Support BIGINT Primary Keys

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)
     {

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

@@ -15,10 +15,11 @@
  */
 package org.labkey.elispot;
 
-import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.assay.AbstractAssayProvider;
 import org.labkey.api.collections.ConcurrentCaseInsensitiveSortedMap;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.DbSchema;
@@ -37,16 +38,12 @@
 import org.labkey.api.exp.property.Domain;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.security.User;
-import org.labkey.api.assay.AbstractAssayProvider;
 
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-/**
- * Created by davebradlee on 3/19/15.
- */
 public class ElispotManager
 {
     private static final Logger _log = LogManager.getLogger(ElispotManager.class);
@@ -82,14 +79,13 @@ public static TableInfo getTableInfoElispotAntigen(ExpProtocol protocol)
         throw new IllegalStateException("Domain not found for protocol: " + protocol.getName());
     }
 
-    public int insertRunDataRow(User user, Map<String, Object> fields)
+    public void insertRunDataRow(User user, Map<String, Object> fields)
     {
-        Map<String, Object> results = Table.insert(user, getTableInfoElispotRunData(), fields);
-        return (Integer)results.get("RowId");
+        Table.insert(user, getTableInfoElispotRunData(), fields);
     }
 
     @Nullable
-    public RunDataRow getRunDataRow(int rowId)
+    public RunDataRow getRunDataRow(long rowId)
     {
         Filter filter = new SimpleFilter(FieldKey.fromString("RowId"), rowId);
         return new TableSelector(getTableInfoElispotRunData()).getObject(filter, RunDataRow.class);
@@ -135,10 +131,9 @@ public void updateRunDataRow(User user, Map<String, Object> fields)
         Table.update(user, getTableInfoElispotRunData(), fields, fields.get("RowId"));
     }
 
-    public String insertAntigenRow(User user, Map<String, Object> fields, ExpProtocol protocol)
+    public void insertAntigenRow(User user, Map<String, Object> fields, ExpProtocol protocol)
     {
-        Map<String, Object> results = Table.insert(user, getTableInfoElispotAntigen(protocol), fields);
-        return results.get("AntigenLsid").toString();
+        Table.insert(user, getTableInfoElispotAntigen(protocol), fields);
     }
 
     public void updateAntigenRow(User user, Map<String, Object> fields, ExpProtocol protocol)
@@ -184,14 +179,14 @@ public void deleteRunData(List<ExpData> datas)
         try (DbScope.Transaction transaction = scope.ensureTransaction())
         {
             // Delete all rows based on the runId
-            Set<Integer> runIds = new HashSet<>();
+            Set<Long> runIds = new HashSet<>();
             for (ExpData data : datas)
             {
                 runIds.add(data.getRunId());
             }
 
             // Since runIds may be from different folders, delete from each separately
-            for (Integer runId : runIds)
+            for (var runId : runIds)
             {
                 if (null != runId)
                 {

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

@@ -17,6 +17,7 @@
 package org.labkey.elispot;
 
 import org.apache.commons.lang3.math.NumberUtils;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.action.SpringActionController;
 import org.labkey.api.data.ActionButton;
 import org.labkey.api.data.ButtonBar;
@@ -45,6 +46,7 @@
 import org.labkey.api.assay.PreviouslyUploadedDataCollector;
 import org.labkey.api.assay.plate.PlateReader;
 import org.labkey.api.util.PageFlowUtil;
+import org.labkey.api.util.logging.LogHelper;
 import org.labkey.api.view.InsertView;
 import org.labkey.elispot.plate.PlateInfo;
 import org.springframework.validation.BindException;
@@ -70,6 +72,8 @@
 @RequiresPermission(InsertPermission.class)
 public class ElispotUploadWizardAction extends UploadWizardAction<ElispotRunUploadForm, ElispotAssayProvider>
 {
+    private static final Logger LOG = LogHelper.getLogger(ElispotUploadWizardAction.class, "Elispot upload errors");
+
     public ElispotUploadWizardAction()
     {
         super(ElispotRunUploadForm.class);
@@ -566,6 +570,7 @@ protected ExpRun finishPost(ElispotRunUploadForm form, BindException errors)
             }
             catch (ExperimentException e)
             {
+                LOG.error("Unexpected exception", e);
                 errors.reject(SpringActionController.ERROR_MSG, e.getMessage());
             }
 

flow/src/org/labkey/flow/FlowServiceImpl.java

@@ -64,7 +64,7 @@ public List<? extends ExpData> getExpDataByPath(Path path, @Nullable Container c
 
             sql.append(" ORDER BY 1");
 
-            Integer[] dataids = new SqlSelector(FlowManager.get().getSchema(), sql).getArray(Integer.class);
+            Long[] dataids = new SqlSelector(FlowManager.get().getSchema(), sql).getArray(Long.class);
 
             return ExperimentService.get().getExpDatas(Arrays.asList(dataids));
         }

flow/src/org/labkey/flow/controllers/BaseFlowController.java

@@ -217,9 +217,9 @@ protected void putParam(ActionURL url, Enum<?> param, String value)
         url.replaceParameter(param.toString(), value);
     }
 
