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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. |
From: <rv...@us...> - 2010-01-14 14:56:45
|
Revision: 437 http://treebase.svn.sourceforge.net/treebase/?rev=437&view=rev Author: rvos Date: 2010-01-14 14:56:33 +0000 (Thu, 14 Jan 2010) Log Message: ----------- Added more logging messages. Modified Paths: -------------- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java =================================================================== --- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-14 14:53:30 UTC (rev 436) +++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-14 14:56:33 UTC (rev 437) @@ -165,9 +165,15 @@ HttpServletResponse pResponse, BindException pBindException, Map pMap) throws Exception { - if (isAuthorizationChecked() || isReviewerAccessGranted(pRequest)) { + if ( isAuthorizationChecked() ) { + LOGGER.info("returning supplied ModelAndView because access was granted explicitly"); return super.showForm(pRequest, pResponse, pBindException, pMap); + } + if (isReviewerAccessGranted(pRequest)) { + LOGGER.info("returning supplied ModelAndView because reviewer access was granted"); + return super.showForm(pRequest, pResponse, pBindException, pMap); } else { + LOGGER.info("returning AUTHORIZATION_VIOLATION_VIEW"); return new ModelAndView(AUTHORIZATION_VIOLATION_VIEW); } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <rv...@us...> - 2010-01-14 14:53:37
|
Revision: 436 http://treebase.svn.sourceforge.net/treebase/?rev=436&view=rev Author: rvos Date: 2010-01-14 14:53:30 +0000 (Thu, 14 Jan 2010) Log Message: ----------- Commented out logging messages. Modified Paths: -------------- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java =================================================================== --- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-14 14:40:32 UTC (rev 435) +++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-14 14:53:30 UTC (rev 436) @@ -177,33 +177,33 @@ Object xAccesCodeObject = pRequest.getSession().getAttribute(Constants.X_ACCESS_CODE); if ( xAccesCodeObject != null ) { String storedHashedStudyId = xAccesCodeObject.toString(); - LOGGER.info("x-access-code="+storedHashedStudyId); + //LOGGER.info("x-access-code="+storedHashedStudyId); if ( ! TreebaseUtil.isEmpty(storedHashedStudyId) ) { Long studyId = ControllerUtil.getStudyId(pRequest); - LOGGER.info("studyId="+studyId); + //LOGGER.info("studyId="+studyId); TreebaseIDString tbidstr = new TreebaseIDString(Study.class,studyId); - LOGGER.info("TreebaseIDString="+tbidstr); + //LOGGER.info("TreebaseIDString="+tbidstr); NamespacedGUID nsguid = tbidstr.getNamespacedGUID(); - LOGGER.info("NamespacedGUID="+nsguid); + //LOGGER.info("NamespacedGUID="+nsguid); String computedHashedStudyId = nsguid.getHashedIDString(); - LOGGER.info("computedHashedStudyId="+computedHashedStudyId); + //LOGGER.info("computedHashedStudyId="+computedHashedStudyId); if ( storedHashedStudyId.equals(computedHashedStudyId) ) { reviewerAccessGranted = true; saveMessage(pRequest,"You are in reviewer access mode."); - LOGGER.info("x-access-code matches computed hashed study id"); - LOGGER.info("Reviewer access is granted"); + //LOGGER.info("x-access-code matches computed hashed study id"); + //LOGGER.info("Reviewer access is granted"); } else { - LOGGER.info("x-access-code doesn't match computed hashed study id"); - LOGGER.info("access denied"); + //LOGGER.info("x-access-code doesn't match computed hashed study id"); + //LOGGER.info("access denied"); } } else { - LOGGER.info("x-access-code is empty"); + //LOGGER.info("x-access-code is empty"); } } else { - LOGGER.info("No x-access-code parameter supplied"); + //LOGGER.info("No x-access-code parameter supplied"); } return reviewerAccessGranted; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <rv...@us...> - 2010-01-14 14:40:38
|
Revision: 435 http://treebase.svn.sourceforge.net/treebase/?rev=435&view=rev Author: rvos Date: 2010-01-14 14:40:32 +0000 (Thu, 14 Jan 2010) Log Message: ----------- Added more logging messages. Modified Paths: -------------- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java =================================================================== --- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-14 14:36:58 UTC (rev 434) +++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-14 14:40:32 UTC (rev 435) @@ -198,6 +198,9 @@ LOGGER.info("access denied"); } } + else { + LOGGER.info("x-access-code is empty"); + } } else { LOGGER.info("No x-access-code parameter supplied"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <rv...@us...> - 2010-01-14 14:37:08
|
Revision: 434 http://treebase.svn.sourceforge.net/treebase/?rev=434&view=rev Author: rvos Date: 2010-01-14 14:36:58 +0000 (Thu, 14 Jan 2010) Log Message: ----------- NPE workaround Modified Paths: -------------- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListSubmissionController.java Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListSubmissionController.java =================================================================== --- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListSubmissionController.java 2010-01-14 14:28:21 UTC (rev 433) +++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListSubmissionController.java 2010-01-14 14:36:58 UTC (rev 434) @@ -1,6 +1,10 @@ package org.cipres.treebase.web.controllers; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; + import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; @@ -8,7 +12,9 @@ import org.springframework.web.servlet.ModelAndView; import org.springframework.web.servlet.mvc.multiaction.MultiActionController; +import org.cipres.treebase.domain.admin.User; import org.cipres.treebase.domain.admin.UserService; +import org.cipres.treebase.domain.study.Submission; import org.cipres.treebase.domain.study.SubmissionService; import org.cipres.treebase.web.Constants; import org.cipres.treebase.web.util.ControllerUtil; @@ -87,8 +93,16 @@ boolean isUser = request.isUserInRole("User"); request.getSession().setAttribute("isUser", Boolean.valueOf(isUser)); - return new ModelAndView("submissionList", Constants.SUBMISSION_LIST, ControllerUtil - .getUser(request, mUserService).getSubmissionIterator()); + User user = ControllerUtil.getUser(request, mUserService); + List<Submission> submissionList = new ArrayList<Submission>(); + Iterator<Submission> submissionIterator = submissionList.iterator(); + if ( user != null ) { + submissionIterator = user.getSubmissionIterator(); + } + return new ModelAndView( + "submissionList", + Constants.SUBMISSION_LIST, + submissionIterator); } /** This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <rv...@us...> - 2010-01-14 14:28:27
