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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 eu.etaxonomy.cdm.common.URI;
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import java.util.List;
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import java.util.UUID;
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import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
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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.SpecimenImportReport;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.molecular.Amplification;
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import eu.etaxonomy.cdm.model.molecular.AmplificationResult;
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import eu.etaxonomy.cdm.model.molecular.DnaQuality;
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import eu.etaxonomy.cdm.model.molecular.DnaSample;
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import eu.etaxonomy.cdm.model.molecular.Primer;
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import eu.etaxonomy.cdm.model.molecular.Sequence;
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import eu.etaxonomy.cdm.model.molecular.SequenceDirection;
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import eu.etaxonomy.cdm.model.molecular.SequenceString;
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import eu.etaxonomy.cdm.model.molecular.SingleRead;
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import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.term.DefinedTerm;
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import eu.etaxonomy.cdm.model.term.DefinedTermBase;
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import eu.etaxonomy.cdm.model.term.OrderedTerm;
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import eu.etaxonomy.cdm.model.term.TermType;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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/**
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* @author pplitzner
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* @since Mar 4, 2015
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*
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*/
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public class AbcdGgbnParser {
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//DNA Quality term
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private static final String HIGH = "high";
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private static final String MEDIUM = "medium";
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private static final String LOW = "low";
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private static final UUID HIGH_QUALITY_TERM = UUID.fromString("ec443c76-5987-4ec5-a66b-da207f70b47f");
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private static final UUID MEDIUM_QUALITY_TERM = UUID.fromString("2a174892-1246-4807-9022-71ce8639346b");
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private static final UUID LOW_QUALITY_TERM = UUID.fromString("a3bf12ff-b041-425f-bdaa-aa51da65eebc");
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private static final String FORWARD = "forward";
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private static final String REVERSE = "reverse";
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private static final Logger logger = LogManager.getLogger(AbcdGgbnParser.class);
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private final String prefix = "ggbn:";
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private final SpecimenImportReport report;
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private final ICdmRepository cdmAppController;
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public AbcdGgbnParser(SpecimenImportReport report, ICdmRepository cdmAppController) {
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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(NodeList ggbn, DnaSample dnaSample, Abcd206ImportState state) {
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for(int i=0;i<ggbn.getLength();i++){
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Node item = ggbn.item(i);
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if(item instanceof Element){
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Element element = (Element) item;
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NodeList methodDeterminationConcentrationAndRatiosList = element.getElementsByTagName(prefix+"methodDeterminationConcentrationAndRatios");
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NodeList volumeList = element.getElementsByTagName(prefix+"volume");
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NodeList weightList = element.getElementsByTagName(prefix+"weight");
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NodeList methodDeterminationWeightList = element.getElementsByTagName(prefix+"methodDeterminationWeight");
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NodeList DNADNAHybridizationList = element.getElementsByTagName(prefix+"DNADNAHybridization");
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NodeList DNAMeltingPointList = element.getElementsByTagName(prefix+"DNAMeltingPoint");
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NodeList estimatedSizeList = element.getElementsByTagName(prefix+"estimated_size");
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NodeList poolDnaExtractsList = element.getElementsByTagName(prefix+"pool_dna_extracts");
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NodeList gelImageList = element.getElementsByTagName(prefix+"gelImage");
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NodeList amplificationsList = element.getElementsByTagName(prefix+"Amplifications");
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dnaSample.setDnaQuality(parseDnaQuality(element, state));
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parseGelImage(gelImageList, state);
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parseAmplifications(amplificationsList, dnaSample, state);
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}
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}
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return dnaSample;
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}
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private DnaQuality parseDnaQuality(Element element, Abcd206ImportState state) {
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DnaQuality dnaQuality = DnaQuality.NewInstance();
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NodeList purificationMethodList = element.getElementsByTagName(prefix+"purificationMethod");
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String purificationMethod = AbcdParseUtility.parseFirstTextContent(purificationMethodList);
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dnaQuality.setPurificationMethod(purificationMethod);
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NodeList concentrationList = element.getElementsByTagName(prefix+"concentration");
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if(concentrationList.getLength()==1){
