Revision b6042ee0
Added by Patrick Plitzner almost 6 years ago
| eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/dataimport/DataImportView.java | ||
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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.util.ArrayList; |
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import java.util.Collection; |
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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.jface.action.IMenuManager; |
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import org.eclipse.jface.action.IToolBarManager; |
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import org.eclipse.jface.viewers.CheckboxTableViewer; |
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import org.eclipse.jface.wizard.IWizard; |
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import org.eclipse.jface.wizard.WizardDialog; |
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import org.eclipse.swt.SWT; |
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import org.eclipse.swt.events.SelectionAdapter; |
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import org.eclipse.swt.events.SelectionEvent; |
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import org.eclipse.swt.layout.GridData; |
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import org.eclipse.swt.layout.GridLayout; |
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import org.eclipse.swt.widgets.Button; |
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import org.eclipse.swt.widgets.Composite; |
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import org.eclipse.swt.widgets.Display; |
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import org.eclipse.swt.widgets.Event; |
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import org.eclipse.swt.widgets.Label; |
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import org.eclipse.swt.widgets.Listener; |
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import org.eclipse.swt.widgets.Table; |
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import org.eclipse.swt.widgets.TableItem; |
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import org.eclipse.swt.widgets.Text; |
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import org.eclipse.ui.IMemento; |
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import org.eclipse.ui.PlatformUI; |
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import org.eclipse.ui.forms.widgets.FormToolkit; |
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import org.eclipse.ui.part.ViewPart; |
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import org.eclipse.wb.swt.ResourceManager; |
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import eu.etaxonomy.cdm.api.conversation.ConversationHolder; |
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import eu.etaxonomy.cdm.api.conversation.IConversationEnabled; |
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import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery; |
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import eu.etaxonomy.cdm.model.taxon.Classification; |
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import eu.etaxonomy.cdm.persistence.hibernate.CdmDataChangeMap; |
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import eu.etaxonomy.taxeditor.databaseAdmin.wizard.ImportPreferencesWizard; |
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import eu.etaxonomy.taxeditor.model.IContextListener; |
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import eu.etaxonomy.taxeditor.model.IPartContentHasDetails; |
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import eu.etaxonomy.taxeditor.model.IPartContentHasFactualData; |
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import eu.etaxonomy.taxeditor.model.IPartContentHasSupplementalData; |
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import eu.etaxonomy.taxeditor.store.CdmStore; |
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import eu.etaxonomy.taxeditor.ui.dialog.selection.SelectionDialogFactory; |
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/** |
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* View which shows a list of "data" that can be imported into the CDM |
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* @author pplitzner |
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* @date Sep 3, 2014 |
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* |
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* @param <T> the CDM type that will be handled by this view |
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*/ |
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public abstract class DataImportView<T> extends ViewPart implements IPartContentHasFactualData, |
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IConversationEnabled, IPartContentHasDetails, IPartContentHasSupplementalData, IContextListener, Listener{
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protected final Logger logger = Logger.getLogger(DataImportView.class); |
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protected Collection<T> results = new ArrayList<T>(); |
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protected boolean updated = false; |
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protected OccurenceQuery query; |
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private static ConversationHolder conversationHolder; |
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private SaveImportedSpecimenAction saveImportedSpecimenAction; |
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private Text textClassification; |
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private Classification classification; |
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private Text textReferenceString; |
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private Button toggleButton; |
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private boolean state; |
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private Button openConfigurator; |
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/** |
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* @return the classification |
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*/ |
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public Classification getClassification() {
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return classification; |
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} |
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/** |
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* @param classification the classification to set |
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*/ |
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public void setClassification(Classification classification) {
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this.classification = classification; |
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} |
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private Button btnBrowseClassification; |
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private Button btnClear; |
