From 954a3406a3ba1feabf05d0419e2da7242e5df6fd Mon Sep 17 00:00:00 2001 From: jorizci Date: Wed, 1 Mar 2017 13:56:32 +0000 Subject: [PATCH 1/3] Removed unused imports across the project. --- .../configuration/JobExecutionDeciderConfiguration.java | 1 - .../pipeline/configuration/PostgreDataSourceConfiguration.java | 2 +- .../uk/ac/ebi/eva/pipeline/io/mappers/VariantVcfFactory.java | 1 - .../java/uk/ac/ebi/eva/pipeline/io/mappers/VcfLineMapper.java | 3 --- .../uk/ac/ebi/eva/pipeline/io/readers/AggregatedVcfReader.java | 1 - .../pipeline/io/readers/NonAnnotatedVariantsMongoReader.java | 2 -- .../uk/ac/ebi/eva/pipeline/jobs/PopulationStatisticsJob.java | 1 - .../jobs/steps/tasklets/PopulationStatisticsGeneratorStep.java | 1 - .../jobs/steps/tasklets/PopulationStatisticsLoaderStep.java | 2 -- .../model/converters/data/VariantToMongoDbObjectConverter.java | 1 - .../runner/exceptions/UnexpectedFileEncodingException.java | 2 -- src/main/java/uk/ac/ebi/eva/utils/TaskletUtils.java | 2 -- .../ebi/eva/pipeline/io/mappers/VariantVcfExacFactoryTest.java | 1 - .../ebi/eva/pipeline/io/readers/AggregatedVcfReaderTest.java | 2 -- .../io/readers/NonAnnotatedVariantsMongoReaderTest.java | 1 - .../ebi/eva/pipeline/io/readers/UnwindingItemReaderTest.java | 1 - .../eva/pipeline/io/readers/UnwindingItemStreamReaderTest.java | 1 - .../uk/ac/ebi/eva/pipeline/io/readers/VcfHeaderReaderTest.java | 1 - .../java/uk/ac/ebi/eva/pipeline/io/readers/VcfReaderTest.java | 1 - .../java/uk/ac/ebi/eva/pipeline/io/writers/GeneWriterTest.java | 1 - .../ebi/eva/pipeline/io/writers/StatisticsMongoWriterTest.java | 1 - .../ac/ebi/eva/pipeline/io/writers/VariantMongoWriterTest.java | 1 - .../eva/pipeline/io/writers/VepAnnotationMongoWriterTest.java | 1 - .../ebi/eva/pipeline/jobs/steps/VepInputGeneratorStepTest.java | 1 - .../java/uk/ac/ebi/eva/runner/JobRestartSynchronousTest.java | 1 - .../test/configuration/AsynchronousBatchTestConfiguration.java | 1 - src/test/java/uk/ac/ebi/eva/test/data/VariantData.java | 2 -- 27 files changed, 1 insertion(+), 35 deletions(-) diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/configuration/JobExecutionDeciderConfiguration.java b/src/main/java/uk/ac/ebi/eva/pipeline/configuration/JobExecutionDeciderConfiguration.java index 132c2cb09..8a28dddfb 100644 --- a/src/main/java/uk/ac/ebi/eva/pipeline/configuration/JobExecutionDeciderConfiguration.java +++ b/src/main/java/uk/ac/ebi/eva/pipeline/configuration/JobExecutionDeciderConfiguration.java @@ -17,7 +17,6 @@ import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing; import org.springframework.batch.core.job.flow.JobExecutionDecider; -import org.springframework.beans.factory.annotation.Value; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; import uk.ac.ebi.eva.pipeline.jobs.deciders.SkipStepDecider; diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/configuration/PostgreDataSourceConfiguration.java b/src/main/java/uk/ac/ebi/eva/pipeline/configuration/PostgreDataSourceConfiguration.java index fda336b37..dc9b954e9 100644 --- a/src/main/java/uk/ac/ebi/eva/pipeline/configuration/PostgreDataSourceConfiguration.java +++ b/src/main/java/uk/ac/ebi/eva/pipeline/configuration/PostgreDataSourceConfiguration.java @@ -16,7 +16,7 @@ package uk.ac.ebi.eva.pipeline.configuration; import javax.sql.DataSource; -import org.springframework.beans.factory.annotation.Autowired; + import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; import org.springframework.context.annotation.Primary; diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/VariantVcfFactory.java b/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/VariantVcfFactory.java index 36fa11815..202a4c1b9 100644 --- a/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/VariantVcfFactory.java +++ b/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/VariantVcfFactory.java @@ -19,7 +19,6 @@ import org.apache.commons.lang3.StringUtils; import org.opencb.biodata.models.feature.Genotype; import org.opencb.biodata.models.variant.VariantFactory; -import org.opencb.biodata.models.variant.VariantSource; import org.opencb.biodata.models.variant.exceptions.NonStandardCompliantSampleField; import org.opencb.biodata.models.variant.exceptions.NotAVariantException; diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/VcfLineMapper.java b/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/VcfLineMapper.java index ada03f3bc..08cdfd0cf 100644 --- a/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/VcfLineMapper.java +++ b/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/VcfLineMapper.java @@ -15,14 +15,11 @@ */ package uk.ac.ebi.eva.pipeline.io.mappers; -import org.opencb.biodata.models.variant.VariantSource; import org.springframework.batch.item.file.LineMapper; import uk.ac.ebi.eva.commons.models.data.Variant; import java.util.List; -import static org.junit.Assert.assertNotNull; - /** * Maps a String (in VCF format) to a list of variants. *

diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/io/readers/AggregatedVcfReader.java b/src/main/java/uk/ac/ebi/eva/pipeline/io/readers/AggregatedVcfReader.java index 24ea0ef0f..9d2b76245 100644 --- a/src/main/java/uk/ac/ebi/eva/pipeline/io/readers/AggregatedVcfReader.java +++ b/src/main/java/uk/ac/ebi/eva/pipeline/io/readers/AggregatedVcfReader.java @@ -20,7 +20,6 @@ import java.io.File; import java.io.IOException; -import java.util.Optional; /** * VCF file reader for VCFs without genotypes (aggregated VCFs). diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/io/readers/NonAnnotatedVariantsMongoReader.java b/src/main/java/uk/ac/ebi/eva/pipeline/io/readers/NonAnnotatedVariantsMongoReader.java index 9ace12e8e..6451cadda 100644 --- a/src/main/java/uk/ac/ebi/eva/pipeline/io/readers/NonAnnotatedVariantsMongoReader.java +++ b/src/main/java/uk/ac/ebi/eva/pipeline/io/readers/NonAnnotatedVariantsMongoReader.java @@ -23,8 +23,6 @@ import org.springframework.data.mongodb.core.MongoOperations; -import java.net.UnknownHostException; - /** * Mongo variant reader using an ItemReader cursor based. This is speeding up * the reading of the variant in big collections. The diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/jobs/PopulationStatisticsJob.java b/src/main/java/uk/ac/ebi/eva/pipeline/jobs/PopulationStatisticsJob.java index 191fa0d32..3ab56281a 100644 --- a/src/main/java/uk/ac/ebi/eva/pipeline/jobs/PopulationStatisticsJob.java +++ b/src/main/java/uk/ac/ebi/eva/pipeline/jobs/PopulationStatisticsJob.java @@ -33,7 +33,6 @@ import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.CALCULATE_STATISTICS_FLOW; import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.CALCULATE_STATISTICS_JOB; -import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.CALCULATE_STATISTICS_OPTIONAL_FLOW; /** * Configuration to run a full Statistics job: variantStatsFlow: statsCreate --> statsLoad diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/jobs/steps/tasklets/PopulationStatisticsGeneratorStep.java b/src/main/java/uk/ac/ebi/eva/pipeline/jobs/steps/tasklets/PopulationStatisticsGeneratorStep.java index 6e9bd6539..7a08b774a 100644 --- a/src/main/java/uk/ac/ebi/eva/pipeline/jobs/steps/tasklets/PopulationStatisticsGeneratorStep.java +++ b/src/main/java/uk/ac/ebi/eva/pipeline/jobs/steps/tasklets/PopulationStatisticsGeneratorStep.java @@ -35,7 +35,6 @@ import uk.ac.ebi.eva.pipeline.parameters.InputParameters; import uk.ac.ebi.eva.pipeline.parameters.MongoConnection; import uk.ac.ebi.eva.pipeline.parameters.OutputParameters; -import