eu.etaxonomy.cdm.database.update.v25_30,
eu.etaxonomy.cdm.database.update.v30_31,
eu.etaxonomy.cdm.ext.bci,
- eu.etaxonomy.cdm.ext.biocase,
+ eu.etaxonomy.cdm.ext.occurrence,
+ eu.etaxonomy.cdm.ext.occurrence.bioCase,
+ eu.etaxonomy.cdm.ext.occurrence.gbif,
eu.etaxonomy.cdm.ext.common,
eu.etaxonomy.cdm.ext.dc,
eu.etaxonomy.cdm.ext.geo,
category="eu.etaxonomy.taxeditor.import.category.cdm"
class="eu.etaxonomy.taxeditor.editor.view.dataimport.SpecimenSearchWizard"
id="eu.etaxonomy.taxeditor.editor.view.dataimport.SpecimenSearchWizard"
- name="Query BioCASE">
+ name="Specimen Search/Import">
<description>
- Query BioCaseProvider
+ Queries data provider (currently only GBIF) for specimens with specified parameters.
</description>
</wizard>
</extension>
setInput(input);
setPartName(input.getName());
setTitleToolTip(input.getName());
- conversation = ((DataImportEditorInput)input).getConversationHolder();
+ conversation = ((DataImportEditorInput<T>)input).getConversationHolder();
}
/* (non-Javadoc)
final ISelection selection = window.getActivePage().getSelection();
if(selection instanceof StructuredSelection){
StructuredSelection structuredSelection = (StructuredSelection)selection;
- Iterator iterator = structuredSelection.iterator();
+ Iterator<?> iterator = structuredSelection.iterator();
while(iterator.hasNext()){
Object next = iterator.next();
if(next instanceof SpecimenOrObservationBase){
IWorkbenchPart activePart = AbstractUtility.getActivePart();
if(activePart instanceof DataImportEditor){
SpecimenImportEditor dataImportEditor = (SpecimenImportEditor)activePart;
- CdmStore.getService(IOccurrenceService.class).saveOrUpdate((SpecimenOrObservationBase) next);
+ CdmStore.getService(IOccurrenceService.class).saveOrUpdate((SpecimenOrObservationBase<?>) next);
dataImportEditor.getConversationHolder().commit(true);
}
}
* @date 20.09.2013
*
*/
-public class SpecimenImportEditor extends DataImportEditor<SpecimenOrObservationBase> {
+public class SpecimenImportEditor extends DataImportEditor<SpecimenOrObservationBase<?>> {
public static final String ID = "eu.etaxonomy.taxeditor.editor.view.dataimport.SpecimenImportEditor";
import org.apache.http.client.ClientProtocolException;
import org.eclipse.swt.widgets.Display;
-import eu.etaxonomy.cdm.ext.biocase.BioCaseQuery;
-import eu.etaxonomy.cdm.ext.biocase.BioCaseQueryServiceWrapper;
-import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator;
+import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;
+import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifQueryServiceWrapper;
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
-import eu.etaxonomy.taxeditor.editor.view.dataimport.transientServices.TransientCdmRepository;
import eu.etaxonomy.taxeditor.store.CdmStore;
/**
* @date 25.02.2014
*
*/
-public class SpecimenImportEditorInput extends DataImportEditorInput<SpecimenOrObservationBase> {
+public class SpecimenImportEditorInput extends DataImportEditorInput<SpecimenOrObservationBase<?>> {
- private final BioCaseQuery query;
+ private final OccurenceQuery query;
/**
* @param results
*/
- public SpecimenImportEditorInput(BioCaseQuery query) {
+ public SpecimenImportEditorInput(OccurenceQuery query) {
super();
this.query = query;
}
public void query(){
- String errorMessage = "Could not execute query " + SpecimenImportEditorInput.this.query;
+ String errorMessage = "Could not execute query " + query;
- Collection<SpecimenOrObservationBase> results = new ArrayList<SpecimenOrObservationBase>();
+ Collection<SpecimenOrObservationBase<?>> results = new ArrayList<SpecimenOrObservationBase<?>>();
try {
- InputStream resultStream = new BioCaseQueryServiceWrapper().query(SpecimenImportEditorInput.this.query);
