Revision 5f152d2b
Added by Patrick Plitzner over 9 years ago
- added new DataImportEditor for GbifResponses
- allows querying for original record via context menu
| .gitattributes | ||
|---|---|---|
| 482 | 482 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/concept/handler/OpenRelatedConceptHandler.java -text |
| 483 | 483 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/concept/operation/CreateConceptRelationOperation.java -text |
| 484 | 484 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/concept/operation/DeleteConceptRelationOperation.java -text |
| 485 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/BioCaseEditorInput.java -text |
|
| 485 | 486 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/DataImportEditor.java -text |
| 486 | 487 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/DataImportEditorInput.java -text |
| 488 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/GbifImportEditor.java -text |
|
| 489 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/GbifImportEditorInput.java -text |
|
| 490 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/QueryOriginalRecordCommand.java -text |
|
| 487 | 491 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/QueryType.java -text |
| 488 | 492 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/SaveSpecimenCommand.java -text |
| 489 | 493 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/SpecimenImportEditor.java -text |
| 490 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/SpecimenImportEditorInput.java -text |
|
| 491 | 494 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/SpecimenProviderSelectionWizardPage.java -text |
| 492 | 495 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/SpecimenSearchWizard.java -text |
| 493 | 496 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/SpecimenSearchWizardPage.java -text |
| eu.etaxonomy.taxeditor.editor/plugin.xml | ||
|---|---|---|
| 71 | 71 |
id="eu.etaxonomy.taxeditor.editor.view.dataimport.SpecimenImportEditor" |
| 72 | 72 |
name="Specimen Import Editor"> |
| 73 | 73 |
</editor> |
| 74 |
<editor |
|
| 75 |
class="eu.etaxonomy.taxeditor.editor.view.dataimport.GbifImportEditor" |
|
| 76 |
default="false" |
|
| 77 |
id="eu.etaxonomy.taxeditor.editor.view.dataimport.GbifImportEditor" |
|
| 78 |
name="Gbif Import Editor"> |
|
| 79 |
</editor> |
|
| 74 | 80 |
</extension> |
| 75 | 81 |
<extension |
| 76 | 82 |
point="org.eclipse.ui.views"> |
| ... | ... | |
| 577 | 583 |
style="push"> |
| 578 | 584 |
</command> |
| 579 | 585 |
</menuContribution> |
| 586 |
<menuContribution |
|
| 587 |
locationURI="popup:eu.etaxonomy.taxeditor.editor.view.dataimport.GbifImportEditor"> |
|
| 588 |
<command |
|
| 589 |
commandId="eu.etaxonomy.taxeditor.editor.view.dataimport.SaveSpecimenCommand" |
|
| 590 |
label="Save Specimen" |
|
| 591 |
style="push"> |
|
| 592 |
</command> |
|
| 593 |
<command |
|
| 594 |
commandId="eu.etaxonomy.taxeditor.editor.view.dataimport.QueryOriginalRecordCommand" |
|
| 595 |
label="Query original data record" |
|
| 596 |
style="push"> |
|
| 597 |
</command> |
|
| 598 |
</menuContribution> |
|
| 580 | 599 |
|
| 581 | 600 |
|
| 582 | 601 |
|
| ... | ... | |
| 1107 | 1126 |
id="eu.etaxonomy.taxeditor.editor.view.dataimport.SaveSpecimenCommand" |
| 1108 | 1127 |
name="Save Specimen"> |
| 1109 | 1128 |
</command> |
| 1129 |
<command |
|
| 1130 |
defaultHandler="eu.etaxonomy.taxeditor.editor.view.dataimport.QueryOriginalRecordCommand" |
|
| 1131 |
id="eu.etaxonomy.taxeditor.editor.view.dataimport.QueryOriginalRecordCommand" |
|
| 1132 |
name="Query original data record"> |
|
| 1133 |
</command> |
|
| 1110 | 1134 |
|
| 1111 | 1135 |
</extension> |
| 1112 | 1136 |
<extension |
| eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/BioCaseEditorInput.java | ||
|---|---|---|
| 1 |
// $Id$ |
|
| 2 |
