[Treebase-guts] SF.net SVN: treebase:[62] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlDocumentConverter.java

[<rv...@us...>]

Revision: 62
          http://treebase.svn.sourceforge.net/treebase/?rev=62&view=rev
Author:   rvos
Date:     2009-06-19 02:12:51 +0000 (Fri, 19 Jun 2009)

Log Message:
-----------
Adding NexmlDocumentConverter class

Added Paths:
-----------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java

Added: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java	                        (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java	2009-06-19 02:12:51 UTC (rev 62)
@@ -0,0 +1,149 @@
+package org.cipres.treebase.domain.nexus.nexml;
+
+import org.cipres.treebase.domain.admin.Person;
+import org.cipres.treebase.domain.nexus.NexusDataSet;
+import org.cipres.treebase.domain.study.ArticleCitation;
+import org.cipres.treebase.domain.study.Citation;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.cipres.treebase.domain.taxon.TaxonLabelSet;
+import org.nexml.model.Document;
+import org.nexml.model.Matrix;
+import org.nexml.model.OTUs;
+import org.nexml.model.TreeBlock;
+
+public class NexmlDocumentConverter extends NexmlObjectConverter {
+
+	/**
+	 * 
+	 * @param study
+	 * @param taxonLabelHome
+	 * @param document
+	 */
+	public NexmlDocumentConverter(Study study, TaxonLabelHome taxonLabelHome,
+			Document document) {
+		super(study, taxonLabelHome, document);
+	}
+	
+	/**
+	 * 
+	 * @param pDocument
+	 * @return
+	 */
+	public NexusDataSet fromXmlToTreeBase(Document pDocument) {
+		NexusDataSet nexusDataSet = new NexusDataSet();
+		nexusDataSet.setNexmlProject(pDocument);
+		
+		NexmlOTUConverter noc = new NexmlOTUConverter(getStudy(),getTaxonLabelHome(),pDocument);
+		for ( OTUs xmlOTUs : pDocument.getOTUsList() ) {
+			TaxonLabelSet taxonLabelSet = noc.fromXmlToTreeBase(xmlOTUs);
+			nexusDataSet.addTaxonLabelSet(xmlOTUs, taxonLabelSet);
+		}
+		
+		NexmlMatrixConverter nmc = new NexmlMatrixConverter(getStudy(),getTaxonLabelHome(),pDocument);
+		for ( Matrix<?> xmlMatrix : pDocument.getMatrices() ) {
+			org.cipres.treebase.domain.matrix.Matrix matrix = nmc.fromXmlToTreeBase(xmlMatrix);
+			nexusDataSet.getMatrices().add(matrix);
+		}
+		
+		NexmlTreeBlockConverter ntc = new NexmlTreeBlockConverter(getStudy(),getTaxonLabelHome(),pDocument);
+		for ( TreeBlock xmlTreeBlock : pDocument.getTreeBlockList() ) {
+			org.cipres.treebase.domain.tree.TreeBlock treeBlock = ntc.fromXmlToTreeBase(xmlTreeBlock);
+			nexusDataSet.getTreeBlocks().add(treeBlock);
+		}
+		
+		return nexusDataSet;		
+	}
+	
+	/**
+	 * 
+	 * @param pNexusDataSet
+	 * @return
+	 */
+	public Document fromTreeBaseToXml(NexusDataSet pNexusDataSet) {
+		
+		NexmlOTUConverter noc = new NexmlOTUConverter(getStudy(),getTaxonLabelHome(),getDocument());
+		for ( TaxonLabelSet taxonLabelSet : pNexusDataSet.getTaxonLabelSets() ) {
+			noc.fromTreeBaseToXml(taxonLabelSet);
+		}
+		
+		NexmlMatrixConverter nmc = new NexmlMatrixConverter(getStudy(),getTaxonLabelHome(),getDocument());
+		for (org.cipres.treebase.domain.matrix.Matrix matrix : pNexusDataSet.getMatrices() ) {
+			nmc.fromTreeBaseToXml(matrix);
+		}
+		