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private final FormToolkit toolkit = new FormToolkit(Display.getCurrent()); |
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private Table table; |
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/** |
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* Constructs a new DataImportEditor and registers it to listen to context changes |
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*/ |
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public DataImportView() {
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CdmStore.getContextManager().addContextListener(this); |
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if(CdmStore.isActive()){
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initConversation(); |
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} |
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} |
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/** |
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* Create contents of the view part. |
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* @param parent |
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*/ |
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@Override |
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public void createPartControl(Composite parent) {
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// final Composite composite = new Composite(parent, SWT.NONE); |
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// |
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// GridLayout gridLayout = new GridLayout(); |
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// gridLayout.numColumns = 3; |
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// composite.setLayout(gridLayout); |
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// composite.setLayoutData(new GridData(SWT.FILL, SWT.TOP, true, false)); |
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Composite composite = new Composite(parent, SWT.NONE); |
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composite.setLayout(new GridLayout(2, false)); |
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Composite composite_1 = new Composite(composite, SWT.NONE); |
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GridData gd_composite_1 = new GridData(SWT.LEFT, SWT.TOP, false, false, 1, 1); |
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gd_composite_1.widthHint = 280; |
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composite_1.setLayoutData(gd_composite_1); |
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composite_1.setLayout(new GridLayout(3, false)); |
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Label label = new Label(composite_1, SWT.TOP); |
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label.setText("Classification");
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label.setLayoutData(new GridData(SWT.LEFT, SWT.CENTER, false, false, 3, 1)); |
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textClassification = new Text(composite_1, SWT.BORDER); |
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textClassification.setEnabled(false); |
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GridData gd_textClassification = new GridData(SWT.LEFT, SWT.CENTER, false, false, 1, 1); |
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gd_textClassification.widthHint = 118; |
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textClassification.setLayoutData(new GridData(SWT.FILL, SWT.LEFT, true, true)); |
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btnBrowseClassification = new Button(composite_1, SWT.NONE); |
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btnBrowseClassification.setImage(ResourceManager.getPluginImage("eu.etaxonomy.taxeditor.store", "icons/open.gif"));
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btnBrowseClassification.addListener(SWT.Selection, this); |
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btnClear = new Button(composite_1, SWT.NONE); |
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btnClear.setImage(ResourceManager.getPluginImage("eu.etaxonomy.taxeditor.store", "icons/trash.gif"));
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btnClear.addListener(SWT.Selection, this); |
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//source reference |
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Label labelRef = new Label(composite_1, SWT.NONE); |
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labelRef.setText("Default import souce reference");
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labelRef.setLayoutData(new GridData(SWT.LEFT, SWT.CENTER, false, false, 3, 1)); |
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textReferenceString = new Text(composite_1, SWT.NONE); |
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textReferenceString.setEnabled(true); |
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GridData gd_textReferenceString = new GridData(SWT.LEFT, SWT.CENTER, true, true, 3, 1); |
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gd_textReferenceString.widthHint = 229; |
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textReferenceString.setLayoutData(gd_textReferenceString); |
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//open configuration |
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openConfigurator = new Button(composite_1, SWT.PUSH); |
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openConfigurator.setText("Configuration");
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new Label(composite_1, SWT.NONE); |
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new Label(composite_1, SWT.NONE); |
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openConfigurator.addSelectionListener(new SelectionAdapter(){
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@Override |
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public void widgetSelected(SelectionEvent e) {
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IWizard wizard = new ImportPreferencesWizard(); |
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WizardDialog dialog = new WizardDialog(PlatformUI.getWorkbench().getActiveWorkbenchWindow().getShell(), wizard); |
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dialog.open(); |
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} |
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}); |
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//checkbox table for result |
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Composite composite_2 = new Composite(composite, SWT.NONE); |
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GridData gd_composite_2 = new GridData(SWT.LEFT, SWT.TOP, true, true, 1, 1); |
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gd_composite_2.heightHint = 454; |
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gd_composite_2.widthHint = 403; |
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composite_2.setLayoutData(gd_composite_2); |
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composite_2.setLayout(new GridLayout(2, false)); |
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CheckboxTableViewer checkboxTableViewer = CheckboxTableViewer.newCheckList(composite_2, SWT.BORDER | SWT.FULL_SELECTION); |
