Thread: [Treebase-guts] SF.net SVN: treebase:[428] trunk/treebase-web/src/main/java/org/cipres/ treebase/w

Status: Beta

Brought to you by: hlapp, naturalis, rvos, sfrgpiel

treebase-guts

[Treebase-guts] SF.net SVN: treebase:[428] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/SearchSummaryController.java

From: <rv...@us...> - 2010-01-13 17:57:45

Revision: 428
          http://treebase.svn.sourceforge.net/treebase/?rev=428&view=rev
Author:   rvos
Date:     2010-01-13 17:57:38 +0000 (Wed, 13 Jan 2010)

Log Message:
-----------
SearchSummaryController now uses super.getConditionalModelAndView to construct the view it returns. This way, an additional access check is performed, so that studies-in-progress are only viewable given an x-access-granted parameter, otherwise an access violation view is returned.

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java	2010-01-13 17:31:31 UTC (rev 427)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java	2010-01-13 17:57:38 UTC (rev 428)
@@ -256,9 +256,8 @@
 	protected ModelAndView processFormSubmission(HttpServletRequest request,
 			HttpServletResponse response, Object command, BindException bindException)
 			throws Exception {
-		// TODO Auto-generated method stub
 		LOGGER.debug("processFormSubmission found study " + (Study) command);
-		return showForm(request, response, bindException);
+		return getConditionalModelAndView(request, showForm(request, response, bindException));
 	}
 
 	@Override
@@ -401,7 +400,7 @@
 		// but what the heck, let's put it in just to be sure
 		newModel.put("study", theStudy);
 
-		return new ModelAndView(pageName, newModel);
+		return getConditionalModelAndView(request, new ModelAndView(pageName, newModel));
 	}
 	
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Treebase-guts] SF.net SVN: treebase:[438] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/SearchSummaryController.java

From: <rv...@us...> - 2010-01-14 15:59:59

Revision: 438
          http://treebase.svn.sourceforge.net/treebase/?rev=438&view=rev
Author:   rvos
Date:     2010-01-14 15:59:53 +0000 (Thu, 14 Jan 2010)

Log Message:
-----------
Added more logging messages

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java	2010-01-14 14:56:33 UTC (rev 437)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java	2010-01-14 15:59:53 UTC (rev 438)
@@ -82,7 +82,7 @@
 	protected Study formBackingObject(HttpServletRequest request)
 			throws Exception {
 		Map<String,String []> param = request.getParameterMap();
-		
+		LOGGER.info("in formBackingObject");
 		theStudy = null;
 		{
 			Long studyID = getIDParam(param, "id");
@@ -133,7 +133,7 @@
 	
 	@Override
 	protected Map<String,Object> referenceData(HttpServletRequest pRequest) throws Exception {
-
+		LOGGER.info("in referenceData");
 		Map<String,Object> resultMap = new HashMap<String,Object>();
 		Study study = ControllerUtil.findStudy(pRequest, getStudyService());
 
@@ -256,6 +256,7 @@
 	protected ModelAndView processFormSubmission(HttpServletRequest request,
 			HttpServletResponse response, Object command, BindException bindException)
 			throws Exception {
+		LOGGER.info("in processFormSubmission");
 		LOGGER.debug("processFormSubmission found study " + (Study) command);
 		return getConditionalModelAndView(request, showForm(request, response, bindException));
 	}
@@ -264,6 +265,7 @@
 	protected ModelAndView showForm(HttpServletRequest request,
 			HttpServletResponse response, BindException errors) throws Exception {
 		String pageName = request.getServletPath();
+		LOGGER.info("in showForm");
 //		LOGGER.debug("GetServletPath returns " + pageName);
 		if (pageName == null) {
 			pageName = getDefaultPage();
@@ -408,6 +410,7 @@
 	// The code should be shared
 	private void setupForPhyloWidget(HttpServletRequest request) {
 		// set up NEWICKSTRINGNAME and NEWICKSTRINGSMAP
+		LOGGER.info("setupForPhyloWidget");
 		String separator = "@";
 		Map<String, String> treeMap = new HashMap<String, String>();
 		String newickStringName = null;
@@ -428,6 +431,7 @@
 	 * The code should be shared
 	 */
 	private String getMapKey(PhyloTree pTree) {
+		LOGGER.info("in getMapKey");
 		StringBuilder key = new StringBuilder("TreeId: " + pTree.getId());
 		if (!TreebaseUtil.isEmpty(pTree.getLabel())) {
 			key.append("|").append(pTree.getLabel());
@@ -446,58 +450,72 @@
 	}
 