+		NexmlTreeBlockConverter ntc = new NexmlTreeBlockConverter(getStudy(),getTaxonLabelHome(),getDocument());
+		for ( org.cipres.treebase.domain.tree.TreeBlock treeBlock : pNexusDataSet.getTreeBlocks() ) {
+			ntc.fromTreeBaseToXML(treeBlock);
+		}
+		
+		return getDocument();
+		
+	}
+	
+	/**
+	 * 
+	 * @param citation
+	 * @param document
+	 */
+	private void copyCitationMetadata(Citation citation,Document document) {
+		attachAnnotation("prism:publicationDate",citation.getPublishYear().toString(),mPrismURI,document);
+		attachAnnotation("prism:doi",citation.getDoi(),mPrismURI,document);
+		String[] pages = citation.getPages().split("-");
+		if ( pages.length > 2 ) {
+			attachAnnotation("prism:startingPage",pages[0],mPrismURI,document);
+			attachAnnotation("prism:endingPage",pages[1],mPrismURI,document);
+			attachAnnotation("prism:pageRange",citation.getPages(),mPrismURI,document);			
+		}
+		String[] keywords = citation.getKeywords().split(", ");
+		for ( int i = 0; i < keywords.length; i++ ) {
+			attachAnnotation("prism:keyword",keywords[i],mPrismURI,document);
+		}		
+		if ( citation instanceof ArticleCitation ) {
+			attachAnnotation("prism:publicationName",((ArticleCitation)citation).getJournal(),mPrismURI,document);
+			attachAnnotation("prism:volume",((ArticleCitation)citation).getVolume(),mPrismURI,document);
+			attachAnnotation("prism:number",((ArticleCitation)citation).getIssue(),mPrismURI,document);
+		}		
+	}
+	
+	/**
+	 * 
+	 * @param pStudy
+	 * @return
+	 */
+	public Document fromTreeBaseToXml(Study pStudy) {
+		attachTreeBaseID(getDocument(), pStudy);
+		attachAnnotation("dc:title", pStudy.getName(), mDCURI, getDocument());
+		attachAnnotation("dc:abstract",pStudy.getCitation().getAbstract(), mDCURI,getDocument());		
+		attachAnnotation(
+				"dc:creator",
+				pStudy.getSubmission().getSubmitter().getPerson().getFullNameCitationStyle(),
+				mDCURI,
+				getDocument()
+		);
+		for ( Person person : pStudy.getAuthors() ) {
+			String personName = person.getFullNameCitationStyle();
+			attachAnnotation("dc:contributor",personName,mDCURI,getDocument());
+		}
+		attachAnnotation("prism:creationDate",pStudy.getSubmission().getCreateDate().toString(),mPrismURI,getDocument());
+		attachAnnotation("prism:embargoDate",pStudy.getReleaseDate().toString(),mPrismURI,getDocument());
+		copyCitationMetadata(pStudy.getCitation(),getDocument());		
+		
+		NexmlOTUConverter noc = new NexmlOTUConverter(getStudy(),getTaxonLabelHome(),getDocument());
+		for ( TaxonLabelSet taxonLabelSet : pStudy.getTaxonLabelSets() ) {
+			noc.fromTreeBaseToXml(taxonLabelSet);
+		}
+		
+		NexmlMatrixConverter nmc = new NexmlMatrixConverter(getStudy(),getTaxonLabelHome(),getDocument());
+		for (org.cipres.treebase.domain.matrix.Matrix matrix : pStudy.getMatrices() ) {
+			nmc.fromTreeBaseToXml(matrix);
+		}
+		
+		NexmlTreeBlockConverter ntc = new NexmlTreeBlockConverter(getStudy(),getTaxonLabelHome(),getDocument());
+		for ( org.cipres.treebase.domain.tree.TreeBlock treeBlock : pStudy.getTreeBlocks() ) {
+			ntc.fromTreeBaseToXML(treeBlock);
+		}		
+		return getDocument();
+	}
+
+}


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