Use helper methods to create IN clauses (#681)

## Rationale
Using helpers to generate SQL IN clauses is more convenient and prevents
broken SQL & injection risks

## Related Pull Requests
- LabKey/platform#8187

Author: labkey-adam

panoramapublic/src/org/labkey/panoramapublic/chromlib/ChromLibStateImporter.java

@@ -16,6 +16,7 @@
 package org.labkey.panoramapublic.chromlib;
 
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Strings;
 import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.DbSchema;
@@ -136,7 +137,7 @@ void parseLibStateRow(Map<String, Object> row) throws ChromLibStateException
     {
         String skyFile = getSkyFile(row);
         String runState = String.valueOf(row.get(RUN_STATE));
-        if (_currentRun == null || !StringUtils.equals(skyFile, _currentRun.getFileName()))
+        if (_currentRun == null || !Strings.CS.equals(skyFile, _currentRun.getFileName()))
         {
             ITargetedMSRun run = _svc.getRunByFileName(skyFile, _container);
             if (run == null)

panoramapublic/src/org/labkey/panoramapublic/model/validation/SpecLibValidation.java

@@ -15,7 +15,7 @@
  */
 package org.labkey.panoramapublic.model.validation;
 
-import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Strings;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.panoramapublic.model.speclib.SpecLibInfo;
@@ -330,7 +330,7 @@ public boolean isPrositLibrary()
         {
             String modelName = getSpectrumFiles().getFirst().getName();
             return "Prositintensity_prosit_publication_v1".equals(modelName)
-                    || StringUtils.startsWith(modelName, "Koina-");
+                    || Strings.CS.startsWith(modelName, "Koina-");
         }
         return false;
     }

panoramapublic/src/org/labkey/panoramapublic/query/ContainerJoin.java

@@ -15,7 +15,7 @@
  */
 package org.labkey.panoramapublic.query;
 
-import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Strings;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.junit.Assert;
@@ -177,8 +177,8 @@ void assertSQLEquals(Object Oexpected, Object Oactual)
             String actual = Oactual instanceof SQLFragment s ? s.getRawSQL() : String.valueOf(Oactual);
 
             // strip "'s to make this less sensitive to SQL generation changes
-            expected = StringUtils.replace(expected, "\"", "").trim();
-            actual = StringUtils.replace(actual, "\"", "").trim();
+            expected = Strings.CS.replace(expected, "\"", "").trim();
+            actual = Strings.CS.replace(actual, "\"", "").trim();
             assertEquals(expected, actual);
         }
 

panoramapublic/src/org/labkey/panoramapublic/query/ExperimentAnnotationsManager.java

@@ -486,18 +486,11 @@ public static boolean hasProteomicData(ExperimentAnnotations experimentAnnotatio
         SQLFragment sql = new SQLFragment("SELECT Id FROM ").append(svc.getTableInfoRuns(), "r")
                 .append(" WHERE PeptideCount > 0 ")
                 .append(" AND Deleted = ? " ).add(Boolean.FALSE)
-                .append(" AND Container IN ");
-        if (experimentAnnotations.isIncludeSubfolders())
-        {
-            List<Container> containers = ContainerManager.getAllChildren(experimentAnnotations.getContainer(), user);
-            sql.append(ContainerManager.getIdsAsCsvList(new HashSet<>(containers), d));
-        }
-        else
-        {
-            sql.append("(");
-            sql.appendValue(experimentAnnotations.getContainer(),d);
-            sql.append(")");
-        }
+                .append(" AND Container");
+        List<Container> containers = experimentAnnotations.isIncludeSubfolders()
+                ? ContainerManager.getAllChildren(experimentAnnotations.getContainer(), user)
+                : List.of(experimentAnnotations.getContainer());
+        sql.appendInClause(containers, d);
 
         return new SqlSelector(targetedmsSchema.getDbSchema(), sql).exists();
     }

panoramapublic/src/org/labkey/panoramapublic/query/ModificationInfoManager.java

@@ -276,8 +276,9 @@ private static boolean runsHaveModifications(List<Long> runIds, TableInfo tableI
                 .append(svc.getTableInfoGeneralMolecule(), "gm").append(" ON gm.Id = mod.peptideId ")
                 .append(" INNER JOIN ")
                 .append(svc.getTableInfoPeptideGroup(), "pg").append(" ON pg.Id = gm.peptideGroupId ")
-                .append(" WHERE pg.runId IN (").append(StringUtils.join(runIds, ",")).append(") ");
+                .append(" WHERE pg.runId");
         var schema = svc.getUserSchema(user, container).getDbSchema();
+        sql.appendInClause(runIds, schema.getSqlDialect());
         sql = schema.getSqlDialect().limitRows(sql, 1);
         return new SqlSelector(schema, sql).exists();
     }