diff --git a/OpenLdapSync/src/org/labkey/openldapsync/OpenLdapSyncController.java b/OpenLdapSync/src/org/labkey/openldapsync/OpenLdapSyncController.java index 07c1bdeb6..3922cba86 100644 --- a/OpenLdapSync/src/org/labkey/openldapsync/OpenLdapSyncController.java +++ b/OpenLdapSync/src/org/labkey/openldapsync/OpenLdapSyncController.java @@ -57,7 +57,7 @@ public OpenLdapSyncController() } @RequiresPermission(AdminOperationsPermission.class) - public class InitiateLdapSyncAction extends MutatingApiAction + public static class InitiateLdapSyncAction extends MutatingApiAction { @Override public ApiResponse execute(InitiateLdapSyncForm form, BindException errors) throws Exception @@ -100,7 +100,7 @@ public void setForPreview(boolean forPreview) } @RequiresPermission(AdminPermission.class) - public class ListLdapGroupsAction extends ReadOnlyApiAction + public static class ListLdapGroupsAction extends ReadOnlyApiAction { @Override public ApiResponse execute(LdapForm form, BindException errors) throws Exception @@ -495,7 +495,7 @@ public void setMemberSyncMode(String memberSyncMode) } @RequiresPermission(AdminOperationsPermission.class) - public class TestLdapConnectionAction extends MutatingApiAction + public static class TestLdapConnectionAction extends MutatingApiAction { @Override public ApiResponse execute(Object form, BindException errors) throws Exception @@ -545,7 +545,7 @@ public ApiResponse execute(Object form, BindException errors) throws Exception } @RequiresPermission(AdminOperationsPermission.class) - public class GetLdapSettingsAction extends ReadOnlyApiAction + public static class GetLdapSettingsAction extends ReadOnlyApiAction { @Override public ApiResponse execute(Object form, BindException errors) @@ -569,7 +569,7 @@ public ApiResponse execute(Object form, BindException errors) @Marshal(Marshaller.Jackson) @RequiresPermission(AdminOperationsPermission.class) - public class SetLdapSettingsAction extends MutatingApiAction + public static class SetLdapSettingsAction extends MutatingApiAction { @Override public ApiResponse execute(LdapForm form, BindException errors) @@ -668,7 +668,7 @@ public ApiResponse execute(LdapForm form, BindException errors) if (form.getSyncMode() != null) props.put(LdapSettings.SYNC_MODE_PROP, form.getSyncMode()); - if (form.getAllowedDn() != null && form.getAllowedDn().length() > 0) + if (form.getAllowedDn() != null && !form.getAllowedDn().isEmpty()) { String allowed = StringUtils.join(form.getAllowedDn().toList(), LdapSettings.DELIM); props.put(LdapSettings.ALLOWED_DN_PROP, allowed); diff --git a/OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapEntry.java b/OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapEntry.java index 91bd18986..ff220b674 100644 --- a/OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapEntry.java +++ b/OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapEntry.java @@ -75,8 +75,8 @@ public boolean isEnabled() try { - Integer value = Integer.parseInt(a); - return (value.intValue() & 2) == 0; + int value = Integer.parseInt(a); + return (value & 2) == 0; } catch (NumberFormatException e) { diff --git a/OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapSettings.java b/OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapSettings.java index 3bb0dca29..0d1761826 100644 --- a/OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapSettings.java +++ b/OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapSettings.java @@ -466,7 +466,6 @@ public Integer getFrequency() /** * Provides a brief sanity check of the settings, designed to identify problems if a sync will run. - * @throws LdapException */ public void validateSettings() throws LdapException { @@ -495,7 +494,7 @@ public void validateSettings() throws LdapException if (LdapSyncMode.groupWhitelist.equals(mode)) { - if (getGroupWhiteList().size() == 0) + if (getGroupWhiteList().isEmpty()) { throw new LdapException("Cannot choose to sync based on specific groups unless you provide a list of groups to sync"); } diff --git a/OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapSyncRunner.java b/OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapSyncRunner.java index 20615a8be..a30d76960 100644 --- a/OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapSyncRunner.java +++ b/OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapSyncRunner.java @@ -14,7 +14,6 @@ import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.data.RuntimeSQLException; -import org.labkey.api.data.Selector; import org.labkey.api.data.SimpleFilter; import org.labkey.api.data.Table; import org.labkey.api.data.TableInfo; @@ -1058,7 +1057,7 @@ public void testIndividualOperations() throws Exception } // This can be used to return LdapEntry objects to support some degree of automated testing without needing a functional LDAP Server - public class DummyConnectionWrapper extends LdapConnectionWrapper + public static class DummyConnectionWrapper extends LdapConnectionWrapper { private final List _users = new ArrayList<>(); private final Map _groupMap = new HashMap<>(); diff --git a/QueryExtensions/src/org/labkey/queryextensions/QueryExtensionsController.java b/QueryExtensions/src/org/labkey/queryextensions/QueryExtensionsController.java index 95772162d..dfeccbf2d 100644 --- a/QueryExtensions/src/org/labkey/queryextensions/QueryExtensionsController.java +++ b/QueryExtensions/src/org/labkey/queryextensions/QueryExtensionsController.java @@ -16,14 +16,7 @@ package org.labkey.queryextensions; -import org.labkey.api.action.SimpleViewAction; import org.labkey.api.action.SpringActionController; -import org.labkey.api.security.RequiresPermission; -import org.labkey.api.security.permissions.ReadPermission; -import org.labkey.api.view.JspView; -import org.labkey.api.view.NavTree; -import org.springframework.validation.BindException; -import org.springframework.web.servlet.ModelAndView; public class QueryExtensionsController extends SpringActionController { diff --git a/QueryExtensions/test/src/org/labkey/test/tests/queryextensions/QueryExtensionsTest.java b/QueryExtensions/test/src/org/labkey/test/tests/queryextensions/QueryExtensionsTest.java index 9065c8158..1991e71c1 100644 --- a/QueryExtensions/test/src/org/labkey/test/tests/queryextensions/QueryExtensionsTest.java +++ b/QueryExtensions/test/src/org/labkey/test/tests/queryextensions/QueryExtensionsTest.java @@ -39,7 +39,7 @@ protected void doCleanup(boolean afterTest) throws TestTimeoutException @BeforeClass public static void setupProject() { - QueryExtensionsTest init = (QueryExtensionsTest)getCurrentTest(); + QueryExtensionsTest init = getCurrentTest(); init.doSetup(); } diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/GenomeTrigger.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/GenomeTrigger.java index 13fc2a48a..4e571e041 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/GenomeTrigger.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/GenomeTrigger.java @@ -16,7 +16,6 @@ package org.labkey.api.sequenceanalysis; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.security.User; diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/SequenceAnalysisService.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/SequenceAnalysisService.java index b718f7588..924b5b666 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/SequenceAnalysisService.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/SequenceAnalysisService.java @@ -113,10 +113,10 @@ static public void setInstance(SequenceAnalysisService instance) abstract public void registerReadsetListener(ReadsetListener listener); - public static interface ReadsetListener + public interface ReadsetListener { - public void onReadsetCreate(User u, Readset rs, @Nullable Readset replacedReadset, @Nullable PipelineJob job); + void onReadsetCreate(User u, Readset rs, @Nullable Readset replacedReadset, @Nullable PipelineJob job); - public boolean isAvailable(Container c, User u); + boolean isAvailable(Container c, User u); } } diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AbstractPipelineStepProvider.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AbstractPipelineStepProvider.java index 36af24665..8cafb83eb 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AbstractPipelineStepProvider.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AbstractPipelineStepProvider.java @@ -20,7 +20,6 @@ import org.json.JSONObject; import org.labkey.api.view.template.ClientDependency; -import java.lang.reflect.ParameterizedType; import java.util.Collection; import java.util.Collections; import java.util.LinkedHashSet; @@ -39,7 +38,7 @@ abstract public class AbstractPipelineStepProvider _clientDependencyPaths; - private List _parameters; + private final List _parameters; public AbstractPipelineStepProvider(String name, String label, @Nullable String toolName, String description, @Nullable List parameters, @Nullable Collection clientDependencyPaths, @Nullable String websiteURL) { diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AlignerIndexUtil.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AlignerIndexUtil.java index 1e55f7e1a..5b86a99d7 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AlignerIndexUtil.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AlignerIndexUtil.java @@ -1,17 +1,13 @@ package org.labkey.api.sequenceanalysis.pipeline; import org.apache.commons.io.FileUtils; -import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.ConvertHelper; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.pipeline.WorkDirectory; -import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper; import java.io.File; import java.io.IOException; -import java.util.Arrays; /** * Created by bimber on 9/6/2014. diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AlignmentStep.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AlignmentStep.java index bef8780a3..672bf202e 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AlignmentStep.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AlignmentStep.java @@ -35,7 +35,6 @@ public interface AlignmentStep extends PipelineStep { /** * Creates any indexes needed by this aligner if not already present. - * @throws PipelineJobException */ IndexOutput createIndex(ReferenceGenome referenceGenome, File outputDir) throws PipelineJobException; @@ -49,7 +48,6 @@ default String getIndexCachedDirName(PipelineJob job) * @param inputFastqs1 The forward FASTQ file(s). In most cases this is a single FASTQ. The aligner must return true for canAlignMultiplePairsAtOnce() otherwise. * @param inputFastqs2 The second FASTQ(s), if using paired end data * @param basename The basename to use as the output - * @throws PipelineJobException */ AlignmentOutput performAlignment(Readset rs, List inputFastqs1, @Nullable List inputFastqs2, File outputDirectory, ReferenceGenome referenceGenome, String basename, String readGroupId, @Nullable String platformUnit) throws PipelineJobException; @@ -102,7 +100,6 @@ interface AlignmentOutput extends PipelineStepOutput /** * Optional. Allows this analysis to gather any information from the server required to execute the alignment. This information needs to be serialized * to run remotely, which could be as simple as writing to a text file. - * @throws PipelineJobException */ default void init(SequenceAnalysisJobSupport support) throws PipelineJobException { diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AnalysisStep.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AnalysisStep.java index dbf7ee5be..1fca4f975 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AnalysisStep.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AnalysisStep.java @@ -31,7 +31,6 @@ public interface AnalysisStep extends PipelineStep /** * Optional. Allows this analysis to gather any information from the server required to execute the analysis. This information needs to be serialized * to run remotely, which could be as simple as writing to a text file. - * @throws PipelineJobException */ default void init(SequenceAnalysisJobSupport support) throws PipelineJobException { diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AssemblyStep.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AssemblyStep.java index ee29bda65..f2cd990c4 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AssemblyStep.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AssemblyStep.java @@ -3,7 +3,6 @@ import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.model.Readset; -import org.labkey.api.util.Pair; import java.io.File; diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/CommandLineParam.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/CommandLineParam.java index 030c67df1..446a32858 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/CommandLineParam.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/CommandLineParam.java @@ -29,7 +29,7 @@ public class CommandLineParam { private final String _argName; - protected boolean _isSwitch = false; + protected boolean _isSwitch; private CommandLineParam(String argName, boolean isSwitch) { diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/PipelineOutputTracker.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/PipelineOutputTracker.java index 5d2c61d95..b535eb9c0 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/PipelineOutputTracker.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/PipelineOutputTracker.java @@ -9,7 +9,6 @@ public interface PipelineOutputTracker { /** * Add an intermediate file. If the user selected 'delete intermediates', this will be deleted on job success. - * @param file */ void addIntermediateFile(File file); @@ -17,13 +16,6 @@ public interface PipelineOutputTracker /** * Add a SequenceOutputFile for this job. These files are tracked and displayed through the browser UI. - * @param file - * @param label - * @param category - * @param readsetId - * @param analysisId - * @param genomeId - * @param description */ void addSequenceOutput(File file, String label, String category, @Nullable Integer readsetId, @Nullable Integer analysisId, @Nullable Integer genomeId, @Nullable String description); diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/PipelineStepOutput.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/PipelineStepOutput.java index e80fc80b4..92aaad56b 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/PipelineStepOutput.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/PipelineStepOutput.java @@ -16,7 +16,6 @@ package org.labkey.api.sequenceanalysis.pipeline; import org.jetbrains.annotations.Nullable; -import org.labkey.api.sequenceanalysis.model.Readset; import org.labkey.api.util.Pair; import java.io.File; @@ -34,15 +33,11 @@ public interface PipelineStepOutput extends PipelineOutputTracker { /** * Add an experiment input to this pipeline step - * @param input - * @param role */ void addInput(File input, String role); /** * Add an experiment output to this pipeline step - * @param output - * @param role */ void addOutput(File output, String role); @@ -65,8 +60,6 @@ public interface PipelineStepOutput extends PipelineOutputTracker /** * Add an intermediate file. If the user selected 'delete intermediates', this will be deleted on job success. * This will also be recorded as a step output with this role. - * @param file - * @param role */ void addIntermediateFile(File file, String role); diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/ProcessUtils.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/ProcessUtils.java index 5064c2398..c3c45f56a 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/ProcessUtils.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/ProcessUtils.java @@ -3,7 +3,6 @@ import org.apache.commons.io.IOUtils; import org.apache.logging.log4j.Level; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.util.StringUtilsLabKey; import java.io.BufferedInputStream; diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SamtoolsIndexer.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SamtoolsIndexer.java index 0aa93644f..2224fd55f 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SamtoolsIndexer.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SamtoolsIndexer.java @@ -1,7 +1,6 @@ package org.labkey.api.sequenceanalysis.pipeline; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.pipeline.PipelineJobException; import java.io.File; diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SamtoolsRunner.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SamtoolsRunner.java index 42b8f9e8b..2e64a32a5 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SamtoolsRunner.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SamtoolsRunner.java @@ -1,7 +1,6 @@ package org.labkey.api.sequenceanalysis.pipeline; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper; diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequenceOutputHandler.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequenceOutputHandler.java index 1f9645621..f8448a485 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequenceOutputHandler.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequenceOutputHandler.java @@ -136,7 +136,6 @@ default boolean isVisible() /** * Provides the opportunity for the handler to validate parameters prior to running - * @param params * @return List of error messages. Null or empty list indicates no errors. */ default List validateParameters(List outputFiles, JSONObject params) @@ -174,8 +173,6 @@ interface SequenceOutputProcessor extends SequenceProcessor * Allows handlers to perform setup on the webserver prior to remote running. This will be run in the background as a pipeline job. * @param ctx Provides context about the active pipeline job * @param inputFiles The list of input files to process - * @param actions - * @param outputsToCreate */ default void init(JobContext ctx, List inputFiles, List actions, List outputsToCreate) throws UnsupportedOperationException, PipelineJobException { @@ -189,10 +186,6 @@ default void init(JobContext ctx, List inputFiles, List inputFiles, JSONObject params, File outputDir, List actions, List outputsToCreate) throws UnsupportedOperationException, PipelineJobException; @@ -211,10 +204,6 @@ interface SequenceReadsetProcessor extends SequenceProcessor * @param job The pipeline job running this task * @param support Provides context about the active pipeline job * @param readsets The list of readsets to process - * @param params - * @param outputDir - * @param actions - * @param outputsToCreate */ void init(PipelineJob job, SequenceAnalysisJobSupport support, List readsets, JSONObject params, File outputDir, List actions, List outputsToCreate) throws UnsupportedOperationException, PipelineJobException; @@ -222,10 +211,6 @@ interface SequenceReadsetProcessor extends SequenceProcessor * * @param support Provides context about the active pipeline job * @param readsets The list of readsets to process - * @param params - * @param outputDir - * @param actions - * @param outputsToCreate */ void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport support, List readsets, JSONObject params, File outputDir, List actions, List outputsToCreate) throws UnsupportedOperationException, PipelineJobException; diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequencePipelineService.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequencePipelineService.java index b57555a1c..e0f8df975 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequencePipelineService.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequencePipelineService.java @@ -129,11 +129,6 @@ static public void setInstance(SequencePipelineService instance) /** * - * @param input - * @param log - * @param startColumnIdx The 1-based column on which to sort. BED files are 2 and GTF/GFF are 4 - * @throws IOException - * @throws PipelineJobException */ abstract public void sortROD(File input, Logger log, Integer startColumnIdx) throws IOException, PipelineJobException; diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SortSamWrapper.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SortSamWrapper.java index ee7fb6388..2dc45ed17 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SortSamWrapper.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SortSamWrapper.java @@ -4,7 +4,6 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.lang3.time.DurationFormatUtils; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.run.PicardWrapper; diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/TaskFileManager.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/TaskFileManager.java index beecdcb51..1c211e399 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/TaskFileManager.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/TaskFileManager.java @@ -56,7 +56,7 @@ public interface TaskFileManager extends PipelineOutputTracker boolean isDeleteIntermediateFiles(); - public boolean performCleanupAfterEachStep(); + boolean performCleanupAfterEachStep(); boolean isCopyInputsLocally(); diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/ToolParameterDescriptor.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/ToolParameterDescriptor.java index 12a054d57..ce31492dc 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/ToolParameterDescriptor.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/ToolParameterDescriptor.java @@ -27,7 +27,6 @@ import java.util.ArrayList; import java.util.List; -import java.util.Map; /** * User: bimber diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java index e9b0df727..dfc4f0232 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java @@ -43,7 +43,7 @@ abstract public class AbstractCommandWrapper implements CommandWrapper { private File _outputDir = null; private File _workingDir = null; - private Logger _log = null; + private Logger _log; private Level _logLevel = Level.DEBUG; private boolean _warnNonZeroExits = true; private boolean _throwNonZeroExits = true; @@ -221,7 +221,7 @@ private void setPath(ProcessBuilder pb) // If the command has a path, then prepend its parent directory to the PATH // environment variable as well. String exePath = pb.command().get(0); - if (exePath != null && !"".equals(exePath) && exePath.indexOf(File.separatorChar) != -1) + if (exePath != null && !exePath.isEmpty() && exePath.indexOf(File.separatorChar) != -1) { File fileExe = new File(exePath); String exeDir = fileExe.getParent(); diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractDiscvrSeqWrapper.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractDiscvrSeqWrapper.java index 41f63e428..2a2569cf5 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractDiscvrSeqWrapper.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractDiscvrSeqWrapper.java @@ -1,7 +1,6 @@ package org.labkey.api.sequenceanalysis.run; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; public class AbstractDiscvrSeqWrapper extends AbstractGatk4Wrapper { diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractGatkWrapper.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractGatkWrapper.java index 98eab53bf..38caf2da7 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractGatkWrapper.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractGatkWrapper.java @@ -1,10 +1,6 @@ package org.labkey.api.sequenceanalysis.run; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.math3.exception.ConvergenceException; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; -import org.labkey.api.data.ConvertHelper; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.pipeline.PipelineJobService; import org.labkey.api.sequenceanalysis.SequenceAnalysisService; diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/CommandWrapper.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/CommandWrapper.java index 2ee8f0769..667cb03a9 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/CommandWrapper.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/CommandWrapper.java @@ -30,8 +30,6 @@ public interface CommandWrapper /** * * @param params A list of params used to create the command. This will be passed directly to ProcessBuilder() - * @return The output of this command. - * @throws PipelineJobException */ void execute(List params) throws PipelineJobException; diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/GeneToNameTranslator.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/GeneToNameTranslator.java index adeb88ef2..f6b8fbdf8 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/GeneToNameTranslator.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/GeneToNameTranslator.java @@ -1,7 +1,6 @@ package org.labkey.api.sequenceanalysis.run; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.reader.Readers; import org.labkey.api.util.FileUtil; diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/PicardWrapper.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/PicardWrapper.java index 63404c554..d32c8767a 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/PicardWrapper.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/PicardWrapper.java @@ -3,10 +3,8 @@ import htsjdk.samtools.ValidationStringency; import org.apache.commons.lang3.StringUtils; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; -import org.labkey.api.pipeline.PipelineJobService; import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; import java.io.File; diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/SelectVariantsWrapper.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/SelectVariantsWrapper.java index 13849200f..039bbcdf3 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/SelectVariantsWrapper.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/SelectVariantsWrapper.java @@ -1,7 +1,6 @@ package org.labkey.api.sequenceanalysis.run; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.pipeline.PipelineJobException; import java.io.File; diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/SimpleScriptWrapper.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/SimpleScriptWrapper.java index 4e48f3b16..7bd140d10 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/SimpleScriptWrapper.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/SimpleScriptWrapper.java @@ -1,7 +1,6 @@ package org.labkey.api.sequenceanalysis.run; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; /** diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/VariantFiltrationWrapper.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/VariantFiltrationWrapper.java index 5e474b225..e7bb587a8 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/VariantFiltrationWrapper.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/VariantFiltrationWrapper.java @@ -1,7 +1,6 @@ package org.labkey.api.sequenceanalysis.run; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.pipeline.PipelineJobException; import java.io.File; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/FileGroup.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/FileGroup.java index 195105108..7ff3914cb 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/FileGroup.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/FileGroup.java @@ -3,7 +3,6 @@ import java.io.File; import java.io.Serializable; import java.util.ArrayList; -import java.util.Arrays; import java.util.Comparator; import java.util.HashSet; import java.util.List; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/OutputIntegrationTests.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/OutputIntegrationTests.java index e58e34001..3b2ba8350 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/OutputIntegrationTests.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/OutputIntegrationTests.java @@ -23,13 +23,11 @@ import org.labkey.api.data.TableSelector; import org.labkey.api.exp.api.ExpData; import org.labkey.api.exp.api.ExperimentService; -import org.labkey.api.laboratory.LaboratoryService; import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.pipeline.PipelineJobService; import org.labkey.api.query.DetailsURL; import org.labkey.api.query.FieldKey; import org.labkey.api.query.QueryService; -import org.labkey.api.sequenceanalysis.SequenceAnalysisService; import org.labkey.api.util.FileUtil; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.TestContext; @@ -149,7 +147,7 @@ protected Set createOutputHandlerJob(String jobName, JSONObject con throw new RuntimeException("Problem creating pipeline job: " + responseJson.getString("exception")); JSONArray guidList = responseJson.getJSONArray("jobGUIDs"); - assert guidList.length() >= 1; + assert !guidList.isEmpty(); Set ret = new HashSet<>(); for (int i = 0; i < guidList.length(); i++) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java index 534381244..3ca197e72 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java @@ -311,7 +311,7 @@ public ModelAndView getView(FastqcForm form, BindException errors) throws Except } } - if (files.size() == 0) + if (files.isEmpty()) { return HtmlView.of("Error: either no files provided or the files did not exist on the server"); } @@ -1100,7 +1100,7 @@ public ApiResponse execute(ValidateReadsetImportForm form, BindException errors) } } - if (datas.size() > 0) + if (!datas.isEmpty()) { for (ExpData d : datas) { @@ -2910,7 +2910,7 @@ public void export(DownloadReferencesForm form, final HttpServletResponse respon public void exec(ResultSet object) throws SQLException { Results rs = new ResultsImpl(object, cols); - Integer rowId = rs.getInt(FieldKey.fromString("rowid")); + int rowId = rs.getInt(FieldKey.fromString("rowid")); String header = se.eval(rs.getFieldKeyRowMap()); RefNtSequenceModel model = new RefNtSequenceModel(); if (rs.getObject(FieldKey.fromString("sequenceFile")) != null) @@ -2920,7 +2920,7 @@ public void exec(ResultSet object) throws SQLException try { - if (intervalMap.has(rowId.toString())) + if (intervalMap.has(Integer.toString(rowId))) { String wholeSequence = model.getSequence(); if (wholeSequence == null) @@ -2929,7 +2929,7 @@ public void exec(ResultSet object) throws SQLException return; } - for (String t : intervalMap.getString(rowId.toString()).split(",")) + for (String t : intervalMap.getString(Integer.toString(rowId)).split(",")) { String[] coordinates = t.split("-"); if (coordinates.length != 2) @@ -3396,7 +3396,7 @@ private static JSONObject getReourceSettingsJson(Container c) } } - if (resourceSettings.length() > 0) + if (!resourceSettings.isEmpty()) { JSONObject json = new JSONObject(); json.put("name", "resourceSettings"); @@ -4487,9 +4487,9 @@ public static SequenceMatch checkReference(String name, DNASequence fastaSequenc private static SequenceMatch doCheck(String name, String seq, String refSeq, RefNtSequenceModel match, DNASequence fastaSequence, boolean isRC) { - boolean sequencesMatch = refSeq.length() > 0 && seq.length() > 0 && seq.equals(refSeq); - boolean fastaSequenceIsSubsetOfReference = refSeq.length() > 0 && seq.length() > 0 && refSeq.contains(seq); - boolean referenceSequenceIsSubsetOfFasta = refSeq.length() > 0 && seq.length() > 0 && seq.contains(refSeq); + boolean sequencesMatch = !refSeq.isEmpty() && !seq.isEmpty() && seq.equals(refSeq); + boolean fastaSequenceIsSubsetOfReference = !refSeq.isEmpty() && !seq.isEmpty() && refSeq.contains(seq); + boolean referenceSequenceIsSubsetOfFasta = !refSeq.isEmpty() && !seq.isEmpty() && seq.contains(refSeq); if (name.equals(match.getName()) || sequencesMatch || fastaSequenceIsSubsetOfReference || referenceSequenceIsSubsetOfFasta) { diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisManager.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisManager.java index b4226eb91..930469cc7 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisManager.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisManager.java @@ -82,7 +82,6 @@ import java.sql.ResultSet; import java.sql.SQLException; import java.util.ArrayList; -import java.util.Arrays; import java.util.Collection; import java.util.Collections; import java.util.Date; @@ -162,7 +161,7 @@ public List getSequencePlatforms() { _platforms = new ArrayList<>(); TableSelector ts = new TableSelector(SequenceAnalysisSchema.getInstance().getSchema().getTable(SequenceAnalysisSchema.TABLE_SEQUENCE_PLATFORMS)); - ts.forEach(new TableSelector.ForEachBlock() + ts.forEach(new TableSelector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java index 2d7ea845f..df804a5aa 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java @@ -510,17 +510,17 @@ protected void registerContainerListeners() public Set getIntegrationTests() { @SuppressWarnings({"unchecked"}) - Set testClasses = new HashSet(Arrays.asList( - Barcoder.TestCase.class, - BamIterator.TestCase.class, - SequenceIntegrationTests.SequenceImportPipelineTestCase.class, - //SequenceIntegrationTests.SequenceAnalysisPipelineTestCase3.class, - SequenceIntegrationTests.SequenceAnalysisPipelineTestCase1.class, - SequenceIntegrationTests.SequenceAnalysisPipelineTestCase2.class, - OutputIntegrationTests.VariantProcessingTest.class, - SequenceRemoteIntegrationTests.class, - SequenceTriggerHelper.TestCase.class, - SequencePipelineServiceImpl.TestCase.class + Set testClasses = new HashSet<>(Arrays.asList( + Barcoder.TestCase.class, + BamIterator.TestCase.class, + SequenceIntegrationTests.SequenceImportPipelineTestCase.class, + //SequenceIntegrationTests.SequenceAnalysisPipelineTestCase3.class, + SequenceIntegrationTests.SequenceAnalysisPipelineTestCase1.class, + SequenceIntegrationTests.SequenceAnalysisPipelineTestCase2.class, + OutputIntegrationTests.VariantProcessingTest.class, + SequenceRemoteIntegrationTests.class, + SequenceTriggerHelper.TestCase.class, + SequencePipelineServiceImpl.TestCase.class )); return testClasses; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisSchema.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisSchema.java index ff3bdc292..452be9a16 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisSchema.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisSchema.java @@ -18,7 +18,6 @@ import org.labkey.api.data.DbSchema; import org.labkey.api.data.DbSchemaType; import org.labkey.api.data.TableInfo; -import org.labkey.api.data.dialect.SqlDialect; public class SequenceAnalysisSchema { diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceIntegrationTests.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceIntegrationTests.java index 9fc9b090c..304a88709 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceIntegrationTests.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceIntegrationTests.java @@ -509,7 +509,7 @@ protected Set createPipelineJob(String jobName, JSONObject config, throw new RuntimeException("Problem creating pipeline job: " + responseJson.getString("exception")); JSONArray guidList = responseJson.getJSONArray("jobGUIDs"); - assert guidList.length() >= 1; + assert !guidList.isEmpty(); Set ret = new HashSet<>(); for (int i = 0; i < guidList.length(); i++) @@ -763,7 +763,6 @@ protected String getProjectName() /** * This is the most basic test of readset import and creation. A single FASTQ is provided, which can be normalized on the webserver * without external tools. - * @throws Exception */ @Test public void basicTest() throws Exception @@ -909,7 +908,7 @@ private void runMergePipelineJob(String jobName, boolean deleteIntermediates, St waitForJobs(jobsUnsorted); List jobs = new ArrayList<>(jobsUnsorted); - Collections.sort(jobs, new Comparator() + Collections.sort(jobs, new Comparator<>() { @Override public int compare(PipelineJob o1, PipelineJob o2) @@ -1005,7 +1004,6 @@ private void verifyJob(File basedir, String jobName, Set expectedOutputs, /** * This test takes 2 input files: a FASTQ and an SFF. The SFF should be converted to FASTQ, and the files merged into a single * FASTQ output. This pipeline is configured to retain intermediate files. - * @throws Exception */ @Test public void mergeTest() throws Exception @@ -1022,7 +1020,6 @@ public void mergeTest() throws Exception /** * This is a variation on mergeTest, except intermediate files are deleting and input file are compressed. - * @throws Exception */ @Test public void mergeTestDeletingIntermediates() throws Exception @@ -1104,7 +1101,6 @@ private Set getBarcodeOutputs(File basedir, String jobName, String prefix) /** * This test uses a barcoded input - * @throws Exception */ @Test public void barcodeTest() throws Exception @@ -1151,7 +1147,6 @@ private File getBaseDir(PipelineJob job) /** * This is an extension of barcodeTest(), except intermediate files are deleted and inputs compressed - * @throws Exception */ @Test public void barcodeTestDeletingIntermediates() throws Exception @@ -1211,7 +1206,6 @@ else if (f.getName().equals("dualBarcodes_SIV_unknowns.fastq.gz")) /** * This imports a readset from two paired end inputs - * @throws Exception */ @Test public void pairedEndTest() throws Exception @@ -1260,7 +1254,6 @@ public void pairedEndTest() throws Exception /** * An extension of pairedEndTest(), except input files are moved to the analysis folder - * @throws Exception */ @Test public void pairedEndTestMovingInputs() throws Exception @@ -1317,7 +1310,6 @@ public void pairedEndTestMovingInputs() throws Exception /** * An extension of pairedEndTest(), except input files are deleted on completion - * @throws Exception */ @Test public void pairedEndTestDeletingInputs() throws Exception @@ -1684,7 +1676,7 @@ protected String[] getFilenamesForReadsets() } } - return files.toArray(new String[files.size()]); + return files.toArray(new String[0]); } protected void appendSamplesForAlignment(JSONObject config, List readsets) @@ -1818,6 +1810,7 @@ public static void cleanup() doCleanup(PROJECT_NAME); } + @Override protected String getProjectName() { return PROJECT_NAME; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceOutputsNavItem.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceOutputsNavItem.java index bc7b3eb04..6bc66f15a 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceOutputsNavItem.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceOutputsNavItem.java @@ -89,7 +89,7 @@ private Map getCategories(Container c, User u) SQLFragment sql = new SQLFragment("SELECT t.category, count(*) as total FROM ").append(ti.getFromSQL("t")).append(" GROUP BY t.category"); SqlSelector ss = new SqlSelector(ti.getSchema(), sql); final TreeMap categories = new TreeMap<>(); - ss.forEach(new Selector.ForEachBlock() + ss.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet object) throws SQLException diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/AbstractCombineGeneCountsHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/AbstractCombineGeneCountsHandler.java index 7a13d0704..fbde2aa7f 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/AbstractCombineGeneCountsHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/AbstractCombineGeneCountsHandler.java @@ -230,7 +230,7 @@ public void prepareFiles(JobContext ctx, List inputFiles, St action.setStartTime(new Date()); String name = params.getString("name"); - Boolean doSkipGenesWithoutData = params.optBoolean("skipGenesWithoutData", false); + boolean doSkipGenesWithoutData = params.optBoolean("skipGenesWithoutData", false); ctx.getLogger().debug("skip genes without data: " + doSkipGenesWithoutData); int gtf = params.optInt("gtf"); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/BamHaplotypeHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/BamHaplotypeHandler.java index 8fde70dac..a936ab0a9 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/BamHaplotypeHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/BamHaplotypeHandler.java @@ -105,7 +105,7 @@ public boolean doSplitJobs() return false; } - public class Processor implements SequenceOutputProcessor + public static class Processor implements SequenceOutputProcessor { @Override public void processFilesRemote(List inputFiles, JobContext ctx) throws UnsupportedOperationException, PipelineJobException diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/CombineSubreadGeneCountsHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/CombineSubreadGeneCountsHandler.java index 926e95898..3d4f4b46f 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/CombineSubreadGeneCountsHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/CombineSubreadGeneCountsHandler.java @@ -76,7 +76,7 @@ protected void processOutputFiles(CountResults results, List results.distinctGenes.add(geneId); - Double count = Double.parseDouble(cells[6]); + double count = Double.parseDouble(cells[6]); Map countMap = results.counts.get(so.getRowid()); if (countMap == null) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/CompareVariantsHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/CompareVariantsHandler.java index 20f8c743c..4ac865c43 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/CompareVariantsHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/CompareVariantsHandler.java @@ -18,7 +18,6 @@ import org.labkey.sequenceanalysis.SequenceAnalysisModule; import java.io.File; -import java.util.Arrays; import java.util.LinkedHashSet; import java.util.List; @@ -106,7 +105,7 @@ public boolean doSplitJobs() return false; } - public class Processor implements SequenceOutputProcessor + public static class Processor implements SequenceOutputProcessor { @Override public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport support, List inputFiles, JSONObject params, File outputDir, List actions, List outputsToCreate) throws UnsupportedOperationException, PipelineJobException diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java index 82d19d3dd..59e462e90 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java @@ -673,8 +673,8 @@ private void processOneInput(JobContext ctx, PipelineJob job, ReferenceGenome ge // See: https://gatk.broadinstitute.org/hc/en-us/articles/4418054384027-GenotypeGVCFs#--genomicsdb-max-alternate-alleles // "A typical value is 3 more than the --max-alternate-alleles value that's used by GenotypeGVCFs and larger differences result in more robustness to PCR-related indel errors" - Integer maxAlt = ctx.getParams().getInt("variantCalling.GenotypeGVCFs.max_alternate_alleles") + 3; - toolParams.add(maxAlt.toString()); + int maxAlt = ctx.getParams().getInt("variantCalling.GenotypeGVCFs.max_alternate_alleles") + 3; + toolParams.add(Integer.toString(maxAlt)); } if (ctx.getParams().optBoolean("variantCalling.GenotypeGVCFs.includeNonVariantSites")) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java index 5b1cda83b..2d579cc28 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java @@ -138,7 +138,7 @@ private static File getUnmappedOutputFile(File liftedVcfFile) private static String getOutputExtension(File inputFile) { - String ext = null; + String ext; if (_bedFileType.isType(inputFile)) { ext = ".bed"; @@ -172,7 +172,7 @@ public class Processor implements SequenceOutputProcessor @Override public void init(JobContext ctx, List inputFiles, List actions, List outputsToCreate) throws UnsupportedOperationException, PipelineJobException { - Integer chainFileId = ctx.getParams().getInt("chainFileId"); + int chainFileId = ctx.getParams().getInt("chainFileId"); ExpData chainData = ExperimentService.get().getExpData(chainFileId); if (chainData == null || !chainData.getFile().exists()) { diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/MultiQCBamHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/MultiQCBamHandler.java index 817667384..f89ac0fcf 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/MultiQCBamHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/MultiQCBamHandler.java @@ -20,7 +20,6 @@ import org.labkey.sequenceanalysis.util.SequenceUtil; import java.io.File; -import java.util.Arrays; import java.util.Date; import java.util.HashSet; import java.util.List; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/MultiQCHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/MultiQCHandler.java index c915c0118..3f9573fc9 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/MultiQCHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/MultiQCHandler.java @@ -20,7 +20,6 @@ import java.io.File; import java.io.IOException; import java.util.ArrayList; -import java.util.Arrays; import java.util.Collections; import java.util.Date; import java.util.HashMap; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/SbtGeneCountHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/SbtGeneCountHandler.java index 472da1529..0ebe5e999 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/SbtGeneCountHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/SbtGeneCountHandler.java @@ -17,7 +17,6 @@ import org.labkey.sequenceanalysis.SequenceAnalysisModule; import java.io.File; -import java.util.Arrays; import java.util.LinkedHashSet; import java.util.List; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/UnmappedSequenceBasedGenotypeHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/UnmappedSequenceBasedGenotypeHandler.java index 7550d4ded..8e500040a 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/UnmappedSequenceBasedGenotypeHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/UnmappedSequenceBasedGenotypeHandler.java @@ -35,7 +35,6 @@ import java.io.OutputStreamWriter; import java.nio.charset.StandardCharsets; import java.util.ArrayList; -import java.util.Arrays; import java.util.Date; import java.util.HashMap; import java.util.HashSet; @@ -95,7 +94,7 @@ public void addSample(String sampleName, String header, int totalReads) { String[] tokens = header.split("-"); - Integer count = Integer.parseInt(tokens[tokens.length - 1]); + int count = Integer.parseInt(tokens[tokens.length - 1]); Integer c = _sampleMap.getOrDefault(sampleName, 0); c += count; _totalReads += count; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/api/picard/CigarPositionIterable.