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table = checkboxTableViewer.getTable(); |
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GridData gd_table = new GridData(SWT.LEFT, SWT.TOP, true, true, 1, 1); |
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gd_table.heightHint = 444; |
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gd_table.widthHint = 312; |
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table.setLayoutData(gd_table); |
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toolkit.paintBordersFor(table); |
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//toggle button |
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toggleButton = new Button(composite_2, SWT.PUSH); |
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GridData gd_toggleButton = new GridData(SWT.LEFT, SWT.TOP, false, false, 1, 1); |
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gd_toggleButton.widthHint = 56; |
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toggleButton.setLayoutData(gd_toggleButton); |
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toggleButton.setText("Toggle");
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toggleButton.addSelectionListener(new SelectionAdapter(){
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@Override |
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public void widgetSelected(SelectionEvent e) {
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state = state ? false : true; |
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for (TableItem item: getTable().getItems()){
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item.setChecked(state); |
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} |
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} |
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}); |
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createActions(); |
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initializeToolBar(); |
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initializeMenu(); |
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} |
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/** |
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* Create the actions. |
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*/ |
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private void createActions() {
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saveImportedSpecimenAction = new SaveImportedSpecimenAction(); |
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} |
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/** |
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* Initialize the toolbar. |
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*/ |
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private void initializeToolBar() {
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IToolBarManager tbm = getViewSite().getActionBars().getToolBarManager(); |
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tbm.add(saveImportedSpecimenAction); |
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} |
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/** |
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* Initialize the menu. |
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*/ |
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private void initializeMenu() {
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IMenuManager manager = getViewSite().getActionBars().getMenuManager(); |
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} |
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public Table getTable() {
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return table; |
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} |
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/** |
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* @param query the query to set |
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*/ |
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public void setQuery(OccurenceQuery query) {
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this.query = query; |
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} |
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/** |
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* @param results the results to set |
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*/ |
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public void setResults(Collection<T> results) {
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this.results = results; |
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updated=false; |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.taxeditor.annotatedlineeditor.AnnotatedLineEditor#dispose() |
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*/ |
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@Override |
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public void dispose() {
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super.dispose(); |
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CdmStore.getContextManager().removeContextListener(this); |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.taxeditor.model.IContextListener#contextRefresh(org.eclipse.core.runtime.IProgressMonitor) |
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*/ |
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@Override |
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public void contextRefresh(IProgressMonitor monitor) {
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refresh(); |
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} |
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protected void refresh(){
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if (!updated){
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if (getTable() != null){
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getTable().removeAll(); |
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} |
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for(T item:results){
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TableItem tableItem = new TableItem(getTable(), SWT.NONE); |
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tableItem.setText(getTextForTableItem(item)); |
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tableItem.setData(item); |
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} |
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updated = true; |
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} |
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} |
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public abstract void query(); |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.persistence.hibernate.ICdmPostDataChangeObserver#update(eu.etaxonomy.cdm.persistence.hibernate.CdmDataChangeMap) |
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*/ |
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@Override |
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public void update(CdmDataChangeMap changeEvents) {
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//nothing |
