Improve logging

Author: bbimber

GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysManager.java

@@ -320,7 +320,7 @@ private void processSet(String assayType, Map<Integer, List<Map<String, Object>>
                 }
                 catch (Exception e)
                 {
-                    _log.error(e);
+                    _log.error(e.getMessage(), e);
                     throw new IllegalArgumentException(e.getMessage());
                 }
             }

mGAP/src/org/labkey/mgap/mGAPController.java

@@ -877,7 +877,7 @@ public boolean handlePost(Object o, BindException errors) throws Exception
             }
             catch (Exception e)
             {
-                _log.error(e);
+                _log.error(e.getMessage(), e);
                 throw e;
             }
 

primeseq/src/org/labkey/primeseq/PrimeseqController.java

@@ -476,7 +476,7 @@ else if (!sf.lookupContainer().hasPermission(getUser(), ReadPermission.class))
                 catch (IOException | PipelineJobException e)
                 {
                     errors.reject(ERROR_MSG, "Unable to read pipeline JSON");
-                    _log.error(e);
+                    _log.error(e.getMessage(), e);
                     return null;
                 }
             }

primeseq/src/org/labkey/primeseq/pipeline/ClusterMaintenanceTask.java

@@ -93,13 +93,13 @@ public void run(Logger log)
             {
                 RemoteWorkTask task = new RemoteWorkTask(jobGuids);
                 PipeRoot pr = PipelineService.get().getPipelineRootSetting(ContainerManager.getHomeContainer());
-                File subdir = new File(pr.getRootPath(), "clusterMaintenance");
+                File subdir = FileUtil.appendName(pr.getRootPath(), "clusterMaintenance");
                 if (!subdir.exists())
                 {
                     subdir.mkdirs();
                 }
 
-                File logFile = new File(subdir, "Maintenance-" + engine.getType() + "." + FileUtil.getTimestamp() + ".log");
+                File logFile = FileUtil.appendName(subdir, "Maintenance-" + engine.getType() + "." + FileUtil.getTimestamp() + ".log");
 
                 jr.execute(new Job()
                 {
@@ -113,7 +113,7 @@ public void run()
                         }
                         catch (PipelineValidationException e)
                         {
-                            _log.error(e);
+                            _log.error(e.getMessage(), e);
                         }
                     }
                 });
@@ -209,7 +209,7 @@ private void inspectFolder(Logger log, File workDirBase)
                         }
                         catch (IOException e)
                         {
-                            _log.error(e);
+                            _log.error(e.getMessage(), e);
                             continue;
                         }