+++ /dev/null
-/**
-* Copyright (C) 2013 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.view.dataimport;
-
-import java.util.ArrayList;
-import java.util.Collection;
-
-import org.apache.log4j.Logger;
-import org.eclipse.core.runtime.IProgressMonitor;
-import org.eclipse.jface.action.IMenuManager;
-import org.eclipse.jface.action.IToolBarManager;
-import org.eclipse.jface.viewers.CheckboxTableViewer;
-import org.eclipse.jface.wizard.IWizard;
-import org.eclipse.jface.wizard.WizardDialog;
-import org.eclipse.swt.SWT;
-import org.eclipse.swt.events.SelectionAdapter;
-import org.eclipse.swt.events.SelectionEvent;
-import org.eclipse.swt.layout.GridData;
-import org.eclipse.swt.layout.GridLayout;
-import org.eclipse.swt.widgets.Button;
-import org.eclipse.swt.widgets.Composite;
-import org.eclipse.swt.widgets.Display;
-import org.eclipse.swt.widgets.Event;
-import org.eclipse.swt.widgets.Label;
-import org.eclipse.swt.widgets.Listener;
-import org.eclipse.swt.widgets.Table;
-import org.eclipse.swt.widgets.TableItem;
-import org.eclipse.swt.widgets.Text;
-import org.eclipse.ui.IMemento;
-import org.eclipse.ui.PlatformUI;
-import org.eclipse.ui.forms.widgets.FormToolkit;
-import org.eclipse.ui.part.ViewPart;
-import org.eclipse.wb.swt.ResourceManager;
-
-import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
-import eu.etaxonomy.cdm.api.conversation.IConversationEnabled;
-import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;
-import eu.etaxonomy.cdm.model.taxon.Classification;
-import eu.etaxonomy.cdm.persistence.hibernate.CdmDataChangeMap;
-import eu.etaxonomy.taxeditor.databaseAdmin.wizard.ImportPreferencesWizard;
-import eu.etaxonomy.taxeditor.model.IContextListener;
-import eu.etaxonomy.taxeditor.model.IPartContentHasDetails;
-import eu.etaxonomy.taxeditor.model.IPartContentHasFactualData;
-import eu.etaxonomy.taxeditor.model.IPartContentHasSupplementalData;
-import eu.etaxonomy.taxeditor.store.CdmStore;
-import eu.etaxonomy.taxeditor.ui.dialog.selection.SelectionDialogFactory;
-
-/**
- * View which shows a list of "data" that can be imported into the CDM
- * @author pplitzner
- * @date Sep 3, 2014
- *
- * @param <T> the CDM type that will be handled by this view
- */
-
-public abstract class DataImportView<T> extends ViewPart implements IPartContentHasFactualData,
-IConversationEnabled, IPartContentHasDetails, IPartContentHasSupplementalData, IContextListener, Listener{
-
- protected final Logger logger = Logger.getLogger(DataImportView.class);
-
- protected Collection<T> results = new ArrayList<T>();
-
- protected boolean updated = false;
-
- protected OccurenceQuery query;
-
- private static ConversationHolder conversationHolder;
-
- private SaveImportedSpecimenAction saveImportedSpecimenAction;
-
- private Text textClassification;
- private Classification classification;
-
- private Text textReferenceString;
-
- private Button toggleButton;
- private boolean state;
-
- private Button openConfigurator;
- /**
- * @return the classification
- */
- public Classification getClassification() {
- return classification;
- }
-
- /**
- * @param classification the classification to set
- */
- public void setClassification(Classification classification) {
- this.classification = classification;
- }
- private Button btnBrowseClassification;
- private Button btnClear;
-
- private final FormToolkit toolkit = new FormToolkit(Display.getCurrent());
-
- private Table table;
-
- /**
- * Constructs a new DataImportEditor and registers it to listen to context changes
- */
- public DataImportView() {
- CdmStore.getContextManager().addContextListener(this);
- if(CdmStore.isActive()){
- initConversation();
- }
- }
-
- /**
- * Create contents of the view part.
