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[Treebase-guts] SF.net SVN: treebase:[82] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers
|
From: <rv...@us...> - 2009-06-23 14:21:02
|
Revision: 82
http://treebase.svn.sourceforge.net/treebase/?rev=82&view=rev
Author: rvos
Date: 2009-06-23 11:10:17 +0000 (Tue, 23 Jun 2009)
Log Message:
-----------
Refactored to take advantage of AbstractDownloadController superclass. Commented out (but kept in place) all now superfluous code.
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAMatrixController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusFileController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusRCTFileController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeBlockController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAnAnalysisStepController.java
Added Paths:
-----------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.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 2009-06-23 11:08:34 UTC (rev 81)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAMatrixController.java 2009-06-23 11:10:17 UTC (rev 82)
@@ -20,25 +20,26 @@
package org.cipres.treebase.web.controllers;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
+//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.apache.log4j.Logger;
import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.mvc.Controller;
import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.domain.matrix.Matrix;
import org.cipres.treebase.domain.matrix.MatrixService;
+import org.cipres.treebase.domain.nexus.NexusDataSet;
import org.cipres.treebase.domain.study.Study;
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;
+//import org.cipres.treebase.web.util.WebUtil;
/**
* DownloadAMatrixController.java
@@ -52,8 +53,8 @@
*
*/
-public class DownloadAMatrixController implements Controller {
- private static final Logger LOGGER = Logger.getLogger(DownloadAMatrixController.class);
+public class DownloadAMatrixController extends AbstractDownloadController implements Controller {
+ //private static final Logger LOGGER = Logger.getLogger(DownloadAMatrixController.class);
private MatrixService mMatrixService;
private StudyService mStudyService;
@@ -103,7 +104,6 @@
// + request.getSession().getServletContext().getRealPath("/NexusFileDownload"));
// System.out.println("PATH INFO: " + request.getPathInfo());
//
- // TODO:
if (request.getParameter("matrixid") == null) {
return null;
@@ -113,40 +113,29 @@
//Study s = getStudyService().findByID(studyId);
long matrixId = Long.parseLong(request.getParameter("matrixid"));
- String fileName = getFileName(matrixId);
+// String fileName = getFileName(matrixId,request);
- String downloadDir = request.getSession().getServletContext().getRealPath(
- TreebaseUtil.FILESEP + "NexusFileDownload")
- + TreebaseUtil.FILESEP + request.getRemoteUser();
+// String downloadDir = request.getSession().getServletContext().getRealPath(
+// TreebaseUtil.FILESEP + "NexusFileDownload")
+// + TreebaseUtil.FILESEP + request.getRemoteUser();
+// String downloadDir = getDownloadDir(request);
- long start = System.currentTimeMillis();
+// long start = System.currentTimeMillis();
- generateAFileDynamically(request, matrixId, downloadDir);
- WebUtil.downloadFile(response, downloadDir, fileName);
+ generateAFileDynamically(request, response, matrixId);
+// WebUtil.downloadFile(response, downloadDir, fileName);
- long end = System.currentTimeMillis();
+// long end = System.currentTimeMillis();
+//
+// if (LOGGER.isDebugEnabled()) {
+// LOGGER.debug("TIME DIFFERENCE FOR A SINGAL FILE IN DOWNLOAD A MATRIX CONTROLLER: "
+// + (end - start));
+// }
- 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);
}
/**
- * This method adds "M" as Prefix to the matrix ID and ".nex" as Suffix.
