LabKey · labkey-jeckels · May 12, 2026 · May 9, 2026
diff --git a/nirc_ehr/src/org/labkey/nirc_ehr/NIRCOrchardFileGenerator.java b/nirc_ehr/src/org/labkey/nirc_ehr/NIRCOrchardFileGenerator.java
@@ -86,7 +86,7 @@ public void run()
             if (orchardFileLocation == null)
             {
                 // Don't run if we don't have a location to write the file
-                _log.warn("Orchard file location is null, cannot generate Orchard file for taskid: " + taskid);
+                _log.warn("Orchard file location is null, cannot generate Orchard file for taskid: {}", taskid);
                 return;
             }
 

diff --git a/nirc_ehr/src/org/labkey/nirc_ehr/buttons/MarkTreatmentCompletedButton.java b/nirc_ehr/src/org/labkey/nirc_ehr/buttons/MarkTreatmentCompletedButton.java
@@ -33,7 +33,7 @@ protected String getJsHandler(TableInfo ti)
         String pkColName = null;
         if (ti.getPkColumnNames() != null && ti.getPkColumnNames().size() == 1)
         {
-            pkColName = ti.getPkColumnNames().get(0);
+            pkColName = ti.getPkColumnNames().getFirst();
         }
 
         return "NIRC_EHR.window.MarkTreatmentCompletedWindow.buttonHandler(dataRegionName, " + PageFlowUtil.jsString(_schemaName) + ", " + PageFlowUtil.jsString(_queryName) + ", " + PageFlowUtil.jsString(xtype) + ", " + PageFlowUtil.jsString(pkColName) + ");";

diff --git a/nirc_ehr/src/org/labkey/nirc_ehr/demographics/CagematesDemographicsProvider.java b/nirc_ehr/src/org/labkey/nirc_ehr/demographics/CagematesDemographicsProvider.java
@@ -45,16 +45,16 @@ public Set<String> getIdsToUpdate(Container c, String id, Map<String, Object> or
         List<Map<String, Object>> newList = newProps == null ? null : (List)newProps.get(_propName);
         Set<String> ret = new TreeSet<>();
 
-        List<String> oldAnimals = oldList == null || oldList.isEmpty() ? Collections.emptyList() : toList(oldList.get(0).get("animals"));
-        List<String> newAnimals = newList == null || newList.isEmpty() ? Collections.emptyList() : toList(newList.get(0).get("animals"));
+        List<String> oldAnimals = oldList == null || oldList.isEmpty() ? Collections.emptyList() : toList(oldList.getFirst().get("animals"));
+        List<String> newAnimals = newList == null || newList.isEmpty() ? Collections.emptyList() : toList(newList.getFirst().get("animals"));
 
         ret.addAll(newAnimals);
         ret.addAll(oldAnimals);
         ret.remove(id);
 
         if (!ret.isEmpty())
         {
-            _log.info(id + ": Triggered additional housing updates for " + ret.size() + " ids: " + StringUtils.join(ret, ";"));
+            _log.info("{}: Triggered additional housing updates for {} ids: {}", id, ret.size(), StringUtils.join(ret, ";"));
         }
 
         return ret;
@@ -75,7 +75,7 @@ else if (input instanceof String)
         }
         else
         {
-            _log.error("Unknown type: " + input.getClass().getName() + ", " + input);
+            _log.error("Unknown type: {}, {}", input.getClass().getName(), input);
             return Collections.emptyList();
         }
     }

diff --git a/nirc_ehr/src/org/labkey/nirc_ehr/notification/NIRCDeathNotification.java b/nirc_ehr/src/org/labkey/nirc_ehr/notification/NIRCDeathNotification.java
@@ -46,12 +46,6 @@ public String getEmailSubject(Container c)
         return "Death Alert " + getDateTimeFormat(c).format(new Date());
     }
 