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} |
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/** |
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* Returns the text label of the given item. |
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* @param item the item for which the label should be returns |
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* @return the label of the item |
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*/ |
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protected abstract String getTextForTableItem(T item); |
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/* (non-Javadoc) |
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* @see org.eclipse.ui.part.WorkbenchPart#setFocus() |
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*/ |
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@Override |
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public void setFocus() {
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getTable().setFocus(); |
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//make sure to bind again if maybe in another view the conversation was unbound |
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if(getConversationHolder()!=null && !getConversationHolder().isBound()){
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getConversationHolder().bind(); |
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} |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.taxeditor.model.IContextListener#contextAboutToStop(org.eclipse.ui.IMemento, org.eclipse.core.runtime.IProgressMonitor) |
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*/ |
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@Override |
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public void contextAboutToStop(IMemento memento, IProgressMonitor monitor) {
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.taxeditor.model.IContextListener#contextStop(org.eclipse.ui.IMemento, org.eclipse.core.runtime.IProgressMonitor) |
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*/ |
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@Override |
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public void contextStop(IMemento memento, IProgressMonitor monitor) {
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// derivateSearchCompositeController.setEnabled(false); |
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// derivateSearchCompositeController.reset(); |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.taxeditor.model.IContextListener#contextStart(org.eclipse.ui.IMemento, org.eclipse.core.runtime.IProgressMonitor) |
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*/ |
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@Override |
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public void contextStart(IMemento memento, IProgressMonitor monitor) {
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initConversation(); |
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// derivateSearchCompositeController.setEnabled(true); |
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} |
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private void initConversation(){
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if(conversationHolder==null){
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conversationHolder = CdmStore.createConversation(); |
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} |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.taxeditor.model.IContextListener#workbenchShutdown(org.eclipse.ui.IMemento, org.eclipse.core.runtime.IProgressMonitor) |
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*/ |
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@Override |
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public void workbenchShutdown(IMemento memento, IProgressMonitor monitor) {
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if(getConversationHolder()!=null && getConversationHolder().isBound() && !getConversationHolder().isClosed()) {
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getConversationHolder().close(); |
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} |
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} |
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/** |
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* @return the conversationHolder |
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*/ |
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@Override |
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public ConversationHolder getConversationHolder() {
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if(CdmStore.isActive() && conversationHolder==null){
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initConversation(); |
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} |
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return conversationHolder; |
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} |
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@Override |
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public void handleEvent(Event event) {
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if(event.widget==btnBrowseClassification){
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classification = SelectionDialogFactory.getSelectionFromDialog(Classification.class, getSite().getShell(), null, null); |
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if(classification!=null){
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textClassification.setText(classification.getTitleCache()); |
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} |
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} |
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else if(event.widget==btnClear){
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classification = null; |
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textClassification.setText("");
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} |
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} |
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/** |
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* @return |
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*/ |
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public String getReferenceString() {
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return textReferenceString.getText(); |
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} |
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} |
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| eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/dataimport/GbifResponseImportView.java | ||
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/** |
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* Copyright (C) 2014 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.net.URISyntaxException; |
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import java.util.Collection; |
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import org.apache.http.client.ClientProtocolException; |
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import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifQueryServiceWrapper; |