- *
- * @param id (Matrix id)
- * @return returns the file name to be used for down loading
- */
-
- private String getFileName(long id) {
-
- return "M" + id + ".nex";
- }
-
- /**
* 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
@@ -155,7 +144,7 @@
* @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);
@@ -183,7 +172,7 @@
matrix.generateNexusBlock(matrixContent);
// matrixContent.append("END;\n"); // Not Needed
- String tmp = getFileName(pMatrixId);
+ String tmp = getFileName(pMatrixId,request);
try {
@@ -203,5 +192,36 @@
}
}
+ */
+ @Override
+ protected String getFileNamePrefix() {
+ return "M";
+ }
+
+ @Override
+ protected String getFileContent(long objectId, HttpServletRequest request) {
+ Study pStudy = ControllerUtil.findStudy(request, getStudyService());
+ Matrix matrix = getMatrixService().findByID(objectId);
+ 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 { // FORMAT_NEXUS or none
+ StringBuilder matrixContent = new StringBuilder();
+ matrixContent.append("#NEXUS\n");
+ TreebaseUtil.attachStudyHeader(pStudy, matrixContent);
+ if (taxa != null) {
+ //one taxon per line, no line number:
+ taxa.buildNexusBlockTaxa(matrixContent, true, false);
+ }
+ matrix.generateNexusBlock(matrixContent);
+ return matrixContent.toString();
+ }
+ }
+
}
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusFileController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusFileController.java 2009-06-23 11:08:34 UTC (rev 81)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusFileController.java 2009-06-23 11:10:17 UTC (rev 82)
@@ -22,17 +22,17 @@
package org.cipres.treebase.web.controllers;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
+//import java.io.File;
+//import java.io.FileWriter;
+//import java.io.IOException;
import java.sql.Clob;
-import java.sql.SQLException;
+//import java.sql.SQLException;
import java.util.Map;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
-import org.apache.log4j.Logger;
+//import org.apache.log4j.Logger;
import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.mvc.Controller;
@@ -42,7 +42,7 @@
import org.cipres.treebase.domain.study.StudyService;
import org.cipres.treebase.domain.tree.PhyloTreeService;
import org.cipres.treebase.web.util.ControllerUtil;
-import org.cipres.treebase.web.util.WebUtil;
+//import org.cipres.treebase.web.util.WebUtil;
/**
*
@@ -54,9 +54,9 @@
* @author madhu
*
*/
-public class DownloadANexusFileController implements Controller {
+public class DownloadANexusFileController extends AbstractDownloadController implements Controller {
- private static final Logger LOGGER = Logger.getLogger(DownloadANexusFileController.class);
+// private static final Logger LOGGER = Logger.getLogger(DownloadANexusFileController.class);
private PhyloTreeService mPhyloTreeService;
private StudyService mStudyService;
@@ -109,39 +109,40 @@
public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response)
throws Exception {
- // TODO Auto-generated method stub
- String sep = System.getProperty("file.separator");
- String downloadDir = request.getSession().getServletContext().getRealPath(
- "/NexusFileDownload")
- + sep + request.getRemoteUser();
+// String sep = System.getProperty("file.separator");
+// String downloadDir = request.getSession().getServletContext().getRealPath(
+// "/NexusFileDownload")
+// + sep + request.getRemoteUser();
+// String downloadDir = getDownloadDir(request);
+//
+// String treeId = request.getParameter("treeid");
+// String matrixId = request.getParameter("matrixid");
+// String nexusFile = request.getParameter("nexusfile");
+//
+// if (treeId == null && matrixId == null && nexusFile == null) {
+// return null;
+// }
+// long clickedParameterId = 0L;
+// String nexusFileName = null;
+//
+// if (treeId != null) {
+// clickedParameterId = Long.parseLong(treeId);
+// nexusFileName = getPhyloTreeService().findByID(clickedParameterId).getNexusFileName();
+// } else if (matrixId != null) {
+// clickedParameterId = Long.parseLong(matrixId);
+// nexusFileName = getMatrixService().findByID(clickedParameterId).getNexusFileName();
+// } else if (nexusFile != null) {
+// nexusFileName = (nexusFile).replaceAll("%20", "_");
+// }
+//
+// if (nexusFileName == null) {
+// return null;
+// }
+
+ generateAFileDynamically(request,response,0L);
+// generateAFileDynamically(request, downloadDir, nexusFileName);
+// WebUtil.downloadFile(response, downloadDir, nexusFileName + org);
- String treeId = request.getParameter("treeid");
- String matrixId = request.getParameter("matrixid");
- String nexusFile = request.getParameter("nexusfile");
-
- if (treeId == null && matrixId == null && nexusFile == null) {
- return null;
- }
- long clickedParameterId = 0L;
- String nexusFileName = null;
-
- if (treeId != null) {
- clickedParameterId = Long.parseLong(treeId);
- nexusFileName = getPhyloTreeService().findByID(clickedParameterId).getNexusFileName();
