Migrate away from deprecated methods

Author: labkey-adam

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

@@ -50,7 +50,7 @@
 import java.util.Map;
 import java.util.Set;
 
-import static org.labkey.api.exp.api.ExperimentService.asInteger;
+import static org.labkey.api.util.IntegerUtils.asInteger;
 
 /**
  * Created by bimber on 9/18/2016.

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

@@ -210,7 +210,7 @@
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipOutputStream;
 
-import static org.labkey.api.exp.api.ExperimentService.asInteger;
+import static org.labkey.api.util.IntegerUtils.asInteger;
 import static org.labkey.sequenceanalysis.SequenceIntegrationTests.PIPELINE_PROP_NAME;
 
 public class SequenceAnalysisController extends SpringActionController

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

@@ -91,7 +91,7 @@
 import java.util.Map;
 import java.util.Set;
 
-import static org.labkey.api.exp.api.ExperimentService.asInteger;
+import static org.labkey.api.util.IntegerUtils.asInteger;
 
 public class SequenceAnalysisManager
 {

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

@@ -69,7 +69,7 @@
 import java.util.Set;
 import java.util.function.Function;
 
-import static org.labkey.api.exp.api.ExperimentService.asLong;
+import static org.labkey.api.util.IntegerUtils.asLong;
 
 /**
  * User: bimber

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

@@ -91,7 +91,7 @@
 import java.util.Set;
 import java.util.stream.Collectors;
 
-import static org.labkey.api.exp.api.ExperimentService.asInteger;
+import static org.labkey.api.util.IntegerUtils.asInteger;
 
 /**
  * User: bimber

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

@@ -69,7 +69,7 @@
 import java.util.Map;
 import java.util.Set;
 
-import static org.labkey.api.exp.api.ExperimentService.asInteger;
+import static org.labkey.api.util.IntegerUtils.asInteger;
 
 /**
  * User: bbimber

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

@@ -42,7 +42,7 @@
 import java.util.Set;
 import java.util.zip.GZIPOutputStream;
 
-import static org.labkey.api.exp.api.ExperimentService.asLong;
+import static org.labkey.api.util.IntegerUtils.asLong;
 
 /**
  * This is designed to parse the FASTQ files produced by a single run on an illumina instructment and produce one gzipped FASTQ

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

@@ -58,7 +58,7 @@
 import java.util.List;
 import java.util.Map;
 
-import static org.labkey.api.exp.api.ExperimentService.asInteger;
+import static org.labkey.api.util.IntegerUtils.asInteger;
 
 /**
  * User: bbimber

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

@@ -82,7 +82,7 @@
 import java.util.Map;
 import java.util.Set;
 
-import static org.labkey.api.exp.api.ExperimentService.asInteger;
+import static org.labkey.api.util.IntegerUtils.asInteger;
 
 /**
  * User: bbimber

Studies/src/org/labkey/studies/StudiesManager.java

@@ -1,6 +1,5 @@
 package org.labkey.studies;
 
-import org.apache.commons.collections.map.CaseInsensitiveMap;
 import org.apache.commons.io.IOUtils;
 import org.json.JSONObject;
 import org.junit.AfterClass;
@@ -19,13 +18,9 @@
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.query.BatchValidationException;
-import org.labkey.api.query.DuplicateKeyException;
 import org.labkey.api.query.FieldKey;
-import org.labkey.api.query.InvalidKeyException;
 import org.labkey.api.query.QueryService;
 import org.labkey.api.query.QueryUpdateService;
-import org.labkey.api.query.QueryUpdateServiceException;
-import org.labkey.api.query.SimpleUserSchema;
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.resource.FileResource;
 import org.labkey.api.resource.Resource;
@@ -34,23 +29,17 @@
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.api.util.TestContext;
-import org.labkey.studies.query.StudiesUserSchema;
-
 
 import java.io.FileInputStream;
 import java.io.InputStream;
-import java.sql.SQLException;
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
-import java.util.stream.Collectors;
 
-import static com.fasterxml.jackson.databind.type.LogicalType.Collection;
-import static org.labkey.api.exp.api.ExperimentService.asInteger;
+import static org.labkey.api.util.IntegerUtils.asInteger;
 
 @RunWith(Enclosed.class)
 public class StudiesManager