Revision 42580bdf
Added by Patrick Plitzner over 9 years ago
- updated SpecimenImportWizard
- refactored BioCase querying to be a separate job
| eu.etaxonomy.taxeditor.bulkeditor/plugin.xml | ||
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| 389 | 389 |
class="eu.etaxonomy.taxeditor.dataimport.wizard.SpecimenSearchWizard" |
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id="eu.etaxonomy.taxeditor.dataimport.wizard.SpecimenSearchWizard" |
| 391 | 391 |
name="Query BioCASE"> |
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<description> |
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Query BioCaseProvider |
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</description> |
|
| 392 | 395 |
</wizard> |
| 393 | 396 |
</extension> |
| 394 | 397 |
<!-- start set marker --> |
| eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/dataimport/DerivedUnitEditorInput.java | ||
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| 12 | 12 |
import java.io.IOException; |
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import java.io.InputStream; |
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import java.net.URISyntaxException; |
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import java.util.Collections; |
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import java.util.List; |
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|
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import org.apache.http.client.ClientProtocolException; |
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import org.apache.log4j.Logger; |
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import org.eclipse.core.runtime.IProgressMonitor; |
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import org.eclipse.core.runtime.IStatus; |
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import org.eclipse.core.runtime.Status; |
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import org.eclipse.core.runtime.jobs.Job; |
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import org.eclipse.jface.resource.ImageDescriptor; |
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import org.eclipse.swt.widgets.Display; |
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import org.eclipse.ui.IEditorInput; |
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import org.eclipse.ui.IPersistableElement; |
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import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
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import eu.etaxonomy.cdm.ext.biocase.BioCaseQuery; |
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import eu.etaxonomy.cdm.ext.biocase.BioCaseQueryServiceWrapper; |
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import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
| ... | ... | |
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|
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private final BioCaseQuery query; |
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private List<SpecimenOrObservationBase> results; |
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|
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/** |
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* @param results |
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*/ |
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public DerivedUnitEditorInput(BioCaseQuery query) {
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this.query = query; |
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Display.getCurrent().asyncExec(new Runnable() {
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@Override |
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public void run() {
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String errorMessage = "Could not execute query " + DerivedUnitEditorInput.this.query; |
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try {
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InputStream resultStream = new BioCaseQueryServiceWrapper().query(DerivedUnitEditorInput.this.query); |
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Abcd206ImportConfigurator configurator = Abcd206ImportConfigurator.NewInstance(resultStream, null, false); |
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TransientCdmRepository repo = |
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new TransientCdmRepository(CdmStore.getCurrentApplicationConfiguration()); |
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configurator.setCdmAppController(repo); |
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|
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CdmDefaultImport<Abcd206ImportConfigurator> importer = new CdmDefaultImport<Abcd206ImportConfigurator>(); |
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importer.invoke(configurator); |
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results = repo.getUnits(); |
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// Abcd206Import abcd206Import = new Abcd206Import(); |
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// Abcd206ImportState state = new Abcd206ImportState(configurator); |
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// abcd206Import.invoke(state); |
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// state.countTrees(); |
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} catch (ClientProtocolException e) {
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logger.error(errorMessage, e); |
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} catch (IOException e) {
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logger.error(errorMessage, e); |
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} catch (URISyntaxException e) {
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logger.error(errorMessage, e); |
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} |
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// return new BioCaseQueryServiceWrapper().dummyData(); |
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} |
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}); |
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} |
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|
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public void query(){
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Job queryJob = new Job("Query Biocase") {
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@Override |
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protected IStatus run(IProgressMonitor monitor) {
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String errorMessage = "Could not execute query " + DerivedUnitEditorInput.this.query; |
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try {
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InputStream resultStream = new BioCaseQueryServiceWrapper().query(DerivedUnitEditorInput.this.query); |
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Abcd206ImportConfigurator configurator = Abcd206ImportConfigurator.NewInstance(resultStream, null, false); |
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TransientCdmRepository repo = |
