Page Actions: Add UserSession Info to Error and Warn logging

Add logging of authUserId, username when project id not parsable or when get exception caught at top level in Page Action.
yeastrc · May 12, 2020 · a7d26a3 · a7d26a3
1 parent 682a14e
commit a7d26a3
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Showing 11 changed files with 590 additions and 80 deletions.
diff --git a/...app/src/main/java/org/yeastrc/xlink/www/actions/ViewMergedSearchCoverageReportAction.java b/...app/src/main/java/org/yeastrc/xlink/www/actions/ViewMergedSearchCoverageReportAction.java
@@ -18,53 +18,31 @@
 import org.apache.struts.action.ActionForward;
 import org.apache.struts.action.ActionMapping;
 import org.yeastrc.xlink.www.dao.SearchDAO;
-import org.yeastrc.xlink.www.objects.ProteinSequenceVersionObject;
 import org.yeastrc.xlink.www.dto.SearchDTO;
-import org.yeastrc.xlink.www.linked_positions.CrosslinkLinkedPositions;
-import org.yeastrc.xlink.www.linked_positions.LinkedPositions_FilterExcludeLinksWith_Param;
-import org.yeastrc.xlink.www.linked_positions.LooplinkLinkedPositions;
-import org.yeastrc.xlink.www.linked_positions.UnlinkedDimerPeptideProteinMapping;
-import org.yeastrc.xlink.www.linked_positions.UnlinkedDimerPeptideProteinMapping.UnlinkedDimerPeptideProteinMappingResult;
 import org.yeastrc.xlink.www.nav_links_image_structure.PopulateRequestDataForImageAndStructureAndQC_NavLinks;
 import org.yeastrc.xlink.www.access_control.result_objects.WebSessionAuthAccessLevel;
 import org.yeastrc.xlink.www.objects.MergedSearchProtein;
-import org.yeastrc.xlink.www.objects.SearchProtein;
-import org.yeastrc.xlink.www.objects.SearchProteinCrosslink;
-import org.yeastrc.xlink.www.objects.SearchProteinCrosslinkWrapper;
-import org.yeastrc.xlink.www.objects.SearchProteinDimer;
-import org.yeastrc.xlink.www.objects.SearchProteinDimerWrapper;
-import org.yeastrc.xlink.www.objects.SearchProteinLooplink;
-import org.yeastrc.xlink.www.objects.SearchProteinLooplinkWrapper;
-import org.yeastrc.xlink.www.objects.SearchProteinUnlinked;
-import org.yeastrc.xlink.www.objects.SearchProteinUnlinkedWrapper;
 import org.yeastrc.xlink.www.searcher.ProjectIdsForProjectSearchIdsSearcher;
-import org.yeastrc.xlink.searcher_psm_peptide_cutoff_objects.SearcherCutoffValuesRootLevel;
-import org.yeastrc.xlink.searcher_psm_peptide_cutoff_objects.SearcherCutoffValuesSearchLevel;
+import org.yeastrc.xlink.www.user_session_management.UserSession;
+import org.yeastrc.xlink.www.user_session_management.UserSessionManager;
 import org.yeastrc.xlink.www.constants.StrutsGlobalForwardNames;
 import org.yeastrc.xlink.www.constants.Struts_Config_Parameter_Values_Constants;
 import org.yeastrc.xlink.www.constants.WebConstants;
 import org.yeastrc.xlink.www.exceptions.ProxlWebappDataException;
-import org.yeastrc.xlink.www.form_query_json_objects.CutoffValuesRootLevel;
 import org.yeastrc.xlink.www.form_query_json_objects.ProteinQueryJSONRoot;
-import org.yeastrc.xlink.www.form_query_json_objects.Z_CutoffValuesObjectsToOtherObjectsFactory;
-import org.yeastrc.xlink.www.form_query_json_objects.Z_CutoffValuesObjectsToOtherObjectsFactory.Z_CutoffValuesObjectsToOtherObjects_RootResult;
 import org.yeastrc.xlink.www.form_utils.GetProteinQueryJSONRootFromFormData;
 import org.yeastrc.xlink.www.forms.MergedSearchViewProteinsForm;
 import org.yeastrc.xlink.www.forms.PeptideProteinCommonForm;
-import org.yeastrc.xlink.www.objects.ProteinCoverageData;
-import org.yeastrc.xlink.www.protein_coverage.ProteinCoverageCompute;
 import org.yeastrc.xlink.www.access_control.access_control_main.GetWebSessionAuthAccessLevelForProjectIds_And_NO_ProjectId.GetWebSessionAuthAccessLevelForProjectIds_And_NO_ProjectId_Result;
 import org.yeastrc.xlink.www.access_control.access_control_main.GetWebSessionAuthAccessLevelForProjectIds_And_NO_ProjectId;
