Merge pull request #836 from virtualcell/834-refine-database-logging

refine database logging, and Biomodel saves
virtualcell · Mar 17, 2023 · aca89dd · aca89dd
2 parents 75037aa + 92d098a
commit aca89dd
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Showing 146 changed files with 653 additions and 462 deletions.
diff --git a/docker/build/vcell-api.log4j.xml b/docker/build/vcell-api.log4j.xml
@@ -18,7 +18,7 @@
     </Root>
     <!--    <Logger name="org.vcell" level="warn" />-->
     <!--    <Logger name="cbit.vcell" level="warn" />-->
-    <!--    <Logger name="cbit.vcell.modeldb" level="warn" />-->
+            <Logger name="cbit.vcell.modeldb" level="debug" />
     <!--    <Logger name="cbit.vcell.message.server.cmd" level="debug" />-->
     <!--    <Logger name="org.vcell.util.exe" level="debug" />-->
     <!--    <Logger name="org.vcell.util.CommentStringTokenizer" level="warn" />-->

diff --git a/docker/build/vcell-data.log4j.xml b/docker/build/vcell-data.log4j.xml
@@ -18,7 +18,7 @@
     </Root>
 <!--    <Logger name="org.vcell" level="warn" />-->
 <!--    <Logger name="cbit.vcell" level="warn" />-->
-<!--    <Logger name="cbit.vcell.modeldb" level="warn" />-->
+        <Logger name="cbit.vcell.modeldb" level="debug" />
 <!--    <Logger name="cbit.vcell.message.server.cmd" level="debug" />-->
 <!--    <Logger name="org.vcell.util.exe" level="debug" />-->
 <!--    <Logger name="org.vcell.util.CommentStringTokenizer" level="warn" />-->

diff --git a/docker/build/vcell-db.log4j.xml b/docker/build/vcell-db.log4j.xml
@@ -18,7 +18,7 @@
     </Root>
 <!--    <Logger name="org.vcell" level="warn" />-->
 <!--    <Logger name="cbit.vcell" level="warn" />-->
-<!--    <Logger name="cbit.vcell.modeldb" level="warn" />-->
+        <Logger name="cbit.vcell.modeldb" level="debug" />
 <!--    <Logger name="cbit.vcell.message.server.cmd" level="debug" />-->
 <!--    <Logger name="org.vcell.util.exe" level="debug" />-->
 <!--    <Logger name="org.vcell.util.CommentStringTokenizer" level="warn" />-->

diff --git a/docker/build/vcell-sched.log4j.xml b/docker/build/vcell-sched.log4j.xml
@@ -18,7 +18,7 @@
     </Root>
 <!--    <Logger name="org.vcell" level="warn" />-->
 <!--    <Logger name="cbit.vcell" level="warn" />-->
-<!--    <Logger name="cbit.vcell.modeldb" level="warn" />-->
+        <Logger name="cbit.vcell.modeldb" level="debug" />
 <!--    <Logger name="cbit.vcell.message.server.cmd" level="warn" />-->
 <!--    <Logger name="org.vcell.util.exe" level="warn" />-->
 <!--    <Logger name="org.vcell.util.CommentStringTokenizer" level="warn" />-->

diff --git a/docker/build/vcell-submit.log4j.xml b/docker/build/vcell-submit.log4j.xml
@@ -22,7 +22,7 @@
 <!--    <Logger name="cbit.vcell.mongodb" level="trace" />-->
 <!--    <Logger name="org.vcell" level="warn" />-->
 <!--    <Logger name="cbit.vcell" level="warn" />-->
-<!--    <Logger name="cbit.vcell.modeldb" level="warn" />-->
+        <Logger name="cbit.vcell.modeldb" level="debug" />
 <!--    <Logger name="cbit.vcell.message.server.cmd" level="warn" />-->
 <!--    <Logger name="org.vcell.util.exe" level="warn" />-->
 <!--    <Logger name="org.vcell.util.CommentStringTokenizer" level="warn" />-->

diff --git a/docker/build/vcell-web.log4j.xml b/docker/build/vcell-web.log4j.xml
@@ -18,7 +18,7 @@
     </Root>
 <!--    <Logger name="org.vcell" level="warn" />-->
 <!--    <Logger name="cbit.vcell" level="warn" />-->
-<!--    <Logger name="cbit.vcell.modeldb" level="warn" />-->
+        <Logger name="cbit.vcell.modeldb" level="debug" />
 <!--    <Logger name="cbit.vcell.message.server.cmd" level="debug" />-->
 <!--    <Logger name="org.vcell.util.exe" level="debug" />-->
 <!--    <Logger name="org.vcell.util.CommentStringTokenizer" level="warn" />-->

diff --git a/vcell-admin/src/main/java/org/vcell/stochtest/StochtestDbUtils.java b/vcell-admin/src/main/java/org/vcell/stochtest/StochtestDbUtils.java
@@ -3,6 +3,9 @@
 import java.sql.ResultSet;
 import java.sql.SQLException;
 