- * @param parent
- */
- @Override
- public void createPartControl(Composite parent) {
-// final Composite composite = new Composite(parent, SWT.NONE);
-//
-// GridLayout gridLayout = new GridLayout();
-// gridLayout.numColumns = 3;
-// composite.setLayout(gridLayout);
-// composite.setLayoutData(new GridData(SWT.FILL, SWT.TOP, true, false));
- Composite composite = new Composite(parent, SWT.NONE);
- composite.setLayout(new GridLayout(2, false));
-
- Composite composite_1 = new Composite(composite, SWT.NONE);
- GridData gd_composite_1 = new GridData(SWT.LEFT, SWT.TOP, false, false, 1, 1);
- gd_composite_1.widthHint = 280;
- composite_1.setLayoutData(gd_composite_1);
- composite_1.setLayout(new GridLayout(3, false));
-
- Label label = new Label(composite_1, SWT.TOP);
- label.setText("Classification");
- label.setLayoutData(new GridData(SWT.LEFT, SWT.CENTER, false, false, 3, 1));
- textClassification = new Text(composite_1, SWT.BORDER);
- textClassification.setEnabled(false);
- GridData gd_textClassification = new GridData(SWT.LEFT, SWT.CENTER, false, false, 1, 1);
- gd_textClassification.widthHint = 118;
- textClassification.setLayoutData(new GridData(SWT.FILL, SWT.LEFT, true, true));
- btnBrowseClassification = new Button(composite_1, SWT.NONE);
- btnBrowseClassification.setImage(ResourceManager.getPluginImage("eu.etaxonomy.taxeditor.store", "icons/open.gif"));
- btnBrowseClassification.addListener(SWT.Selection, this);
- btnClear = new Button(composite_1, SWT.NONE);
- btnClear.setImage(ResourceManager.getPluginImage("eu.etaxonomy.taxeditor.store", "icons/trash.gif"));
- btnClear.addListener(SWT.Selection, this);
- //source reference
-
- Label labelRef = new Label(composite_1, SWT.NONE);
- labelRef.setText("Default import souce reference");
- labelRef.setLayoutData(new GridData(SWT.LEFT, SWT.CENTER, false, false, 3, 1));
- textReferenceString = new Text(composite_1, SWT.NONE);
- textReferenceString.setEnabled(true);
- GridData gd_textReferenceString = new GridData(SWT.LEFT, SWT.CENTER, true, true, 3, 1);
- gd_textReferenceString.widthHint = 229;
- textReferenceString.setLayoutData(gd_textReferenceString);
-
- //open configuration
- openConfigurator = new Button(composite_1, SWT.PUSH);
- openConfigurator.setText("Configuration");
- new Label(composite_1, SWT.NONE);
- new Label(composite_1, SWT.NONE);
- openConfigurator.addSelectionListener(new SelectionAdapter(){
- @Override
- public void widgetSelected(SelectionEvent e) {
-
- IWizard wizard = new ImportPreferencesWizard();
- WizardDialog dialog = new WizardDialog(PlatformUI.getWorkbench().getActiveWorkbenchWindow().getShell(), wizard);
- dialog.open();
- }
- });
-
- //checkbox table for result
- Composite composite_2 = new Composite(composite, SWT.NONE);
- GridData gd_composite_2 = new GridData(SWT.LEFT, SWT.TOP, true, true, 1, 1);
- gd_composite_2.heightHint = 454;
- gd_composite_2.widthHint = 403;
- composite_2.setLayoutData(gd_composite_2);
- composite_2.setLayout(new GridLayout(2, false));
-
-
- CheckboxTableViewer checkboxTableViewer = CheckboxTableViewer.newCheckList(composite_2, SWT.BORDER | SWT.FULL_SELECTION);
-
-
- table = checkboxTableViewer.getTable();
- GridData gd_table = new GridData(SWT.LEFT, SWT.TOP, true, true, 1, 1);
- gd_table.heightHint = 444;
- gd_table.widthHint = 312;
- table.setLayoutData(gd_table);
- toolkit.paintBordersFor(table);
- //toggle button
- toggleButton = new Button(composite_2, SWT.PUSH);
- GridData gd_toggleButton = new GridData(SWT.LEFT, SWT.TOP, false, false, 1, 1);
- gd_toggleButton.widthHint = 56;
- toggleButton.setLayoutData(gd_toggleButton);
- toggleButton.setText("Toggle");
- toggleButton.addSelectionListener(new SelectionAdapter(){
- @Override
- public void widgetSelected(SelectionEvent e) {
- state = state ? false : true;
- for (TableItem item: getTable().getItems()){
- item.setChecked(state);
- }
-
- }
- });
- createActions();
- initializeToolBar();
- initializeMenu();
- }
-
- /**
- * Create the actions.
- */
- private void createActions() {
- saveImportedSpecimenAction = new SaveImportedSpecimenAction();
- }
-
- /**
- * Initialize the toolbar.