 import org.yeastrc.xlink.www.web_utils.AnyPDBFilesForProjectId;
 import org.yeastrc.xlink.www.web_utils.ExcludeLinksWith_Remove_NonUniquePSMs_Checkbox_PopRequestItems;
-import org.yeastrc.xlink.www.web_utils.ExcludeOnTaxonomyForProteinSequenceVersionIdSearchId;
 import org.yeastrc.xlink.www.web_utils.GetAnnotationDisplayUserSelectionDetailsData;
 import org.yeastrc.xlink.www.web_utils.GetMinimumPSMsDefaultForProject_PutInRequestScope;
 import org.yeastrc.xlink.www.web_utils.GetPageHeaderData;
 import org.yeastrc.xlink.www.web_utils.GetSearchDetailsData;
 import org.yeastrc.xlink.www.web_utils.ProjectSearchIdsSearchIds_SetRequestParameter;
 import org.yeastrc.xlink.www.web_utils.ProteinListingTooltipConfigUtil;
-import org.yeastrc.xlink.www.web_utils.TaxonomiesForSearchOrSearches;
 import org.yeastrc.xlink.www.web_utils.URLEncodeDecodeAURL;
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
@@ -83,6 +61,8 @@ public ActionForward execute( ActionMapping mapping,
 			  HttpServletRequest request,
 			  HttpServletResponse response ) throws Exception {
 
+		Integer projectId = null;
+
 		//  Detect which Struts action mapping was called by examining the value of the "parameter" attribute
 		//     accessed by calling mapping.getParameter()
 		String strutsActionMappingParameter = mapping.getParameter();
@@ -119,7 +99,9 @@ public ActionForward execute( ActionMapping mapping,
 				//  Invalid request, searches across projects
 				return mapping.findForward( StrutsGlobalForwardNames.INVALID_REQUEST_SEARCHES_ACROSS_PROJECTS );
 			}
-			int projectId = projectIdsFromSearchIds.get( 0 );
+
+			projectId = projectIdsFromSearchIds.get( 0 );
+
 			request.setAttribute( "projectId", projectId ); 
 			request.setAttribute( "project_id", projectId );
 			///////////////////////
@@ -265,14 +247,63 @@ public int compare(SearchDTO o1, SearchDTO o2) {
 			PopulateRequestDataForImageAndStructureAndQC_NavLinks.getInstance()
 			.populateRequestDataForImageAndStructureNavLinksForProtein( proteinQueryJSONRoot, projectId, authAccessLevel, form, request );
 			//////////////////////////////////////
+
 			return mapping.findForward( "Success" );
+
 		} catch ( ProxlWebappDataException e ) {
-			String msg = "Exception processing request data";
+
+			Integer authUserId = null;
+			Integer userMgmtUserId = null;
+			String username = null;
+
+			try {	
+				UserSession userSession = UserSessionManager.getSinglesonInstance().getUserSession(request);
+
+				if ( userSession != null ) {
+
+					authUserId = userSession.getAuthUserId();
+					userMgmtUserId = userSession.getUserMgmtUserId();
+					username = userSession.getUsername();
+				}	
+			} catch ( Exception e2 ) {
+				log.error( "In Main } catch ( Exception e ) {: Error getting User Id and Username: ", e2 );
+			}
+
+			String msg = "Exception processing request data. authUserId (null if no session): " 
+					+ authUserId
+					+ ", userMgmtUserId (null if no session): " + userMgmtUserId
+					+ ", username (null if no session): " + username
+					+ e.toString();
 			log.error( msg, e );
+
 			return mapping.findForward( StrutsGlobalForwardNames.INVALID_REQUEST_DATA );
+
 		} catch ( Exception e ) {
-			String msg = "Exception caught: " + e.toString();
+
+			Integer authUserId = null;
+			Integer userMgmtUserId = null;
+			String username = null;
+
+			try {	
+				UserSession userSession = UserSessionManager.getSinglesonInstance().getUserSession(request);
+
+				if ( userSession != null ) {
+
+					authUserId = userSession.getAuthUserId();
+					userMgmtUserId = userSession.getUserMgmtUserId();
+					username = userSession.getUsername();
+				}	
+			} catch ( Exception e2 ) {
+				log.error( "In Main } catch ( Exception e ) {: Error getting User Id and Username: ", e2 );
