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[Treebase-guts] SF.net SVN: treebase:[732] trunk/treebase-web/src/main
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From: <yo...@us...> - 2010-07-14 02:17:04
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Revision: 732
http://treebase.svn.sourceforge.net/treebase/?rev=732&view=rev
Author: youjun
Date: 2010-07-14 02:16:55 +0000 (Wed, 14 Jul 2010)
Log Message:
-----------
handshaking page, controller, 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/DryadUtil.java
trunk/treebase-web/src/main/webapp/WEB-INF/pages/loginForm.jsp
Added Paths:
-----------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/CitationParser.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 2010-07-13 16:38:00 UTC (rev 731)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ProcessUserController.java 2010-07-14 02:16:55 UTC (rev 732)
@@ -21,7 +21,12 @@
public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response)
throws Exception {
- String importKey = (String)request.getSession().getAttribute("importKey");
+ String importKey = null;
+ if(request.getParameter("importKey") != null){
+ importKey = (String)request.getAttribute("importKey");
+ request.getSession().setAttribute("importKey",importKey);
+ }
+
if (importKey != null && importKey.length()>0) {
return new ModelAndView("redirect:/user/studyForm.html");
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 2010-07-13 16:38:00 UTC (rev 731)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudyFormController.java 2010-07-14 02:16:55 UTC (rev 732)
@@ -2,6 +2,7 @@
package org.cipres.treebase.web.controllers;
import java.io.File;
+import java.io.FileFilter;
import java.util.Collection;
import javax.servlet.ServletException;
@@ -127,32 +128,41 @@
ControllerUtil.saveStudy(request, submission.getStudy());
} else if(importKey != null && importKey.length()>0){
-
- String uploadDir = getServletContext()
- .getRealPath(TreebaseUtil.FILESEP + "DryadUpload")
- + TreebaseUtil.FILESEP + importKey;
+ String uploadpath = getServletContext()
+ .getRealPath(TreebaseUtil.FILESEP + "DryadFileUpload")
+ + TreebaseUtil.FILESEP + importKey;
String importStatus="";
- File bagitPath= new File(uploadDir, "data");
- if(!bagitPath.exists())importStatus = "NOT FOUND";
- else{
- try{
+ File uploadDir=new File(uploadpath);
+ if(!uploadDir.exists()){
+ importStatus = "NOT FOUND";
+ return new ModelAndView(new RedirectView("submissionList.html"));
+ }
+
+ File[] uploadFiles = uploadDir.listFiles(new FileFilter(){public boolean accept(File file){return file.isDirectory();}});
+ if(uploadDir.length()==0){
+ importStatus = "NOT FOUND";
+ return new ModelAndView(new RedirectView("submissionList.html"));
+ }
+ File bagitPath = uploadFiles[0];
+ File dataPath = new File(bagitPath, "data");
+
+ try{
Submission submission = mSubmissionService.createSubmission(user, new Study());
-
- Citation citation = DryadUtil.createCitation(bagitPath);
+ Citation citation = DryadUtil.createCitation(dataPath);
submission.getStudy().setCitation(citation);
citation.setStudy(submission.getStudy());
- Collection<File> files = DryadUtil.getDataFiles(bagitPath);
+ Collection<File> files = DryadUtil.getDataFiles(dataPath);
MyProgressionListener listener = new MyProgressionListener();
getSubmissionService().addNexusFilesJDBC(submission, files, listener);
// save Study object to session
ControllerUtil.saveStudy(request, submission.getStudy());
importStatus = "OK";
- }catch (Exception e) {
+ }catch (Exception e) {
importStatus = "FAILED";
- }
}
+
request.setAttribute("importStatus", importStatus);
//request.getSession().removeAttribute("importKey");
return new ModelAndView(new RedirectView("submissionList.html"));
Added: 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 (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/CitationParser.java 2010-07-14 02:16:55 UTC (rev 732)
@@ -0,0 +1,93 @@
+package org.cipres.treebase.web.util;
+
+import java.io.File;
+import java.util.List;
+
+import org.cipres.treebase.domain.study.ArticleCitation;
+import org.cipres.treebase.domain.study.Citation;
+import org.dom4j.Document;
+import org.dom4j.DocumentException;
+import org.dom4j.Element;
+import org.dom4j.Namespace;
+import org.dom4j.Node;
+import org.dom4j.QName;
+import org.dom4j.io.SAXReader;
+
+public class CitationParser {
+
+ 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 ;
+ try {
+ pubDoc = pubReader.read(pubFile);
+ pubRoot = pubDoc.getRootElement();
+ } catch (DocumentException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+
+ File pkgFile = new File(path, "dryadpkg.xml");
+ SAXReader pkgReader = new SAXReader();
+ Document pkgDoc= null ;
+ try {
+ pkgDoc = pkgReader.read(pkgFile);
+ pkgRoot = pkgDoc.getRootElement();
+ } catch (DocumentException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ loadData();
+ }
+
+
+ private void loadData(){
+
+ citation.setAbstract(getNode(pubRoot,"description",dcterms).getText());
+ citation.setDoi(getNode(pubRoot,"identifier",dcterms).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());
+
+ //citation.setKeywords(getNode(pubRoot,"description",dcterms).getText());
+ //citation.setAuthors(pAuthors);
+
+ //citation.setPublishYear(getNode(pubRoot,"issued",dcterms).getText());
+ //citation.setPublished(getNode(pubRoot,"description",dcterms).getText());
+
+ }
+
+ private Node getNode(Element root, String localName, Namespace namespace){
+
+ return root.element(new QName(localName, namespace));
+ }
+
+ private List<Node> getNodes(Element root, String localName, Namespace namespace){
+
+ return root.elements(new QName(localName, namespace));
+ }
+
+
+ public Citation 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 2010-07-13 16:38:00 UTC (rev 731)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/DryadUtil.java 2010-07-14 02:16:55 UTC (rev 732)
@@ -15,6 +15,7 @@
public class DryadUtil {
+
public static Citation createCitation(File path){
Citation citation = new Citation();
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/loginForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/loginForm.jsp 2010-07-13 16:38:00 UTC (rev 731)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/loginForm.jsp 2010-07-14 02:16:55 UTC (rev 732)
@@ -2,13 +2,15 @@
<form method="post" id="loginForm" action="<c:url value="/j_security_check"/>" >
+<!--
<%
if(request.getParameter("importKey") != null){
session.setAttribute("importKey",request.getParameter("importKey"));
}
%>
-
+-->
+
<fieldset>
<legend>Login</legend>
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