+import cbit.vcell.modeldb.DbDriver;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.vcell.db.ConnectionFactory;
 import org.vcell.stochtest.TimeSeriesMultitrialData.SummaryStatistics;
 import org.vcell.util.DataAccessException;
@@ -14,6 +17,7 @@
 import cbit.vcell.modeldb.StochtestTable;
 
 public class StochtestDbUtils {
+	private static final Logger lg = LogManager.getLogger(StochtestDbUtils.class);
 
 	public static StochtestRun getStochtestRun(ConnectionFactory conFactory, KeyValue stochtestRunKey) throws IllegalArgumentException, SQLException, DataAccessException {
 
@@ -112,11 +116,13 @@ public static void finalizeAcceptedStochtestRun(ConnectionFactory conFactory, St
 								stochtestRunTable.networkGenProbs.getUnqualifiedColName() + " = " + networkGenProbsRHS + " " +
 						" WHERE "+stochtestRunTable.id.getUnqualifiedColName()+" = " + acceptedStochtestRun.key.toString();
 				stmt = con.createStatement();
-System.out.println(sql);
-			    int numrows = stmt.executeUpdate(sql);
-			    if (numrows != 1){
-			    	throw new DataAccessException("failed to update mathgen status for id = "+acceptedStochtestRun.key);
-			    }
+				if (lg.isDebugEnabled()) {
+					lg.debug("executeUpdate() SQL: '" + sql + "'", new DbDriver.StackTraceGenerationException());
+				}
+				int numrows = stmt.executeUpdate(sql); // jcs: added logging
+				if (numrows != 1) {
+					throw new DataAccessException("failed to update mathgen status for id = " + acceptedStochtestRun.key);
+				}
 			} finally {
 				if (stmt != null) {
 					stmt.close();
@@ -171,11 +177,13 @@ public static void finalizeAcceptedStochtestCompare(ConnectionFactory conFactory
 					}
 					sql += " WHERE "+stochtestCompareTable.id.getUnqualifiedColName()+" = " + acceptedStochtestCompare.key.toString();
 				stmt = con.createStatement();
-System.out.println(sql);
-			    int numrows = stmt.executeUpdate(sql);
-			    if (numrows != 1){
-			    	throw new DataAccessException("failed to update mathgen status for id = "+acceptedStochtestCompare.key);
-			    }
+				if (lg.isDebugEnabled()) {
+					lg.debug("executeUpdate() SQL: '" + sql + "'", new DbDriver.StackTraceGenerationException());
+				}
+				int numrows = stmt.executeUpdate(sql); // jcs: added logging
+				if (numrows != 1) {
+					throw new DataAccessException("failed to update mathgen status for id = " + acceptedStochtestCompare.key);
+				}
 			} finally {
 				if (stmt != null) {
 					stmt.close();
@@ -262,11 +270,13 @@ public static StochtestRun acceptNextWaitingStochtestRun(ConnectionFactory conFa
 						" SET "+stochtestRunTable.status.getUnqualifiedColName() + " = " + "'"+StochtestRun.StochtestRunStatus.accepted+"'" +
 						" WHERE "+stochtestRunTable.id.getUnqualifiedColName()+" = " + stochtestRun.key.toString();
 				stmt = con.createStatement();
-System.out.println(sql);
-			    int numrows = stmt.executeUpdate(sql);
-			    if (numrows != 1){
-			    	throw new DataAccessException("failed to update mathgen status for id = "+stochtestRun.key);
-			    }
+				if (lg.isDebugEnabled()) {
+					lg.debug("executeUpdate() SQL: '" + sql + "'", new DbDriver.StackTraceGenerationException());
+				}
+				int numrows = stmt.executeUpdate(sql); // jcs: added logging
+				if (numrows != 1) {
+					throw new DataAccessException("failed to update mathgen status for id = " + stochtestRun.key);
+				}
 			} finally {
 				if (stmt != null) {
 					stmt.close();
@@ -341,11 +351,13 @@ public static StochtestCompare acceptNextWaitingStochtestCompare(ConnectionFacto
 						" SET "+stochtestCompareTable.status.getUnqualifiedColName() + " = " + "'"+StochtestCompare.StochtestCompareStatus.accepted+"'" +
 						" WHERE "+stochtestCompareTable.id.getUnqualifiedColName()+" = " + stochtestCompare.key.toString();
 				stmt = con.createStatement();
-System.out.println(sql);
-			    int numrows = stmt.executeUpdate(sql);
-			    if (numrows != 1){
-			    	throw new DataAccessException("failed to update mathgen status for id = "+stochtestCompare.key);
-			    }
+				if (lg.isDebugEnabled()) {
+					lg.debug("executeUpdate() SQL: '" + sql + "'", new DbDriver.StackTraceGenerationException());
+				}
+				int numrows = stmt.executeUpdate(sql); // jcs: added logging
+				if (numrows != 1) {
+					throw new DataAccessException("failed to update mathgen status for id = " + stochtestCompare.key);
+				}
 			} finally {
 				if (stmt != null) {
 					stmt.close();

