diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/OutputIntegrationTests.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/OutputIntegrationTests.java index 41b45779e..7d8e716d8 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/OutputIntegrationTests.java +++ b/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. diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java index 25a8b5268..3f74c0df3 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java +++ b/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 diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisManager.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisManager.java index 59fe53d6d..c2bca075c 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisManager.java +++ b/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 { diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisServiceImpl.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisServiceImpl.java index 976c9009e..11cbb37c3 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisServiceImpl.java +++ b/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 diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceIntegrationTests.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceIntegrationTests.java index 45d1737d4..4ee5aa85f 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceIntegrationTests.java +++ b/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 diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CreateReferenceLibraryTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CreateReferenceLibraryTask.java index b2784cf17..7a6f149db 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CreateReferenceLibraryTask.java +++ b/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 diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaFastqSplitter.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaFastqSplitter.java index a88fd7f5d..5e6a3f900 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaFastqSplitter.java +++ b/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 diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaImportTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaImportTask.java index 8c320d331..b436f501d 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaImportTask.java +++ b/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 diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java index 53578ab71..6c13f1249 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java +++ b/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 diff --git a/Studies/src/org/labkey/studies/StudiesManager.java b/Studies/src/org/labkey/studies/StudiesManager.java index eedaedba3..f7c23f2b3 100644 --- a/Studies/src/org/labkey/studies/StudiesManager.java +++ b/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 diff --git a/jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseSessionTask.java b/jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseSessionTask.java index dd8b9b0f6..2739ef11c 100644 --- a/jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseSessionTask.java +++ b/jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseSessionTask.java @@ -44,7 +44,7 @@ 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