From: Patric Plitzner
Date: Wed, 12 Nov 2014 14:35:23 +0000 (+0000)
Subject: - updated molecular DetailsViews according to requirements
X-Git-Tag: 3.6.0~367
X-Git-Url: https://dev.e-taxonomy.eu/gitweb/taxeditor.git/commitdiff_plain/686f8a4c887d08bf8e08d6f18378abddec0d03fa
- updated molecular DetailsViews according to requirements
---
diff --git a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationGeneralDetailElement.java b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationGeneralDetailElement.java
index 6b335ba22..1844b0025 100644
--- a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationGeneralDetailElement.java
+++ b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationGeneralDetailElement.java
@@ -10,15 +10,15 @@
package eu.etaxonomy.taxeditor.ui.section.occurrence.dna;
import eu.etaxonomy.cdm.model.agent.AgentBase;
+import eu.etaxonomy.cdm.model.agent.Institution;
import eu.etaxonomy.cdm.model.common.DefinedTerm;
import eu.etaxonomy.cdm.model.common.TermType;
+import eu.etaxonomy.cdm.model.common.TimePeriod;
import eu.etaxonomy.cdm.model.molecular.Amplification;
-import eu.etaxonomy.cdm.model.occurrence.MaterialOrMethodEvent;
+import eu.etaxonomy.cdm.model.molecular.Primer;
import eu.etaxonomy.taxeditor.ui.combo.TermComboElement;
import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
-import eu.etaxonomy.taxeditor.ui.element.CheckboxElement;
import eu.etaxonomy.taxeditor.ui.element.ICdmFormElement;
-import eu.etaxonomy.taxeditor.ui.element.NumberWithLabelElement;
import eu.etaxonomy.taxeditor.ui.element.TextWithLabelElement;
import eu.etaxonomy.taxeditor.ui.element.TimePeriodElement;
import eu.etaxonomy.taxeditor.ui.section.AbstractCdmDetailElement;
@@ -31,20 +31,24 @@ import eu.etaxonomy.taxeditor.ui.selection.EntitySelectionElement;
*/
public class AmplificationGeneralDetailElement extends AbstractCdmDetailElement {
- private TextWithLabelElement textDescription;
+ private TextWithLabelElement textDesignation;
+ private TextWithLabelElement textNotes;
private TermComboElement comboMarker;
private TimePeriodElement dateAmplification;
+ private EntitySelectionElement selectionInstitution;
private EntitySelectionElement selectionAmplificationStaff;
- private CheckboxElement checkBoxAmplificationSuccess;
- private TextWithLabelElement textAmplificationSuccessDetails;
- private TermComboElement comboAmplificationMaterialOrMethod;
+ private EntitySelectionElement selectionPrimerFW;
+ private EntitySelectionElement selectionPrimerRW;
+// private CheckboxElement checkBoxAmplificationSuccess;
+// private TextWithLabelElement textAmplificationSuccessDetails;
+// private TermComboElement comboAmplificationMaterialOrMethod;
- private NumberWithLabelElement numberGelVoltage;
- private NumberWithLabelElement numberGelConcentration;
- private NumberWithLabelElement numberGelRunningTime;
- private TextWithLabelElement textLadderUsed;
+// private NumberWithLabelElement numberGelVoltage;
+// private NumberWithLabelElement numberGelConcentration;
+// private NumberWithLabelElement numberGelRunningTime;
+// private TextWithLabelElement textLadderUsed;
- private TermComboElement comboPurificationMaterialOrMethod;
+// private TermComboElement comboPurificationMaterialOrMethod;
/**
@@ -64,10 +68,14 @@ public class AmplificationGeneralDetailElement extends AbstractCdmDetailElement<
*/
@Override
protected void createControls(ICdmFormElement formElement, Amplification entity, int style) {
- textDescription = formFactory.createTextWithLabelElement(formElement, "Description", entity.getDescription(), style);
+ textDesignation = formFactory.createTextWithLabelElement(formElement, "Designation", entity.getDescription(), style);
+ textDesignation.setEnabled(false);
+ //TODO institution
