Support BIGINT Primary Keys (#912)

Author: labkey-matthewb

elisa/src/org/labkey/elisa/ElisaAssayProvider.java

@@ -434,7 +434,7 @@ public Collection<StatsService.CurveFitType> getCurveFits()
     protected void moveAssayResults(List<ExpRun> runs, ExpProtocol protocol, Container sourceContainer, Container targetContainer, User user, AssayMoveData assayMoveData) throws ExperimentException
     {
         super.moveAssayResults(runs, protocol, sourceContainer, targetContainer, user, assayMoveData); // assay results
-        List<Integer> runRowIds = runs.stream().map(ExpRun::getRowId).toList();
+        List<Long> runRowIds = runs.stream().map(ExpRun::getRowId).toList();
 
         // move specimen
         String tableName = AssayProtocolSchema.DATA_TABLE_NAME;

elisa/src/org/labkey/elisa/ElisaController.java

@@ -55,17 +55,17 @@ public ElisaController()
 
     public static class RunDetailsForm
     {
-        private int _protocolId;
-        private int _runId;
+        private long _protocolId;
+        private long _runId;
         private String _runName;
         private String _schemaName;
 
-        public int getRunId()
+        public long getRunId()
         {
             return _runId;
         }
 
-        public void setRunId(int runId)
+        public void setRunId(long runId)
         {
             _runId = runId;
         }
@@ -90,12 +90,12 @@ public void setSchemaName(String schemaName)
             _schemaName = schemaName;
         }
 
-        public int getProtocolId()
+        public long getProtocolId()
         {
             return _protocolId;
         }
 
-        public void setProtocolId(int protocolId)
+        public void setProtocolId(long protocolId)
         {
             _protocolId = protocolId;
         }

elisa/src/org/labkey/elisa/ElisaDataHandler.java

@@ -431,7 +431,7 @@ public void beforeDeleteData(List<ExpData> datas, User user) throws ExperimentEx
         {
             super.beforeDeleteData(datas, user);
 
-            Set<Integer> runIds = new HashSet<>();
+            Set<Long> runIds = new HashSet<>();
             for (ExpData data : datas)
             {
                 if (null != data.getRunId())

elisa/src/org/labkey/elisa/HighThroughputImportHelper.java

@@ -10,6 +10,7 @@
 import org.labkey.api.assay.plate.PositionImpl;
 import org.labkey.api.assay.plate.Well;
 import org.labkey.api.assay.plate.WellGroup;
+import org.labkey.api.collections.IntHashMap;
 import org.labkey.api.data.statistics.CurveFit;
 import org.labkey.api.exp.ExperimentException;
 import org.labkey.api.exp.api.ExpMaterial;
@@ -139,7 +140,7 @@ public Set<String> getPlates()
     @Override
     public Map<Integer, Plate> getAnalyteToPlate(String plateName) throws ExperimentException
     {
-        Map<Integer, Plate> analyteToPlate = new HashMap<>();
+        Map<Integer, Plate> analyteToPlate = new IntHashMap<>();
         for (Map.Entry<Integer, double[][]> entry : _plateMap.get(plateName).getDataMap().entrySet())
         {
             Plate plate = PlateService.get().createPlate(_plateTemplate, entry.getValue(), null);
@@ -171,8 +172,8 @@ public Map<String, Object> getExtraProperties(String plateName, Position positio
 
     private static class AnalytePlate
     {
-        private final Map<Integer, Map<String, Double>> _stdConcentrations = new HashMap<>();
-        private final Map<Integer, double[][]> _dataMap = new HashMap<>();
+        private final Map<Integer, Map<String, Double>> _stdConcentrations = new IntHashMap<>();
+        private final Map<Integer, double[][]> _dataMap = new IntHashMap<>();
         private final String _plateName;
         private final Plate _plateTemplate;
         // contains the mapping of (well/analyte) to extra row data to merge during data import

