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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.List;
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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.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DefinedTerm;
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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.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 Set<SingleRead> multiLinkSingleReads;
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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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return getDerivateText(element);
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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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conversation.bind();
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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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if(CdmStore.getService(IOccurrenceService.class).exists(fieldUnit.getUuid()) && !conversation.getSession().contains(gatheringEvent)){
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fieldUnit = (FieldUnit) CdmStore.getService(IOccurrenceService.class).load(fieldUnit.getUuid());
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gatheringEvent = fieldUnit.getGatheringEvent();
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}
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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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java.util.Collection<FieldUnit> fieldUnits = CdmStore.getService(IOccurrenceService.class).getFieldUnits(derivedUnit.getUuid());
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if(fieldUnits!=null && !fieldUnits.isEmpty()){
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FieldUnit fieldUnit = fieldUnits.iterator().next();
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GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
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// gatheringEvent = HibernateProxyHelper.deproxy(gatheringEvent, GatheringEvent.class);
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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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eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.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()+"), ":emptyString;
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}
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String mostSignificantIdentifier = CdmStore.getService(IOccurrenceService.class).getMostSignificantIdentifier(derivedUnit);
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label += mostSignificantIdentifier!=null?mostSignificantIdentifier+separator:emptyString;
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label += derivedUnit.getBarcode()!=null?derivedUnit.getBarcode():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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if(label.isEmpty()){
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label = derivate.toString();
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}
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//remove last comma
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else if(label.endsWith(separator)){
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label = label.substring(0, label.length()-separator.length());
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}
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return label;
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}
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/* (non-Javadoc)
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* @see org.eclipse.jface.viewers.ColumnLabelProvider#getImage(java.lang.Object)
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*/
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@Override
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public Image getImage(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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if(element instanceof CdmBase){
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CdmBase cdmBase = (CdmBase)element;
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// boolean hasCharacterData = false;
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// if(cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
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// SpecimenOrObservationBase specimen = HibernateProxyHelper.deproxy(cdmBase, SpecimenOrObservationBase.class);
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// if(!CdmStore.getService(IOccurrenceService.class).getCharacterDataForSpecimen(specimen).isEmpty()){
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// hasCharacterData = true;
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// return ImageResources.getImage(ImageResources.CHARACTER_DATA_DERIVATE);
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// }
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// }
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if(cdmBase.isInstanceOf(FieldUnit.class)){
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return ImageResources.getImage(ImageResources.FIELD_UNIT);
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}
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else if(cdmBase.isInstanceOf(DerivedUnit.class)){
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DerivedUnit derivedUnit = (DerivedUnit)element;
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if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.FieldUnit){
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return ImageResources.getImage(ImageResources.FIELD_UNIT);
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}
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else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.DnaSample){
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return ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE);
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}
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else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
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return ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE);
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}
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else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
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return ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE);
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}
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else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.Media){
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if(derivedUnit.getKindOfUnit()!=null){
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if(derivedUnit.getKindOfUnit().equals(getArtworkTerm())){
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334
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return ImageResources.getImage(ImageResources.ARTWORK_DERIVATE);
|
|
335
|
}
|
|
336
|
else if(derivedUnit.getKindOfUnit().equals(getLivingPlantPhotoTerm())){
|
|
337
|
return ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE);
|
|
338
|
}
|
|
339
|
else if(derivedUnit.getKindOfUnit().equals(getSpecimenScanTerm())){
|
|
340
|
return ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE);
|
|
341
|
}
|
|
342
|
else if(derivedUnit.getKindOfUnit().equals(getDetailImageTerm())){
|
|
343
|
return ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE);
|
|
344
|
}
|
|
345
|
}
|
|
346
|
}
|
|
347
|
}
|
|
348
|
else if(cdmBase.isInstanceOf(Sequence.class)){
|
|
349
|
return ImageResources.getImage(ImageResources.SEQUENCE_DERIVATE);
|
|
350
|
}
|
|
351
|
|
|
352
|
else if(cdmBase.isInstanceOf(SingleRead.class)){
|
|
353
|
if(multiLinkSingleReads.contains(element)){
|
|
354
|
return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE_MULTILINK);
|
|
355
|
}
|
|
356
|
else{
|
|
357
|
return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE);
|
|
358
|
}
|
|
359
|
}
|
|
360
|
}
|
|
361
|
return super.getImage(element);
|
|
362
|
}
|
|
363
|
|
|
364
|
public static Identifier<DnaSample> getCurrentSampleDesignation(CdmBase entity) {
|
|
365
|
if(entity instanceof DnaSample){
|
|
366
|
DnaSample dnaSample = (DnaSample)entity;
|
|
367
|
for (Identifier<DnaSample> identifier : dnaSample.getIdentifiers()) {
|
|
368
|
if(identifier.getType()!=null && identifier.getType().equals(DerivateLabelProvider.getSampleDesignationTerm())){
|
|
369
|
//first sample designation is the current
|
|
370
|
return identifier;
|
|
371
|
}
|
|
372
|
}
|
|
373
|
}
|
|
374
|
else if(entity instanceof Sequence){
|
|
375
|
Sequence sequence = (Sequence)entity;
|
|
376
|
if(sequence.getDnaSample()!=null){
|
|
377
|
return getCurrentSampleDesignation(sequence.getDnaSample());
|
|
378
|
}
|
|
379
|
}
|
|
380
|
return null;
|
|
381
|
}
|
|
382
|
|
|
383
|
/**
|
|
384
|
* @param multiLinkSingleReads2
|
|
385
|
*/
|
|
386
|
public void setMultiLinkSingleReads(Set<SingleRead> multiLinkSingleReads) {
|
|
387
|
this.multiLinkSingleReads = multiLinkSingleReads;
|
|
388
|
}
|
|
389
|
|
|
390
|
}
|