Specimen module cleanup

specimen/src/org/labkey/specimen/importer/ImportableColumn.java

@@ -24,7 +24,7 @@ public class ImportableColumn
     private final boolean _maskOnExport;
     private final boolean _unique;
     private final int _size;
-    private final Class _javaClass;
+    private final Class<?> _javaClass;
     private final JdbcType _jdbcType;
     private Object _defaultValue = null;
 
@@ -88,7 +88,7 @@ public ImportableColumn(String tsvColumnName, Collection<String> tsvColumnAliase
     }
 
     // Can't use standard JdbcType.valueOf() method since this uses contains()
-    private static Class determineJavaType(String dbType)
+    private static Class<?> determineJavaType(String dbType)
     {
         if (dbType.contains(ImportTypes.DATETIME_TYPE))
             throw new IllegalStateException("Java types for DateTime/Timestamp columns should be previously initialized.");
@@ -148,7 +148,7 @@ public boolean isUnique()
         return _unique;
     }
 
-    public Class getJavaClass()
+    public Class<?> getJavaClass()
     {
         return _javaClass;
     }

specimen/src/org/labkey/specimen/importer/RequestabilityManager.java

@@ -395,8 +395,6 @@ public RequestableRule(Container container)
         public int updateRequestability(User user, List<Vial> vials) throws InvalidRuleException
         {
             TableInfo tableInfoVial = SpecimenSchema.get().getTableInfoVial(_container);
-            if (null == tableInfoVial)
-                throw new IllegalStateException("Expected Vial table to exist.");
 
             SQLFragment reason = getAvailabilityReason();
             SQLFragment updateSQL = new SQLFragment("UPDATE ");
@@ -573,7 +571,7 @@ public SQLFragment getFilterSQL(Container container, User user, List<Vial> vials
         @Override
         public SQLFragment getAvailabilityReason()
         {
-            return new SQLFragment("'This vial is " + getMarkType().getLabel().toLowerCase() + " because it was found in the set called \"" + _queryName + "\".'");
+            return new SQLFragment("?", "This vial is " + getMarkType().getLabel().toLowerCase() + " because it was found in the set called \"" + _queryName + "\".");
         }
 
         @Override
@@ -695,8 +693,6 @@ public LockedWhileProcessingRule(Container container)
         public SQLFragment getFilterSQL(Container container, User user, List<Vial> vials)
         {
             TableInfo tableInfoVial = SpecimenSchema.get().getTableInfoVial(_container);
-            if (null == tableInfoVial)
-                throw new IllegalStateException("Expected Vial table to exist.");
 
             SQLFragment sql = new SQLFragment();
             if (vials != null && !vials.isEmpty())
@@ -792,8 +788,6 @@ private void updateRequestability(Container container, User user, boolean resetT
         if (resetToAvailable)
         {
             TableInfo tableInfoVial = SpecimenSchema.get().getTableInfoVial(container);
-            if (null == tableInfoVial)
-                throw new IllegalStateException("Expected Vial table to exist.");
 
             if (logger != null)
                 logger.info("\tResetting vials to default available state.");
@@ -847,10 +841,9 @@ public void updateRequestability(Container container, User user, boolean resetTo
 
     public static String makeSpecimenUnavailableMessage(Vial vial, @Nullable String additionalText)
     {
-        String message = String.format("Specimen %s%s%s",
+        return String.format("Specimen %s%s%s",
                 vial.getGlobalUniqueId(),
                 null != vial.getAvailabilityReason() ? vial.getAvailabilityReason().replaceFirst("This vial", "") : " is not available.",
                 null != additionalText ? " " + additionalText : "");
-        return message;
     }
 }

specimen/src/org/labkey/specimen/importer/SimpleSpecimenImporter.java

@@ -84,11 +84,6 @@ public class SimpleSpecimenImporter extends SpecimenImporter
     private final Map<String, String> _columnLabels;
     private final TimepointType _timepointType;
 
-    public SimpleSpecimenImporter(Container container, User user)
-    {
-        this(container, user, TimepointType.DATE, "Subject");
-    }
-
     public SimpleSpecimenImporter(Container container, User user, TimepointType timepointType, String participantIdLabel)
     {
         super(container, user);
@@ -130,15 +125,6 @@ public void fixupSpecimenColumns(TabLoader tl) throws IOException
         tl.setColumns(mappedCols);
     }
 
-    // UNDONE: Converting values belongs in _process
-    public List<Map<String, Object>> fixupSpecimenRows(List<Map<String, Object>> rows)
-    {
-        List<Map<String, Object>> result = new ArrayList<>();
-        for (Map<String, Object> row : rows)
-            result.add(fixupSpecimenRow(row));
-        return result;
-    }
-
     private Map<String, Object> fixupSpecimenRow(Map<String, Object> row)
     {
         Map<String, Object> result = new HashMap<>();

specimen/src/org/labkey/specimen/importer/SpecimenSchemaImporter.java

@@ -185,7 +185,7 @@ public void process(SimpleStudyImportContext ctx, VirtualFile studyDir, BindExce
                     current.put(pd.getName(), pd);
                 }
 
-                DomainURIFactory factory = name -> new Pair<>(domain.getTypeURI(), container);
+                DomainURIFactory factory = _ -> new Pair<>(domain.getTypeURI(), container);
 
                 ImportPropertyDescriptorsList pds = importHelper.getImportPropertyDescriptors(factory, propErrors, container);
                 if (!propErrors.isEmpty())