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[Treebase-guts] SF.net SVN: treebase:[730] trunk/treebase-web/src/main
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From: <yo...@us...> - 2010-07-07 20:08:39
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Revision: 730
http://treebase.svn.sourceforge.net/treebase/?rev=730&view=rev
Author: youjun
Date: 2010-07-07 19:32:38 +0000 (Wed, 07 Jul 2010)
Log Message:
-----------
handshacking web path
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/webapp/WEB-INF/pages/loginForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionList.jsp
Added Paths:
-----------
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 2010-07-02 16:30:32 UTC (rev 729)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ProcessUserController.java 2010-07-07 19:32:38 UTC (rev 730)
@@ -21,7 +21,11 @@
public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response)
throws Exception {
+ String importKey = (String)request.getSession().getAttribute("importKey");
+ if (importKey != null && importKey.length()>0) {
+ return new ModelAndView("redirect:/user/studyForm.html");
+ }
if (request.isUserInRole(UserRole.ROLE_ADMIN) || request.isUserInRole(UserRole.ROLE_ASSO_EDITOR)) {
return new ModelAndView("redirect:/admin/administrationPage.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 2010-07-02 16:30:32 UTC (rev 729)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudyFormController.java 2010-07-07 19:32:38 UTC (rev 730)
@@ -1,6 +1,9 @@
package org.cipres.treebase.web.controllers;
+import java.io.File;
+import java.util.Collection;
+
import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
@@ -14,12 +17,15 @@
import org.cipres.treebase.domain.admin.User;
import org.cipres.treebase.domain.admin.UserService;
+import org.cipres.treebase.domain.study.Citation;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.study.StudyService;
import org.cipres.treebase.domain.study.Submission;
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.ControllerUtil;
+import org.cipres.treebase.web.util.DryadUtil;
/**
* StudyFormController.java
@@ -96,7 +102,9 @@
Study study = (Study) command;
User user = ControllerUtil.getUser(request, mUserService);
-
+ 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
@@ -118,7 +126,38 @@
// save Study object to session and remove
ControllerUtil.saveStudy(request, submission.getStudy());
- } else if (request.getParameter(ACTION_UPDATE) != null) {
+ } else if(importKey != null && importKey.length()>0){
+
+ String uploadDir = getServletContext()
+ .getRealPath(TreebaseUtil.FILESEP + "DryadUpload")
+ + TreebaseUtil.FILESEP + importKey;
+ String importStatus="";
+ File bagitPath= new File(uploadDir, "data");
+ if(!bagitPath.exists())importStatus = "NOT FOUND";
+ else{
+
+ try{
+ Submission submission = mSubmissionService.createSubmission(user, new Study());
+
+ Citation citation = DryadUtil.createCitation(bagitPath);
+ submission.getStudy().setCitation(citation);
+ citation.setStudy(submission.getStudy());
+
+ Collection<File> files = DryadUtil.getDataFiles(bagitPath);
+ MyProgressionListener listener = new MyProgressionListener();
+ getSubmissionService().addNexusFilesJDBC(submission, files, listener);
+ // save Study object to session
+ ControllerUtil.saveStudy(request, submission.getStudy());
+ importStatus = "OK";
+ }catch (Exception e) {
+ importStatus = "FAILED";
+ }
+ }
+ request.setAttribute("importStatus", importStatus);
+ //request.getSession().removeAttribute("importKey");
+ return new ModelAndView(new RedirectView("submissionList.html"));
+
+ }else if (request.getParameter(ACTION_UPDATE) != null) {
mStudyService.update(study);
} else if (request.getParameter(ACTION_DELETE) != null) {
Added: 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 (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/DryadUtil.java 2010-07-07 19:32:38 UTC (rev 730)
@@ -0,0 +1,54 @@
+package org.cipres.treebase.web.util;
+
+import java.io.File;
+import java.io.FilenameFilter;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+
+import org.cipres.treebase.domain.admin.Person;
+import org.cipres.treebase.domain.study.Citation;
+import org.dom4j.*;
+import org.dom4j.io.*;
+
+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;
+ }}));
+ return flist;
+ }
+
+}
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/loginForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/loginForm.jsp 2010-07-02 16:30:32 UTC (rev 729)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/loginForm.jsp 2010-07-07 19:32:38 UTC (rev 730)
@@ -2,6 +2,13 @@
<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>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionList.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionList.jsp 2010-07-02 16:30:32 UTC (rev 729)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionList.jsp 2010-07-07 19:32:38 UTC (rev 730)
@@ -101,7 +101,19 @@
</display:footer>
<display:setProperty name="basic.empty.showtable" value="true"/>
-
+
</display:table>
</fieldset>
+<fieldset>
+<legend>Dryad Import Result
+<a href="#" class="openHelp" onclick="openHelp('dryadImport')"><img class="iconButton" src="<fmt:message key="icons.help"/>" /></a>
+</legend>
+ <div align="center">
+ <c:choose>
+ <c:when test="${importStatus =='NOT FOUND'}"><c:out value="Sorry, we cannot find your data"/></c:when>
+ <c:when test="${importStatus =='OK'}"><c:out value="Import finished"/></c:when>
+ <c:when test="${importStatus =='FAILED'}"><c:out value="Sorry, One or more data file cannot parsed correctly, you may add your data via treebase interfaces"/></c:when>
+ </c:choose>
+ </div>
+</fieldset>
</form>
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