import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
import eu.etaxonomy.cdm.api.service.IOccurrenceService;
+import eu.etaxonomy.cdm.model.common.CdmBase;
import eu.etaxonomy.cdm.model.common.DefinedTerm;
+import eu.etaxonomy.cdm.model.common.Identifier;
import eu.etaxonomy.cdm.model.molecular.DnaSample;
import eu.etaxonomy.cdm.model.molecular.Sequence;
import eu.etaxonomy.cdm.model.molecular.SingleRead;
*/
public class DerivateLabelProvider extends ColumnLabelProvider {
+ private static final String NO_SAMPLE_DESIGNATION = "[no sample designation]";
+
private Set<SingleRead> multiLinkSingleReads;
private ConversationHolder conversation;
private static DefinedTerm drawingTerm = null;
private static DefinedTerm specimenScanTerm = null;
private static DefinedTerm detailImageTerm = null;
+ private static DefinedTerm sampleDesignationTerm = null;
+ //FIXME: move static term getters to new singleton utility class
private static void initializeTerms() {
List<DefinedTerm> preferredTerms = CdmStore.getTermManager().getPreferredTerms(DefinedTerm.class);
for (DefinedTerm definedTerm : preferredTerms) {
else if(definedTerm.getUuid().equals(UUID.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))){
detailImageTerm = definedTerm;
}
+ else if(definedTerm.getUuid().equals(UUID.fromString("fadeba12-1be3-4bc7-9ff5-361b088d86fc"))){
+ sampleDesignationTerm = definedTerm;
+ }
}
}
return detailImageTerm;
}
+ public static DefinedTerm getSampleDesignationTerm(){
+ if(sampleDesignationTerm==null){
+ initializeTerms();
+ }
+ return sampleDesignationTerm;
+ }
+
/** {@inheritDoc} */
@Override
this.conversation = conversation;
}
- /**
- *
- * @param element
- * @return
- */
public String getDerivateText(Object element){
+ return getDerivateText(element, conversation);
+ }
+
+ public static String getDerivateText(Object element, ConversationHolder conversation){
+ //TODO: use list of strings to assemble labels to avoid adding the separator every time and to allow null values
TreeNode parentNode = null;
+ TreeNode node = null;
+ Object derivate = element;
if(element instanceof TreeNode){
- parentNode = ((TreeNode) element).getParent();
+ node = (TreeNode) element;
+ parentNode = node.getParent();
//unwrap specimen from TreeNode
- element = ((TreeNode) element).getValue();
+ derivate = node.getValue();
}
conversation.bind();
- String label = "";
- if(element instanceof FieldUnit){
- FieldUnit fieldUnit = (FieldUnit)element;
+ final String emptyString = "";
+ final String separator = ", ";
+
+ String label = emptyString;
+
+ //Field Unit
+ if(derivate instanceof FieldUnit){
+ FieldUnit fieldUnit = (FieldUnit)derivate;
if(fieldUnit.getGatheringEvent()!=null){
GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
- if(!conversation.getSession().contains(gatheringEvent)){
+ if(CdmStore.getService(IOccurrenceService.class).exists(fieldUnit.getUuid()) && !conversation.getSession().contains(gatheringEvent)){
fieldUnit = (FieldUnit) CdmStore.getService(IOccurrenceService.class).load(fieldUnit.getUuid());
gatheringEvent = fieldUnit.getGatheringEvent();
}
- label += gatheringEvent.getCountry()!=null?gatheringEvent.getCountry().getLabel()+", ":"";
- label += gatheringEvent.getLocality()!=null?gatheringEvent.getLocality().getText()+", ":"";
- label += gatheringEvent.getGatheringDate()!=null?gatheringEvent.getGatheringDate()+", ":"";
- label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+", ":"";
+ label += gatheringEvent.getCountry()!=null?gatheringEvent.getCountry().getLabel()+separator:emptyString;
+ label += gatheringEvent.getLocality()!=null?gatheringEvent.getLocality().getText()+separator:emptyString;
+ label += gatheringEvent.getGatheringDate()!=null?gatheringEvent.getGatheringDate()+separator:emptyString;
+ label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
}
- label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber():"";
