[Treebase-guts] SF.net SVN: treebase:[125] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers

[<rv...@us...>]

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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