 	public String getDefaultPage() {
+		LOGGER.info("in getDefaultPage");
 		return defaultPage;
 	}
 
 	public void setDefaultPage(String defaultView) {
+		LOGGER.info("in setDefaultPage");
 		this.defaultPage = defaultView;
 	}
 
 	public StudyService getStudyService() {
+		LOGGER.info("in getStudyService");
 		return studyService;
 	}
 
 	public void setStudyService(StudyService studyService) {
+		LOGGER.info("in setStudyService");
 		this.studyService = studyService;
 	}
 
 	public MatrixService getMatrixService() {
+		LOGGER.info("in getMatrixService");
 		return matrixService;
 	}
 
 	public void setMatrixService(MatrixService matrixService) {
+		LOGGER.info("in setMatrixService");
 		this.matrixService = matrixService;
 	}
 
 	public MatrixRowService getMatrixRowService() {
+		LOGGER.info("in getMatrixRowService");
 		return matrixRowService;
 	}
 
 	public void setMatrixRowService(MatrixRowService matrixRowService) {
+		LOGGER.info("in setMatrixRowService");
 		this.matrixRowService = matrixRowService;
 	}
 
 	public PhyloTreeService getPhyloTreeService() {
+		LOGGER.info("in getPhyloTreeService");
 		return phyloTreeService;
 	}
 
 	public void setPhyloTreeService(PhyloTreeService phyloTreeService) {
+		LOGGER.info("in setPhyloTreeService");
 		this.phyloTreeService = phyloTreeService;
 	}
 
 	public AnalysisService getAnalysisService() {
+		LOGGER.info("in getAnalysisService");
 		return analysisService;
 	}
 
 	public void setAnalysisService(AnalysisService analysisService) {
+		LOGGER.info("in setAnalysisService");
 		this.analysisService = analysisService;
 	}
 
 	public TaxonLabelService getTaxonLabelService() {
+		LOGGER.info("in getTaxonLabelService");
 		return taxonLabelService;
 	}
 
 	public void setTaxonLabelService(TaxonLabelService taxonLabelService) {
+		LOGGER.info("in setTaxonLabelService");
 		this.taxonLabelService = taxonLabelService;
 	}
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Treebase-guts] SF.net SVN: treebase:[439] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/SearchSummaryController.java

From: <rv...@us...> - 2010-01-14 16:12:34

Revision: 439
          http://treebase.svn.sourceforge.net/treebase/?rev=439&view=rev
Author:   rvos
Date:     2010-01-14 16:12:28 +0000 (Thu, 14 Jan 2010)

Log Message:
-----------
Now throws exception if access isn't granted through x-access-code

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java	2010-01-14 15:59:53 UTC (rev 438)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java	2010-01-14 16:12:28 UTC (rev 439)
@@ -70,6 +70,7 @@
 	
 	class NoStudySpecifiedError extends Error { }
 	class UnknownStudyError extends Error { }
+	class RestrictedStudyError extends Error { }
 	
 	Study theStudy = null;
 	CharacterMatrix theMatrix = null; // XXX What if it isn't a CharacterMatrix?
@@ -90,6 +91,13 @@
 			theStudy = getStudyService().findByID(studyID);
 			if (theStudy == null) { throw new UnknownStudyError(); }
 			LOGGER.debug("formBackingObject found study " + theStudy);
+			if ( ! theStudy.isPublished() ) {
+				String hashedId = theStudy.getNamespacedGUID().getHashedIDString();
+				String xAccessCode = request.getParameter(Constants.X_ACCESS_CODE);
+				if ( ! hashedId.equals(xAccessCode) ) {
+					throw new RestrictedStudyError();
+				}
+			}
 		}
 		
 		theTree = null;


