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[Treebase-guts] SF.net SVN: treebase:[735] trunk/treebase-web/src/main
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From: <yo...@us...> - 2010-07-15 20:52:04
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Revision: 735
http://treebase.svn.sourceforge.net/treebase/?rev=735&view=rev
Author: youjun
Date: 2010-07-15 20:51:58 +0000 (Thu, 15 Jul 2010)
Log Message:
-----------
handshaking add new citation object to a user
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
trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
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 2010-07-15 00:13:45 UTC (rev 734)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ProcessUserController.java 2010-07-15 20:51:58 UTC (rev 735)
@@ -1,13 +1,30 @@
package org.cipres.treebase.web.controllers;
+import java.io.File;
+import java.io.FileFilter;
+import java.util.Collection;
+import java.util.List;
+
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.log4j.Logger;
import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.mvc.Controller;
+import org.springframework.web.servlet.view.RedirectView;
+import org.cipres.treebase.TreebaseUtil;
+import org.cipres.treebase.domain.admin.User;
import org.cipres.treebase.domain.admin.UserRole;
+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.Submission;
+import org.cipres.treebase.domain.study.SubmissionService;
+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;
/**
* @author madhu
@@ -16,17 +33,86 @@
*
*/
public class ProcessUserController implements Controller {
+ private SubmissionService mSubmissionService;
+ private UserService mUserService;
+
+ public UserService getUserService() {
+ return mUserService;
+ }
+ public void setUserService(UserService mUserService) {
+ this.mUserService = mUserService;
+ }
+
+ public SubmissionService getSubmissionService() {
+ return mSubmissionService;
+ }
+
+ public void setSubmissionService(SubmissionService mSubmissionService) {
+ this.mSubmissionService = mSubmissionService;
+ }
+
private static final Logger LOGGER = Logger.getLogger(ProcessUserController.class);
public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response)
throws Exception {
+
String importKey = (String)request.getSession().getAttribute("importKey");
+ User user = ControllerUtil.getUser(request, mUserService);
- if (importKey != null && importKey.length()>0) {
-
- return new ModelAndView("redirect:/user/studyForm.html");
- }
+ if(importKey != null && importKey.length()>0){
+
+ String uploadpath = request.getSession().getServletContext()
+ .getRealPath(TreebaseUtil.FILESEP + "DryadFileUpload")
+ + TreebaseUtil.FILESEP + importKey;
+ String importStatus="";
+
+ File uploadDir=new File(uploadpath);
+ if(!uploadDir.exists()){
+ importStatus = "NOT FOUND";
+ request.setAttribute("importStatus", importStatus);
+ return new ModelAndView("redirect:/user/submissionList.html");
+ }
+
+ File[] uploadFiles = uploadDir.listFiles(new FileFilter(){public boolean accept(File file){return file.isDirectory();}});
+ if(uploadFiles.length==0){
+ importStatus = "NOT FOUND";
+ request.setAttribute("importStatus", importStatus);
+ return new ModelAndView("redirect:/user/submissionList.html");
+ }
+ File bagitPath = uploadFiles[0];
+ File dataPath = new File(bagitPath, "data");
+
+ try{
+ CitationParser cparser= new CitationParser(dataPath);
+ Citation citation = cparser.getCitation();
+ Study study = new Study();
+
+ study.setCitation(citation);
+ citation.setStudy(study);
+ Submission submission = mSubmissionService.createSubmission(user, study);
+
+ List<File> files = DryadUtil.getDataFiles(dataPath);
+ for(int i=0; i<files.size(); i++ )
+ submission.getStudy().addNexusFile(files.get(i).getName(), "NEXUS");
+ MyProgressionListener listener = new MyProgressionListener();
+ //getSubmissionService().addNexusFilesJDBC(submission, files, listener);
+
+ // save Study object to session
+ //mSubmissionService.save(submission);
+ mSubmissionService.save(study);
+ //mSubmissionService.save(citation);
+
+ importStatus = "OK";
+ }catch (Exception e) {
+ importStatus = "FAILED";
+ }
+
+ request.setAttribute("importStatus", importStatus);
+ request.getSession().removeAttribute("importKey");
+ return new ModelAndView("redirect:/user/submissionList.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 2010-07-15 00:13:45 UTC (rev 734)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudyFormController.java 2010-07-15 20:51:58 UTC (rev 735)
@@ -1,33 +1,24 @@
package org.cipres.treebase.web.controllers;
-import java.io.File;
-import java.io.FileFilter;
-import java.util.Collection;
-
import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
-import org.cipres.treebase.TreebaseUtil;
import org.apache.log4j.Logger;
-import org.springframework.validation.BindException;
-import org.springframework.web.bind.ServletRequestUtils;
-import org.springframework.web.servlet.ModelAndView;
-import org.springframework.web.servlet.view.RedirectView;
-
+import org.cipres.treebase.TreebaseUtil;
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.CitationParser;
import org.cipres.treebase.web.util.ControllerUtil;
-import org.cipres.treebase.web.util.DryadUtil;
+import org.springframework.validation.BindException;
+import org.springframework.web.bind.ServletRequestUtils;
+import org.springframework.web.servlet.ModelAndView;
+import org.springframework.web.servlet.view.RedirectView;
/**
* StudyFormController.java
@@ -104,54 +95,7 @@
Study study = (Study) command;
User user = ControllerUtil.getUser(request, mUserService);
- String importKey = (String)request.getSession().getAttribute("importKey");
- //request.getSession().removeAttribute("importKey");
- if(importKey != null && importKey.length()>0){
- String uploadpath = getServletContext()
- .getRealPath(TreebaseUtil.FILESEP + "DryadFileUpload")
- + TreebaseUtil.FILESEP + importKey;
- String importStatus="";
-
- 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());
- 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);
- // 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"));
-
- }
-
-
-
if (request.getParameter(ACTION_SUBMIT) != null) {
// Study must be submitted with citation together
// here we are just saving the data to the session
@@ -214,10 +158,7 @@
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 2010-07-15 00:13:45 UTC (rev 734)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/CitationParser.java 2010-07-15 20:51:58 UTC (rev 735)
@@ -56,7 +56,7 @@
private void loadData(){
-
+
Node description = getNode(pubRoot,"description",dcterms);
if(description!=null)citation.setAbstract(description.getText());
@@ -104,11 +104,12 @@
}
- if(getNode(pubRoot,"pubStatus",null).getText()!=null){
+ if(getNode(pubRoot,"pubStatus",null)!=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){
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 2010-07-15 00:13:45 UTC (rev 734)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/DryadUtil.java 2010-07-15 20:51:58 UTC (rev 735)
@@ -16,7 +16,7 @@
public class DryadUtil {
- public static Collection<File> getDataFiles(File path) {
+ public static List<File> getDataFiles(File path) {
// TODO Auto-generated method stub
File[] files = path.listFiles(new FileFilter() {
public boolean accept(File file) {
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2010-07-15 00:13:45 UTC (rev 734)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2010-07-15 20:51:58 UTC (rev 735)
@@ -21,8 +21,10 @@
<!-- LIST OF CONTROLLERS FOR WEB-TIER -->
<!-- ========================================================== -->
- <bean id="processUserController" class="org.cipres.treebase.web.controllers.ProcessUserController"/>
-
+ <bean id="processUserController" class="org.cipres.treebase.web.controllers.ProcessUserController">
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
+ <property name="userService"><ref bean="userService"></ref></property>
+ </bean>
<bean id="anyObjectAsRDFController" class="org.cipres.treebase.web.controllers.AnyObjectAsRDFController">
<property name="studyService"><ref bean="studyService"></ref></property>
</bean>
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