Revision 94fbdc99
Added by Katja Luther over 7 years ago
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/dataimport/SpecimenSearchWizard.java | ||
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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.dataimport; |
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import java.io.IOException; |
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import java.io.InputStream; |
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import java.net.URI; |
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import org.apache.log4j.Logger; |
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import org.eclipse.core.runtime.IProgressMonitor; |
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import org.eclipse.core.runtime.IStatus; |
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import org.eclipse.core.runtime.Status; |
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import org.eclipse.core.runtime.jobs.Job; |
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import org.eclipse.jface.viewers.IStructuredSelection; |
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import org.eclipse.jface.wizard.Wizard; |
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import org.eclipse.swt.widgets.Display; |
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import org.eclipse.ui.IImportWizard; |
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import org.eclipse.ui.IWorkbench; |
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import org.eclipse.ui.IWorkbenchPage; |
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import org.eclipse.ui.IWorkbenchWindow; |
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import org.eclipse.ui.PartInitException; |
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import org.eclipse.ui.PlatformUI; |
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import org.w3c.dom.NodeList; |
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import eu.etaxonomy.cdm.database.DbSchemaValidation; |
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import eu.etaxonomy.cdm.ext.common.ServiceWrapperBase; |
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import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery; |
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import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper; |
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator; |
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportReport; |
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdParseUtility; |
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport; |
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.UnitAssociationWrapper; |
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import eu.etaxonomy.taxeditor.store.CdmStore; |
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/** |
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* Wizard for querying specimen provider. |
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* @author pplitzner |
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* @date 11.09.2013 |
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* |
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*/ |
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public class SpecimenSearchWizard extends Wizard implements IImportWizard { |
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private static final Logger logger = Logger.getLogger(SpecimenSearchWizard.class); |
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private OccurenceQuery query = null; |
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private SpecimenProviderSelectionWizardPage providerSelectionPage; |
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private SpecimenSearchWizardPage searchPage; |
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/** |
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* Creates a new SpecimenSearchWizard |
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*/ |
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public SpecimenSearchWizard() { |
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//default constructor needed for RCP extension points |
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//check if connected to a data source. If not this will open an error dialog |
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CdmStore.getCurrentApplicationConfiguration(); |
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this.setWindowTitle("Search Specimens"); |
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} |
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/* (non-Javadoc) |
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* @see org.eclipse.jface.wizard.Wizard#performFinish() |
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*/ |
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@Override |
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public boolean performFinish() { |
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searchPage.getController().saveLastSate(); |
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providerSelectionPage.getController().saveLastState(); |
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ServiceWrapperBase serviceWrapper; |
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DataImportView<?> dataImportView = null; |
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query = searchPage.getQuery(); |
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Abcd206ImportConfigurator configurator = CdmStore.getImportManager().AbcdConfigurator(); |
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configurator.setOccurenceQuery(query); |
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configurator.setSourceUri(providerSelectionPage.getEndPoint()); |
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configurator.setDbSchemaValidation(DbSchemaValidation.CREATE); |
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if(CdmStore.getCurrentSessionManager().isRemoting() ) { |
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//Job job = CdmStore.getImportManager().createIOServiceJob(configurator, new File(source), SOURCE_TYPE.INPUTSTREAM); |
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//CdmStore.getImportManager().run(job); |
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try { |
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serviceWrapper = providerSelectionPage.getQueryServiceWrapper(); |
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InputStream stream = null; |
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final IWorkbenchWindow window = PlatformUI.getWorkbench().getActiveWorkbenchWindow(); |
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IWorkbenchPage activePart = window.getActivePage(); |
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if (providerSelectionPage.getQueryType().equals(QueryType.BIOCASE)){ |
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stream =((BioCaseQueryServiceWrapper) serviceWrapper).query(query, configurator.getSourceUri()); |
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SpecimenImportReport report = new SpecimenImportReport(); |
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UnitAssociationWrapper unitNodesList = AbcdParseUtility.parseUnitsNodeList(stream, report); |
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NodeList nodeList = unitNodesList.getAssociatedUnits(); |
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String prefix = unitNodesList.getPrefix(); |
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String associationType = unitNodesList.getAssociationType(); |
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URI uri =AbcdParseUtility.parseFirstUri(nodeList, report); |
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String content = AbcdParseUtility.parseFirstTextContent(nodeList); |
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System.out.println(content); |
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SpecimenImportView specimenImportView = new SpecimenImportView(); |
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try { |
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specimenImportView = (SpecimenImportView) activePart.showView(SpecimenImportView.ID); |
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specimenImportView.setEndpoint(providerSelectionPage.getEndPoint()); |
