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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.e4;
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import java.io.IOException;
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import java.io.InputStream;
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import java.net.URI;
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import java.time.LocalDate;
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import java.time.format.DateTimeFormatter;
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import java.util.ArrayList;
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import java.util.Collection;
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import org.apache.http.client.ClientProtocolException;
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import org.w3c.dom.Element;
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import org.w3c.dom.NodeList;
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import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper;
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import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseResponse;
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206DataHolder;
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator;
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportParser;
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportState;
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206XMLFieldGetter;
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdParseUtility;
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.Identification;
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.UnitAssociationWrapper;
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/**
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* @author pplitzner
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* @date Sep 3, 2014
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*
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*/
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public class SpecimenImportViewE4 extends DataImportViewE4<BioCaseResponse> {
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public static final String ID = "eu.etaxonomy.taxeditor.view.dataimport.SpecimenImportView"; //$NON-NLS-1$
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private URI endPoint;
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public SpecimenImportViewE4() {
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}
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/**
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* @param endPoint
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*/
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public void setEndpoint(URI endPoint) {
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this.endPoint = endPoint;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.taxeditor.view.dataimport.DataImportView#getTextForTableItem(java.lang.Object)
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*/
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@Override
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protected String getTextForTableItem(BioCaseResponse item) {
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//TODO: could be defined in user preferences...
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String name = null;
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if(!(((Abcd206DataHolder)item.getAbcdDataHolder()).getIdentificationList() == null) && !((Abcd206DataHolder)item.getAbcdDataHolder()).getIdentificationList().isEmpty()){
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Identification identification = ((Abcd206DataHolder)item.getAbcdDataHolder()).getIdentificationList().iterator().next();
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name = identification.getScientificName();
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}
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if (name != null){
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return name +" - "+((Abcd206DataHolder)item.getAbcdDataHolder()).getCollectionCode() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getUnitID() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getKindOfUnit();
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}else {
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return ((Abcd206DataHolder)item.getAbcdDataHolder()).getCollectionCode() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getUnitID() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getKindOfUnit();
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}
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.taxeditor.view.dataimport.DataImportView#query()
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*/
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@Override
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public void query() {
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String errorMessage = "Could not execute query " + query;
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Collection<BioCaseResponse> results = new ArrayList<BioCaseResponse>();
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try {
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//FIXME move ABCD import to cdmlib -> this will also get rid of the transient services
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InputStream resultStream;
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resultStream = new BioCaseQueryServiceWrapper().query(query, endPoint);
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Abcd206ImportConfigurator configurator = Abcd206ImportConfigurator.NewInstance(null, null);
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configurator.setSourceUri(endPoint);
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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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//TODO: do not query all data but with the selected triple IDs -> see GbifResponseImportView
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configurator.setAddMediaAsMediaSpecimen(true);
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configurator.setAllowReuseOtherClassifications(true);
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configurator.setMoveNewTaxaToDefaultClassification(false);
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UnitAssociationWrapper unitAssociationWrapper = AbcdParseUtility.parseUnitsNodeList(resultStream, null);
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NodeList unitsList = unitAssociationWrapper.getAssociatedUnits();
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Abcd206DataHolder dataHolder = new Abcd206DataHolder();
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Abcd206XMLFieldGetter abcdFieldGetter = new Abcd206XMLFieldGetter(dataHolder, unitAssociationWrapper.getPrefix());
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Abcd206ImportState state = new Abcd206ImportState(configurator);
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state.setDataHolder(dataHolder);
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BioCaseResponse response = null;
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if (unitsList != null){
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for (int i = 0; i <unitsList.getLength(); i++){
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Element item = (Element) unitsList.item(i);
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dataHolder = new Abcd206DataHolder();
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abcdFieldGetter = new Abcd206XMLFieldGetter(dataHolder, unitAssociationWrapper.getPrefix());
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state.setPrefix(unitAssociationWrapper.getPrefix());
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Abcd206ImportParser.setUnitPropertiesXML(item, abcdFieldGetter, state);
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String[] tripleIdBioCase = new String[3];
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tripleIdBioCase[0] =dataHolder.getUnitID();
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tripleIdBioCase[1] = dataHolder.getInstitutionCode();
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tripleIdBioCase[2] = dataHolder.getCollectionCode();
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response = new BioCaseResponse(dataHolder, endPoint, tripleIdBioCase );
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results.add(response);
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}
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}
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// Job job = CdmStore.getImportManager().createIOServiceJob(configurator, resultStream, SOURCE_TYPE.INPUTSTREAM);
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// CdmStore.getImportManager().run(job);
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setResults(results);
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DateTimeFormatter dtf = DateTimeFormatter.ofPattern("yyyy/MM/dd");
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LocalDate localDate = LocalDate.now();
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System.out.println(dtf.format(localDate));
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textReferenceString.setText("Biocase Import " + localDate.toString());
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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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}
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// setResults(results);
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}
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}
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