- } else if (matrixId != null) {
- clickedParameterId = Long.parseLong(matrixId);
- nexusFileName = getMatrixService().findByID(clickedParameterId).getNexusFileName();
- } else if (nexusFile != null) {
- nexusFileName = (nexusFile).replaceAll("%20", "_");
- }
-
- if (nexusFileName == null) {
- return null;
- }
-
- generateAFileDynamically(request, downloadDir, nexusFileName);
- WebUtil.downloadFile(response, downloadDir, nexusFileName + org);
-
return null;
}
@@ -149,7 +150,8 @@
* @param req HttpServletRequest
* @param downloadDirName String Name of the directory where file(s) will be downloaded
* @param fileName String name of the download file
- */
+ */
+ /*
private void generateAFileDynamically(
HttpServletRequest req,
String downloadDirName,
@@ -199,6 +201,72 @@
sqle.printStackTrace();
}
+ }
+ */
+
+ @Override
+ protected String getFileName(long objectId,HttpServletRequest req) {
+ String treeId = req.getParameter("treeid");
+ String matrixId = req.getParameter("matrixid");
+ String nexusFile = req.getParameter("nexusfile");
+
+ if (treeId == null && matrixId == null && nexusFile == null) {
+ return null;
+ }
+ long clickedParameterId = 0L;
+ String nexusFileName = null;
+ if (treeId != null) {
+ clickedParameterId = Long.parseLong(treeId);
+ nexusFileName = getPhyloTreeService().findByID(clickedParameterId).getNexusFileName();
+ } else if (matrixId != null) {
+ clickedParameterId = Long.parseLong(matrixId);
+ nexusFileName = getMatrixService().findByID(clickedParameterId).getNexusFileName();
+ } else if (nexusFile != null) {
+ nexusFileName = (nexusFile).replaceAll("%20", "_");
+ }
+ return ( nexusFileName + org ).replaceAll(TreebaseUtil.ANEMPTYSPACE, "_");
+ }
+
+ @Override
+ protected String getFileNamePrefix() {
+ // Not necessary because we override getFileName
+ return null;
+ }
+
+ @Override
+ protected String getFileContent(long objectId, HttpServletRequest req) {
+ String nexusFileName = null;
+ String treeId = req.getParameter("treeid");
+ String matrixId = req.getParameter("matrixid");
+ String nexusFile = req.getParameter("nexusfile");
+ long clickedParameterId = 0L;
+ if (treeId != null) {
+ clickedParameterId = Long.parseLong(treeId);
+ nexusFileName = getPhyloTreeService().findByID(clickedParameterId).getNexusFileName();
+ } else if (matrixId != null) {
+ clickedParameterId = Long.parseLong(matrixId);
+ nexusFileName = getMatrixService().findByID(clickedParameterId).getNexusFileName();
+ } else if (nexusFile != null) {
+ nexusFileName = (nexusFile).replaceAll("%20", "_");
+ }
+ if (nexusFileName == null) {
+ return null;
+ }
+ Study study = ControllerUtil.findStudy(req, mStudyService);
+ Map<String, Clob> nexusMap = study.getNexusFiles();
+ Clob clob = nexusMap.get(nexusFileName);
+ String clobStr = "File Not Found. File Name is: " + nexusFileName;
+ if (clob != null) {
+ try {
+ int clobLength = (int) clob.length();
+ char[] clobchars = new char[clobLength];
+ clob.getCharacterStream().read(clobchars);
+ clobStr = new String(clobchars);
+ } catch ( Exception e ) {
+ e.printStackTrace();
+ }
+ }
+ return clobStr;
}
}
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusRCTFileController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusRCTFileController.java 2009-06-23 11:08:34 UTC (rev 81)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusRCTFileController.java 2009-06-23 11:10:17 UTC (rev 82)
@@ -21,8 +21,8 @@
*/
package org.cipres.treebase.web.controllers;
-import java.io.File;
-import java.io.FileWriter;
+//import java.io.File;
+//import java.io.FileWriter;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
@@ -36,7 +36,7 @@
import org.cipres.treebase.domain.study.StudyService;
import org.cipres.treebase.domain.study.Submission;
import org.cipres.treebase.web.util.ControllerUtil;
-import org.cipres.treebase.web.util.WebUtil;
+//import org.cipres.treebase.web.util.WebUtil;
/**
* @author madhu
@@ -46,7 +46,7 @@
* Modified on April 28, 2008
*
*/
-public class DownloadANexusRCTFileController implements Controller {
+public class DownloadANexusRCTFileController extends AbstractDownloadController implements Controller {
Logger LOGGER = Logger.getLogger(DownloadANexusRCTFileController.class);
@@ -78,52 +78,91 @@
Long study_id = ControllerUtil.getStudyId(pRequest);
Study study = mStudyService.findByID(study_id);
Submission submission = study.getSubmission();
+ generateAFileDynamically(pRequest, pResponse, submission.getId());
+ return null;
- String fileName = pRequest.getParameter("nexusfile");
+// String fileName = pRequest.getParameter("nexusfile");
+// if (fileName == null) {
+// return null;
+// }
+//
+// String nexFileName = (fileName + "rct").replaceAll(TreebaseUtil.ANEMPTYSPACE, "_");
+//
+// if (LOGGER.isInfoEnabled()) {
+// LOGGER.info("Submission id: " + submission.getId() + ", FileName: " + nexFileName);
+// }
+
+// String downloadDir = pRequest.getSession().getServletContext().getRealPath(
+// TreebaseUtil.FILESEP + "NexusFileDownload")
+// + TreebaseUtil.FILESEP + pRequest.getRemoteUser();
+// String downloadDir = getDownloadDir(pRequest);
+//
+// long start = System.currentTimeMillis();
+//
+// File dirPath = new File(downloadDir);
+// if (!dirPath.exists()) {
+// dirPath.mkdirs();
+// }
+//
+// String pathName = downloadDir + TreebaseUtil.FILESEP + nexFileName;
+// File file = new File(pathName);
+//
+// if (LOGGER.isDebugEnabled()) {
+// LOGGER.debug("path=" + pathName);
+// }
+//
+// FileWriter fwriter = new FileWriter(file);
+// StringBuilder bldr = new StringBuilder("#NEXUS");
+// bldr.append(TreebaseUtil.getLineSeparators(2));
+// bldr
+// .append(getStudyService().generateReconstructedNexusFile(submission.getId(), fileName));
+//
+// fwriter.write(bldr.toString());
+// fwriter.close();
+// WebUtil.downloadFile(pResponse, downloadDir, nexFileName);
+//
+// if (LOGGER.isDebugEnabled()) {
+// long end = System.currentTimeMillis();
+// LOGGER.debug(" file download time=" + (end-start));
+// }
+//
+// return null;
+ }
+
+ @Override
+ protected String getFileName(long objectId,HttpServletRequest req) {
+ String fileName = req.getParameter("nexusfile");
if (fileName == null) {
return null;
}
+ return (fileName + "rct").replaceAll(TreebaseUtil.ANEMPTYSPACE, "_");
+ }
- String nexFileName = (fileName + "rct").replaceAll(TreebaseUtil.ANEMPTYSPACE, "_");
+ @Override
+ protected String getFileNamePrefix() {
+ // Not necessary because we override getFileName
+ return null;
+ }
- if (LOGGER.isInfoEnabled()) {
- LOGGER.info("Submission id: " + submission.getId() + ", FileName: " + nexFileName);
+ @Override
+ protected String getFileContent(long submisionId, HttpServletRequest request) {
+ if ( getFormat(request) == FORMAT_NEXML ) {
+ Long study_id = ControllerUtil.getStudyId(request);
+ Study study = mStudyService.findByID(study_id);
+ return getNexmlService().serialize(study);
}
-
- String downloadDir = pRequest.getSession().getServletContext().getRealPath(
- TreebaseUtil.FILESEP + "NexusFileDownload")
- + TreebaseUtil.FILESEP + pRequest.getRemoteUser();
-
- long start = System.currentTimeMillis();
-
- File dirPath = new File(downloadDir);
- if (!dirPath.exists()) {
- dirPath.mkdirs();
+ else {
+ String fileName = request.getParameter("nexusfile");
+ if (fileName == null) {
+ return null;
+ }
+ StringBuilder bldr = new StringBuilder("#NEXUS");
+ bldr
+ .append(TreebaseUtil.getLineSeparators(2))
+ .append(getStudyService()
+ .generateReconstructedNexusFile(submisionId, fileName));
+ return bldr.toString();
}
-
- String pathName = downloadDir + TreebaseUtil.FILESEP + nexFileName;
- File file = new File(pathName);
-
- if (LOGGER.isDebugEnabled()) {
- LOGGER.debug("path=" + pathName);
- }
-
- FileWriter fwriter = new FileWriter(file);
- StringBuilder bldr = new StringBuilder("#NEXUS");
- bldr.append(TreebaseUtil.getLineSeparators(2));
- bldr
- .append(getStudyService().generateReconstructedNexusFile(submission.getId(), fileName));
-
- fwriter.write(bldr.toString());
- fwriter.close();
- WebUtil.downloadFile(pResponse, downloadDir, nexFileName);
-
- if (LOGGER.isDebugEnabled()) {
- long end = System.currentTimeMillis();
- LOGGER.debug(" file download time=" + (end-start));
- }
-
- return null;
}
}
Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java 2009-06-23 11:10:17 UTC (rev 82)
@@ -0,0 +1,92 @@
+/**
+ *
+ */
+package org.cipres.treebase.web.controllers;
+
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.cipres.treebase.TreebaseIDString;
+import org.cipres.treebase.TreebaseUtil;
+import org.cipres.treebase.domain.matrix.Matrix;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.study.StudyService;
+import org.cipres.treebase.domain.taxon.TaxonLabelSet;
+import org.cipres.treebase.domain.tree.TreeBlock;
+import org.springframework.web.servlet.ModelAndView;
+import org.springframework.web.servlet.mvc.Controller;
+
+/**
+ * @author rvosa
+ *
+ */
+public class DownloadAStudyController extends AbstractDownloadController
+ implements Controller {
+ private StudyService mStudyService;
+
+ public StudyService getStudyService() {
+ return mStudyService;
+ }
+
+ public void setStudyService(StudyService studyService) {
+ mStudyService = studyService;
+ }
+
+ /* (non-Javadoc)
+ * @see org.cipres.treebase.web.controllers.AbstractDownloadController#getFileContent(long, javax.servlet.http.HttpServletRequest)
+ */
+ @Override
+ protected String getFileContent(long pStudyID, HttpServletRequest request) {
+ Study study = getStudyService().findByID(pStudyID);
+ if ( getFormat(request) == FORMAT_NEXML ) {
+ return getNexmlService().serialize(study);
+ }
+ else {
+ StringBuilder builder = new StringBuilder();
+ builder.append("#NEXUS\n\n");
+
+ // header:
+ TreebaseUtil.attachStudyHeader(study, builder);
+
+ // taxa:
+ for ( TaxonLabelSet tls : study.getTaxonLabelSets() ) {
+ // one taxon label per line, no line number.
