Example usage for org.springframework.batch.test MetaDataInstanceFactory createStepExecution

Introduction

In this page you can find the example usage for org.springframework.batch.test MetaDataInstanceFactory createStepExecution.

Prototype

public static StepExecution createStepExecution() 

Source Link

Document

Create a StepExecution with default parameters.

Usage

From source file:uk.ac.ebi.eva.pipeline.io.readers.GeneReaderTest.java

@Test
public void shouldReadAllLinesInGtf() throws Exception {
    ExecutionContext executionContext = MetaDataInstanceFactory.createStepExecution().getExecutionContext();

    //simulate VEP output file
    File file = JobTestUtils.makeGzipFile(GtfStaticTestData.GTF_CONTENT);

    GeneReader geneReader = new GeneReader(file);
    geneReader.setSaveState(false);/*from  www  .  ja v a2 s.  c om*/
    geneReader.open(executionContext);

    FeatureCoordinates gene;
    int chromosomeCount = 0;
    int count = 0;
    while ((gene = geneReader.read()) != null) {
        count++;
        if (gene.getChromosome() != null && !gene.getChromosome().isEmpty()) {
            chromosomeCount++;
        }
    }
    // all should have at least the chromosome field
    assertEquals(count, chromosomeCount);

    // GeneReader should get all the lines from the file
    long actualCount = JobTestUtils.getLines(new GZIPInputStream(new FileInputStream(file)));
    assertEquals(actualCount, count);
}

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From source file:uk.ac.ebi.eva.pipeline.jobs.steps.processor.GeneFilterProcessorTest.java

@Test
public void shouldKeepGenesAndTranscripts() throws Exception {
    ExecutionContext executionContext = MetaDataInstanceFactory.createStepExecution().getExecutionContext();
    GeneFilterProcessor geneFilterProcessor = new GeneFilterProcessor();

    //simulate VEP output file
    File file = JobTestUtils.makeGzipFile(GtfStaticTestData.GTF_CONTENT);

    GeneReader geneReader = new GeneReader(file);
    geneReader.setSaveState(false);// w  w w. j a va 2 s  .c o m
    geneReader.open(executionContext);

    FeatureCoordinates gene;
    int count = 0;
    int keptGenes = 0;
    while ((gene = geneReader.read()) != null) {
        count++;
        FeatureCoordinates processedGene = geneFilterProcessor.process(gene);
        if (processedGene != null) {
            keptGenes++;
        }
    }

    assertEquals(7, count);
    assertEquals(4, keptGenes);
}

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From source file:uk.ac.ebi.eva.pipeline.io.writers.VepInputFlatFileWriterTest.java

@Test
public void shouldWriteAllFieldsToFile() throws Exception {
    ExecutionContext executionContext = MetaDataInstanceFactory.createStepExecution().getExecutionContext();

    DBObjectToVariantConverter converter = new DBObjectToVariantConverter();
    VariantWrapper variant = new VariantWrapper(converter
            .convertToDataModelType(JobTestUtils.constructDbo(VariantData.getVariantWithAnnotation())));

    File tempFile = JobTestUtils.createTempFile();
    VepInputFlatFileWriter writer = new VepInputFlatFileWriter(tempFile);
    writer.open(executionContext);/*from   w  w w.  j  a v a2s.com*/
    writer.write(Collections.singletonList(variant));
    assertEquals("20\t60344\t60348\tG/A\t+", readFirstLine(tempFile));
    writer.close();
}

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From source file:uk.ac.ebi.eva.pipeline.io.readers.AnnotationFlatFileReaderTest.java

@Test
public void shouldReadAllLinesInVepOutput() throws Exception {
    ExecutionContext executionContext = MetaDataInstanceFactory.createStepExecution().getExecutionContext();

    //simulate VEP output file
    File file = JobTestUtils.makeGzipFile(VepOutputContent.vepOutputContent);

    AnnotationFlatFileReader annotationFlatFileReader = new AnnotationFlatFileReader(file);
    annotationFlatFileReader.setSaveState(false);
    annotationFlatFileReader.open(executionContext);

    VariantAnnotation variantAnnotation;
    int consequenceTypeCount = 0;
    int count = 0;
    while ((variantAnnotation = annotationFlatFileReader.read()) != null) {
        count++;/*w ww  . j a v a  2s . co m*/
        if (variantAnnotation.getConsequenceTypes() != null
                && !variantAnnotation.getConsequenceTypes().isEmpty()) {
            consequenceTypeCount++;
        }
    }
    // all should have at least consequence type annotations
    assertEquals(count, consequenceTypeCount);

    // annotationFlatFileReader should get all the lines from the file
    long actualCount = JobTestUtils.getLines(new GZIPInputStream(new FileInputStream(file)));
    assertEquals(actualCount, count);
}