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specimenImportView.setQuery(query); |
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dataImportView = specimenImportView; |
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} catch (PartInitException e) { |
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// TODO Auto-generated catch block |
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e.printStackTrace(); |
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} |
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} else{ |
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try { |
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dataImportView = (GbifResponseImportView) activePart.showView(GbifResponseImportView.ID, "query_"+query.toString().replaceAll(",", ""), IWorkbenchPage.VIEW_ACTIVATE); |
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dataImportView.setQuery(query); |
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// (GbifResponseImportView) activePart.showView(GbifResponseImportView.ID);getWorkbench().getActiveWorkbenchWindow().getActivePage() |
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// .showView(GbifResponseImportView.ID, "query_"+query.toString().replaceAll(",", ""),IWorkbenchPage.VIEW_ACTIVATE); |
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} catch (PartInitException e) { |
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// TODO Auto-generated catch block |
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e.printStackTrace(); |
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} |
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} |
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} catch (IOException e) { |
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// TODO Auto-generated catch block |
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e.printStackTrace(); |
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} |
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// CdmStore.getImportManager().run(configurator); |
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} |
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// try { |
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// switch (providerSelectionPage.getQueryType()) { |
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// case BIOCASE: |
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// SpecimenImportView specimenImportView = (SpecimenImportView) TaxeditorEditorPlugin.getDefault().getWorkbench().getActiveWorkbenchWindow().getActivePage() |
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// .showView(SpecimenImportView.ID, "query_"+query.toString().replaceAll(",", ""),IWorkbenchPage.VIEW_ACTIVATE); |
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// specimenImportView.setEndpoint(providerSelectionPage.getEndPoint()); |
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// dataImportView = specimenImportView; |
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// break; |
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// case GBIF: |
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// dataImportView = (GbifResponseImportView) TaxeditorEditorPlugin.getDefault().getWorkbench().getActiveWorkbenchWindow().getActivePage() |
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// .showView(GbifResponseImportView.ID, "query_"+query.toString().replaceAll(",", ""),IWorkbenchPage.VIEW_ACTIVATE); |
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// break; |
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// } |
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// } catch ( PartInitException e ) { |
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// logger.error("Could not open import view for query: " + query.toString(), e); |
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// } |
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// if(dataImportView!=null){ |
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// dataImportView.setQuery(query); |
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//// dataImportView.query(); |
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//// Display.getDefault().asyncExec(new Runnable() { |
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//// |
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//// @Override |
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//// public void run() { |
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//// CdmStore.getContextManager().notifyContextRefresh(); |
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//// } |
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//// }); |
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Job queryJob = new QueryJob("Query specimen provider", dataImportView); |
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queryJob.schedule(); |
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return true; |
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} |
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/* (non-Javadoc) |
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* @see org.eclipse.jface.wizard.Wizard#addPages() |
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*/ |
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@Override |
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public void addPages() { |
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addPage(providerSelectionPage); |
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addPage(searchPage); |
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} |
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/* (non-Javadoc) |
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* @see org.eclipse.ui.IWorkbenchWizard#init(org.eclipse.ui.IWorkbench, org.eclipse.jface.viewers.IStructuredSelection) |
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*/ |
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@Override |
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public void init(IWorkbench workbench, IStructuredSelection selection) { |
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providerSelectionPage = new SpecimenProviderSelectionWizardPage("Select specimen provider"); |
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searchPage = new SpecimenSearchWizardPage("Specimen Search"); |
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} |
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private class QueryJob extends Job{ |
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private final DataImportView<?> view; |
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/** |
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* @param name |
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*/ |
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public QueryJob(String name, DataImportView<?> view) { |
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super(name); |
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this.view = view; |
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} |
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/* (non-Javadoc) |
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* @see org.eclipse.core.runtime.jobs.Job#run(org.eclipse.core.runtime.IProgressMonitor) |
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*/ |
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@Override |
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protected IStatus run(IProgressMonitor monitor) { |
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view.getConversationHolder().bind(); |
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view.query(); |
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Display.getDefault().asyncExec(new Runnable() { |
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@Override |
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public void run() { |
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CdmStore.getContextManager().notifyContextRefresh(); |
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} |
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}); |
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return Status.OK_STATUS; |
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} |
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} |