+ tls.buildNexusBlockTaxa(builder, true, false);
+ }
+
+ // matrices::
+ for ( Matrix m : study.getMatrices() ) {
+ m.generateNexusBlock(builder);
+ }
+
+ //tree blocks:
+ for ( TreeBlock tb : study.getTreeBlocks() ) {
+ tb.generateAFileDynamically(builder);
+ }
+
+ return builder.toString();
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see org.cipres.treebase.web.controllers.AbstractDownloadController#getFileNamePrefix()
+ */
+ @Override
+ protected String getFileNamePrefix() {
+ return TreebaseIDString.getPrefixForClass(Study.class);
+ }
+
+ /* (non-Javadoc)
+ * @see org.springframework.web.servlet.mvc.Controller#handleRequest(javax.servlet.http.HttpServletRequest, javax.servlet.http.HttpServletResponse)
+ */
+ public ModelAndView handleRequest(HttpServletRequest request,
+ HttpServletResponse response) throws Exception {
+ if (request.getParameter("id") == null) {
+ return null;
+ }
+ long pStudyId = Long.parseLong(request.getParameter("id"));
+ generateAFileDynamically(request, response, pStudyId);
+ return null;
+ }
+
+}
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeBlockController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeBlockController.java 2009-06-23 11:08:34 UTC (rev 81)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeBlockController.java 2009-06-23 11:10:17 UTC (rev 82)
@@ -20,19 +20,21 @@
package org.cipres.treebase.web.controllers;
-import java.io.File;
-import java.io.FileWriter;
+//import java.io.File;
+//import java.io.FileWriter;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
-import org.apache.log4j.Logger;
+//import org.apache.log4j.Logger;
import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.mvc.Controller;
+//import org.cipres.treebase.TreebaseUtil;
+import org.cipres.treebase.domain.nexus.NexusDataSet;
import org.cipres.treebase.domain.tree.PhyloTreeHome;
import org.cipres.treebase.domain.tree.TreeBlock;
-import org.cipres.treebase.web.util.WebUtil;
+//import org.cipres.treebase.web.util.WebUtil;
/**
*
@@ -40,8 +42,8 @@
*
*/
-public class DownloadATreeBlockController implements Controller {
- private static final Logger LOGGER = Logger.getLogger(DownloadATreeBlockController.class);
+public class DownloadATreeBlockController extends AbstractDownloadController implements Controller {
+// private static final Logger LOGGER = Logger.getLogger(DownloadATreeBlockController.class);
private PhyloTreeHome mPhyloTreeHome;
@@ -67,53 +69,66 @@
public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response)
throws Exception {
- // TODO:
- String sep = System.getProperty("file.separator");
+// String sep = System.getProperty("file.separator");
if (request.getParameter("treeblockid") == null) {
return null;
}
long blockid = Long.parseLong(request.getParameter("treeblockid"));
- String fileName = getFileName(blockid);
+ generateAFileDynamically(request, response, blockid);
+ return null;
+ //String fileName = getFileName(blockid,request);
- String downloadDir = request.getSession().getServletContext().getRealPath(
- "/NexusFileDownload")
- + sep + request.getRemoteUser();
+// String downloadDir = request.getSession().getServletContext().getRealPath(
+// "/NexusFileDownload")
+// + sep + request.getRemoteUser();
+// String downloadDir = getDownloadDir(request);
+//
+// long start = System.currentTimeMillis();
+//
+// TreeBlock treeBlock = getPhyloTreeHome().findTreeBlockById(blockid);
+//
+// File dirPath = new File(downloadDir);
+// if (!dirPath.exists()) {
+// dirPath.mkdirs();
+// }
+// File file = new File(downloadDir + System.getProperty("file.separator")
+// + getFileName(blockid,request));
+// FileWriter fwriter = new FileWriter(file);
+// StringBuilder bldr = new StringBuilder("#NEXUS\n\n");
+// treeBlock.generateAFileDynamically(bldr);
+// fwriter.write(bldr.toString());
+// fwriter.close();
+// generateAFileDynamically(request, blockid);
+// WebUtil.downloadFile(response, downloadDir, getFileName(blockid,request));
+//
+// long end = System.currentTimeMillis();
+//
+// if (LOGGER.isDebugEnabled()) {
+// LOGGER.debug("TIME DIFFERENCE FOR A SINGAL FILE: " + (end - start));
+// }
+//
+// return null;
+ }
- long start = System.currentTimeMillis();
+ @Override
+ protected String getFileNamePrefix() {
+ return "TB";
+ }
- TreeBlock element = getPhyloTreeHome().findTreeBlockById(blockid);
-
- File dirPath = new File(downloadDir);
- if (!dirPath.exists()) {
- dirPath.mkdirs();
+ @Override
+ protected String getFileContent(long blockid, HttpServletRequest request) {
