Better error reporting for invalid chromosomes

src/main/java/genepi/imputationserver/steps/InputValidationCommand.java

@@ -168,18 +168,19 @@ private boolean checkVcfFiles() throws Exception {
 			try {
 
 				VcfFile vcfFile = VcfFileUtil.load(filename, chunksize, !noIndex);
+				String chromosome = vcfFile.getChromosome();
 
-				if (VcfFileUtil.isChrMT(vcfFile.getChromosome())) {
+				if (VcfFileUtil.isChrMT(chromosome)) {
 					vcfFile.setPhased(true);
 				}
 
-				if (!VcfFileUtil.isValidChromosome(vcfFile.getChromosome())) {
-					output.error("No valid chromosomes found!");
+				if (!VcfFileUtil.isValidChromosome(chromosome)) {
+					output.error("Invalid chromosome found: " + chromosome);
 					return false;
 				}
 
 				validVcfFiles.add(vcfFile);
-				chromosomes.add(vcfFile.getChromosome());
+				chromosomes.add(chromosome);
 
 				// check if all files have same amount of samples
 				if (noSamples != 0 && noSamples != vcfFile.getNoSamples()) {
@@ -210,14 +211,14 @@ private boolean checkVcfFiles() throws Exception {
 				if (build.equals("hg19") && vcfFile.hasChrPrefix()) {
 					output.error("Your upload data contains chromosome '" + vcfFile.getRawChromosome()
 							+ "'. This is not a valid hg19 encoding. Please ensure that your input data is build hg19 and chromosome is encoded as '"
-							+ vcfFile.getChromosome() + "'.");
+							+ chromosome + "'.");
 					return false;
 				}
 
 				if (build.equals("hg38") && !vcfFile.hasChrPrefix()) {
 					output.error("Your upload data contains chromosome '" + vcfFile.getRawChromosome()
 							+ "'. This is not a valid hg38 encoding. Please ensure that your input data is build hg38 and chromosome is encoded as 'chr"
-							+ vcfFile.getChromosome() + "'.");
+							+ chromosome + "'.");
 					return false;
 				}
 

src/test/java/genepi/imputationserver/steps/InputValidationCommandTest.java

@@ -20,6 +20,38 @@ public class InputValidationCommandTest extends AbstractTestcase {
 
 	private static final String CLOUDGENE_LOG = "cloudgene.report";
 
+	@Test
+	public void testMissingReferencePanel() throws Exception {
+		String inputFolder = "test-data/data/chr20-phased";
+
+		InputValidationCommand command = buildCommand(inputFolder);
+		command.setReference("this-path/does-not-exist.json");
+		command.setBuild("hg38");
+
+		assertEquals(1, (int)command.call());
+
+		OutputReader log = new OutputReader(CLOUDGENE_LOG);
+		log.view();
+		assertTrue(log.hasInMemory("::error:: Unable to parse reference panel: this-path/does-not-exist.json (No such file or directory)"));
+	}
+
+	@Test
+	public void testInvalidChromosome() throws Exception {
+
+		String inputFolder = "test-data/data/chrY-fake";
+
+		InputValidationCommand command = buildCommand(inputFolder);
+		command.setReference("test-data/configs/hapmap-chr1/hapmap2.json");
+		command.setPopulation("mixed");
+
+		assertEquals(1, (int)command.call());
+
+		OutputReader log = new OutputReader(CLOUDGENE_LOG);
+		log.view();
+		assertTrue(log.hasInMemory("::error:: Invalid chromosome found: Y"));
+
+	}
+
 	@Test
 	public void testVcfWithHeaderOnly() throws Exception {