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/api/picard/CigarPositionIterable.java index a8abc065d..020974609 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/api/picard/CigarPositionIterable.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/api/picard/CigarPositionIterable.java @@ -139,7 +139,7 @@ public PositionInfo next() * Describes a specific position in an alignment, including the position relative to the start of both the reference and read * sequences. */ - public class PositionInfo + public static class PositionInfo { private final SAMRecord _record; private final CigarOperator _op; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/button/ArchiveReadsetsButton.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/button/ArchiveReadsetsButton.java index e19f572c3..0a6044f41 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/button/ArchiveReadsetsButton.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/button/ArchiveReadsetsButton.java @@ -3,8 +3,6 @@ import org.labkey.api.laboratory.security.LaboratoryAdminPermission; import org.labkey.api.ldk.table.SimpleButtonConfigFactory; import org.labkey.api.module.ModuleLoader; -import org.labkey.api.security.permissions.AdminPermission; -import org.labkey.api.security.permissions.UpdatePermission; import org.labkey.api.view.template.ClientDependency; import org.labkey.sequenceanalysis.SequenceAnalysisModule; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/button/ChangeReadsetStatusButton.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/button/ChangeReadsetStatusButton.java index cf04dee1c..e9bf0ff3b 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/button/ChangeReadsetStatusButton.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/button/ChangeReadsetStatusButton.java @@ -5,7 +5,6 @@ import org.labkey.api.view.template.ClientDependency; import org.labkey.sequenceanalysis.SequenceAnalysisModule; -import java.util.Arrays; import java.util.List; /** diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/button/ChangeReadsetStatusForAnalysesButton.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/button/ChangeReadsetStatusForAnalysesButton.java index 694f943d2..b78634f13 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/button/ChangeReadsetStatusForAnalysesButton.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/button/ChangeReadsetStatusForAnalysesButton.java @@ -5,7 +5,6 @@ import org.labkey.api.view.template.ClientDependency; import org.labkey.sequenceanalysis.SequenceAnalysisModule; -import java.util.Arrays; import java.util.List; /** diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/button/ReprocessLibraryButton.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/button/ReprocessLibraryButton.java index 14f08a47e..98c5ee2af 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/button/ReprocessLibraryButton.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/button/ReprocessLibraryButton.java @@ -5,7 +5,6 @@ import org.labkey.api.view.template.ClientDependency; import org.labkey.sequenceanalysis.SequenceAnalysisModule; -import java.util.Arrays; import java.util.List; /** diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/model/UnderscoreBeanObjectFactory.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/model/UnderscoreBeanObjectFactory.java index fddada1a3..b659ce8d1 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/model/UnderscoreBeanObjectFactory.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/model/UnderscoreBeanObjectFactory.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.model; import org.labkey.api.data.BeanObjectFactory; -import org.labkey.api.data.ObjectFactory; /** * Created by bimber on 2/20/2015. diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/AlignmentAnalysisJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/AlignmentAnalysisJob.java index 82cd77df9..093371229 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/AlignmentAnalysisJob.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/AlignmentAnalysisJob.java @@ -23,7 +23,6 @@ import java.io.IOException; import java.util.ArrayList; -import java.util.Arrays; import java.util.Collections; import java.util.HashMap; import java.util.List; @@ -65,7 +64,7 @@ public static List createForAnalyses(Container c, User u, List ret = new ArrayList<>(); for (int i=0;i parseAndCreateAnalyses() throws PipelineJobException Integer runId = SequenceTaskHelper.getExpRunIdForJob(getJob()); ExpRun run = ExperimentService.get().getExpRun(runId); List datas = run.getInputDatas(SequenceAlignmentTask.FINAL_BAM_ROLE, ExpProtocol.ApplicationType.ExperimentRunOutput); - if (datas.size() > 0) + if (!datas.isEmpty()) { for (ExpData d : datas) { diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/AlignmentInitTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/AlignmentInitTask.java index 4636cc2e6..00df2a90c 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/AlignmentInitTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/AlignmentInitTask.java @@ -15,7 +15,6 @@ import org.labkey.api.util.FileType; import java.io.File; -import java.util.Arrays; import java.util.Collections; import java.util.List; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/AlignmentNormalizationTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/AlignmentNormalizationTask.java index b8417b5ae..aa2caf833 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/AlignmentNormalizationTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/AlignmentNormalizationTask.java @@ -31,7 +31,6 @@ import java.io.File; import java.io.IOException; import java.util.ArrayList; -import java.util.Arrays; import java.util.Collections; import java.util.Date; import java.util.HashMap; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CacheAlignerIndexesTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CacheAlignerIndexesTask.java index 08fcaca50..a6d7d8935 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CacheAlignerIndexesTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CacheAlignerIndexesTask.java @@ -21,7 +21,6 @@ import java.io.File; import java.io.IOException; -import java.util.Arrays; import java.util.Collections; import java.util.List; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CacheGenomePipelineJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CacheGenomePipelineJob.java index f59d13986..670b6bb28 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CacheGenomePipelineJob.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CacheGenomePipelineJob.java @@ -30,7 +30,6 @@ import java.io.File; import java.io.IOException; -import java.util.Arrays; import java.util.Collections; import java.util.List; import java.util.Map; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ConvertToCramHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ConvertToCramHandler.java index 1d3a08c56..6fdb4e338 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ConvertToCramHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ConvertToCramHandler.java @@ -91,7 +91,7 @@ public SequenceOutputProcessor getProcessor() return new Processor(); } - public class Processor implements SequenceOutputProcessor + public static class Processor implements SequenceOutputProcessor { @Override public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport support, List inputFiles, JSONObject params, File outputDir, List actions, List outputsToCreate) throws UnsupportedOperationException, PipelineJobException diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CreateReferenceLibraryTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CreateReferenceLibraryTask.java index 92eff93b8..785e1e628 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CreateReferenceLibraryTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CreateReferenceLibraryTask.java @@ -62,7 +62,6 @@ import java.io.IOException; import java.io.PrintWriter; import java.util.ArrayList; -import java.util.Arrays; import java.util.Collections; import java.util.HashMap; import java.util.HashSet; @@ -199,7 +198,7 @@ public RecordedActionSet run() throws PipelineJobException libraryRow.put("description", getPipelineJob().getLibraryDescription()); BatchValidationException errors = new BatchValidationException(); - List> inserted = libraryTable.getUpdateService().insertRows(getJob().getUser(), getJob().getContainer(), List.of(libraryRow), errors, null, new HashMap()); + List> inserted = libraryTable.getUpdateService().insertRows(getJob().getUser(), getJob().getContainer(), List.of(libraryRow), errors, null, new HashMap<>()); if (errors.hasErrors()) { throw errors; @@ -419,7 +418,7 @@ public RecordedActionSet run() throws PipelineJobException getJob().getLogger().info("updating database"); BatchValidationException errors = new BatchValidationException(); TableInfo libraryMembersTable = QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), SequenceAnalysisSchema.SCHEMA_NAME).getTable(SequenceAnalysisSchema.TABLE_REF_LIBRARY_MEMBERS); - libraryMembersTable.getUpdateService().insertRows(getJob().getUser(), getJob().getContainer(), toInsert, errors, null, new HashMap()); + libraryMembersTable.getUpdateService().insertRows(getJob().getUser(), getJob().getContainer(), toInsert, errors, null, new HashMap<>()); if (errors.hasErrors()) { throw errors; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaFastqSplitter.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaFastqSplitter.java index 136b65f81..41a633f76 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaFastqSplitter.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaFastqSplitter.java @@ -22,7 +22,6 @@ import htsjdk.samtools.fastq.FastqRecord; import htsjdk.samtools.fastq.FastqWriter; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.util.FileType; @@ -133,7 +132,7 @@ public Map, File> parseFastqFiles() throws PipelineJ FastqRecord fq = reader.next(); String header = fq.getReadHeader(); IlluminaReadHeader parsedHeader = new IlluminaReadHeader(header); - String illuminaSampleId = null; + String illuminaSampleId; if (parsedHeader.getIndexSequenceString() != null) { illuminaSampleId = parsedHeader.getIndexSequenceString(); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaImportJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaImportJob.java index b51e11a54..f96fddba1 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaImportJob.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaImportJob.java @@ -19,7 +19,6 @@ import java.io.File; import java.io.IOException; import java.util.ArrayList; -import java.util.Arrays; import java.util.Collection; import java.util.Collections; import java.util.List; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaImportTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaImportTask.java index e1541489b..3928cc015 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaImportTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaImportTask.java @@ -49,7 +49,6 @@ import java.io.File; import java.io.IOException; import java.util.ArrayList; -import java.util.Arrays; import java.util.Collections; import java.util.Date; import java.util.HashMap; @@ -130,7 +129,7 @@ public RecordedActionSet run() throws PipelineJobException String prefix = job.getParameters().get("fastqPrefix"); List inputFiles = getSupport().getInputFiles(); - if (inputFiles.size() == 0) + if (inputFiles.isEmpty()) throw new PipelineJobException("No input files"); DbSchema schema = SequenceAnalysisSchema.getInstance().getSchema(); @@ -336,7 +335,7 @@ private Map parseCsv(File sampleFile, DbSchema schema) throws P Map sampleMap = new HashMap<>(); sampleMap.put("S0", 0); //placeholder for control and unmapped reads - Boolean inSamples = false; + boolean inSamples = false; int sampleIdx = 0; while ((nextLine = reader.readNext()) != null) { diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaReadsetCreationTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaReadsetCreationTask.java index 8882623b0..5dd3ccd0b 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaReadsetCreationTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/IlluminaReadsetCreationTask.java @@ -22,7 +22,6 @@ import org.labkey.sequenceanalysis.SequenceAnalysisSchema; import java.util.ArrayList; -import java.util.Arrays; import java.util.Collections; import java.util.HashMap; import java.util.List; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportFastaSequencesTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportFastaSequencesTask.java index 0c84f13ff..464d8a0b7 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportFastaSequencesTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportFastaSequencesTask.java @@ -28,7 +28,6 @@ import java.io.File; import java.util.ArrayList; -import java.util.Arrays; import java.util.Collections; import java.util.List; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackPipelineJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackPipelineJob.java index 703e10df7..3897b650e 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackPipelineJob.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackPipelineJob.java @@ -13,7 +13,6 @@ import org.labkey.api.query.DetailsURL; import org.labkey.api.security.User; import org.labkey.api.security.permissions.InsertPermission; -import org.labkey.api.util.FileType; import org.labkey.api.util.FileUtil; import org.labkey.api.view.ActionURL; import org.labkey.api.view.ViewBackgroundInfo; @@ -22,7 +21,6 @@ import java.io.File; import java.io.IOException; -import java.util.Arrays; /** * User: bimber diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java index 50add8b12..5c6498d0c 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java @@ -229,7 +229,7 @@ private int addTrackForLibrary(File file, String trackName, String trackDescript knownChrs.put(m.getName(), m.getName()); } - SAMSequenceDictionary dict = null; + SAMSequenceDictionary dict; if (!genome.getSequenceDictionary().exists()) { SequencePipelineService.get().ensureSequenceDictionaryExists(genome.getWorkingFastaFile(), getJob().getLogger(), false); @@ -410,12 +410,12 @@ private Map> getNameTranslationMap(List> getNameTranslationMap(List getActions() return _actions; } + @Override public Collection getDockerVolumes() { return _job.getDockerVolumes(); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java index e6a657190..69f1bef17 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java @@ -289,7 +289,7 @@ private Map> getDataMapForContainer(Container c, Map> dataMap = new HashMap<>(); - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/PipelineStepCtxImpl.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/PipelineStepCtxImpl.java index 2154b5fd7..f63eab681 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/PipelineStepCtxImpl.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/PipelineStepCtxImpl.java @@ -10,7 +10,7 @@ public class PipelineStepCtxImpl implements PipelineStepCtx { private final PipelineStepProvider _provider; - private int _stepIdx = 0; + private int _stepIdx; public PipelineStepCtxImpl(PipelineStepProvider provider, int stepIdx) { diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/PrepareAlignerIndexesTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/PrepareAlignerIndexesTask.java index 445e6dad0..ef75c5297 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/PrepareAlignerIndexesTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/PrepareAlignerIndexesTask.java @@ -16,7 +16,6 @@ import org.labkey.sequenceanalysis.run.util.FastaIndexer; import java.io.File; -import java.util.Arrays; import java.util.Collections; import java.util.List; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ProcessVariantsHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ProcessVariantsHandler.java index 1d28158d9..fab9620ad 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ProcessVariantsHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ProcessVariantsHandler.java @@ -36,7 +36,6 @@ import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport; import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler; import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; -import org.labkey.api.sequenceanalysis.pipeline.TaskFileManager; import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor; import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStep; import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetCreationTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetCreationTask.java index 15da5149c..4900f8c99 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetCreationTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetCreationTask.java @@ -254,7 +254,7 @@ private void importReadsets() throws PipelineJobException File f2 = rd.getFile2(); getJob().getLogger().debug("Total exp data files: " + datas.size()); - if (datas.size() > 0) + if (!datas.isEmpty()) { boolean found = false; boolean found2 = false; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetImportJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetImportJob.java index 6bdeeeb04..bfd38bce2 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetImportJob.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetImportJob.java @@ -30,7 +30,6 @@ import java.io.File; import java.io.IOException; import java.util.ArrayList; -import java.util.Arrays; import java.util.HashMap; import java.util.HashSet; import java.util.List; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReblockGvcfHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReblockGvcfHandler.java index aa3abdd30..496fb4052 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReblockGvcfHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReblockGvcfHandler.java @@ -90,7 +90,7 @@ public SequenceOutputProcessor getProcessor() return new Processor(); } - public class Processor implements SequenceOutputProcessor + public static class Processor implements SequenceOutputProcessor { @Override public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport support, List inputFiles, JSONObject params, File outputDir, List actions, List outputsToCreate) throws UnsupportedOperationException, PipelineJobException diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentJob.java index e504cf0e3..23195cb0c 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentJob.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentJob.java @@ -61,7 +61,7 @@ public static List createForReadsets(Container c, User u, List ret = new ArrayList<>(); for (int i=0;i sequenceIds, String name, S { d.append(description); } - if (d.length() > 0) + if (!d.isEmpty()) { d.append(", "); } diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJobSupportImpl.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJobSupportImpl.java index 6fb8ca8e2..f84922a68 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJobSupportImpl.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJobSupportImpl.java @@ -3,7 +3,6 @@ import com.fasterxml.jackson.databind.JavaType; import com.fasterxml.jackson.databind.ObjectMapper; import htsjdk.samtools.util.IOUtil; -import org.apache.logging.log4j.Logger; import org.junit.Assert; import org.junit.Test; import org.labkey.api.exp.api.ExpData; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceNormalizationTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceNormalizationTask.java index 1184d9c07..1cb082521 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceNormalizationTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceNormalizationTask.java @@ -156,7 +156,7 @@ public static boolean shouldRunRemote(PipelineJob job) throws FileNotFoundExcept { SequencePipelineSettings settings = new SequencePipelineSettings(job.getParameters()); - return settings.isRunFastqc() || getFilesToNormalize(job, ((FileAnalysisJobSupport) job).getInputFiles(), true).size() > 0; + return settings.isRunFastqc() || !getFilesToNormalize(job, ((FileAnalysisJobSupport) job).getInputFiles(), true).isEmpty(); } private ReadsetImportJob getPipelineJob() @@ -517,7 +517,7 @@ else if (lane.isEmpty()) } } - if (outputs.size() > 0) + if (!outputs.isEmpty()) { for (FileGroup.FilePair fp : fg.filePairs) { @@ -772,7 +772,7 @@ private Barcoder getBarcoder() throws PipelineJobException barcoder.setCreateDetailedLog(true); } - if (getBarcodeGroupsToScan(getHelper().getSettings()).size() > 0) + if (!getBarcodeGroupsToScan(getHelper().getSettings()).isEmpty()) barcoder.setScanAll(true); return barcoder; @@ -887,7 +887,7 @@ private File normalizeFastqSequence(File input, List actions) th workingDir.mkdirs(); FileType gz = new FileType("gz"); - File output = null; + File output; //NOTE: if the file is ASCII33 FASTQ, it should not reach this stage, unless we're doing barcoding or merging if (type.equals(SequenceUtil.FILETYPE.fastq)) { diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceOutputHandlerJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceOutputHandlerJob.java index 709c116ba..d892e6eb8 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceOutputHandlerJob.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceOutputHandlerJob.java @@ -111,7 +111,9 @@ protected List readOutputFilesFromFile() throws PipelineJobE try (InputStream is = IOUtil.maybeBufferInputStream(IOUtil.openFileForReading(xml))) { ObjectMapper objectMapper = createObjectMapper(); - List ret = objectMapper.readValue(is, new TypeReference>(){}); + List ret = objectMapper.readValue(is, new TypeReference<>() + { + }); getLogger().debug("read SequenceOutputFiles from file, total: " + ret.size()); for (SequenceOutputFile so : ret) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceOutputHandlerRemoteTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceOutputHandlerRemoteTask.java index 06cf83837..647c9438e 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceOutputHandlerRemoteTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceOutputHandlerRemoteTask.java @@ -16,7 +16,6 @@ import org.labkey.api.util.FileType; import org.labkey.sequenceanalysis.SequenceAnalysisServiceImpl; -import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.Collections; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceTaskHelper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceTaskHelper.java index 97b1ad53f..5805c92d7 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceTaskHelper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceTaskHelper.java @@ -346,6 +346,7 @@ public void cacheExpDatasForParams() throws PipelineJobException } } + @Override public Collection getDockerVolumes() { return _job.getDockerVolumes(); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/TaskFileManagerImpl.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/TaskFileManagerImpl.java index dc5ce05e5..91d06a881 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/TaskFileManagerImpl.