- Abcd206ImportConfigurator configurator = Abcd206ImportConfigurator.NewInstance(resultStream, null, false);
- TransientCdmRepository repo =
- new TransientCdmRepository(CdmStore.getCurrentApplicationConfiguration());
- configurator.setCdmAppController(repo);
-
- CdmDefaultImport<Abcd206ImportConfigurator> importer = new CdmDefaultImport<Abcd206ImportConfigurator>();
- importer.invoke(configurator);
- results = repo.getUnits();
+ InputStream resultStream = new GbifQueryServiceWrapper().query(query);
+// JSONObject jsonObject = JSONObject.fromObject(dummyJson);
+// Object java = JSONSerializer.toJava(jsonObject);
} catch (ClientProtocolException e) {
logger.error(errorMessage, e);
} catch (IOException e) {
import org.eclipse.ui.PartInitException;
import org.eclipse.ui.PlatformUI;
-import eu.etaxonomy.cdm.ext.biocase.BioCaseQuery;
+import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;
import eu.etaxonomy.taxeditor.store.CdmStore;
/**
- * Wizard for querying BioCASe provider.
+ * Wizard for querying specimen provider.
* @author pplitzner
* @date 11.09.2013
*
@SuppressWarnings("unused")
private static final Logger logger = Logger.getLogger(SpecimenSearchWizard.class);
- private BioCaseQuery query;
+ private OccurenceQuery query = null;
private SpecimenSearchWizardPage searchPage;
/**
query = searchPage.getQuery();
final SpecimenImportEditorInput input = new SpecimenImportEditorInput(query);
- Job queryJob = new Job("Query Biocase") {
+ Job queryJob = new Job("Query specimen provider") {
@Override
protected IStatus run(IProgressMonitor monitor) {
*/
@Override
public void init(IWorkbench workbench, IStructuredSelection selection) {
- query = new BioCaseQuery();
searchPage = new SpecimenSearchWizardPage("Specimen Search");
}
/**
- * Return a {@link BioCaseQuery} with the parameters entered in the wizard
+ * Return a {@link OccurenceQuery} with the parameters entered in the wizard
* @return the query
*/
- public BioCaseQuery getQuery() {
+ public OccurenceQuery getQuery() {
return query;
}
import org.eclipse.jface.wizard.WizardPage;
import org.eclipse.swt.widgets.Composite;
-import eu.etaxonomy.cdm.ext.biocase.BioCaseQuery;
+import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;
import eu.etaxonomy.taxeditor.view.specimenSearch.SpecimenSearchController;
}
/**
- * Returns a {@link BioCaseQuery} filled with the parameters defined in this wizard page
+ * Returns an {@link OccurenceQuery} filled with the parameters defined in this wizard page
* @return
*/
- public BioCaseQuery getQuery() {
- BioCaseQuery query = new BioCaseQuery();
- query.accessionNumber = specimenSearchController.getAccessionNumber();
- query.collector = specimenSearchController.getCollector();
- query.collectorsNumber = specimenSearchController.getCollectorNumber();
- query.country = specimenSearchController.getCountry();
-// query.date = specimenSearchController.getDate();
- query.herbarium = specimenSearchController.getHerbarium();
- query.locality = specimenSearchController.getLocality();
- query.taxonName = specimenSearchController.getTaxonName();
- return query;
+ public OccurenceQuery getQuery() {
+ String accessionNumber = specimenSearchController.getAccessionNumber();
+ String collector = specimenSearchController.getCollector();
+ String collectorsNumber = specimenSearchController.getCollectorNumber();
+ String country = specimenSearchController.getCountry();
+// date = specimenSearchController.getDate();
+ String herbarium = specimenSearchController.getHerbarium();
+ String locality = specimenSearchController.getLocality();
+ String taxonName = specimenSearchController.getTaxonName();
+ return new OccurenceQuery(taxonName, collector, collectorsNumber, accessionNumber, herbarium, country, locality, null);
}
}