+			}
+
+			String msg = "Exception caught. authUserId (null if no session): " 
+					+ authUserId
+					+ ", userMgmtUserId (null if no session): " + userMgmtUserId
+					+ ", username (null if no session): " + username
+					+ e.toString();
 			log.error( msg, e );
+
 			throw e;
 		}
 	}

diff --git a/proxl_web_app/src/main/java/org/yeastrc/xlink/www/actions/ViewMergedSearchImageAction.java b/proxl_web_app/src/main/java/org/yeastrc/xlink/www/actions/ViewMergedSearchImageAction.java
@@ -20,17 +20,17 @@
 import org.yeastrc.xlink.www.dao.SearchDAO;
 import org.yeastrc.xlink.www.dto.SearchDTO;
 import org.yeastrc.xlink.www.dao.ConfigSystemDAO;
-import org.yeastrc.xlink.www.form_query_json_objects.CutoffValuesRootLevel;
 import org.yeastrc.xlink.www.form_query_json_objects.ImageStructure_QC_QueryJSONRoot;
 import org.yeastrc.xlink.www.forms.MergedSearchViewProteinsForm;
 import org.yeastrc.xlink.www.forms.PeptideProteinCommonForm;
 import org.yeastrc.xlink.www.access_control.result_objects.WebSessionAuthAccessLevel;
 import org.yeastrc.xlink.www.constants.ConfigSystemsKeysConstants;
 import org.yeastrc.xlink.www.constants.StrutsGlobalForwardNames;
 import org.yeastrc.xlink.www.constants.WebConstants;
-import org.yeastrc.xlink.www.cutoff_processing_web.GetDefaultPsmPeptideCutoffs;
 import org.yeastrc.xlink.www.cutoff_processing_web.Set__A_QueryBase_JSONRoot__Defaults;
 import org.yeastrc.xlink.www.searcher.ProjectIdsForProjectSearchIdsSearcher;
+import org.yeastrc.xlink.www.user_session_management.UserSession;
+import org.yeastrc.xlink.www.user_session_management.UserSessionManager;
 import org.yeastrc.xlink.www.access_control.access_control_main.GetWebSessionAuthAccessLevelForProjectIds_And_NO_ProjectId.GetWebSessionAuthAccessLevelForProjectIds_And_NO_ProjectId_Result;
 import org.yeastrc.xlink.www.access_control.access_control_main.GetWebSessionAuthAccessLevelForProjectIds_And_NO_ProjectId;
 import org.yeastrc.xlink.www.web_utils.AnyPDBFilesForProjectId;
@@ -57,6 +57,9 @@ public ActionForward execute( ActionMapping mapping,
 			  ActionForm actionForm,
 			  HttpServletRequest request,
 			  HttpServletResponse response ) throws Exception {
+
+		Integer projectId = null;
+
 		try {
 			MergedSearchViewProteinsForm form = (MergedSearchViewProteinsForm) actionForm;
 			int[] projectSearchIdsFromForm = form.getProjectSearchId();
@@ -85,7 +88,9 @@ public ActionForward execute( ActionMapping mapping,
 				//  Invalid request, searches across projects
 				return mapping.findForward( StrutsGlobalForwardNames.INVALID_REQUEST_SEARCHES_ACROSS_PROJECTS );
 			}
-			int projectId = projectIdsFromSearchIds.get( 0 );
+
+			projectId = projectIdsFromSearchIds.get( 0 );
+
 			request.setAttribute( "projectId", projectId ); 
 			request.setAttribute( "project_id", projectId );
 			///////////////////////
@@ -230,8 +235,31 @@ public int compare(SearchDTO o1, SearchDTO o2) {
 			return mapping.findForward( "Success" );
 
 		} catch ( Exception e ) {
-			String msg = "Exception caught: " + e.toString();
+
+			Integer authUserId = null;
+			Integer userMgmtUserId = null;
+			String username = null;
+
+			try {	
+				UserSession userSession = UserSessionManager.getSinglesonInstance().getUserSession(request);
+
+				if ( userSession != null ) {
+
+					authUserId = userSession.getAuthUserId();
+					userMgmtUserId = userSession.getUserMgmtUserId();
+					username = userSession.getUsername();
+				}	
+			} catch ( Exception e2 ) {
+				log.error( "In Main } catch ( Exception e ) {: Error getting User Id and Username: ", e2 );
+			}
+
+			String msg = "Exception caught. authUserId (null if no session): " 
+					+ authUserId
+					+ ", userMgmtUserId (null if no session): " + userMgmtUserId
+					+ ", username (null if no session): " + username