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/TaskFileManagerImpl.java @@ -1060,7 +1060,7 @@ private File decompressFile(File i, List actions) //NOTE: because we can initate runs on readsets from different containers, we cannot rely on dataDirectory() to be consistent //b/c inputs are always copied to the root of the analysis folder, we will use relative paths FileType gz = new FileType(".gz"); - File unzipped = null; + File unzipped; if (gz.isType(i)) { RecordedAction action = new RecordedAction(SequenceAlignmentTask.DECOMPRESS_ACTIONNAME); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java index 35d173da5..d9f7e4462 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java @@ -26,7 +26,6 @@ import org.labkey.api.pipeline.PipelineService; import org.labkey.api.pipeline.TaskId; import org.labkey.api.pipeline.TaskPipeline; -import org.labkey.api.pipeline.WorkDirectory; import org.labkey.api.query.FieldKey; import org.labkey.api.reader.Readers; import org.labkey.api.security.User; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingRemoteMergeTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingRemoteMergeTask.java index e7a9be1d7..f8e043f29 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingRemoteMergeTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingRemoteMergeTask.java @@ -17,7 +17,6 @@ import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler; import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStep; import org.labkey.api.util.FileType; -import org.labkey.sequenceanalysis.run.variant.OutputVariantsStartingInIntervalsStep; import java.io.File; import java.io.IOException; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/DownloadSequenceDisplayColumnFactory.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/DownloadSequenceDisplayColumnFactory.java index 86e8ec9a3..6f563d735 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/DownloadSequenceDisplayColumnFactory.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/DownloadSequenceDisplayColumnFactory.java @@ -8,7 +8,6 @@ import org.labkey.api.data.RenderContext; import org.labkey.api.query.FieldKey; import org.labkey.api.util.LinkBuilder; -import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.HttpView; import org.labkey.api.view.template.ClientDependency; import org.labkey.api.writer.HtmlWriter; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/GenbankDisplayColumnFactory.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/GenbankDisplayColumnFactory.java index d3fe19645..005a2d129 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/GenbankDisplayColumnFactory.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/GenbankDisplayColumnFactory.java @@ -6,13 +6,8 @@ import org.labkey.api.data.DisplayColumnFactory; import org.labkey.api.data.RenderContext; import org.labkey.api.util.LinkBuilder; -import org.labkey.api.util.PageFlowUtil; -import org.labkey.api.util.URLHelper; import org.labkey.api.writer.HtmlWriter; -import java.io.IOException; -import java.io.Writer; - /** * Created by bimber on 2/8/2017. */ diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisUserSchema.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisUserSchema.java index aa54bf6ac..9757cfc34 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisUserSchema.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisUserSchema.java @@ -192,7 +192,7 @@ private TableInfo createOutputFiles(TableInfo sourceTable, ContainerFilter cf) } } - ret.getButtonBarConfig().setScriptIncludes(scriptIncludes.toArray(new String[scriptIncludes.size()])); + ret.getButtonBarConfig().setScriptIncludes(scriptIncludes.toArray(new String[0])); if (ret.getColumn("analysisSets") == null) { diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceTriggerHelper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceTriggerHelper.java index 5a0d3e9bf..f6eb36e24 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceTriggerHelper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceTriggerHelper.java @@ -43,8 +43,8 @@ */ public class SequenceTriggerHelper { - private Container _container = null; - private User _user = null; + private Container _container; + private User _user; private static final Logger _log = LogManager.getLogger(SequenceTriggerHelper.class); private TableInfo _refNts = null; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/MultiQcRunner.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/MultiQcRunner.java index 50406156d..7f7920288 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/MultiQcRunner.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/MultiQcRunner.java @@ -2,7 +2,6 @@ import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.pipeline.PipelineJobService; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BWAMem2Wrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BWAMem2Wrapper.java index 73d1e6412..24a959dc3 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BWAMem2Wrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BWAMem2Wrapper.java @@ -1,29 +1,19 @@ package org.labkey.sequenceanalysis.run.alignment; -import org.apache.commons.lang3.StringUtils; import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.json.JSONObject; import org.labkey.api.pipeline.PipelineJob; -import org.labkey.api.pipeline.PipelineJobException; -import org.labkey.api.sequenceanalysis.model.Readset; import org.labkey.api.sequenceanalysis.pipeline.AbstractAlignmentStepProvider; -import org.labkey.api.sequenceanalysis.pipeline.AlignmentOutputImpl; import org.labkey.api.sequenceanalysis.pipeline.AlignmentStep; import org.labkey.api.sequenceanalysis.pipeline.AlignmentStepProvider; import org.labkey.api.sequenceanalysis.pipeline.CommandLineParam; import org.labkey.api.sequenceanalysis.pipeline.PipelineContext; -import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome; -import org.labkey.api.sequenceanalysis.pipeline.SamtoolsRunner; import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor; -import org.labkey.api.util.FileUtil; -import org.labkey.sequenceanalysis.util.SequenceUtil; import java.io.File; -import java.util.ArrayList; import java.util.Arrays; -import java.util.List; /** * User: bimber diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BWASWWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BWASWWrapper.java index ce0e55fee..8350f7ff5 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BWASWWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BWASWWrapper.java @@ -2,7 +2,6 @@ import htsjdk.samtools.ValidationStringency; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.pipeline.PipelineJobException; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/FastaToTwoBitRunner.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/FastaToTwoBitRunner.java index 67bd5f690..bef15afd4 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/FastaToTwoBitRunner.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/FastaToTwoBitRunner.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.run.alignment; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.pipeline.AlignerIndexUtil; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/FastqCollapser.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/FastqCollapser.java index 375054dae..0930d032c 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/FastqCollapser.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/FastqCollapser.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.run.alignment; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java index 258bdbfec..630ef7c7b 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java @@ -196,7 +196,7 @@ else if (!svVcf.exists()) // id path depth read length // IB18 ../IB18.cram 29.77 150 File coverageFile = new File(ctx.getWorkingDirectory(), "coverage.txt"); - String rgId = null; + String rgId; try (PrintWriter writer = PrintWriters.getPrintWriter(coverageFile); SamReader reader = SamReaderFactory.makeDefault().open(so.getFile())) { SAMFileHeader header = reader.getFileHeader(); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/StarWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/StarWrapper.java index 38c635908..b729970ea 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/StarWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/StarWrapper.java @@ -405,15 +405,15 @@ public IndexOutput createIndex(ReferenceGenome referenceGenome, File outputDir) getPipelineCtx().getLogger().info("reference has " + refNumber + " contigs, adjusting parameters"); getPipelineCtx().getLogger().info("genome length: " + genomeLength); - Double scale = Math.min(18.0, (Math.log((genomeLength / refNumber)) / Math.log(2))); + double scale = Math.min(18.0, (Math.log((genomeLength / refNumber)) / Math.log(2))); args.add("--genomeChrBinNbits"); - args.add(String.valueOf(scale.intValue())); + args.add(String.valueOf((int) scale)); } //and small genomes may require this - Double genomeSAindexNbases = Math.min(14.0, ((Math.log(genomeLength) / Math.log(2)) / 2) - 1); + double genomeSAindexNbases = Math.min(14.0, ((Math.log(genomeLength) / Math.log(2)) / 2) - 1); args.add("--genomeSAindexNbases"); - args.add(String.valueOf(genomeSAindexNbases.intValue())); + args.add(String.valueOf((int) genomeSAindexNbases)); } catch (IOException e) { diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/VulcanWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/VulcanWrapper.java index ea3937be9..0974bb32e 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/VulcanWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/VulcanWrapper.java @@ -20,7 +20,6 @@ import java.io.File; import java.util.ArrayList; -import java.util.Arrays; import java.util.List; //// vulcan -i $FASTQ -clr -t 12 -r $REF -w $WORK_DIR -o $OUT_DIR/${OUT}.bam diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AASnpByCodonAggregator.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AASnpByCodonAggregator.java index bd7659216..6a55a32f9 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AASnpByCodonAggregator.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AASnpByCodonAggregator.java @@ -164,7 +164,7 @@ public List> getResults(User u, Container c, AnalysisModel m if (depth != null && !info.getReadResidue().equals(":")) { - Double adj_depth = info.calculateNtDepth(true); + double adj_depth = info.calculateNtDepth(true); double pct = depth == 0 ? 0 : ((double) readCount / adj_depth ) * 100.0; row.put("adj_depth", adj_depth); row.put("pct", pct); @@ -322,7 +322,7 @@ public void addSNP(AASnp snp) String ntPosString = snp.getNtPositionString(); if (!_readnamesByPos.containsKey(ntPosString)) { - _readnamesByPos.put(ntPosString, new HashSet()); + _readnamesByPos.put(ntPosString, new HashSet<>()); } if (_readnamesByPos.get(ntPosString).contains(snp.getNtSnp().getReadname())) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AASnpByReadAggregator.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AASnpByReadAggregator.java index d64b92606..df8bd0f29 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AASnpByReadAggregator.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AASnpByReadAggregator.java @@ -65,7 +65,7 @@ public void inspectAlignment(SAMRecord record, ReferenceSequence ref, Map 0) + if (!highQualitySnpsByPos.isEmpty()) { for (AASnp snp : translateSnpsForRead(record, highQualitySnpsByPos)) { diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AbstractAlignmentAggregator.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AbstractAlignmentAggregator.java index 25550ea90..6309f89db 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AbstractAlignmentAggregator.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AbstractAlignmentAggregator.java @@ -19,7 +19,6 @@ import htsjdk.samtools.reference.ReferenceSequence; import org.apache.commons.lang3.StringUtils; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.ReferenceLibraryHelper; import org.labkey.sequenceanalysis.run.util.AASnp; @@ -28,7 +27,6 @@ import org.labkey.sequenceanalysis.util.TranslatingReferenceSequence; import java.io.File; -import java.util.Arrays; import java.util.HashMap; import java.util.List; import java.util.Map; @@ -320,7 +318,7 @@ public void setMinDipQual(int minDipQual) _minDipQual = minDipQual; } - protected class CacheKeyInfo + protected static class CacheKeyInfo { private final String _refName; private final Integer _refPosition; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AvgBaseQualityAggregator.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AvgBaseQualityAggregator.java index 2f132ae28..62e973304 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AvgBaseQualityAggregator.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AvgBaseQualityAggregator.java @@ -48,7 +48,7 @@ public class AvgBaseQualityAggregator private final File _bai; private final File _ref; private Map> _quals = null; - private List _filters = null; + private List _filters; public AvgBaseQualityAggregator(Logger log, File bam, File refFasta) throws FileNotFoundException { diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/BamIterator.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/BamIterator.java index 23991eefb..6e138c513 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/BamIterator.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/BamIterator.java @@ -164,7 +164,6 @@ public void iterateReads(String refName, int start, int stop) throws IOException /** * Iterates all reads in the alignment - * @return */ public void iterateReads() throws IOException, PipelineJobException { @@ -206,7 +205,7 @@ private void processAlignment(SAMRecord r, IndexedFastaSequenceFile indexedRef) } } - if (snps.size() > 0) + if (!snps.isEmpty()) snpPositions.put(pi.getLastRefPosition(), snps); } @@ -218,7 +217,7 @@ private void processAlignment(SAMRecord r, IndexedFastaSequenceFile indexedRef) { Integer pos1 = snp1.getLastRefPosition(); Integer idx1 = snp1.getInsertIndex(); - Integer compare1 = pos1.compareTo(snp2.getLastRefPosition()); + int compare1 = pos1.compareTo(snp2.getLastRefPosition()); return compare1 != 0 ? compare1 : idx1.compareTo(snp2.getInsertIndex()); }); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/ExportOverlappingReadsAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/ExportOverlappingReadsAnalysis.java index f53e161d9..9b73d3993 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/ExportOverlappingReadsAnalysis.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/ExportOverlappingReadsAnalysis.java @@ -110,8 +110,8 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc } String refName = m.group(1); - Integer start = Integer.parseInt(m.group(2)); - Integer stop = Integer.parseInt(m.group(3)); + int start = Integer.parseInt(m.group(2)); + int stop = Integer.parseInt(m.group(3)); getPipelineCtx().getLogger().info("calculating bases over " + refName + ": " + start + "-" + stop); int added = calculateForInterval(inputBam, refName, start, stop, distinctReadNames); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java index eb6dbb4fc..c33383ff0 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java @@ -132,7 +132,7 @@ public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport private static final double NO_DATA_VAL = -1.0; - private class SiteAndAlleles + private static class SiteAndAlleles { private final String _contig; private final int _start; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NextCladeHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NextCladeHandler.java index fe4b571c3..0b02e947c 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NextCladeHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NextCladeHandler.java @@ -299,10 +299,10 @@ public static void processAndImportNextCladeAa(PipelineJob job, File jsonFile, i throw new PipelineJobException("Expected variant for AA position: " + aaName + " " + pos); } - Double depth; - Double alleleDepth; - Double af; - Double dp; + double depth; + double alleleDepth; + double af; + double dp; List ntPositions = new ArrayList<>(); if (vcList.size() == 1) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NtCoverageAggregator.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NtCoverageAggregator.java index a5a4ee3bd..5a34244d8 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NtCoverageAggregator.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NtCoverageAggregator.java @@ -18,7 +18,6 @@ import htsjdk.samtools.SAMRecord; import htsjdk.samtools.reference.ReferenceSequence; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.data.DbScope; import org.labkey.api.data.SimpleFilter; @@ -388,7 +387,7 @@ public void writeOutput(User u, Container c, AnalysisModel model) for (char base : _baseMap.keySet()) { String fieldSuffix = _baseMap.get(base); - Integer baseTotal = getValueForPositionAndBase(refName, position, index, base, _totalCoverageByBase); + int baseTotal = getValueForPositionAndBase(refName, position, index, base, _totalCoverageByBase); row.put("total_" + fieldSuffix, baseTotal); @@ -397,7 +396,7 @@ public void writeOutput(User u, Container c, AnalysisModel model) n_total += baseTotal; double totalQual = getValueForPositionAndBase(refName, position, index, base, _totalQualByBase); - double avgQual = baseTotal == 0 ? 0 : totalQual / baseTotal.doubleValue(); + double avgQual = baseTotal == 0 ? 0 : totalQual / (double) baseTotal; row.put("avgqual_" + fieldSuffix, avgQual); if (index == 0 && base == wtBase) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NtSnpByPosAggregator.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NtSnpByPosAggregator.java index 05ba8c39f..b0195f693 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NtSnpByPosAggregator.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NtSnpByPosAggregator.java @@ -18,7 +18,6 @@ import htsjdk.samtools.SAMRecord; import htsjdk.samtools.reference.ReferenceSequence; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.data.DbScope; import org.labkey.api.data.SimpleFilter; @@ -30,7 +29,6 @@ import org.labkey.api.security.User; import org.labkey.api.sequenceanalysis.model.AnalysisModel; import org.labkey.sequenceanalysis.SequenceAnalysisSchema; -import org.labkey.sequenceanalysis.api.picard.CigarPositionIterable; import org.labkey.sequenceanalysis.run.util.NTSnp; import java.io.File; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PARalyzerAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PARalyzerAnalysis.java index 3fe265254..4bc98bffc 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PARalyzerAnalysis.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PARalyzerAnalysis.java @@ -19,7 +19,6 @@ import java.io.File; import java.util.Arrays; import java.util.HashMap; -import java.util.List; import java.util.Map; /** diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PindelAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PindelAnalysis.java index ce90daa7c..2541c91e6 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PindelAnalysis.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PindelAnalysis.java @@ -146,9 +146,9 @@ private static String parseInsertMetrics(File inputFile, int minInsertSize) thro { if (m.PAIR_ORIENTATION == SamPairUtil.PairOrientation.FR) { - Double insertSize = Math.ceil(m.MEAN_INSERT_SIZE); + double insertSize = Math.ceil(m.MEAN_INSERT_SIZE); - return String.valueOf(Math.max(minInsertSize, insertSize.intValue())); + return String.valueOf(Math.max(minInsertSize, (int) insertSize)); } } } diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/SequenceBasedTypingAlignmentAggregator.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/SequenceBasedTypingAlignmentAggregator.java index d2273f700..5e1581cd0 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/SequenceBasedTypingAlignmentAggregator.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/SequenceBasedTypingAlignmentAggregator.java @@ -187,7 +187,7 @@ public void inspectAlignment(SAMRecord record, ReferenceSequence ref, Map doFilterStage1(CSVWriter writer) List refNames2 = null; //if this read has an aligned mate, we find the intersect between its alignments - Boolean hasMate = false; + boolean hasMate = false; if (_alignmentsByReadM2.containsKey(readName)) { refNames2 = new ArrayList<>(_alignmentsByReadM2.get(readName)); @@ -383,11 +383,11 @@ private Map doFilterStage1(CSVWriter writer) for (String refName : names) { - writer.writeNext(new String[]{"Forward", readName, String.valueOf(_alignmentsByReadM1.get(readName).size()), String.valueOf(refNames.size()), refName, String.valueOf(refNames.contains(refName)), hasMate.toString()}); + writer.writeNext(new String[]{"Forward", readName, String.valueOf(_alignmentsByReadM1.get(readName).size()), String.valueOf(refNames.size()), refName, String.valueOf(refNames.contains(refName)), Boolean.toString(hasMate)}); } } - if (refNames.size() > 0) + if (!refNames.isEmpty()) { if (!_onlyImportValidPairs || hasMate) { @@ -434,7 +434,7 @@ private Map doFilterStage1(CSVWriter writer) List refNames = new ArrayList(_alignmentsByReadM2.get(mateName)); if (!_onlyImportValidPairs) { - if (refNames.size() > 0) + if (!refNames.isEmpty()) { appendReadToTotals(mateName, refNames, totals, false, true); _singletonCalls++; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/SequenceBasedTypingAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/SequenceBasedTypingAnalysis.java index 3ad16b82a..58a4e41af 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/SequenceBasedTypingAnalysis.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/SequenceBasedTypingAnalysis.java @@ -35,7 +35,6 @@ import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome; import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport; import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor; -import org.labkey.api.util.Compress; import org.labkey.api.util.FileUtil; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.Pair; @@ -184,7 +183,7 @@ public static void prepareLineageMapFiles(SequenceAnalysisJobSupport support, Lo log.info("writing lineage map file"); SQLFragment sql = new SQLFragment("SELECT r.name, r.lineage FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_REF_NT_SEQUENCES + " r WHERE r.rowid IN (SELECT ref_nt_id FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_REF_LIBRARY_MEMBERS + " WHERE library_id = ?)", genome.getGenomeId()); SqlSelector ss = new SqlSelector(DbScope.getLabKeyScope(), sql); - ss.forEach(new Selector.ForEachBlock() + ss.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/SnpCountAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/SnpCountAnalysis.java index eb46ca2a4..e554bba5d 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/SnpCountAnalysis.