+ TreeBlock treeBlock = getPhyloTreeHome().findTreeBlockById(blockid);
+ if ( getFormat(request) == FORMAT_NEXML ) {
+ NexusDataSet nexusDataSet = new NexusDataSet();
+ nexusDataSet.getTaxonLabelSets().add(treeBlock.getTaxonLabelSet());
+ nexusDataSet.getTreeBlocks().add(treeBlock);
+ return getNexmlService().serialize(nexusDataSet);
}
- File file = new File(downloadDir + System.getProperty("file.separator")
- + getFileName(blockid));
- FileWriter fwriter = new FileWriter(file);
- StringBuilder bldr = new StringBuilder("#NEXUS\n\n");
- element.generateAFileDynamically(bldr);
- fwriter.write(bldr.toString());
- fwriter.close();
- WebUtil.downloadFile(response, downloadDir, fileName);
-
- long end = System.currentTimeMillis();
-
- if (LOGGER.isDebugEnabled()) {
- LOGGER.debug("TIME DIFFERENCE FOR A SINGAL FILE: " + (end - start));
+ else {
+ StringBuilder bldr = new StringBuilder("#NEXUS\n\n");
+ treeBlock.generateAFileDynamically(bldr);
+ return bldr.toString();
}
-
- return null;
}
- /**
- * This method adds "TB" as Prefix to the tree block ID and ".tre" as Suffix.
- *
- * @param id (TreeBlock id)
- * @return returns the file name to be used for down loading
- */
- private String getFileName(long id) {
-
- return "TB" + id + ".tre";
- }
-
}
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeController.java 2009-06-23 11:08:34 UTC (rev 81)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeController.java 2009-06-23 11:10:17 UTC (rev 82)
@@ -20,24 +20,26 @@
package org.cipres.treebase.web.controllers;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
+//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.apache.log4j.Logger;
import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.mvc.Controller;
import org.cipres.treebase.TreebaseUtil;
+import org.cipres.treebase.domain.nexus.NexusDataSet;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.study.StudyService;
import org.cipres.treebase.domain.tree.PhyloTree;
import org.cipres.treebase.domain.tree.PhyloTreeService;
+import org.cipres.treebase.domain.tree.TreeBlock;
import org.cipres.treebase.web.util.ControllerUtil;
-import org.cipres.treebase.web.util.WebUtil;
+//import org.cipres.treebase.web.util.WebUtil;
import org.cipres.treebase.domain.taxon.TaxonLabelSet;
@@ -53,8 +55,8 @@
*
*/
-public class DownloadATreeController implements Controller {
- private static final Logger LOGGER = Logger.getLogger(DownloadATreeController.class);
+public class DownloadATreeController extends AbstractDownloadController implements Controller {
+// private static final Logger LOGGER = Logger.getLogger(DownloadATreeController.class);
private PhyloTreeService mPhyloTreeService;
private StudyService mStudyService;
@@ -94,50 +96,42 @@
public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response)
throws Exception {
- // TODO:
- String sep = System.getProperty("file.separator");
+// String sep = System.getProperty("file.separator");
if (request.getParameter("treeid") == null) {
return null;
}
long treeid = Long.parseLong(request.getParameter("treeid"));
- String fileName = getFileName(treeid);
-
- String downloadDir = request.getSession().getServletContext().getRealPath(
- "/NexusFileDownload")
- + sep + request.getRemoteUser();
-
- long start = System.currentTimeMillis();
-
- generateAFileDynamically(request, treeid, downloadDir);
- WebUtil.downloadFile(response, downloadDir, fileName);
-
- long end = System.currentTimeMillis();
-
- if (LOGGER.isDebugEnabled()) {
- LOGGER.debug("TIME DIFFERENCE FOR A SINGAL FILE: " + (end - start));
- }
-
- return null; // new ModelAndView("treeList", Constants.TREE_LIST, phyloTrees);
+ generateAFileDynamically(request, response, treeid);
+ return null;
+// String fileName = getFileName(treeid,request);
+//
+// String downloadDir = request.getSession().getServletContext().getRealPath(
+// "/NexusFileDownload")
+// + sep + request.getRemoteUser();
+// String downloadDir = getDownloadDir(request);
+//
+// long start = System.currentTimeMillis();
+//
+// generateAFileDynamically(request, treeid, downloadDir);
+// WebUtil.downloadFile(response, downloadDir, fileName);
+//
+// long end = System.currentTimeMillis();
+//
+// if (LOGGER.isDebugEnabled()) {
+// LOGGER.debug("TIME DIFFERENCE FOR A SINGAL FILE: " + (end - start));
+// }
+//
+// return null; // new ModelAndView("treeList", Constants.TREE_LIST, phyloTrees);
}
/**
- * This method adds "T" as Prefix to the tree ID and ".tre" as Suffix.
