treebase-guts Mailing List for TreeBASE (Page 21)

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Revision: 733
          http://treebase.svn.sourceforge.net/treebase/?rev=733&view=rev
Author:   youjun
Date:     2010-07-14 20:45:11 +0000 (Wed, 14 Jul 2010)

Log Message:
-----------
handshaking controller and util

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ProcessUserController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudyFormController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/CitationParser.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/DryadUtil.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ProcessUserController.java
===================================================================

--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ProcessUserController.java	2010-07-14 02:16:55 UTC (rev 732)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ProcessUserController.java	2010-07-14 20:45:11 UTC (rev 733)
@@ -21,11 +21,7 @@
 
 	public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response)
 		throws Exception {
-		String importKey = null;
-		if(request.getParameter("importKey") != null){
-               importKey = (String)request.getAttribute("importKey");
-		       request.getSession().setAttribute("importKey",importKey);
-		}
+		String importKey = (String)request.getSession().getAttribute("importKey");
 		
 		if (importKey != null && importKey.length()>0) {
 

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudyFormController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudyFormController.java	2010-07-14 02:16:55 UTC (rev 732)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudyFormController.java	2010-07-14 20:45:11 UTC (rev 733)
@@ -25,6 +25,7 @@
 import org.cipres.treebase.domain.study.SubmissionService;
 import org.cipres.treebase.web.Constants;
 import org.cipres.treebase.web.model.MyProgressionListener;
+import org.cipres.treebase.web.util.CitationParser;
 import org.cipres.treebase.web.util.ControllerUtil;
 import org.cipres.treebase.web.util.DryadUtil;
 
@@ -106,28 +107,7 @@
 		String importKey = (String)request.getSession().getAttribute("importKey");
 		request.getSession().removeAttribute("importKey");
 		
-		if (request.getParameter(ACTION_SUBMIT) != null) {
-			// Study must be submitted with citation together
-			// here we are just saving the data to the session
-			// request.getSession().setAttribute(Constants.STUDY_KEY, study);
-
-			// BeanUtils.copyProperties(citationCommand.getCitationMap(citationType),
-			// citationCommand);
-
-			// FIXME citation
-			// Citation c = new ArticleCitation();
-			// c.setStudy(study);
-			// study.setCitation(c);
-
-			// retrieve Study object from session to be submitted with citation
-			// Study study = (Study) request.getSession().getAttribute(Constants.STUDY_KEY);
-			// citationCommand.getCitationMap(citationType).setStudy(study);
-			Submission submission = mSubmissionService.createSubmission(user, study);
-
-			// save Study object to session and remove
-			ControllerUtil.saveStudy(request, submission.getStudy());
-
-		} else if(importKey != null && importKey.length()>0){
+		if(importKey != null && importKey.length()>0){
 			String uploadpath = getServletContext()
         	.getRealPath(TreebaseUtil.FILESEP + "DryadFileUpload")
         	+ TreebaseUtil.FILESEP +  importKey;			
@@ -149,13 +129,14 @@
 			
 			try{
 					Submission submission = mSubmissionService.createSubmission(user, new Study());
-					Citation citation = DryadUtil.createCitation(dataPath);
+					CitationParser cparser= new CitationParser(dataPath);
+					Citation citation = cparser.getCitation();
 					submission.getStudy().setCitation(citation);
 					citation.setStudy(submission.getStudy());
 			
 					Collection<File> files = DryadUtil.getDataFiles(dataPath);
 					MyProgressionListener listener = new MyProgressionListener();
-					getSubmissionService().addNexusFilesJDBC(submission, files, listener);
+					//getSubmissionService().addNexusFilesJDBC(submission, files, listener);
 					// save Study object to session
 					ControllerUtil.saveStudy(request, submission.getStudy());
 					importStatus = "OK";
@@ -167,7 +148,32 @@
 			//request.getSession().removeAttribute("importKey");
 			return new ModelAndView(new RedirectView("submissionList.html"));
 			