-    @Override
-    public String getCronString()
-    {
-        return null;
-    }
-
     @Override
     public String getScheduleDescription()
     {

diff --git a/nirc_ehr/src/org/labkey/nirc_ehr/notification/NIRCPregnancyOutcomeNotification.java b/nirc_ehr/src/org/labkey/nirc_ehr/notification/NIRCPregnancyOutcomeNotification.java
@@ -46,12 +46,6 @@ public String getEmailSubject(Container c)
         return "Pregnancy Outcome Alert " + getDateTimeFormat(c).format(new Date());
     }
 
-    @Override
-    public String getCronString()
-    {
-        return null;
-    }
-
     @Override
     public String getScheduleDescription()
     {

diff --git a/nirc_ehr/src/org/labkey/nirc_ehr/query/NIRC_EHRTriggerHelper.java b/nirc_ehr/src/org/labkey/nirc_ehr/query/NIRC_EHRTriggerHelper.java
@@ -146,7 +146,7 @@ else if (enddate == null || enddate.after(deathDate))
             TableSelector ts = new TableSelector(ti, PageFlowUtil.set("date"), nextFilter, new Sort("date"));
             List<Date> dates = ts.getArrayList(Date.class);
             if (!dates.isEmpty())
-                enddate = dates.get(0);
+                enddate = dates.getFirst();
         }
 
         String qcstate = ConvertHelper.convert(row.get("qcstate"), String.class);
@@ -383,8 +383,8 @@ public void clinicalMoveNotification(final String animalId, final String date)
                             return;
                         }
 
-                        String remark = (String) EHRDemographicsService.get().getAnimal(container, animalId).getActiveHousing().get(0).get("remark");
-                        String performedBy = (String) EHRDemographicsService.get().getAnimal(container, animalId).getActiveHousing().get(0).get("performedBy");
+                        String remark = (String) EHRDemographicsService.get().getAnimal(container, animalId).getActiveHousing().getFirst().get("remark");
+                        String performedBy = (String) EHRDemographicsService.get().getAnimal(container, animalId).getActiveHousing().getFirst().get("performedBy");
 
                         //construct html for email notification
                         final StringBuilder html = new StringBuilder();
@@ -396,15 +396,15 @@ public void clinicalMoveNotification(final String animalId, final String date)
                         appendAnimalDetails(html, animalId, container);
 
                         // send Clinical Move Notification
-                        _log.debug("NIRC Clinical Move notification job sending email for animal " + animalId + " in container " + container.getPath());
+                        _log.debug("NIRC Clinical Move notification job sending email for animal {} in container {}", animalId, container.getPath());
                         TriggerScriptNotification.sendMessage(subject, html.toString(), recipients, container, user);
                     }), DbScope.CommitTaskOption.POSTCOMMIT);
 
             transaction.commit();
         }
     }
 
-    public void sendDeathNotification(final String animalId) throws Exception
+    public void sendDeathNotification(final String animalId)
     {
         //check whether Death Notification is enabled
         if (!NotificationService.get().isActive(new NIRCDeathNotification(), _container) || !NotificationService.get().isServiceEnabled())
@@ -450,36 +450,36 @@ public void sendDeathNotification(final String animalId) throws Exception
 
                         //construct html for email notification
                         final StringBuilder html = new StringBuilder();
-                        if (deathDate.getValue() == null)
+                        if (deathDate.get() == null)
                         {
-                            _log.error("NIRC death notification job found no death date for animal " + animalId + " in container " + _container.getPath());
+                            _log.error("NIRC death notification job found no death date for animal {} in container {}", animalId, _container.getPath());
                             html.append("Death date not found. Please contact system administrator.").append("<br>");
                             return;
                         }
-                        html.append("Animal '").append(PageFlowUtil.filter(animalId)).append("' has been declared dead on '").append(_dateFormat.format(deathDate.getValue())).append("'.<br>");
-                        html.append("Performed By: ").append(PageFlowUtil.filter(performedBy.getValue())).append("<br>");
-                        html.append("Disposition: ").append(PageFlowUtil.filter(disposition.getValue())).append("<br><br>");
+                        html.append("Animal '").append(PageFlowUtil.filter(animalId)).append("' has been declared dead on '").append(_dateFormat.format(deathDate.get())).append("'.<br>");
+                        html.append("Performed By: ").append(PageFlowUtil.filter(performedBy.get())).append("<br>");
+                        html.append("Disposition: ").append(PageFlowUtil.filter(disposition.get())).append("<br><br>");
 