- */
- private void initializeToolBar() {
- IToolBarManager tbm = getViewSite().getActionBars().getToolBarManager();
- tbm.add(saveImportedSpecimenAction);
- }
-
- /**
- * Initialize the menu.
- */
- private void initializeMenu() {
- IMenuManager manager = getViewSite().getActionBars().getMenuManager();
- }
-
- public Table getTable() {
- return table;
- }
-
- /**
- * @param query the query to set
- */
- public void setQuery(OccurenceQuery query) {
- this.query = query;
- }
-
- /**
- * @param results the results to set
- */
- public void setResults(Collection<T> results) {
- this.results = results;
- updated=false;
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.annotatedlineeditor.AnnotatedLineEditor#dispose()
- */
- @Override
- public void dispose() {
- super.dispose();
- CdmStore.getContextManager().removeContextListener(this);
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.model.IContextListener#contextRefresh(org.eclipse.core.runtime.IProgressMonitor)
- */
- @Override
- public void contextRefresh(IProgressMonitor monitor) {
- refresh();
- }
-
- protected void refresh(){
-
- if (!updated){
- if (getTable() != null){
- getTable().removeAll();
- }
- for(T item:results){
- TableItem tableItem = new TableItem(getTable(), SWT.NONE);
- tableItem.setText(getTextForTableItem(item));
- tableItem.setData(item);
- }
- updated = true;
- }
- }
-
- public abstract void query();
-
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.persistence.hibernate.ICdmPostDataChangeObserver#update(eu.etaxonomy.cdm.persistence.hibernate.CdmDataChangeMap)
- */
- @Override
- public void update(CdmDataChangeMap changeEvents) {
- //nothing
- }
-
- /**
- * Returns the text label of the given item.
- * @param item the item for which the label should be returns
- * @return the label of the item
- */
- protected abstract String getTextForTableItem(T item);
-
- /* (non-Javadoc)
- * @see org.eclipse.ui.part.WorkbenchPart#setFocus()
- */
- @Override
- public void setFocus() {
- getTable().setFocus();
- //make sure to bind again if maybe in another view the conversation was unbound
- if(getConversationHolder()!=null && !getConversationHolder().isBound()){
- getConversationHolder().bind();
- }
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.model.IContextListener#contextAboutToStop(org.eclipse.ui.IMemento, org.eclipse.core.runtime.IProgressMonitor)
- */
- @Override
- public void contextAboutToStop(IMemento memento, IProgressMonitor monitor) {
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.model.IContextListener#contextStop(org.eclipse.ui.IMemento, org.eclipse.core.runtime.IProgressMonitor)
- */
- @Override
- public void contextStop(IMemento memento, IProgressMonitor monitor) {
-// derivateSearchCompositeController.setEnabled(false);
-// derivateSearchCompositeController.reset();
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.model.IContextListener#contextStart(org.eclipse.ui.IMemento, org.eclipse.core.runtime.IProgressMonitor)
- */
- @Override
- public void contextStart(IMemento memento, IProgressMonitor monitor) {
- initConversation();
-// derivateSearchCompositeController.setEnabled(true);
- }
-
- private void initConversation(){
- if(conversationHolder==null){
- conversationHolder = CdmStore.createConversation();
- }
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.model.IContextListener#workbenchShutdown(org.eclipse.ui.IMemento, org.eclipse.core.runtime.IProgressMonitor)
- */
- @Override
- public void workbenchShutdown(IMemento memento, IProgressMonitor monitor) {
- if(getConversationHolder()!=null && getConversationHolder().isBound() && !getConversationHolder().isClosed()) {
- getConversationHolder().close();
- }
- }
-
- /**
- * @return the conversationHolder
- */
- @Override
- public ConversationHolder getConversationHolder() {
- if(CdmStore.isActive() && conversationHolder==null){
- initConversation();
- }
- return conversationHolder;
- }
- @Override
- public void handleEvent(Event event) {
- if(event.widget==btnBrowseClassification){
- classification = SelectionDialogFactory.getSelectionFromDialog(Classification.class, getSite().getShell(), null, null);
- if(classification!=null){
- textClassification.setText(classification.getTitleCache());
- }
- }
- else if(event.widget==btnClear){
- classification = null;
- textClassification.setText("");
- }
- }
-
- /**
- * @return
- */