|
Revision: 433 http://treebase.svn.sourceforge.net/treebase/?rev=433&view=rev Author: rvos Date: 2010-01-14 14:28:21 +0000 (Thu, 14 Jan 2010) Log Message: ----------- Added more logging messages. Modified Paths: -------------- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AddAnalyzedDataController.java trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AnalysisFormController.java trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AnalysisStepFormController.java trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DeleteStudyController.java trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTreeController.java trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SummaryController.java Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AddAnalyzedDataController.java =================================================================== --- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AddAnalyzedDataController.java 2010-01-14 14:04:24 UTC (rev 432) +++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AddAnalyzedDataController.java 2010-01-14 14:28:21 UTC (rev 433) @@ -9,6 +9,7 @@ import org.springframework.web.servlet.ModelAndView; import org.springframework.web.servlet.view.RedirectView; +import org.apache.log4j.Logger; import org.cipres.treebase.TreebaseUtil; import org.cipres.treebase.domain.admin.UserRole.TBPermission; import org.cipres.treebase.domain.matrix.Matrix; @@ -31,6 +32,7 @@ import org.cipres.treebase.web.util.ControllerUtil; public class AddAnalyzedDataController extends BaseFormController { + private static final Logger LOGGER = Logger.getLogger(AddAnalyzedDataController.class); private AnalysisService mAnalysisService; private StudyService mStudyService; private AnalysisStepService mAnalysisStepService; @@ -241,6 +243,7 @@ Study study; if (TreebaseUtil.isEmpty(submission_id)) { study = ControllerUtil.findStudy(request, mStudyService); + LOGGER.info("setAuthorizationChecked(true)"); setAuthorizationChecked(true);// This is needed in case one is clicking at Summary // link at the bottom of the menu list on the right hand // side. @@ -255,8 +258,10 @@ Long.parseLong(submission_id)); if (perm2 == TBPermission.WRITE || perm2 == TBPermission.READ_ONLY || perm2 == TBPermission.SUBMITTED_WRITE) { + LOGGER.info("setAuthorizationChecked(true)"); setAuthorizationChecked(true); } else { + LOGGER.info("setAuthorizationChecked(false)"); setAuthorizationChecked(false); return new ArticleCitation(); } Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AnalysisFormController.java =================================================================== --- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AnalysisFormController.java 2010-01-14 14:04:24 UTC (rev 432) +++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AnalysisFormController.java 2010-01-14 14:28:21 UTC (rev 433) @@ -176,9 +176,11 @@ if (TreebaseUtil.isEmpty(analysis_id)) { if (perm == TBPermission.WRITE) { + LOGGER.info("setAuthorizationChecked(true)"); setAuthorizationChecked(true); return new Analysis(); } else { + LOGGER.info("setAuthorizationChecked(false)"); setAuthorizationChecked(false); return null; } @@ -195,11 +197,12 @@ // FIXME set a session variable to hide the edit buttons. } - + LOGGER.info("setAuthorizationChecked(true)"); setAuthorizationChecked(true); return analysis; } else { LOGGER.debug("NULL CONDITION SATISFIED"); + LOGGER.info("setAuthorizationChecked(false)"); setAuthorizationChecked(false); return new Analysis(); } Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AnalysisStepFormController.java =================================================================== --- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AnalysisStepFormController.java 2010-01-14 14:04:24 UTC (rev 432) +++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AnalysisStepFormController.java 2010-01-14 14:28:21 UTC (rev 433) @@ -326,9 +326,11 @@ if (TreebaseUtil.isEmpty(analysisStep_id)) { if (perm == TBPermission.WRITE) { + LOGGER.info("setAuthorizationChecked(true)"); setAuthorizationChecked(true); return analysisStepCommand; } else { + LOGGER.info("setAuthorizationChecked(false)"); setAuthorizationChecked(false); return null; } @@ -360,14 +362,14 @@ // FIXME set a session variable to hide the edit buttons. } - + LOGGER.info("setAuthorizationChecked(true)"); setAuthorizationChecked(true); return analysisStepCommand; } else { if (LOGGER.isDebugEnabled()) { LOGGER.debug("NULL CONDITION SATISFIED"); } - + LOGGER.info("setAuthorizationChecked(false)"); setAuthorizationChecked(false); return analysisStepCommand; } Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DeleteStudyController.java =================================================================== --- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DeleteStudyController.java 2010-01-14 14:04:24 UTC (rev 432) +++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DeleteStudyController.java 2010-01-14 14:28:21 UTC (rev 433) @@ -135,8 +135,10 @@ TBPermission perm = getSubmissionService().getPermission(username, Long.parseLong(subid)); if (perm == TBPermission.WRITE) { + LOGGER.info("setAuthorizationChecked(true)"); setAuthorizationChecked(true); } else { + LOGGER.info("setAuthorizationChecked(false)"); setAuthorizationChecked(false); } Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTreeController.java =================================================================== --- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTreeController.java 2010-01-14 14:04:24 UTC (rev 432) +++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTreeController.java 2010-01-14 14:28:21 UTC (rev 433) @@ -171,6 +171,7 @@ request.getRemoteUser(), submission_id); if (perm2 == TBPermission.WRITE || perm2 == TBPermission.SUBMITTED_WRITE) { + LOGGER.info("setAuthorizationChecked(true)"); setAuthorizationChecked(true); Collection<PhyloTree> phyloTreeList = treeblock.getTreeList(); ControllerUtil.setTreeBlockId(TBID, request); @@ -178,6 +179,7 @@ // This ID has to be saved for success/cancel view. return new AGenericList<Collection<PhyloTree>>(phyloTreeList); } else { + LOGGER.info("setAuthorizationChecked(false)"); setAuthorizationChecked(false); return new AGenericList<Collection<PhyloTree>>(new ArrayList<PhyloTree>()); } Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SummaryController.java =================================================================== --- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SummaryController.java 2010-01-14 14:04:24 UTC (rev 432) +++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SummaryController.java 2010-01-14 14:28:21 UTC (rev 433) @@ -108,6 +108,7 @@ Study study; if (TreebaseUtil.isEmpty(submission_id)) { study = ControllerUtil.findStudy(request, mStudyService); + LOGGER.info("setAuthorizationChecked(true)"); setAuthorizationChecked(true);// This is needed in case one is clicking at Summary // link at the bottom of the menu list on the right hand // side. @@ -122,8 +123,10 @@ Long.parseLong(submission_id)); if (perm2 == TBPermission.WRITE || perm2 == TBPermission.READ_ONLY || perm2 == TBPermission.SUBMITTED_WRITE) { + LOGGER.info("setAuthorizationChecked(true)"); setAuthorizationChecked(true); } else { + LOGGER.info("setAuthorizationChecked(false)"); setAuthorizationChecked(false); return new ArticleCitation(); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <rv...@us...> - 2010-01-14 14:04:35
|
Revision: 432 http://treebase.svn.sourceforge.net/treebase/?rev=432&view=rev Author: rvos Date: 2010-01-14 14:04:24 +0000 (Thu, 14 Jan 2010) Log Message: ----------- Added more logging messages. Modified Paths: -------------- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java =================================================================== --- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-13 18:18:27 UTC (rev 431) +++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-14 14:04:24 UTC (rev 432) @@ -131,6 +131,7 @@ * @return */ private boolean isAuthorizationChecked() { + LOGGER.info("Checking whether explicit access is granted, value="+mAuthorizationChecked); return mAuthorizationChecked; } @@ -175,18 +176,32 @@ boolean reviewerAccessGranted = false; Object xAccesCodeObject = pRequest.getSession().getAttribute(Constants.X_ACCESS_CODE); if ( xAccesCodeObject != null ) { - String storedHashedStudyId = xAccesCodeObject.toString(); + String storedHashedStudyId = xAccesCodeObject.toString(); + LOGGER.info("x-access-code="+storedHashedStudyId); if ( ! TreebaseUtil.isEmpty(storedHashedStudyId) ) { Long studyId = ControllerUtil.getStudyId(pRequest); - TreebaseIDString treebaseIDString = new TreebaseIDString(Study.class,studyId); - NamespacedGUID namespacedGUID = treebaseIDString.getNamespacedGUID(); - String computedHashedStudyId = namespacedGUID.getHashedIDString(); + LOGGER.info("studyId="+studyId); + TreebaseIDString tbidstr = new TreebaseIDString(Study.class,studyId); + LOGGER.info("TreebaseIDString="+tbidstr); + NamespacedGUID nsguid = tbidstr.getNamespacedGUID(); + LOGGER.info("NamespacedGUID="+nsguid); + String computedHashedStudyId = nsguid.getHashedIDString(); + LOGGER.info("computedHashedStudyId="+computedHashedStudyId); if ( storedHashedStudyId.equals(computedHashedStudyId) ) { reviewerAccessGranted = true; saveMessage(pRequest,"You are in reviewer access mode."); + LOGGER.info("x-access-code matches computed hashed study id"); + LOGGER.info("Reviewer access is granted"); } + else { + LOGGER.info("x-access-code doesn't match computed hashed study id"); + LOGGER.info("access denied"); + } } } + else { + LOGGER.info("No x-access-code parameter supplied"); + } return reviewerAccessGranted; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: SourceForge.net <no...@so...> - 2010-01-13 20:37:58
|
Bugs item #2931595, was opened at 2010-01-13 15:37 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2931595&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: phylows gives access to data belonging to non-public studies Initial Comment: The phylows API, even without a special access parameter, is giving access to data from studies that are still either "in progress" or "ready" (but not "published"). For example, this URL resolves, when it ought not to: http://treebasedb-dev.nescent.org:6666/treebase-web/phylows/study/TB2:S44 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2931595&group_id=248804 |
From: SourceForge.net <no...@so...> - 2010-01-13 20:32:42
|
Bugs item #2931592, was opened at 2010-01-13 15:32 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2931592&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: data Group: None Status: Open Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Mark Dominus (mjdominus) Summary: submissions with orphaned records cannot be deleted Initial Comment: Study_id 22 and 23 have treeblock records that lack phylotree records. This causes errors in the unit tests. But additionally, we cannot delete these submission. (i.e. http://treebasedb-dev.nescent.org:8180/treebase-web/user/deleteStudy.html?submissionid=22 throws and error). Either the orphans should be deleted separately (e.g. with a SQL statement), or the deletion feature should be make capable for deleting them. The orphaned records can be found like so: SELECT tb.treeblock_id FROM study st JOIN submission sub ON (st.study_id = sub.study_id) JOIN sub_treeblock stb ON (sub.submission_id = stb.submission_id) JOIN treeblock tb ON (stb.treeblock_id = tb.treeblock_id) LEFT JOIN phylotree pt ON (pt.treeblock_id = tb.treeblock_id) WHERE pt.phylotree_id IS NULL AND st.study_id = 22 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2931592&group_id=248804 |