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import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifResponse; |
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/** |
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| 21 |
* @author pplitzner |
|
| 22 |
* @date Sep 5, 2014 |
|
| 23 |
* |
|
| 24 |
*/ |
|
| 25 |
public class GbifResponseImportView extends DataImportView<GbifResponse> {
|
|
| 26 |
|
|
| 27 |
|
|
| 28 |
public static final String ID = "eu.etaxonomy.taxeditor.view.dataimport.GbifResponseImportView"; |
|
| 29 |
|
|
| 30 |
/* (non-Javadoc) |
|
| 31 |
* @see eu.etaxonomy.taxeditor.view.dataimport.DataImportView#getTextForTableItem(java.lang.Object) |
|
| 32 |
*/ |
|
| 33 |
@Override |
|
| 34 |
protected String getTextForTableItem(GbifResponse item) {
|
|
| 35 |
String text = ""; |
|
| 36 |
if(item.getDataSetProtocol()!=null){
|
|
| 37 |
text += "["+item.getDataSetProtocol()+"] "; |
|
| 38 |
} |
|
| 39 |
text += item.getDerivedUnitFacade().innerDerivedUnit().generateTitle(); |
|
| 40 |
return text; |
|
| 41 |
} |
|
| 42 |
|
|
| 43 |
/* (non-Javadoc) |
|
| 44 |
* @see eu.etaxonomy.taxeditor.view.dataimport.DataImportView#query() |
|
| 45 |
*/ |
|
| 46 |
@Override |
|
| 47 |
public void query() {
|
|
| 48 |
String errorMessage = "Could not execute query " + query; |
|
| 49 |
try{
|
|
| 50 |
//Collection<GbifResponse> results = new GbifQueryServiceWrapper().query(query); |
|
| 51 |
//setResults(results); |
|
| 52 |
|
|
| 53 |
// String errorMessage = "Could not execute query " + query; |
|
| 54 |
|
|
| 55 |
// Collection<SpecimenOrObservationBase<?>> results = new ArrayList<SpecimenOrObservationBase<?>>(); |
|
| 56 |
Collection<GbifResponse> results = new GbifQueryServiceWrapper().query(query); |
|
| 57 |
|
|
| 58 |
setResults(results); |
|
| 59 |
|
|
| 60 |
|
|
| 61 |
// |
|
| 62 |
// results = repo.getUnits(); |
|
| 63 |
|
|
| 64 |
} catch (ClientProtocolException e) {
|
|
| 65 |
logger.error(errorMessage, e); |
|
| 66 |
} catch (IOException e) {
|
|
| 67 |
logger.error(errorMessage, e); |
|
| 68 |
} catch (URISyntaxException e) {
|
|
| 69 |
// TODO Auto-generated catch block |
|
| 70 |
e.printStackTrace(); |
|
| 71 |
} |
|
| 72 |
} |
|
| 73 |
|
|
| 74 |
// setResults(results); |
|
| 75 |
// |
|
| 76 |
// } |
|
| 77 |
// } catch (ClientProtocolException e) {
|
|
| 78 |
// logger.error(errorMessage, e); |
|
| 79 |
// } catch (IOException e) {
|
|
| 80 |
// logger.error(errorMessage, e); |
|
| 81 |
// } catch (URISyntaxException e) {
|
|
| 82 |
// logger.error(errorMessage, e); |
|
| 83 |
// } |
|
| 84 |
|
|
| 85 |
// } |
|
| 86 |
|
|
| 87 |
|
|
| 88 |
|
|
| 89 |
|
|
| 90 |
|
|
| 91 |
|
|
| 92 |
} |
|
| eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/dataimport/SaveImportedSpecimenAction.java | ||
|---|---|---|
| 1 |
package eu.etaxonomy.taxeditor.view.dataimport; |
|
| 2 |
|
|
| 3 |
import java.net.URI; |
|
| 4 |
import java.util.ArrayList; |
|
| 5 |
import java.util.Collection; |
|
| 6 |
import java.util.Collections; |
|
| 7 |
import java.util.Comparator; |
|
| 8 |
import java.util.HashSet; |
|
| 9 |
import java.util.List; |
|
| 10 |
import java.util.Set; |
|
| 11 |
|
|
| 12 |
import org.apache.log4j.Logger; |
|
| 13 |
import org.eclipse.core.runtime.jobs.Job; |
|
| 14 |
import org.eclipse.jface.action.Action; |
|
| 15 |
import org.eclipse.swt.widgets.Table; |
|
| 16 |
import org.eclipse.swt.widgets.TableItem; |
|
| 17 |
import org.eclipse.ui.IWorkbenchPart; |
|
| 18 |
import org.eclipse.ui.IWorkbenchWindow; |
|
| 19 |
import org.eclipse.ui.PlatformUI; |
|
| 20 |
|
|
| 21 |
import eu.etaxonomy.cdm.api.conversation.ConversationHolder; |
|
| 22 |
import eu.etaxonomy.cdm.api.service.ITermService; |
|
| 23 |
import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery; |
|
| 24 |
import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseResponse; |
|
| 25 |
import eu.etaxonomy.cdm.ext.occurrence.gbif.DataSetResponse; |
|
| 26 |
import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifDataSetProtocol; |
|
| 27 |
import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifResponse; |
|
| 28 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator; |
|
| 29 |
import eu.etaxonomy.cdm.io.specimen.gbif.in.GbifImportConfigurator; |
|
| 30 |
import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
|
| 31 |
import eu.etaxonomy.taxeditor.preference.PreferencesUtil; |
|
| 32 |
import eu.etaxonomy.taxeditor.store.CdmStore; |
|
| 33 |
|
|
| 34 |
public class SaveImportedSpecimenAction extends Action {
|
|
| 35 |
|
|
| 36 |
private final Logger logger = Logger.getLogger(SaveImportedSpecimenAction.class); |
|
| 37 |
|
|
| 38 |
private Comparator<GbifResponse> comparator; |
|
| 39 |
|
|
| 40 |
/* (non-Javadoc) |
|
| 41 |
* @see org.eclipse.jface.action.Action#run() |
|
| 42 |
*/ |
|
| 43 |
@Override |
|
| 44 |
public void run() {
|
|
| 45 |
final IWorkbenchWindow window = PlatformUI.getWorkbench().getActiveWorkbenchWindow(); |
|
| 46 |
IWorkbenchPart activePart = window.getActivePage().getActivePart(); |
|
| 47 |
if(activePart instanceof DataImportView<?>){
|
|
| 48 |
DataImportView<?> dataImportView = (DataImportView<?>)activePart; |
|
| 49 |
Table table = dataImportView.getTable(); |
|
| 50 |
Collection<GbifResponse> checkedResults = new HashSet<GbifResponse>(); |
|
| 51 |
Collection<BioCaseResponse> checkedAbcdResults = new HashSet<BioCaseResponse>(); |
|
| 52 |
Object data; |
|
| 53 |
Set<String[]> unitIdsGbif = new HashSet<String[]>(); |
|
| 54 |
Set<String[]> unitIdsBioCase = new HashSet<String[]>(); |
|
| 55 |
List<GbifResponse> biocaseResponses = new ArrayList<GbifResponse>(); |
|
| 56 |
|
|
| 57 |
for(TableItem item:table.getItems()){
|
|
| 58 |
if(item.getChecked()){
|
|
| 59 |
//Save Specimen |
|
| 60 |
data = item.getData(); |
|
| 61 |
if(data instanceof GbifResponse){
|
|
| 62 |
checkedResults.add((GbifResponse)item.getData()); |
|
| 63 |
} |
|
| 64 |
if(data instanceof BioCaseResponse){
|
|
| 65 |
checkedAbcdResults.add((BioCaseResponse)data); |
|
| 66 |
} |
|
| 67 |
} |
|
| 68 |
} |
|
| 69 |
String[] tripleId ; |
|
| 70 |
for (GbifResponse response:checkedResults){
|
|
| 71 |
if (response != null){
|
|
| 72 |
tripleId = response.getTripleID(); |
|
| 73 |
|
|
| 74 |
if (response.getDataSetProtocol().equals(GbifDataSetProtocol.BIOCASE)){
|
|
| 75 |
biocaseResponses.add(response); |
|
| 76 |
|
|
| 77 |
}else{
|
|
| 78 |
unitIdsGbif.add(tripleId); |
|
| 79 |
} |
|
| 80 |
|
|
| 81 |
|
|
| 82 |
} |
|
| 83 |
} |
|
| 84 |
Collections.sort(biocaseResponses, getComparator()); |
|
| 85 |
|
|
| 86 |
Abcd206ImportConfigurator configuratorAbcd; |
|
| 87 |
List<Abcd206ImportConfigurator> abcdConfigurators = new ArrayList<Abcd206ImportConfigurator>(); |
|
| 88 |
DataSetResponse dataSetResponse; |
|
| 89 |
OccurenceQuery bioCaseOccurrenceQuery = null; |
|
| 90 |
URI dataSetUri = null; |
|
| 91 |
for (BioCaseResponse response:checkedAbcdResults){
|
|
| 92 |
|
|
| 93 |
if (!response.getDataSetUri().equals(dataSetUri)){
|
|
| 94 |
dataSetUri = response.getDataSetUri(); |
|
| 95 |
|
|
| 96 |
configuratorAbcd = PreferencesUtil.getAbcdImportConfigurationPreference(true); |
|
| 97 |
configuratorAbcd.setSourceUri(dataSetUri); |
|
| 98 |
// configuratorAbcd.addMediaAsMediaSpecimen(true); |
|