+ selectionAmplificationStaff = formFactory.createSelectionElement(AgentBase.class, getConversationHolder(), formElement, "Amplification staff", entity.getActor(), EntitySelectionElement.ALL, style);
+ dateAmplification = formFactory.createTimePeriodElement(formElement, "Date", entity.getTimeperiod(), style);
comboMarker = formFactory.createDefinedTermComboElement(TermType.DnaMarker, formElement, "DNA Marker", entity.getDnaMarker(), style);
-// dateAmplification = formFactory.createTimePeriodElement(formElement, "Amplification Date", entity.getTimeperiod(), style);
-// selectionAmplificationStaff = formFactory.createSelectionElement(AgentBase.class, getConversationHolder(), formElement, "Amplification staff", entity.getActor(), EntitySelectionElement.ALL, style);
+ selectionPrimerFW = formFactory.createSelectionElement(Primer.class, getConversationHolder(), formElement, "Primer FW", entity.getForwardPrimer(), EntitySelectionElement.ALL, style);
+ selectionPrimerRW = formFactory.createSelectionElement(Primer.class, getConversationHolder(), formElement, "Primer RW", entity.getReversePrimer(), EntitySelectionElement.ALL, style);
// checkBoxAmplificationSuccess = formFactory.createCheckbox(formElement, "Amplification Success", entity.getSuccessful(), style);
// textAmplificationSuccessDetails = formFactory.createTextWithLabelElement(formElement, "Ampl. Success Details", entity.getSuccessText(), style);
// comboAmplificationMaterialOrMethod = formFactory.createTermComboElement(DefinedTerm.class, formElement, "Ampl. Mat. & Meth.", entity.get, style)
@@ -75,8 +83,47 @@ public class AmplificationGeneralDetailElement extends AbstractCdmDetailElement<
// numberGelConcentration = formFactory.createNumberTextWithLabelElement(formElement, "Gel Concentration", entity.getGelConcentration(), style);
// numberGelRunningTime = formFactory.createNumberTextWithLabelElement(formElement, "Gel Ruinning Time (Min)", entity.getGelRunningTime(), style);
// textLadderUsed = formFactory.createTextWithLabelElement(formElement, "Ladder Used", entity.getLadderUsed(), style);
- comboPurificationMaterialOrMethod = formFactory.createDefinedTermComboElement(TermType.MaterialOrMethod, formElement, "Purification Mat. & Meth.",
- entity.getPurification()==null?null:entity.getPurification().getDefinedMaterialOrMethod(), style);
+// comboPurificationMaterialOrMethod = formFactory.createDefinedTermComboElement(TermType.MaterialOrMethod, formElement, "Purification Mat. & Meth.",
+// entity.getPurification()==null?null:entity.getPurification().getDefinedMaterialOrMethod(), style);
+ //TODO notes
+ updateDesignationText();
+ }
+
+ private void updateDesignationText(){
+ String institutionName = "";
+ String staffName = "";
+ String dateString = "";
+ //TODO institution
+// Institution selection = selectionInstitution.getSelection();
+// if(selection!=null){
+// institutionName = selection.getName();
+// }
+ AgentBase staff = selectionAmplificationStaff.getSelection();
+ if(staff!=null){
+ staffName = staff.getTitleCache();
+ }
+ TimePeriod timePeriod = dateAmplification.getTimePeriod();
+ if(timePeriod!=null){
+ dateString = timePeriod.toString()!=null?timePeriod.toString():"";
+ }
+ String designation = "";
+ if(!institutionName.equals("")){
+ designation += institutionName;
+ }
+ if(!staffName.equals("")){
+ if(!designation.equals("")){
+ designation += "_";
+ }
+ designation += staffName;
+ }
+ if(!dateString.equals("")){
+ if(!designation.equals("")){
+ designation += "_";
+ }
+ designation += dateString;
+ }
+ textDesignation.setText(designation);
+ getEntity().setDescription(designation);
}
/*
@@ -88,46 +135,58 @@ public class AmplificationGeneralDetailElement extends AbstractCdmDetailElement<
*/
@Override
public void handleEvent(Object eventSource) {
- if(eventSource==textDescription){
- getEntity().setDescription(textDescription.getText());
+ if(eventSource==textNotes){
