From 10abf3017506bbd315569eb8855471aeeb60b7ff Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Thu, 4 Sep 2025 17:33:19 -0700
Subject: [PATCH] Improve generics and other warnings

---
 flow/src/org/labkey/flow/controllers/FlowController.java | 2 +-
 .../editscript/CompensationCalculationPage.java          | 9 +++++----
 .../microarray/matrix/ExpressionMatrixAssayProvider.java | 6 +++---
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/flow/src/org/labkey/flow/controllers/FlowController.java b/flow/src/org/labkey/flow/controllers/FlowController.java
index 4dc09b289..e3823a2b8 100644
--- a/flow/src/org/labkey/flow/controllers/FlowController.java
+++ b/flow/src/org/labkey/flow/controllers/FlowController.java
@@ -164,7 +164,7 @@ public ModelAndView getView(Object o, BindException errors)
             run = schema.getRun();
 //            script = schema.getScript();
 
-            QueryView view = schema.createView(getViewContext(), settings);
+            QueryView view = schema.createView(getViewContext(), settings, errors);
             if (view.getQueryDef() == null)
             {
                 throw new NotFoundException("Query definition '" + settings.getQueryName() + "' in flow schema not found");
diff --git a/flow/src/org/labkey/flow/controllers/editscript/CompensationCalculationPage.java b/flow/src/org/labkey/flow/controllers/editscript/CompensationCalculationPage.java
index 50dcba86c..1d060513c 100644
--- a/flow/src/org/labkey/flow/controllers/editscript/CompensationCalculationPage.java
+++ b/flow/src/org/labkey/flow/controllers/editscript/CompensationCalculationPage.java
@@ -17,6 +17,7 @@
 package org.labkey.flow.controllers.editscript;
 
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Strings;
 import org.fhcrc.cpas.flow.script.xml.ChannelDef;
 import org.fhcrc.cpas.flow.script.xml.ChannelSubsetDef;
 import org.fhcrc.cpas.flow.script.xml.CompensationCalculationDef;
@@ -263,14 +264,14 @@ public SelectBuilder selectKeywordValues(Sign sign, int index)
 
     private boolean subsetNameMatches(String subsetUser, String subsetWorkspace, Sign sign, String channel)
     {
-        if (StringUtils.equals(subsetUser, subsetWorkspace))
+        if (Strings.CS.equals(subsetUser, subsetWorkspace))
             return true;
-        if (StringUtils.equals(subsetUser, channel + subsetWorkspace))
+        if (Strings.CS.equals(subsetUser, channel + subsetWorkspace))
             return true;
         String strSign = sign == Sign.positive ? "+" : "-";
-        if (StringUtils.equals(subsetUser, channel + strSign + subsetWorkspace))
+        if (Strings.CS.equals(subsetUser, channel + strSign + subsetWorkspace))
             return true;
-        if (StringUtils.equals(subsetUser, strSign + subsetWorkspace))
+        if (Strings.CS.equals(subsetUser, strSign + subsetWorkspace))
             return true;
         return false;
     }
diff --git a/microarray/src/org/labkey/microarray/matrix/ExpressionMatrixAssayProvider.java b/microarray/src/org/labkey/microarray/matrix/ExpressionMatrixAssayProvider.java
index 59cb9b4e6..42e730c24 100644
--- a/microarray/src/org/labkey/microarray/matrix/ExpressionMatrixAssayProvider.java
+++ b/microarray/src/org/labkey/microarray/matrix/ExpressionMatrixAssayProvider.java
@@ -16,7 +16,7 @@
 
 package org.labkey.microarray.matrix;
 
-import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Strings;
 import org.fhcrc.cpas.exp.xml.ExperimentRunType;
 import org.fhcrc.cpas.exp.xml.SimpleTypeNames;
 import org.fhcrc.cpas.exp.xml.SimpleValueType;
@@ -234,7 +234,7 @@ public void beforeXarExportRun(ExpRun run, ExperimentRunType xrun)
                 }
                 for (SimpleValueType sv : xrun.getProperties().getSimpleValArray())
                 {
-                    if (StringUtils.equals("featureSet",sv.getName()))
+                    if (Strings.CS.equals("featureSet",sv.getName()))
                     {
                         int featureAnnotationSetRowId = (int)Float.parseFloat(sv.getStringValue());
                         String featureAnnotationSetName = mapRowIdName.get(featureAnnotationSetRowId);
@@ -267,7 +267,7 @@ public void beforeXarImportRun(ExperimentRunType xrun)
                 }
                 for (SimpleValueType sv : xrun.getProperties().getSimpleValArray())
                 {
-                    if (StringUtils.equals(FEATURE_SET_PROPERTY_NAME,sv.getName()))
+                    if (Strings.CS.equals(FEATURE_SET_PROPERTY_NAME,sv.getName()))
                     {
                         String featureAnnotationSetName = sv.getStringValue();
                         Long featureAnnotationRowId = mapNameRowId.get(featureAnnotationSetName);