase.isInstanceOf(DerivedUnit.class)){
|
|
460
|
derivedUnits.add(HibernateProxyHelper.deproxy(specimenOrObservationBase, DerivedUnit.class));
|
|
461
|
}
|
|
462
|
}
|
|
463
|
typeDesignations = CdmStore.getService(IOccurrenceService.class).listTypeDesignations(derivedUnits, null, null, null, null);
|
|
464
|
}
|
|
465
|
}
|
|
466
|
|
|
467
|
}
|