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package eu.etaxonomy.taxeditor.view.dataimport.e4;
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import java.net.URI;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.Comparator;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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import org.apache.commons.lang.StringUtils;
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import org.eclipse.core.runtime.jobs.Job;
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import org.eclipse.jface.action.Action;
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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 eu.etaxonomy.cdm.api.conversation.ConversationHolder;
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import eu.etaxonomy.cdm.api.service.ITermService;
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import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;
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import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseResponse;
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import eu.etaxonomy.cdm.ext.occurrence.gbif.DataSetResponse;
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import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifDataSetProtocol;
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import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifResponse;
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator;
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import eu.etaxonomy.cdm.io.specimen.gbif.in.GbifImportConfigurator;
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import eu.etaxonomy.cdm.model.metadata.PreferencePredicate;
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import eu.etaxonomy.cdm.model.term.DefinedTermBase;
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import eu.etaxonomy.taxeditor.preference.IPreferenceKeys;
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import eu.etaxonomy.taxeditor.preference.PreferencesUtil;
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import eu.etaxonomy.taxeditor.store.CdmStore;
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import eu.etaxonomy.taxeditor.view.dataimport.GbifResponseComparator;
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/**
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*
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* @author pplitzner
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* @since Oct 4, 2017
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*
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*/
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public class SaveImportedSpecimenActionE4 extends Action {
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private Comparator<GbifResponse> comparator;
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private DataImportViewE4<?> dataImportView;
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public SaveImportedSpecimenActionE4(DataImportViewE4<?> dataImportView) {
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super();
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this.dataImportView = dataImportView;
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}
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@Override
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public void run() {
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Table table = dataImportView.getTable();
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Collection<GbifResponse> checkedResults = new HashSet<GbifResponse>();
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Collection<BioCaseResponse> checkedAbcdResults = new HashSet<BioCaseResponse>();
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Object data;
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Set<String[]> unitIdsGbif = new HashSet<String[]>();
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Set<String[]> unitIdsBioCase = new HashSet<String[]>();
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List<GbifResponse> biocaseResponses = new ArrayList<GbifResponse>();
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for(TableItem item:table.getItems()){
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if(item.getChecked()){
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//Save Specimen
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data = item.getData();
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if(data instanceof GbifResponse){
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checkedResults.add((GbifResponse)item.getData());
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}
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if(data instanceof BioCaseResponse){
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checkedAbcdResults.add((BioCaseResponse)data);
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}
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}
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}
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String[] tripleId ;
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for (GbifResponse response:checkedResults){
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if (response != null){
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tripleId = response.getTripleID();
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if (response.getDataSetProtocol()!=null && response.getDataSetProtocol().equals(GbifDataSetProtocol.BIOCASE)){
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biocaseResponses.add(response);
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}else{
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unitIdsGbif.add(tripleId);
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}
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}
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}
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Collections.sort(biocaseResponses, getComparator());
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Abcd206ImportConfigurator configuratorAbcd;
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List<Abcd206ImportConfigurator> abcdConfigurators = new ArrayList<Abcd206ImportConfigurator>();
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DataSetResponse dataSetResponse;
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OccurenceQuery bioCaseOccurrenceQuery = null;
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URI dataSetUri = null;
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for (BioCaseResponse response:checkedAbcdResults){
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if (!response.getDataSetUri().equals(dataSetUri)){
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dataSetUri = response.getDataSetUri();
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configuratorAbcd = Abcd206ImportConfigurator.NewInstance(null, null);
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String configString = PreferencesUtil.getStringValue(IPreferenceKeys.LAST_USED_ABCD_CONFIG);
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if (StringUtils.isBlank(configString)){
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configString = PreferencesUtil.getStringValue(PreferencePredicate.AbcdImportConfig.getKey(), false);
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PreferencesUtil.extractAbcdConfiguratorFromPreferenceString(configuratorAbcd, configString);
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if (configuratorAbcd.getNomenclaturalCode() == null){
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configuratorAbcd.setNomenclaturalCode(PreferencesUtil.getPreferredNomenclaturalCode());
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}
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}else{
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configuratorAbcd = Abcd206ImportConfigurator.NewInstance(null, null);
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PreferencesUtil.extractAbcdConfiguratorFromPreferenceString(configuratorAbcd, configString);
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if (configuratorAbcd.getNomenclaturalCode() == null){
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configuratorAbcd.setNomenclaturalCode(PreferencesUtil.getPreferredNomenclaturalCode());
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}
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}