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/SnpCountAnalysis.java @@ -32,7 +32,6 @@ import java.io.File; import java.io.FileWriter; import java.io.IOException; -import java.util.Arrays; import java.util.HashMap; import java.util.Iterator; import java.util.List; @@ -123,8 +122,8 @@ public Output performAnalysisPerSampleLocal(AnalysisModel model, File inputBam, } String refName = m.group(1); - Integer start = Integer.parseInt(m.group(2)); - Integer stop = Integer.parseInt(m.group(3)); + int start = Integer.parseInt(m.group(2)); + int stop = Integer.parseInt(m.group(3)); getPipelineCtx().getLogger().info("calculating bases over " + refName + ": " + start + "-" + stop); calculateForInterval(writer, inputBam, indexFile, indexedFastaSequenceFile, inputBam.getName(), rs.getName(), refName, start, stop); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/UnmappedReadExportAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/UnmappedReadExportAnalysis.java index 3ab136087..c11c3f16e 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/UnmappedReadExportAnalysis.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/UnmappedReadExportAnalysis.java @@ -35,7 +35,6 @@ import java.io.PrintWriter; import java.io.Writer; import java.util.ArrayList; -import java.util.Arrays; import java.util.List; /** diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/assembly/TrinityRunner.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/assembly/TrinityRunner.java index 9f0e77be9..2441ab2b6 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/assembly/TrinityRunner.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/assembly/TrinityRunner.java @@ -20,7 +20,6 @@ import java.io.File; import java.util.ArrayList; -import java.util.Arrays; import java.util.List; /** diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/bampostprocessing/ClipOverlappingAlignmentsWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/bampostprocessing/ClipOverlappingAlignmentsWrapper.java index e1784c9e7..57828cf54 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/bampostprocessing/ClipOverlappingAlignmentsWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/bampostprocessing/ClipOverlappingAlignmentsWrapper.java @@ -18,7 +18,6 @@ import java.io.File; import java.util.ArrayList; -import java.util.Arrays; import java.util.LinkedHashSet; import java.util.List; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/bampostprocessing/DiscardUnmappedReadsStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/bampostprocessing/DiscardUnmappedReadsStep.java index 356017125..7955b71b9 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/bampostprocessing/DiscardUnmappedReadsStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/bampostprocessing/DiscardUnmappedReadsStep.java @@ -1,7 +1,5 @@ package org.labkey.sequenceanalysis.run.bampostprocessing; -import htsjdk.samtools.SAMFileHeader; -import htsjdk.samtools.ValidationStringency; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.model.Readset; import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider; @@ -11,14 +9,10 @@ import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider; import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome; import org.labkey.api.sequenceanalysis.pipeline.SamtoolsRunner; -import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; -import org.labkey.api.sequenceanalysis.pipeline.SortSamWrapper; import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep; import org.labkey.api.util.FileUtil; -import org.labkey.sequenceanalysis.util.SequenceUtil; import java.io.File; -import java.io.IOException; import java.util.ArrayList; import java.util.List; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/bampostprocessing/IndelRealignerStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/bampostprocessing/IndelRealignerStep.java index 887ecead8..28674283b 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/bampostprocessing/IndelRealignerStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/bampostprocessing/IndelRealignerStep.java @@ -1,6 +1,5 @@ package org.labkey.sequenceanalysis.run.bampostprocessing; -import org.json.JSONObject; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.model.Readset; import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider; @@ -9,13 +8,11 @@ import org.labkey.api.sequenceanalysis.pipeline.PipelineContext; import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider; import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome; -import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor; import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep; import org.labkey.api.util.FileUtil; import org.labkey.sequenceanalysis.run.util.IndelRealignerWrapper; import java.io.File; -import java.util.Arrays; import java.util.Collections; /** diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/BlastFilterPipelineStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/BlastFilterPipelineStep.java index 2389457d9..5eb589002 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/BlastFilterPipelineStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/BlastFilterPipelineStep.java @@ -174,7 +174,7 @@ public PreprocessingOutputImpl processInputFile(File inputFile1, @Nullable File try (CSVReader reader = new CSVReader(Readers.getReader(blastOutput), '\t')) { String[] line; - while ((line = reader.readNext()) != null) + while (reader.readNext() != null) { } diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/CutadaptWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/CutadaptWrapper.java index ea181f661..be370eef0 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/CutadaptWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/CutadaptWrapper.java @@ -11,7 +11,6 @@ import org.labkey.api.sequenceanalysis.pipeline.PipelineContext; import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider; import org.labkey.api.sequenceanalysis.pipeline.PreprocessingStep; -import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep; import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper; import org.labkey.api.sequenceanalysis.pipeline.CommandLineParam; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/DownsampleFastqWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/DownsampleFastqWrapper.java index e5dbd4ece..c1c2939e8 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/DownsampleFastqWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/DownsampleFastqWrapper.java @@ -20,7 +20,6 @@ import org.labkey.sequenceanalysis.util.FastqUtils; import java.io.File; -import java.util.Arrays; import java.util.List; /** diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/SeqtkRunner.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/SeqtkRunner.java index a4cad8dbe..7aecb1e55 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/SeqtkRunner.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/SeqtkRunner.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.run.preprocessing; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/Sff2FastqRunner.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/Sff2FastqRunner.java index ea43218f9..eb8815aa3 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/Sff2FastqRunner.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/Sff2FastqRunner.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.run.preprocessing; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; @@ -10,8 +9,6 @@ import java.io.File; import java.util.LinkedList; import java.util.List; -import java.util.regex.Matcher; -import java.util.regex.Pattern; /** * User: bimber diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/TrimmomaticWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/TrimmomaticWrapper.java index 97870629c..2494c8504 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/TrimmomaticWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/TrimmomaticWrapper.java @@ -152,7 +152,7 @@ public List getAdditionalParams(PipelineContext ctx, PreprocessingOutput @Override public Double getThreshold(PipelineContext ctx, int stepIdx) { - Double ret = 0.0; + double ret = 0.0; for (Pair provider : _providers) { Double val = provider.first.getParameterByName(MIN_PCT_RETAINED).extractValue(ctx.getJob(), this, stepIdx, Double.class); @@ -795,8 +795,8 @@ else if ((header != null && header.getPairNumber() == 2) || name.endsWith("/2")) } } - Double avgBasesTrimmed = totalReadsTrimmed == 0 ? 0 : (double)totalBasesTrimmed / (double)totalReadsTrimmed; - Double avgReadLength = totalReadsTrimmed == 0 ? 0 : (double)totalLength / (double)totalReadsRetained; + double avgBasesTrimmed = totalReadsTrimmed == 0 ? 0 : (double)totalBasesTrimmed / (double)totalReadsTrimmed; + double avgReadLength = totalReadsTrimmed == 0 ? 0 : (double)totalLength / (double)totalReadsRetained; Double pctRetained =(double)totalReadsRetained / totalInspected; results.add(pctRetained); StringBuilder summary = new StringBuilder(); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/AASnp.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/AASnp.java index 83f79d974..79f774cf0 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/AASnp.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/AASnp.java @@ -97,7 +97,7 @@ private void calculateResidues() _log.error("unable to translate string: " + _codon, e); } - if (_residueString == null || "".equals(_residueString)) + if (_residueString == null || _residueString.isEmpty()) { _residueString = "*"; } diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/AbstractGenomicsDBImportHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/AbstractGenomicsDBImportHandler.java index a44f756c5..4b281369c 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/AbstractGenomicsDBImportHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/AbstractGenomicsDBImportHandler.java @@ -629,7 +629,7 @@ else if (genomeIds.isEmpty()) } Integer maxRam = SequencePipelineService.get().getMaxRam(); - Integer nativeMemoryBuffer = ctx.getParams().optInt("nativeMemoryBuffer", 0); + int nativeMemoryBuffer = ctx.getParams().optInt("nativeMemoryBuffer", 0); if (maxRam != null && nativeMemoryBuffer > 0) { ctx.getLogger().info("Adjusting RAM based on memory buffer (" + nativeMemoryBuffer + "), from: " + maxRam); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/BlastNWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/BlastNWrapper.java index 9a7ce1075..278d9cdbf 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/BlastNWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/BlastNWrapper.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.run.util; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.pipeline.PipelineJobService; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/CollectWgsMetricsWithNonZeroCoverageWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/CollectWgsMetricsWithNonZeroCoverageWrapper.java index 2a658ccb8..19cde181f 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/CollectWgsMetricsWithNonZeroCoverageWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/CollectWgsMetricsWithNonZeroCoverageWrapper.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.run.util; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; /** * Created by bimber on 6/29/2017. diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/CombineGVCFsHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/CombineGVCFsHandler.java index 302b460a8..b4940a6c7 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/CombineGVCFsHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/CombineGVCFsHandler.java @@ -170,7 +170,7 @@ public void processFilesRemote(List inputFiles, JobContext c } } - wrapper.execute(genome.getWorkingFastaFile(), outputFile, options, vcfsToProcess.toArray(new File[vcfsToProcess.size()])); + wrapper.execute(genome.getWorkingFastaFile(), outputFile, options, vcfsToProcess.toArray(new File[0])); } if (!outputFile.exists()) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/CombineGVCFsWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/CombineGVCFsWrapper.java index cb60e086f..11d71fad0 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/CombineGVCFsWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/CombineGVCFsWrapper.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.run.util; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.SequenceAnalysisService; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/DepthOfCoverageWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/DepthOfCoverageWrapper.java index cb3524686..89d2dfd19 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/DepthOfCoverageWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/DepthOfCoverageWrapper.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.run.util; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.run.AbstractGatk4Wrapper; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/DownsampleSamWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/DownsampleSamWrapper.java index 1b8a7bcd1..048d47a5a 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/DownsampleSamWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/DownsampleSamWrapper.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.run.util; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.run.PicardWrapper; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/EstimateLibraryComplexityWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/EstimateLibraryComplexityWrapper.java index 5c93dc51d..a15102d07 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/EstimateLibraryComplexityWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/EstimateLibraryComplexityWrapper.java @@ -2,7 +2,6 @@ import htsjdk.samtools.SAMFileHeader; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.pipeline.SamSorter; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastaIndexer.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastaIndexer.java index d34f47e91..401d4944e 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastaIndexer.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastaIndexer.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.run.util; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.pipeline.SamtoolsRunner; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqToSamWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqToSamWrapper.java index 447056f9f..33cfc5a0c 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqToSamWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqToSamWrapper.java @@ -4,7 +4,6 @@ import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.samtools.util.FastqQualityFormat; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.run.PicardWrapper; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java index 8252c7876..8871efc4a 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java @@ -46,13 +46,11 @@ import java.io.InputStreamReader; import java.io.StringWriter; import java.util.ArrayList; -import java.util.Arrays; import java.util.HashSet; import java.util.LinkedList; import java.util.List; import java.util.Map; import java.util.Set; -import java.util.stream.Collectors; import java.util.zip.GZIPInputStream; /** diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FixMateInformationWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FixMateInformationWrapper.java index 345146b6a..09512ba1d 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FixMateInformationWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FixMateInformationWrapper.java @@ -2,7 +2,6 @@ import htsjdk.samtools.SAMFileHeader; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.run.PicardWrapper; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FlagStatRunner.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FlagStatRunner.java index c6d6342c2..6da5d24ce 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FlagStatRunner.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FlagStatRunner.java @@ -2,7 +2,6 @@ import org.apache.logging.log4j.Level; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.pipeline.SamtoolsRunner; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FlashWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FlashWrapper.java index f2e0f63d7..cbd57fffc 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FlashWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FlashWrapper.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.run.util; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GFFReadWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GFFReadWrapper.java index 3d5b5ec25..239c2d47d 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GFFReadWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GFFReadWrapper.java @@ -2,10 +2,8 @@ import org.apache.commons.io.FileUtils; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; -import org.labkey.api.sequenceanalysis.SequenceAnalysisService; import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper; import org.labkey.api.util.FileUtil; @@ -66,7 +64,7 @@ public File sortGxf(File gxf, @Nullable File output) throws PipelineJobException } Double lineCountStart = ((Long)SequencePipelineService.get().getLineCount(gxf)).doubleValue(); - Double lineCountEnd = ((Long)SequencePipelineService.get().getLineCount(outputFile)).doubleValue(); + double lineCountEnd = ((Long)SequencePipelineService.get().getLineCount(outputFile)).doubleValue(); if (lineCountEnd == 0) { throw new PipelineJobException("No lines remain after sorting"); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/IdxStatsRunner.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/IdxStatsRunner.java index 872b7b68a..900f8d889 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/IdxStatsRunner.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/IdxStatsRunner.java @@ -2,7 +2,6 @@ import org.apache.logging.log4j.Level; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.pipeline.SamtoolsRunner; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/ImmunoGenotypingWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/ImmunoGenotypingWrapper.java index 6a9a42484..b79adfb0c 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/ImmunoGenotypingWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/ImmunoGenotypingWrapper.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.run.util; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.run.AbstractDiscvrSeqWrapper; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/LiftoverVcfWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/LiftoverVcfWrapper.java index 032e9bd50..165d551df 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/LiftoverVcfWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/LiftoverVcfWrapper.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.run.util; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.SequenceAnalysisService; @@ -9,7 +8,6 @@ import java.io.File; import java.io.IOException; -import java.util.Date; import java.util.List; /** diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/MarkDuplicatesWithMateCigarWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/MarkDuplicatesWithMateCigarWrapper.java index 4401676c7..ec0eaacaa 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/MarkDuplicatesWithMateCigarWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/MarkDuplicatesWithMateCigarWrapper.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.run.util; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; /** * Created by bimber on 5/5/2016. diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/MergeBamAlignmentWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/MergeBamAlignmentWrapper.java index 171bf5d07..4e58dd717 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/MergeBamAlignmentWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/MergeBamAlignmentWrapper.java @@ -74,7 +74,7 @@ public File executeCommand(File refFasta, File alignedBam, List try (SamReader reader = fact.open(alignedBam)) { SAMFileHeader header = reader.getFileHeader(); - if (header.getReadGroups().size() == 0) + if (header.getReadGroups().isEmpty()) { getLogger().warn("No read groups found in input BAM"); } diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/MultiAllelicPositionWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/MultiAllelicPositionWrapper.java index d6aae4137..801cdc082 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/MultiAllelicPositionWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/MultiAllelicPositionWrapper.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.run.util; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.run.AbstractDiscvrSeqWrapper; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/NTSnp.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/NTSnp.java index 64f62ea0e..6156d97f3 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/NTSnp.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/NTSnp.java @@ -37,7 +37,6 @@ public NTSnp(CigarPositionIterable.PositionInfo pi) /** * 0-based, -1 indicates an insertion - * @return */ public int getReferencePosition() { @@ -46,7 +45,6 @@ public int getReferencePosition() /** * 0-based, -1 indicates a deletion - * @return */ public int getReadPosition() { @@ -79,7 +77,6 @@ public int getLastReadPosition() /** * Returns the last reference position that was overlapped (0-based). Primarily used for insertions relative to the reference, * in order to find the previous reference position. For non-insertions, this will return the same value as getRefPosition() - * @return */ public int getLastRefPosition() { diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/PARalyzerRunner.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/PARalyzerRunner.java index 989fd8d72..08bbfcc58 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/PARalyzerRunner.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/PARalyzerRunner.java @@ -2,7 +2,6 @@ import htsjdk.samtools.SAMFileHeader; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.pipeline.SamSorter; @@ -38,7 +37,7 @@ public File execute(File inputBam, File outDir, File twoBit, Map setOutputDir(outDir); //ensure sort order - File bam = inputBam; + File bam; if (SequenceUtil.getBamSortOrder(inputBam) != SAMFileHeader.SortOrder.queryname) { getLogger().info("Queryname Sorting BAM: " + inputBam.getPath()); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/RnaSeQCWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/RnaSeQCWrapper.java index 9cb630b60..aeb02da02 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/RnaSeQCWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/RnaSeQCWrapper.java @@ -4,7 +4,6 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.lang3.StringUtils; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.pipeline.PipelineJobService; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/SFFExtractRunner.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/SFFExtractRunner.java index 59df24a4d..1ed2beb34 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/SFFExtractRunner.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/SFFExtractRunner.