uk.ac.ebi.eva.utils.MongoDBHelper; import uk.ac.ebi.eva.utils.URLHelper; import java.net.URI; diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/jobs/steps/tasklets/PopulationStatisticsLoaderStep.java b/src/main/java/uk/ac/ebi/eva/pipeline/jobs/steps/tasklets/PopulationStatisticsLoaderStep.java index 226563d6e..61bf69a66 100644 --- a/src/main/java/uk/ac/ebi/eva/pipeline/jobs/steps/tasklets/PopulationStatisticsLoaderStep.java +++ b/src/main/java/uk/ac/ebi/eva/pipeline/jobs/steps/tasklets/PopulationStatisticsLoaderStep.java @@ -29,10 +29,8 @@ import org.opencb.opencga.storage.core.variant.VariantStorageManager; import org.opencb.opencga.storage.core.variant.adaptors.VariantDBAdaptor; import org.opencb.opencga.storage.core.variant.io.json.VariantStatsJsonMixin; -import org.opencb.opencga.storage.core.variant.stats.VariantStatisticsManager; import org.opencb.opencga.storage.core.variant.stats.VariantStatsWrapper; import org.opencb.opencga.storage.mongodb.utils.MongoCredentials; -import org.opencb.opencga.storage.mongodb.variant.MongoDBVariantStorageManager; import org.opencb.opencga.storage.mongodb.variant.VariantMongoDBAdaptor; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/model/converters/data/VariantToMongoDbObjectConverter.java b/src/main/java/uk/ac/ebi/eva/pipeline/model/converters/data/VariantToMongoDbObjectConverter.java index 2a311b69b..d6ad1c0ad 100644 --- a/src/main/java/uk/ac/ebi/eva/pipeline/model/converters/data/VariantToMongoDbObjectConverter.java +++ b/src/main/java/uk/ac/ebi/eva/pipeline/model/converters/data/VariantToMongoDbObjectConverter.java @@ -17,7 +17,6 @@ import com.mongodb.BasicDBObject; import com.mongodb.DBObject; -import org.opencb.opencga.storage.core.variant.VariantStorageManager; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.core.convert.converter.Converter; diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/runner/exceptions/UnexpectedFileEncodingException.java b/src/main/java/uk/ac/ebi/eva/pipeline/runner/exceptions/UnexpectedFileEncodingException.java index 50e80983f..7b0078000 100644 --- a/src/main/java/uk/ac/ebi/eva/pipeline/runner/exceptions/UnexpectedFileEncodingException.java +++ b/src/main/java/uk/ac/ebi/eva/pipeline/runner/exceptions/UnexpectedFileEncodingException.java @@ -15,8 +15,6 @@ */ package uk.ac.ebi.eva.pipeline.runner.exceptions; -import java.io.IOException; - /** * Exception used to express a codification problem while interpreting a file */ diff --git a/src/main/java/uk/ac/ebi/eva/utils/TaskletUtils.java b/src/main/java/uk/ac/ebi/eva/utils/TaskletUtils.java index aa8a6f97a..835e83206 100644 --- a/src/main/java/uk/ac/ebi/eva/utils/TaskletUtils.java +++ b/src/main/java/uk/ac/ebi/eva/utils/TaskletUtils.java @@ -5,8 +5,6 @@ import org.springframework.batch.core.step.builder.TaskletStepBuilder; import org.springframework.batch.core.step.tasklet.Tasklet; import org.springframework.batch.core.step.tasklet.TaskletStep; -import uk.ac.ebi.eva.pipeline.parameters.JobOptions; -import uk.ac.ebi.eva.pipeline.parameters.JobParametersNames; public class TaskletUtils { diff --git a/src/test/java/uk/ac/ebi/eva/pipeline/io/mappers/VariantVcfExacFactoryTest.java b/src/test/java/uk/ac/ebi/eva/pipeline/io/mappers/VariantVcfExacFactoryTest.java index 2bf48eb2d..5b005eb13 100644 --- a/src/test/java/uk/ac/ebi/eva/pipeline/io/mappers/VariantVcfExacFactoryTest.java +++ b/src/test/java/uk/ac/ebi/eva/pipeline/io/mappers/VariantVcfExacFactoryTest.java @@ -17,7 +17,6 @@ import org.junit.Test; import org.opencb.biodata.models.feature.Genotype; -import org.opencb.biodata.models.variant.VariantSource; import org.opencb.commons.test.GenericTest; import uk.ac.ebi.eva.commons.models.data.Variant; diff --git a/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/AggregatedVcfReaderTest.java