From: <rv...@us...> - 2010-01-13 18:18:36
|
Revision: 431 http://treebase.svn.sourceforge.net/treebase/?rev=431&view=rev Author: rvos Date: 2010-01-13 18:18:27 +0000 (Wed, 13 Jan 2010) Log Message: ----------- Added list of alternative studies to navigate to Modified Paths: -------------- trunk/treebase-web/src/main/webapp/WEB-INF/pages/errors/studyAccessFailure.jsp Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/errors/studyAccessFailure.jsp =================================================================== --- trunk/treebase-web/src/main/webapp/WEB-INF/pages/errors/studyAccessFailure.jsp 2010-01-13 18:15:21 UTC (rev 430) +++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/errors/studyAccessFailure.jsp 2010-01-13 18:18:27 UTC (rev 431) @@ -7,4 +7,6 @@ <img src="<c:url value="/images/iconWarning.gif"/>" alt="<fmt:message key="icon.warning"/>" class="icon" /> <c:out value="${requestScope.exception.message}"/> -</p> \ No newline at end of file +</p> + +<c:import url="/user/submissionList.html"/> \ No newline at end of file This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <rv...@us...> - 2010-01-13 18:15:28
|
Revision: 430 http://treebase.svn.sourceforge.net/treebase/?rev=430&view=rev Author: rvos Date: 2010-01-13 18:15:21 +0000 (Wed, 13 Jan 2010) Log Message: ----------- Removed old code. Modified Paths: -------------- trunk/treebase-web/src/main/webapp/WEB-INF/pages/errors/studyAccessFailure.jsp Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/errors/studyAccessFailure.jsp =================================================================== --- trunk/treebase-web/src/main/webapp/WEB-INF/pages/errors/studyAccessFailure.jsp 2010-01-13 18:09:36 UTC (rev 429) +++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/errors/studyAccessFailure.jsp 2010-01-13 18:15:21 UTC (rev 430) @@ -7,12 +7,4 @@ <img src="<c:url value="/images/iconWarning.gif"/>" alt="<fmt:message key="icon.warning"/>" class="icon" /> <c:out value="${requestScope.exception.message}"/> -</p> - -<c:import url="/user/submissionList.html"/> - -<!-- % -Exception ex = (Exception) request.getAttribute("exception"); -ex.printStackTrace(new java.io.PrintWriter(out)); -% --> -<!-- a href="/user/submissionList.html" onclick="history.back();return false">« Back</a --> +</p> \ No newline at end of file This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <rv...@us...> - 2010-01-13 18:09:43
|
Revision: 429 http://treebase.svn.sourceforge.net/treebase/?rev=429&view=rev Author: rvos Date: 2010-01-13 18:09:36 +0000 (Wed, 13 Jan 2010) Log Message: ----------- NPE workaround Modified Paths: -------------- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java =================================================================== --- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-13 17:57:38 UTC (rev 428) +++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-13 18:09:36 UTC (rev 429) @@ -173,15 +173,18 @@ private boolean isReviewerAccessGranted(HttpServletRequest pRequest) { boolean reviewerAccessGranted = false; - String storedHashedStudyId = pRequest.getSession().getAttribute(Constants.X_ACCESS_CODE).toString(); - if ( ! TreebaseUtil.isEmpty(storedHashedStudyId) ) { - Long studyId = ControllerUtil.getStudyId(pRequest); - TreebaseIDString treebaseIDString = new TreebaseIDString(Study.class,studyId); - NamespacedGUID namespacedGUID = treebaseIDString.getNamespacedGUID(); - String computedHashedStudyId = namespacedGUID.getHashedIDString(); - if ( storedHashedStudyId.equals(computedHashedStudyId) ) { - reviewerAccessGranted = true; - saveMessage(pRequest,"You are in reviewer access mode."); + Object xAccesCodeObject = pRequest.getSession().getAttribute(Constants.X_ACCESS_CODE); + if ( xAccesCodeObject != null ) { + String storedHashedStudyId = xAccesCodeObject.toString(); + if ( ! TreebaseUtil.isEmpty(storedHashedStudyId) ) { + Long studyId = ControllerUtil.getStudyId(pRequest); + TreebaseIDString treebaseIDString = new TreebaseIDString(Study.class,studyId); + NamespacedGUID namespacedGUID = treebaseIDString.getNamespacedGUID(); + String computedHashedStudyId = namespacedGUID.getHashedIDString(); + if ( storedHashedStudyId.equals(computedHashedStudyId) ) { + reviewerAccessGranted = true; + saveMessage(pRequest,"You are in reviewer access mode."); + } } } return reviewerAccessGranted; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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. |
From: <rv...@us...> - 2010-01-13 17:31:37
|
Revision: 427 http://treebase.svn.sourceforge.net/treebase/?rev=427&view=rev Author: rvos Date: 2010-01-13 17:31:31 +0000 (Wed, 13 Jan 2010) Log Message: ----------- Implemented getDomainName() method, which returns the domain name as specified in the treebase.properties file. This domain name is to be used in the view layer if we want to display absolute URLs that cannot be computed by the web app (e.g. if we start using PURLs). Modified Paths: -------------- trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java =================================================================== --- trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2010-01-13 17:29:26 UTC (rev 426) +++ trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2010-01-13 17:31:31 UTC (rev 427) @@ -3,6 +3,8 @@ import java.io.BufferedReader; import java.io.File; +import java.io.FileInputStream; +import java.io.FileNotFoundException; import java.io.FileReader; import java.io.IOException; import java.text.ParseException; @@ -12,6 +14,7 @@ import java.util.Collection; import java.util.Date; import java.util.Iterator; +import java.util.Properties; import java.util.TimeZone; import org.cipres.treebase.domain.study.Citation; @@ -422,6 +425,27 @@ return date + " GMT"; } + + /** + * This method returns the domain name (possibly with port number) + * which can be used to construct URLs by prefixing with "http://" + * and suffixing with the full path (e.g. "/treebase-web") + * + * @return domain name + */ + public static String getDomainName() { + Properties properties = new Properties(); + String domainName = ""; + try { + properties.load( new FileInputStream("treebase.properties") ); + domainName = properties.getProperty("treebase.domain.name"); + } catch (FileNotFoundException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + } + return domainName; + } /** * This method appends header information upon formatting to the nexus file. This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <rv...@us...> - 2010-01-13 17:29:33