| 99 |
// configuratorAbcd.setIgnoreAuthorship(true); |
|
| 100 |
// configuratorAbcd.setMoveNewTaxaToDefaultClassification(false); |
|
| 101 |
|
|
| 102 |
unitIdsBioCase = new HashSet<String[]>(); |
|
| 103 |
bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase); |
|
| 104 |
configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery); |
|
| 105 |
// configuratorAbcd.setGetSiblings(true); |
|
| 106 |
if (dataImportView.getClassification() != null){
|
|
| 107 |
configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid()); |
|
| 108 |
} |
|
| 109 |
if (dataImportView.getReferenceString() != null){
|
|
| 110 |
configuratorAbcd.setSourceReferenceTitle(dataImportView.getReferenceString()); |
|
| 111 |
} |
|
| 112 |
abcdConfigurators.add(configuratorAbcd); |
|
| 113 |
|
|
| 114 |
} |
|
| 115 |
tripleId = response.getTripleID(); |
|
| 116 |
unitIdsBioCase.add(tripleId); |
|
| 117 |
|
|
| 118 |
|
|
| 119 |
} |
|
| 120 |
|
|
| 121 |
|
|
| 122 |
// if (!unitIdsBioCase.isEmpty()){
|
|
| 123 |
// configuratorAbcd = Abcd206ImportConfigurator.NewInstance(dataSetUri, null, false); |
|
| 124 |
// configuratorAbcd.addMediaAsMediaSpecimen(true); |
|
| 125 |
// configuratorAbcd.setIgnoreAuthorship(true); |
|
| 126 |
// configuratorAbcd.setMoveNewTaxaToDefaultClassification(false); |
|
| 127 |
// if (configuratorAbcd != null){
|
|
| 128 |
// abcdConfigurators.add(configuratorAbcd); |
|
| 129 |
// } |
|
| 130 |
//// unitIdsBioCase = new HashSet<String[]>(); |
|
| 131 |
// bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase); |
|
| 132 |
// configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery); |
|
| 133 |
// configuratorAbcd.setGetSiblings(true); |
|
| 134 |
// if (dataImportView.getClassification() != null){
|
|
| 135 |
// configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid()); |
|
| 136 |
// } |
|
| 137 |
// } |
|
| 138 |
|
|
| 139 |
// for (GbifResponse response: biocaseResponses){
|
|
| 140 |
// try {
|
|
| 141 |
// dataSetResponse = new GbifQueryServiceWrapper().queryOriginalDataSet(response); |
|
| 142 |
// dataSetUri = dataSetResponse.getEndpoint(); |
|
| 143 |
// } catch (ClientProtocolException e) {
|
|
| 144 |
// // TODO Auto-generated catch block |
|
| 145 |
// e.printStackTrace(); |
|
| 146 |
// } catch (IOException e) {
|
|
| 147 |
// // TODO Auto-generated catch block |
|
| 148 |
// e.printStackTrace(); |
|
| 149 |
// } |
|
| 150 |
// if (!response.getDataSetUri().equals(dataSetUri)){
|
|
| 151 |
// configuratorAbcd = Abcd206ImportConfigurator.NewInstance(dataSetUri, null, false); |
|
| 152 |
// configuratorAbcd.addMediaAsMediaSpecimen(true); |
|
| 153 |
// configuratorAbcd.setIgnoreAuthorship(true); |
|
| 154 |
// configuratorAbcd.setMoveNewTaxaToDefaultClassification(false); |
|
| 155 |
// if (configuratorAbcd != null){
|
|
| 156 |
// abcdConfigurators.add(configuratorAbcd); |
|
| 157 |
// } |
|
| 158 |
// unitIdsBioCase = new HashSet<String[]>(); |
|
| 159 |
// bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase); |
|
| 160 |
// configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery); |
|
| 161 |
// configuratorAbcd.setGetSiblings(true); |
|
| 162 |
// if (dataImportView.getClassification() != null){
|
|
| 163 |
// configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid()); |
|
| 164 |
// } |
|
| 165 |
// |
|
| 166 |
// } |
|
| 167 |
// tripleId = response.getTripleID(); |
|
| 168 |
// unitIdsBioCase.add(tripleId); |
|
| 169 |
// } |
|
| 170 |
|
|
| 171 |
|
|
| 172 |
|
|
| 173 |
|
|
| 174 |
// configurator.setQuery(query); |
|
| 175 |
if (!checkedAbcdResults.isEmpty()){
|
|
| 176 |
Job bioCaseJob = CdmStore.getImportManager().createIOServiceJob(abcdConfigurators); |
|
| 177 |
CdmStore.getImportManager().run(bioCaseJob); |
|
| 178 |
} |
|
| 179 |
|
|
| 180 |
if (!unitIdsGbif.isEmpty()){
|
|
| 181 |
OccurenceQuery query = new OccurenceQuery(unitIdsGbif); |
|
| 182 |
GbifImportConfigurator configurator = GbifImportConfigurator.newInstance(query); |
|
| 183 |
configurator.setSourceReferenceTitle("Import Gbif data");
|
|
| 184 |
|
|
| 185 |
Job gbifJob = CdmStore.getImportManager().createIOServiceJob(configurator); |
|
| 186 |
CdmStore.getImportManager().run(gbifJob); |
|
| 187 |
} |
|
| 188 |
|
|
| 189 |
|
|
| 190 |
|
|
| 191 |
} |
|
| 192 |
} |
|
| 193 |
|
|
| 194 |
|
|
| 195 |
private void persistTerm(DefinedTermBase<?> term, ITermService termService, ConversationHolder conversation){
|
|
| 196 |
if(term!=null){
|
|
| 197 |
//if the term does not exist in the DB save it |
|
| 198 |
if(termService.find(term.getUuid())==null){
|
|
| 199 |
termService.saveOrUpdate(term); |
|
| 200 |
} |
|
| 201 |
} |
|
| 202 |
} |
|
| 203 |
|
|
| 204 |
/* (non-Javadoc) |
|
| 205 |
* @see org.eclipse.jface.action.Action#getText() |
|
| 206 |
*/ |
|
| 207 |
@Override |
|
| 208 |
public String getText() {
|
|
| 209 |
return "Import"; |
|
| 210 |
} |
|
| 211 |
|
|
| 212 |
private Comparator<GbifResponse> getComparator(){
|
|
| 213 |
if (comparator == null){
|
|
| 214 |
comparator = new GbifResponseComparator(); |
|
| 215 |
} |
|
| 216 |
return comparator; |
|
| 217 |
} |
|
| 218 |
|
|
| 219 |
|
|
| 220 |
} |
|
| eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/dataimport/SpecimenImportView.java | ||
|---|---|---|
| 1 |
/** |
|
| 2 |
* Copyright (C) 2014 EDIT |
|
| 3 |
* European Distributed Institute of Taxonomy |
|
| 4 |
* http://www.e-taxonomy.eu |
|
| 5 |
* |
|
| 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
| 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
| 8 |
*/ |
|
| 9 |
package eu.etaxonomy.taxeditor.view.dataimport; |
|
| 10 |
|
|
| 11 |
import java.io.IOException; |
|
| 12 |
import java.io.InputStream; |
|
| 13 |
import java.net.URI; |
|
| 14 |
import java.util.ArrayList; |
|
| 15 |
import java.util.Collection; |
|
| 16 |
|
|
| 17 |
import org.apache.http.client.ClientProtocolException; |
|
| 18 |
import org.w3c.dom.Element; |
|
| 19 |
import org.w3c.dom.NodeList; |
|
| 20 |
|
|
| 21 |
import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper; |
|
| 22 |
import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseResponse; |
|
| 23 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206DataHolder; |
|
| 24 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator; |
|
| 25 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportParser; |
|
| 26 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportState; |
|
| 27 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206XMLFieldGetter; |
|
| 28 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdParseUtility; |
|
| 29 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Identification; |
|
| 30 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.UnitAssociationWrapper; |
|
| 31 |
|
|
| 32 |
/** |
|
| 33 |
* @author pplitzner |
|
| 34 |
* @date Sep 3, 2014 |
|
| 35 |
* |
|
| 36 |
*/ |
|
| 37 |
public class SpecimenImportView extends DataImportView<BioCaseResponse> {
|
|
| 38 |
|
|
| 39 |
public static final String ID = "eu.etaxonomy.taxeditor.view.dataimport.SpecimenImportView"; //$NON-NLS-1$ |
|
| 40 |
|
|
| 41 |
private URI endPoint; |
|
| 42 |
|
|
| 43 |
public SpecimenImportView() {
|
|
| 44 |
} |
|
| 45 |
|
|
| 46 |
/** |
|
| 47 |
* @param endPoint |
|
| 48 |
*/ |
|
| 49 |
public void setEndpoint(URI endPoint) {
|
|
| 50 |