diff --git a/vcell-api/src/main/java/org/vcell/rest/UserVerifier.java b/vcell-api/src/main/java/org/vcell/rest/UserVerifier.java
@@ -169,7 +169,7 @@ public AuthenticationStatus verify(ChallengeResponse challengeResponse) {
 					return AuthenticationStatus.valid;
 				}
 			}catch (Exception e){
-				lg.error(e);
+				lg.error(e.getMessage(), e);
 				return AuthenticationStatus.invalid;
 			}
 		}else{

diff --git a/vcell-api/src/main/java/org/vcell/rest/VCellCookieAuthenticator.java b/vcell-api/src/main/java/org/vcell/rest/VCellCookieAuthenticator.java
@@ -85,7 +85,7 @@ protected int logout(Request request, Response response) {
 	        }
 
 		}catch (Exception e){
-			lg.error(e);
+			lg.error(e.getMessage(), e);
 			getLogger().log(Level.SEVERE,"MyCookieAuthenticator.logout(request,response) - exception while invalidating '"+CustomAuthHelper.ACCESS_TOKEN+"'",e);
 		}
 

diff --git a/vcell-api/src/main/java/org/vcell/rest/admin/AdminJobsRestlet.java b/vcell-api/src/main/java/org/vcell/rest/admin/AdminJobsRestlet.java
@@ -112,7 +112,7 @@ public void handle(Request req, Response response) {
 
 			} catch (Exception e) {
 				getLogger().severe("failed to retrieve job status: "+e.getMessage());
-				lg.error(e);
+				lg.error(e.getMessage(), e);
 				response.setStatus(Status.SERVER_ERROR_INTERNAL);
 				response.setEntity("failed to retrieve job status: "+e.getMessage(), MediaType.TEXT_PLAIN);
 			}

diff --git a/vcell-api/src/main/java/org/vcell/rest/events/EventsRestlet.java b/vcell-api/src/main/java/org/vcell/rest/events/EventsRestlet.java
@@ -48,7 +48,7 @@ public void handle(Request req, Response response) {
 				response.setEntity(new JsonRepresentation(eventWrappersJSON));
 			} catch (Exception e) {
 				getLogger().severe("internal error retrieving events: "+e.getMessage());
-				lg.error(e);
+				lg.error(e.getMessage(), e);
 				response.setStatus(Status.SERVER_ERROR_INTERNAL);
 				response.setEntity("internal error retrieving events: "+e.getMessage(), MediaType.TEXT_PLAIN);
 			}

diff --git a/vcell-api/src/main/java/org/vcell/rest/health/HealthRestlet.java b/vcell-api/src/main/java/org/vcell/rest/health/HealthRestlet.java
@@ -110,7 +110,7 @@ public void handle(Request req, Response response) {
 					}
 				}
 			} catch (Exception e) {
-				lg.error(e);
+				lg.error(e.getMessage(), e);
 				response.setStatus(Status.SERVER_ERROR_INTERNAL);
 				response.setEntity("failed to retrieve system health: "+e.getMessage(), MediaType.TEXT_PLAIN);
 			}