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From source file:de.langmi.spring.batch.examples.complex.file.split.GetLineCountTaskletTest.java

@Test
public void testExecute() throws Exception {
    // setup//from ww  w. j ava2s . co m
    tasklet = new GetLineCountTasklet();
    tasklet.setResource(new FileSystemResource(INPUT));
    StepExecution stepExecution = MetaDataInstanceFactory.createStepExecution();

    // execute
    RepeatStatus status = tasklet.execute(new StepContribution(stepExecution),
            new ChunkContext(new StepContext(stepExecution)));
    // assertions
    assertEquals(RepeatStatus.FINISHED, status);
    assertEquals(EXPECTED_COUNT, stepExecution.getExecutionContext().get("line.count"));
}

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From source file:de.langmi.spring.batch.examples.readers.file.flatfileitemreader.FlatFileItemReaderTest.java

/**
 * Test should read succesfully./*  w  ww. jav  a 2 s.  c  om*/
 *
 * @throws Exception 
 */
@Test
public void testSuccessfulReading() throws Exception {
    // init reader
    reader.setLineMapper(new PassThroughLineMapper());
    reader.setResource(new FileSystemResource(INPUT_FILE));
    // open, provide "mock" ExecutionContext
    reader.open(MetaDataInstanceFactory.createStepExecution().getExecutionContext());
    // read
    try {
        int count = 0;
        String line;
        while ((line = reader.read()) != null) {
            assertEquals(String.valueOf(count), line);
            count++;
        }
        assertEquals(EXPECTED_COUNT, count);
    } catch (Exception e) {
        throw e;
    } finally {
        reader.close();
    }
}

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From source file:de.langmi.spring.batch.examples.readers.file.peekable.SimplePeekableItemReaderTest.java

/**
 * Test should read succesfully.//from w  w  w .  jav a 2s.c om
 *
 * @throws Exception 
 */
@Test
public void testSuccessfulPeekAhead() throws Exception {
    // init delegate
    delegateReader.setLineMapper(new PassThroughLineMapper());
    delegateReader.setResource(new FileSystemResource(INPUT_FILE));
    // init peekable
    SingleItemPeekableItemReader<String> peekable = new SingleItemPeekableItemReader<String>();
    peekable.setDelegate(delegateReader);
    // open, provide "mock" ExecutionContext
    peekable.open(MetaDataInstanceFactory.createStepExecution().getExecutionContext());
    // read
    try {
        int count = 0;
        String line;
        while ((line = peekable.read()) != null) {
            assertEquals(String.valueOf(count), line);
            // test for peek
            String lineAhead = peekable.peek();
            if (count + 1 < EXPECTED_COUNT) {
                assertEquals(String.valueOf(count + 1), lineAhead);
            } else {
                assertNull(lineAhead);
            }
            count++;
        }
        assertEquals(EXPECTED_COUNT, count);
    } catch (Exception e) {
        throw e;
    } finally {
        peekable.close();
    }
}

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From source file:fr.acxio.tools.agia.alfresco.MultiLineNodeListItemReaderTest.java

public StepExecution getStepExection() {
    StepExecution execution = MetaDataInstanceFactory.createStepExecution();
    return execution;
}

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From source file:com.github.jrrdev.mantisbtsync.core.jobs.projects.ProjectsVersionsWriterTest.java

public StepExecution getStepExecution() {

    final StepExecution stepExecution = MetaDataInstanceFactory.createStepExecution();
    stepExecution.getExecutionContext().putInt("mantis.loop.project_id", 1);

    return stepExecution;
}

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From source file:de.langmi.spring.batch.examples.readers.file.zip.ZipMultiResourceItemReaderTest.java

/**
 * Test with one ZIP file containing one text file with 20 lines.
 *
 * @throws Exception //  w  w w  .ja  v a  2  s .co m
 */
@Test
public void testOneZipFile() throws Exception {
    LOG.debug("testOneZipFile");
    ZipMultiResourceItemReader<String> mReader = new ZipMultiResourceItemReader<String>();
    // setup multResourceReader
    mReader.setArchives(new Resource[] { new FileSystemResource(ZIP_INPUT_SINGLE_FILE) });

    // call general setup last
    generalMultiResourceReaderSetup(mReader);

    // open with mock context
    mReader.open(MetaDataInstanceFactory.createStepExecution().getExecutionContext());

    // read
    try {
        String item = null;
        int count = 0;
        do {
            item = mReader.read();
            if (item != null) {
                assertEquals(String.valueOf(count), item);
                count++;
            }
        } while (item != null);
        assertEquals(20, count);
    } catch (Exception e) {
        throw e;
    } finally {
        mReader.close();
    }
}

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