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[Treebase-guts] SF.net SVN: treebase:[103] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/DownloadAMatrixController.java
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From: <rv...@us...> - 2009-06-25 02:38:59
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Revision: 103
http://treebase.svn.sourceforge.net/treebase/?rev=103&view=rev
Author: rvos
Date: 2009-06-25 02:38:58 +0000 (Thu, 25 Jun 2009)
Log Message:
-----------
Added NeXML->RDF serialization, removed old, commented out code.
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAMatrixController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAMatrixController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAMatrixController.java 2009-06-25 02:33:04 UTC (rev 102)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAMatrixController.java 2009-06-25 02:38:58 UTC (rev 103)
@@ -20,14 +20,9 @@
package org.cipres.treebase.web.controllers;
-//import java.io.File;
-//import java.io.FileWriter;
-//import java.io.IOException;
-
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;
@@ -39,7 +34,6 @@
import org.cipres.treebase.domain.study.StudyService;
import org.cipres.treebase.domain.taxon.TaxonLabelSet;
import org.cipres.treebase.web.util.ControllerUtil;
-//import org.cipres.treebase.web.util.WebUtil;
/**
* DownloadAMatrixController.java
@@ -54,7 +48,6 @@
*/
public class DownloadAMatrixController extends AbstractDownloadController implements Controller {
- //private static final Logger LOGGER = Logger.getLogger(DownloadAMatrixController.class);
private MatrixService mMatrixService;
private StudyService mStudyService;
@@ -98,102 +91,14 @@
*/
public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response)
throws Exception {
- //
- // System.out.println("CONTEXT PATH IS: " + request.getContextPath());
- // System.out.println("REAL PATH IS: "
- // + request.getSession().getServletContext().getRealPath("/NexusFileDownload"));
- // System.out.println("PATH INFO: " + request.getPathInfo());
- //
-
if (request.getParameter("matrixid") == null) {
return null;
}
-
- //Long studyId = ControllerUtil.getStudyId(request);
- //Study s = getStudyService().findByID(studyId);
-
long matrixId = Long.parseLong(request.getParameter("matrixid"));
-// String fileName = getFileName(matrixId,request);
-
-// String downloadDir = request.getSession().getServletContext().getRealPath(
-// TreebaseUtil.FILESEP + "NexusFileDownload")
-// + TreebaseUtil.FILESEP + request.getRemoteUser();
-// String downloadDir = getDownloadDir(request);
-
-// long start = System.currentTimeMillis();
-
generateAFileDynamically(request, response, matrixId);
-// WebUtil.downloadFile(response, downloadDir, fileName);
-
-// long end = System.currentTimeMillis();
-//
-// if (LOGGER.isDebugEnabled()) {
-// LOGGER.debug("TIME DIFFERENCE FOR A SINGAL FILE IN DOWNLOAD A MATRIX CONTROLLER: "
-// + (end - start));
-// }
-
- return null; // new ModelAndView("treeList", Constants.TREE_LIST, phyloTrees);
+ return null;
}
- /**
- * This method is responsible for generating a Matrix file in a particular down load directory.
- * But first It should get All the Taxa associated with a Matrix id and get the max length of
- * the Taxon Labels and put Taxa and remaining matrix information in a separate ArrayLists
- *
- * @param request
- * @param pMatrixId It is Matrix id.
- * @param downloadDirName down load directory where files will be created
- */
- /*
- private void generateAFileDynamically(HttpServletRequest request, long pMatrixId, String downloadDirName) {
-
- Study pStudy = ControllerUtil.findStudy(request, mStudyService);
-
- Matrix matrix = mMatrixService.findByID(pMatrixId);
-
- File dirPath = new File(downloadDirName);
- if (!dirPath.exists()) {
- dirPath.mkdirs();
- }
-
- StringBuilder matrixContent = new StringBuilder();
- matrixContent.append("#NEXUS\n");
-
- //header:
- TreebaseUtil.attachStudyHeader(pStudy, matrixContent);
-
- // taxa:
- TaxonLabelSet taxa = matrix.getTaxa();
- if (taxa != null) {
- //one taxon per line, no line number:
- taxa.buildNexusBlockTaxa(matrixContent, true, false);
- }
-
- matrix.generateNexusBlock(matrixContent);
- // matrixContent.append("END;\n"); // Not Needed
-
- String tmp = getFileName(pMatrixId,request);
-
- try {
-
- File file = new File(downloadDirName + TreebaseUtil.FILESEP + tmp);
- FileWriter out = new FileWriter(file);
-
- out.write(matrixContent.toString());
-
- out.close();
- // File did not exist and was created
- // } else {
- // File already exists
- // }
-
- } catch (IOException e) {
- e.printStackTrace();
- }
-
- }
- */
-
@Override
protected String getFileNamePrefix() {
return "M";
@@ -203,14 +108,19 @@
protected String getFileContent(long objectId, HttpServletRequest request) {
Study pStudy = ControllerUtil.findStudy(request, getStudyService());
Matrix matrix = getMatrixService().findByID(objectId);
- TaxonLabelSet taxa = matrix.getTaxa();
-
+ TaxonLabelSet taxa = matrix.getTaxa();
if ( getFormat(request) == FORMAT_NEXML ) {
NexusDataSet pNexusDataSet = new NexusDataSet();
pNexusDataSet.getTaxonLabelSets().add(taxa);
pNexusDataSet.getMatrices().add(matrix);
return getNexmlService().serialize(pNexusDataSet);
}
+ else if ( getFormat(request) == FORMAT_RDF ) {
+ NexusDataSet pNexusDataSet = new NexusDataSet();
+ pNexusDataSet.getTaxonLabelSets().add(taxa);
+ pNexusDataSet.getMatrices().add(matrix);
+ return getRdfaService().serialize(pNexusDataSet);
+ }
else { // FORMAT_NEXUS or none
StringBuilder matrixContent = new StringBuilder();
matrixContent.append("#NEXUS\n");
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