                         //append animal details
                         appendAnimalDetails(html, animalId, container);
 
                         //append link to Necropsy form
                         String url = AppProps.getInstance().getBaseServerUrl() + AppProps.getInstance().getContextPath() + "/ehr" +
-                                container.getPath() + "/dataEntryForm.view?formType=Necropsy&taskid=" + taskId.getValue();
+                                container.getPath() + "/dataEntryForm.view?formType=Necropsy&taskid=" + taskId.get();
                         html.append("<a href='").append(PageFlowUtil.filter(url)).append("'>");
 
                         html.append("Click here to record Necropsy</a><br>");
 
                         // send Death Notification
-                        _log.debug("NIRC Death notification job sending email for animal " + animalId + " in container " + container.getPath());
+                        _log.debug("NIRC Death notification job sending email for animal {} in container {}", animalId, container.getPath());
                         TriggerScriptNotification.sendMessage(subject, html.toString(), recipients, container, user);
                     }), DbScope.CommitTaskOption.POSTCOMMIT);
 
             transaction.commit();
         }
     }
 
-    public void generateOrchardFile(final String taskid) throws Exception
+    public void generateOrchardFile(final String taskid)
     {
         NIRCOrchardFileGenerator orchardFileGenerator = NIRC_EHRManager.getOrchardFileGenerator();
         orchardFileGenerator.generateOrchardFile(_container, _user, taskid);
@@ -500,7 +500,7 @@ private void appendAnimalDetails(StringBuilder html, String id, final Container
         List<Map<String, Object>> activeHousing = EHRDemographicsService.get().getAnimal(container, id).getActiveHousing();
         if (null != activeHousing && !activeHousing.isEmpty())
         {
-            cage = (String) activeHousing.get(0).get("cage/cage");
+            cage = (String) activeHousing.getFirst().get("cage/cage");
         }
         else
         {
@@ -524,10 +524,8 @@ private String getProject(String id)
         SimpleFilter filter = new SimpleFilter(FieldKey.fromString("Id"), id);
         TableSelector ts = new TableSelector(ti, PageFlowUtil.set("project"), filter, null);
         final Mutable<String> project = new MutableObject<>();
-        ts.forEach(rs -> {
-            project.setValue(rs.getString("project"));
-        });
-        return project.getValue();
+        ts.forEach(rs -> project.setValue(rs.getString("project")));
+        return project.get();
     }
 
     private String getProtocol(String id)
@@ -557,7 +555,7 @@ private String getProtocol(String id)
                 protocol.setValue(title + (inves == null ? "" : " - " + inves));
             }
         });
-        return protocol.getValue();
+        return protocol.get();
     }
 
     public String createAssignmentRecord(String dataset, String id, Map<String, Object> row) throws SQLException, BatchValidationException, QueryUpdateServiceException, InvalidKeyException, DuplicateKeyException
@@ -682,7 +680,7 @@ public boolean canCloseCase(String category)
         return false;
     }
 
-    public void closeDailyClinicalObs(String caseid, String enddate) throws SQLException
+    public void closeDailyClinicalObs(String caseid, String enddate)
     {
         TableInfo ti = getTableInfo("study", "observation_order");
         SimpleFilter filter = new SimpleFilter(FieldKey.fromString("caseid"), caseid);
@@ -708,7 +706,7 @@ public void closeDailyClinicalObs(String caseid, String enddate) throws SQLExcep
         }
     }
 
