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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.molecular;
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import java.util.Date;
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import org.apache.commons.lang3.StringUtils;
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import org.w3c.dom.Element;
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import org.w3c.dom.Node;
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import org.w3c.dom.NodeList;
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import eu.etaxonomy.cdm.api.application.ICdmRepository;
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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.AbcdParseUtility;
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdPersonParser;
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.molecular.DnaSample;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
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import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
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import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
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import eu.etaxonomy.cdm.model.term.DefinedTerm;
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/**
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* @author pplitzner
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* @since 15.06.2015
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*
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*/
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public class AbcdDnaParser {
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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 AbcdDnaParser(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 DnaSample parse(Element item, Abcd206ImportState state) {
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FieldUnit fieldUnit = null;
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if (StringUtils.isNotBlank(state.getDataHolder().getFieldNumber())){
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fieldUnit = state.getFieldUnit(state.getDataHolder().getFieldNumber());
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}
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if (fieldUnit == null){
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fieldUnit = state.getLastFieldUnit();
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if (fieldUnit == null){
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fieldUnit = FieldUnit.NewInstance();
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if (StringUtils.isNotBlank(state.getDataHolder().getFieldNumber())){
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fieldUnit.setFieldNumber(state.getDataHolder().getFieldNumber());
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}
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}
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state.setFieldUnit(fieldUnit);
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state.setLastFieldUnit(fieldUnit);
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}
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DnaSample dnaSample = DnaSample.NewInstance();
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DerivationEvent.NewSimpleInstance(fieldUnit, dnaSample, DerivationEventType.DNA_EXTRACTION());
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//specimen unit
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NodeList specimenUnitList = item.getElementsByTagName(prefix+"SpecimenUnit");
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if(specimenUnitList.item(0)!=null && specimenUnitList.item(0) instanceof Element){
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parseSpecimenUnit((Element)specimenUnitList.item(0), dnaSample);
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}
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NodeList unitExtensions = item.getElementsByTagName(prefix+"UnitExtensions");
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System.err.println(item.toString());
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for(int i=0;i<unitExtensions.getLength();i++){
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if(unitExtensions.item(i) instanceof Element){
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Element unitExtension = (Element) unitExtensions.item(i);
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NodeList ggbn = unitExtension.getElementsByTagName("ggbn:GGBN");
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if(ggbn.getLength()>0){
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AbcdGgbnParser ggbnParser = new AbcdGgbnParser(report, cdmAppController);
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ggbnParser.parse(ggbn, dnaSample, state);
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}
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}
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}
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return dnaSample;
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}
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private void parseSpecimenUnit(Element item, DnaSample dnaSample) {
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NodeList preparationsList = item.getElementsByTagName(prefix+"Preparations");
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if(preparationsList.item(0)!=null && preparationsList.item(0) instanceof Element){
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parsePreparations((Element) preparationsList.item(0), dnaSample);
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}
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NodeList preservationsList = item.getElementsByTagName(prefix+"Preservations");
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if(preservationsList.item(0)!=null && preservationsList.item(0) instanceof Element){
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parsePreservations((Element) preservationsList.item(0), dnaSample);
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}
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}
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private void parsePreparations(Element item, DnaSample dnaSample) {
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NodeList preparationList = item.getElementsByTagName(prefix+"preparation");
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for(int i=0;i<preparationList.getLength();i++){
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Node node = preparationList.item(i);
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if(node instanceof Element){
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DerivationEvent derivedFrom = dnaSample.getDerivedFrom();
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String preparationType = AbcdParseUtility.parseFirstTextContent(((Element) node).getElementsByTagName(prefix+"preparationType"));
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//preparation materials
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String preparationMaterials = AbcdParseUtility.parseFirstTextContent(((Element) node).getElementsByTagName(prefix+"preparationMaterials"));
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derivedFrom.setDescription(preparationMaterials);
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//preparation actor
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NodeList preparationAgentList = ((Element) node).getElementsByTagName(prefix+"preparationAgent");
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if(preparationAgentList.item(0)!=null && preparationAgentList.item(0) instanceof Element){
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AgentBase<?> preparationAgent = parsePreparationAgent((Element)preparationAgentList.item(0));
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derivedFrom.setActor(preparationAgent);
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}
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//preparation date
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Date preparationDate = AbcdParseUtility.parseFirstDate(((Element) node).getElementsByTagName(prefix+"preparationDate"));
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derivedFrom.setTimeperiod(TimePeriod.NewInstance(preparationDate, null));
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//sample designation
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NodeList sampleDesignationsList = ((Element) node).getElementsByTagName(prefix+"sampleDesignations");
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if(sampleDesignationsList.item(0)!=null && sampleDesignationsList.item(0) instanceof Element){
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parseSampleDesignations((Element)sampleDesignationsList.item(0), dnaSample);
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}
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}
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}
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}
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/**
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* @param item
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* @param dnaSample
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*/
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private void parseSampleDesignations(Element item, DnaSample dnaSample) {
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NodeList sampleDesignationList = item.getElementsByTagName(prefix+"sampleDesignation");
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for(int i=0;i<sampleDesignationList.getLength();i++){
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dnaSample.addIdentifier(sampleDesignationList.item(i).getTextContent(), (DefinedTerm)cdmAppController.getTermService().find(DefinedTerm.uuidSampleDesignation));
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}
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}
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private AgentBase<?> parsePreparationAgent(Element item) {
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AgentBase<?> agentBase = null;
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NodeList personList = item.getElementsByTagName(prefix+"Person");
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if(personList.item(0)!=null && personList.item(0) instanceof Element){
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agentBase = new AbcdPersonParser(prefix,report, cdmAppController).parse((Element)personList.item(0));
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}
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return agentBase;
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}
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private void parsePreservations(Element item, DnaSample dnaSample) {
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NodeList preservationList = item.getElementsByTagName(prefix+"preservation");
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for(int i=0;i<preservationList.getLength();i++){
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Node node = preservationList.item(i);
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if(node instanceof Element){
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PreservationMethod preservation = PreservationMethod.NewInstance();
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dnaSample.setPreservation(preservation);
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String preservationType = AbcdParseUtility.parseFirstTextContent(((Element) node).getElementsByTagName(prefix+"preservationType"));
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Double preservationTemperature = AbcdParseUtility.parseFirstDouble(((Element) node).getElementsByTagName(prefix+"preservationTemperature"), report);
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preservation.setTemperature(preservationTemperature);
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}
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}
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}
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}
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