-		}else if (request.getParameter(ACTION_UPDATE) != null) {
+		}
+		
+		
+		
+		if (request.getParameter(ACTION_SUBMIT) != null) {
+			// Study must be submitted with citation together
+			// here we are just saving the data to the session
+			// request.getSession().setAttribute(Constants.STUDY_KEY, study);
+
+			// BeanUtils.copyProperties(citationCommand.getCitationMap(citationType),
+			// citationCommand);
+
+			// FIXME citation
+			// Citation c = new ArticleCitation();
+			// c.setStudy(study);
+			// study.setCitation(c);
+
+			// retrieve Study object from session to be submitted with citation
+			// Study study = (Study) request.getSession().getAttribute(Constants.STUDY_KEY);
+			// citationCommand.getCitationMap(citationType).setStudy(study);
+			Submission submission = mSubmissionService.createSubmission(user, study);
+
+			// save Study object to session and remove
+			ControllerUtil.saveStudy(request, submission.getStudy());
+
+		} else if (request.getParameter(ACTION_UPDATE) != null) {
 			mStudyService.update(study);
 		} else if (request.getParameter(ACTION_DELETE) != null) {
 
@@ -208,6 +214,10 @@
 			request.getSession().removeAttribute(Constants.STUDY_MAP);
 			return new Study();
 		}
+		
+		if(request.getSession().getAttribute("importKey") != null)
+			return new Study();
+		
 		// if we are updating a data that's already in the db (access from RHS menu)
 		study = ControllerUtil.findStudy(request, mStudyService);
 		return study;

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/CitationParser.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/CitationParser.java	2010-07-14 02:16:55 UTC (rev 732)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/CitationParser.java	2010-07-14 20:45:11 UTC (rev 733)
@@ -3,6 +3,7 @@
 import java.io.File;
 import java.util.List;
 
+import org.cipres.treebase.domain.admin.Person;
 import org.cipres.treebase.domain.study.ArticleCitation;
 import org.cipres.treebase.domain.study.Citation;
 import org.dom4j.Document;
@@ -14,21 +15,18 @@
 import org.dom4j.io.SAXReader;
 
 public class CitationParser {
-
+	private ArticleCitation citation;
 	private static final Namespace xs = new Namespace("xs","http://www.w3.org/2001/XMLSchema");
 	private static final Namespace dwc= new Namespace("dwc", "http://rs.tdwg.org/dwc/terms/");
 	private static final Namespace dcterms= new Namespace("dcterms", "http://purl.org/dc/terms/");
 	private static final Namespace prism= new Namespace("prism", "http://prismstandard.org/namespaces/basic/2.0/");
 
-	private ArticleCitation citation; 
 	private Element pubRoot;
 	private Element pkgRoot;
 
 
 	public CitationParser(File path){
-
-		citation = new ArticleCitation();
-
+	
 		File pubFile = new File(path, "dryadpub.xml");
 		SAXReader pubReader = new SAXReader();
 		Document pubDoc= null ;
@@ -52,31 +50,69 @@
 			e.printStackTrace();
 		}
 		
+		citation = new ArticleCitation();
 		loadData();
 	}
 
 		
 	private void loadData(){
-	    		
-		citation.setAbstract(getNode(pubRoot,"description",dcterms).getText());
-		citation.setDoi(getNode(pubRoot,"identifier",dcterms).getText());;
+	    
+		Node description = getNode(pubRoot,"description",dcterms);		
+		if(description!=null)citation.setAbstract(description.getText());
 		
-		citation.setTitle(getNode(pubRoot,"title",dcterms).getText());
-		citation.setIssue(getNode(pubRoot,"issueIdentifier",prism).getText());
-		citation.setJournal(getNode(pubRoot,"publicationName",prism).getText());
-		citation.setVolume(getNode(pubRoot,"volume",prism).getText());		
-		citation.setPages(getNode(pubRoot,":pageRange",prism).getText());
+		Node identifier = getNode(pubRoot,"identifier",dcterms);		
+		if(identifier!=null)citation.setDoi(identifier.getText());;
 		
-		//citation.setKeywords(getNode(pubRoot,"description",dcterms).getText());
-		//citation.setAuthors(pAuthors);
+	    Node title = getNode(pubRoot,"title",dcterms);		
+	    if(title!=null)citation.setTitle(title.getText());
 		
-		//citation.setPublishYear(getNode(pubRoot,"issued",dcterms).getText());			
-		//citation.setPublished(getNode(pubRoot,"description",dcterms).getText());
+		Node issueIdentifier = getNode(pubRoot,"issueIdentifier",prism);		
+		if(issueIdentifier!=null)citation.setIssue(issueIdentifier.getText());
 		
