[Treebase-guts] SF.net SVN: treebase:[571] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlDocumentConverter.java

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

Revision: 571
          http://treebase.svn.sourceforge.net/treebase/?rev=571&view=rev
Author:   rvos
Date:     2010-03-15 01:04:39 +0000 (Mon, 15 Mar 2010)

Log Message:
-----------
Now calls getAnnotations() to let the object decide what metadata to add as opposed to fiddling with the object here.

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

Modified: 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	2010-03-15 01:02:39 UTC (rev 570)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java	2010-03-15 01:04:39 UTC (rev 571)
@@ -1,10 +1,11 @@
 package org.cipres.treebase.domain.nexus.nexml;
 
-import org.cipres.treebase.domain.admin.Person;
+//import org.cipres.treebase.Constants;
+//import org.cipres.treebase.domain.admin.Person;
 import org.cipres.treebase.domain.matrix.CharacterMatrix;
 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.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;
@@ -91,55 +92,11 @@
 	
 	/**
 	 * 
-	 * @param citation
-	 * @param document
-	 */
-	private void copyCitationMetadata(Citation citation,Document document) {
-		attachAnnotation("dcterms:bibliographicCitation",citation.getAuthorsCitationStyleWithoutHtml(),mDCURI,document);
-		if ( null != citation.getTitle() ) {
-			attachAnnotation("tb:title.study",citation.getTitle(),mTBTermsURI,document);
-		}
-		if ( null != citation.getPublishYear() ) {
-			attachAnnotation("prism:publicationDate",citation.getPublishYear().toString(),mPrismURI,document);
-		}
-		if ( null != citation.getDoi() ) {
-			attachAnnotation("prism:doi",citation.getDoi(),mPrismURI,document);
-		}
-		if ( null != citation.getPages() ) {
-			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);			
-			}
-		}
-		if ( null != citation.getKeywords() ) {
-			String[] keywords = citation.getKeywords().split(", ");
-			for ( int i = 0; i < keywords.length; i++ ) {
-				attachAnnotation("dcterms:subject",keywords[i],mDCURI,document);
-			}		
-		}
-		if ( citation instanceof ArticleCitation ) {
-			ArticleCitation ac = (ArticleCitation)citation;
-			if ( null != ac.getJournal() ) {
-				attachAnnotation("prism:publicationName",ac.getJournal(),mPrismURI,document);
-			}
-			if ( null != ac.getVolume() ) {
-				attachAnnotation("prism:volume",ac.getVolume(),mPrismURI,document);
-			}
-			if ( null != ac.getIssue() ) {
-				attachAnnotation("prism:number",ac.getIssue(),mPrismURI,document);
-			}
-		}		
-	}
-	
-	/**
-	 * 
 	 * @param pStudy
 	 * @return
 	 */
 	public Document fromTreeBaseToXml(Study pStudy) {
-		copyMetadata(pStudy);		
+		attachTreeBaseID(getDocument(), pStudy,Study.class);
 		
 		NexmlOTUConverter noc = new NexmlOTUConverter(getStudy(),getTaxonLabelHome(),getDocument());
 		for ( TaxonLabelSet taxonLabelSet : pStudy.getTaxonLabelSets() ) {
@@ -161,37 +118,4 @@
 		return getDocument();
 	}
 
-	private void copyMetadata(Study pStudy) {
-		attachTreeBaseID(getDocument(), pStudy,Study.class);
-		attachAnnotation("tb:identifier.study",pStudy.getId().toString(), mTBTermsURI, getDocument());
-		attachAnnotation("tb:identifier.study.tb1",pStudy.getTB1StudyID(), mTBTermsURI, getDocument());
-		if ( null != pStudy.getName() ) {
-			attachAnnotation("tb:title.study", pStudy.getName(), mTBTermsURI, getDocument());
-		}		
-		for ( Person person : pStudy.getAuthors() ) {
-			String personName = person.getFullNameCitationStyle();
-			attachAnnotation("dcterms:contributor",personName,mDCURI,getDocument());
-		}
-		if ( null != pStudy.getReleaseDate() ) {
-			attachAnnotation("prism:embargoDate",pStudy.getReleaseDate().toString(),mPrismURI,getDocument());
-		}
-		if ( null != pStudy.getSubmission() ) {
-			if ( null != pStudy.getSubmission().getSubmitter() ) {
-				attachAnnotation(
-						"dcterms:creator",
-						pStudy.getSubmission().getSubmitter().getPerson().getFullNameCitationStyle(),
-						mDCURI,
-						getDocument()
-				);		
-			}
-			if ( null != pStudy.getSubmission().getCreateDate() ) {
-				attachAnnotation("prism:creationDate",pStudy.getSubmission().getCreateDate().toString(),mPrismURI,getDocument());
-			}
-		}		
-		if ( null != pStudy.getCitation() ) {			
-			//attachAnnotation("dc:abstract",forXML(pStudy.getCitation().getAbstract()), mDCURI,getDocument());
-			copyCitationMetadata(pStudy.getCitation(),getDocument());
-		}
-	}
-
 }


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