+ getEntity().setDescription(textNotes.getText());
}
else if(eventSource==comboMarker){
getEntity().setDnaMarker(comboMarker.getSelection());
}
else if(eventSource==dateAmplification){
getEntity().setTimeperiod(dateAmplification.getTimePeriod());
+ updateDesignationText();
}
else if(eventSource==selectionAmplificationStaff){
getEntity().setActor(selectionAmplificationStaff.getEntity());
+ updateDesignationText();
}
- else if(eventSource==checkBoxAmplificationSuccess){
- getEntity().setSuccessful(checkBoxAmplificationSuccess.getSelection());
- }
- else if(eventSource==textAmplificationSuccessDetails){
- getEntity().setSuccessText(textAmplificationSuccessDetails.getText());
- }
- else if(eventSource==comboAmplificationMaterialOrMethod){
-
- }
- else if(eventSource==numberGelVoltage){
- getEntity().setElectrophoresisVoltage(numberGelVoltage.getDouble());
- }
- else if(eventSource==numberGelConcentration){
- getEntity().setGelConcentration(numberGelConcentration.getDouble());
+ else if(eventSource==selectionInstitution){
+ //TODO implement
+ updateDesignationText();
}
- else if(eventSource==numberGelRunningTime){
- getEntity().setGelRunningTime(numberGelRunningTime.getDouble());
+ else if(eventSource==selectionPrimerFW){
+ getEntity().setForwardPrimer(selectionPrimerFW.getSelection());
}
- else if(eventSource==textLadderUsed){
- getEntity().setLadderUsed(textLadderUsed.getText());
- }
- else if(eventSource==comboPurificationMaterialOrMethod){
- MaterialOrMethodEvent purification = getEntity().getPurification();
- if(purification==null){
- purification = MaterialOrMethodEvent.NewInstance();
- getEntity().setPurification(purification);
- }
- purification.setDefinedMaterialOrMethod(comboPurificationMaterialOrMethod.getSelection());
+ else if(eventSource==selectionPrimerRW){
+ getEntity().setReversePrimer(selectionPrimerRW.getSelection());
}
+// else if(eventSource==checkBoxAmplificationSuccess){
+// getEntity().setSuccessful(checkBoxAmplificationSuccess.getSelection());
+// }
+// else if(eventSource==textAmplificationSuccessDetails){
+// getEntity().setSuccessText(textAmplificationSuccessDetails.getText());
+// }
+// else if(eventSource==comboAmplificationMaterialOrMethod){
+//
+// }
+// else if(eventSource==numberGelVoltage){
+// getEntity().setElectrophoresisVoltage(numberGelVoltage.getDouble());
+// }
+// else if(eventSource==numberGelConcentration){
+// getEntity().setGelConcentration(numberGelConcentration.getDouble());
+// }
+// else if(eventSource==numberGelRunningTime){
+// getEntity().setGelRunningTime(numberGelRunningTime.getDouble());
+// }
+// else if(eventSource==textLadderUsed){
+// getEntity().setLadderUsed(textLadderUsed.getText());
+// }
+// else if(eventSource==comboPurificationMaterialOrMethod){
+// MaterialOrMethodEvent purification = getEntity().getPurification();
+// if(purification==null){
+// purification = MaterialOrMethodEvent.NewInstance();
+// getEntity().setPurification(purification);
+// }
+// purification.setDefinedMaterialOrMethod(comboPurificationMaterialOrMethod.getSelection());
+// }
}
}
\ No newline at end of file
diff --git a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/DnaQualityDetailElement.java b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/DnaQualityDetailElement.java
index 039f2f745..3384b2571 100644
--- a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/DnaQualityDetailElement.java
+++ b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/DnaQualityDetailElement.java
@@ -64,9 +64,10 @@ public class DnaQualityDetailElement extends AbstractCdmDetailElement
Double ratioOfAbsorbance260_230 = dnaQuality.getRatioOfAbsorbance260_230();
Double ratioOfAbsorbance260_280 = dnaQuality.getRatioOfAbsorbance260_280();
Double concentration = dnaQuality.getConcentration();
+ //TODO quality term