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} |
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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.dataimport; |
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import java.io.IOException; |
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import java.io.InputStream; |
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import java.net.URI; |
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|
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import org.apache.log4j.Logger; |
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import org.eclipse.core.runtime.IProgressMonitor; |
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import org.eclipse.core.runtime.IStatus; |
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import org.eclipse.core.runtime.Status; |
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import org.eclipse.core.runtime.jobs.Job; |
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import org.eclipse.jface.viewers.IStructuredSelection; |
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import org.eclipse.jface.wizard.Wizard; |
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import org.eclipse.swt.widgets.Display; |
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import org.eclipse.ui.IImportWizard; |
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import org.eclipse.ui.IWorkbench; |
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import org.eclipse.ui.IWorkbenchPage; |
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import org.eclipse.ui.IWorkbenchWindow; |
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import org.eclipse.ui.PartInitException; |
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import org.eclipse.ui.PlatformUI; |
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import org.w3c.dom.NodeList; |
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import eu.etaxonomy.cdm.database.DbSchemaValidation; |
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import eu.etaxonomy.cdm.ext.common.ServiceWrapperBase; |
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import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery; |
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import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper; |
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator; |
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdParseUtility; |
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport; |
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.UnitAssociationWrapper; |
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import eu.etaxonomy.taxeditor.store.CdmStore; |
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|
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/** |
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* Wizard for querying specimen provider. |
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* @author pplitzner |
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* @date 11.09.2013 |
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* |
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*/ |
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public class SpecimenSearchWizard extends Wizard implements IImportWizard { |
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private static final Logger logger = Logger.getLogger(SpecimenSearchWizard.class); |
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private OccurenceQuery query = null; |
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private SpecimenProviderSelectionWizardPage providerSelectionPage; |
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private SpecimenSearchWizardPage searchPage; |
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/** |
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* Creates a new SpecimenSearchWizard |
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*/ |
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public SpecimenSearchWizard() { |
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//default constructor needed for RCP extension points |
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//check if connected to a data source. If not this will open an error dialog |
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CdmStore.getCurrentApplicationConfiguration(); |
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this.setWindowTitle("Search Specimens"); |
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} |
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/* (non-Javadoc) |
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* @see org.eclipse.jface.wizard.Wizard#performFinish() |
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*/ |
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@Override |
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public boolean performFinish() { |
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searchPage.getController().saveLastSate(); |
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providerSelectionPage.getController().saveLastState(); |
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ServiceWrapperBase serviceWrapper; |
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DataImportView<?> dataImportView = null; |
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query = searchPage.getQuery(); |
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Abcd206ImportConfigurator configurator = CdmStore.getImportManager().AbcdConfigurator(); |
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configurator.setOccurenceQuery(query); |
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configurator.setSourceUri(providerSelectionPage.getEndPoint()); |
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configurator.setDbSchemaValidation(DbSchemaValidation.CREATE); |
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if(CdmStore.getCurrentSessionManager().isRemoting() ) { |
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//Job job = CdmStore.getImportManager().createIOServiceJob(configurator, new File(source), SOURCE_TYPE.INPUTSTREAM); |
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//CdmStore.getImportManager().run(job); |
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try { |
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serviceWrapper = providerSelectionPage.getQueryServiceWrapper(); |
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InputStream stream = null; |
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final IWorkbenchWindow window = PlatformUI.getWorkbench().getActiveWorkbenchWindow(); |
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IWorkbenchPage activePart = window.getActivePage(); |
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if (providerSelectionPage.getQueryType().equals(QueryType.BIOCASE)){ |
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stream =((BioCaseQueryServiceWrapper) serviceWrapper).query(query, configurator.getSourceUri()); |
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SpecimenImportReport report = new SpecimenImportReport(); |
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UnitAssociationWrapper unitNodesList = AbcdParseUtility.parseUnitsNodeList(stream, report); |
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NodeList nodeList = unitNodesList.getAssociatedUnits(); |
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String prefix = unitNodesList.getPrefix(); |
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String associationType = unitNodesList.getAssociationType(); |
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URI uri =AbcdParseUtility.parseFirstUri(nodeList, report); |
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String content = AbcdParseUtility.parseFirstTextContent(nodeList); |
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System.out.println(content); |
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SpecimenImportView specimenImportView = new SpecimenImportView(); |
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try { |
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specimenImportView = (SpecimenImportView) activePart.showView(SpecimenImportView.ID); |
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specimenImportView.setEndpoint(providerSelectionPage.getEndPoint()); |