diff --git a/vcell-api/src/main/java/org/vcell/rest/health/HealthService.java b/vcell-api/src/main/java/org/vcell/rest/health/HealthService.java
@@ -309,7 +309,7 @@ public void setMessage(String message) { }
 						try {
 							vcellConnection.getSimulationController().stopSimulation(runningSimId);
 						}catch (Exception e) {
-							lg.error(e);
+							lg.error(e.getMessage(), e);
 						}
 					}
 					if (savedBioModelKey!=null) {

diff --git a/vcell-api/src/main/java/org/vcell/rest/rpc/RpcRestlet.java b/vcell-api/src/main/java/org/vcell/rest/rpc/RpcRestlet.java
@@ -89,7 +89,7 @@ public void handle(Request req, Response response) {
 			} catch (Exception e) {
 				String errMesg = "<html><body>Error RpcRestlet.handle(...) req='"+req.toString()+"' <br>err='"+e.getMessage()+"'</br>"+"</body></html>";
 				getLogger().severe(errMesg);
-				lg.error(e);
+				lg.error(e.getMessage(), e);
 				response.setStatus(Status.SERVER_ERROR_INTERNAL);
 				response.setEntity(errMesg, MediaType.TEXT_HTML);
 			}
@@ -185,7 +185,7 @@ public void handle(Request req, Response response) {
 						response.setEntity(new ByteArrayRepresentation(serializedResultObject));
 						return;
 					} catch (Exception e1) {
-						lg.error(e1);
+						lg.error(e1.getMessage(), e1);
 						//continue and send error message
 					}
 				}

diff --git a/vcell-api/src/main/java/org/vcell/rest/server/BiomodelDiagramServerResource.java b/vcell-api/src/main/java/org/vcell/rest/server/BiomodelDiagramServerResource.java
@@ -95,7 +95,7 @@ public ByteArrayRepresentation get_png() {
 			byte[] imageBytes = outputStream.toByteArray();
 			return new ByteArrayRepresentation(imageBytes, MediaType.IMAGE_PNG, imageBytes.length);
 		} catch (Exception e) {
-			lg.error(e);
+			lg.error(e.getMessage(), e);
 			throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
 		}
 	}

diff --git a/vcell-api/src/main/java/org/vcell/rest/server/BiomodelSimulationSaveServerResource.java b/vcell-api/src/main/java/org/vcell/rest/server/BiomodelSimulationSaveServerResource.java
@@ -127,7 +127,7 @@ public void save(JsonRepresentation jsonOverrides) throws JSONException {
 			lg.error(e);
 			throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "simulation not found");
 		} catch (Exception e){
-			lg.error(e);
+			lg.error(e.getMessage(), e);
 			throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
 		}
 	}

diff --git a/vcell-api/src/main/java/org/vcell/rest/server/BiomodelVCMLModelInfoResource.java b/vcell-api/src/main/java/org/vcell/rest/server/BiomodelVCMLModelInfoResource.java
@@ -100,7 +100,7 @@ public StringRepresentation get_html() {
 			StringBuffer sb = createHtml(bm);
 			return new StringRepresentation(sb.toString(), MediaType.TEXT_HTML);
 		} catch (Exception e) {
-			lg.error(e);
+			lg.error(e.getMessage(), e);
 			if(e instanceof ResourceException) {
 				throw (ResourceException)e;
 			}

diff --git a/vcell-api/src/main/java/org/vcell/rest/server/OptimizationRunServerResource.java b/vcell-api/src/main/java/org/vcell/rest/server/OptimizationRunServerResource.java
@@ -46,9 +46,9 @@ public OptSocketStreams(Socket optSocket, ObjectInputStream ois, ObjectOutputStr
 		}
 		public void closeAll(String optID) {
 			paramOptActiveSockets.remove(optID);
-			try{ois.close();}catch(Exception e2) { lg.error(e2); }
-			try{oos.close();}catch(Exception e2) { lg.error(e2); }
-			try{optSocket.close();}catch(Exception e2) { lg.error(e2); }
+			try{ois.close();}catch(Exception e2) { lg.error(e2.getMessage(), e2); }
+			try{oos.close();}catch(Exception e2) { lg.error(e2.getMessage(), e2); }
+			try{optSocket.close();}catch(Exception e2) { lg.error(e2.getMessage(), e2); }
 		}
 		public OptMessage.OptResponseMessage sendCommand(OptMessage.OptCommandMessage optCommandMessage) throws IOException,ClassNotFoundException{
 			lg.info("sending command "+optCommandMessage+" with ID="+optCommandMessage.optID);