- public String getReferenceString() {
-
- return textReferenceString.getText();
- }
-}
+++ /dev/null
-/**
-* Copyright (C) 2014 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.view.dataimport;
-
-import java.io.IOException;
-import java.net.URISyntaxException;
-import java.util.Collection;
-
-import org.apache.http.client.ClientProtocolException;
-
-import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifQueryServiceWrapper;
-import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifResponse;
-
-/**
- * @author pplitzner
- * @date Sep 5, 2014
- *
- */
-public class GbifResponseImportView extends DataImportView<GbifResponse> {
-
-
- public static final String ID = "eu.etaxonomy.taxeditor.view.dataimport.GbifResponseImportView";
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.view.dataimport.DataImportView#getTextForTableItem(java.lang.Object)
- */
- @Override
- protected String getTextForTableItem(GbifResponse item) {
- String text = "";
- if(item.getDataSetProtocol()!=null){
- text += "["+item.getDataSetProtocol()+"] ";
- }
- text += item.getDerivedUnitFacade().innerDerivedUnit().generateTitle();
- return text;
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.view.dataimport.DataImportView#query()
- */
- @Override
- public void query() {
- String errorMessage = "Could not execute query " + query;
- try{
- //Collection<GbifResponse> results = new GbifQueryServiceWrapper().query(query);
- //setResults(results);
-
- // String errorMessage = "Could not execute query " + query;
-
- // Collection<SpecimenOrObservationBase<?>> results = new ArrayList<SpecimenOrObservationBase<?>>();
- Collection<GbifResponse> results = new GbifQueryServiceWrapper().query(query);
-
- setResults(results);
-
-
-//
- // results = repo.getUnits();
-
- } catch (ClientProtocolException e) {
- logger.error(errorMessage, e);
- } catch (IOException e) {
- logger.error(errorMessage, e);
- } catch (URISyntaxException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }
-
-// setResults(results);
-//
-// }
-// } catch (ClientProtocolException e) {
-// logger.error(errorMessage, e);
-// } catch (IOException e) {
-// logger.error(errorMessage, e);
-// } catch (URISyntaxException e) {
-// logger.error(errorMessage, e);
-// }
-
- // }
-
-
-
-
-
-
-}
+++ /dev/null
-package eu.etaxonomy.taxeditor.view.dataimport;
-
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.eclipse.core.runtime.jobs.Job;
-import org.eclipse.jface.action.Action;
-import org.eclipse.swt.widgets.Table;
-import org.eclipse.swt.widgets.TableItem;
-import org.eclipse.ui.IWorkbenchPart;
-import org.eclipse.ui.IWorkbenchWindow;
-import org.eclipse.ui.PlatformUI;
-
-import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
-import eu.etaxonomy.cdm.api.service.ITermService;
-import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;
-import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseResponse;
-import eu.etaxonomy.cdm.ext.occurrence.gbif.DataSetResponse;
-import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifDataSetProtocol;
-import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifResponse;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator;
-import eu.etaxonomy.cdm.io.specimen.gbif.in.GbifImportConfigurator;
-import eu.etaxonomy.cdm.model.common.DefinedTermBase;
-import eu.etaxonomy.taxeditor.preference.PreferencesUtil;
-import eu.etaxonomy.taxeditor.store.CdmStore;
-
-public class SaveImportedSpecimenAction extends Action {
-
- private final Logger logger = Logger.getLogger(SaveImportedSpecimenAction.class);
-
- private Comparator<GbifResponse> comparator;
-
- /* (non-Javadoc)
- * @see org.eclipse.jface.action.Action#run()
- */
- @Override
- public void run() {
- final IWorkbenchWindow window = PlatformUI.getWorkbench().getActiveWorkbenchWindow();
- IWorkbenchPart activePart = window.getActivePage().getActivePart();
- if(activePart instanceof DataImportView<?>){
- DataImportView<?> dataImportView = (DataImportView<?>)activePart;
- Table table = dataImportView.getTable();
- Collection<GbifResponse> checkedResults = new HashSet<GbifResponse>();
- Collection<BioCaseResponse> checkedAbcdResults = new HashSet<BioCaseResponse>();
- Object data;
- Set<String[]> unitIdsGbif = new HashSet<String[]>();
- Set<String[]> unitIdsBioCase = new HashSet<String[]>();
- List<GbifResponse> biocaseResponses = new ArrayList<GbifResponse>();