|
Revision: 426 http://treebase.svn.sourceforge.net/treebase/?rev=426&view=rev Author: rvos Date: 2010-01-13 17:29:26 +0000 (Wed, 13 Jan 2010) Log Message: ----------- Implemented getConditionalModelAndView, which checks whether the supplied ModelAndView should be returned (which is the case if an x-access-granted parameter was supplied or access was explicitly granted), or an authorization violation view. Modified Paths: -------------- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java =================================================================== --- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-13 17:25:37 UTC (rev 425) +++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-13 17:29:26 UTC (rev 426) @@ -141,6 +141,22 @@ protected void setAuthorizationChecked(boolean pAuthorizationChecked) { mAuthorizationChecked = pAuthorizationChecked; } + + /** + * + * @param pRequest + * @param pModelAndView + * @return + */ + protected ModelAndView getConditionalModelAndView( + HttpServletRequest pRequest, + ModelAndView pModelAndView) { + if ( isReviewerAccessGranted(pRequest) || isAuthorizationChecked() ) { + return pModelAndView; + } else { + return new ModelAndView(AUTHORIZATION_VIOLATION_VIEW); + } + } @Override protected ModelAndView showForm( This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <rv...@us...> - 2010-01-13 17:25:44
|
Revision: 425 http://treebase.svn.sourceforge.net/treebase/?rev=425&view=rev Author: rvos Date: 2010-01-13 17:25:37 +0000 (Wed, 13 Jan 2010) Log Message: ----------- SummaryController now uses super.getConditionalModelAndView to construct the view it returns on submit. 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/SummaryController.java Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SummaryController.java =================================================================== --- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SummaryController.java 2010-01-13 17:20:49 UTC (rev 424) +++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SummaryController.java 2010-01-13 17:25:37 UTC (rev 425) @@ -92,8 +92,7 @@ HttpServletResponse response, Object command, BindException errors) throws Exception { - - return new ModelAndView(getSuccessView()); + return getConditionalModelAndView(request, new ModelAndView(getSuccessView())); } protected Object formBackingObject(HttpServletRequest request) throws ServletException { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <rv...@us...> - 2010-01-13 17:20:56
|
Revision: 424 http://treebase.svn.sourceforge.net/treebase/?rev=424&view=rev Author: rvos Date: 2010-01-13 17:20:49 +0000 (Wed, 13 Jan 2010) Log Message: ----------- Added treebase.domain.name property. This property is used to construct absolute URLs in the view layer. The domain name we want to display is not necessarily the domain on which the web application runs (e.g. we may want to display PURLs instead), which is why this is an editable property, and not something we simply compute at runtime. Modified Paths: -------------- trunk/treebase-core/src/main/resources/treebase.properties Modified: trunk/treebase-core/src/main/resources/treebase.properties =================================================================== --- trunk/treebase-core/src/main/resources/treebase.properties 2010-01-13 17:04:03 UTC (rev 423) +++ trunk/treebase-core/src/main/resources/treebase.properties 2010-01-13 17:20:49 UTC (rev 424) @@ -1,3 +1,3 @@ #options are: NexusServiceMesquite | NexusServiceNCL nexus.parser.impl=NexusServiceMesquite - +treebase.domain.name=treebase-dev.nescent.org:6666 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <vga...@us...> - 2010-01-13 17:04:12
|
Revision: 423 http://treebase.svn.sourceforge.net/treebase/?rev=423&view=rev Author: vgapeyev Date: 2010-01-13 17:04:03 +0000 (Wed, 13 Jan 2010) Log Message: ----------- Switching to use JNDI for the DataSource in the web app. The standalone apps still get their db credentials from jdbc.properties. Description of the new setup is at https://sourceforge.net/apps/mediawiki/treebase/index.php?title=Databases Modified Paths: -------------- trunk/treebase-core/src/main/java/org/cipres/treebase/core/CoreServiceLauncher.java trunk/treebase-core/src/main/resources/applicationContext-dao.xml trunk/treebase-web/src/main/webapp/WEB-INF/web.xml Added Paths: ----------- trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml trunk/treebase-core/src/main/resources/jdbc.properties.example trunk/treebase-web/src/main/webapp/META-INF/context.xml.example Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/core/CoreServiceLauncher.java =================================================================== --- trunk/treebase-core/src/main/java/org/cipres/treebase/core/CoreServiceLauncher.java 2010-01-12 18:28:42 UTC (rev 422) +++ trunk/treebase-core/src/main/java/org/cipres/treebase/core/CoreServiceLauncher.java 2010-01-13 17:04:03 UTC (rev 423) @@ -18,6 +18,7 @@ private static final Logger LOGGER = Logger.getLogger(CoreServiceLauncher.class); private static final String[] SPRING_CONFIG_FILES = new String[] {// "applicationContext.xml", + "applicationContext-db-standalone.xml", // 2010-01-12 VG "applicationContext-dao.xml", "applicationContext-service.xml", "applicationContext-standalone.xml" // 20090222 MJD Modified: trunk/treebase-core/src/main/resources/applicationContext-dao.xml =================================================================== --- trunk/treebase-core/src/main/resources/applicationContext-dao.xml 2010-01-12 18:28:42 UTC (rev 422) +++ trunk/treebase-core/src/main/resources/applicationContext-dao.xml 2010-01-13 17:04:03 UTC (rev 423) @@ -22,24 +22,31 @@ </property> </bean> + +<!