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[Treebase-guts] SF.net SVN: treebase:[125] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers
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From: <rv...@us...> - 2009-06-25 14:56:44
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Revision: 125
http://treebase.svn.sourceforge.net/treebase/?rev=125&view=rev
Author: rvos
Date: 2009-06-25 13:41:20 +0000 (Thu, 25 Jun 2009)
Log Message:
-----------
Changed base URI handling
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAMatrixController.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/DownloadAStudyController.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
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java 2009-06-25 13:40:41 UTC (rev 124)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java 2009-06-25 13:41:20 UTC (rev 125)
@@ -2,6 +2,7 @@
import java.io.File;
import java.io.FileWriter;
+import java.util.Properties;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
@@ -21,6 +22,18 @@
private static String mNexmlContentType = "application/xml";
private static String mRdfContentType = "application/rdf+xml";
+ protected Properties getDefaultProperties(HttpServletRequest request) {
+ Properties properties = new Properties();
+ StringBuffer baseURI = new StringBuffer("http://");
+ baseURI
+ .append(request.getServerName())
+ .append(':')
+ .append(request.getServerPort())
+ .append("/treebase-web/PhyloWS/");
+ properties.setProperty("nexml.uri.base", baseURI.toString());
+ return properties;
+ }
+
/**
*
* @param request
@@ -54,6 +67,9 @@
if ( getFormat(request) == FORMAT_NEXML ) {
return getFileNamePrefix() + id + ".xml";
}
+ if ( getFormat(request) == FORMAT_RDF ) {
+ return getFileNamePrefix() + id + ".rdf";
+ }
return getFileNamePrefix() + id + ".nex";
}
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 13:40:41 UTC (rev 124)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAMatrixController.java 2009-06-25 13:41:20 UTC (rev 125)
@@ -113,13 +113,13 @@
NexusDataSet pNexusDataSet = new NexusDataSet();
pNexusDataSet.getTaxonLabelSets().add(taxa);
pNexusDataSet.getMatrices().add(matrix);
- return getNexmlService().serialize(pNexusDataSet);
+ return getNexmlService().serialize(pNexusDataSet,getDefaultProperties(request));
}
else if ( getFormat(request) == FORMAT_RDF ) {
NexusDataSet pNexusDataSet = new NexusDataSet();
pNexusDataSet.getTaxonLabelSets().add(taxa);
pNexusDataSet.getMatrices().add(matrix);
- return getRdfaService().serialize(pNexusDataSet);
+ return getRdfaService().serialize(pNexusDataSet,getDefaultProperties(request));
}
else { // FORMAT_NEXUS or none
StringBuilder matrixContent = new StringBuilder();
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 2009-06-25 13:40:41 UTC (rev 124)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusRCTFileController.java 2009-06-25 13:41:20 UTC (rev 125)
@@ -98,12 +98,12 @@
if ( getFormat(request) == FORMAT_NEXML ) {
Long study_id = ControllerUtil.getStudyId(request);
Study study = mStudyService.findByID(study_id);
- return getNexmlService().serialize(study);
+ return getNexmlService().serialize(study,getDefaultProperties(request));
}
else if ( getFormat(request) == FORMAT_RDF ) {
Long study_id = ControllerUtil.getStudyId(request);
Study study = mStudyService.findByID(study_id);
- return getRdfaService().serialize(study);
+ return getRdfaService().serialize(study,getDefaultProperties(request));
}
else {
String fileName = request.getParameter("nexusfile");
Modified: 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 2009-06-25 13:40:41 UTC (rev 124)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java 2009-06-25 13:41:20 UTC (rev 125)
@@ -39,10 +39,10 @@
protected String getFileContent(long pStudyID, HttpServletRequest request) {
Study study = getStudyService().findByID(pStudyID);
if ( getFormat(request) == FORMAT_NEXML ) {
- return getNexmlService().serialize(study);