b/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/AggregatedVcfReaderTest.java index 762f2e3ab..2fa826395 100644 --- a/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/AggregatedVcfReaderTest.java +++ b/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/AggregatedVcfReaderTest.java @@ -10,12 +10,10 @@ import uk.ac.ebi.eva.commons.models.data.VariantSourceEntry; import uk.ac.ebi.eva.test.rules.PipelineTemporaryFolderRule; import uk.ac.ebi.eva.test.utils.JobTestUtils; -import uk.ac.ebi.eva.test.utils.TestFileUtils; import java.io.File; import java.io.FileInputStream; import java.util.List; -import java.util.Optional; import java.util.zip.GZIPInputStream; import static org.junit.Assert.assertEquals; diff --git a/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/NonAnnotatedVariantsMongoReaderTest.java b/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/NonAnnotatedVariantsMongoReaderTest.java index d557b625b..bcfd1adc4 100644 --- a/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/NonAnnotatedVariantsMongoReaderTest.java +++ b/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/NonAnnotatedVariantsMongoReaderTest.java @@ -32,7 +32,6 @@ import uk.ac.ebi.eva.pipeline.Application; import uk.ac.ebi.eva.pipeline.configuration.MongoConfiguration; import uk.ac.ebi.eva.pipeline.parameters.MongoConnection; -import uk.ac.ebi.eva.test.configuration.BaseTestConfiguration; import uk.ac.ebi.eva.test.data.VariantData; import uk.ac.ebi.eva.test.rules.TemporaryMongoRule; diff --git a/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/UnwindingItemReaderTest.java b/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/UnwindingItemReaderTest.java index b29a1b2f1..0f5311e33 100644 --- a/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/UnwindingItemReaderTest.java +++ b/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/UnwindingItemReaderTest.java @@ -27,7 +27,6 @@ import uk.ac.ebi.eva.commons.models.data.VariantSourceEntry; import uk.ac.ebi.eva.test.rules.PipelineTemporaryFolderRule; import uk.ac.ebi.eva.test.utils.JobTestUtils; -import uk.ac.ebi.eva.test.utils.TestFileUtils; import java.io.File; import java.io.FileInputStream; diff --git a/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/UnwindingItemStreamReaderTest.java b/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/UnwindingItemStreamReaderTest.java index 85acec6f2..7a6dff7bc 100644 --- a/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/UnwindingItemStreamReaderTest.java +++ b/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/UnwindingItemStreamReaderTest.java @@ -27,7 +27,6 @@ import uk.ac.ebi.eva.commons.models.data.VariantSourceEntry; import uk.ac.ebi.eva.test.rules.PipelineTemporaryFolderRule; import uk.ac.ebi.eva.test.utils.JobTestUtils; -import uk.ac.ebi.eva.test.utils.TestFileUtils; import java.io.File; import java.io.FileInputStream; diff --git a/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/VcfHeaderReaderTest.java b/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/VcfHeaderReaderTest.java index b04b0e36d..a0c560304 100644 --- a/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/VcfHeaderReaderTest.java +++ b/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/VcfHeaderReaderTest.java @@ -12,7 +12,6 @@ import uk.ac.ebi.eva.commons.models.data.VariantSourceEntity; import uk.ac.ebi.eva.test.rules.PipelineTemporaryFolderRule; import uk.ac.ebi.eva.test.utils.JobTestUtils; -import uk.ac.ebi.eva.test.utils.TestFileUtils; import java.io.File; import java.util.Arrays; diff --git a/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/VcfReaderTest.java b/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/VcfReaderTest.java index 8e9c08f28..cf8f11661 100644 --- a/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/VcfReaderTest.java +++ b/src/test/java/uk/ac/ebi/eva/pipeline/io/readers/VcfReaderTest.java @@ -10,7 +10,6 @@ import uk.ac.ebi.eva.commons.models.data.VariantSourceEntry; import uk.ac.ebi.eva.test.rules.PipelineTemporaryFolderRule; import uk.ac.ebi.eva.test.utils.JobTestUtils; -import uk.ac.ebi.eva.test.utils.TestFileUtils; import java.io.File; import java.io.FileInputStream; diff --git a/src/test/java/uk/ac/ebi/eva/pipeline/io/writers/GeneWriterTest.java b/src/test/java/uk/ac/ebi/eva/pipeline/io/writers/GeneWriterTest.java index 278b738b9..3c2fd5b63 100644 --- a/src/test/java/uk/ac/ebi/eva/pipeline/io/writers/GeneWriterTest.java +++ b/src/test/java/uk/ac/ebi/eva/pipeline/io/writers/GeneWriterTest.java @@ -32,7 +32,6 @@ import uk.ac.ebi.eva.pipeline.io.mappers.GeneLineMapper; import uk.ac.ebi.eva.pipeline.model.FeatureCoordinates; import uk.ac.ebi.eva.pipeline.parameters.MongoConnection; -import uk.ac.ebi.eva.test.configuration.BaseTestConfiguration; import uk.ac.ebi.eva.test.data.GtfStaticTestData; import uk.ac.ebi.eva.test.rules.TemporaryMongoRule; diff --git a/src/test/java/uk/ac/ebi/eva/pipeline/io/writers/StatisticsMongoWriterTest.java b/src/test/java/uk/ac/ebi/eva/pipeline/io/writers/StatisticsMongoWriterTest.java index a6f6c286f..4815053f9 100644 --- a/src/test/java/uk/ac/ebi/eva/pipeline/io/writers/StatisticsMongoWriterTest.java +++ b/src/test/java/uk/ac/ebi/eva/pipeline/io/writers/StatisticsMongoWriterTest.java @@ -33,7 +33,6 @@ import uk.ac.ebi.eva.pipeline.configuration.MongoConfiguration; import uk.ac.ebi.eva.pipeline.model.PopulationStatistics; import uk.ac.ebi.eva.pipeline.parameters.MongoConnection; -import uk.ac.ebi.eva.test.configuration.BaseTestConfiguration; import uk.ac.ebi.eva.test.data.VariantData; import uk.ac.ebi.eva.test.rules.TemporaryMongoRule; diff --git a/src/test/java/uk/ac/ebi/eva/pipeline/io/writers/VariantMongoWriterTest.java b/src/test/java/uk/ac/ebi/eva/pipeline/io/writers/VariantMongoWriterTest.java index 994c8e7f0..4941aad5c 100644 --- a/src/test/java/uk/ac/ebi/eva/pipeline/io/writers/VariantMongoWriterTest.java +++ b/src/test/java/uk/ac/ebi/eva/pipeline/io/writers/VariantMongoWriterTest.java @@ -33,7 +33,6 @@ import uk.ac.ebi.eva.pipeline.configuration.MongoConfiguration; import uk.ac.ebi.eva.pipeline.model.converters.data.VariantToMongoDbObjectConverter; import uk.ac.ebi.eva.pipeline.parameters.MongoConnection; -import uk.ac.ebi.eva.test.configuration.BaseTestConfiguration; import uk.ac.ebi.eva.test.rules.TemporaryMongoRule; import uk.ac.ebi.eva.utils.MongoDBHelper; diff --git a/src/test/java/uk/ac/ebi/eva/pipeline/io/writers/VepAnnotationMongoWriterTest.java b/src/test/java/uk/ac/ebi/eva/pipeline/io/writers/VepAnnotationMongoWriterTest.java index e0909ef7e..e07be440d 100644 --- a/src/test/java/uk/ac/ebi/eva/pipeline/io/writers/VepAnnotationMongoWriterTest.java +++ b/src/test/java/uk/ac/ebi/eva/pipeline/io/writers/VepAnnotationMongoWriterTest.java @@ -37,7 +37,6 @@ import uk.ac.ebi.eva.pipeline.configuration.MongoConfiguration; import uk.ac.ebi.eva.pipeline.io.mappers.AnnotationLineMapper; import uk.ac.ebi.eva.pipeline.parameters.MongoConnection; -import uk.ac.ebi.eva.test.configuration.BaseTestConfiguration; import uk.ac.ebi.eva.test.rules.TemporaryMongoRule; import uk.ac.ebi.eva.utils.MongoDBHelper; diff --git a/src/test/java/uk/ac/ebi/eva/pipeline/jobs/steps/VepInputGeneratorStepTest.java b/src/test/java/uk/ac/ebi/eva/pipeline/jobs/steps/VepInputGeneratorStepTest.java index fc4f3f141..43e1862df 100644 --- a/src/test/java/uk/ac/ebi/eva/pipeline/jobs/steps/VepInputGeneratorStepTest.java +++ b/src/test/java/uk/ac/ebi/eva/pipeline/jobs/steps/VepInputGeneratorStepTest.java @@ -24,7 +24,6 @@ import