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/**
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* Copyright (C) 2015 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.cdm.io.specimen.abcd206.in;
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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.util.HashSet;
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import java.util.Set;
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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.w3c.dom.Element;
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import eu.etaxonomy.cdm.api.application.ICdmRepository;
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import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;
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import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper;
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/**
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* @author pplitzner
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\* @since 16.06.2015
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*
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*/
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public class UnitAssociationParser {
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private static final Logger logger = Logger.getLogger(UnitAssociationParser.class);
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private final String prefix;
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private final SpecimenImportReport report;
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private final ICdmRepository cdmAppController;
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public UnitAssociationParser(String prefix, SpecimenImportReport report, ICdmRepository cdmAppController) {
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this.prefix = prefix;
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this.report = report;
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this.cdmAppController = cdmAppController;
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}
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public UnitAssociationWrapper parse(Element unitAssociation){
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if(prefix.equals("abcd:")){
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}
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else if(prefix.equals("abcd21:")){
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}
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//unit id
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String unitId = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"UnitID"));
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if(unitId==null){
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unitId = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"AssociatedUnitID"));//abcd 2.0.6
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}
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//institution code
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String institutionCode = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"SourceInstitutionCode"));
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if(institutionCode==null){
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institutionCode = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"AssociatedUnitSourceInstitutionCode"));//abcd 2.0.6
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}
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//institution name
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String institutionName = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"SourceName"));
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if(institutionName==null){
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institutionName = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"AssociatedUnitSourceName"));//abcd 2.0.6
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}
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//data access point
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URI datasetAccessPoint = AbcdParseUtility.parseFirstUri(unitAssociation.getElementsByTagName(prefix+"DatasetAccessPoint"), report);
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if(datasetAccessPoint==null){
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datasetAccessPoint = AbcdParseUtility.parseFirstUri(unitAssociation.getElementsByTagName(prefix+"Comment"), report);//abcd 2.0.6
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}
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//association type
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String associationType = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"AssociationType"));
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String unableToLoadMessage = String.format("Unable to load unit %s from %s", unitId, datasetAccessPoint);
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if(unitId!=null && datasetAccessPoint!=null){
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BioCaseQueryServiceWrapper serviceWrapper = new BioCaseQueryServiceWrapper();
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Set<String[]> unitIds = new HashSet<String[]>();
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String[] unitIdArray = {unitId};
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unitIds.add(unitIdArray);
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OccurenceQuery query = new OccurenceQuery(unitIds);
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try {
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InputStream inputStream = serviceWrapper.query(query, datasetAccessPoint);
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if(inputStream!=null){
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UnitAssociationWrapper unitAssociationWrapper = null;
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try {
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unitAssociationWrapper = AbcdParseUtility.parseUnitsNodeList(inputStream, report);
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} catch (Exception e) {
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String exceptionMessage = "An exception occurred during parsing of associated units!";
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logger.error(exceptionMessage, e);
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report.addException(exceptionMessage, e);
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}
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if(unitAssociationWrapper!=null){
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unitAssociationWrapper.setAssociationType(associationType);
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unitAssociationWrapper.setAccesPoint(datasetAccessPoint);
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if(unitAssociationWrapper.getAssociatedUnits()!=null && unitAssociationWrapper.getAssociatedUnits().getLength()>1){
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String moreThanOneUnitFoundMessage = String.format("More than one unit was found for unit association to %s", unitId);
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logger.warn(moreThanOneUnitFoundMessage);
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report.addInfoMessage(moreThanOneUnitFoundMessage);
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}
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}
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return unitAssociationWrapper;
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}
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else{
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logger.error(unableToLoadMessage);
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report.addInfoMessage(unableToLoadMessage);
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}
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} catch (ClientProtocolException e) {
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logger.error(unableToLoadMessage, e);
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report.addInfoMessage(unableToLoadMessage);
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} catch (IOException e) {
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logger.error(unableToLoadMessage, e);
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report.addInfoMessage(unableToLoadMessage);
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}
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}
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else{
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report.addInfoMessage(unableToLoadMessage);
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}
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return null;
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}
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public UnitAssociationWrapper parseSiblings(String unitID, URI datasetAccessPoint){
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String unableToLoadMessage = String.format("Unable to load unit %s from %s", unitID, datasetAccessPoint);
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if(unitID!=null && datasetAccessPoint!=null){
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BioCaseQueryServiceWrapper serviceWrapper = new BioCaseQueryServiceWrapper();
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OccurenceQuery query = new OccurenceQuery(unitID);
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InputStream inputStream;
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try {
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inputStream = serviceWrapper.querySiblings(query, datasetAccessPoint);
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if(inputStream!=null){
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UnitAssociationWrapper unitAssociationWrapper = null;
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try {
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unitAssociationWrapper = AbcdParseUtility.parseUnitsNodeList(inputStream, report);
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} catch (Exception e) {
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String exceptionMessage = "An exception occurred during parsing of associated units!";
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logger.error(exceptionMessage, e);
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report.addException(exceptionMessage, e);
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}
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return unitAssociationWrapper;
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}
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else{
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logger.error(unableToLoadMessage);
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report.addInfoMessage(unableToLoadMessage);
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}
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} catch (ClientProtocolException e1) {
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// TODO Auto-generated catch block
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e1.printStackTrace();
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} catch (IOException e1) {
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// TODO Auto-generated catch block
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e1.printStackTrace();
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}
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}
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else{
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report.addInfoMessage(unableToLoadMessage);
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}
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return null;
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}
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}
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