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configuratorAbcd.setSourceUri(dataSetUri);
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unitIdsBioCase = new HashSet<String[]>();
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bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase);
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configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery);
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if (dataImportView.getClassification() != null){
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configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid());
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}
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if (dataImportView.getReferenceString() != null){
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configuratorAbcd.setSourceReferenceTitle(dataImportView.getReferenceString());
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}
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abcdConfigurators.add(configuratorAbcd);
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}
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tripleId = response.getTripleID();
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unitIdsBioCase.add(tripleId);
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}
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// if (!unitIdsBioCase.isEmpty()){
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// configuratorAbcd = Abcd206ImportConfigurator.NewInstance(dataSetUri, null, false);
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// configuratorAbcd.addMediaAsMediaSpecimen(true);
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// configuratorAbcd.setIgnoreAuthorship(true);
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// configuratorAbcd.setMoveNewTaxaToDefaultClassification(false);
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// if (configuratorAbcd != null){
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// abcdConfigurators.add(configuratorAbcd);
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// }
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//// unitIdsBioCase = new HashSet<String[]>();
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// bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase);
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// configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery);
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// configuratorAbcd.setGetSiblings(true);
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// if (dataImportView.getClassification() != null){
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// configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid());
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// }
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// }
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// for (GbifResponse response: biocaseResponses){
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// try {
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// dataSetResponse = new GbifQueryServiceWrapper().queryOriginalDataSet(response);
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// dataSetUri = dataSetResponse.getEndpoint();
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// } catch (ClientProtocolException e) {
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// // TODO Auto-generated catch block
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// e.printStackTrace();
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// } catch (IOException e) {
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// // TODO Auto-generated catch block
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// e.printStackTrace();
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// }
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// if (!response.getDataSetUri().equals(dataSetUri)){
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// configuratorAbcd = Abcd206ImportConfigurator.NewInstance(dataSetUri, null, false);
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// configuratorAbcd.addMediaAsMediaSpecimen(true);
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// configuratorAbcd.setIgnoreAuthorship(true);
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// configuratorAbcd.setMoveNewTaxaToDefaultClassification(false);
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// if (configuratorAbcd != null){
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// abcdConfigurators.add(configuratorAbcd);
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// }
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// unitIdsBioCase = new HashSet<String[]>();
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// bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase);
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// configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery);
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// configuratorAbcd.setGetSiblings(true);
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// if (dataImportView.getClassification() != null){
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// configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid());
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// }
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//
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// }
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// tripleId = response.getTripleID();
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// unitIdsBioCase.add(tripleId);
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// }
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// configurator.setQuery(query);
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if (!checkedAbcdResults.isEmpty()){
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Job bioCaseJob = CdmStore.getImportManager().createIOServiceJob(abcdConfigurators);
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CdmStore.getImportManager().run(bioCaseJob);
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}
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if (!unitIdsGbif.isEmpty()){
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OccurenceQuery query = new OccurenceQuery(unitIdsGbif);
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GbifImportConfigurator configurator = GbifImportConfigurator.newInstance(query);
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configurator.setSourceReferenceTitle("Import Gbif data");
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Job gbifJob = CdmStore.getImportManager().createIOServiceJob(configurator);
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CdmStore.getImportManager().run(gbifJob);
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}
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}
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private void persistTerm(DefinedTermBase<?> term, ITermService termService, ConversationHolder conversation){
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if(term!=null){
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//if the term does not exist in the DB save it
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if(termService.find(term.getUuid())==null){
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termService.saveOrUpdate(term);
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}
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}
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}
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@Override
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public String getText() {
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return "Import";
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}
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private Comparator<GbifResponse> getComparator(){
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if (comparator == null){
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comparator = new GbifResponseComparator();
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}
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return comparator;
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}
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}
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