-- VG 2010-01-11 instead, see applicationContext-db-webapp.xml and applicationContext-db-standalone.xml <bean id="dataSource" class="com.mchange.v2.c3p0.ComboPooledDataSource" destroy-method="close"> <property name="driverClass" value="${jdbc.driverClassName}" /> <property name="jdbcUrl" value="${jdbc.url}" /> <property name="user" value="${jdbc.username}" /> <property name="password" value="${jdbc.password}" /> <property name="minPoolSize" value="5" /> +--> <!-- reduce to expose connection leak problem, if any property name="maxPoolSize" value="100" /--> +<!-- <property name="maxPoolSize" value="10" /> <property name="initialPoolSize" value="6" /> <property name="maxIdleTime" value="3600" /> +--> <!--property name="maxIdleTime" value="9000" /--> +<!-- <property name="maxConnectionAge" value="18000" /> <property name="idleConnectionTestPeriod" value="300" /> <property name="maxIdleTimeExcessConnections" value="300" /> <property name="maxStatementsPerConnection" value="100" /> <property name="numHelperThreads" value="5" /> </bean> +--> <bean id="sessionFactory" class="org.springframework.orm.hibernate3.annotation.AnnotationSessionFactoryBean"> Added: trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml =================================================================== --- trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml (rev 0) +++ trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml 2010-01-13 17:04:03 UTC (rev 423) @@ -0,0 +1,34 @@ +<?xml version="1.0" encoding="UTF-8"?> + +<beans xmlns="http://www.springframework.org/schema/beans" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xmlns:dwr="http://www.directwebremoting.org/schema/spring-dwr" + xsi:schemaLocation="http://www.springframework.org/schema/beans + http://www.springframework.org/schema/beans/spring-beans-2.0.xsd + http://www.directwebremoting.org/schema/spring-dwr + http://www.directwebremoting.org/schema/spring-dwr-2.0.xsd" + default-autowire="no"> + + <bean id="dataSource" class="com.mchange.v2.c3p0.ComboPooledDataSource" destroy-method="close"> + <property name="driverClass" value="${jdbc.driverClassName}" /> + <property name="jdbcUrl" value="${jdbc.url}" /> + <property name="user" value="${jdbc.username}" /> + <property name="password" value="${jdbc.password}" /> + <property name="minPoolSize" value="5" /> + <!-- reduce to expose connection leak problem, if any + property name="maxPoolSize" value="100" /--> + <property name="maxPoolSize" value="10" /> + <property name="initialPoolSize" value="6" /> + <property name="maxIdleTime" value="3600" /> + <!--property name="maxIdleTime" value="9000" /--> + <property name="maxConnectionAge" value="18000" /> + <property name="idleConnectionTestPeriod" value="300" /> + <property name="maxIdleTimeExcessConnections" value="300" /> + <property name="maxStatementsPerConnection" value="100" /> + <property name="numHelperThreads" value="5" /> + </bean> + + + +</beans> + \ No newline at end of file Added: trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml =================================================================== --- trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml (rev 0) +++ trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml 2010-01-13 17:04:03 UTC (rev 423) @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> + +<beans xmlns="http://www.springframework.org/schema/beans" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xmlns:dwr="http://www.directwebremoting.org/schema/spring-dwr" + xsi:schemaLocation="http://www.springframework.org/schema/beans + http://www.springframework.org/schema/beans/spring-beans-2.0.xsd + http://www.directwebremoting.org/schema/spring-dwr + http://www.directwebremoting.org/schema/spring-dwr-2.0.xsd" + default-autowire="no"> + + <bean id="dataSource" class="org.springframework.jndi.JndiObjectFactoryBean"> + <property name="jndiName" value="java:comp/env/jdbc/TreebaseDB"/> + </bean> + +</beans> \ No newline at end of file Added: trunk/treebase-core/src/main/resources/jdbc.properties.example =================================================================== --- trunk/treebase-core/src/main/resources/jdbc.properties.example (rev 0) +++ trunk/treebase-core/src/main/resources/jdbc.properties.example 2010-01-13 17:04:03 UTC (rev 423) @@ -0,0 +1,27 @@ +#### VG 2010-01-12 DB credentials that are used by the web application are now in JNDI -- see /treebase-web/src/main/webapp/META-INF/context.xml +#### The credentials below are only used by tests and, possibly, by data importing classes in cipres.teebase.util +#### (see treebase-core/src/main/java/org/cipres/treebase/core/CoreServiceLauncher.java) + +jdbc.driverClassName=org.postgresql.Driver + +# Login credentials, obtain the actual values from +# other developers (or create your own on a fresh install). +jdbc.url=jdbc:postgresql://YOUR.SERVER.ORG/YOUR-DB +jdbc.username=YOUR_USERNAME +jdbc.password=YOUT_PASSWORD + + +# This tells our object-relational mapping libraries +# to use postgres-specific SQL dialect +hibernate.dialect=org.hibernate.dialect.PostgreSQLDialect + +# for development only: +hibernate.show_sql=false +hibernate.format_sql=true +hibernate.generate_statistics=false + +# options are: validate | update | create | create-drop +hibernate.hbm2ddl.auto= + +# Mesquite installation directory +mesquite.folder_dir=/home/rvosa/applications/mesquiteHeadless/Mesquite_Folder/ Added: trunk/treebase-web/src/main/webapp/META-INF/context.xml.example =================================================================== --- trunk/treebase-web/src/main/webapp/META-INF/context.xml.example (rev 0) +++ trunk/treebase-web/src/main/webapp/META-INF/context.xml.example 2010-01-13 17:04:03 UTC (rev 423) @@ -0,0 +1,28 @@ +<?xml version="1.0" encoding="UTF-8"?