diff --git a/vcell-api/src/main/java/org/vcell/rest/server/RestDatabaseService.java b/vcell-api/src/main/java/org/vcell/rest/server/RestDatabaseService.java
@@ -194,7 +194,7 @@ public SimulationRep startSimulation(BiomodelSimulationStartServerResource resou
 			try {
 				userLoginInfo.setUser(vcellUser);
 			} catch (Exception e) {
-				lg.error(e);
+				lg.error(e.getMessage(), e);
 				throw new DataAccessException(e.getMessage());
 			}
 			RpcSimServerProxy rpcSimServerProxy = new RpcSimServerProxy(userLoginInfo, rpcSession);
@@ -223,7 +223,7 @@ public SimulationRep stopSimulation(BiomodelSimulationStopServerResource resourc
 			try {
 				userLoginInfo.setUser(vcellUser);
 			} catch (Exception e) {
-				lg.error(e);
+				lg.error(e.getMessage(), e);
 				throw new DataAccessException(e.getMessage());
 			}
 			RpcSimServerProxy rpcSimServerProxy = new RpcSimServerProxy(userLoginInfo, rpcSession);
@@ -713,7 +713,7 @@ public SimpleJobStatus[] query(SimulationTasksServerResource resource, User vcel
 			try {
 				userLoginInfo.setUser(vcellUser);
 			} catch (Exception e) {
-				lg.error(e);
+				lg.error(e.getMessage(), e);
 				throw new DataAccessException(e.getMessage());
 			}
 			RpcSimServerProxy rpcSimServerProxy = new RpcSimServerProxy(userLoginInfo, rpcSession);
@@ -778,7 +778,7 @@ public SimulationStatusRepresentation[] query(SimulationStatusServerResource res
 			try {
 				userLoginInfo.setUser(vcellUser);
 			} catch (Exception e) {
-				lg.error(e);
+				lg.error(e.getMessage(), e);
 				throw new DataAccessException(e.getMessage());
 			}
 			RpcSimServerProxy rpcSimServerProxy = new RpcSimServerProxy(userLoginInfo, rpcSession);

diff --git a/vcell-api/src/main/java/org/vcell/rest/server/SimDataServerResource.java b/vcell-api/src/main/java/org/vcell/rest/server/SimDataServerResource.java
@@ -91,7 +91,7 @@ public Representation get_html() {
 		try {
 			simData = getSimDataRepresentation(vcellUser);
 		}catch (Exception e){
-			lg.error(e);
+			lg.error(e.getMessage(), e);
 		}
 		Map<String,Object> dataModel = new HashMap<String,Object>();
 

diff --git a/vcell-api/src/main/java/org/vcell/rest/server/TestRestServerBlinov.java b/vcell-api/src/main/java/org/vcell/rest/server/TestRestServerBlinov.java
@@ -112,7 +112,7 @@ public boolean accept(File pathname) {
 					mapBMidToBiomodelRep.put(bm.getVersion().getVersionKey().toString(), bmrep);
 				} catch (Exception e) {
 					// TODO Auto-generated catch block
-					lg.error(e);
+					lg.error(e.getMessage(), e);
 				}
 			}
 			//Create a Restlet server on local machine that will accept queries from a regular web browser
@@ -130,7 +130,7 @@ public boolean accept(File pathname) {
 			restletComponent.start();
 		} catch (Exception e) {
 			// TODO Auto-generated catch block
-			lg.error(e);
+			lg.error(e.getMessage(), e);
 		}
 
 	}

diff --git a/vcell-api/src/main/java/org/vcell/rest/users/ContactUsRestlet.java b/vcell-api/src/main/java/org/vcell/rest/users/ContactUsRestlet.java
@@ -67,7 +67,7 @@ public void handle(Request request, Response response) {
 
 				sendErrorReportEmail(errorReport);
 			} catch (Exception e) {
-				lg.error(e);
+				lg.error(e.getMessage(), e);
 				response.setStatus(Status.SERVER_ERROR_INTERNAL);
 				response.setEntity("We failed to report an error to VCell support", MediaType.TEXT_PLAIN);
 				return;

