Add unit test around Fastqc JARs

Author: bbimber

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

@@ -131,6 +131,7 @@
 import org.labkey.sequenceanalysis.run.reference.SavedReferenceLibraryStep;
 import org.labkey.sequenceanalysis.run.reference.VirusReferenceLibraryStep;
 import org.labkey.sequenceanalysis.run.util.CombineGVCFsHandler;
+import org.labkey.sequenceanalysis.run.util.FastqcRunner;
 import org.labkey.sequenceanalysis.run.util.GenomicsDBAppendHandler;
 import org.labkey.sequenceanalysis.run.util.GenomicsDBImportHandler;
 import org.labkey.sequenceanalysis.run.variant.CombineVariantsHandler;
@@ -476,7 +477,8 @@ public Set<Class> getUnitTests()
                 ProcessVariantsHandler.TestCase.class,
                 VariantProcessingJob.TestCase.class,
                 ScatterGatherUtils.TestCase.class,
-                ChainFileValidator.TestCase.class
+                ChainFileValidator.TestCase.class,
+                FastqcRunner.TestCase.class
         );
     }
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java

@@ -20,6 +20,8 @@
 import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.Nullable;
+import org.junit.Assert;
+import org.junit.Test;
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.pipeline.PipelineJobService;
@@ -410,5 +412,18 @@ private List<String> getParams(File f) throws FileNotFoundException
 
         return params;
     }
+
+    public static class TestCase extends Assert
+    {
+        @Test
+        public void testApacheJar() throws Exception
+        {
+            //This will error if JARs are not found:
+            FastqcRunner runner = new FastqcRunner(null);
+            List<String> params = runner.getBaseParams();
+
+            assertEquals("Incorrect params", 5, params.size());
+        }
+    }
 }