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new TransientCdmRepository(CdmStore.getCurrentApplicationConfiguration()); |
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configurator.setCdmAppController(repo); |
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|
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CdmDefaultImport<Abcd206ImportConfigurator> importer = new CdmDefaultImport<Abcd206ImportConfigurator>(); |
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importer.invoke(configurator); |
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results = repo.getUnits(); |
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// Abcd206Import abcd206Import = new Abcd206Import(); |
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// Abcd206ImportState state = new Abcd206ImportState(configurator); |
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// abcd206Import.invoke(state); |
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// state.countTrees(); |
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} catch (ClientProtocolException e) {
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logger.error(errorMessage, e); |
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} catch (IOException e) {
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logger.error(errorMessage, e); |
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} catch (URISyntaxException e) {
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logger.error(errorMessage, e); |
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} |
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Display.getDefault().asyncExec(new Runnable() {
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@Override |
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public void run() {
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CdmStore.getContextManager().notifyContextRefresh(); |
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} |
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}); |
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return Status.OK_STATUS; |
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} |
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}; |
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} |
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/* (non-Javadoc) |
| ... | ... | |
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* @return the results |
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*/ |
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public List<SpecimenOrObservationBase> getResults() {
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String errorMessage = "Could not execute query " + query; |
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List<SpecimenOrObservationBase> results = Collections.EMPTY_LIST; |
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try {
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InputStream resultStream = new BioCaseQueryServiceWrapper().query(query); |
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Abcd206ImportConfigurator configurator = Abcd206ImportConfigurator.NewInstance(resultStream, null, false); |
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TransientCdmRepository repo = |
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new TransientCdmRepository((ICdmApplicationConfiguration)CdmStore.getCurrentApplicationConfiguration()); |
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configurator.setCdmAppController(repo); |
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CdmDefaultImport<Abcd206ImportConfigurator> importer = new CdmDefaultImport<Abcd206ImportConfigurator>(); |
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importer.invoke(configurator); |
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results = repo.getUnits(); |
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// Abcd206Import abcd206Import = new Abcd206Import(); |
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// Abcd206ImportState state = new Abcd206ImportState(configurator); |
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// abcd206Import.invoke(state); |
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// state.countTrees(); |
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} catch (ClientProtocolException e) {
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logger.error(errorMessage, e); |
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} catch (IOException e) {
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logger.error(errorMessage, e); |
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} catch (URISyntaxException e) {
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logger.error(errorMessage, e); |
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} |
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// return new BioCaseQueryServiceWrapper().dummyData(); |
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return results; |
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} |
| 131 | 182 |
|
| eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/dataimport/wizard/SpecimenSearchWizard.java | ||
|---|---|---|
| 44 | 44 |
|
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//check if connected to a data source. If not this will open an error dialog |
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CdmStore.getCurrentApplicationConfiguration(); |
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this.setWindowTitle("Search Specimens");
|
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} |
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|
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|
| ... | ... | |
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try {
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query = searchPage.getQuery(); |
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DerivedUnitEditorInput input = new DerivedUnitEditorInput(query); |
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input.query(); |
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page.openEditor(input, DataImportEditor.ID, true); |
| 61 | 63 |
} catch ( PartInitException e ) {
|
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//Put your exception handler here if you wish to |
| eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/dataimport/wizard/SpecimenSearchWizardPage.java | ||
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| 28 | 28 |
|
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protected SpecimenSearchWizardPage(String pageName) {
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super(pageName); |
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setDescription("Specify search parameters for external search query.");
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setTitle("Search Specimens");
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} |
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/* (non-Javadoc) |
| eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/specimenSearch/SpecimenSearchComposite.java | ||
|---|---|---|
| 25 | 25 |
*/ |
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public class SpecimenSearchComposite extends Composite {