+ return getNexmlService().serialize(study,getDefaultProperties(request));
}
else if ( getFormat(request) == FORMAT_RDF ) {
- return getRdfaService().serialize(study);
+ return getRdfaService().serialize(study,getDefaultProperties(request));
}
else {
StringBuilder builder = new StringBuilder();
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 2009-06-25 13:40:41 UTC (rev 124)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeBlockController.java 2009-06-25 13:41:20 UTC (rev 125)
@@ -81,13 +81,13 @@
NexusDataSet nexusDataSet = new NexusDataSet();
nexusDataSet.getTaxonLabelSets().add(treeBlock.getTaxonLabelSet());
nexusDataSet.getTreeBlocks().add(treeBlock);
- return getNexmlService().serialize(nexusDataSet);
+ return getNexmlService().serialize(nexusDataSet,getDefaultProperties(request));
}
else if ( getFormat(request) == FORMAT_RDF ) {
NexusDataSet nexusDataSet = new NexusDataSet();
nexusDataSet.getTaxonLabelSets().add(treeBlock.getTaxonLabelSet());
nexusDataSet.getTreeBlocks().add(treeBlock);
- return getRdfaService().serialize(nexusDataSet);
+ return getRdfaService().serialize(nexusDataSet,getDefaultProperties(request));
}
else {
StringBuilder bldr = new StringBuilder("#NEXUS\n\n");
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 2009-06-25 13:40:41 UTC (rev 124)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeController.java 2009-06-25 13:41:20 UTC (rev 125)
@@ -20,6 +20,8 @@
package org.cipres.treebase.web.controllers;
+import java.util.Properties;
+
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
@@ -113,7 +115,7 @@
treeBlock.setTaxonLabelSet(tls);
treeBlock.addPhyloTree(tree);
nds.getTreeBlocks().add(treeBlock);
- return getNexmlService().serialize(nds);
+ return getNexmlService().serialize(nds,getDefaultProperties(request));
}
else if ( getFormat(request) == FORMAT_RDF ) {
NexusDataSet nds = new NexusDataSet();
@@ -122,7 +124,7 @@
treeBlock.setTaxonLabelSet(tls);
treeBlock.addPhyloTree(tree);
nds.getTreeBlocks().add(treeBlock);
- return getRdfaService().serialize(nds);
+ return getRdfaService().serialize(nds,getDefaultProperties(request));
}
else {
StringBuilder builder = new StringBuilder();
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 2009-06-25 13:40:41 UTC (rev 124)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAnAnalysisStepController.java 2009-06-25 13:41:20 UTC (rev 125)
@@ -111,97 +111,14 @@
*/
public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response)
throws Exception {
-
if ( request.getParameter("analysisid") == null ) {
return null;
}
-
- long analysisId = Long.parseLong(request.getParameter("analysisid"));
-// String fileName = getFileName(analysisId,request);
-
-// String downloadDir = request.getSession().getServletContext().getRealPath(
-// TreebaseUtil.FILESEP + "NexusFileDownload")
-// + TreebaseUtil.FILESEP + request.getRemoteUser();
-// String downloadDir = getDownloadDir(request);
-
+ long analysisId = Long.parseLong(request.getParameter("analysisid"));
generateAFileDynamically(request, response, analysisId);
-// WebUtil.downloadFile(response, downloadDir, fileName);
-
return null;
}
- /**
- *
- *
- * @param request
- * @param analysisId
- * @param downloadDirName
- */
- /*
- private void generateAFileDynamically(HttpServletRequest request, long analysisId, String downloadDirName) {
-
- AnalysisStep step = getAnalysisStepService().findByID(analysisId);
-
- File dirPath = new File(downloadDirName);
- if (!dirPath.exists()) {
- dirPath.mkdirs();
- }
-
- 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);
- }
- }
- }
-
- String tmp = getFileName(analysisId,request);
- try {
- File file = new File(downloadDirName + TreebaseUtil.FILESEP + tmp);
- FileWriter out = new FileWriter(file);
- out.write(stepContent.toString());
- out.close();
- } catch (IOException e) {
- e.printStackTrace();
- }
-
- }
- */
-
@Override
protected String getFileNamePrefix() {
return "AnalysisStep";
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