DefinedTerm qualityTerm = dnaQuality.getQualityTerm();
-// textPurificationMethod = formFactory.createTextWithLabelElement(formElement, "Purification Method", dnaQuality.getPurificationMethod(), style);
+ textPurificationMethod = formFactory.createTextWithLabelElement(formElement, "DNA Purification Details", dnaQuality.getPurificationMethod(), style);
numberRatioOfAbsorbance260_280 = formFactory.createNumberTextWithLabelElement(formElement, "Ratio of absorbance 260-280", ratioOfAbsorbance260_280, style);
numberRatioOfAbsorbance260_230 = formFactory.createNumberTextWithLabelElement(formElement, "Ratio of absorbance 260-230", ratioOfAbsorbance260_230, style);
numberConcentration = formFactory.createNumberTextWithLabelElement(formElement, "Concentration", concentration, style);
@@ -85,8 +86,7 @@ public class DnaQualityDetailElement extends AbstractCdmDetailElement
public void handleEvent(Object eventSource) {
DnaQuality dnaQuality = getEntity().getDnaQuality();
if(eventSource==textPurificationMethod){
- //TODO
-// dnaQuality.setPurificationMethod(textPurificationMethod.getText());
+ dnaQuality.setPurificationMethod(textPurificationMethod.getText());
}
else if(eventSource==numberRatioOfAbsorbance260_230){
dnaQuality.setRatioOfAbsorbance260_230(numberRatioOfAbsorbance260_230.getDouble());
diff --git a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/DnaSampleGeneralDetailElement.java b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/DnaSampleGeneralDetailElement.java
index 3b5dc4d88..4461471b5 100644
--- a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/DnaSampleGeneralDetailElement.java
+++ b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/DnaSampleGeneralDetailElement.java
@@ -12,7 +12,6 @@ package eu.etaxonomy.taxeditor.ui.section.occurrence.dna;
import eu.etaxonomy.cdm.model.agent.AgentBase;
import eu.etaxonomy.cdm.model.common.DefinedTerm;
import eu.etaxonomy.cdm.model.common.TermType;
-import eu.etaxonomy.cdm.model.common.TimePeriod;
import eu.etaxonomy.cdm.model.molecular.DnaSample;
import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
import eu.etaxonomy.taxeditor.ui.combo.TermComboElement;
@@ -54,18 +53,14 @@ public class DnaSampleGeneralDetailElement extends AbstractCdmDetailElement actor = null;
Double temperature = null;
DefinedTerm definedMaterialOrMethod = null;
if(entity.getPreservation()!=null){
- timePeriod= entity.getPreservation().getTimeperiod();
- actor = entity.getPreservation().getActor();
temperature = entity.getPreservation().getTemperature();
definedMaterialOrMethod = entity.getPreservation().getDefinedMaterialOrMethod();
}
- datePreservationDate = formFactory.createTimePeriodElement(formElement, "Preservation date", timePeriod, style);
- selectionPreparedBy = formFactory.createSelectionElement(AgentBase.class, getConversationHolder(), formElement, "Prepared by", actor, EntitySelectionElement.ALL, style);
+// datePreservationDate = formFactory.createTimePeriodElement(formElement, "Preparation date", timePeriod, style);
+// selectionPreparedBy = formFactory.createSelectionElement(AgentBase.class, getConversationHolder(), formElement, "Prepared by", actor, EntitySelectionElement.ALL, style);
numberPreservationTemperature = formFactory.createNumberTextWithLabelElement(formElement, "Preservation Temp. [C°]", temperature, style);
comboMaterialOrMethods = formFactory.createDefinedTermComboElement(TermType.MaterialOrMethod, formElement, "Materials & Methods", definedMaterialOrMethod, style);
//TODO preparation date
diff --git a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/PrimerGeneralDetailElement.java b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/PrimerGeneralDetailElement.java
index 3ec0627e4..b415ef04b 100644
--- a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/PrimerGeneralDetailElement.java
+++ b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/PrimerGeneralDetailElement.java
@@ -9,9 +9,11 @@
*/
package eu.etaxonomy.taxeditor.ui.section.occurrence.dna;
+import eu.etaxonomy.cdm.model.common.DefinedTerm;
import eu.etaxonomy.cdm.model.molecular.Primer;
import eu.etaxonomy.cdm.model.molecular.SequenceString;
import eu.etaxonomy.cdm.model.reference.Reference;
+import eu.etaxonomy.taxeditor.ui.combo.TermComboElement;
import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
import eu.etaxonomy.taxeditor.ui.element.ICdmFormElement;
import eu.etaxonomy.taxeditor.ui.element.TextWithLabelElement;
@@ -31,6 +33,11 @@ public class PrimerGeneralDetailElement extends AbstractCdmDetailElement
// This is a bit of a overhead as we may just need the sequence string. This may change in future in both directions:
// either extending this view to support the remaining fields of Sequence or by switching to the more basic SequenceString model element
private TextWithLabelElement textPrimerSequence;
+ private TermComboElement comboMarker;
+ /**
+ * free text notes field is backed up by an annotation
+ */
+ private TextWithLabelElement textNotes;
private EntitySelectionElement selectionReference;
/**
@@ -56,6 +63,8 @@ public class PrimerGeneralDetailElement extends AbstractCdmDetailElement
sequenceString = entity.getSequence().getString();
}
textPrimerSequence = formFactory.createTextWithLabelElement(formElement, "Primer seq. 5'->3'", sequenceString, style);
+ //TODO: marker
+ //TODO: notes
selectionReference = formFactory
.createSelectionElement(Reference.class,
diff --git a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SequenceGeneralDetailElement.java b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SequenceGeneralDetailElement.java
index 10fb8e3c5..e4ac9865c 100644
--- a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SequenceGeneralDetailElement.java
+++ b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SequenceGeneralDetailElement.java
@@ -37,7 +37,6 @@ public class SequenceGeneralDetailElement extends AbstractCdmDetailElement comboMarker;
private TextWithLabelElement textConsensusSequence;
private NumberWithLabelElement textConsensusSequenceLength;
- private TextWithLabelElement textBarcodeSequence;
private TextWithLabelElement textGeneticAccessNo;
private UriWithLabelElement textNCBIUri;
private UriWithLabelElement textENAUri;
@@ -63,10 +62,7 @@ public class SequenceGeneralDetailElement extends AbstractCdmDetailElement3'", entity.getConsensusSequence().getString(), style);
-// textConsensusSequenceLength = formFactory.createNumberTextWithLabelElement(formElement, "Consensus Seq. Length", entity.getConsensusSequence().getLength(), style);
-// ((Text) textConsensusSequenceLength.getMainControl()).setEditable(false);
- textBarcodeSequence = formFactory.createTextWithLabelElement(formElement, "Barcode Sequence 5'->3'", entity.getBarcodeSequencePart()==null?"":entity.getBarcodeSequencePart().getString(), style);
+ textConsensusSequence = formFactory.createTextWithLabelElement(formElement, "Consensus Sequence 5'->3'", entity.getConsensusSequence().getString(), style);
URI genBankUri = null;
URI emblUri = null;
@@ -115,14 +111,6 @@ public class SequenceGeneralDetailElement extends AbstractCdmDetailElement comboKindOfTissue;
+ private EntitySelectionElement selectionInstitution;
+ private EntitySelectionElement selectionStaff;
private TimePeriodElement datePreparation;
- private EntitySelectionElement selectionPreparedBy;
private TermComboElement comboPreservationMedium;
- private TimePeriodElement datePreservation;
private EntitySelectionElement selectionCollection;
private TextWithLabelElement textAccessionNumber;
private TextWithLabelElement textBarcode;
@@ -64,19 +64,20 @@ public class TissueSampleGeneralDetailElement extends AbstractCdmDetailElement