this.endPoint = endPoint; |
|
| 51 |
} |
|
| 52 |
|
|
| 53 |
/* (non-Javadoc) |
|
| 54 |
* @see eu.etaxonomy.taxeditor.view.dataimport.DataImportView#getTextForTableItem(java.lang.Object) |
|
| 55 |
*/ |
|
| 56 |
@Override |
|
| 57 |
protected String getTextForTableItem(BioCaseResponse item) {
|
|
| 58 |
//TODO: could be defined in user preferences... |
|
| 59 |
String name = null; |
|
| 60 |
if(!(((Abcd206DataHolder)item.getAbcdDataHolder()).getIdentificationList() == null) && !((Abcd206DataHolder)item.getAbcdDataHolder()).getIdentificationList().isEmpty()){
|
|
| 61 |
Identification identification = ((Abcd206DataHolder)item.getAbcdDataHolder()).getIdentificationList().iterator().next(); |
|
| 62 |
name = identification.getScientificName(); |
|
| 63 |
} |
|
| 64 |
if (name != null){
|
|
| 65 |
return name +" - "+((Abcd206DataHolder)item.getAbcdDataHolder()).getCollectionCode() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getUnitID() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getKindOfUnit(); |
|
| 66 |
}else {
|
|
| 67 |
return ((Abcd206DataHolder)item.getAbcdDataHolder()).getCollectionCode() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getUnitID() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getKindOfUnit(); |
|
| 68 |
} |
|
| 69 |
} |
|
| 70 |
|
|
| 71 |
/* (non-Javadoc) |
|
| 72 |
* @see eu.etaxonomy.taxeditor.view.dataimport.DataImportView#query() |
|
| 73 |
*/ |
|
| 74 |
@Override |
|
| 75 |
public void query() {
|
|
| 76 |
String errorMessage = "Could not execute query " + query; |
|
| 77 |
|
|
| 78 |
Collection<BioCaseResponse> results = new ArrayList<BioCaseResponse>(); |
|
| 79 |
try {
|
|
| 80 |
//FIXME move ABCD import to cdmlib -> this will also get rid of the transient services |
|
| 81 |
InputStream resultStream; |
|
| 82 |
resultStream = new BioCaseQueryServiceWrapper().query(query, endPoint); |
|
| 83 |
Abcd206ImportConfigurator configurator = Abcd206ImportConfigurator.NewInstance(null, null); |
|
| 84 |
configurator.setSourceUri(endPoint); |
|
| 85 |
|
|
| 86 |
// TransientCdmRepository repo = |
|
| 87 |
// new TransientCdmRepository(CdmStore.getCurrentApplicationConfiguration()); |
|
| 88 |
//configurator.setCdmAppController(repo); |
|
| 89 |
|
|
| 90 |
//TODO: do not query all data but with the selected triple IDs -> see GbifResponseImportView |
|
| 91 |
configurator.setAddMediaAsMediaSpecimen(true); |
|
| 92 |
configurator.setAllowReuseOtherClassifications(true); |
|
| 93 |
configurator.setMoveNewTaxaToDefaultClassification(false); |
|
| 94 |
UnitAssociationWrapper unitAssociationWrapper = AbcdParseUtility.parseUnitsNodeList(resultStream, null); |
|
| 95 |
NodeList unitsList = unitAssociationWrapper.getAssociatedUnits(); |
|
| 96 |
Abcd206DataHolder dataHolder = new Abcd206DataHolder(); |
|
| 97 |
Abcd206XMLFieldGetter abcdFieldGetter = new Abcd206XMLFieldGetter(dataHolder, unitAssociationWrapper.getPrefix()); |
|
| 98 |
Abcd206ImportState state = new Abcd206ImportState(configurator); |
|
| 99 |
state.setDataHolder(dataHolder); |
|
| 100 |
BioCaseResponse response = null; |
|
| 101 |
if (unitsList != null){
|
|
| 102 |
for (int i = 0; i <unitsList.getLength(); i++){
|
|
| 103 |
Element item = (Element) unitsList.item(i); |
|
| 104 |
dataHolder = new Abcd206DataHolder(); |
|
| 105 |
abcdFieldGetter = new Abcd206XMLFieldGetter(dataHolder, unitAssociationWrapper.getPrefix()); |
|
| 106 |
state.setPrefix(unitAssociationWrapper.getPrefix()); |
|
| 107 |
Abcd206ImportParser.setUnitPropertiesXML(item, abcdFieldGetter, state); |
|
| 108 |
String[] tripleIdBioCase = new String[3]; |
|
| 109 |
tripleIdBioCase[0] =dataHolder.getUnitID(); |
|
| 110 |
tripleIdBioCase[1] = dataHolder.getInstitutionCode(); |
|
| 111 |
tripleIdBioCase[2] = dataHolder.getCollectionCode(); |
|
| 112 |
|
|
| 113 |
response = new BioCaseResponse(dataHolder, endPoint, tripleIdBioCase ); |
|
| 114 |
results.add(response); |
|
| 115 |
} |
|
| 116 |
} |
|
| 117 |
|
|
| 118 |
// Job job = CdmStore.getImportManager().createIOServiceJob(configurator, resultStream, SOURCE_TYPE.INPUTSTREAM); |
|
| 119 |
// CdmStore.getImportManager().run(job); |
|
| 120 |
|
|
| 121 |
setResults(results); |
|
| 122 |
} catch (ClientProtocolException e) {
|
|
| 123 |
logger.error(errorMessage, e); |
|
| 124 |
} catch (IOException e) {
|
|
| 125 |
logger.error(errorMessage, e); |
|
| 126 |
} |
|
| 127 |
|
|
| 128 |
// setResults(results); |
|
| 129 |
|
|
| 130 |
} |
|
| 131 |
|
|
| 132 |
|
|
| 133 |
|
|
| 134 |
} |
|
| eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/dataimport/SpecimenSearchWizard.java | ||
|---|---|---|
| 1 |
/** |
|
| 2 |
* Copyright (C) 2013 EDIT |
|
| 3 |
* European Distributed Institute of Taxonomy |
|
| 4 |
* http://www.e-taxonomy.eu |
|
| 5 |
* |
|
| 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
| 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
| 8 |
*/ |
|
| 9 |
package eu.etaxonomy.taxeditor.view.dataimport; |
|
| 10 |
|
|
| 11 |
import java.io.IOException; |
|
| 12 |
import java.io.InputStream; |
|
| 13 |
import java.net.URI; |
|
| 14 |
|
|
| 15 |
import org.apache.log4j.Logger; |
|
| 16 |
import org.eclipse.core.runtime.IProgressMonitor; |
|
| 17 |
import org.eclipse.core.runtime.IStatus; |
|
| 18 |
import org.eclipse.core.runtime.Status; |
|
| 19 |
import org.eclipse.core.runtime.jobs.Job; |
|
| 20 |
import org.eclipse.jface.viewers.IStructuredSelection; |
|
| 21 |
import org.eclipse.jface.wizard.Wizard; |
|
| 22 |
import org.eclipse.swt.widgets.Display; |
|
| 23 |
import org.eclipse.ui.IImportWizard; |
|
| 24 |
import org.eclipse.ui.IWorkbench; |
|
| 25 |
import org.eclipse.ui.IWorkbenchPage; |
|
| 26 |
import org.eclipse.ui.IWorkbenchWindow; |
|
| 27 |
import org.eclipse.ui.PartInitException; |
|
| 28 |
import org.eclipse.ui.PlatformUI; |
|
| 29 |
import org.w3c.dom.NodeList; |
|
| 30 |
|
|
| 31 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
|
| 32 |
import eu.etaxonomy.cdm.ext.common.ServiceWrapperBase; |
|
| 33 |
import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery; |
|
| 34 |
import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper; |
|
| 35 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator; |
|
| 36 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdParseUtility; |
|
| 37 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport; |
|
| 38 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.UnitAssociationWrapper; |
|
| 39 |
import eu.etaxonomy.taxeditor.store.CdmStore; |
|
| 40 |
|
|
| 41 |
/** |
|
| 42 |
* Wizard for querying specimen provider. |
|
| 43 |
* @author pplitzner |
|
| 44 |
* @date 11.09.2013 |
|
| 45 |
* |
|
| 46 |
*/ |
|
| 47 |
public class SpecimenSearchWizard extends Wizard implements IImportWizard {
|
|
| 48 |
private static final Logger logger = Logger.getLogger(SpecimenSearchWizard.class); |
|
| 49 |
|
|
| 50 |
private OccurenceQuery query = null; |
|
| 51 |
private SpecimenProviderSelectionWizardPage providerSelectionPage; |
|
| 52 |
private SpecimenSearchWizardPage searchPage; |
|
| 53 |
|
|
| 54 |
/** |
|
| 55 |
* Creates a new SpecimenSearchWizard |
|
| 56 |
*/ |
|
| 57 |
public SpecimenSearchWizard() {
|
|
| 58 |
//default constructor needed for RCP extension points |
|
| 59 |
|
|
| 60 |
//check if connected to a data source. If not this will open an error dialog |