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.run.util; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.util.FileUtil; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/SamFormatConverterWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/SamFormatConverterWrapper.java index 8f2830fd4..bb15b5f13 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/SamFormatConverterWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/SamFormatConverterWrapper.java @@ -2,7 +2,6 @@ import org.apache.commons.lang3.time.DurationFormatUtils; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.run.PicardWrapper; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/SortVcfWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/SortVcfWrapper.java index bb2431144..17a0f583a 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/SortVcfWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/SortVcfWrapper.java @@ -2,7 +2,6 @@ import org.apache.commons.io.FileUtils; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.SequenceAnalysisService; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/SplitNCigarReadsWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/SplitNCigarReadsWrapper.java index 1dc0f4584..512192409 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/SplitNCigarReadsWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/SplitNCigarReadsWrapper.java @@ -2,7 +2,6 @@ import htsjdk.samtools.SAMFileHeader; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.pipeline.SamSorter; import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/TabixRunner.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/TabixRunner.java index a242b5549..528cadd8e 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/TabixRunner.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/TabixRunner.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.run.util; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/VariantEvalWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/VariantEvalWrapper.java index ca1751879..2448152b3 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/VariantEvalWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/VariantEvalWrapper.java @@ -2,7 +2,6 @@ import htsjdk.samtools.util.Interval; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.run.AbstractGatk4Wrapper; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/DepthOfCoverageHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/DepthOfCoverageHandler.java index 6ac70c371..893f56d8a 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/DepthOfCoverageHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/DepthOfCoverageHandler.java @@ -131,20 +131,20 @@ public void processFilesRemote(List inputFiles, JobContext c extraArgs.addAll(DepthOfCoverageWrapper.generateIntervalArgsForFullGenome(rg, intervalList)); } - Integer mmq = ctx.getParams().optInt("mmq"); + int mmq = ctx.getParams().optInt("mmq"); if (mmq > 0) { extraArgs.add("--read-filter"); extraArgs.add("MappingQualityReadFilter"); extraArgs.add("--minimum-mapping-quality"); - extraArgs.add(mmq.toString()); + extraArgs.add(Integer.toString(mmq)); } - Integer mbq = ctx.getParams().optInt("mbq"); + int mbq = ctx.getParams().optInt("mbq"); if (mbq > 0) { extraArgs.add("--min-base-quality"); - extraArgs.add(mbq.toString()); + extraArgs.add(Integer.toString(mbq)); } extraArgs.add("--omit-locus-table"); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeConcordanceStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeConcordanceStep.java index 0ee8d3488..61b82cc4e 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeConcordanceStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeConcordanceStep.java @@ -208,7 +208,7 @@ private boolean annotationsPresent(File inputVcf) } } - private class DiscordantTracker + private static class DiscordantTracker { long totalCompared = 0L; long totalDiscordant = 0L; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/MultiAllelicPositionsHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/MultiAllelicPositionsHandler.java index 8839549c8..5488eea27 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/MultiAllelicPositionsHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/MultiAllelicPositionsHandler.java @@ -111,11 +111,11 @@ public void processFilesRemote(List inputFiles, JobContext c File outputFile = new File(ctx.getOutputDir(), basename + ".bed"); List options = new ArrayList<>(); - Integer minDepth = ctx.getParams().optInt("minDepth", 0); + int minDepth = ctx.getParams().optInt("minDepth", 0); if (minDepth > 0) { options.add("-minDepth"); - options.add(minDepth.toString()); + options.add(Integer.toString(minDepth)); } MultiAllelicPositionWrapper wrapper = new MultiAllelicPositionWrapper(ctx.getLogger()); @@ -125,7 +125,7 @@ public void processFilesRemote(List inputFiles, JobContext c throw new PipelineJobException("Unable to find expected file:" + outputFile.getPath()); } - Integer callThreshold = ctx.getParams().optInt("callThreshold", 0); + int callThreshold = ctx.getParams().optInt("callThreshold", 0); if (callThreshold > 0) { ctx.getLogger().info("will only report sites present in at least " + callThreshold + " samples"); @@ -140,7 +140,7 @@ public void processFilesRemote(List inputFiles, JobContext c while ((line = reader.readNext()) != null) { totalLines++; - Integer val = Integer.parseInt(line[4]); + int val = Integer.parseInt(line[4]); if (val < callThreshold) { linesFiltered++; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SnpEffWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SnpEffWrapper.java index 70f91bcf7..4f82587d4 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SnpEffWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SnpEffWrapper.java @@ -2,7 +2,6 @@ import org.apache.commons.io.FileUtils; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.pipeline.PipelineJobService; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SplitVcfBySamplesStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SplitVcfBySamplesStep.java index 20c076c54..de8480264 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SplitVcfBySamplesStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SplitVcfBySamplesStep.java @@ -13,7 +13,6 @@ import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider; import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome; import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler; -import org.labkey.api.sequenceanalysis.pipeline.TaskFileManager; import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor; import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStep; import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStepOutputImpl; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/VariantQCWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/VariantQCWrapper.java index ce6bdfa0c..58ed0c88b 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/VariantQCWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/VariantQCWrapper.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.run.variant; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.run.AbstractDiscvrSeqWrapper; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/AbstractSequenceMatcher.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/AbstractSequenceMatcher.java index 22e5b67ec..56a325281 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/AbstractSequenceMatcher.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/AbstractSequenceMatcher.java @@ -5,7 +5,6 @@ import htsjdk.samtools.fastq.FastqWriter; import org.apache.commons.lang3.StringUtils; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.util.Pair; import org.labkey.sequenceanalysis.model.SequenceTag; @@ -223,7 +222,7 @@ protected void scanForMatches(FastqRecord rec, Collection barcodes5 } i++; - if (matches5.size() > 0) + if (!matches5.isEmpty()) break; } } @@ -240,7 +239,7 @@ protected void scanForMatches(FastqRecord rec, Collection barcodes5 } i++; - if (matches5.size() > 0) + if (!matches5.isEmpty()) break; } } @@ -280,7 +279,7 @@ protected void scanForMatches(FastqRecord rec, Collection barcodes5 } i++; - if (matches3.size() > 0) + if (!matches3.isEmpty()) break; } } @@ -297,7 +296,7 @@ protected void scanForMatches(FastqRecord rec, Collection barcodes5 } i++; - if (matches3.size() > 0) + if (!matches3.isEmpty()) break; } } @@ -306,7 +305,7 @@ protected void scanForMatches(FastqRecord rec, Collection barcodes5 protected SequenceMatch findBestMatch(Map> matchesMap, Map counter) { SequenceMatch bestMatch = null; - if (matchesMap.size() > 0) + if (!matchesMap.isEmpty()) { //get the match w/ the lowest edit distance Map matches = matchesMap.get(matchesMap.keySet().iterator().next()); @@ -335,7 +334,7 @@ public File getSummaryLogFile() return _createSummaryLog ? _summaryLog : null; } - protected class SequenceMatch + protected static class SequenceMatch { private final FastqRecord _rec; private final SequenceTag _tag; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/Barcoder.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/Barcoder.java index 2a112db8c..43b40ba6e 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/Barcoder.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/Barcoder.java @@ -35,7 +35,6 @@ import java.io.PrintStream; import java.text.NumberFormat; import java.util.ArrayList; -import java.util.Arrays; import java.util.Collection; import java.util.Collections; import java.util.HashMap; @@ -277,7 +276,7 @@ public Set demultiplexPairs(List> fastqPairs, List 0) + if (!_otherMatches.isEmpty()) { _logger.info("Reads Not Matching A Readset:"); for (String key : _otherMatches.keySet()) @@ -657,13 +656,13 @@ private void testBarcoder(Logger log, int editDistance, int offset, int deletion String mid5 = readname[0].split("-")[0]; String mid3 = readname[1].split("-")[0]; - Integer editDist5 = Integer.parseInt(readname[0].split("-")[1].substring(0, 1)); - Integer offset5 = Integer.parseInt(readname[0].split("-")[1].substring(1, 2)); - Integer deletion5 = Integer.parseInt(readname[0].split("-")[1].substring(2, 3)); + int editDist5 = Integer.parseInt(readname[0].split("-")[1].substring(0, 1)); + int offset5 = Integer.parseInt(readname[0].split("-")[1].substring(1, 2)); + int deletion5 = Integer.parseInt(readname[0].split("-")[1].substring(2, 3)); - Integer editDist3 = Integer.parseInt(readname[1].split("-")[1].substring(0, 1)); - Integer offset3 = Integer.parseInt(readname[1].split("-")[1].substring(1, 2)); - Integer deletion3 = Integer.parseInt(readname[1].split("-")[1].substring(2, 3)); + int editDist3 = Integer.parseInt(readname[1].split("-")[1].substring(0, 1)); + int offset3 = Integer.parseInt(readname[1].split("-")[1].substring(1, 2)); + int deletion3 = Integer.parseInt(readname[1].split("-")[1].substring(2, 3)); boolean shouldFindMid5 = editDist5 <= editDistance && offset5 <= offset && deletion5 <= deletions; @@ -672,8 +671,8 @@ private void testBarcoder(Logger log, int editDistance, int offset, int deletion Assert.assertEquals("Incorrect 5' barcode on line: " + lineNum, (shouldFindMid5 ? mid5 : ""), line[2]); Assert.assertEquals("Incorrect 3' barcode on line: " + lineNum, (shouldFindMid3 ? mid3 : ""), line[3]); - Assert.assertEquals("Incorrect 5' editDistance on line: " + lineNum, (shouldFindMid5 ? editDist5.toString() : ""), line[4]); - Assert.assertEquals("Incorrect 3' editDistance on line: " + lineNum, (shouldFindMid3 ? editDist3.toString() : ""), line[5]); + Assert.assertEquals("Incorrect 5' editDistance on line: " + lineNum, (shouldFindMid5 ? Integer.toString(editDist5) : ""), line[4]); + Assert.assertEquals("Incorrect 3' editDistance on line: " + lineNum, (shouldFindMid3 ? Integer.toString(editDist3) : ""), line[5]); Integer barcodeLength = 10; //all barcodes are 10bp in this test @@ -768,7 +767,7 @@ private BarcodeModel[] getBarcodes() names.add(rs.getBarcode3()); } - return BarcodeModel.getByNames(names.toArray(new String[names.size()])); + return BarcodeModel.getByNames(names.toArray(new String[0])); } private List getReadsets() diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/ChainFileValidator.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/ChainFileValidator.java index 9055c0cbe..a3715b491 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/ChainFileValidator.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/ChainFileValidator.java @@ -77,7 +77,7 @@ public File processChainFile(File chainFile, int sourceGenome, int targetGenome, List errors = new ArrayList<>(); while ((line = reader.readLine()) != null) { - if (line.equals("") || line.startsWith("#")) + if (line.isEmpty() || line.startsWith("#")) { continue; } @@ -292,7 +292,7 @@ private String resolveSequenceId(String refName, int genomeId) { final Map cachedReferences = new CaseInsensitiveHashMap<>(); SqlSelector ss = new SqlSelector(DbScope.getLabKeyScope(), new SQLFragment("SELECT r.rowid, r.name, r.genbank, r.refSeqId, r.aliases FROM sequenceanalysis.ref_nt_sequences r WHERE r.rowid IN (SELECT ref_nt_id FROM sequenceanalysis.reference_library_members m WHERE m.library_id = ?) ", genomeId)); - ss.forEach(new Selector.ForEachBlock() + ss.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException @@ -340,16 +340,16 @@ else if (name.startsWith("chr")) TableSelector ts = new TableSelector(SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_REF_LIBRARY_MEMBERS), PageFlowUtil.set("ref_nt_id", "alias"), filter, null); if (ts.exists()) { - ts.forEachResults(new Selector.ForEachBlock() - { - @Override - public void exec(Results rs) throws SQLException - { - String name = RefNtSequenceModel.getForRowId(rs.getInt(FieldKey.fromString("ref_nt_id"))).getName(); - String alias = rs.getString(FieldKey.fromString("alias")); - cachedReferences.put(alias, name); - } - }); + ts.forEachResults(new Selector.ForEachBlock<>() + { + @Override + public void exec(Results rs) throws SQLException + { + String name = RefNtSequenceModel.getForRowId(rs.getInt(FieldKey.fromString("ref_nt_id"))).getName(); + String alias = rs.getString(FieldKey.fromString("alias")); + cachedReferences.put(alias, name); + } + }); } _cachedReferencesByGenome.put(genomeId, cachedReferences); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/CreateUnalignedFastq.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/CreateUnalignedFastq.java index 1e47fe50c..3f4b64a2a 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/CreateUnalignedFastq.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/CreateUnalignedFastq.java @@ -8,7 +8,6 @@ import htsjdk.samtools.fastq.FastqWriter; import htsjdk.samtools.fastq.FastqWriterFactory; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.util.FileUtil; import org.labkey.api.util.Pair; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/FastaToFastqConverter.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/FastaToFastqConverter.java index 5f7d908da..86e4bb35f 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/FastaToFastqConverter.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/FastaToFastqConverter.java @@ -6,7 +6,6 @@ import htsjdk.samtools.reference.FastaSequenceFile; import htsjdk.samtools.reference.ReferenceSequence; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import java.io.File; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/FastqMerger.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/FastqMerger.java index 156dfc79b..013f0f5f5 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/FastqMerger.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/FastqMerger.java @@ -3,7 +3,6 @@ import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.SystemUtils; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.reader.Readers; import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/FastqToFastaConverter.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/FastqToFastaConverter.java index 545dcda92..2c833b8c9 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/FastqToFastaConverter.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/FastqToFastaConverter.java @@ -4,7 +4,6 @@ import htsjdk.samtools.fastq.FastqRecord; import htsjdk.samtools.util.IOUtil; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.pipeline.PipelineJobException; import java.io.BufferedWriter; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/FastqUtils.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/FastqUtils.java index 2aea8b583..785a45ead 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/FastqUtils.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/FastqUtils.java @@ -23,7 +23,6 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.util.FileType; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/MultiFeatureIterator.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/MultiFeatureIterator.java index feaf23272..cd78cc183 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/MultiFeatureIterator.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/MultiFeatureIterator.java @@ -34,7 +34,7 @@ public MultiFeatureIterator(Collection> readers, Comparator< for (FeatureReader reader : readers) { - _queue.add(new ComparableFeatureIterator(reader.iterator(), comparator)); + _queue.add(new ComparableFeatureIterator<>(reader.iterator(), comparator)); } } @@ -52,7 +52,7 @@ private void startIterationIfRequired() for (final Iterator iterator : _iterators) { - addIfNotEmpty(new ComparableFeatureIterator(iterator, _comparator)); + addIfNotEmpty(new ComparableFeatureIterator<>(iterator, _comparator)); } _initialized = true; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/ReferenceLibraryHelperImpl.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/ReferenceLibraryHelperImpl.java index 3490758a2..d6514891b 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/ReferenceLibraryHelperImpl.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/ReferenceLibraryHelperImpl.java @@ -1,7 +1,6 @@ package org.labkey.sequenceanalysis.util; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.reader.Readers; import org.labkey.api.sequenceanalysis.ReferenceLibraryHelper; @@ -21,7 +20,7 @@ public class ReferenceLibraryHelperImpl implements ReferenceLibraryHelper { private final File _refFasta; - private Logger _log = null; + private Logger _log; private final Map _cachedIds = new HashMap<>(); private final Map _cachedAccessions = new HashMap<>(); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/TranslatingReferenceSequence.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/TranslatingReferenceSequence.java index 666edabe9..6dce152df 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/TranslatingReferenceSequence.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/TranslatingReferenceSequence.java @@ -71,8 +71,6 @@ private void queryDb() /** * - * @param readSnps - * @return */ public List translateSnpsForRead(Map> readSnps) { @@ -233,7 +231,7 @@ private List translateSnp(NTSnp pi, Map> readSnps) StringBuilder codon = new StringBuilder(); //to track the SNPs that comprise this codon, 0-based - Map snpMap = new HashMap(); + Map snpMap = new HashMap<>(); Integer positionInCodon = null; //0-based for (Integer p : positions) //1-based { @@ -242,7 +240,7 @@ private List translateSnp(NTSnp pi, Map> readSnps) { StringBuilder thisSegment = new StringBuilder(); int positionInSegment = 0; - Map snpMapForSegment = new HashMap(); //0-based + Map snpMapForSegment = new HashMap<>(); //0-based //force sorting by idx List otherSnps = readSnps.get(position); @@ -300,7 +298,7 @@ private List translateSnp(NTSnp pi, Map> readSnps) assert positionInCodon != null; if (codon.length() <= 4) { - List snpList = new ArrayList(snpMap.values()); + List snpList = new ArrayList<>(snpMap.values()); snps.add(new AASnp(pi, model, aaPosInProtein, 0, codon.toString(), frame, snpList, _nt.getSequenceBases())); } else @@ -309,7 +307,7 @@ private List translateSnp(NTSnp pi, Map> readSnps) int start = aaInsertIndex * 3; int stop = (codon.length() - start) <= 4 ? codon.length() : start + 3; String tmpCodon = codon.substring(start, stop); - List snpList = new ArrayList(); + List snpList = new ArrayList<>(); for (int j = start; j 0) { - Integer rowId2 = Integer.valueOf(srr.getRows().get(0).get("rowid").toString()); + int rowId2 = Integer.parseInt(srr.getRows().get(0).get("rowid").toString()); log("initial rowId: " + rowId + ", after: " + rowId2); } diff --git a/Studies/test/src/org/labkey/test/tests/studies/StudiesTest.java b/Studies/test/src/org/labkey/test/tests/studies/StudiesTest.java index 35db63d66..baf7d1d3b 100644 --- a/Studies/test/src/org/labkey/test/tests/studies/StudiesTest.java +++ b/Studies/test/src/org/labkey/test/tests/studies/StudiesTest.java @@ -23,7 +23,7 @@ protected void doCleanup(boolean afterTest) throws TestTimeoutException @BeforeClass public static void setupProject() { - StudiesTest init = (StudiesTest)getCurrentTest(); + StudiesTest init = getCurrentTest(); init.doSetup(); } diff --git a/blast/src/org/labkey/blast/BLASTController.java b/blast/src/org/labkey/blast/BLASTController.java index d511beae8..06ec27082 100644 --- a/blast/src/org/labkey/blast/BLASTController.java +++ b/blast/src/org/labkey/blast/BLASTController.java @@ -88,7 +88,7 @@ public BLASTController() } @RequiresPermission(AdminPermission.class) - public class GetSettingsAction extends ReadOnlyApiAction + public static class GetSettingsAction extends ReadOnlyApiAction { @Override public ApiResponse execute(Object form, BindException errors) @@ -104,7 +104,7 @@ public ApiResponse execute(Object form, BindException errors) } @RequiresSiteAdmin - public class SetSettingsAction extends MutatingApiAction + public static class SetSettingsAction extends MutatingApiAction { @Override public ApiResponse execute(SettingsForm form, BindException errors) @@ -150,7 +150,7 @@ public void setBlastBinDir(String blastBinDir) } @RequiresPermission(InsertPermission.class) - public class CreateDatabaseAction extends MutatingApiAction + public static class CreateDatabaseAction extends MutatingApiAction { @Override public ApiResponse execute(DatabaseForm form, BindException errors) @@ -179,7 +179,7 @@ public ApiResponse execute(DatabaseForm form, BindException errors) } @RequiresPermission(ReadPermission.class) - public class RunBlastAction extends AbstractFileUploadAction + public static class RunBlastAction extends AbstractFileUploadAction { @Override protected void setContentType(HttpServletResponse response) @@ -467,7 +467,7 @@ public void setLibraryIds(Integer[] libraryIds) } @RequiresPermission(AdminPermission.class) - public class RecreateDatabaseAction extends MutatingApiAction + public static class RecreateDatabaseAction extends MutatingApiAction { @Override public ApiResponse execute(RecreateDatabaseForm form, BindException errors) @@ -530,7 +530,7 @@ public void setDatabaseIds(String[] databaseIds) } @RequiresPermission(ReadPermission.class) - public class JobDetailsAction extends SimpleViewAction + public static class JobDetailsAction extends SimpleViewAction { @Override public ModelAndView