org.springframework.batch.core.JobParameters; import org.springframework.batch.test.JobLauncherTestUtils; import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.context.annotation.Profile; import org.springframework.test.context.ActiveProfiles; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.TestPropertySource; diff --git a/src/test/java/uk/ac/ebi/eva/runner/JobRestartSynchronousTest.java b/src/test/java/uk/ac/ebi/eva/runner/JobRestartSynchronousTest.java index 8b902bda1..9f92b256b 100644 --- a/src/test/java/uk/ac/ebi/eva/runner/JobRestartSynchronousTest.java +++ b/src/test/java/uk/ac/ebi/eva/runner/JobRestartSynchronousTest.java @@ -20,7 +20,6 @@ import org.springframework.batch.core.JobParameters; import org.springframework.batch.core.Step; import org.springframework.batch.core.StepContribution; -import org.springframework.batch.core.configuration.annotation.SimpleBatchConfiguration; import org.springframework.batch.core.scope.context.ChunkContext; import org.springframework.batch.core.step.tasklet.Tasklet; import org.springframework.batch.repeat.RepeatStatus; diff --git a/src/test/java/uk/ac/ebi/eva/test/configuration/AsynchronousBatchTestConfiguration.java b/src/test/java/uk/ac/ebi/eva/test/configuration/AsynchronousBatchTestConfiguration.java index e78fb2df6..b0710e1b8 100644 --- a/src/test/java/uk/ac/ebi/eva/test/configuration/AsynchronousBatchTestConfiguration.java +++ b/src/test/java/uk/ac/ebi/eva/test/configuration/AsynchronousBatchTestConfiguration.java @@ -29,7 +29,6 @@ import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor; -import org.springframework.scheduling.concurrent.ThreadPoolTaskScheduler; /** * Specific configuration to use a spring batch context with an asynchronous thread pool executor. The standard base diff --git a/src/test/java/uk/ac/ebi/eva/test/data/VariantData.java b/src/test/java/uk/ac/ebi/eva/test/data/VariantData.java index 39917605e..33bf7ee51 100644 --- a/src/test/java/uk/ac/ebi/eva/test/data/VariantData.java +++ b/src/test/java/uk/ac/ebi/eva/test/data/VariantData.java @@ -17,8 +17,6 @@ import org.apache.commons.io.FileUtils; -import uk.ac.ebi.eva.test.utils.TestFileUtils; - import java.io.IOException; import static uk.ac.ebi.eva.utils.FileUtils.getResource; From 708dda487456ac490ccf04a918c02bfaaefb0ddc Mon Sep 17 00:00:00 2001 From: jorizci Date: Wed, 1 Mar 2017 14:33:53 +0000 Subject: [PATCH 2/3] Exception thrown when trying to run a unknown job from the command line runner. --- .../runner/EvaPipelineJobLauncherCommandLineRunner.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/runner/EvaPipelineJobLauncherCommandLineRunner.java b/src/main/java/uk/ac/ebi/eva/pipeline/runner/EvaPipelineJobLauncherCommandLineRunner.java index 37ab70b47..bfa86e994 100644 --- a/src/main/java/uk/ac/ebi/eva/pipeline/runner/EvaPipelineJobLauncherCommandLineRunner.java +++ b/src/main/java/uk/ac/ebi/eva/pipeline/runner/EvaPipelineJobLauncherCommandLineRunner.java @@ -221,9 +221,9 @@ private void launchJob(JobParameters jobParameters) throws JobExecutionException } catch (NoSuchJobException ex) { logger.error("No job found in registry for job name: " + jobName); } - } else { - logger.error("Job not found and no JobRegistry initializated."); } + + throw new UnknownJobException(jobName); } @Override From 9ec9b336d37af2bf6b7200a1226e06790f72bddc Mon Sep 17 00:00:00 2001 From: jorizci Date: Wed, 1 Mar 2017 14:39:42 +0000 Subject: [PATCH 3/3] Removed unused exceptions. --- .../pipeline/configuration/readers/VcfReaderConfiguration.java | 2 +- src/main/java/uk/ac/ebi/eva/pipeline/parameters/JobOptions.java | 2 +- .../java/uk/ac/ebi/eva/test/utils/GenotypedVcfJobTestUtils.java | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) 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)); }