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specimenImportView.setQuery(query); |
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dataImportView = specimenImportView; |
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} catch (PartInitException e) { |
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// TODO Auto-generated catch block |
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e.printStackTrace(); |
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|
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} |
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|
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} else{ |
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try { |
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dataImportView = (GbifResponseImportView) activePart.showView(GbifResponseImportView.ID, "query_"+query.toString().replaceAll(",", ""), IWorkbenchPage.VIEW_ACTIVATE); |
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dataImportView.setQuery(query); |
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// (GbifResponseImportView) activePart.showView(GbifResponseImportView.ID);getWorkbench().getActiveWorkbenchWindow().getActivePage() |
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// .showView(GbifResponseImportView.ID, "query_"+query.toString().replaceAll(",", ""),IWorkbenchPage.VIEW_ACTIVATE); |
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|
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} catch (PartInitException e) { |
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// TODO Auto-generated catch block |
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e.printStackTrace(); |
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} |
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|
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} |
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|
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|
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} catch (IOException e) { |
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// TODO Auto-generated catch block |
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e.printStackTrace(); |
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} |
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// CdmStore.getImportManager().run(configurator); |
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} |
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// try { |
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// switch (providerSelectionPage.getQueryType()) { |
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// case BIOCASE: |
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// SpecimenImportView specimenImportView = (SpecimenImportView) TaxeditorEditorPlugin.getDefault().getWorkbench().getActiveWorkbenchWindow().getActivePage() |
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// .showView(SpecimenImportView.ID, "query_"+query.toString().replaceAll(",", ""),IWorkbenchPage.VIEW_ACTIVATE); |
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// specimenImportView.setEndpoint(providerSelectionPage.getEndPoint()); |
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// dataImportView = specimenImportView; |
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// break; |
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// case GBIF: |
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// dataImportView = (GbifResponseImportView) TaxeditorEditorPlugin.getDefault().getWorkbench().getActiveWorkbenchWindow().getActivePage() |
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// .showView(GbifResponseImportView.ID, "query_"+query.toString().replaceAll(",", ""),IWorkbenchPage.VIEW_ACTIVATE); |
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// break; |
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// } |
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// } catch ( PartInitException e ) { |
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// logger.error("Could not open import view for query: " + query.toString(), e); |
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// } |
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// if(dataImportView!=null){ |
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// dataImportView.setQuery(query); |
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//// dataImportView.query(); |
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//// Display.getDefault().asyncExec(new Runnable() { |
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//// |
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//// @Override |
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//// public void run() { |
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//// CdmStore.getContextManager().notifyContextRefresh(); |
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//// } |
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//// }); |
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Job queryJob = new QueryJob("Query specimen provider", dataImportView); |
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queryJob.schedule(); |
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|
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return true; |
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} |
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|
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/* (non-Javadoc) |
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* @see org.eclipse.jface.wizard.Wizard#addPages() |
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*/ |
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@Override |
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public void addPages() { |
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addPage(providerSelectionPage); |
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addPage(searchPage); |
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} |
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|
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/* (non-Javadoc) |
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* @see org.eclipse.ui.IWorkbenchWizard#init(org.eclipse.ui.IWorkbench, org.eclipse.jface.viewers.IStructuredSelection) |
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*/ |
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@Override |
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public void init(IWorkbench workbench, IStructuredSelection selection) { |
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providerSelectionPage = new SpecimenProviderSelectionWizardPage("Select specimen provider"); |
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searchPage = new SpecimenSearchWizardPage("Specimen Search"); |
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} |
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|
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private class QueryJob extends Job{ |
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|
|
189 |
private final DataImportView<?> view; |
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190 |
|
|
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/** |
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* @param name |
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*/ |
|
194 |
public QueryJob(String name, DataImportView<?> view) { |
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195 |
super(name); |
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this.view = view; |
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197 |
} |
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|
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199 |
/* (non-Javadoc) |
|
200 |
* @see org.eclipse.core.runtime.jobs.Job#run(org.eclipse.core.runtime.IProgressMonitor) |
|
201 |
*/ |
|
202 |
@Override |
|
203 |
protected IStatus run(IProgressMonitor monitor) { |
|
204 |
view.getConversationHolder().bind(); |
|
205 |
view.query(); |
|
206 |
Display.getDefault().asyncExec(new Runnable() { |
|
207 |
|
|
208 |
@Override |
|
209 |
public void run() { |
|
210 |
CdmStore.getContextManager().notifyContextRefresh(); |
|
211 |
} |
|
212 |
}); |
|
213 |
return Status.OK_STATUS; |
|
214 |
} |
|
215 |
|
|
216 |
} |
|
217 |
} |
Also available in: Unified diff
fix specimenSearchWizard