-
- for(TableItem item:table.getItems()){
- if(item.getChecked()){
- //Save Specimen
- data = item.getData();
- if(data instanceof GbifResponse){
- checkedResults.add((GbifResponse)item.getData());
- }
- if(data instanceof BioCaseResponse){
- checkedAbcdResults.add((BioCaseResponse)data);
- }
- }
- }
- String[] tripleId ;
- for (GbifResponse response:checkedResults){
- if (response != null){
- tripleId = response.getTripleID();
-
- if (response.getDataSetProtocol().equals(GbifDataSetProtocol.BIOCASE)){
- biocaseResponses.add(response);
-
- }else{
- unitIdsGbif.add(tripleId);
- }
-
-
- }
- }
- Collections.sort(biocaseResponses, getComparator());
-
- Abcd206ImportConfigurator configuratorAbcd;
- List<Abcd206ImportConfigurator> abcdConfigurators = new ArrayList<Abcd206ImportConfigurator>();
- DataSetResponse dataSetResponse;
- OccurenceQuery bioCaseOccurrenceQuery = null;
- URI dataSetUri = null;
- for (BioCaseResponse response:checkedAbcdResults){
-
- if (!response.getDataSetUri().equals(dataSetUri)){
- dataSetUri = response.getDataSetUri();
-
- configuratorAbcd = PreferencesUtil.getAbcdImportConfigurationPreference(true);
- configuratorAbcd.setSourceUri(dataSetUri);
-// configuratorAbcd.addMediaAsMediaSpecimen(true);
-// configuratorAbcd.setIgnoreAuthorship(true);
-// configuratorAbcd.setMoveNewTaxaToDefaultClassification(false);
-
- unitIdsBioCase = new HashSet<String[]>();
- bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase);
- configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery);
- // configuratorAbcd.setGetSiblings(true);
- if (dataImportView.getClassification() != null){
- configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid());
- }
- if (dataImportView.getReferenceString() != null){
- configuratorAbcd.setSourceReferenceTitle(dataImportView.getReferenceString());
- }
- abcdConfigurators.add(configuratorAbcd);
-
- }
- tripleId = response.getTripleID();
- unitIdsBioCase.add(tripleId);
-
-
- }
-
-
-// if (!unitIdsBioCase.isEmpty()){
-// configuratorAbcd = Abcd206ImportConfigurator.NewInstance(dataSetUri, null, false);
-// configuratorAbcd.addMediaAsMediaSpecimen(true);
-// configuratorAbcd.setIgnoreAuthorship(true);
-// configuratorAbcd.setMoveNewTaxaToDefaultClassification(false);
-// if (configuratorAbcd != null){
-// abcdConfigurators.add(configuratorAbcd);
-// }
-//// unitIdsBioCase = new HashSet<String[]>();
-// bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase);
-// configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery);
-// configuratorAbcd.setGetSiblings(true);
-// if (dataImportView.getClassification() != null){
-// configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid());
-// }
-// }
-
-// for (GbifResponse response: biocaseResponses){
-// try {
-// dataSetResponse = new GbifQueryServiceWrapper().queryOriginalDataSet(response);
-// dataSetUri = dataSetResponse.getEndpoint();
-// } catch (ClientProtocolException e) {
-// // TODO Auto-generated catch block
-// e.printStackTrace();
-// } catch (IOException e) {
-// // TODO Auto-generated catch block
-// e.printStackTrace();
-// }
-// if (!response.getDataSetUri().equals(dataSetUri)){
-// configuratorAbcd = Abcd206ImportConfigurator.NewInstance(dataSetUri, null, false);
-// configuratorAbcd.addMediaAsMediaSpecimen(true);
-// configuratorAbcd.setIgnoreAuthorship(true);
-// configuratorAbcd.setMoveNewTaxaToDefaultClassification(false);
-// if (configuratorAbcd != null){
-// abcdConfigurators.add(configuratorAbcd);
-// }
-// unitIdsBioCase = new HashSet<String[]>();
-// bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase);
-// configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery);
-// configuratorAbcd.setGetSiblings(true);
-// if (dataImportView.getClassification() != null){
-// configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid());
-// }
-//
-// }
-// tripleId = response.getTripleID();
-// unitIdsBioCase.add(tripleId);
-// }
-
-
-
-
- // configurator.setQuery(query);
- if (!checkedAbcdResults.isEmpty()){
- Job bioCaseJob = CdmStore.getImportManager().createIOServiceJob(abcdConfigurators);
- CdmStore.getImportManager().run(bioCaseJob);
- }
-
- if (!unitIdsGbif.isEmpty()){
- OccurenceQuery query = new OccurenceQuery(unitIdsGbif);
- GbifImportConfigurator configurator = GbifImportConfigurator.newInstance(query);
- configurator.setSourceReferenceTitle("Import Gbif data");