> + +<!-- An example of META-INF/context.xml - a Tomcat-specific shorthand to specify JNDI resources during development. + See http://tomcat.apache.org/tomcat-5.5-doc/jndi-datasource-examples-howto.html + --> + +<!-- Copy this file (context.xml.example) to context.xml and replace YOUR-XXX strings with suitable credentials. + (Note that context.xml is set to be ignored by SVN, so storing passwords there is safe.) + Make sure that $CATALINA_HOME/common/lib contains a postgres JDBC driver jar. + Now, dropping treebase-web.war to $CATALINA_HOME/webapps of a vanilla Tomcat should automatically create + config file $CATALINA_HOME/conf/Catalina/localhost/treebase-web.xml, + which instructs Tomcat to provide a JNDI DataSource. + FYI: If this config is created or modified by hand, it is not affected by WAR (re-)deployments. + (I.e., server-side configuration supercedes WAR-side.) +--> + +<Context reloadable="true"> + + <Resource name="jdbc/TreebaseDB" auth="Container" + type="javax.sql.DataSource" driverClassName="org.postgresql.Driver" + url="jdbc:postgresql://YOUR-URL" + username="YOUR-NAME" password="YOUR-PASS" + maxActive="20" maxIdle="10" maxWait="-1" + /> + +</Context> + + Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml =================================================================== --- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2010-01-12 18:28:42 UTC (rev 422) +++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2010-01-13 17:04:03 UTC (rev 423) @@ -18,6 +18,7 @@ <context-param> <param-name>contextConfigLocation</param-name> <param-value> + classpath*:applicationContext-db-webapp.xml, classpath*:applicationContext-dao.xml, classpath*:applicationContext-service.xml, /WEB-INF/applicationContext.xml, @@ -37,6 +38,16 @@ <param-value>en</param-value> </context-param> + + <!-- =================================================================== --> + <!-- Declarations of JNDI Resources expected from the Tomcat container --> + <!-- =================================================================== --> + <resource-ref> + <description>The JNDI DataSource of the Treebase postgres instance that should be supplied by Tomcat.</description> + <res-ref-name>jdbc/TreebaseDB</res-ref-name> + <res-type>javax.sql.DataSource</res-type> + <res-auth>Container</res-auth> + </resource-ref> <!-- ========================================================== --> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: SourceForge.net <no...@so...> - 2010-01-13 16:51:24
|
Bugs item #2931463, was opened at 2010-01-13 11:51 Message generated for change (Tracker Item Submitted) made by vgapeyev You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2931463&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: internals Group: None Status: Open Priority: 5 Private: No Submitted By: Vladimir Gapeyev (vgapeyev) Assigned to: Nobody/Anonymous (nobody) Summary: Rationalize DB connection creation: in webapp vs in tests Initial Comment: Background: There are at least three parts of TB Java code that need DB connections: the web application (WAR), the tests, and data importing utilities (in /treebase-core/src/main/java/org/cipres/treebase/util). After Jan 2010 switch to using JNDI DataSource, DB credentials needed by the webapp are specified in /treebase-web/target/treebase-web/META-INF/context.xml as a JNDI resource. DB credentials used by tests and import utilities are still read from /treebase-core/src/main/resources/jdbc.properties. (See treebase-core/src/main/java/org/cipres/treebase/core/CoreServiceLauncher.java) The corresponding Spring dataSource beans are declared in /treebase-core/src/main/resources/{applicationContext-db-webapp.xml,applicationContext-db-standalone.xml} The problems: (1) The standalone datasource still uses com.mchange.v2.c3p0.ComboPooledDataSource rather than Apache commons-dbcp supplied by Tomcat to the web app. (2) The fact that the standalone apps retrieve DB credentials from inside the code tree (jdbc.properties) is still somewhat uncomfortable. Any solution should keep it possible to specify separate DB credentials for each separate application. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2931463&group_id=248804 |
From: <rv...@us...> - 2010-01-12 18:28:55
|
Revision: 422 http://treebase.svn.sourceforge.net/treebase/?rev=422&view=rev Author: rvos Date: 2010-01-12 18:28:42 +0000 (Tue, 12 Jan 2010) Log Message: ----------- Added icons for email and reviewer permalink Modified Paths: -------------- trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp =================================================================== --- trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp 2010-01-12 18:26:19 UTC (rev 421) +++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp 2010-01-12 18:28:42 UTC (rev 422) @@ -17,7 +17,7 @@ </a> <br/> <a href="/treebase-web/phylows/<c:out value="${submission.study.phyloWSPath}"/>?x-access-code=<c:out value="${submission.study.namespacedGUID.hashedIDString}"/>&format=html"> - <img class="iconButton" alt="link" src="<fmt:message key="icons.permalink"/>" /> + <img class="iconButton" alt="link" src="<fmt:message key="icons.weblink"/>" /> Reviewer access URL: right-click and copy me </a> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <rv...@us...> - 2010-01-12 18:26:27
|
