remove (Integer) casts

bulk search/replace

Author: labkey-matthewb

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java

@@ -209,6 +209,7 @@
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipOutputStream;
 
+import static org.labkey.api.exp.api.ExperimentService.asInteger;
 import static org.labkey.sequenceanalysis.SequenceIntegrationTests.PIPELINE_PROP_NAME;
 
 public class SequenceAnalysisController extends SpringActionController
@@ -3239,8 +3240,8 @@ public ApiResponse execute(CheckFileStatusForm form, BindException errors)
                         continue;
                     }
 
-                    Integer dataId = (Integer) rowMap.get("dataid");
-                    Integer libraryId = (Integer) rowMap.get("library_id");
+                    Integer dataId = asInteger(rowMap.get("dataid"));
+                    Integer libraryId = asInteger(rowMap.get("library_id"));
                     ExpData d = ExperimentService.get().getExpData(dataId);
                     if (d == null)
                     {

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisManager.java

@@ -91,6 +91,8 @@
 import java.util.Map;
 import java.util.Set;
 
+import static org.labkey.api.exp.api.ExperimentService.asInteger;
+
 public class SequenceAnalysisManager
 {
     private static final SequenceAnalysisManager _instance = new SequenceAnalysisManager();
@@ -783,7 +785,7 @@ public List<Integer> importRefSequencesFromFasta(Container c, User u, File file,
                         map.put("jobId", jobId);
 
                     map = Table.insert(u, dnaTable, map);
-                    sequenceIds.add((Integer) map.get("rowid"));
+                    sequenceIds.add(asInteger(map.get("rowid")));
 
                     RefNtSequenceModel m = new TableSelector(dnaTable, new SimpleFilter(FieldKey.fromString("rowid"), map.get("rowid")), null).getObject(RefNtSequenceModel.class);
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisServiceImpl.java

@@ -69,6 +69,8 @@
 import java.util.Set;
 import java.util.function.Function;
 
+import static org.labkey.api.exp.api.ExperimentService.asLong;
+
 /**
  * User: bimber
  * Date: 10/27/13
@@ -231,7 +233,7 @@ public ReferenceGenomeImpl getReferenceGenome(int genomeId, User u) throws Pipel
             throw new UnauthorizedException("Cannot read data in container: " + c.getPath());
         }
 
-        ExpData d = ExperimentService.get().getExpData((Integer)map.get("fasta_file"));
+        ExpData d = ExperimentService.get().getExpData(asLong(map.get("fasta_file")));
         if (d.getFile() == null)
         {
             throw new PipelineJobException("No FASTA file found for genome: " + genomeId);

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceIntegrationTests.java

@@ -90,6 +90,8 @@
 import java.util.Set;
 import java.util.stream.Collectors;
 
+import static org.labkey.api.exp.api.ExperimentService.asInteger;
+
 /**
  * User: bimber
  * Date: 11/25/12
@@ -1753,11 +1755,11 @@ protected Integer createSavedLibrary() throws Exception
             if (ts.exists())
             {
                 Map<String, Object> rowMap = ts.getMap();
-                Integer fasta_file = (Integer)rowMap.get("fasta_file");
+                Integer fasta_file = asInteger(rowMap.get("fasta_file"));
                 ExpData d = fasta_file == null ? null : ExperimentService.get().getExpData(fasta_file);
                 if (d != null && d.getFile() != null && d.getFile().exists())
                 {
-                    return (Integer) rowMap.get("rowid");
+                    return asInteger(rowMap.get("rowid"));
                 }
                 else
                 {

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaImportTask.java

@@ -57,6 +57,8 @@
 import java.util.List;
 import java.util.Map;
 
+import static org.labkey.api.exp.api.ExperimentService.asInteger;
+
 /**
  * User: bbimber
  * Date: 4/22/12
@@ -292,7 +294,7 @@ private void handleInstrumentRun(DbSchema schema)
 
         runRow = Table.insert(getJob().getUser(), runTable, runRow);
 
-        _instrumentRunId = (Integer)runRow.get("rowid");
+        _instrumentRunId = asInteger(runRow.get("rowid"));
         getJob().getLogger().info("Created run: " + _instrumentRunId);
     }
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java

@@ -81,6 +81,8 @@
 import java.util.Map;
 import java.util.Set;
 
+import static org.labkey.api.exp.api.ExperimentService.asInteger;
+
 /**
  * User: bbimber
  * Date: 8/6/12
@@ -338,7 +340,7 @@ else if (SequenceUtil.FILETYPE.bw.getFileType().isType(file))
             throw new PipelineJobException("Unable to find rowid for new track");
         }
 
-        return (Integer)map.get("rowid");
+        return asInteger(map.get("rowid"));
     }
 
     private void sortGxf(File gxf) throws PipelineJobException