|
| 61 |
CdmStore.getCurrentApplicationConfiguration(); |
|
| 62 |
this.setWindowTitle("Search Specimens");
|
|
| 63 |
} |
|
| 64 |
|
|
| 65 |
|
|
| 66 |
/* (non-Javadoc) |
|
| 67 |
* @see org.eclipse.jface.wizard.Wizard#performFinish() |
|
| 68 |
*/ |
|
| 69 |
@Override |
|
| 70 |
public boolean performFinish() {
|
|
| 71 |
searchPage.getController().saveLastSate(); |
|
| 72 |
providerSelectionPage.getController().saveLastState(); |
|
| 73 |
ServiceWrapperBase serviceWrapper; |
|
| 74 |
DataImportView<?> dataImportView = null; |
|
| 75 |
query = searchPage.getQuery(); |
|
| 76 |
Abcd206ImportConfigurator configurator = CdmStore.getImportManager().AbcdConfigurator(); |
|
| 77 |
configurator.setOccurenceQuery(query); |
|
| 78 |
configurator.setSourceUri(providerSelectionPage.getEndPoint()); |
|
| 79 |
configurator.setAddMediaAsMediaSpecimen(true); |
|
| 80 |
configurator.setDbSchemaValidation(DbSchemaValidation.CREATE); |
|
| 81 |
configurator.setIgnoreAuthorship(true); |
|
| 82 |
configurator.setMoveNewTaxaToDefaultClassification(false); |
|
| 83 |
|
|
| 84 |
|
|
| 85 |
//Job job = CdmStore.getImportManager().createIOServiceJob(configurator, new File(source), SOURCE_TYPE.INPUTSTREAM); |
|
| 86 |
//CdmStore.getImportManager().run(job); |
|
| 87 |
try {
|
|
| 88 |
serviceWrapper = providerSelectionPage.getQueryServiceWrapper(); |
|
| 89 |
InputStream stream = null; |
|
| 90 |
|
|
| 91 |
final IWorkbenchWindow window = PlatformUI.getWorkbench().getActiveWorkbenchWindow(); |
|
| 92 |
IWorkbenchPage activePart = window.getActivePage(); |
|
| 93 |
if (providerSelectionPage.getQueryType().equals(QueryType.BIOCASE)){
|
|
| 94 |
stream =((BioCaseQueryServiceWrapper) serviceWrapper).query(query, configurator.getSourceUri()); |
|
| 95 |
SpecimenImportReport report = new SpecimenImportReport(); |
|
| 96 |
UnitAssociationWrapper unitNodesList = AbcdParseUtility.parseUnitsNodeList(stream, report); |
|
| 97 |
NodeList nodeList = unitNodesList.getAssociatedUnits(); |
|
| 98 |
String prefix = unitNodesList.getPrefix(); |
|
| 99 |
String associationType = unitNodesList.getAssociationType(); |
|
| 100 |
if (nodeList != null){
|
|
| 101 |
URI uri =AbcdParseUtility.parseFirstUri(nodeList, report); |
|
| 102 |
String content = AbcdParseUtility.parseFirstTextContent(nodeList); |
|
| 103 |
System.out.println(content); |
|
| 104 |
} |
|
| 105 |
|
|
| 106 |
|
|
| 107 |
|
|
| 108 |
SpecimenImportView specimenImportView = new SpecimenImportView(); |
|
| 109 |
try {
|
|
| 110 |
specimenImportView = (SpecimenImportView) activePart.showView(SpecimenImportView.ID); |
|
| 111 |
specimenImportView.setEndpoint(providerSelectionPage.getEndPoint()); |
|
| 112 |
specimenImportView.setQuery(query); |
|
| 113 |
dataImportView = specimenImportView; |
|
| 114 |
} catch (PartInitException e) {
|
|
| 115 |
// TODO Auto-generated catch block |
|
| 116 |
e.printStackTrace(); |
|
| 117 |
|
|
| 118 |
} |
|
| 119 |
|
|
| 120 |
} else{
|
|
| 121 |
try {
|
|
| 122 |
|
|
| 123 |
dataImportView = (GbifResponseImportView) activePart.showView(GbifResponseImportView.ID, "query_"+query.toString().replaceAll(",", ""), IWorkbenchPage.VIEW_ACTIVATE);
|
|
| 124 |
dataImportView.setQuery(query); |
|
| 125 |
// (GbifResponseImportView) activePart.showView(GbifResponseImportView.ID);getWorkbench().getActiveWorkbenchWindow().getActivePage() |
|
| 126 |
// .showView(GbifResponseImportView.ID, "query_"+query.toString().replaceAll(",", ""),IWorkbenchPage.VIEW_ACTIVATE);
|
|
| 127 |
|
|
| 128 |
} catch (PartInitException e) {
|
|
| 129 |
// TODO Auto-generated catch block |
|
| 130 |
e.printStackTrace(); |
|
| 131 |
} |
|
| 132 |
|
|
| 133 |
} |
|
| 134 |
|
|
| 135 |
|
|
| 136 |
} catch (IOException e) {
|
|
| 137 |
// TODO Auto-generated catch block |
|
| 138 |
e.printStackTrace(); |
|
| 139 |
} |
|
| 140 |
// CdmStore.getImportManager().run(configurator); |
|
| 141 |
|
|
| 142 |
// try {
|
|
| 143 |
// switch (providerSelectionPage.getQueryType()) {
|
|
| 144 |
// case BIOCASE: |
|
| 145 |
// SpecimenImportView specimenImportView = (SpecimenImportView) TaxeditorEditorPlugin.getDefault().getWorkbench().getActiveWorkbenchWindow().getActivePage() |
|
| 146 |
// .showView(SpecimenImportView.ID, "query_"+query.toString().replaceAll(",", ""),IWorkbenchPage.VIEW_ACTIVATE);
|
|
| 147 |
// specimenImportView.setEndpoint(providerSelectionPage.getEndPoint()); |
|
| 148 |
// dataImportView = specimenImportView; |
|
| 149 |
// break; |
|
| 150 |
// case GBIF: |
|
| 151 |
// dataImportView = (GbifResponseImportView) TaxeditorEditorPlugin.getDefault().getWorkbench().getActiveWorkbenchWindow().getActivePage() |
|
| 152 |
// .showView(GbifResponseImportView.ID, "query_"+query.toString().replaceAll(",", ""),IWorkbenchPage.VIEW_ACTIVATE);
|
|
| 153 |
// break; |
|
| 154 |
// } |
|
| 155 |
// } catch ( PartInitException e ) {
|
|
| 156 |
// logger.error("Could not open import view for query: " + query.toString(), e);
|
|
| 157 |
// } |
|
| 158 |
// if(dataImportView!=null){
|
|
| 159 |
// dataImportView.setQuery(query); |
|
| 160 |
//// dataImportView.query(); |
|
| 161 |
//// Display.getDefault().asyncExec(new Runnable() {
|
|
| 162 |
//// |
|
| 163 |
//// @Override |
|
| 164 |
//// public void run() {
|
|
| 165 |
//// CdmStore.getContextManager().notifyContextRefresh(); |
|
| 166 |
//// } |
|
| 167 |
//// }); |
|
| 168 |
Job queryJob = new QueryJob("Query specimen provider", dataImportView);
|
|
| 169 |
queryJob.schedule(); |
|
| 170 |
|
|
| 171 |
return true; |
|
| 172 |
} |
|
| 173 |
|
|
| 174 |
/* (non-Javadoc) |
|
| 175 |
* @see org.eclipse.jface.wizard.Wizard#addPages() |
|
| 176 |
*/ |
|
| 177 |
@Override |
|
| 178 |
public void addPages() {
|
|
| 179 |
addPage(providerSelectionPage); |
|
| 180 |
addPage(searchPage); |
|
| 181 |
} |
|
| 182 |
|
|
| 183 |
/* (non-Javadoc) |
|
| 184 |
* @see org.eclipse.ui.IWorkbenchWizard#init(org.eclipse.ui.IWorkbench, org.eclipse.jface.viewers.IStructuredSelection) |
|
| 185 |
*/ |
|
| 186 |
@Override |
|
| 187 |
public void init(IWorkbench workbench, IStructuredSelection selection) {
|
|
| 188 |
providerSelectionPage = new SpecimenProviderSelectionWizardPage("Select specimen provider");
|
|
| 189 |
searchPage = new SpecimenSearchWizardPage("Specimen Search");
|
|
| 190 |
} |
|
| 191 |
|
|
| 192 |
private class QueryJob extends Job{
|
|
| 193 |
|
|
| 194 |
private final DataImportView<?> view; |
|
| 195 |
|
|
| 196 |
/** |
|
| 197 |
* @param name |
|
| 198 |
*/ |
|
| 199 |
public QueryJob(String name, DataImportView<?> view) {
|
|
| 200 |
super(name); |
|
| 201 |
this.view = view; |
|
| 202 |
} |
|
| 203 |
|
|
| 204 |
/* (non-Javadoc) |
|
| 205 |
* @see org.eclipse.core.runtime.jobs.Job#run(org.eclipse.core.runtime.IProgressMonitor) |
|
| 206 |
*/ |
|
| 207 |
@Override |
|
| 208 |
protected IStatus run(IProgressMonitor monitor) {
|
|
| 209 |
view.getConversationHolder().bind(); |
|
| 210 |
view.query(); |
|
| 211 |
Display.getDefault().asyncExec(new Runnable() {
|
|
| 212 |
|
|
| 213 |
@Override |
|
| 214 |
public void run() {
|
|
| 215 |
CdmStore.getContextManager().notifyContextRefresh(); |
|
| 216 |
} |
|
| 217 |
}); |
|
| 218 |
return Status.OK_STATUS; |
|
| 219 |
} |
|
| 220 |
|
|
| 221 |
} |
|
| 222 |
} |
|
Also available in: Unified diff
ref #6913 Remove data import view