diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/configuration/readers/VcfReaderConfiguration.java b/src/main/java/uk/ac/ebi/eva/pipeline/configuration/readers/VcfReaderConfiguration.java index ba7a05d03..b4ccd5a8b 100644 --- a/src/main/java/uk/ac/ebi/eva/pipeline/configuration/readers/VcfReaderConfiguration.java +++ b/src/main/java/uk/ac/ebi/eva/pipeline/configuration/readers/VcfReaderConfiguration.java @@ -39,7 +39,7 @@ public class VcfReaderConfiguration { @Bean(VARIANT_READER) @StepScope - public ItemStreamReader unwindingReader(VcfReader vcfReader) throws Exception { + public ItemStreamReader unwindingReader(VcfReader vcfReader) { return new UnwindingItemStreamReader<>(vcfReader); } diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/parameters/JobOptions.java b/src/main/java/uk/ac/ebi/eva/pipeline/parameters/JobOptions.java index 1c023064f..01b1b36df 100644 --- a/src/main/java/uk/ac/ebi/eva/pipeline/parameters/JobOptions.java +++ b/src/main/java/uk/ac/ebi/eva/pipeline/parameters/JobOptions.java @@ -41,7 +41,7 @@ public class JobOptions { @Value("${" + JobParametersNames.CONFIG_RESTARTABILITY_ALLOW + ":false}") private boolean allowStartIfComplete; @PostConstruct - public void loadArgs() throws IOException { + public void loadArgs() { logger.info("Loading job arguments"); if (opencgaAppHome == null || opencgaAppHome.isEmpty()) { diff --git a/src/test/java/uk/ac/ebi/eva/test/utils/GenotypedVcfJobTestUtils.java b/src/test/java/uk/ac/ebi/eva/test/utils/GenotypedVcfJobTestUtils.java index 3d0119d15..a9dcd5a46 100644 --- a/src/test/java/uk/ac/ebi/eva/test/utils/GenotypedVcfJobTestUtils.java +++ b/src/test/java/uk/ac/ebi/eva/test/utils/GenotypedVcfJobTestUtils.java @@ -178,7 +178,7 @@ public static File getSourceStatsFile(String outputDirStats) throws URISyntaxExc return new File(URLHelper.getSourceStatsUri(outputDirStats, INPUT_STUDY_ID, INPUT_VCF_ID)); } - public static File getVepInputFile(String outputDirAnnotation) throws URISyntaxException { + public static File getVepInputFile(String outputDirAnnotation) { return new File(URLHelper.resolveVepInput(outputDirAnnotation, INPUT_STUDY_ID, INPUT_VCF_ID)); }