-
- Job gbifJob = CdmStore.getImportManager().createIOServiceJob(configurator);
- CdmStore.getImportManager().run(gbifJob);
- }
-
-
-
- }
- }
-
-
- private void persistTerm(DefinedTermBase<?> term, ITermService termService, ConversationHolder conversation){
- if(term!=null){
- //if the term does not exist in the DB save it
- if(termService.find(term.getUuid())==null){
- termService.saveOrUpdate(term);
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.eclipse.jface.action.Action#getText()
- */
- @Override
- public String getText() {
- return "Import";
- }
-
- private Comparator<GbifResponse> getComparator(){
- if (comparator == null){
- comparator = new GbifResponseComparator();
- }
- return comparator;
- }
-
-
-}
+++ /dev/null
-/**
-* Copyright (C) 2014 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.view.dataimport;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.Collection;
-
-import org.apache.http.client.ClientProtocolException;
-import org.w3c.dom.Element;
-import org.w3c.dom.NodeList;
-
-import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper;
-import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseResponse;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206DataHolder;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportParser;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportState;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206XMLFieldGetter;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdParseUtility;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.Identification;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.UnitAssociationWrapper;
-
-/**
- * @author pplitzner
- * @date Sep 3, 2014
- *
- */
-public class SpecimenImportView extends DataImportView<BioCaseResponse> {
-
- public static final String ID = "eu.etaxonomy.taxeditor.view.dataimport.SpecimenImportView"; //$NON-NLS-1$
-
- private URI endPoint;
-
- public SpecimenImportView() {
- }
-
- /**
- * @param endPoint
- */
- public void setEndpoint(URI endPoint) {
- this.endPoint = endPoint;
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.view.dataimport.DataImportView#getTextForTableItem(java.lang.Object)
- */
- @Override
- protected String getTextForTableItem(BioCaseResponse item) {
- //TODO: could be defined in user preferences...
- String name = null;
- if(!(((Abcd206DataHolder)item.getAbcdDataHolder()).getIdentificationList() == null) && !((Abcd206DataHolder)item.getAbcdDataHolder()).getIdentificationList().isEmpty()){
- Identification identification = ((Abcd206DataHolder)item.getAbcdDataHolder()).getIdentificationList().iterator().next();
- name = identification.getScientificName();
- }
- if (name != null){
- return name +" - "+((Abcd206DataHolder)item.getAbcdDataHolder()).getCollectionCode() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getUnitID() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getKindOfUnit();
- }else {
- return ((Abcd206DataHolder)item.getAbcdDataHolder()).getCollectionCode() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getUnitID() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getKindOfUnit();
- }
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.view.dataimport.DataImportView#query()
- */
- @Override
- public void query() {
- String errorMessage = "Could not execute query " + query;
-
- Collection<BioCaseResponse> results = new ArrayList<BioCaseResponse>();
- try {
- //FIXME move ABCD import to cdmlib -> this will also get rid of the transient services
- InputStream resultStream;
- resultStream = new BioCaseQueryServiceWrapper().query(query, endPoint);
- Abcd206ImportConfigurator configurator = Abcd206ImportConfigurator.NewInstance(null, null);
- configurator.setSourceUri(endPoint);
-
- // TransientCdmRepository repo =
-// new TransientCdmRepository(CdmStore.getCurrentApplicationConfiguration());
- //configurator.setCdmAppController(repo);
-
- //TODO: do not query all data but with the selected triple IDs -> see GbifResponseImportView
- configurator.setAddMediaAsMediaSpecimen(true);
- configurator.setAllowReuseOtherClassifications(true);
- configurator.setMoveNewTaxaToDefaultClassification(false);
- UnitAssociationWrapper unitAssociationWrapper = AbcdParseUtility.parseUnitsNodeList(resultStream, null);
- NodeList unitsList = unitAssociationWrapper.getAssociatedUnits();