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Treebase-guts] SF.net SVN: treebase:[444] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/SearchSummaryController.java

From: <rv...@us...> - 2010-01-15 13:32:14

Revision: 444
          http://treebase.svn.sourceforge.net/treebase/?rev=444&view=rev
Author:   rvos
Date:     2010-01-15 13:32:07 +0000 (Fri, 15 Jan 2010)

Log Message:
-----------
Removed early throwing of RestrictedStudyError

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java	2010-01-15 12:41:32 UTC (rev 443)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java	2010-01-15 13:32:07 UTC (rev 444)
@@ -91,6 +91,7 @@
 			theStudy = getStudyService().findByID(studyID);
 			if (theStudy == null) { throw new UnknownStudyError(); }
 			LOGGER.debug("formBackingObject found study " + theStudy);
+			/*
 			if ( ! theStudy.isPublished() ) {
 				String hashedId = theStudy.getNamespacedGUID().getHashedIDString();
 				String xAccessCode = request.getParameter(Constants.X_ACCESS_CODE);
@@ -98,6 +99,7 @@
 					throw new RestrictedStudyError();
 				}
 			}
+			*/
 		}
 		
 		theTree = null;


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Treebase-guts] SF.net SVN: treebase:[445] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/SearchSummaryController.java

From: <rv...@us...> - 2010-01-15 13:56:35

Revision: 445
          http://treebase.svn.sourceforge.net/treebase/?rev=445&view=rev
Author:   rvos
Date:     2010-01-15 13:56:27 +0000 (Fri, 15 Jan 2010)

Log Message:
-----------
Now a priori explicitly denies access to unpublished studies.

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java	2010-01-15 13:32:07 UTC (rev 444)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java	2010-01-15 13:56:27 UTC (rev 445)
@@ -91,15 +91,13 @@
 			theStudy = getStudyService().findByID(studyID);
 			if (theStudy == null) { throw new UnknownStudyError(); }
 			LOGGER.debug("formBackingObject found study " + theStudy);
-			/*
 			if ( ! theStudy.isPublished() ) {
-				String hashedId = theStudy.getNamespacedGUID().getHashedIDString();
-				String xAccessCode = request.getParameter(Constants.X_ACCESS_CODE);
-				if ( ! hashedId.equals(xAccessCode) ) {
-					throw new RestrictedStudyError();
-				}
+				// we assume access is denied, unless specifically granted!
+				setAuthorizationChecked(false);
 			}
-			*/
+			else {
+				setAuthorizationChecked(true);
+			}
 		}
 		
 		theTree = null;


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Treebase-guts] SF.net SVN: treebase:[697] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/SearchSummaryController.java

From: <hl...@us...> - 2010-05-24 16:54:34

Revision: 697
          http://treebase.svn.sourceforge.net/treebase/?rev=697&view=rev
Author:   hlapp
Date:     2010-05-24 16:54:27 +0000 (Mon, 24 May 2010)

Log Message:
-----------
Fix for the null pointer exception in TaxonLabelByLabelComparator.

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java	2010-05-01 15:13:17 UTC (rev 696)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java	2010-05-24 16:54:27 UTC (rev 697)
@@ -547,7 +547,11 @@
 
 	private class TaxonLabelByLabelComparator implements Comparator<TaxonLabel> {
 		public int compare(TaxonLabel a, TaxonLabel b) {
-			return a.getTaxonLabel().compareTo(b.getTaxonLabel());
+                    String l1 = (a == null) ? "" : a.getTaxonLabel();
+                    String l2 = (b == null) ? "" : b.getTaxonLabel();
+                    if (l1 == null) l1 = "";
+                    if (l2 == null) l2 = "";
+                    return l1.compareTo(l2);
 		}	
 	}
 }
\ No newline at end of file


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.