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Node concentration = concentrationList.item(0);
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dnaQuality.setConcentration(AbcdParseUtility.parseDouble(concentration, report));
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if(concentration instanceof Element){
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String unit = ((Element) concentration).getAttribute("Unit");
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//TODO
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// dnaQuality.setConcentrationUnit(concentrationUnit)
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}
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}
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NodeList ratioOfAbsorbance260_280List = element.getElementsByTagName(prefix+"ratioOfAbsorbance260_280");
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dnaQuality.setRatioOfAbsorbance260_280(AbcdParseUtility.parseFirstDouble(ratioOfAbsorbance260_280List, report));
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NodeList ratioOfAbsorbance260_230List = element.getElementsByTagName(prefix+"ratioOfAbsorbance260_230");
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dnaQuality.setRatioOfAbsorbance260_230(AbcdParseUtility.parseFirstDouble(ratioOfAbsorbance260_230List, report));
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NodeList qualityCheckDateList = element.getElementsByTagName(prefix+"qualityCheckDate");
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if(qualityCheckDateList.item(0)!=null){
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dnaQuality.setQualityCheckDate(AbcdParseUtility.parseFirstDateTime(qualityCheckDateList));
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}
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NodeList qualityList = element.getElementsByTagName(prefix+"quality");
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String quality = AbcdParseUtility.parseFirstTextContent(qualityList);
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if(LOW.equals(quality)){
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dnaQuality.setQualityTerm((OrderedTerm) state.getCdmRepository().getTermService().load(LOW_QUALITY_TERM));
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}
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else if(MEDIUM.equals(quality)){
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dnaQuality.setQualityTerm((OrderedTerm) state.getCdmRepository().getTermService().load(MEDIUM_QUALITY_TERM));
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}
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else if(HIGH.equals(quality)){
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dnaQuality.setQualityTerm((OrderedTerm) state.getCdmRepository().getTermService().load(HIGH_QUALITY_TERM));
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}
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NodeList qualityRemarksList = element.getElementsByTagName(prefix+"qualityRemarks");
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return dnaQuality;
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}
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private void parseGelImage(NodeList gelImageList, Abcd206ImportState state) {
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if(gelImageList.item(0)!=null && gelImageList.item(0) instanceof Element){
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Element gelImage = (Element)gelImageList.item(0);
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NodeList fileURIList = gelImage.getElementsByTagName("fileURI");
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NodeList gelVoltageList = gelImage.getElementsByTagName("gelVoltage");
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NodeList gelConcentrationList = gelImage.getElementsByTagName("gelConcentration");
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NodeList gelDurationList = gelImage.getElementsByTagName("gelDuration");
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NodeList gelLadderList = gelImage.getElementsByTagName("gelLadder");
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NodeList gelStainList = gelImage.getElementsByTagName("gelStain");
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NodeList gelRemarksList = gelImage.getElementsByTagName("gelRemarks");
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}
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}
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private void parseAmplifications(NodeList amplificationsList, DnaSample dnaSample, Abcd206ImportState state) {
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if(amplificationsList.item(0)!=null && amplificationsList.item(0) instanceof Element){
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AmplificationResult amplificationResult = AmplificationResult.NewInstance();
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Amplification amplification = Amplification.NewInstance();
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NodeList amplificationList = ((Element) amplificationsList.item(0)).getElementsByTagName(prefix+"amplification");
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for(int i=0;i<amplificationList.getLength();i++){
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if(amplificationList.item(i) instanceof Element){
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Element amplificationElement = (Element)amplificationList.item(i);
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NodeList amplificationDateList = amplificationElement.getElementsByTagName(prefix+"amplificationDate");
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NodeList amplificationStaffList = amplificationElement.getElementsByTagName(prefix+"amplificationStaff");
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//amplification dna marker
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NodeList markerList = amplificationElement.getElementsByTagName(prefix+"marker");
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if(markerList.item(0)!=null){
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String amplificationMarker = markerList.item(0).getTextContent();
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DefinedTerm dnaMarker = null;
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List<DefinedTerm> markersFound = cdmAppController.getTermService().findByTitleWithRestrictions(DefinedTerm.class, amplificationMarker, MatchMode.EXACT, null, null, null, null, null).getRecords();
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if(markersFound.size()==1){
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dnaMarker = markersFound.get(0);
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}
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else{
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dnaMarker = DefinedTerm.NewDnaMarkerInstance(amplificationMarker, amplificationMarker, amplificationMarker);
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List<TermVocabulary<DefinedTermBase>> vocs = cdmAppController.getVocabularyService().findByTermType(TermType.DnaMarker, null);