- Abcd206DataHolder dataHolder = new Abcd206DataHolder();
- Abcd206XMLFieldGetter abcdFieldGetter = new Abcd206XMLFieldGetter(dataHolder, unitAssociationWrapper.getPrefix());
- Abcd206ImportState state = new Abcd206ImportState(configurator);
- state.setDataHolder(dataHolder);
- BioCaseResponse response = null;
- if (unitsList != null){
- for (int i = 0; i <unitsList.getLength(); i++){
- Element item = (Element) unitsList.item(i);
- dataHolder = new Abcd206DataHolder();
- abcdFieldGetter = new Abcd206XMLFieldGetter(dataHolder, unitAssociationWrapper.getPrefix());
- state.setPrefix(unitAssociationWrapper.getPrefix());
- Abcd206ImportParser.setUnitPropertiesXML(item, abcdFieldGetter, state);
- String[] tripleIdBioCase = new String[3];
- tripleIdBioCase[0] =dataHolder.getUnitID();
- tripleIdBioCase[1] = dataHolder.getInstitutionCode();
- tripleIdBioCase[2] = dataHolder.getCollectionCode();
-
- response = new BioCaseResponse(dataHolder, endPoint, tripleIdBioCase );
- results.add(response);
- }
- }
-
-// Job job = CdmStore.getImportManager().createIOServiceJob(configurator, resultStream, SOURCE_TYPE.INPUTSTREAM);
-// CdmStore.getImportManager().run(job);
-
- setResults(results);
- } catch (ClientProtocolException e) {
- logger.error(errorMessage, e);
- } catch (IOException e) {
- logger.error(errorMessage, e);
- }
-
- // setResults(results);
-
- }
-
-
-
-}
+++ /dev/null
-/**
-* Copyright (C) 2013 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.view.dataimport;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URI;
-
-import org.apache.log4j.Logger;
-import org.eclipse.core.runtime.IProgressMonitor;
-import org.eclipse.core.runtime.IStatus;
-import org.eclipse.core.runtime.Status;
-import org.eclipse.core.runtime.jobs.Job;
-import org.eclipse.jface.viewers.IStructuredSelection;
-import org.eclipse.jface.wizard.Wizard;
-import org.eclipse.swt.widgets.Display;
-import org.eclipse.ui.IImportWizard;
-import org.eclipse.ui.IWorkbench;
-import org.eclipse.ui.IWorkbenchPage;
-import org.eclipse.ui.IWorkbenchWindow;
-import org.eclipse.ui.PartInitException;
-import org.eclipse.ui.PlatformUI;
-import org.w3c.dom.NodeList;
-
-import eu.etaxonomy.cdm.database.DbSchemaValidation;
-import eu.etaxonomy.cdm.ext.common.ServiceWrapperBase;
-import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;
-import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdParseUtility;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.UnitAssociationWrapper;
-import eu.etaxonomy.taxeditor.store.CdmStore;
-
-/**
- * Wizard for querying specimen provider.
- * @author pplitzner
- * @date 11.09.2013
- *
- */
-public class SpecimenSearchWizard extends Wizard implements IImportWizard {
- private static final Logger logger = Logger.getLogger(SpecimenSearchWizard.class);
-
- private OccurenceQuery query = null;
- private SpecimenProviderSelectionWizardPage providerSelectionPage;
- private SpecimenSearchWizardPage searchPage;
-
- /**
- * Creates a new SpecimenSearchWizard
- */
- public SpecimenSearchWizard() {
- //default constructor needed for RCP extension points
-
- //check if connected to a data source. If not this will open an error dialog
- CdmStore.getCurrentApplicationConfiguration();
- this.setWindowTitle("Search Specimens");
- }
-
-
- /* (non-Javadoc)
- * @see org.eclipse.jface.wizard.Wizard#performFinish()
- */
- @Override
- public boolean performFinish() {
- searchPage.getController().saveLastSate();
- providerSelectionPage.getController().saveLastState();
- ServiceWrapperBase serviceWrapper;
- DataImportView<?> dataImportView = null;
- query = searchPage.getQuery();
- Abcd206ImportConfigurator configurator = CdmStore.getImportManager().AbcdConfigurator();
- configurator.setOccurenceQuery(query);
- configurator.setSourceUri(providerSelectionPage.getEndPoint());
- configurator.setAddMediaAsMediaSpecimen(true);
- configurator.setDbSchemaValidation(DbSchemaValidation.CREATE);
- configurator.setIgnoreAuthorship(true);
- configurator.setMoveNewTaxaToDefaultClassification(false);
-
-
- //Job job = CdmStore.getImportManager().createIOServiceJob(configurator, new File(source), SOURCE_TYPE.INPUTSTREAM);
- //CdmStore.getImportManager().run(job);
- try {
- serviceWrapper = providerSelectionPage.getQueryServiceWrapper();
- InputStream stream = null;
-
- final IWorkbenchWindow window = PlatformUI.getWorkbench().getActiveWorkbenchWindow();