*
- * @param id (Tree id)
- * @return returns the file name to be used for downloading
- */
- private String getFileName(long id) {
-
- return "T" + id + ".tre";
- }
-
- /**
- *
* @param request
* @param pTreeId It is tree id.
* @param downloadDirName download directory where files will be created
*/
+ /*
private void generateAFileDynamically(
HttpServletRequest request,
long pTreeId,
@@ -145,15 +139,15 @@
Study study = ControllerUtil.findStudy(request, mStudyService);
- File dirPath = new File(downloadDirName);
- if (!dirPath.exists()) {
- dirPath.mkdirs();
- }
+// File dirPath = new File(downloadDirName);
+// if (!dirPath.exists()) {
+// dirPath.mkdirs();
+// }
PhyloTree tree = getPhyloTreeService().findByID(pTreeId);
TaxonLabelSet tbnlblSet = tree.getTreeBlock().getTaxonLabelSet();
- String tmp = getFileName(pTreeId);
+// String tmp = getFileName(pTreeId,request);
StringBuilder builder = new StringBuilder();
@@ -168,19 +162,60 @@
//tree block:
tree.buildNexusBlock(builder);
+
+ generateAFileDynamically(request, pTreeId);
- try {
+// try {
+//
+// File file = new File(downloadDirName + TreebaseUtil.FILESEP + tmp);
+// FileWriter out = new FileWriter(file);
+//
+// out.write(builder.toString());
+//
+// out.close();
+//
+// } catch (IOException e) {
+// e.printStackTrace();
+// }
+ }
+*/
+ @Override
+ protected String getFileNamePrefix() {
+ return "T";
+ }
- File file = new File(downloadDirName + TreebaseUtil.FILESEP + tmp);
- FileWriter out = new FileWriter(file);
-
- out.write(builder.toString());
-
- out.close();
-
- } catch (IOException e) {
- e.printStackTrace();
+ @Override
+ protected String getFileContent(long pTreeId, HttpServletRequest request) {
+ Study study = ControllerUtil.findStudy(request, mStudyService);
+ PhyloTree tree = getPhyloTreeService().findByID(pTreeId);
+ tree = getPhyloTreeService().resurrect(tree);
+ TreeBlock enclosingTreeBlock = getPhyloTreeService().resurrect(tree.getTreeBlock());
+ TaxonLabelSet tls = getPhyloTreeService().resurrect(enclosingTreeBlock.getTaxonLabelSet());
+ if ( getFormat(request) == FORMAT_NEXML ) {
+ NexusDataSet nds = new NexusDataSet();
+ nds.getTaxonLabelSets().add(tls);
+ TreeBlock treeBlock = new TreeBlock();
+ treeBlock.setTaxonLabelSet(tls);
+ treeBlock.addPhyloTree(tree);
+ nds.getTreeBlocks().add(treeBlock);
+ return getNexmlService().serialize(nds);
}
+ else {
+ StringBuilder builder = new StringBuilder();
+ builder.append("#NEXUS\n\n");
+
+ // header:
+ TreebaseUtil.attachStudyHeader(study, builder);
+
+ // taxa:
+ // one taxon label per line, no line number.
