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[Treebase-guts] SF.net SVN: treebase:[733] trunk/treebase-web/src/main/java/org/cipres/ treebase/web
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From: <yo...@us...> - 2010-07-14 20:45:18
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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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