diff --git a/vcell-api/src/main/java/org/vcell/rest/users/LostPasswordRestlet.java b/vcell-api/src/main/java/org/vcell/rest/users/LostPasswordRestlet.java
@@ -51,7 +51,7 @@ public void handle(Request request, Response response) {
 				VCellApiApplication vcellApiApplication = (VCellApiApplication)getApplication();
 				vcellApiApplication.getRestDatabaseService().sendLostPassword(userid);
 			} catch (Exception e) {
-				lg.error(e);
+				lg.error(e.getMessage(), e);
 				response.setStatus(Status.SERVER_ERROR_INTERNAL);
 				response.setEntity("we failed to send a verification email for account '"+userid+"': "+e.getMessage(), MediaType.TEXT_PLAIN);
 				return;

diff --git a/vcell-api/src/main/java/org/vcell/rest/users/NewUserRestlet.java b/vcell-api/src/main/java/org/vcell/rest/users/NewUserRestlet.java
@@ -113,7 +113,7 @@ private void handleJsonRequest(Request request, Response response) {
 					request.getResourceRef().getHostIdentifier()+"/"+VCellApiApplication.NEWUSER_VERIFY+"?"+VCellApiApplication.EMAILVERIFYTOKEN_FORMNAME+"="+emailVerifyToken.getString()
 				);
 			} catch (Exception e) {
-				lg.error(e);
+				lg.error(e.getMessage(), e);
 				response.setStatus(Status.SERVER_ERROR_INTERNAL);
 				response.setEntity("we failed to send a verification email to "+newUserInfo.email, MediaType.TEXT_PLAIN);
 				return;
@@ -227,7 +227,7 @@ public void handle(Request request, Response response) {
 					request.getResourceRef().getHostIdentifier()+"/"+VCellApiApplication.NEWUSER_VERIFY+"?"+VCellApiApplication.EMAILVERIFYTOKEN_FORMNAME+"="+emailVerifyToken.getString()
 				);
 			} catch (Exception e) {
-				lg.error(e);
+				lg.error(e.getMessage(), e);
 				response.setStatus(Status.SERVER_ERROR_INTERNAL);
 				response.setEntity("we failed to send a verification email to "+newUserInfo.email, MediaType.TEXT_PLAIN);
 			}

diff --git a/vcell-client/src/main/java/org/vcell/optimization/gui/ParameterEstimationRunTaskPanel.java b/vcell-client/src/main/java/org/vcell/optimization/gui/ParameterEstimationRunTaskPanel.java
@@ -583,7 +583,7 @@ public void propertyChange(java.beans.PropertyChangeEvent evt) {
 						}
 					}
 				} catch (Exception e) {
-					lg.error(e);
+					lg.error(e.getMessage(), e);
 				}
 			}
 			if (evt.getSource() == optSolverCallbacks && (evt.getPropertyName().equals(CopasiOptSolverCallbacks.STOP_REQUESTED))) {
@@ -592,7 +592,7 @@ public void propertyChange(java.beans.PropertyChangeEvent evt) {
 						OptimizationResultSet optimizationResultSet = CopasiUtils.getOptimizationResultSet(parameterEstimationTask, optSolverCallbacks.getProgressReport());
 						parameterEstimationTask.setOptimizationResultSet(optimizationResultSet);
 					} catch (Exception e) {
-						lg.error(e);
+						lg.error(e.getMessage(), e);
 					}
 				}
 			}

diff --git a/vcell-core/src/main/java/cbit/gui/graph/GraphModel.java b/vcell-core/src/main/java/cbit/gui/graph/GraphModel.java
@@ -347,7 +347,7 @@ public void paint(java.awt.Graphics2D g) {
 			g.setColor(Color.red);
 			g.drawString("EXCEPTION IN GraphModel.paint(): " + e.getMessage(),
 					20, 20);
-			lg.error(e);
+			lg.error(e.getMessage(), e);
 			return;
 		}
 	}

diff --git a/vcell-core/src/main/java/cbit/gui/graph/groups/VCGroupManager.java b/vcell-core/src/main/java/cbit/gui/graph/groups/VCGroupManager.java
@@ -68,7 +68,7 @@ public void collapseAsNewGroup() {
 			ShapeGroupUtil.collapseGroup(groupShape);
 			graphView.repaint();
 		} catch (Exception e) {
-			lg.error(e);
+			lg.error(e.getMessage(), e);
 		}
 	}