+		Node publicationName = getNode(pubRoot,"publicationName",prism);		
+		if(publicationName!=null)citation.setJournal(publicationName.getText());
+		
+		Node volume = getNode(pubRoot,"volume",prism);		
+		if(volume!=null)citation.setVolume(volume.getText());		
+		
+		Node pageRange = getNode(pubRoot,"pageRange",prism);		
+		if(pageRange!=null)citation.setPages(pageRange.getText());						
+	
+		List<Node> kl = getNodes(pkgRoot,"subject",dcterms);
+		String keywords="";
+		for(int i = 0; i<kl.size(); i++) {
+		     keywords+= kl.get(i).getText()+",";			
+		}		
+		citation.setKeywords(keywords.substring(0, keywords.length()-1));
+				
+		List<Node> al = getNodes(pubRoot,"creator",dcterms);
+		for(int i = 0; i<al.size(); i++) {
+		    String []names = al.get(i).getText().split(",");
+			if(names.length >1 ){
+				Person p = new Person ();
+				p.setFirstName(names[1]);
+				p.setLastName(names[0]);
+				citation.addAuthor(p);
+			}
+		}		
+		
+		try{
+		    int issue = Integer.parseInt(getNode(pubRoot,"issued",dcterms).getText());
+		    citation.setPublishYear(issue);			
+		}catch(Exception e){
+			
+		}
+		
+		
+		if(getNode(pubRoot,"pubStatus",null).getText()!=null){
+			if("published".compareToIgnoreCase(getNode(pubRoot,"pubStatus",null).getText())==0)
+		     	citation.setPublished(true);
+		    else citation.setPublished(false);
+		}
 	}
 
 	private Node getNode(Element root, String localName, Namespace namespace){
-
+        if(namespace==null)return root.element(new QName(localName));
 		return root.element(new QName(localName, namespace));
 	}
 
@@ -85,8 +121,7 @@
 		return root.elements(new QName(localName, namespace));	
 	}
 
-
-	public Citation getCitation() {
+	public ArticleCitation getCitation() {
 		return citation;
 	}
 

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/DryadUtil.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/DryadUtil.java	2010-07-14 02:16:55 UTC (rev 732)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/DryadUtil.java	2010-07-14 20:45:11 UTC (rev 733)
@@ -1,7 +1,9 @@
 package org.cipres.treebase.web.util;
 
 import java.io.File;
+import java.io.FileFilter;
 import java.io.FilenameFilter;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Iterator;
@@ -14,41 +16,26 @@
 
 public class DryadUtil {
 	
-	
-	
-	public static Citation createCitation(File path){
-		Citation citation = new Citation();
-		
-		File f = new File(path, "citation.xml");
-		SAXReader reader = new SAXReader();
-		Document doc= null ;
-		try {
-			doc = reader.read(f);
-		} catch (DocumentException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-		Element root = doc.getRootElement();
-		Element node;
-		for (Iterator i = root.elementIterator("author"); i.hasNext();) {
-			node = (Element) i.next();
-			Person p = new Person();
-			//node.getName();
-			citation.addAuthor(p);
-		}
-		citation.setTitle(root.element("title").getName());
-		
-		
-		return citation;
-	}
-
 	public static Collection<File> getDataFiles(File path) {
 		// TODO Auto-generated method stub
-		List<File> flist=Arrays.asList(path.listFiles(new FilenameFilter() {
-            public boolean accept(File file, String name) {
-                boolean ret = !(name.endsWith("xml")); 
-                return ret;
-            }}));		
+		 File[] files = path.listFiles(new FileFilter() {
+	            public boolean accept(File file) {	                 
+	                return file.isDirectory();
+	     }});		
+	            
+		 List<File> flist = new ArrayList<File>();
+		 
+		 for(int i=0; i<files.length; i++){
+			 
+			 File[] nexus = files[i].listFiles(new FilenameFilter() {
+		            public boolean accept(File file, String name) {
+		            boolean ret = !(name.endsWith("nexus")); 
+		            return ret;
+		     }});
+			 
+			 if (nexus!=null && nexus.length>0) flist.addAll(Arrays.asList(nexus));
+		 }				 
+				
 		return flist;
 	}
 


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treebase-guts Mailing List for TreeBASE (Page 21)

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