-    protected void putParam(ActionURL url, Enum<?> param, int value)
+    protected void putParam(ActionURL url, Enum<?> param, long value)
     {
-        putParam(url, param, Integer.toString(value));
+        putParam(url, param, Long.toString(value));
     }
 
     public HttpServletRequest getRequest()

flow/src/org/labkey/flow/controllers/ReportsController.java

@@ -408,7 +408,7 @@ else if (r.saveToDomain())
                         PipelineService.get().queueJob(job);
 
                         // navigate to the job status page
-                        int jobId = PipelineService.get().getJobId(getUser(), getContainer(), job.getJobGUID());
+                        long jobId = PipelineService.get().getJobId(getUser(), getContainer(), job.getJobGUID());
                         throw new RedirectException(urlProvider(PipelineStatusUrls.class).urlDetails(getContainer(), jobId));
                     }
                 }

flow/src/org/labkey/flow/controllers/attribute/summary.jsp

@@ -44,7 +44,7 @@
             FlowEntry primary = entry.getKey();
             Collection<FlowEntry> aliases = entry.getValue();
 
-            Map<Integer, Number> counts = FlowManager.get().getUsageCount(primary._type, primary._rowId);
+            Map<Long, Number> counts = FlowManager.get().getUsageCount(primary._type, primary._rowId);
             long totalCount = 0;
             for (Number count : counts.values())
                 totalCount += count.longValue();

flow/src/org/labkey/flow/controllers/editscript/EditScriptForm.java

@@ -97,12 +97,12 @@ public void reset()
             _run = FlowRun.fromURL(getViewContext().getActionURL(), getRequest(), getViewContext().getContainer(), getUser());
             if (_run != null)
             {
-                FlowPreference.editScriptRunId.setValue(getRequest(), Integer.toString(_run.getRunId()));
+                FlowPreference.editScriptRunId.setValue(getRequest(), Long.toString(_run.getRunId()));
             }
             _comp = FlowCompensationMatrix.fromURL(getViewContext().getActionURL(), getRequest(), getContainer(), getUser());
             if (_comp != null)
             {
-                FlowPreference.editScriptCompId.setValue(getRequest(), Integer.toString(_comp.getRowId()));
+                FlowPreference.editScriptCompId.setValue(getRequest(), Long.toString(_comp.getRowId()));
             }
             String strWellId = getRequest().getParameter(FlowParam.wellId.toString());
             if (strWellId != null)
@@ -320,14 +320,14 @@ public boolean canEdit()
         return getContainer().hasPermission(getUser(), UpdatePermission.class) && _runCount == 0;
     }
 
-    public Map<Integer, String> getExperimentRuns()
+    public Map<Long, String> getExperimentRuns()
     {
         return getExperimentRuns(false);
     }
 
-    public Map<Integer, String> getExperimentRuns(boolean realFiles)
+    public Map<Long, String> getExperimentRuns(boolean realFiles)
     {
-        LinkedHashMap<Integer, String> ret = new LinkedHashMap<>();
+        LinkedHashMap<Long, String> ret = new LinkedHashMap<>();
         List<FlowRun> runs = realFiles ?
                 FlowRun.getRunsWithRealFCSFiles(getContainer(), FlowProtocolStep.keywords) :
                 FlowRun.getRunsForContainer(getContainer(), FlowProtocolStep.keywords);

flow/src/org/labkey/flow/controllers/executescript/AnalysisScriptController.java

@@ -1216,7 +1216,7 @@ private void resolveSamples(ImportAnalysisForm form, @Nullable FlowRun keywordRu
                     if (matches != null)
                     {
                         FlowFCSFile perfectMatch = matches.first;
-                        int perfectMatchId = perfectMatch != null ? perfectMatch.getRowId() : 0;
+                        long perfectMatchId = perfectMatch != null ? perfectMatch.getRowId() : 0;
                         List<FlowFCSFile> candidates = matches.second;
 
                         if (perfectMatchId != 0 || (candidates != null && !candidates.isEmpty()))

flow/src/org/labkey/flow/controllers/executescript/ChooseRunsToAnalyzeForm.java

@@ -170,7 +170,7 @@ public void populate(BindException errors)
             FlowExperiment analysis = FlowExperiment.getMostRecentAnalysis(getContainer());
             if (analysis != null)
             {
-                ff_targetExperimentId = Integer.toString(analysis.getExperimentId());
+                ff_targetExperimentId = Long.toString(analysis.getExperimentId());
             }
         }
         Collection<FlowScript> availableProtocols = Arrays.asList(FlowScript.getScripts(getContainer()));