-    public void ensureDailyClinicalObservationOrders(String id, String caseid, final Date date, String performedby, String qcstate, String taskid, List<Map<String, Object>> ordersInTransaction) throws SQLException
+    public void ensureDailyClinicalObservationOrders(String id, String caseid, final Date date, String performedby, String qcstate, String taskid, List<Map<String, Object>> ordersInTransaction)
     {
         TableInfo ti = getTableInfo("study", "observation_order");
         SimpleFilter filter = new SimpleFilter(FieldKey.fromParts("category","value"), "Activity");
@@ -898,7 +896,7 @@ public boolean isProcedureOrderEntered(String orderid)
         TableInfo ti = getTableInfo("study", "prc_order");
         SimpleFilter filter = new SimpleFilter(FieldKey.fromString("objectid"), orderid);
         TableSelector ts = new TableSelector(ti, PageFlowUtil.set("qcstate"), filter, null);
-        Integer qcstate = ts.getArrayList(Integer.class).get(0);
+        Integer qcstate = ts.getArrayList(Integer.class).getFirst();
         if (EHRService.get().getQCStates(_container).get("Completed").getRowId() == qcstate)
             return true;
 
@@ -967,7 +965,7 @@ public void updateProcedureOrdersToCompleted(List<String> ids)
         try
         {
             ti.getUpdateService().updateRows(_user, _container, rows, null, null, getExtraContext());
-            _log.info("Successfully updated " + rows.size() + " prc_order rows to 'Completed' status");
+            _log.info("Successfully updated {} prc_order rows to 'Completed' status", rows.size());
         }
         catch (Exception e)
         {
@@ -1023,7 +1021,7 @@ public void sendPregnancyOutcomeNotification(final String animalId, Map<String,
                         appendAnimalDetails(html, animalId, container);
 
                         // send Pregnancy Outcome notification
-                        _log.debug("NIRC Pregnancy Outcome notification job sending email for animal " + animalId + " in container " + container.getPath());
+                        _log.debug("NIRC Pregnancy Outcome notification job sending email for animal {} in container {}", animalId, container.getPath());
                         TriggerScriptNotification.sendMessage(subject, html.toString(), recipients, container, user);
                     }), DbScope.CommitTaskOption.POSTCOMMIT);
 

diff --git a/nirc_ehr/src/org/labkey/nirc_ehr/table/NIRC_EHRSharedDatasetTrigger.java b/nirc_ehr/src/org/labkey/nirc_ehr/table/NIRC_EHRSharedDatasetTrigger.java
@@ -35,7 +35,7 @@ private void verifyPerformedBy(TableInfo table, @Nullable Map<String, Object> ne
     }
 
     @Override
-    public void beforeInsert(TableInfo table, Container c, User user, @Nullable QueryUpdateService.InsertOption insertOption, @Nullable Map<String, Object> newRow, ValidationException errors, Map<String, Object> extraContext) throws ValidationException
+    public void beforeInsert(TableInfo table, Container c, User user, @Nullable QueryUpdateService.InsertOption insertOption, @Nullable Map<String, Object> newRow, ValidationException errors, Map<String, Object> extraContext)
     {
         transformAnimalIdToUpperCase(newRow);
         verifyPerformedBy(table, newRow, errors);
@@ -44,7 +44,7 @@ public void beforeInsert(TableInfo table, Container c, User user, @Nullable Quer
     @Override
     public void beforeUpdate(TableInfo table, Container c,
                              User user, @Nullable QueryUpdateService.InsertOption insertOption, @Nullable Map<String, Object> newRow, @Nullable Map<String, Object> oldRow,
-                             ValidationException errors, Map<String, Object> extraContext) throws ValidationException
+                             ValidationException errors, Map<String, Object> extraContext)
     {
         verifyPerformedBy(table, newRow, errors);
     }

diff --git a/nirc_ehr/src/org/labkey/nirc_ehr/table/NIRC_EHRTriggerScriptFactory.java b/nirc_ehr/src/org/labkey/nirc_ehr/table/NIRC_EHRTriggerScriptFactory.java
@@ -14,7 +14,7 @@ public class NIRC_EHRTriggerScriptFactory extends ScriptTriggerFactory
 {
     @Override
     @NotNull
-    protected Collection<Trigger> createTriggerScript(Container c, TableInfo table) throws ScriptException
+    protected Collection<Trigger> createTriggerScript(@NotNull Container c, TableInfo table) throws ScriptException
     {
         return Collections.singleton(new NIRC_EHRSharedDatasetTrigger());
     }