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EVA-501 using FeatureCoordinates from variation commons #31

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EVA-501 using FeatureCoordinates from variation commons #31

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7 changes: 6 additions & 1 deletion pom.xml
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<biodata.version>0.4.5</biodata.version>
<cellbase.version>3.1.3</cellbase.version>
</properties>

<dependencies>
<dependency>
<groupId>uk.ac.ebi.eva</groupId>
<artifactId>variation-commons</artifactId>
<version>0.1</version>
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@sundarvenkata-EBI sundarvenkata-EBI Jul 1, 2020 •
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This version should be changed to use the variation commons version post EVA-1984.

</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
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2 changes: 1 addition & 1 deletion src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/GeneLineMapper.java
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import org.springframework.batch.item.file.LineMapper;

import uk.ac.ebi.eva.pipeline.model.FeatureCoordinates;
import uk.ac.ebi.eva.commons.models.data.FeatureCoordinates;

import java.util.Map;
import java.util.TreeMap;
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2 changes: 1 addition & 1 deletion src/main/java/uk/ac/ebi/eva/pipeline/io/readers/GeneReader.java
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import org.springframework.batch.item.file.FlatFileItemReader;
import org.springframework.core.io.Resource;
import uk.ac.ebi.eva.commons.models.data.FeatureCoordinates;
import uk.ac.ebi.eva.pipeline.io.GzipLazyResource;
import uk.ac.ebi.eva.pipeline.io.mappers.GeneLineMapper;
import uk.ac.ebi.eva.pipeline.model.FeatureCoordinates;

import java.io.File;

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2 changes: 1 addition & 1 deletion src/main/java/uk/ac/ebi/eva/pipeline/io/writers/GeneWriter.java
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import org.springframework.batch.item.data.MongoItemWriter;
import org.springframework.data.mongodb.core.MongoOperations;
import uk.ac.ebi.eva.pipeline.model.FeatureCoordinates;
import uk.ac.ebi.eva.commons.models.data.FeatureCoordinates;

/**
* @author Jose Miguel Mut Lopez &lt;[email protected]&gt;
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2 changes: 1 addition & 1 deletion src/main/java/uk/ac/ebi/eva/pipeline/jobs/steps/GeneLoaderStep.java
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import uk.ac.ebi.eva.pipeline.io.mappers.GeneLineMapper;
import uk.ac.ebi.eva.pipeline.jobs.steps.processors.GeneFilterProcessor;
import uk.ac.ebi.eva.pipeline.listeners.SkippedItemListener;
import uk.ac.ebi.eva.pipeline.model.FeatureCoordinates;
import uk.ac.ebi.eva.commons.models.data.FeatureCoordinates;

import java.io.IOException;

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3 changes: 1 addition & 2 deletions src/main/java/uk/ac/ebi/eva/pipeline/jobs/steps/processors/GeneFilterProcessor.java
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package uk.ac.ebi.eva.pipeline.jobs.steps.processors;

import org.springframework.batch.item.ItemProcessor;

import uk.ac.ebi.eva.pipeline.model.FeatureCoordinates;
import uk.ac.ebi.eva.commons.models.data.FeatureCoordinates;

/**
* @author Jose Miguel Mut Lopez &lt;[email protected]&gt;
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91 changes: 0 additions & 91 deletions src/main/java/uk/ac/ebi/eva/pipeline/model/FeatureCoordinates.java
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This file was deleted.

2 changes: 1 addition & 1 deletion src/test/java/uk/ac/ebi/eva/pipeline/io/mappers/GeneLineMapperTest.java
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package uk.ac.ebi.eva.pipeline.io.mappers;

import org.junit.Test;
import uk.ac.ebi.eva.pipeline.model.FeatureCoordinates;
import uk.ac.ebi.eva.commons.models.data.FeatureCoordinates;
import uk.ac.ebi.eva.test.data.GtfStaticTestData;

import static org.junit.Assert.assertNotNull;
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4 changes: 3 additions & 1 deletion src/test/java/uk/ac/ebi/eva/pipeline/io/readers/GeneReaderTest.java
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import org.junit.Test;
import org.springframework.batch.item.ExecutionContext;
import org.springframework.batch.test.MetaDataInstanceFactory;
import uk.ac.ebi.eva.pipeline.model.FeatureCoordinates;
import uk.ac.ebi.eva.commons.models.data.FeatureCoordinates;
import uk.ac.ebi.eva.test.data.GtfStaticTestData;
import uk.ac.ebi.eva.test.utils.JobTestUtils;

import java.io.File;
import java.io.FileInputStream;
import java.util.zip.GZIPInputStream;

import static junit.framework.TestCase.assertEquals;

/**
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2 changes: 1 addition & 1 deletion src/test/java/uk/ac/ebi/eva/pipeline/io/writers/GeneWriterTest.java
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import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import uk.ac.ebi.eva.commons.models.data.FeatureCoordinates;
import uk.ac.ebi.eva.pipeline.configuration.DatabaseInitializationConfiguration;
import uk.ac.ebi.eva.pipeline.configuration.JobOptions;
import uk.ac.ebi.eva.pipeline.io.mappers.GeneLineMapper;
import uk.ac.ebi.eva.pipeline.model.FeatureCoordinates;
import uk.ac.ebi.eva.test.data.GtfStaticTestData;
import uk.ac.ebi.eva.test.utils.JobTestUtils;

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2 changes: 1 addition & 1 deletion src/test/java/uk/ac/ebi/eva/pipeline/jobs/steps/processor/GeneFilterProcessorTest.java
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import org.junit.Test;
import org.springframework.batch.item.ExecutionContext;
import org.springframework.batch.test.MetaDataInstanceFactory;
import uk.ac.ebi.eva.commons.models.data.FeatureCoordinates;
import uk.ac.ebi.eva.pipeline.io.readers.GeneReader;
import uk.ac.ebi.eva.pipeline.jobs.steps.processors.GeneFilterProcessor;
import uk.ac.ebi.eva.pipeline.model.FeatureCoordinates;
import uk.ac.ebi.eva.test.data.GtfStaticTestData;
import uk.ac.ebi.eva.test.utils.JobTestUtils;

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