Merge pull request #99 from jorizci/code-cleaning

Code cleaning
EBIvariation · Mar 1, 2017 · 25e07c6 · 25e07c6
2 parents 3225152 + 9ec9b33
commit 25e07c6
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Showing 31 changed files with 6 additions and 40 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
@@ -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
@@ -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/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<Variant> unwindingReader(VcfReader vcfReader) throws Exception {
+    public ItemStreamReader<Variant> unwindingReader(VcfReader vcfReader) {
         return new UnwindingItemStreamReader<>(vcfReader);
     }
 

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
@@ -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
@@ -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.
  * <p>

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
@@ -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
@@ -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
@@ -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/...in/java/uk/ac/ebi/eva/pipeline/jobs/steps/tasklets/PopulationStatisticsGeneratorStep.java b/...in/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
@@ -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/...in/java/uk/ac/ebi/eva/pipeline/model/converters/data/VariantToMongoDbObjectConverter.java b/...in/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/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/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

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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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;

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
@@ -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));
     }
-Original file line number
+Diff line change
@@ Expand Up / @@ -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
      */
@@ Expand Down @@