- IWorkbenchPage activePart = window.getActivePage();
- if (providerSelectionPage.getQueryType().equals(QueryType.BIOCASE)){
- stream =((BioCaseQueryServiceWrapper) serviceWrapper).query(query, configurator.getSourceUri());
- SpecimenImportReport report = new SpecimenImportReport();
- UnitAssociationWrapper unitNodesList = AbcdParseUtility.parseUnitsNodeList(stream, report);
- NodeList nodeList = unitNodesList.getAssociatedUnits();
- String prefix = unitNodesList.getPrefix();
- String associationType = unitNodesList.getAssociationType();
- if (nodeList != null){
- URI uri =AbcdParseUtility.parseFirstUri(nodeList, report);
- String content = AbcdParseUtility.parseFirstTextContent(nodeList);
- System.out.println(content);
- }
-
-
-
- SpecimenImportView specimenImportView = new SpecimenImportView();
- try {
- specimenImportView = (SpecimenImportView) activePart.showView(SpecimenImportView.ID);
- specimenImportView.setEndpoint(providerSelectionPage.getEndPoint());
- specimenImportView.setQuery(query);
- dataImportView = specimenImportView;
- } catch (PartInitException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
-
- }
-
- } else{
- try {
-
- dataImportView = (GbifResponseImportView) activePart.showView(GbifResponseImportView.ID, "query_"+query.toString().replaceAll(",", ""), IWorkbenchPage.VIEW_ACTIVATE);
- dataImportView.setQuery(query);
- // (GbifResponseImportView) activePart.showView(GbifResponseImportView.ID);getWorkbench().getActiveWorkbenchWindow().getActivePage()
- // .showView(GbifResponseImportView.ID, "query_"+query.toString().replaceAll(",", ""),IWorkbenchPage.VIEW_ACTIVATE);
-
- } catch (PartInitException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-
- }
-
-
- } catch (IOException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- // CdmStore.getImportManager().run(configurator);
-
-// try {
-// switch (providerSelectionPage.getQueryType()) {
-// case BIOCASE:
-// SpecimenImportView specimenImportView = (SpecimenImportView) TaxeditorEditorPlugin.getDefault().getWorkbench().getActiveWorkbenchWindow().getActivePage()
-// .showView(SpecimenImportView.ID, "query_"+query.toString().replaceAll(",", ""),IWorkbenchPage.VIEW_ACTIVATE);
-// specimenImportView.setEndpoint(providerSelectionPage.getEndPoint());
-// dataImportView = specimenImportView;
-// break;
-// case GBIF:
-// dataImportView = (GbifResponseImportView) TaxeditorEditorPlugin.getDefault().getWorkbench().getActiveWorkbenchWindow().getActivePage()
-// .showView(GbifResponseImportView.ID, "query_"+query.toString().replaceAll(",", ""),IWorkbenchPage.VIEW_ACTIVATE);
-// break;
-// }
-// } catch ( PartInitException e ) {
-// logger.error("Could not open import view for query: " + query.toString(), e);
-// }
-// if(dataImportView!=null){
-// dataImportView.setQuery(query);
-//// dataImportView.query();
-//// Display.getDefault().asyncExec(new Runnable() {
-////
-//// @Override
-//// public void run() {
-//// CdmStore.getContextManager().notifyContextRefresh();
-//// }
-//// });
- Job queryJob = new QueryJob("Query specimen provider", dataImportView);
- queryJob.schedule();
-
- return true;
- }
-
- /* (non-Javadoc)
- * @see org.eclipse.jface.wizard.Wizard#addPages()
- */
- @Override
- public void addPages() {
- addPage(providerSelectionPage);
- addPage(searchPage);
- }
-
- /* (non-Javadoc)
- * @see org.eclipse.ui.IWorkbenchWizard#init(org.eclipse.ui.IWorkbench, org.eclipse.jface.viewers.IStructuredSelection)
- */
- @Override
- public void init(IWorkbench workbench, IStructuredSelection selection) {
- providerSelectionPage = new SpecimenProviderSelectionWizardPage("Select specimen provider");
- searchPage = new SpecimenSearchWizardPage("Specimen Search");
- }
-
- private class QueryJob extends Job{
-
- private final DataImportView<?> view;
-
- /**
- * @param name
- */
- public QueryJob(String name, DataImportView<?> view) {
- super(name);
- this.view = view;
- }
-
- /* (non-Javadoc)
- * @see org.eclipse.core.runtime.jobs.Job#run(org.eclipse.core.runtime.IProgressMonitor)
- */
- @Override
- protected IStatus run(IProgressMonitor monitor) {
- view.getConversationHolder().bind();
- view.query();
- Display.getDefault().asyncExec(new Runnable() {
-
- @Override
- public void run() {
- CdmStore.getContextManager().notifyContextRefresh();
- }
- });
- return Status.OK_STATUS;
- }
-
- }
-}
BGBM BDI Projects / taxeditor.git / commitdiff