+ tls.buildNexusBlockTaxa(builder, true, false);
+
+ //tree block:
+ tree.buildNexusBlock(builder);
+
+ return builder.toString();
+ }
}
}
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAnAnalysisStepController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAnAnalysisStepController.java 2009-06-23 11:08:34 UTC (rev 81)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAnAnalysisStepController.java 2009-06-23 11:10:17 UTC (rev 82)
@@ -20,9 +20,9 @@
package org.cipres.treebase.web.controllers;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
+//import java.io.File;
+//import java.io.FileWriter;
+//import java.io.IOException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
@@ -39,7 +39,7 @@
import org.cipres.treebase.domain.taxon.TaxonLabelSet;
import org.cipres.treebase.domain.tree.PhyloTree;
import org.cipres.treebase.domain.tree.PhyloTreeService;
-import org.cipres.treebase.web.util.WebUtil;
+//import org.cipres.treebase.web.util.WebUtil;
/**
*
@@ -49,7 +49,7 @@
* @author rvosa
*
*/
-public class DownloadAnAnalysisStepController implements Controller {
+public class DownloadAnAnalysisStepController extends AbstractDownloadController implements Controller {
private MatrixService mMatrixService;
private PhyloTreeService mPhyloTreeService;
private AnalysisStepService mAnalysisStepService;
@@ -117,14 +117,15 @@
}
long analysisId = Long.parseLong(request.getParameter("analysisid"));
- String fileName = getFileName(analysisId);
+// String fileName = getFileName(analysisId,request);
- String downloadDir = request.getSession().getServletContext().getRealPath(
- TreebaseUtil.FILESEP + "NexusFileDownload")
- + TreebaseUtil.FILESEP + request.getRemoteUser();
+// String downloadDir = request.getSession().getServletContext().getRealPath(
+// TreebaseUtil.FILESEP + "NexusFileDownload")
+// + TreebaseUtil.FILESEP + request.getRemoteUser();
+// String downloadDir = getDownloadDir(request);
- generateAFileDynamically(request, analysisId, downloadDir);
- WebUtil.downloadFile(response, downloadDir, fileName);
+ generateAFileDynamically(request, response, analysisId);
+// WebUtil.downloadFile(response, downloadDir, fileName);
return null;
}
@@ -136,6 +137,7 @@
* @param analysisId
* @param downloadDirName
*/
+ /*
private void generateAFileDynamically(HttpServletRequest request, long analysisId, String downloadDirName) {
AnalysisStep step = getAnalysisStepService().findByID(analysisId);
@@ -187,7 +189,7 @@
}
}
- String tmp = getFileName(analysisId);
+ String tmp = getFileName(analysisId,request);
try {
File file = new File(downloadDirName + TreebaseUtil.FILESEP + tmp);
FileWriter out = new FileWriter(file);
@@ -198,9 +200,57 @@
}
}
-
- private String getFileName(long id) {
- return "AnalysisStep" + id + ".nex";
+ */
+
+ @Override
+ protected String getFileNamePrefix() {
+ return "AnalysisStep";
}
+ @Override
+ protected String getFileContent(long analysisId, HttpServletRequest request) {
+ AnalysisStep step = getAnalysisStepService().findByID(analysisId);
+ StringBuilder stepContent = new StringBuilder();
+ stepContent.append("#NEXUS\n");
+
+ //header:
+ TreebaseUtil.attachStudyHeader(step.getAnalysis().getStudy(), stepContent);
+ stepContent.append("[ The following blocks are input data for analysis step " + analysisId + " ]\n");
+ TaxonLabelSet inputLabelSet = step.getInputTaxonLabelSet();
+ inputLabelSet.buildNexusBlockTaxa(stepContent, true, false);
+ for ( AnalyzedData data : step.getDataSetReadOnly() ) {
+ if ( data.isInputData() ) {
+ PhyloTree tree = data.getTreeData();
+ Matrix matrix = data.getMatrixData();
+ if ( tree != null ) {
+ tree.getTreeBlock().setTaxonLabelSet(inputLabelSet);
+ tree.buildNexusBlock(stepContent);
+ }
+ if ( matrix != null ) {
+ matrix.setTaxa(inputLabelSet);
+ matrix.generateNexusBlock(stepContent);
+ }
+ }
+ }
+
+ stepContent.append("[ The following blocks are output data for analysis step " + analysisId + " ]\n");
+ TaxonLabelSet outputLabelSet = step.getOutputTaxonLabelSet();
+ outputLabelSet.buildNexusBlockTaxa(stepContent, true, false);
+ for ( AnalyzedData data : step.getDataSetReadOnly() ) {
+ if ( ! data.isInputData() ) {
+ PhyloTree tree = data.getTreeData();
+ Matrix matrix = data.getMatrixData();
+ if ( tree != null ) {
+ tree.getTreeBlock().setTaxonLabelSet(outputLabelSet);
+ tree.buildNexusBlock(stepContent);
+ }
+ if ( matrix != null ) {
+ matrix.setTaxa(outputLabelSet);
+ matrix.generateNexusBlock(stepContent);
+ }
+ }
+ }
+ return stepContent.toString();
+ }
+
}
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