+ label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber():emptyString;
}
- else if(element instanceof MediaSpecimen){
- MediaSpecimen mediaSpecimen = (MediaSpecimen)element;
+ //MediaSpecimen
+ else if(derivate instanceof MediaSpecimen){
+ MediaSpecimen mediaSpecimen = (MediaSpecimen)derivate;
if(mediaSpecimen.getMediaSpecimen()!=null){
- label += mediaSpecimen.getMediaSpecimen().getTitle()!=null?mediaSpecimen.getMediaSpecimen().getTitle().getText()+", ":"[no motif]";
- label += mediaSpecimen.getMediaSpecimen().getArtist()!=null?mediaSpecimen.getMediaSpecimen().getArtist()+", ":"";
+ label += mediaSpecimen.getMediaSpecimen().getTitle()!=null?mediaSpecimen.getMediaSpecimen().getTitle().getText()+separator:"[no motif]";
+ label += mediaSpecimen.getMediaSpecimen().getArtist()!=null?mediaSpecimen.getMediaSpecimen().getArtist()+separator:emptyString;
}
eu.etaxonomy.cdm.model.occurrence.Collection collection = mediaSpecimen.getCollection();
if(collection!=null){
- label += collection.getName()!=null?collection.getName()+" ":"";
- label += collection.getCode()!=null?"("+collection.getCode()+"), ":"";
+ label += collection.getName()!=null?collection.getName()+" ":emptyString;
+ label += collection.getCode()!=null?"("+collection.getCode()+")"+separator:emptyString;
}
- label += mediaSpecimen.getAccessionNumber()!=null?mediaSpecimen.getAccessionNumber()+", ":"";
+ label += mediaSpecimen.getAccessionNumber()!=null?mediaSpecimen.getAccessionNumber()+separator:emptyString;
}
- else if(element instanceof DnaSample
- || (element instanceof DerivedUnit
- && ((SpecimenOrObservationBase<?>) element).getRecordBasis()==SpecimenOrObservationType.DnaSample)){
- label += "[no sample designation]";
+ //TissueSample + DnaSample
+ else if(derivate instanceof DnaSample){
+ DnaSample dnaSample = (DnaSample)derivate;
+ if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.DnaSample){
+ Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
+ if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
+ label += currentSampleDesignation.getIdentifier()+separator;
+ }
+ else{
+ label += NO_SAMPLE_DESIGNATION+separator;
+ }
+ }
+ else if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.TissueSample){
+ label += dnaSample.getKindOfUnit()+separator;
+ Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
+ if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
+ label += currentSampleDesignation.getIdentifier()+separator;
+ }
+ else{
+ label += NO_SAMPLE_DESIGNATION+separator;
+ }
+ }
}
- else if(element instanceof DerivedUnit){
- DerivedUnit derivedUnit = (DerivedUnit)element;
+ //DerivedUnit + TissueSample
+ else if(derivate instanceof DerivedUnit){
+ DerivedUnit derivedUnit = (DerivedUnit)derivate;
if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
java.util.Collection<FieldUnit> fieldUnits = CdmStore.getService(IOccurrenceService.class).getFieldUnits(derivedUnit.getUuid());
if(fieldUnits!=null && !fieldUnits.isEmpty()){
FieldUnit fieldUnit = fieldUnits.iterator().next();
GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
-// gatheringEvent = HibernateProxyHelper.deproxy(gatheringEvent, GatheringEvent.class);
+// gatheringEvent = HibernateProxyHelper.deproxy(gatheringEvent, GatheringEvent.class);
if(gatheringEvent!=null){
- label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+", ":"";
+ label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
}
- label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber()+", ":"";
+ label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber()+separator:emptyString;
}
eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
if(collection!=null){
- label += collection.getName()!=null?collection.getName()+" ":"";
- label += collection.getCode()!=null?"("+collection.getCode()+"), ":"";
+ label += collection.getName()!=null?collection.getName()+" ":emptyString;
+ label += collection.getCode()!=null?"("+collection.getCode()+"), ":emptyString;
