Haplotype assay cleanup (#200)

#### Rationale
Lint cleanup and SQL improvements

#### Changes
* Clear assorted IntelliJ warnings
* Use JDBC parameter

Author: labkey-jeckels

genotyping/src/org/labkey/genotyping/HaplotypeProtocolBean.java

@@ -22,22 +22,7 @@
  * Date: 12/14/12
  */
 
-public class HaplotypeProtocolBean
+public record HaplotypeProtocolBean(HaplotypeDataCollector<?> dataCollector, ExpProtocol protocol)
 {
-    private final HaplotypeDataCollector dataCollector;
-    private final ExpProtocol protocol;
-
-    public HaplotypeProtocolBean(HaplotypeDataCollector dataCollector, ExpProtocol protocol){
-        this.dataCollector = dataCollector;
-        this.protocol = protocol;
-    }
-
-    public HaplotypeDataCollector getDataCollector(){
-        return dataCollector;
-    }
-
-    public ExpProtocol getProtocol(){
-        return protocol;
-    }
 
 }

genotyping/src/org/labkey/genotyping/HaplotypeProtocolSchema.java

@@ -102,7 +102,7 @@ public TableInfo getTable(String name, @Nullable ContainerFilter cf, boolean inc
     @Override
     public @Nullable TableInfo createDataTable(ContainerFilter cf, boolean includeCopiedToStudyColumns)
     {
-        FilteredTable<?> table = (FilteredTable)new GenotypingQuerySchema(getUser(), getContainer()).getTable(GenotypingQuerySchema.TableType.AnimalAnalysis.name(), cf,true, true);
+        FilteredTable<?> table = (FilteredTable<?>)new GenotypingQuerySchema(getUser(), getContainer()).getTable(GenotypingQuerySchema.TableType.AnimalAnalysis.name(), cf,true, true);
         List<FieldKey> keys = new ArrayList<>(table.getDefaultVisibleColumns());
         HashSet<String> defaults = HaplotypeAssayProvider.getDefaultColumns();
         List<? extends DomainProperty> props = HaplotypeAssayProvider.getDomainProps(getProtocol());
@@ -147,14 +147,15 @@ private ExprColumn makeColumnFromRunField(DomainProperty prop, boolean max, SQLF
 
         String field = prop.getName();
         String label = prop.getLabel() != null ? prop.getLabel() : ColumnInfo.labelFromName(prop.getName());
-        String type = field.substring(0, prop.getName().length()-1).replaceAll("Haplotype", ""); //ColumnInfo.labelFromName(prop.getName()).split(" ")[0];
+        String type = field.substring(0, prop.getName().length()-1).replace("Haplotype", ""); //ColumnInfo.labelFromName(prop.getName()).split(" ")[0];
 
         SQLFragment sql = new SQLFragment("(SELECT ");
         sql.append("min");
         sql.append("(x.Haplotype) FROM (");
         sql.append(selectStatement);
-        sql.append(") AS x WHERE x.DiploidNumber = ? AND x.Type = '" + type + "' AND x.AnimalAnalysisId = " + ExprColumn.STR_TABLE_ALIAS + ".RowID)");
+        sql.append(") AS x WHERE x.DiploidNumber = ? AND x.Type = ? AND x.AnimalAnalysisId = " + ExprColumn.STR_TABLE_ALIAS + ".RowID)");
         sql.add(max ? 2 : 1);
+        sql.add(type);
         ExprColumn column = new ExprColumn(table, field, sql, JdbcType.VARCHAR);
         TableInfo haplotypeDetailsTableInfo = getHaplotypeDetailsTableInfo();
         if (haplotypeDetailsTableInfo != null && haplotypeDetailsTableInfo.getGridURL(getContainer()) != null)
@@ -180,8 +181,7 @@ public DataView createDataView()
             {
                 DataView result = super.createDataView();
                 DataRegion rgn = result.getDataRegion();
-
-                ButtonBar bar = result.getDataRegion().getButtonBar(DataRegion.MODE_GRID);
+                ButtonBar bar = rgn.getButtonBar(DataRegion.MODE_GRID);
                 if (!bar.isLocked())
                 {
                     ActionButton reportButton = new ActionButton(GenotypingController.HaplotypeAssignmentReportAction.class, "Produce Report");

genotyping/src/org/labkey/genotyping/IlluminaFastqParser.java

@@ -20,8 +20,8 @@
 import org.apache.commons.collections4.ListValuedMap;
 import org.apache.commons.collections4.multimap.ArrayListValuedHashMap;
 import org.apache.commons.io.FileUtils;
-import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
 import org.junit.Assert;
 import org.junit.Before;
@@ -57,10 +57,6 @@
  * This is designed to parse the FASTQ files produced by a single run on an Illumina instrument and produce one gzipped FASTQ
  * for each sample in that run.  Parsing that CSV file to obtain the sample list is upstream of this class.
  * It is designed to be called from a pipeline job, although it should not need to be.
- *
- * User: bbimber
- * Date: 4/18/12
- * Time: 11:35 AM
  */
 public class IlluminaFastqParser
 {
@@ -350,7 +346,7 @@ else if(rc == 0 && readCount != 0)
                 return fileName + " has " + readCount + " reads, while its pair file is empty and has 0 reads.";
         }
         else
-            m.put(fileNameWithoutPairingInfo, Integer.valueOf(readCount));
+            m.put(fileNameWithoutPairingInfo, readCount);
 
         return null;
 

genotyping/src/org/labkey/genotyping/view/importHaplotypeAssignments.jsp

@@ -28,7 +28,7 @@
 <%
     JspView<HaplotypeProtocolBean> me = HttpView.currentView();
     HaplotypeProtocolBean bean = me.getModelBean();
-    HaplotypeDataCollector dataCollector = bean.getDataCollector();
+    HaplotypeDataCollector dataCollector = bean.dataCollector();
     String[] reshowData = {};
     if (dataCollector.getReshowValue("data") != null && !dataCollector.getReshowValue("data").isEmpty())
     {
@@ -42,7 +42,7 @@
 <script type="text/javascript" nonce="<%=getScriptNonce()%>">
     var expectedHeaders = [];
     <%
-    for (Map.Entry<String, HaplotypeColumnMappingProperty> property : HaplotypeAssayProvider.getColumnMappingProperties(bean.getProtocol()).entrySet())
+    for (Map.Entry<String, HaplotypeColumnMappingProperty> property : HaplotypeAssayProvider.getColumnMappingProperties(bean.protocol()).entrySet())
     {
         %>expectedHeaders.push({name: '<%=h(property.getKey())%>', label: '<%=h(property.getValue().getLabel())%>', reshowValue: '<%=h(dataCollector.getReshowValue(property.getKey()))%>', required: <%=property.getValue().isRequired()%>});<%
     }