+					+ e.toString();
 			log.error( msg, e );
+
 			throw e;
 		}
 	}

diff --git a/...l_web_app/src/main/java/org/yeastrc/xlink/www/actions/ViewMergedSearchPeptidesAction.java b/...l_web_app/src/main/java/org/yeastrc/xlink/www/actions/ViewMergedSearchPeptidesAction.java
@@ -24,6 +24,8 @@
 import org.yeastrc.xlink.www.access_control.result_objects.WebSessionAuthAccessLevel;
 import org.yeastrc.xlink.www.searcher.ProjectIdsForProjectSearchIdsSearcher;
 import org.yeastrc.xlink.www.searcher.SearchModMassDistinctSearcher;
+import org.yeastrc.xlink.www.user_session_management.UserSession;
+import org.yeastrc.xlink.www.user_session_management.UserSessionManager;
 import org.yeastrc.xlink.www.constants.PeptideViewLinkTypesConstants;
 import org.yeastrc.xlink.www.constants.StrutsGlobalForwardNames;
 import org.yeastrc.xlink.www.constants.WebConstants;
@@ -72,6 +74,9 @@ public ActionForward execute( ActionMapping mapping,
 			webappTiming = WebappTiming.getInstance( log );
 			request.setAttribute( "webappTiming", webappTiming );
 		}
+
+		Integer projectId = null;
+
 		try {
 			// our form
 			MergedSearchViewPeptidesForm form = (MergedSearchViewPeptidesForm) actionForm;
@@ -102,7 +107,9 @@ public ActionForward execute( ActionMapping mapping,
 				//  Invalid request, searches across projects
 				return mapping.findForward( StrutsGlobalForwardNames.INVALID_REQUEST_SEARCHES_ACROSS_PROJECTS );
 			}
-			int projectId = projectIdsFromSearchIds.get( 0 );
+
+			projectId = projectIdsFromSearchIds.get( 0 );
+
 			request.setAttribute( "projectId", projectId );
 			request.setAttribute( "project_id", projectId );
 			///////////////////////
@@ -282,14 +289,64 @@ public int compare(SearchDTO o1, SearchDTO o2) {
 			if ( webappTiming != null ) {
 				webappTiming.markPoint( "Before send to JSP" );
 			}
+
 			return mapping.findForward( "Success" );
+
+
 		} catch ( ProxlWebappDataException e ) {
-			String msg = "Exception processing request data";
+
+			Integer authUserId = null;
+			Integer userMgmtUserId = null;
+			String username = null;
+
+			try {	
+				UserSession userSession = UserSessionManager.getSinglesonInstance().getUserSession(request);
+
+				if ( userSession != null ) {
+
+					authUserId = userSession.getAuthUserId();
+					userMgmtUserId = userSession.getUserMgmtUserId();
+					username = userSession.getUsername();
+				}	
+			} catch ( Exception e2 ) {
+				log.error( "In Main } catch ( Exception e ) {: Error getting User Id and Username: ", e2 );
+			}
+
+			String msg = "Exception processing request data. authUserId (null if no session): " 
+					+ authUserId
+					+ ", userMgmtUserId (null if no session): " + userMgmtUserId
+					+ ", username (null if no session): " + username
+					+ e.toString();
 			log.error( msg, e );
+
 			return mapping.findForward( StrutsGlobalForwardNames.INVALID_REQUEST_DATA );
+
 		} catch ( Exception e ) {
-			String msg = "Exception caught: " + e.toString();
+
+			Integer authUserId = null;
+			Integer userMgmtUserId = null;
+			String username = null;
+
+			try {	
+				UserSession userSession = UserSessionManager.getSinglesonInstance().getUserSession(request);
+
+				if ( userSession != null ) {
+
+					authUserId = userSession.getAuthUserId();
+					userMgmtUserId = userSession.getUserMgmtUserId();
+					username = userSession.getUsername();
+				}	
+			} catch ( Exception e2 ) {
+				log.error( "In Main } catch ( Exception e ) {: Error getting User Id and Username: ", e2 );
+			}
+
+			String msg = "Exception caught. authUserId (null if no session): " 
+					+ authUserId
+					+ ", userMgmtUserId (null if no session): " + userMgmtUserId
+					+ ", username (null if no session): " + username
+					+ e.toString();
 			log.error( msg, e );
+
 			throw e;
 		}
 	}