/** |
|
| 3 |
* Copyright (C) 2014 EDIT |
|
| 4 |
* European Distributed Institute of Taxonomy |
|
| 5 |
* http://www.e-taxonomy.eu |
|
| 6 |
* |
|
| 7 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
| 8 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
| 9 |
*/ |
|
| 10 |
package eu.etaxonomy.taxeditor.editor.view.dataimport; |
|
| 11 |
|
|
| 12 |
import java.io.IOException; |
|
| 13 |
import java.io.InputStream; |
|
| 14 |
import java.net.URISyntaxException; |
|
| 15 |
import java.util.ArrayList; |
|
| 16 |
import java.util.Collection; |
|
| 17 |
|
|
| 18 |
import org.apache.http.client.ClientProtocolException; |
|
| 19 |
import org.eclipse.swt.widgets.Display; |
|
| 20 |
|
|
| 21 |
import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery; |
|
| 22 |
import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper; |
|
| 23 |
import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
|
| 24 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator; |
|
| 25 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
|
| 26 |
import eu.etaxonomy.taxeditor.editor.view.dataimport.transientServices.TransientCdmRepository; |
|
| 27 |
import eu.etaxonomy.taxeditor.store.CdmStore; |
|
| 28 |
|
|
| 29 |
/** |
|
| 30 |
* @author pplitzner |
|
| 31 |
* @date 25.02.2014 |
|
| 32 |
* |
|
| 33 |
*/ |
|
| 34 |
public class BioCaseEditorInput extends DataImportEditorInput<SpecimenOrObservationBase<?>> {
|
|
| 35 |
|
|
| 36 |
private final OccurenceQuery query; |
|
| 37 |
|
|
| 38 |
/** |
|
| 39 |
* @param results |
|
| 40 |
*/ |
|
| 41 |
public BioCaseEditorInput(OccurenceQuery query) {
|
|
| 42 |
super(); |
|
| 43 |
this.query = query; |
|
| 44 |
} |
|
| 45 |
|
|
| 46 |
@Override |
|
| 47 |
public void query(){
|
|
| 48 |
String errorMessage = "Could not execute query " + query; |
|
| 49 |
|
|
| 50 |
Collection<SpecimenOrObservationBase<?>> results = new ArrayList<SpecimenOrObservationBase<?>>(); |
|
| 51 |
try {
|
|
| 52 |
InputStream resultStream; |
|
| 53 |
resultStream = new BioCaseQueryServiceWrapper().query(query); |
|
| 54 |
Abcd206ImportConfigurator configurator = Abcd206ImportConfigurator.NewInstance(resultStream, null, false); |
|
| 55 |
TransientCdmRepository repo = |
|
| 56 |
new TransientCdmRepository(CdmStore.getCurrentApplicationConfiguration()); |
|
| 57 |
configurator.setCdmAppController(repo); |
|
| 58 |
|
|
| 59 |
CdmDefaultImport<Abcd206ImportConfigurator> importer = new CdmDefaultImport<Abcd206ImportConfigurator>(); |
|
| 60 |
importer.invoke(configurator); |
|
| 61 |
results = repo.getUnits(); |
|
| 62 |
setResults(results); |
|
| 63 |
} catch (ClientProtocolException e) {
|
|
| 64 |
logger.error(errorMessage, e); |
|
| 65 |
} catch (IOException e) {
|
|
| 66 |
logger.error(errorMessage, e); |
|
| 67 |
} catch (URISyntaxException e) {
|
|
| 68 |
logger.error(errorMessage, e); |
|
| 69 |
} |
|
| 70 |
|
|
| 71 |
setResults(results); |
|
| 72 |
|
|
| 73 |
Display.getDefault().asyncExec(new Runnable() {
|
|
| 74 |
|
|
| 75 |
@Override |
|
| 76 |
public void run() {
|
|
| 77 |
CdmStore.getContextManager().notifyContextRefresh(); |
|
| 78 |
} |
|
| 79 |
}); |
|
| 80 |
} |
|
| 81 |
|
|
| 82 |
/* (non-Javadoc) |
|
| 83 |
* @see org.eclipse.ui.IEditorInput#getName() |
|
| 84 |
*/ |
|
| 85 |
@Override |
|
| 86 |
public String getName() {
|
|
| 87 |
return "[BioCASE] " + query.toString(); |
|
| 88 |
} |
|
| 89 |
|
|
| 90 |
/* (non-Javadoc) |
|
| 91 |
* @see org.eclipse.ui.IEditorInput#getToolTipText() |
|
| 92 |
*/ |
|
| 93 |
@Override |
|
| 94 |
public String getToolTipText() {
|
|
| 95 |
return "[BioCASE] " + query.toString(); |
|
| 96 |
} |
|
| 97 |
|
|
| 98 |
/* (non-Javadoc) |
|
| 99 |
* @see java.lang.Object#hashCode() |
|
| 100 |
*/ |
|
| 101 |
@Override |
|
| 102 |
public int hashCode() {
|
|
| 103 |
final int prime = 31; |
|
| 104 |
int result = 1; |
|
| 105 |
result = prime * result + ((query == null) ? 0 : query.hashCode()); |
|
| 106 |
return result; |
|
| 107 |
} |
|
| 108 |
|
|
| 109 |
/* (non-Javadoc) |
|
| 110 |
* @see java.lang.Object#equals(java.lang.Object) |
|
| 111 |
*/ |
|
| 112 |
@Override |
|
| 113 |
public boolean equals(Object obj) {
|
|
| 114 |
if (this == obj) {
|
|
| 115 |
return true; |
|
| 116 |
} |
|
| 117 |
if (obj == null) {
|
|
| 118 |
return false; |
|
| 119 |
} |
|
| 120 |
if (getClass() != obj.getClass()) {
|
|
| 121 |
return false; |
|
| 122 |
} |
|
| 123 |
BioCaseEditorInput other = (BioCaseEditorInput) obj; |
|
| 124 |
if (query == null) {
|
|
| 125 |
if (other.query != null) {
|
|
| 126 |
return false; |
|
| 127 |
} |
|
| 128 |
} else if (!query.equals(other.query)) {
|
|
| 129 |
return false; |
|
| 130 |
} |
|
| 131 |
return true; |
|
| 132 |
} |
|
| 133 |
} |
|
| eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/DataImportEditor.java | ||
|---|---|---|
| 28 | 28 |
|
| 29 | 29 |
import eu.etaxonomy.cdm.api.conversation.ConversationHolder; |
| 30 | 30 |
import eu.etaxonomy.cdm.api.conversation.IConversationEnabled; |
| 31 |
import eu.etaxonomy.cdm.model.common.IIdentifiableEntity; |
|
| 32 | 31 |
import eu.etaxonomy.cdm.persistence.hibernate.CdmDataChangeMap; |
| 33 | 32 |
import eu.etaxonomy.taxeditor.model.IContextListener; |
| 34 | 33 |
import eu.etaxonomy.taxeditor.model.IDirtyMarkableSelectionProvider; |
| ... | ... | |
| 43 | 42 |
* @date 20.09.2013 |
| 44 | 43 |
* |
| 45 | 44 |
*/ |
| 46 |
public abstract class DataImportEditor<T extends IIdentifiableEntity> extends EditorPart implements IPartContentHasFactualData, IDirtyMarkableSelectionProvider,
|
|
| 45 |
public abstract class DataImportEditor<T> extends EditorPart implements IPartContentHasFactualData, IDirtyMarkableSelectionProvider, |
|
| 47 | 46 |
IConversationEnabled, IPartContentHasDetails, IPartContentHasSupplementalData, IContextListener{
|
| 48 | 47 |
|
| 49 | 48 |
private ConversationHolder conversation; |
| ... | ... | |
| 54 | 53 |
* Constructs a new DataImportEditor and registers it to listen to context changes |
| 55 | 54 |
*/ |
| 56 | 55 |
public DataImportEditor() {
|
| 57 |
CdmStore.getContextManager().addContextListener(this); |
|
| 58 | 56 |
} |
| 59 | 57 |
|
| 60 | 58 |
/* (non-Javadoc) |
| ... | ... | |
| 64 | 62 |
public void createPartControl(Composite parent) {
|
| 65 | 63 |
|
| 66 | 64 |
Table table = new Table(parent, SWT.BORDER | SWT.MULTI | SWT.FULL_SELECTION); |
| 67 |
table.setHeaderVisible(true);//TODO: set header title as BioCase query
|
|
| 65 |
table.setHeaderVisible(true);//TODO: set header title as query |
|
| 68 | 66 |
table.setLinesVisible(true); |
| 69 | 67 |
tableViewer = new TableViewer(table); |
| 70 | 68 |
|
| ... | ... | |
| 96 | 94 |
*/ |
| 97 | 95 |
@Override |
| 98 | 96 |
public void init(IEditorSite site, IEditorInput input) throws PartInitException {
|
| 97 |
CdmStore.getContextManager().addContextListener(this); |
|
| 99 | 98 |
setSite(site); |
| 100 | 99 |
setInput(input); |
| 101 | 100 |
setPartName(input.getName()); |
| ... | ... | |
| 147 | 146 |
tableViewer.getTable().removeAll(); |
| 148 | 147 |
Collection<T> results = ((DataImportEditorInput<T>) editorInput).getResults(); |
| 149 | 148 |
if(results!=null){
|
| 150 |
for(T specimen:results){
|
|
| 149 |
for(T item:results){
|
|
| 151 | 150 |
TableItem tableItem = new TableItem(tableViewer.getTable(), SWT.NONE); |
| 152 |
tableItem.setText(specimen.generateTitle());
|
|
| 153 |
tableItem.setData(specimen);
|
|
| 151 |
tableItem.setText(getTextForTableItem(item));
|
|
| 152 |
tableItem.setData(item);
|
|
| 154 | 153 |
} |
| 155 | 154 |
} |
| 156 | 155 |
} |
| 157 | 156 |
} |
| 158 | 157 |
|
| 158 |
protected abstract String getTextForTableItem(T item); |
|
| 159 |
|
|
| 159 | 160 |
/* (non-Javadoc) |
| 160 | 161 |
* @see eu.etaxonomy.taxeditor.model.IContextListener#workbenchShutdown(org.eclipse.ui.IMemento, org.eclipse.core.runtime.IProgressMonitor) |
| 161 | 162 |
*/ |
| eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/DataImportEditorInput.java | ||
|---|---|---|
| 17 | 17 |
import org.eclipse.ui.IPersistableElement; |
| 18 | 18 |
|
| 19 | 19 |
import eu.etaxonomy.cdm.api.conversation.ConversationHolder; |
| 20 |
import eu.etaxonomy.cdm.model.common.IIdentifiableEntity; |
|
| 21 | 20 |
import eu.etaxonomy.taxeditor.store.CdmStore; |
| 22 | 21 |
|
| 23 | 22 |
/** |
| ... | ... | |
| 25 | 24 |
* @date 25.02.2014 |
| 26 | 25 |
* |
| 27 | 26 |
*/ |
| 28 |
public abstract class DataImportEditorInput<T extends IIdentifiableEntity> implements IEditorInput {
|
|
| 27 |
public abstract class DataImportEditorInput<T> implements IEditorInput {
|
|
| 29 | 28 |
|
| 30 | 29 |
protected static Logger logger = Logger.getLogger(DataImportEditorInput.class); |
| 31 | 30 |
|
| ... | ... | |
| 101 | 100 |
|
| 102 | 101 |
@Override |
| 103 | 102 |
public abstract boolean equals(Object obj); |
| 103 |
|
|
| 104 |
|
|
| 105 |
public abstract void query(); |
|
| 104 | 106 |
} |
| eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/GbifImportEditor.java | ||
|---|---|---|
| 1 |
// $Id$ |
|
| 2 |
/** |
|
| 3 |
* Copyright (C) 2014 EDIT |
|
| 4 |
* European Distributed Institute of Taxonomy |
|
| 5 |
* http://www.e-taxonomy.eu |
|
| 6 |
* |
|
| 7 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
| 8 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
| 9 |
*/ |
|
| 10 |
package eu.etaxonomy.taxeditor.editor.view.dataimport; |
|
| 11 |
|
|
| 12 |
import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifResponse; |
|
| 13 |
|
|
| 14 |
/** |
|
| 15 |
* @author pplitzner |
|
| 16 |
* @date 27.05.2014 |
|
| 17 |
* |
|
| 18 |
*/ |
|
| 19 |
public class GbifImportEditor extends DataImportEditor<GbifResponse>{
|
|
| 20 |
|
|
| 21 |
public static final String ID = "eu.etaxonomy.taxeditor.editor.view.dataimport.GbifImportEditor"; |
|
| 22 |
|
|
| 23 |
/** |
|
| 24 |
* Required for extension point |
|
| 25 |
*/ |
|
| 26 |
public GbifImportEditor() {
|
|
| 27 |
super(); |
|
| 28 |
} |
|
| 29 |
|
|
| 30 |
/* (non-Javadoc) |
|
| 31 |
* @see eu.etaxonomy.taxeditor.editor.view.dataimport.DataImportEditor#getTextForTableItem(java.lang.Object) |
|
| 32 |
*/ |
|
| 33 |
@Override |
|
| 34 |
protected String getTextForTableItem(GbifResponse item) {
|
|
| 35 |
return item.getDerivedUnitFacade().innerDerivedUnit().generateTitle(); |
|
| 36 |
} |
|
| 37 |
|
|
| 38 |
} |
|
| eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/GbifImportEditorInput.java | ||
|---|---|---|
| 1 |
// $Id$ |
|
| 2 |
/** |
|
| 3 |
* Copyright (C) 2014 EDIT |
|
| 4 |
* European Distributed Institute of Taxonomy |
|
| 5 |
* http://www.e-taxonomy.eu |
|
| 6 |
* |
|
| 7 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
| 8 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
| 9 |
*/ |
|
| 10 |
package eu.etaxonomy.taxeditor.editor.view.dataimport; |
|
| 11 |
|
|
| 12 |
import java.util.ArrayList; |
|
| 13 |
import java.util.Collection; |
|
| 14 |
|
|
| 15 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
|
| 16 |
import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery; |
|
| 17 |
import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifResponse; |
|
| 18 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType; |
|
| 19 |
|
|
| 20 |
/** |
|
| 21 |
* @author pplitzner |
|
| 22 |
* @date 27.05.2014 |
|
| 23 |
* |
|
| 24 |
*/ |
|
| 25 |
public class GbifImportEditorInput extends DataImportEditorInput<GbifResponse> {
|
|
| 26 |
|
|
| 27 |
private final OccurenceQuery query; |
|
| 28 |
|
|
| 29 |
/** |
|
| 30 |
* @param query |
|
| 31 |
*/ |
|
| 32 |
public GbifImportEditorInput(OccurenceQuery query) {
|
|
| 33 |
super(); |
|
| 34 |
this.query = query; |
|
| 35 |
} |
|
| 36 |
|
|
| 37 |
@Override |
|
| 38 |
public void query(){
|
|
| 39 |
String errorMessage = "Could not execute query " + query; |
|
| 40 |
// try{
|
|
| 41 |
// Collection<GbifResponse> results = new GbifQueryServiceWrapper().query(query); |
|
| 42 |
Collection<GbifResponse> results = new ArrayList<GbifResponse>(); |
|
| 43 |
DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(SpecimenOrObservationType.PreservedSpecimen); |
|
| 44 |
facade.setLocality("outbanks of seashore");
|
|
| 45 |
GbifResponse gbifResponse = new GbifResponse(facade, "endPointURL"); |
|
| 46 |
results.add(gbifResponse); |
|
| 47 |
setResults(results); |
|
| 48 |
// } catch (ClientProtocolException e) {
|
|
| 49 |
// logger.error(errorMessage, e); |
|
| 50 |
// } catch (IOException e) {
|
|
| 51 |
// logger.error(errorMessage, e); |
|
| 52 |
// } catch (URISyntaxException e) {
|
|
| 53 |
// logger.error(errorMessage, e); |
|
| 54 |
// } |
|
| 55 |
} |
|
| 56 |
|
|
| 57 |
|
|
| 58 |
/* (non-Javadoc) |
|
| 59 |
* @see org.eclipse.ui.IEditorInput#getName() |
|
| 60 |
*/ |
|
| 61 |
@Override |
|
| 62 |
public String getName() {
|
|
| 63 |
return "[GBIF] " + query.toString(); |
|
| 64 |
} |
|
| 65 |
|
|
| 66 |
/* (non-Javadoc) |
|
| 67 |
* @see org.eclipse.ui.IEditorInput#getToolTipText() |
|
| 68 |
*/ |
|
| 69 |
@Override |
|
| 70 |
public String getToolTipText() {
|
|
| 71 |
return "[GBIF] " + query.toString(); |
|
| 72 |
} |
|
| 73 |
|
|
| 74 |
/* (non-Javadoc) |
|
| 75 |
* @see java.lang.Object#hashCode() |
|
| 76 |
*/ |
|
| 77 |
@Override |
|
| 78 |
public int hashCode() {
|
|
| 79 |
final int prime = 31; |
|
| 80 |
int result = 1; |
|
| 81 |
result = prime * result + ((query == null) ? 0 : query.hashCode()); |
|
| 82 |
return result; |
|
| 83 |
} |
|
| 84 |
|
|
| 85 |
/* (non-Javadoc) |
|
| 86 |
* @see java.lang.Object#equals(java.lang.Object) |
|
| 87 |
*/ |
|
| 88 |
@Override |
|
| 89 |
public boolean equals(Object obj) {
|
|
| 90 |
if (this == obj) {
|
|
| 91 |
return true; |
|
| 92 |
} |
|
| 93 |
if (obj == null) {
|
|
| 94 |
return false; |
|
| 95 |
} |
|
| 96 |
if (getClass() != obj.getClass()) {
|
|
| 97 |
return false; |
|
| 98 |
} |
|
| 99 |
GbifImportEditorInput other = (GbifImportEditorInput) obj; |
|
| 100 |
if (query == null) {
|
|
| 101 |
if (other.query != null) {
|
|
| 102 |
return false; |
|
| 103 |
} |
|
| 104 |
} else if (!query.equals(other.query)) {
|
|
| 105 |
return false; |
|
| 106 |
} |
|
| 107 |
return true; |
|
| 108 |
} |
|
| 109 |
|
|
| 110 |
} |
|
| eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/QueryOriginalRecordCommand.java | ||
|---|---|---|
| 1 |
package eu.etaxonomy.taxeditor.editor.view.dataimport; |
|
| 2 |
|
|
| 3 |
import org.eclipse.core.commands.AbstractHandler; |
|
| 4 |
import org.eclipse.core.commands.ExecutionEvent; |
|
| 5 |
import org.eclipse.core.commands.ExecutionException; |
|
| 6 |
import org.eclipse.jface.viewers.ISelection; |
|
| 7 |
import org.eclipse.jface.viewers.StructuredSelection; |
|
| 8 |
import org.eclipse.ui.IWorkbenchWindow; |
|
| 9 |
import org.eclipse.ui.PlatformUI; |
|
| 10 |
|
|
| 11 |
import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifResponse; |
|
| 12 |
|
|
| 13 |
public class QueryOriginalRecordCommand extends AbstractHandler {
|
|
| 14 |
|
|
| 15 |
/* (non-Javadoc) |
|
| 16 |
* @see org.eclipse.core.commands.IHandler#execute(org.eclipse.core.commands.ExecutionEvent) |
|
| 17 |
*/ |
|
| 18 |
@Override |
|
| 19 |
public Object execute(ExecutionEvent event) throws ExecutionException {
|
|
| 20 |
final IWorkbenchWindow window = PlatformUI.getWorkbench().getActiveWorkbenchWindow(); |
|
| 21 |
final ISelection selection = window.getActivePage().getSelection(); |
|
| 22 |
if(selection instanceof StructuredSelection){
|
|
| 23 |
StructuredSelection structuredSelection = (StructuredSelection)selection; |
|
| 24 |
if(structuredSelection.size()==1){
|
|
| 25 |
Object next = structuredSelection.iterator().next(); |
|
| 26 |
if(next instanceof GbifResponse){
|
|
| 27 |
String endPoint = ((GbifResponse) next).getEndPointQuery(); |
|
| 28 |
} |
|
| 29 |
} |
|
| 30 |
} |
|
| 31 |
return null; |
|
| 32 |
} |
|
| 33 |
|
|
| 34 |
} |
|
| eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/SaveSpecimenCommand.java | ||
|---|---|---|
| 34 | 34 |
if(next instanceof SpecimenOrObservationBase){
|
| 35 | 35 |
IWorkbenchPart activePart = AbstractUtility.getActivePart(); |
| 36 | 36 |
if(activePart instanceof DataImportEditor){
|
| 37 |
SpecimenImportEditor dataImportEditor = (SpecimenImportEditor)activePart;
|
|
| 37 |
DataImportEditor dataImportEditor = (DataImportEditor)activePart;
|
|
| 38 | 38 |
CdmStore.getService(IOccurrenceService.class).saveOrUpdate((SpecimenOrObservationBase<?>) next); |
| 39 | 39 |
dataImportEditor.getConversationHolder().commit(true); |
| 40 | 40 |
} |
| eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/SpecimenImportEditor.java | ||
|---|---|---|
| 22 | 22 |
public static final String ID = "eu.etaxonomy.taxeditor.editor.view.dataimport.SpecimenImportEditor"; |
| 23 | 23 |
|
| 24 | 24 |
/** |
| 25 |
* |
|
| 25 |
* Required for extension point
|
|
| 26 | 26 |
*/ |
| 27 | 27 |
public SpecimenImportEditor() {
|
| 28 | 28 |
super(); |
| 29 | 29 |
} |
| 30 |
|
|
| 31 |
/* (non-Javadoc) |
|
| 32 |
* @see eu.etaxonomy.taxeditor.editor.view.dataimport.DataImportEditor#getTextForTableItem(eu.etaxonomy.cdm.model.common.IIdentifiableEntity) |
|
| 33 |
*/ |
|
| 34 |
@Override |
|
| 35 |
protected String getTextForTableItem(SpecimenOrObservationBase<?> item) {
|
|
| 36 |
return item.generateTitle(); |
|
| 37 |
} |
|
| 30 | 38 |
} |
| eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/SpecimenImportEditorInput.java | ||
|---|---|---|
| 1 |
// $Id$ |
|
| 2 |
/** |
|
| 3 |
* Copyright (C) 2014 EDIT |
|
| 4 |
* European Distributed Institute of Taxonomy |
|
| 5 |
* http://www.e-taxonomy.eu |
|
| 6 |
* |
|
| 7 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
| 8 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
| 9 |
*/ |
|
| 10 |
package eu.etaxonomy.taxeditor.editor.view.dataimport; |
|
| 11 |
|
|
| 12 |
import java.io.IOException; |
|
| 13 |
import java.io.InputStream; |
|
| 14 |
import java.net.URISyntaxException; |
|
| 15 |
import java.util.ArrayList; |
|
| 16 |
import java.util.Collection; |
|
| 17 |
|
|
| 18 |
import org.apache.http.client.ClientProtocolException; |
|
| 19 |
import org.eclipse.swt.widgets.Display; |
|
| 20 |
|
|
| 21 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
|
| 22 |
import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery; |
|
| 23 |
import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper; |
|
| 24 |
import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifQueryServiceWrapper; |
|
| 25 |
import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
|
| 26 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator; |
|
| 27 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
|
| 28 |
import eu.etaxonomy.taxeditor.editor.view.dataimport.transientServices.TransientCdmRepository; |
|
| 29 |
import eu.etaxonomy.taxeditor.store.CdmStore; |
|
| 30 |
|
|
| 31 |
/** |
|
| 32 |
* @author pplitzner |
|
| 33 |
* @date 25.02.2014 |
|
| 34 |
* |
|
| 35 |
*/ |
|
| 36 |
public class SpecimenImportEditorInput extends DataImportEditorInput<SpecimenOrObservationBase<?>> {
|
|
| 37 |
|
|
| 38 |
private final OccurenceQuery query; |
|
| 39 |
private final QueryType queryType; |
|
| 40 |
|
|
| 41 |
/** |
|
| 42 |
* @param results |
|
| 43 |
*/ |
|
| 44 |
public SpecimenImportEditorInput(OccurenceQuery query, QueryType queryType) {
|
|
| 45 |
super(); |
|
| 46 |
this.query = query; |
|
| 47 |
this.queryType = queryType; |
|
| 48 |
} |
|
| 49 |
|
|
| 50 |
public void query(){
|
|
| 51 |
String errorMessage = "Could not execute query " + query; |
|
| 52 |
|
|
| 53 |
Collection<SpecimenOrObservationBase<?>> results = new ArrayList<SpecimenOrObservationBase<?>>(); |
|
| 54 |
try {
|
|
| 55 |
InputStream resultStream; |
|
| 56 |
switch (queryType) {
|
|
| 57 |
case GBIF: |
|
| 58 |
Collection<DerivedUnitFacade> facades = new GbifQueryServiceWrapper().query(query); |
|
| 59 |
for(DerivedUnitFacade facade:facades){
|
|
| 60 |
results.add(facade.innerDerivedUnit()); |
|
| 61 |
} |
|
| 62 |
break; |
|
| 63 |
case BIOCASE: |
|
| 64 |
resultStream = new BioCaseQueryServiceWrapper().query(query); |
|
| 65 |
Abcd206ImportConfigurator configurator = Abcd206ImportConfigurator.NewInstance(resultStream, null, false); |
|
| 66 |
TransientCdmRepository repo = |
|
| 67 |
new TransientCdmRepository(CdmStore.getCurrentApplicationConfiguration()); |
|
| 68 |
configurator.setCdmAppController(repo); |
|
| 69 |
|
|
| 70 |
CdmDefaultImport<Abcd206ImportConfigurator> importer = new CdmDefaultImport<Abcd206ImportConfigurator>(); |
|
| 71 |
importer.invoke(configurator); |
|
| 72 |
results = repo.getUnits(); |
|
| 73 |
setResults(results); |
|
| 74 |
break; |
|
| 75 |
} |
|
| 76 |
} catch (ClientProtocolException e) {
|
|
| 77 |
logger.error(errorMessage, e); |
|
| 78 |
} catch (IOException e) {
|
|
| 79 |
logger.error(errorMessage, e); |
|
| 80 |
} catch (URISyntaxException e) {
|
|
| 81 |
logger.error(errorMessage, e); |
|
| 82 |
} |
|
| 83 |
|
|
| 84 |
setResults(results); |
|
| 85 |
|
|
| 86 |
Display.getDefault().asyncExec(new Runnable() {
|
|
| 87 |
|
|
| 88 |
@Override |
|
| 89 |
public void run() {
|
|
| 90 |
CdmStore.getContextManager().notifyContextRefresh(); |
|
| 91 |
} |
|
| 92 |
}); |
|
| 93 |
} |
|
| 94 |
|
|
| 95 |
/* (non-Javadoc) |
|
| 96 |
* @see org.eclipse.ui.IEditorInput#getName() |
|
| 97 |
*/ |
|
| 98 |
@Override |
|
| 99 |
public String getName() {
|
|
| 100 |
return queryType + " " + query.toString(); |
|
| 101 |
} |
|
| 102 |
|
|
| 103 |
/* (non-Javadoc) |
|
| 104 |
* @see org.eclipse.ui.IEditorInput#getToolTipText() |
|
| 105 |
*/ |
|
| 106 |
@Override |
|
| 107 |
public String getToolTipText() {
|
|
| 108 |
return query.toString(); |
|
| 109 |
} |
|
| 110 |
|
|
| 111 |
/* (non-Javadoc) |
|
| 112 |
* @see java.lang.Object#hashCode() |
|
| 113 |
*/ |
|
| 114 |
@Override |
|
| 115 |
public int hashCode() {
|
|
| 116 |
final int prime = 31; |
|
| 117 |
int result = 1; |
|
| 118 |
result = prime * result + ((query == null) ? 0 : query.hashCode()); |
|
| 119 |
return result; |
|
| 120 |
} |
|
| 121 |
|
|
| 122 |
/* (non-Javadoc) |
|
| 123 |
* @see java.lang.Object#equals(java.lang.Object) |
|
| 124 |
*/ |
|
| 125 |
@Override |
|
| 126 |
public boolean equals(Object obj) {
|
|
| 127 |
if (this == obj) {
|
|
| 128 |
return true; |
|
| 129 |
} |
|
| 130 |
if (obj == null) {
|
|
| 131 |
return false; |
|
| 132 |
} |
|
| 133 |
if (getClass() != obj.getClass()) {
|
|
| 134 |
return false; |
|
| 135 |
} |
|
| 136 |
SpecimenImportEditorInput other = (SpecimenImportEditorInput) obj; |
|
| 137 |
if (query == null) {
|
|
| 138 |
if (other.query != null) {
|
|
| 139 |
return false; |
|
| 140 |
} |
|
| 141 |
} else if (!query.equals(other.query)) {
|
|
| 142 |
return false; |
|
| 143 |
} |
|
| 144 |
return true; |
|
| 145 |
} |
|
| 146 |
} |
|
| eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/SpecimenSearchWizard.java | ||
|---|---|---|
| 16 | 16 |
import org.eclipse.core.runtime.jobs.Job; |
| 17 | 17 |
import org.eclipse.jface.viewers.IStructuredSelection; |
| 18 | 18 |
import org.eclipse.jface.wizard.Wizard; |
| 19 |
import org.eclipse.swt.widgets.Display; |
|
| 19 | 20 |
import org.eclipse.ui.IImportWizard; |
| 20 | 21 |
import org.eclipse.ui.IWorkbench; |
| 21 | 22 |
import org.eclipse.ui.IWorkbenchPage; |
| ... | ... | |
| 57 | 58 |
@Override |
| 58 | 59 |
public boolean performFinish() {
|
| 59 | 60 |
final IWorkbenchPage page = PlatformUI.getWorkbench().getActiveWorkbenchWindow().getActivePage(); |
| 60 |
|
|
| 61 |
query = searchPage.getQuery(); |
|
| 62 |
final SpecimenImportEditorInput input = new SpecimenImportEditorInput(query, providerSelectionPage.getQueryType()); |
|
| 63 |
Job queryJob = new Job("Query specimen provider") {
|
|
| 64 |
|
|
| 65 |
@Override |
|
| 66 |
protected IStatus run(IProgressMonitor monitor) {
|
|
| 67 |
input.query(); |
|
| 68 |
return Status.OK_STATUS; |
|
| 69 |
} |
|
| 70 |
}; |
|
| 71 |
queryJob.schedule(); |
|
| 72 |
try {
|
|
| 73 |
page.openEditor(input, SpecimenImportEditor.ID, true); |
|
| 74 |
} catch ( PartInitException e ) {
|
|
| 75 |
//Put your exception handler here if you wish to |
|
| 76 |
} |
|
| 61 |
DataImportEditorInput<?> input = null; |
|
| 62 |
String editorId = null; |
|
| 63 |
query = searchPage.getQuery(); |
|
| 64 |
switch (providerSelectionPage.getQueryType()) {
|
|
| 65 |
case BIOCASE: |
|
| 66 |
input = new BioCaseEditorInput(query); |
|
| 67 |
editorId = SpecimenImportEditor.ID; |
|
| 68 |
break; |
|
| 69 |
case GBIF: |
|
| 70 |
input = new GbifImportEditorInput(query); |
|
| 71 |
editorId = GbifImportEditor.ID; |
|
| 72 |
break; |
|
| 73 |
} |
|
| 74 |
try {
|
|
| 75 |
page.openEditor(input, editorId, true); |
|
| 76 |
} catch ( PartInitException e ) {
|
|
| 77 |
//Put your exception handler here if you wish to |
|
| 78 |
} |
|
| 79 |
Job queryJob = new QueryJob("Query specimen provider", input);
|
|
| 80 |
queryJob.schedule(); |
|
| 77 | 81 |
return true; |
| 78 | 82 |
} |
| 79 | 83 |
|
| ... | ... | |
| 95 | 99 |
searchPage = new SpecimenSearchWizardPage("Specimen Search");
|
| 96 | 100 |
} |
| 97 | 101 |
|
| 102 |
private class QueryJob extends Job{
|
|
| 103 |
|
|
| 104 |
private final DataImportEditorInput<?> input; |
|
| 105 |
|
|
| 106 |
/** |
|
| 107 |
* @param name |
|
| 108 |
*/ |
|
| 109 |
public QueryJob(String name, DataImportEditorInput<?> input) {
|
|
| 110 |
super(name); |
|
| 111 |
this.input = input; |
|
| 112 |
} |
|
| 113 |
|
|
| 114 |
/* (non-Javadoc) |
|
| 115 |
* @see org.eclipse.core.runtime.jobs.Job#run(org.eclipse.core.runtime.IProgressMonitor) |
|
| 116 |
*/ |
|
| 117 |
@Override |
|
| 118 |
protected IStatus run(IProgressMonitor monitor) {
|
|
| 119 |
input.query(); |
|
| 120 |
Display.getDefault().asyncExec(new Runnable() {
|
|
| 121 |
|
|
| 122 |
@Override |
|
| 123 |
public void run() {
|
|
| 124 |
CdmStore.getContextManager().notifyContextRefresh(); |
|
| 125 |
} |
|
| 126 |
}); |
|
| 127 |
return Status.OK_STATUS; |
|
| 128 |
} |
|
| 129 |
|
|
| 130 |
} |
|
| 98 | 131 |
} |
| eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/detail/DetailsViewer.java | ||
|---|---|---|
| 23 | 23 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
| 24 | 24 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException; |
| 25 | 25 |
import eu.etaxonomy.cdm.api.service.ITermService; |
| 26 |
import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifResponse; |
|
| 26 | 27 |
import eu.etaxonomy.cdm.model.agent.Person; |
| 27 | 28 |
import eu.etaxonomy.cdm.model.agent.Team; |
| 28 | 29 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
| ... | ... | |
| 168 | 169 |
if(input instanceof TreeNode){
|
| 169 | 170 |
input = ((TreeNode) input).getValue(); |
| 170 | 171 |
} |
| 172 |
if(input instanceof GbifResponse){
|
|
| 173 |
input = ((GbifResponse) input).getDerivedUnitFacade(); |
|
| 174 |
} |
|
| 171 | 175 |
if (input.getClass().equals(DerivedUnit.class)) {
|
| 172 | 176 |
DerivedUnit derivedUnit = (DerivedUnit)input; |
| 173 | 177 |
try {
|
Also available in: Unified diff