elisa/src/org/labkey/elisa/ManualImportHelper.java

@@ -10,6 +10,7 @@
 import org.labkey.api.assay.plate.Position;
 import org.labkey.api.assay.plate.Well;
 import org.labkey.api.assay.plate.WellGroup;
+import org.labkey.api.collections.IntHashMap;
 import org.labkey.api.data.statistics.CurveFit;
 import org.labkey.api.exp.ExperimentException;
 import org.labkey.api.exp.api.ExpMaterial;
@@ -45,7 +46,7 @@ public Set<String> getPlates()
     @Override
     public Map<Integer, Plate> getAnalyteToPlate(String plateName) throws ExperimentException
     {
-        Map<Integer, Plate> analyteMap = new HashMap<>();
+        Map<Integer, Plate> analyteMap = new IntHashMap<>();
         PlateReader reader = _provider.getPlateReader(BioTekPlateReader.LABEL);
         if (reader != null)
         {

elisa/src/org/labkey/elisa/query/CurveFitDb.java

@@ -5,8 +5,8 @@
 public class CurveFitDb extends Entity
 {
     private Integer _rowId;
-    private Integer _runId;
-    private Integer _protocolId;
+    private Long _runId;
+    private Long _protocolId;
     private String _plateName;
     private Integer _spot;
     private Double _rSquared;
@@ -27,22 +27,22 @@ public void setRowId(Integer rowId)
         _rowId = rowId;
     }
 
-    public Integer getRunId()
+    public Long getRunId()
     {
         return _runId;
     }
 
-    public void setRunId(Integer runId)
+    public void setRunId(Long runId)
     {
         _runId = runId;
     }
 
-    public Integer getProtocolId()
+    public Long getProtocolId()
     {
         return _protocolId;
     }
 
-    public void setProtocolId(Integer protocolId)
+    public void setProtocolId(Long protocolId)
     {
         _protocolId = protocolId;
     }

elisa/src/org/labkey/elisa/query/ElisaManager.java

@@ -36,7 +36,6 @@ public static CurveFitDb getCurveFit(Container c, ExpRun run, String plateName,
         filter.addCondition(FieldKey.fromParts("PlateName"), plateName);
         filter.addCondition(FieldKey.fromParts("Spot"), spot);
         return new TableSelector(ElisaProtocolSchema.getTableInfoCurveFit(), filter, null).getObject(CurveFitDb.class);
-
     }
 
     public static void deleteContainerData(Container container)

elispotassay/src/org/labkey/elispot/AbstractElispotDataHandler.java

@@ -156,7 +156,7 @@ public static Lsid getAntigenRowLsid(String dataLsid, String sampleName)
         return dataRowLsid.build();
     }
 
-    public static Lsid getAntigenLsid(String antigenWellgroupName, String sampleName, int runId, String assayName, String analyte)
+    public static Lsid getAntigenLsid(String antigenWellgroupName, String sampleName, long runId, String assayName, String analyte)
     {
         assert (antigenWellgroupName != null);
         assert (sampleName != null);

elispotassay/src/org/labkey/elispot/ElispotAssayProvider.java

@@ -174,10 +174,10 @@ public ElispotAssayProvider()
     }
 
     @Override
-    public Set<ExpData> getDatasForResultRows(Collection<Integer> rowIds, ExpProtocol protocol, ResolverCache cache)
+    public Set<ExpData> getDatasForResultRows(Collection<Long> rowIds, ExpProtocol protocol, ResolverCache cache)
     {
         Set<ExpData> result = new HashSet<>();
-        for (Integer rowId : rowIds)
+        for (var rowId : rowIds)
         {
             RunDataRow dataRow = ElispotManager.get().getRunDataRow(rowId);
             if (dataRow == null)

elispotassay/src/org/labkey/elispot/ElispotDataHandler.java

@@ -523,7 +523,7 @@ public static void populateAntigenRunProperties(ExpRun run, Plate plate, PlateRe
         }
     }
 
-    private static Map<String, Object> makeAntigenRow(int runId, String specimenLsid, String wellgroupName, String antigenName,
+    private static Map<String, Object> makeAntigenRow(long runId, String specimenLsid, String wellgroupName, String antigenName,
                                                       Double mean, Double median, String objectUri, String protocolName,
                                                       String antigenWellgroupName, String analyte, Object cytokine)
     {