}
- label += derivedUnit.getAccessionNumber()!=null?derivedUnit.getAccessionNumber()+", ":"";
- label += derivedUnit.getBarcode()!=null?derivedUnit.getBarcode():"";
+ label += derivedUnit.getAccessionNumber()!=null?derivedUnit.getAccessionNumber()+separator:emptyString;
+ label += derivedUnit.getBarcode()!=null?derivedUnit.getBarcode():emptyString;
}
else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
- //TODO: implement
- label += "kindofTissue? + [no sample designation]";
+ //TissueSample should only be created by using it's own class
+ //in future using only one class with different SpecimenOrObservationTypes is desired
+// label += derivedUnit.getKindOfUnit() + NO_SAMPLE_DESIGNATION;
}
}
- else if(element instanceof Sequence){
- Sequence sequence = (Sequence)element;
- label += "[no sample designation]"+", ";
- label += sequence.getDnaMarker()!=null?sequence.getDnaMarker():"";
+ //Sequence
+ else if(derivate instanceof Sequence){
+ Sequence sequence = (Sequence)derivate;
+ Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
+ if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
+ label += currentSampleDesignation.getIdentifier()+separator;
+ }
+ else{
+ label += NO_SAMPLE_DESIGNATION+separator;
+ }
+ label += sequence.getDnaMarker()!=null?sequence.getDnaMarker():emptyString;
}
- else if(element instanceof SingleRead){
- SingleRead singleRead = (SingleRead)element;
- label += "[no sample designation]"+", ";
- label += singleRead.getPrimer()!=null?singleRead.getPrimer().getLabel()+", ":"";
+ //SingleRead
+ else if(derivate instanceof SingleRead){
+ SingleRead singleRead = (SingleRead)derivate;
if(parentNode!=null && parentNode.getValue() instanceof Sequence){
Sequence sequence = (Sequence) parentNode.getValue();
- label += sequence.getDnaMarker()!=null?sequence.getDnaMarker():"";
+ Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
+ if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
+ label = currentSampleDesignation.getIdentifier()+separator;
+ }
+ else{
+ label += NO_SAMPLE_DESIGNATION+separator;
+ }
+ label += singleRead.getPrimer()!=null?singleRead.getPrimer().getLabel()+separator:emptyString;
+ if(sequence!=null){
+ label += sequence.getDnaMarker()!=null?sequence.getDnaMarker():emptyString;
+ }
}
}
- else if(element instanceof SpecimenOrObservationBase){
- SpecimenOrObservationBase<?> derivate = (SpecimenOrObservationBase<?>) element;
- SpecimenOrObservationType type = derivate.getRecordBasis();
- return derivate.getTitleCache() + (type!=null?" ["+type.toString()+"]":"");
+ //SOOB
+ else if(derivate instanceof SpecimenOrObservationBase){
+ SpecimenOrObservationBase<?> specimen = (SpecimenOrObservationBase<?>) derivate;
+ SpecimenOrObservationType type = specimen.getRecordBasis();
+ return specimen.getTitleCache() + (type!=null?" ["+type.toString()+"]":emptyString);
}
if(label.isEmpty()){
- label = element.toString();
+ label = derivate.toString();
}
//remove last comma
- else if(label.endsWith(", ")){
- label = label.substring(0, label.length()-2);
+ else if(label.endsWith(separator)){
+ label = label.substring(0, label.length()-separator.length());
}
return label;
}
return super.getImage(element);
}
+ public static Identifier<DnaSample> getCurrentSampleDesignation(CdmBase entity) {
+ if(entity instanceof DnaSample){
+ DnaSample dnaSample = (DnaSample)entity;
+ for (Identifier<DnaSample> identifier : dnaSample.getIdentifiers()) {
+ if(identifier.getType()!=null && identifier.getType().equals(DerivateLabelProvider.getSampleDesignationTerm())){
+ //first sample designation is the current
+ return identifier;
+ }
+ }
+ }
+ else if(entity instanceof Sequence){
+ Sequence sequence = (Sequence)entity;
+ if(sequence.getDnaSample()!=null){
+ return getCurrentSampleDesignation(sequence.getDnaSample());
+ }
+ }
+ return null;
+ }
+
/**
* @param multiLinkSingleReads2
*/
BGBM BDI Projects / taxeditor.git / blobdiff