getView(BlastResultForm form, BindException errors) throws Exception @@ -571,7 +571,7 @@ public void setJobId(String jobId) @RequiresPermission(ReadPermission.class) @IgnoresTermsOfUse - public class DownloadBlastResultsAction extends ExportAction + public static class DownloadBlastResultsAction extends ExportAction { @Override public void export(DownloadBlastResultsForm form, HttpServletResponse response, BindException errors) throws Exception diff --git a/blast/src/org/labkey/blast/BLASTMaintenanceTask.java b/blast/src/org/labkey/blast/BLASTMaintenanceTask.java index b1d3fa8d7..87c70d870 100644 --- a/blast/src/org/labkey/blast/BLASTMaintenanceTask.java +++ b/blast/src/org/labkey/blast/BLASTMaintenanceTask.java @@ -1,7 +1,6 @@ package org.labkey.blast; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.apache.tomcat.util.http.fileupload.FileUtils; import org.labkey.api.collections.CaseInsensitiveHashSet; import org.labkey.api.data.Container; diff --git a/blast/src/org/labkey/blast/BLASTUpgradeCode.java b/blast/src/org/labkey/blast/BLASTUpgradeCode.java index 547d676d5..8651ce0fd 100644 --- a/blast/src/org/labkey/blast/BLASTUpgradeCode.java +++ b/blast/src/org/labkey/blast/BLASTUpgradeCode.java @@ -5,7 +5,6 @@ import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; -import org.labkey.api.data.DbSchema; import org.labkey.api.data.DbScope; import org.labkey.api.data.PropertyManager; import org.labkey.api.data.SQLFragment; @@ -17,12 +16,9 @@ import org.labkey.api.module.ModuleContext; import org.labkey.api.pipeline.PipelineService; import org.labkey.api.query.FieldKey; -import org.labkey.api.util.FileUtil; import org.labkey.api.util.PageFlowUtil; -import org.labkey.blast.model.BlastJob; import java.io.File; -import java.io.IOException; import java.util.List; import java.util.Map; diff --git a/blast/src/org/labkey/blast/BlastGenomeTrigger.java b/blast/src/org/labkey/blast/BlastGenomeTrigger.java index 2326b5797..3359fcc74 100644 --- a/blast/src/org/labkey/blast/BlastGenomeTrigger.java +++ b/blast/src/org/labkey/blast/BlastGenomeTrigger.java @@ -1,7 +1,6 @@ package org.labkey.blast; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.data.SimpleFilter; diff --git a/blast/src/org/labkey/blast/button/CreateDatabaseButton.java b/blast/src/org/labkey/blast/button/CreateDatabaseButton.java index 8b85fd1b0..ce6fe2166 100644 --- a/blast/src/org/labkey/blast/button/CreateDatabaseButton.java +++ b/blast/src/org/labkey/blast/button/CreateDatabaseButton.java @@ -5,7 +5,6 @@ import org.labkey.api.view.template.ClientDependency; import org.labkey.blast.BLASTModule; -import java.util.Arrays; import java.util.List; /** diff --git a/blast/src/org/labkey/blast/model/BlastJob.java b/blast/src/org/labkey/blast/model/BlastJob.java index 86890a9de..fd1e6923d 100644 --- a/blast/src/org/labkey/blast/model/BlastJob.java +++ b/blast/src/org/labkey/blast/model/BlastJob.java @@ -375,7 +375,7 @@ private void addAlignment(String sname, int qLen, int sLen, int alignLen) } } - class Alignment + static class Alignment { final int qLength; final int sLength; diff --git a/blast/src/org/labkey/blast/pipeline/BlastDatabaseTask.java b/blast/src/org/labkey/blast/pipeline/BlastDatabaseTask.java index d92154943..d65cc3ab8 100644 --- a/blast/src/org/labkey/blast/pipeline/BlastDatabaseTask.java +++ b/blast/src/org/labkey/blast/pipeline/BlastDatabaseTask.java @@ -32,7 +32,6 @@ import java.io.File; import java.io.IOException; import java.io.PrintWriter; -import java.util.Arrays; import java.util.Collections; import java.util.List; diff --git a/blast/src/org/labkey/blast/pipeline/BlastFinalTask.java b/blast/src/org/labkey/blast/pipeline/BlastFinalTask.java index 6824d3a6f..9e868b666 100644 --- a/blast/src/org/labkey/blast/pipeline/BlastFinalTask.java +++ b/blast/src/org/labkey/blast/pipeline/BlastFinalTask.java @@ -19,13 +19,9 @@ import org.labkey.api.pipeline.AbstractTaskFactorySettings; import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.pipeline.PipelineJobException; -import org.labkey.api.pipeline.RecordedAction; import org.labkey.api.pipeline.RecordedActionSet; import org.labkey.api.util.FileType; -import org.labkey.blast.BLASTWrapper; -import java.io.IOException; -import java.util.Arrays; import java.util.Collections; import java.util.List; diff --git a/blast/src/org/labkey/blast/pipeline/BlastWorkTask.java b/blast/src/org/labkey/blast/pipeline/BlastWorkTask.java index b94a39f29..6f8e34919 100644 --- a/blast/src/org/labkey/blast/pipeline/BlastWorkTask.java +++ b/blast/src/org/labkey/blast/pipeline/BlastWorkTask.java @@ -25,7 +25,6 @@ import org.labkey.blast.BLASTWrapper; import java.io.IOException; -import java.util.Arrays; import java.util.Collections; import java.util.List; diff --git a/cluster/api-src/org/labkey/api/cluster/ClusterService.java b/cluster/api-src/org/labkey/api/cluster/ClusterService.java index 00f6aa059..d9f7f3505 100644 --- a/cluster/api-src/org/labkey/api/cluster/ClusterService.java +++ b/cluster/api-src/org/labkey/api/cluster/ClusterService.java @@ -1,7 +1,6 @@ package org.labkey.api.cluster; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.pipeline.PipelineValidationException; diff --git a/cluster/src/org/labkey/cluster/ClusterController.java b/cluster/src/org/labkey/cluster/ClusterController.java index 4028cd757..f17c50518 100644 --- a/cluster/src/org/labkey/cluster/ClusterController.java +++ b/cluster/src/org/labkey/cluster/ClusterController.java @@ -107,7 +107,7 @@ public boolean handlePost(Object form, BindException errors) throws Exception } @RequiresSiteAdmin - public class ForcePipelineCancelAction extends ConfirmAction + public static class ForcePipelineCancelAction extends ConfirmAction { @Override public void validateCommand(JobIdsForm form, Errors errors) @@ -213,7 +213,7 @@ public void setFilePath(String filePath) } @RequiresSiteAdmin - public class ResetPipelineJobLogFileAction extends ConfirmAction + public static class ResetPipelineJobLogFileAction extends ConfirmAction { @Override public void validateCommand(ResetPipelineJobLogFileForm form, Errors errors) diff --git a/cluster/src/org/labkey/cluster/pipeline/AbstractClusterExecutionEngine.java b/cluster/src/org/labkey/cluster/pipeline/AbstractClusterExecutionEngine.java index dd9fcc125..ba520f4d6 100644 --- a/cluster/src/org/labkey/cluster/pipeline/AbstractClusterExecutionEngine.java +++ b/cluster/src/org/labkey/cluster/pipeline/AbstractClusterExecutionEngine.java @@ -3,7 +3,6 @@ import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashSet; diff --git a/cluster/src/org/labkey/cluster/pipeline/HTCondorExecutionEngineConfig.java b/cluster/src/org/labkey/cluster/pipeline/HTCondorExecutionEngineConfig.java index 206eb177d..e45cfe263 100644 --- a/cluster/src/org/labkey/cluster/pipeline/HTCondorExecutionEngineConfig.java +++ b/cluster/src/org/labkey/cluster/pipeline/HTCondorExecutionEngineConfig.java @@ -1,11 +1,6 @@ package org.labkey.cluster.pipeline; import org.jetbrains.annotations.NotNull; -import org.labkey.api.util.StringExpression; -import org.labkey.api.util.StringExpressionFactory; - -import java.util.ArrayList; -import java.util.List; /** * Created by bimber on 10/31/2015. diff --git a/cluster/src/org/labkey/cluster/pipeline/SlurmExecutionEngine.java b/cluster/src/org/labkey/cluster/pipeline/SlurmExecutionEngine.java index 017ce8e46..e13c918d3 100644 --- a/cluster/src/org/labkey/cluster/pipeline/SlurmExecutionEngine.java +++ b/cluster/src/org/labkey/cluster/pipeline/SlurmExecutionEngine.java @@ -124,7 +124,7 @@ protected Set updateStatusForAllJobs() throws PipelineJobException { //verify success boolean headerFound = false; - List header = null; + List header; int jobIdx = -1; int stateIdx = -1; int hostnameIdx = -1; @@ -721,7 +721,7 @@ private Pair getStatusFromQueue(ClusterJob job) if (ret != null) { boolean headerFound = false; - List header = null; + List header; int jobIdx = -1; int stateIdx = -1; int hostnameIdx = -1; diff --git a/cluster/src/org/labkey/cluster/pipeline/TestCase.java b/cluster/src/org/labkey/cluster/pipeline/TestCase.java index 00a8be7c3..51caea543 100644 --- a/cluster/src/org/labkey/cluster/pipeline/TestCase.java +++ b/cluster/src/org/labkey/cluster/pipeline/TestCase.java @@ -113,7 +113,7 @@ public void basicTest() throws Exception public static class TestRunner implements ClusterService.ClusterRemoteTask { - public long _sleep = 0l; + public long _sleep; public TestRunner(long sleep) { diff --git a/discvrcore/src/org/labkey/discvrcore/AuditSummaryUserSchema.java b/discvrcore/src/org/labkey/discvrcore/AuditSummaryUserSchema.java index afbf634b6..ce7236f5c 100644 --- a/discvrcore/src/org/labkey/discvrcore/AuditSummaryUserSchema.java +++ b/discvrcore/src/org/labkey/discvrcore/AuditSummaryUserSchema.java @@ -236,13 +236,13 @@ public void testAuditTables() throws Exception TableInfo qa = QueryService.get().getUserSchema(TestContext.get().getUser(), c, NAME).getTable(DATASET_AUDIT); TableSelector ts1 = new TableSelector(qa, PageFlowUtil.set("primaryKey")); - assertEquals("Incorrect row count", ts1.getRowCount(), 2L); + assertEquals("Incorrect row count", 2L, ts1.getRowCount()); assertEquals("Incorrect PK", new TableSelector(qa, PageFlowUtil.set("primaryKey"), new SimpleFilter(FieldKey.fromString("Comment"), "inserted", CompareType.CONTAINS).addCondition(FieldKey.fromString("DatasetId"), d1.getDatasetId()), null).getObject(String.class), guid1); - assertEquals("Incorrect PK", new TableSelector(qa, PageFlowUtil.set("primaryKey"), new SimpleFilter(FieldKey.fromString("Comment"), "inserted", CompareType.CONTAINS).addCondition(FieldKey.fromString("DatasetId"), d2.getDatasetId()), null).getObject(String.class), "P1"); + assertEquals("Incorrect PK", "P1", new TableSelector(qa, PageFlowUtil.set("primaryKey"), new SimpleFilter(FieldKey.fromString("Comment"), "inserted", CompareType.CONTAINS).addCondition(FieldKey.fromString("DatasetId"), d2.getDatasetId()), null).getObject(String.class)); assertEquals("Incorrect PK", new TableSelector(qa, PageFlowUtil.set("primaryKey"), new SimpleFilter(FieldKey.fromString("Comment"), "inserted", CompareType.CONTAINS).addCondition(FieldKey.fromString("DatasetId/Name"), d1.getName()), null).getObject(String.class), guid1); - assertEquals("Incorrect PK", new TableSelector(qa, PageFlowUtil.set("primaryKey"), new SimpleFilter(FieldKey.fromString("Comment"), "inserted", CompareType.CONTAINS).addCondition(FieldKey.fromString("DatasetId/Name"), d2.getName()), null).getObject(String.class), "P1"); + assertEquals("Incorrect PK", "P1", new TableSelector(qa, PageFlowUtil.set("primaryKey"), new SimpleFilter(FieldKey.fromString("Comment"), "inserted", CompareType.CONTAINS).addCondition(FieldKey.fromString("DatasetId/Name"), d2.getName()), null).getObject(String.class)); t1.getUpdateService().deleteRows(TestContext.get().getUser(), c, Collections.singletonList(new CaseInsensitiveHashMap<>(Map.of("ObjectId", guid1))), null, null); assertEquals("Incorrect PK", new TableSelector(qa, PageFlowUtil.set("primaryKey"), new SimpleFilter(FieldKey.fromString("Comment"), "deleted", CompareType.CONTAINS), null).getObject(String.class), guid1); @@ -251,7 +251,7 @@ public void testAuditTables() throws Exception User reader = getReaderUser(true); qa = QueryService.get().getUserSchema(reader, c, NAME).getTable(DATASET_AUDIT); assertEquals("Incorrect PK", new TableSelector(qa, PageFlowUtil.set("primaryKey"), new SimpleFilter(FieldKey.fromString("Comment"), "inserted", CompareType.CONTAINS).addCondition(FieldKey.fromString("DatasetId/Name"), d1.getName()), null).getObject(String.class), guid1); - assertEquals("Incorrect PK", new TableSelector(qa, PageFlowUtil.set("primaryKey"), new SimpleFilter(FieldKey.fromString("Comment"), "inserted", CompareType.CONTAINS).addCondition(FieldKey.fromString("DatasetId/Name"), d2.getName()), null).getObject(String.class), "P1"); + assertEquals("Incorrect PK", "P1", new TableSelector(qa, PageFlowUtil.set("primaryKey"), new SimpleFilter(FieldKey.fromString("Comment"), "inserted", CompareType.CONTAINS).addCondition(FieldKey.fromString("DatasetId/Name"), d2.getName()), null).getObject(String.class)); } @AfterClass diff --git a/discvrcore/test/src/org/labkey/test/tests/discvrcore/DiscvrCoreTest.java b/discvrcore/test/src/org/labkey/test/tests/discvrcore/DiscvrCoreTest.java index 7b1150048..ad3a41506 100644 --- a/discvrcore/test/src/org/labkey/test/tests/discvrcore/DiscvrCoreTest.java +++ b/discvrcore/test/src/org/labkey/test/tests/discvrcore/DiscvrCoreTest.java @@ -27,8 +27,6 @@ import java.util.Collections; import java.util.List; -import static org.junit.Assert.*; - @Category({InDevelopment.class}) public class DiscvrCoreTest extends BaseWebDriverTest { @@ -41,7 +39,7 @@ protected void doCleanup(boolean afterTest) throws TestTimeoutException @BeforeClass public static void setupProject() { - DiscvrCoreTest init = (DiscvrCoreTest)getCurrentTest(); + DiscvrCoreTest init = getCurrentTest(); init.doSetup(); } diff --git a/jbrowse/api-src/org/labkey/api/jbrowse/JBrowseFieldCustomizer.java b/jbrowse/api-src/org/labkey/api/jbrowse/JBrowseFieldCustomizer.java index 1ea7cfccc..2c0e87c9c 100644 --- a/jbrowse/api-src/org/labkey/api/jbrowse/JBrowseFieldCustomizer.java +++ b/jbrowse/api-src/org/labkey/api/jbrowse/JBrowseFieldCustomizer.java @@ -7,9 +7,9 @@ import java.util.List; public interface JBrowseFieldCustomizer { - public void customizeField(JBrowseFieldDescriptor field, Container c, User u); + void customizeField(JBrowseFieldDescriptor field, Container c, User u); - public List getPromotedFilters(Collection indexedFields, Container c, User u); + List getPromotedFilters(Collection indexedFields, Container c, User u); - public boolean isAvailable(Container c, User u); + boolean isAvailable(Container c, User u); } diff --git a/jbrowse/api-src/org/labkey/api/jbrowse/JBrowseFieldDescriptor.java b/jbrowse/api-src/org/labkey/api/jbrowse/JBrowseFieldDescriptor.java index c6a3ba61c..4c6dc45b2 100644 --- a/jbrowse/api-src/org/labkey/api/jbrowse/JBrowseFieldDescriptor.java +++ b/jbrowse/api-src/org/labkey/api/jbrowse/JBrowseFieldDescriptor.java @@ -18,7 +18,7 @@ public class JBrowseFieldDescriptor { private List _allowableValues = null; private boolean _isHidden = false; private String _colWidth = null; - private Integer _orderKey = 8; + private Integer _orderKey; // NOTE: this should support "jexl:xxxxxx" syntax, like other JBrowse formatting private String _formatString = null; diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseGenomeTrigger.java b/jbrowse/src/org/labkey/jbrowse/JBrowseGenomeTrigger.java index cc3e1eed3..7078bde92 100644 --- a/jbrowse/src/org/labkey/jbrowse/JBrowseGenomeTrigger.java +++ b/jbrowse/src/org/labkey/jbrowse/JBrowseGenomeTrigger.java @@ -3,7 +3,6 @@ import org.apache.logging.log4j.Logger; import org.labkey.api.data.Container; import org.labkey.api.module.ModuleLoader; -import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.security.User; import org.labkey.api.sequenceanalysis.GenomeTrigger; diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseLuceneSearch.java b/jbrowse/src/org/labkey/jbrowse/JBrowseLuceneSearch.java index d4a58e168..532d76156 100644 --- a/jbrowse/src/org/labkey/jbrowse/JBrowseLuceneSearch.java +++ b/jbrowse/src/org/labkey/jbrowse/JBrowseLuceneSearch.java @@ -261,7 +261,7 @@ private SearchConfig createSearchConfig(User u, String searchString, final int p while (tokenizer.hasMoreTokens() && !searchString.equals(ALL_DOCS)) { String queryString = tokenizer.nextToken(); - Query query = null; + Query query; String fieldName = extractFieldName(queryString); @@ -693,7 +693,7 @@ public void shutdownStarted() } } - private class SearchConfig { + private static class SearchConfig { CacheEntry cacheEntry; Query query; int pageSize; diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseManager.java b/jbrowse/src/org/labkey/jbrowse/JBrowseManager.java index f3e56434b..ec0f92945 100644 --- a/jbrowse/src/org/labkey/jbrowse/JBrowseManager.java +++ b/jbrowse/src/org/labkey/jbrowse/JBrowseManager.java @@ -48,7 +48,6 @@ import org.labkey.api.util.Path; import org.labkey.api.view.UnauthorizedException; import org.labkey.jbrowse.model.JBrowseSession; -import org.labkey.jbrowse.model.JsonFile; import org.labkey.jbrowse.pipeline.JBrowseSessionPipelineJob; import java.io.File; @@ -58,7 +57,6 @@ import java.util.Arrays; import java.util.List; import java.util.Set; -import java.util.stream.Collectors; public class JBrowseManager { @@ -187,7 +185,7 @@ public File getJbrowseCli() throws PipelineJobException throw new PipelineJobException("Unable to find expected folder: " + toolDir.getPath()); } - File exe = null; + File exe; if (SystemUtils.IS_OS_WINDOWS) { exe = new File(toolDir, "cli-win.exe"); diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseSequenceOutputHandler.java b/jbrowse/src/org/labkey/jbrowse/JBrowseSequenceOutputHandler.java index c1b8ac373..f7aab18d6 100644 --- a/jbrowse/src/org/labkey/jbrowse/JBrowseSequenceOutputHandler.java +++ b/jbrowse/src/org/labkey/jbrowse/JBrowseSequenceOutputHandler.java @@ -14,7 +14,6 @@ import org.labkey.api.view.ActionURL; import java.io.File; -import java.util.Arrays; import java.util.LinkedHashSet; import java.util.List; @@ -100,7 +99,7 @@ public boolean doSplitJobs() return false; } - public class Processor implements SequenceOutputProcessor + public static class Processor implements SequenceOutputProcessor { @Override public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport support, List inputFiles, JSONObject params, File outputDir, List actions, List outputsToCreate) throws UnsupportedOperationException, PipelineJobException diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseServiceImpl.java b/jbrowse/src/org/labkey/jbrowse/JBrowseServiceImpl.java index 6ad23749a..df8905483 100644 --- a/jbrowse/src/org/labkey/jbrowse/JBrowseServiceImpl.java +++ b/jbrowse/src/org/labkey/jbrowse/JBrowseServiceImpl.java @@ -178,10 +178,6 @@ public void customizeField(User u, Container c, JBrowseFieldDescriptor field) { } /*** - * @param groupName - * @param u - * @param c - * @return */ public List resolveGroups(String trackId, String groupName, User u, Container c) { diff --git a/jbrowse/src/org/labkey/jbrowse/button/AddDataButton.java b/jbrowse/src/org/labkey/jbrowse/button/AddDataButton.java index 6303e8cf0..171010b93 100644 --- a/jbrowse/src/org/labkey/jbrowse/button/AddDataButton.java +++ b/jbrowse/src/org/labkey/jbrowse/button/AddDataButton.java @@ -6,7 +6,6 @@ import org.labkey.api.view.template.ClientDependency; import org.labkey.jbrowse.JBrowseModule; -import java.util.Arrays; import java.util.List; /** diff --git a/jbrowse/src/org/labkey/jbrowse/button/AddLibraryButton.java b/jbrowse/src/org/labkey/jbrowse/button/AddLibraryButton.java index d5554956d..8333f5e33 100644 --- a/jbrowse/src/org/labkey/jbrowse/button/AddLibraryButton.java +++ b/jbrowse/src/org/labkey/jbrowse/button/AddLibraryButton.java @@ -6,7 +6,6 @@ import org.labkey.api.view.template.ClientDependency; import org.labkey.jbrowse.JBrowseModule; -import java.util.Arrays; import java.util.List; /** diff --git a/jbrowse/src/org/labkey/jbrowse/button/AddTrackButton.java b/jbrowse/src/org/labkey/jbrowse/button/AddTrackButton.java index df7d268a1..002f19df2 100644 --- a/jbrowse/src/org/labkey/jbrowse/button/AddTrackButton.java +++ b/jbrowse/src/org/labkey/jbrowse/button/AddTrackButton.java @@ -6,7 +6,6 @@ import org.labkey.api.view.template.ClientDependency; import org.labkey.jbrowse.JBrowseModule; -import java.util.Arrays; import java.util.List; /** diff --git a/jbrowse/src/org/labkey/jbrowse/button/ModifyTrackConfigButton.java b/jbrowse/src/org/labkey/jbrowse/button/ModifyTrackConfigButton.java index 59601ad47..6d7488d28 100644 --- a/jbrowse/src/org/labkey/jbrowse/button/ModifyTrackConfigButton.java +++ b/jbrowse/src/org/labkey/jbrowse/button/ModifyTrackConfigButton.java @@ -6,7 +6,6 @@ import org.labkey.api.view.template.ClientDependency; import org.labkey.jbrowse.JBrowseModule; -import java.util.Arrays; import java.util.List; /** diff --git a/jbrowse/src/org/labkey/jbrowse/button/ReprocessResourcesButton.java b/jbrowse/src/org/labkey/jbrowse/button/ReprocessResourcesButton.java index 5d11feaf2..36dcfdddf 100644 --- a/jbrowse/src/org/labkey/jbrowse/button/ReprocessResourcesButton.java +++ b/jbrowse/src/org/labkey/jbrowse/button/ReprocessResourcesButton.java @@ -6,7 +6,6 @@ import org.labkey.api.view.template.ClientDependency; import org.labkey.jbrowse.JBrowseModule; -import java.util.Arrays; import java.util.List; /** diff --git a/jbrowse/src/org/labkey/jbrowse/button/ReprocessSessionsButton.java b/jbrowse/src/org/labkey/jbrowse/button/ReprocessSessionsButton.java index 5ed8fd817..408cdf466 100644 --- a/jbrowse/src/org/labkey/jbrowse/button/ReprocessSessionsButton.java +++ b/jbrowse/src/org/labkey/jbrowse/button/ReprocessSessionsButton.java @@ -6,7 +6,6 @@ import org.labkey.api.view.template.ClientDependency; import org.labkey.jbrowse.JBrowseModule; -import java.util.Arrays; import java.util.List; /** diff --git a/jbrowse/src/org/labkey/jbrowse/model/JBrowseSession.java b/jbrowse/src/org/labkey/jbrowse/model/JBrowseSession.java index 5fb45c17e..f8cbecc26 100644 --- a/jbrowse/src/org/labkey/jbrowse/model/JBrowseSession.java +++ b/jbrowse/src/org/labkey/jbrowse/model/JBrowseSession.java @@ -28,7 +28,6 @@ import org.labkey.jbrowse.JBrowseManager; import org.labkey.jbrowse.JBrowseSchema; -import java.io.File; import java.net.URI; import java.nio.file.Path; import java.nio.file.Paths; diff --git a/jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseSessionTask.java b/jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseSessionTask.java index a7482d12f..a4a7b7134 100644 --- a/jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseSessionTask.java +++ b/jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseSessionTask.java @@ -39,7 +39,6 @@ import org.labkey.jbrowse.model.JsonFile; import java.util.ArrayList; -import java.util.Arrays; import java.util.Collections; import java.util.Date; import java.util.List; diff --git a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java index 9ee4094ac..b267d0c76 100644 --- a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java +++ b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java @@ -1954,25 +1954,25 @@ private void testLuceneColumnSerializationFirstRow() { switch(elem.getAttribute("aria-colindex")) { case "1": - Assert.assertEquals(value, "1"); + Assert.assertEquals("1", value); break; case "2": - Assert.assertEquals(value, "2"); + Assert.assertEquals("2", value); break; case "3": - Assert.assertEquals(value, "A"); + Assert.assertEquals("A", value); break; case "4": - Assert.assertEquals(value, "T"); + Assert.assertEquals("T", value); break; case "6": - Assert.assertEquals(value, "0.029"); + Assert.assertEquals("0.029", value); break; case "7": - Assert.assertEquals(value, "7.292"); + Assert.assertEquals("7.292", value); break; case "8": - Assert.assertEquals(value, "HIGH"); + Assert.assertEquals("HIGH", value); break; } } @@ -1997,19 +1997,19 @@ private void testLuceneColumnSerialization(String sessionId) { parentOfCaddScoreToggle.click(); String colVisModelString = "%257B%2522contig%2522%253Atrue%252C%2522start%2522%253Atrue%252C%2522ref%2522%253Atrue%252C%2522alt%2522%253Atrue%252C%2522variableSamples%2522%253Atrue%252C%2522AF%2522%253Atrue%252C%2522CADD_PH%2522%253Atrue%252C%2522IMPACT%2522%253Atrue%257D"; - Assert.assertEquals(getUrlParam("colVisModel"), colVisModelString); + Assert.assertEquals(colVisModelString, getUrlParam("colVisModel")); getDriver().navigate().refresh(); waitForElement(TOP_ROW); - Assert.assertEquals(getUrlParam("colVisModel"), colVisModelString); + Assert.assertEquals(colVisModelString, getUrlParam("colVisModel")); testLuceneColumnSerializationFirstRow(); waitAndClick(Locator.tagWithText("button", "Search")); waitAndClick(Locator.tagWithClass("button", "filter-form-select-button")); waitForElement(TOP_ROW); - Assert.assertEquals(getUrlParam("colVisModel"), colVisModelString); + Assert.assertEquals(colVisModelString, getUrlParam("colVisModel")); testLuceneColumnSerializationFirstRow(); } } \ No newline at end of file diff --git a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTestHelper.java b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTestHelper.java index b4efebabc..de884641b 100644 --- a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTestHelper.java +++ b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTestHelper.java @@ -6,7 +6,6 @@ import org.labkey.test.Locator; import org.labkey.test.TestFileUtils; import org.labkey.test.WebDriverWrapper; -import org.labkey.test.categories.Base; import org.labkey.test.components.ext4.Window; import org.labkey.test.util.DataRegionTable; import org.labkey.test.util.Ext4Helper; diff --git a/singlecell/api-src/org/labkey/api/singlecell/pipeline/SingleCellStep.java b/singlecell/api-src/org/labkey/api/singlecell/pipeline/SingleCellStep.java index d2b48a501..66911ed57 100644 --- a/singlecell/api-src/org/labkey/api/singlecell/pipeline/SingleCellStep.java +++ b/singlecell/api-src/org/labkey/api/singlecell/pipeline/SingleCellStep.java @@ -1,18 +1,5 @@ package org.labkey.api.singlecell.pipeline; -import com.fasterxml.jackson.annotation.JsonIgnore; -import org.jetbrains.annotations.Nullable; -import org.labkey.api.pipeline.PipelineJobException; -import org.labkey.api.sequenceanalysis.SequenceOutputFile; -import org.labkey.api.sequenceanalysis.pipeline.PipelineStep; -import org.labkey.api.sequenceanalysis.pipeline.PipelineStepOutput; -import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler; - -import java.io.File; -import java.io.Serializable; -import java.util.Collection; -import java.util.List; - public interface SingleCellStep extends AbstractSingleCellStep { String STEP_TYPE = "singleCell"; diff --git a/singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java b/singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java index a291d1aa7..c8fba2dd3 100644 --- a/singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java +++ b/singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java @@ -913,7 +913,7 @@ public void processMetrics(SequenceOutputFile so, PipelineJob job, boolean updat description.append(StringUtils.trimToNull(so.getDescription())); } - String delim = description.length() > 0 ? "\n" : ""; + String delim = !description.isEmpty() ? "\n" : ""; DecimalFormat fmt = new DecimalFormat("##.##%"); List metricNames = new ArrayList<>(Arrays.asList("PassingCellBarcodes", "TotalLowCounts", "TotalSinglet", "FractionCalled", "FractionSinglet", "FractionDoublet", "FractionDiscordant", "UniqueHtos")); diff --git a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java index 6e9c2fb0d..3356f9a15 100644 --- a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java +++ b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java @@ -36,7 +36,6 @@ import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor; import org.labkey.api.singlecell.CellHashingService; import org.labkey.api.singlecell.pipeline.AbstractSingleCellPipelineStep; -import org.labkey.api.singlecell.pipeline.AbstractSingleCellStep; import org.labkey.api.singlecell.pipeline.SingleCellRawDataStep; import org.labkey.api.singlecell.pipeline.SingleCellStep; import org.labkey.api.util.FileUtil; diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendCiteSeq.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendCiteSeq.java index d9d58fa37..41c92ed63 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendCiteSeq.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendCiteSeq.java @@ -94,7 +94,7 @@ protected Map prepareCountData(SingleCellOutput output, SequenceO for (SeuratObjectWrapper wrapper : inputObjects) { File localCopyUmiCountDir = null; - File localAggregateCountFile = null; + File localAggregateCountFile; if (wrapper.getSequenceOutputFileId() == null) { throw new PipelineJobException("Append CITE-seq is only support using seurat objects will a single input dataset. Consider moving this step easier in your pipeline, before merging or subsetting"); diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendMetadata.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendMetadata.java index c88aa3775..3dc04863e 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendMetadata.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendMetadata.java @@ -4,7 +4,6 @@ import org.labkey.api.sequenceanalysis.pipeline.PipelineContext; import org.labkey.api.singlecell.pipeline.SingleCellStep; -import java.util.Arrays; import java.util.List; public class AppendMetadata extends AbstractRDiscvrStep diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendSaturation.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendSaturation.java index 0314d69d1..3b1a1ebec 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendSaturation.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendSaturation.java @@ -25,7 +25,6 @@ import java.io.File; import java.io.IOException; import java.util.ArrayList; -import java.util.Arrays; import java.util.HashMap; import java.util.HashSet; import java.util.List; diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendTcr.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendTcr.java index 0176d2766..2a09ad6dd 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendTcr.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendTcr.java @@ -6,7 +6,6 @@ import org.labkey.api.singlecell.pipeline.SeuratToolParameter; import org.labkey.api.singlecell.pipeline.SingleCellStep; -import java.util.Arrays; import java.util.List; public class AppendTcr extends AbstractRDiscvrStep diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CalculateGeneComponentScores.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CalculateGeneComponentScores.java index 898e2e218..5b4f8a98a 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CalculateGeneComponentScores.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CalculateGeneComponentScores.java @@ -7,7 +7,6 @@ import org.labkey.api.singlecell.pipeline.SingleCellStep; import org.labkey.api.util.PageFlowUtil; -import java.util.Arrays; import java.util.Collection; import java.util.Collections; diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CiteSeqPlots.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CiteSeqPlots.java index 531aba464..e3648cb8d 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CiteSeqPlots.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CiteSeqPlots.java @@ -6,7 +6,6 @@ import org.labkey.api.singlecell.pipeline.SeuratToolParameter; import org.labkey.api.singlecell.pipeline.SingleCellStep; -import java.util.Arrays; import java.util.List; public class CiteSeqPlots extends AbstractCellMembraneStep diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/ClearCommands.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/ClearCommands.java index 98155f3d8..19702b01a 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/ClearCommands.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/ClearCommands.java @@ -4,7 +4,6 @@ import org.labkey.api.sequenceanalysis.pipeline.PipelineContext; import org.labkey.api.singlecell.pipeline.SingleCellStep; -import java.util.Arrays; import java.util.List; public class ClearCommands extends AbstractCellMembraneStep diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CustomUCell.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CustomUCell.java index dada70d2d..9807014ca 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CustomUCell.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CustomUCell.java @@ -3,7 +3,6 @@ import org.json.JSONObject; import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider; import org.labkey.api.sequenceanalysis.pipeline.PipelineContext; -import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor; import org.labkey.api.singlecell.pipeline.SeuratToolParameter; import org.labkey.api.singlecell.pipeline.SingleCellStep; diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DietSeurat.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DietSeurat.java index 9da979e5e..14e54cabd 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DietSeurat.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DietSeurat.java @@ -4,7 +4,6 @@ import org.labkey.api.sequenceanalysis.pipeline.PipelineContext; import org.labkey.api.singlecell.pipeline.SingleCellStep; -import java.util.Arrays; import java.util.List; public class DietSeurat extends AbstractCellMembraneStep diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DimPlots.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DimPlots.java index 76ab8c38d..c7d3c2a83 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DimPlots.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DimPlots.java @@ -7,7 +7,6 @@ import org.labkey.api.singlecell.pipeline.SingleCellStep; import org.labkey.api.util.PageFlowUtil; -import java.util.Arrays; import java.util.Collection; import java.util.Collections; import java.util.List; diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DoubletFinder.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DoubletFinder.java index 026279afb..b423ff2a8 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DoubletFinder.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DoubletFinder.java @@ -6,7 +6,6 @@ import org.labkey.api.singlecell.pipeline.SeuratToolParameter; import org.labkey.api.singlecell.pipeline.SingleCellStep; -import java.util.Arrays; import java.util.List; public class DoubletFinder extends AbstractCellMembraneStep diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DropAssays.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DropAssays.java index 7f5280d73..a457b7a3e 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DropAssays.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DropAssays.java @@ -6,7 +6,6 @@ import org.labkey.api.singlecell.pipeline.SeuratToolParameter; import org.labkey.api.singlecell.pipeline.SingleCellStep; -import java.util.Arrays; import java.util.Collections; import java.util.List; diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DropCiteSeq.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DropCiteSeq.java index 9b40e6e72..037d710ab 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DropCiteSeq.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/DropCiteSeq.java @@ -4,7 +4,6 @@ import org.labkey.api.sequenceanalysis.pipeline.PipelineContext; import org.labkey.api.singlecell.pipeline.SingleCellStep; -import java.util.Arrays; import java.util.List; public class DropCiteSeq extends AbstractCellMembraneStep diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/FeaturePlots.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/FeaturePlots.java index 493ba8803..5d09f92e2 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/FeaturePlots.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/FeaturePlots.java @@ -7,7 +7,6 @@ import org.labkey.api.singlecell.pipeline.SingleCellStep; import org.labkey.api.util.PageFlowUtil; -import java.util.Arrays; import java.util.Collection; import java.util.Collections; import java.util.List; diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/FindClustersAndDimRedux.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/FindClustersAndDimRedux.java index 81f6edb73..86e16b494 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/FindClustersAndDimRedux.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/FindClustersAndDimRedux.java @@ -6,7 +6,6 @@ import org.labkey.api.singlecell.pipeline.SeuratToolParameter; import org.labkey.api.singlecell.pipeline.SingleCellStep; -import java.util.Arrays; import java.util.List; public class FindClustersAndDimRedux extends AbstractCellMembraneStep diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PhenotypePlots.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PhenotypePlots.java index c93f0f6d4..b3e54b3fc 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PhenotypePlots.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PhenotypePlots.java @@ -5,7 +5,6 @@ import org.labkey.api.singlecell.pipeline.SingleCellStep; import org.labkey.api.util.PageFlowUtil; -import java.util.Arrays; import java.util.Collection; import java.util.List; diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PlotAssayFeatures.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PlotAssayFeatures.java index 4519f47da..549735fb0 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PlotAssayFeatures.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PlotAssayFeatures.java @@ -6,7 +6,6 @@ import org.labkey.api.singlecell.pipeline.SeuratToolParameter; import org.labkey.api.singlecell.pipeline.SingleCellStep; -import java.util.Arrays; import java.util.Collections; public class PlotAssayFeatures extends AbstractCellMembraneStep diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PredictScTour.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PredictScTour.java index dd1d7af87..6fae8f256 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PredictScTour.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PredictScTour.java @@ -1,6 +1,5 @@ package org.labkey.singlecell.pipeline.singlecell; -import org.apache.commons.io.FileUtils; import org.json.JSONObject; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider; @@ -10,12 +9,10 @@ import org.labkey.api.singlecell.pipeline.SingleCellStep; import java.io.File; -import java.io.IOException; import java.util.Arrays; import java.util.Collection; import java.util.Collections; import java.util.List; -import java.util.Set; public class PredictScTour extends AbstractRiraStep { diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunEscape.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunEscape.java index 639f4f094..5de04773d 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunEscape.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunEscape.java @@ -7,7 +7,6 @@ import org.labkey.api.singlecell.pipeline.SingleCellStep; import java.util.Arrays; -import java.util.Collections; public class RunEscape extends AbstractCellMembraneStep { diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunLDA.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunLDA.java index 65bd08f3a..58b2d69a2 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunLDA.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunLDA.java @@ -89,7 +89,7 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List wrappers = inputObjects.stream().filter(x -> datasetId.equals(x.getDatasetId())).collect(Collectors.toSet()); - if (wrappers.size() == 0) + if (wrappers.isEmpty()) { throw new PipelineJobException("Unable to find seurat object wrapper for: " + datasetId); } diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunPCA.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunPCA.java index 5269b96df..ba253938d 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunPCA.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunPCA.java @@ -6,7 +6,6 @@ import org.labkey.api.singlecell.pipeline.SeuratToolParameter; import org.labkey.api.singlecell.pipeline.SingleCellStep; -import java.util.Arrays; import java.util.List; public class RunPCA extends AbstractCellMembraneStep diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunPHATE.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunPHATE.java index 9f110252c..12d9cc342 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunPHATE.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunPHATE.java @@ -5,7 +5,6 @@ import org.labkey.api.singlecell.pipeline.SeuratToolParameter; import org.labkey.api.singlecell.pipeline.SingleCellStep; -import java.util.Arrays; import java.util.List; public class RunPHATE extends AbstractCellMembraneStep diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunSDA.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunSDA.java index 5a07e8736..0dc3a5e4f 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunSDA.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunSDA.java @@ -9,7 +9,6 @@ import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider; import org.labkey.api.sequenceanalysis.pipeline.PipelineContext; import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler; -import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor; import org.labkey.api.singlecell.pipeline.SeuratToolParameter; import org.labkey.api.singlecell.pipeline.SingleCellStep; @@ -129,7 +128,7 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List wrappers = inputObjects.stream().filter(x -> datasetId.equals(x.getDatasetId())).collect(Collectors.toSet()); - if (wrappers.size() == 0) + if (wrappers.isEmpty()) { throw new PipelineJobException("Unable to find seurat object wrapper for: " + datasetId); } diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunTricycle.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunTricycle.java index 5e059a782..4e79d7673 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunTricycle.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunTricycle.java @@ -1,9 +1,7 @@ package org.labkey.singlecell.pipeline.singlecell; -import org.json.JSONObject; import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider; import org.labkey.api.sequenceanalysis.pipeline.PipelineContext; -import org.labkey.api.singlecell.pipeline.SeuratToolParameter; import org.labkey.api.singlecell.pipeline.SingleCellStep; import java.util.Arrays; diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunVision.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunVision.java index 6e0fbbd69..0dbda2015 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunVision.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunVision.java @@ -13,7 +13,6 @@ import java.io.File; import java.io.IOException; -import java.util.Arrays; import java.util.Collections; import java.util.List; import java.util.Set; @@ -84,7 +83,7 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List wrappers = inputObjects.stream().filter(x -> datasetId.equals(x.getDatasetId())).collect(Collectors.toSet()); - if (wrappers.size() == 0) + if (wrappers.isEmpty()) { throw new PipelineJobException("Unable to find seurat object wrapper for: " + datasetId); } diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/SubsetSeurat.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/SubsetSeurat.java index 13ae96797..ec56a127c 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/SubsetSeurat.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/SubsetSeurat.java @@ -9,7 +9,6 @@ import org.labkey.api.singlecell.pipeline.SingleCellStep; import java.util.ArrayList; -import java.util.Arrays; import java.util.Collection; import java.util.HashSet; import java.util.List; diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/TcrFilter.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/TcrFilter.java index bb7f97289..6818d58fd 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/TcrFilter.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/TcrFilter.java @@ -7,7 +7,6 @@ import org.labkey.api.singlecell.pipeline.SingleCellStep; import java.util.Arrays; -import java.util.Collections; import java.util.List; public class TcrFilter extends AbstractCellMembraneStep diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java index f750cf2bf..9a9329b96 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java @@ -25,7 +25,6 @@ import java.util.Collections; import java.util.List; import java.util.Map; -import java.util.Queue; import static org.labkey.singlecell.analysis.AbstractSingleCellHandler.SEURAT_PROTOTYPE; diff --git a/singlecell/src/org/labkey/singlecell/run/CellRangerFeatureBarcodeHandler.java b/singlecell/src/org/labkey/singlecell/run/CellRangerFeatureBarcodeHandler.java index 60a265113..b03b7faa0 100644 --- a/singlecell/src/org/labkey/singlecell/run/CellRangerFeatureBarcodeHandler.java +++ b/singlecell/src/org/labkey/singlecell/run/CellRangerFeatureBarcodeHandler.java @@ -22,7 +22,6 @@ import org.labkey.api.query.FieldKey; import org.labkey.api.query.QueryService; import org.labkey.api.reader.Readers; -import org.labkey.api.sequenceanalysis.SequenceAnalysisService; import org.labkey.api.sequenceanalysis.SequenceOutputFile; import org.labkey.api.sequenceanalysis.model.Readset; import org.labkey.api.sequenceanalysis.pipeline.AbstractParameterizedOutputHandler; @@ -313,7 +312,7 @@ private void processType(List> inputFastqs, AlignmentOutputImpl if (ctx.getParams().optBoolean("useGEX", false)) { description = description + "\n" + "HTO and GEX Counts"; - }; + } output.addSequenceOutput(outputHtmlRename, rs.getName() + " 10x " + rs.getApplication() + " Summary", "10x Run Summary", rs.getRowId(), null, null, description); File rawCounts = new File(outsdir, "raw_feature_bc_matrix/matrix.mtx.gz"); diff --git a/singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java b/singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java index 17972552c..d2969cb63 100644 --- a/singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java +++ b/singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java @@ -3,7 +3,6 @@ import au.com.bytecode.opencsv.CSVReader; import org.apache.commons.io.FileUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.commons.lang3.stream.IntStreams; import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.json.JSONObject; diff --git a/singlecell/src/org/labkey/singlecell/run/RepeatNimbleReportHandler.java b/singlecell/src/org/labkey/singlecell/run/RepeatNimbleReportHandler.java index c0e40daee..d95e562bf 100644 --- a/singlecell/src/org/labkey/singlecell/run/RepeatNimbleReportHandler.java +++ b/singlecell/src/org/labkey/singlecell/run/RepeatNimbleReportHandler.java @@ -196,7 +196,7 @@ public void complete(JobContext ctx, List inputs, List