Minor cleanup

Author: labkey-jeckels

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

@@ -1,5 +1,6 @@
 package org.labkey.sequenceanalysis.pipeline;
 
+import org.jetbrains.annotations.NotNull;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.pipeline.RecordedAction;
@@ -98,7 +99,7 @@ private SequenceAlignmentJob getPipelineJob()
     }
 
     @Override
-    public RecordedActionSet run() throws PipelineJobException
+    public @NotNull RecordedActionSet run() throws PipelineJobException
     {
         _taskHelper = new SequenceTaskHelper(getPipelineJob(), _wd);
 

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

@@ -16,6 +16,7 @@
 package org.labkey.sequenceanalysis.pipeline;
 
 import org.apache.commons.lang3.StringUtils;
+import org.jetbrains.annotations.NotNull;
 import org.labkey.api.pipeline.AbstractTaskFactory;
 import org.labkey.api.pipeline.AbstractTaskFactorySettings;
 import org.labkey.api.pipeline.PipelineJob;
@@ -84,7 +85,7 @@ public boolean isJobComplete(PipelineJob job)
     }
 
     @Override
-    public RecordedActionSet run() throws PipelineJobException
+    public @NotNull RecordedActionSet run() throws PipelineJobException
     {
         getJob().getLogger().info("Importing sequences from file(s): ");
         for (File f : getPipelineJob().getFastas())

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

@@ -32,6 +32,7 @@
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.SystemUtils;
+import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.data.CompareType;
@@ -136,7 +137,7 @@ public boolean isJobComplete(PipelineJob job)
     }
 
     @Override
-    public RecordedActionSet run() throws PipelineJobException
+    public @NotNull RecordedActionSet run() throws PipelineJobException
     {
         getJob().getLogger().info("Importing tracks from file(s): ");
         RecordedAction action = new RecordedAction(ACTION_NAME);

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

@@ -1,5 +1,6 @@
 package org.labkey.sequenceanalysis.pipeline;
 
+import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.CompareType;
 import org.labkey.api.data.SimpleFilter;
@@ -85,7 +86,7 @@ private SequenceOutputHandlerJob getPipelineJob()
     }
 
     @Override
-    public RecordedActionSet run() throws PipelineJobException
+    public @NotNull RecordedActionSet run() throws PipelineJobException
     {
         Long runId = SequenceTaskHelper.getExpRunIdForJob(getJob());
         getPipelineJob().setExperimentRunRowId(runId);

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

@@ -1,5 +1,6 @@
 package org.labkey.sequenceanalysis.pipeline;
 
+import org.jetbrains.annotations.NotNull;
 import org.labkey.api.pipeline.AbstractTaskFactory;
 import org.labkey.api.pipeline.AbstractTaskFactorySettings;
 import org.labkey.api.pipeline.PipelineJob;
@@ -69,7 +70,7 @@ private SequenceReadsetHandlerJob  getPipelineJob()
     }
 
     @Override
-    public RecordedActionSet run() throws PipelineJobException
+    public @NotNull RecordedActionSet run() throws PipelineJobException
     {
         Long runId = SequenceTaskHelper.getExpRunIdForJob(getJob());
         getPipelineJob().setExperimentRunRowId(runId);

blast/src/org/labkey/blast/pipeline/BlastDatabaseTask.java

@@ -15,6 +15,7 @@
  */
 package org.labkey.blast.pipeline;
 
+import org.jetbrains.annotations.NotNull;
 import org.labkey.api.pipeline.AbstractTaskFactory;
 import org.labkey.api.pipeline.AbstractTaskFactorySettings;
 import org.labkey.api.pipeline.PipelineJob;
@@ -88,7 +89,7 @@ public boolean isJobComplete(PipelineJob job)
     }
 
     @Override
-    public RecordedActionSet run() throws PipelineJobException
+    public @NotNull RecordedActionSet run() throws PipelineJobException
     {
         getJob().getLogger().info("creating BLAST database for library: " + getPipelineJob().getLibraryId());
 

blast/src/org/labkey/blast/pipeline/BlastFinalTask.java

@@ -15,6 +15,7 @@
  */
 package org.labkey.blast.pipeline;
 
+import org.jetbrains.annotations.NotNull;
 import org.labkey.api.pipeline.AbstractTaskFactory;
 import org.labkey.api.pipeline.AbstractTaskFactorySettings;
 import org.labkey.api.pipeline.PipelineJob;
@@ -80,7 +81,7 @@ public boolean isJobComplete(PipelineJob job)
     }
 
     @Override
-    public RecordedActionSet run() throws PipelineJobException
+    public @NotNull RecordedActionSet run() throws PipelineJobException
     {
         getPipelineJob().getBlastJob().setComplete(getJob().getUser(), getJob());
 

blast/src/org/labkey/blast/pipeline/BlastWorkTask.java

@@ -15,6 +15,7 @@
  */
 package org.labkey.blast.pipeline;
 
+import org.jetbrains.annotations.NotNull;
 import org.labkey.api.pipeline.AbstractTaskFactory;
 import org.labkey.api.pipeline.AbstractTaskFactorySettings;
 import org.labkey.api.pipeline.PipelineJob;
@@ -81,7 +82,7 @@ public boolean isJobComplete(PipelineJob job)
     }
 
     @Override
-    public RecordedActionSet run() throws PipelineJobException
+    public @NotNull RecordedActionSet run() throws PipelineJobException
     {
         try
         {