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TermVocabulary<DefinedTermBase> voc = null;
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if (vocs == null || vocs.size() == 0 ){
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voc = TermVocabulary.NewInstance(TermType.DnaMarker);
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voc.setLabel("Dna Marker");
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cdmAppController.getVocabularyService().saveOrUpdate(voc);
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}else{
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voc = vocs.get(0);
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}
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voc.addTerm(dnaMarker);
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cdmAppController.getTermService().saveOrUpdate(dnaMarker);
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}
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amplification.setDnaMarker(dnaMarker);
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}
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NodeList markerSubfragmentList = amplificationElement.getElementsByTagName(prefix+"markerSubfragment");
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NodeList amplificationSuccessList = amplificationElement.getElementsByTagName(prefix+"amplificationSuccess");
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NodeList amplificationSuccessDetailsList = amplificationElement.getElementsByTagName(prefix+"amplificationSuccessDetails");
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NodeList amplificationMethodList = amplificationElement.getElementsByTagName(prefix+"amplificationMethod");
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NodeList purificationMethodList = amplificationElement.getElementsByTagName(prefix+"purificationMethod");
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NodeList libReadsSeqdList = amplificationElement.getElementsByTagName(prefix+"lib_reads_seqd");
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NodeList libScreenList = amplificationElement.getElementsByTagName(prefix+"lib_screen");
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NodeList libVectorList = amplificationElement.getElementsByTagName(prefix+"lib_vector");
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NodeList libConstMethList = amplificationElement.getElementsByTagName(prefix+"lib_const_meth");
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NodeList plasmidList = amplificationElement.getElementsByTagName(prefix+"plasmid");
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//consensus sequence
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NodeList sequencingsList = amplificationElement.getElementsByTagName(prefix+"Sequencings");
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if(sequencingsList.item(0)!=null) {
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if ( sequencingsList.item(0) instanceof Element){
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Element el = (Element)sequencingsList.item(0);
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parseAmplificationSequencings(el, amplification, amplificationResult, dnaSample, state);
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}
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}
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parseAmplificationPrimers(amplificationElement.getElementsByTagName(prefix+"AmplificationPrimers"));
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}
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}
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//check if amplification already exists (can only be checked after all fields are initialized because comparison is done on the label cache))
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List<Amplification> matchingAmplifications = cdmAppController.getAmplificationService().findByLabelCache(amplification.getLabelCache(), MatchMode.EXACT, null, null, null, null, null).getRecords();
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if(matchingAmplifications.size()==1){
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amplification = matchingAmplifications.iterator().next();
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}
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cdmAppController.getAmplificationService().save(amplification);
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amplificationResult.setAmplification(amplification);
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dnaSample.addAmplificationResult(amplificationResult);
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}
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}
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private void parseAmplificationPrimers(NodeList elementsByTagName) {
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// TODO Auto-generated method stub
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}
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private void parseAmplificationSequencings(Element sequencings, Amplification amplification, AmplificationResult amplificationResult, DnaSample dnaSample, Abcd206ImportState state) {
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NodeList sequencingList = sequencings.getElementsByTagName(prefix+"sequencing");
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for(int i=0;i<sequencingList.getLength();i++){
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Sequence sequence = Sequence.NewInstance("");
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dnaSample.addSequence(sequence);
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sequence.setDnaMarker(amplification.getDnaMarker());
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if(sequencingList.item(i) instanceof Element){
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Element sequencing = (Element)sequencingList.item(i);
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//singleSequencings
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NodeList singleSequencingsList = sequencing.getElementsByTagName(prefix+"SingleSequencings");
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parseSingleSequencings(singleSequencingsList, amplification, amplificationResult, sequence);
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//Consensus sequence
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NodeList consensusSequencesList = sequencing.getElementsByTagName(prefix+"consensusSequence");
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sequence.setConsensusSequence(SequenceString.NewInstance(AbcdParseUtility.parseFirstTextContent(consensusSequencesList)));
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//sequence length
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Double consensusSequenceLength = AbcdParseUtility.parseFirstDouble(sequencing.getElementsByTagName(prefix+"consensusSequenceLength"), report);
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if(sequence.getConsensusSequence()!=null && consensusSequenceLength!=null){
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//TODO: this can be different from the actual length in ABCD but not in CDM!
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sequence.getConsensusSequence().setLength(consensusSequenceLength.intValue());
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}
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//contig file URL geneticAccessionNumberURI
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NodeList consensusSequenceChromatogramFileURIList = sequencing.getElementsByTagName(prefix+"consensusSequenceChromatogramFileURI");
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//NodeList consensusSequenceChromatogramFileURIList = sequencing.getElementsByTagName(prefix+"geneticAccessionNumberURI");
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URI uri = AbcdParseUtility.parseFirstUri(consensusSequenceChromatogramFileURIList, report);
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if (uri != null && uri.toString().endsWith("fasta")){
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state.putSequenceDataStableIdentifier(uri);
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sequence.addAnnotation(Annotation.NewInstance(uri.toString(), Language.DEFAULT()));
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}else{
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Media contigFile = Media.NewInstance(uri, null, null, null);
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sequence.setContigFile(contigFile);
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}
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//genetic Accession
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NodeList geneticAccessionList = sequencing.getElementsByTagName(prefix+"geneticAccession");
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parseGeneticAccession(geneticAccessionList, sequence);
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//references
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NodeList referencesList = sequencing.getElementsByTagName(prefix+"References");
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if(referencesList.item(0)!=null && referencesList.item(0) instanceof Element){
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parseSequencingReferences((Element) referencesList.item(0), sequence);
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}
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}
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}
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// if(nodeList.item(0)!=null && nodeList.item(0) instanceof Element){
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// NodeList plasmidList = amplificationElement.getElementsByTagName(prefix+"plasmid");
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}
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private void parseSequencingReferences(Element references, Sequence sequence) {
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NodeList referenceList = references.getElementsByTagName(prefix+"Reference");
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for(int i=0;i<referenceList.getLength();i++){
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if(referenceList.item(i) instanceof Element){
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Element element = (Element)referenceList.item(i);
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NodeList referenceCitationList = element.getElementsByTagName(prefix+"ReferenceCitation");
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Reference reference = AbcdParseUtility.parseFirstReference(referenceCitationList, cdmAppController);
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sequence.addCitation(reference);
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}
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}
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}
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private void parseSingleSequencings(NodeList singleSequencingsList, Amplification amplification, AmplificationResult amplificationResult, Sequence sequence) {
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if(singleSequencingsList.item(0)!=null && singleSequencingsList.item(0) instanceof Element){
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Element singleSequencings = (Element)singleSequencingsList.item(0);
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NodeList singleSequencingList = singleSequencings.getElementsByTagName(prefix+"singleSequencing");
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308
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for(int i=0;i<singleSequencingList.getLength();i++){
|
|
309
|
//single read
|
|
310
|
SingleRead singleRead = SingleRead.NewInstance();
|
|
311
|
SingleReadAlignment.NewInstance(sequence, singleRead);
|
|
312
|
amplificationResult.addSingleRead(singleRead);
|
|
313
|
if(singleSequencingList.item(i) instanceof Element){