Revision: 421 http://treebase.svn.sourceforge.net/treebase/?rev=421&view=rev Author: rvos Date: 2010-01-12 18:26:19 +0000 (Tue, 12 Jan 2010) Log Message: ----------- Added icons for email and reviewer permalink Modified Paths: -------------- trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp =================================================================== --- trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp 2010-01-12 18:01:53 UTC (rev 420) +++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp 2010-01-12 18:26:19 UTC (rev 421) @@ -11,17 +11,22 @@ </legend> Submission: <c:out value="${submissionNumber}"/>, <c:out value="${studyStatus}"/>, <a href="/treebase-web/admin/changeStudyStatus.html"> Update Status</a><br/> Submission initiated: <c:out value="${initiatedDate}"/><br/> -<a href='mailto:${submission.submitter.emailAddressString}?subject=TreeBASE Submission S${submission.id}'>Contact Submitter</a><br/> +<a href='mailto:${submission.submitter.emailAddressString}?subject=TreeBASE Submission S${submission.id}'> + <img class="iconButton" alt="mail" src="<fmt:message key="icons.email"/>" /> + Contact Submitter +</a> +<br/> +<a href="/treebase-web/phylows/<c:out value="${submission.study.phyloWSPath}"/>?x-access-code=<c:out value="${submission.study.namespacedGUID.hashedIDString}"/>&format=html"> + <img class="iconButton" alt="link" src="<fmt:message key="icons.permalink"/>" /> + Reviewer access URL: right-click and copy me +</a> + <c:if test="${not empty citationsummary.study}"> <c:if test="${not empty citationsummary.study.name}"> Study name: <c:out value="${citationsummary.study.name}"/> </c:if> </c:if> -<a href="/treebase-web/phylows/<c:out value="${submission.study.phyloWSPath}"/>?x-access-code=<c:out value="${submission.study.namespacedGUID.hashedIDString}"/>&format=html"> - Reviewer access URL -</a> - <br/> <br/> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <rv...@us...> - 2010-01-12 18:02:02
|
Revision: 420 http://treebase.svn.sourceforge.net/treebase/?rev=420&view=rev Author: rvos Date: 2010-01-12 18:01:53 +0000 (Tue, 12 Jan 2010) Log Message: ----------- Added default html format specifier in reviewer access url Modified Paths: -------------- trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp =================================================================== --- trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp 2010-01-12 17:45:51 UTC (rev 419) +++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp 2010-01-12 18:01:53 UTC (rev 420) @@ -18,7 +18,7 @@ </c:if> </c:if> -<a href="/treebase-web/phylows/<c:out value="${submission.study.phyloWSPath}"/>?x-access-code=<c:out value="${submission.study.namespacedGUID.hashedIDString}"/>"> +<a href="/treebase-web/phylows/<c:out value="${submission.study.phyloWSPath}"/>?x-access-code=<c:out value="${submission.study.namespacedGUID.hashedIDString}"/>&format=html"> Reviewer access URL </a> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <rv...@us...> - 2010-01-12 17:45:57
|
Revision: 419 http://treebase.svn.sourceforge.net/treebase/?rev=419&view=rev Author: rvos Date: 2010-01-12 17:45:51 +0000 (Tue, 12 Jan 2010) Log Message: ----------- Changed JSP to get study from submission instead of citation Modified Paths: -------------- trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp =================================================================== --- trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp 2010-01-12 17:28:29 UTC (rev 418) +++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp 2010-01-12 17:45:51 UTC (rev 419) @@ -16,11 +16,12 @@ <c:if test="${not empty citationsummary.study.name}"> Study name: <c:out value="${citationsummary.study.name}"/> </c:if> - <a href="/treebase-web/phylows/<c:out value="${citationsummary.study.phyloWSPath}"/>?x-access-code=<c:out value="${citationsummary.study.namespacedGUID.hashedIDString}"/>"> - Reviewer access URL - </a> </c:if> +<a href="/treebase-web/phylows/<c:out value="${submission.study.phyloWSPath}"/>?x-access-code=<c:out value="${submission.study.namespacedGUID.hashedIDString}"/>"> + Reviewer access URL +</a> + <br/> <br/> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <rv...@us...> - 2010-01-12 17:28:36
|
Revision: 418 http://treebase.svn.sourceforge.net/treebase/?rev=418&view=rev Author: rvos Date: 2010-01-12 17:28:29 +0000 (Tue, 12 Jan 2010) Log Message: ----------- The PhyloWSController now stores the x-access-granted QUERY_STRING parameter as a session variable so that it can be referred to by other pages in the same session. Modified Paths: -------------- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java =================================================================== --- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2010-01-12 17:23:04 UTC (rev 417) +++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2010-01-12 17:28:29 UTC (rev 418) @@ -16,6 +16,7 @@ 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.web.Constants; public class PhyloWSController implements Controller { private static String ncbiBaseUrl = "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="; @@ -61,6 +62,11 @@ res.setContentType("text/plain"); String url = null; String domain = "http://" + req.getServerName() + ":" + req.getServerPort(); + if ( ! TreebaseUtil.isEmpty(req.getParameter(Constants.X_ACCESS_CODE)) ) { + req.getSession().setAttribute( + Constants.X_ACCESS_CODE, + req.getParameter(Constants.X_ACCESS_CODE)); + } try { String pathInfo = req.getPathInfo(); if ( TreebaseUtil.isEmpty(pathInfo) ) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <rv...@us...> - 2010-01-12 17:23:10
|
Revision: 417 http://treebase.svn.sourceforge.net/treebase/?rev=417&view=rev Author: rvos Date: 2010-01-12 17:23:04 +0000 (Tue, 12 Jan 2010) Log Message: ----------- Added X_ACCESS_CODE constant Modified Paths: -------------- trunk/treebase-web/src/main/java/org/cipres/treebase/web/Constants.java Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/Constants.java =================================================================== --- trunk/treebase-web/src/main/java/org/cipres/treebase/web/Constants.java 2010-01-12 17:21:50 UTC (rev 416) +++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/Constants.java 2010-01-12 17:23:04 UTC (rev 417) @@ -24,6 +24,7 @@ /* * objects to be stores in the session */ + public static final String X_ACCESS_CODE = "x-access-code"; public static final String STUDY_MAP = "studyMap"; public static final String ANALYSIS_MAP = "analysisMap"; public static final String ANALYSIS_STEP_MAP = "analysisStepMap"; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |