Support BIGINT Primary Keys

LDK/test/src/org/labkey/test/tests/external/labModules/LabModulesTest.java

@@ -494,7 +494,7 @@ else if (serverVal instanceof Date)
                     Date d = dateFormat.parse(expectations[idx]);
                     assertEquals("Incorrect value for: " + col + " on row " + i, d, serverVal);
                 }
-                else if ((serverVal instanceof Integer || serverVal instanceof Double))
+                else if ((serverVal instanceof Integer || serverVal instanceof Long || serverVal instanceof Double))
                 {
                     double d = Double.parseDouble(expectations[idx]);
                     assertEquals("Incorrect value for: " + col + " on row " + i, d, Double.parseDouble(serverVal.toString()), DELTA);

laboratory/api-src/org/labkey/api/laboratory/LaboratoryService.java

@@ -76,7 +76,7 @@ static public void setInstance(LaboratoryService instance)
 
     abstract public Set<AssayDataProvider> getRegisteredAssayProviders();
 
-    abstract public AssayDataProvider getDataProviderForAssay(int protocolId);
+    abstract public AssayDataProvider getDataProviderForAssay(long protocolId);
 
     abstract public AssayDataProvider getDataProviderForAssay(AssayProvider ap);
 

laboratory/api-src/org/labkey/api/laboratory/assay/AbstractAssayDataProvider.java

@@ -166,7 +166,7 @@ public AssayImportMethod getImportMethodByName(String methodName)
     }
 
     @Override
-    public String getDefaultImportMethodName(Container c, User u, int protocolId)
+    public String getDefaultImportMethodName(Container c, User u, long protocolId)
     {
         Container targetContainer = c.isWorkbook() ? c.getParent() : c;
         Map<String, String> props = PropertyManager.getProperties(targetContainer, PROPERTY_CATEGORY);
@@ -176,7 +176,7 @@ public String getDefaultImportMethodName(Container c, User u, int protocolId)
             return _importMethods.isEmpty() ?  null : _importMethods.iterator().next().getName();
     }
 
-    private String getDefaultMethodPropertyKey(int protocolId)
+    private String getDefaultMethodPropertyKey(long protocolId)
     {
         return getKey() + "||" + protocolId;
     }

laboratory/api-src/org/labkey/api/laboratory/assay/AssayDataProvider.java

@@ -55,7 +55,7 @@ public interface AssayDataProvider extends DataProvider
 
     AssayImportMethod getImportMethodByName(String methodName);
 
-    String getDefaultImportMethodName(Container c, User u, int protocolId);
+    String getDefaultImportMethodName(Container c, User u, long protocolId);
 
     boolean isModuleEnabled(Container c);
 }

laboratory/api-src/org/labkey/api/laboratory/assay/DefaultAssayParser.java

@@ -462,7 +462,7 @@ protected void validateRows(List<Map<String, Object>> rows, ImportContext contex
         errors.confirmNoErrors();
     }
 
-    protected void saveTemplate(ViewContext ctx, int templateId, int runId) throws BatchValidationException
+    protected void saveTemplate(ViewContext ctx, int templateId, long runId) throws BatchValidationException
     {
         try
         {

laboratory/api-src/org/labkey/api/laboratory/assay/PivotingAssayParser.java

@@ -18,6 +18,7 @@
 import au.com.bytecode.opencsv.CSVWriter;
 import org.apache.commons.lang3.StringUtils;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
+import org.labkey.api.collections.IntHashMap;
 import org.labkey.api.data.Container;
 import org.labkey.api.exp.property.DomainProperty;
 import org.labkey.api.query.BatchValidationException;
@@ -27,7 +28,6 @@
 import java.io.IOException;
 import java.io.StringWriter;
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -122,7 +122,7 @@ protected String readRawFile(ImportContext context) throws BatchValidationExcept
      */
     private Map<Integer, String> inspectHeader(List<String> header, ImportContext context) throws BatchValidationException
     {
-        Map<Integer, String> resultMap = new HashMap<>();
+        Map<Integer, String> resultMap = new IntHashMap<>();
         Map<String, String> allowable = new CaseInsensitiveHashMap<>();
         BatchValidationException errors = new BatchValidationException();
 

laboratory/api-src/org/labkey/api/laboratory/query/ContainerIncrementingTable.java

@@ -41,6 +41,8 @@
 import java.util.Set;
 import java.util.concurrent.Callable;
 
+import static org.labkey.api.exp.api.ExperimentService.asInteger;
+
 /**
  * User: bimber
  * Date: 3/12/13
@@ -153,6 +155,8 @@ private Integer getInteger(Object value) throws ValidationException
             return null;
         else if (value instanceof Integer)
             return (Integer)value;
+        else if (value instanceof Long)
+            return asInteger(value);
         else if (value instanceof Double)
             return ((Double)value).intValue();
         try
@@ -326,9 +330,9 @@ public Object call() throws Exception
                         Object selfAssignedId = it.getInputColumnValue(inputColMap.get(_incrementingCol));
                         if (selfAssignedId != null)
                         {
-                            if (selfAssignedId instanceof Integer)
+                            if (selfAssignedId instanceof Integer || selfAssignedId instanceof Long)
                             {
-                                rowId = (Integer)selfAssignedId;
+                                rowId = asInteger(selfAssignedId);
 
                                 if (idGen.hasRowWithId(c, rowId))
                                     _context.getErrors().addRowError(new ValidationException("A record is already present with ID: " + rowId));

laboratory/src/org/labkey/laboratory/LaboratoryServiceImpl.java

@@ -172,7 +172,7 @@ public Set<AssayDataProvider> getRegisteredAssayProviders()
     }
 
     @Override
-    public AssayDataProvider getDataProviderForAssay(int protocolId)
+    public AssayDataProvider getDataProviderForAssay(long protocolId)
     {
         ExpProtocol protocol = ExperimentService.get().getExpProtocol(protocolId);
         if (protocol == null)

laboratory/src/org/labkey/laboratory/assay/RunUploadContext.java

@@ -196,7 +196,7 @@ public void setTransformResult(TransformResult result)
      * The RowId for the run that is being deleted and reuploaded, or null if this is a new run
      */
     @Override
-    public Integer getReRunId()
+    public Long getReRunId()
     {
         return null;
     }