|
|
314
|
Element singleSequencing = (Element)singleSequencingList.item(i);
|
|
315
|
NodeList sequencingDirectionList = singleSequencing.getElementsByTagName(prefix+"sequencingDirection");
|
|
316
|
//read direction
|
|
317
|
String singleReadDirection = AbcdParseUtility.parseFirstTextContent(sequencingDirectionList);
|
|
318
|
|
|
319
|
if(singleReadDirection != null && singleReadDirection.equals(FORWARD)){
|
|
320
|
singleRead.setDirection(SequenceDirection.Forward);
|
|
321
|
}
|
|
322
|
else if(singleReadDirection != null && singleReadDirection.equals(REVERSE)){
|
|
323
|
singleRead.setDirection(SequenceDirection.Reverse);
|
|
324
|
}
|
|
325
|
//read pherogram URI
|
|
326
|
NodeList chromatogramFileURIList = singleSequencing.getElementsByTagName(prefix+"chromatogramFileURI");
|
|
327
|
singleRead.setPherogram(Media.NewInstance(AbcdParseUtility.parseFirstUri(chromatogramFileURIList, report), null, null, null));
|
|
328
|
NodeList sequencingPrimersList = singleSequencing.getElementsByTagName(prefix+"SequencingPrimers");
|
|
329
|
parseSequencingPrimers(sequencingPrimersList, singleRead, amplification);
|
|
330
|
}
|
|
331
|
}
|
|
332
|
}
|
|
333
|
}
|
|
334
|
|
|
335
|
private void parseSequencingPrimers(NodeList sequencingPrimersList, SingleRead singleRead, Amplification amplification) {
|
|
336
|
if(sequencingPrimersList.item(0)!=null && sequencingPrimersList.item(0) instanceof Element){
|
|
337
|
Element sequencingPrimers = (Element)sequencingPrimersList.item(0);
|
|
338
|
NodeList sequencingPrimerList = sequencingPrimers.getElementsByTagName(prefix+"sequencingPrimer");
|
|
339
|
for(int i=0;i<sequencingPrimerList.getLength();i++){
|
|
340
|
if(sequencingPrimerList.item(i) instanceof Element){
|
|
341
|
Element sequencingPrimer = (Element)sequencingPrimerList.item(i);
|
|
342
|
//primer name
|
|
343
|
String primerName = AbcdParseUtility.parseFirstTextContent(sequencingPrimer.getElementsByTagName(prefix+"primerName"));
|
|
344
|
//check if primer already exists
|
|
345
|
List<Primer> matchingPrimers = cdmAppController.getPrimerService().findByLabel(primerName, MatchMode.EXACT, null, null, null, null, null).getRecords();
|
|
346
|
Primer primer = null;
|
|
347
|
if(matchingPrimers.size()==1){
|
|
348
|
primer = matchingPrimers.iterator().next();
|
|
349
|
return;
|
|
350
|
}
|
|
351
|
else{
|
|
352
|
primer = Primer.NewInstance(null);
|
|
353
|
primer.setLabel(primerName);
|
|
354
|
}
|
|
355
|
singleRead.setPrimer(primer);
|
|
356
|
//primer sequence
|
|
357
|
NodeList primerSequenceList = sequencingPrimer.getElementsByTagName(prefix+"primerSequence");
|
|
358
|
primer.setSequence(SequenceString.NewInstance(AbcdParseUtility.parseFirstTextContent(primerSequenceList)));
|
|
359
|
//primer direction
|
|
360
|
String direction = parseFirstAttribute("Direction", primerSequenceList);
|
|
361
|
if(direction!=null){
|
|
362
|
if(direction.equals(FORWARD)){
|
|
363
|
amplification.setForwardPrimer(primer);
|
|
364
|
}
|
|
365
|
else if(direction.equals(REVERSE)){
|
|
366
|
amplification.setReversePrimer(primer);
|
|
367
|
}
|
|
368
|
}
|
|
369
|
//reference citation
|
|
370
|
NodeList primerReferenceCitationList = sequencingPrimer.getElementsByTagName(prefix+"primerReferenceCitation");
|
|
371
|
String primerReferenceCitation = AbcdParseUtility.parseFirstTextContent(primerReferenceCitationList);
|
|
372
|
Reference reference = AbcdParseUtility.parseFirstReference(primerReferenceCitationList, cdmAppController);
|
|
373
|
primer.setPublishedIn(reference);
|
|
374
|
|
|
375
|
cdmAppController.getPrimerService().save(primer);
|
|
376
|
}
|
|
377
|
}
|
|
378
|
}
|
|
379
|
}
|
|
380
|
|
|
381
|
private String parseFirstAttribute(String attributeName, NodeList nodeList) {
|
|
382
|
String attribute = null;
|
|
383
|
if(nodeList.item(0)!=null && nodeList.item(0) instanceof Element){
|
|
384
|
Element element = (Element)nodeList.item(0);
|
|
385
|
attribute = element.getAttribute(attributeName);
|
|
386
|
}
|
|
387
|
return attribute;
|
|
388
|
}
|
|
389
|
|
|
390
|
private void parseGeneticAccession(NodeList geneticAccessionList, Sequence sequence) {
|
|
391
|
for(int i=0;i<geneticAccessionList.getLength();i++){
|
|
392
|
if(geneticAccessionList.item(i) instanceof Element){
|
|
393
|
//genetic accession number
|
|
394
|
NodeList geneticAccessionNumberList = ((Element)geneticAccessionList.item(i)).getElementsByTagName(prefix+"geneticAccessionNumber");
|
|
395
|
sequence.setGeneticAccessionNumber(AbcdParseUtility.parseFirstTextContent(geneticAccessionNumberList));
|
|
396
|
|
|
397
|
//genetic accession number uri
|
|
398
|
NodeList geneticAccessionNumberUriList = ((Element)geneticAccessionList.item(i)).getElementsByTagName(prefix+"geneticAccessionNumberURI");
|
|
399
|
//TODO: this is different from the geneticAccessionNumber
|
|
400
|
|
|
401
|
}
|
|
402
|
}
|
|
403
|
}
|
|
404
|
|
|
405
|
}
|