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private final FormToolkit formToolkit = new FormToolkit(Display.getDefault()); |
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private Text textTaxonName; |
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private Text textCollector; |
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private Text textCollectorNumber; |
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private Text textAccessionNumber; |
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private Text textLocality; |
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private Text textHerbarium; |
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private Text textCountry; |
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private final Text textTaxonName;
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private final Text textCollector;
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private final Text textCollectorNumber;
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private final Text textAccessionNumber;
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private final Text textLocality;
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private final Text textHerbarium;
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private final Text textCountry;
|
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/** |
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* Create the composite. |
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* @param parent |
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* @param style |
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* @setBackgroundMode(SWT.INHERIT_DEFAULT); |
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param style |
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*/ |
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public SpecimenSearchComposite(Composite parent, int style) {
|
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super(parent, style); |
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setBackgroundMode(SWT.INHERIT_DEFAULT); |
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{
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TableWrapLayout tableWrapLayout = new TableWrapLayout(); |
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tableWrapLayout.numColumns = 2; |
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setLayout(tableWrapLayout); |
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} |
| 49 | 49 |
|
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Label lblTaxonName = formToolkit.createLabel(this, "Taxon Name", SWT.NONE); |
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Label lblTaxonName = new Label(this, SWT.NONE); |
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lblTaxonName.setText("Taxon Name");
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textTaxonName = new Text(this, SWT.BORDER);
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textTaxonName = new Text(this, SWT.NONE);
|
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textTaxonName.setLayoutData(new TableWrapData(TableWrapData.FILL_GRAB, TableWrapData.TOP, 1, 1)); |
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formToolkit.adapt(textTaxonName, true, true); |
|
| 55 | 55 |
|
| 56 | 56 |
Label lblCollectors = new Label(this, SWT.NONE); |
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formToolkit.adapt(lblCollectors, true, true); |
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lblCollectors.setText("Collector(s)");
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textCollector = new Text(this, SWT.BORDER);
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textCollector = new Text(this, SWT.NONE);
|
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textCollector.setLayoutData(new TableWrapData(TableWrapData.FILL_GRAB, TableWrapData.TOP, 1, 1)); |
| 62 | 61 |
formToolkit.adapt(textCollector, true, true); |
| 63 | 62 |
|
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Label lblCollectorsNumber = new Label(this, SWT.NONE); |
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formToolkit.adapt(lblCollectorsNumber, true, true); |
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lblCollectorsNumber.setText("Collector(s) Number");
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| 67 | 65 |
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textCollectorNumber = new Text(this, SWT.BORDER);
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textCollectorNumber = new Text(this, SWT.NONE);
|
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| 69 | 67 |
textCollectorNumber.setLayoutData(new TableWrapData(TableWrapData.FILL_GRAB, TableWrapData.TOP, 1, 1)); |
| 70 | 68 |
formToolkit.adapt(textCollectorNumber, true, true); |
| 71 | 69 |
|
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Label lblAccessionNumber = new Label(this, SWT.NONE); |
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formToolkit.adapt(lblAccessionNumber, true, true); |
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lblAccessionNumber.setText("Accession Number");
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| 75 | 72 |
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textAccessionNumber = new Text(this, SWT.BORDER);
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textAccessionNumber = new Text(this, SWT.NONE);
|
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| 77 | 74 |
textAccessionNumber.setLayoutData(new TableWrapData(TableWrapData.FILL_GRAB, TableWrapData.TOP, 1, 1)); |
| 78 | 75 |
formToolkit.adapt(textAccessionNumber, true, true); |
| 79 | 76 |
|
| 80 | 77 |
Label lblHerbarium = new Label(this, SWT.NONE); |
| 81 |
formToolkit.adapt(lblHerbarium, true, true); |
|
| 82 | 78 |
lblHerbarium.setText("Herbarium");
|
| 83 | 79 |
|
| 84 | 80 |
textHerbarium = new Text(this, SWT.NONE); |
| 85 | 81 |
textHerbarium.setLayoutData(new TableWrapData(TableWrapData.FILL_GRAB, TableWrapData.TOP, 1, 1)); |
| 86 | 82 |
|
| 87 | 83 |
Label lblCountry = new Label(this, SWT.NONE); |
| 88 |
formToolkit.adapt(lblCountry, true, true); |
|
| 89 | 84 |
lblCountry.setText("Country");
|
| 90 | 85 |
|
| 91 | 86 |
textCountry = new Text(this, SWT.NONE); |
| 92 | 87 |
textCountry.setLayoutData(new TableWrapData(TableWrapData.FILL_GRAB, TableWrapData.TOP, 1, 1)); |
| 93 | 88 |
|
| 94 | 89 |
Label lblLocality = new Label(this, SWT.NONE); |
| 95 |
formToolkit.adapt(lblLocality, true, true); |
|
| 96 | 90 |
lblLocality.setText("Locality");
|
| 97 | 91 |
|
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textLocality = new Text(this, SWT.BORDER);
|
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textLocality = new Text(this, SWT.NONE);
|
|
| 99 | 93 |
textLocality.setLayoutData(new TableWrapData(TableWrapData.FILL_GRAB, TableWrapData.TOP, 1, 1)); |
| 100 | 94 |
formToolkit.adapt(textLocality, true, true); |
| 101 | 95 |
|
| 102 | 96 |
Label lblCollectionDate = new Label(this, SWT.NONE); |
| 103 |
formToolkit.adapt(lblCollectionDate, true, true); |
|
| 104 | 97 |
lblCollectionDate.setText("Collection Date");
|
| 105 | 98 |
new Label(this, SWT.NONE); |
| 106 | 99 |
|
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