Example usage for org.springframework.batch.item.file FlatFileItemReader close

Introduction

In this page you can find the example usage for org.springframework.batch.item.file FlatFileItemReader close.

Prototype

void close() throws ItemStreamException;

Source Link

Document

If any resources are needed for the stream to operate they need to be destroyed here.

Usage

From source file:de.mediait.batch.FlatFileItemReaderTest.java

@Test
public void testFlatFileReader2() throws Exception {

    final FlatFileItemReader<String[]> reader = createFlatFileReader(',', '\'');

    reader.setResource(new ClassPathResource("csv-fix-samples/fixcomma.txt"));

    final ExecutionContext executionContext = new ExecutionContext();
    reader.open(executionContext);//from  w  w w .  ja v a  2  s. c  o m
    final String[] object = (String[]) reader.read();
    reader.close();

    assertArrayEquals(new String[] { "begin", "abc' \"d\" 'ef", "end" }, object);
}

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From source file:de.mediait.batch.FlatFileItemReaderTest.java

@Test
public void testFlatFileReader() throws Exception {

    final FlatFileItemReader<String[]> reader = createFlatFileReader(';', '\'');

    reader.setResource(new ClassPathResource("csv-fix-samples/fixsemicolon.txt"));

    final ExecutionContext executionContext = new ExecutionContext();
    reader.open(executionContext);/*from  w  ww. ja va 2  s.c o  m*/
    final String[] object = (String[]) reader.read();
    reader.close();

    assertArrayEquals(new String[] { "begin", "abc' \"d\" 'ef", "end" }, object);
}

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From source file:org.cbioportal.annotation.pipeline.MutationRecordReader.java

@Override
public void open(ExecutionContext ec) throws ItemStreamException {

    processComments(ec);/* w  w  w .  j  a  v a2s. c  o  m*/

    FlatFileItemReader<MutationRecord> reader = new FlatFileItemReader<>();
    reader.setResource(new FileSystemResource(filename));
    DefaultLineMapper<MutationRecord> mapper = new DefaultLineMapper<>();
    final DelimitedLineTokenizer tokenizer = new DelimitedLineTokenizer();
    tokenizer.setDelimiter("\t");
    mapper.setLineTokenizer(tokenizer);
    mapper.setFieldSetMapper(new MutationFieldSetMapper());
    reader.setLineMapper(mapper);
    reader.setLinesToSkip(1);
    reader.setSkippedLinesCallback(new LineCallbackHandler() {
        @Override
        public void handleLine(String line) {
            tokenizer.setNames(line.split("\t"));
        }
    });
    reader.open(ec);

    LOG.info("Loading records from: " + filename);
    MutationRecord mutationRecord;
    try {
        while ((mutationRecord = reader.read()) != null) {
            mutationRecords.add(mutationRecord);
        }
    } catch (Exception e) {
        throw new ItemStreamException(e);
    }
    reader.close();

    int variantsToAnnotateCount = mutationRecords.size();
    int annotatedVariantsCount = 0;
    LOG.info(String.valueOf(variantsToAnnotateCount) + " records to annotate");
    for (MutationRecord record : mutationRecords) {
        annotatedVariantsCount++;
        if (annotatedVariantsCount % 2000 == 0) {
            LOG.info("\tOn record " + String.valueOf(annotatedVariantsCount) + " out of "
                    + String.valueOf(variantsToAnnotateCount) + ", annotation "
                    + String.valueOf((int) (((annotatedVariantsCount * 1.0) / variantsToAnnotateCount) * 100))
                    + "% complete");
        }
        // save variant details for logging
        String variantDetails = "(sampleId,chr,start,end,ref,alt,url)= (" + record.getTUMOR_SAMPLE_BARCODE()
                + "," + record.getCHROMOSOME() + "," + record.getSTART_POSITION() + ","
                + record.getEND_POSITION() + "," + record.getREFERENCE_ALLELE() + ","
                + record.getTUMOR_SEQ_ALLELE2() + "," + annotator.getUrlForRecord(record, isoformOverride)
                + ")";

        // init annotated record w/o genome nexus in case server error occurs
        // if no error then annotated record will get overwritten anyway with genome nexus response
        String serverErrorMessage = "";
        AnnotatedRecord annotatedRecord = new AnnotatedRecord(record);
        try {
            annotatedRecord = annotator.annotateRecord(record, replace, isoformOverride, true);
        } catch (HttpServerErrorException ex) {
            serverErrorMessage = "Failed to annotate variant due to internal server error";
        } catch (HttpClientErrorException ex) {
            serverErrorMessage = "Failed to annotate variant due to client error";
        } catch (HttpMessageNotReadableException ex) {
            serverErrorMessage = "Failed to annotate variant due to message not readable error";
        } catch (GenomeNexusAnnotationFailureException ex) {
            serverErrorMessage = "Failed to annotate variant due to Genome Nexus : " + ex.getMessage();
        }
        annotatedRecords.add(annotatedRecord);
        header.addAll(annotatedRecord.getHeaderWithAdditionalFields());

        // log server failure message if applicable
        if (!serverErrorMessage.isEmpty()) {
            LOG.warn(serverErrorMessage);
            failedAnnotations++;
            failedServerAnnotations++;
            if (errorReportLocation != null)
                updateErrorMessages(record, record.getVARIANT_CLASSIFICATION(),
                        annotator.getUrlForRecord(record, isoformOverride), serverErrorMessage);
            continue;
        }
        String annotationErrorMessage = "";
        if (MafUtil.variantContainsAmbiguousTumorSeqAllele(record.getREFERENCE_ALLELE(),
                record.getTUMOR_SEQ_ALLELE1(), record.getTUMOR_SEQ_ALLELE2())) {
            snpAndIndelVariants++;
            annotationErrorMessage = "Record contains ambiguous SNP and INDEL allele change - SNP allele will be used";
        }
        if (annotatedRecord.getHGVSC().isEmpty() && annotatedRecord.getHGVSP().isEmpty()) {
            if (annotator.isHgvspNullClassifications(annotatedRecord.getVARIANT_CLASSIFICATION())) {
                failedNullHgvspAnnotations++;
                annotationErrorMessage = "Ignoring record with HGVSp null classification '"
                        + annotatedRecord.getVARIANT_CLASSIFICATION() + "'";
            } else {
                annotationErrorMessage = "Failed to annotate variant";
            }
            failedAnnotations++;
        }
        if (!annotationErrorMessage.isEmpty()) {
            if (verbose)
                LOG.info(annotationErrorMessage + ": " + variantDetails);
            if (errorReportLocation != null)
                updateErrorMessages(record, annotatedRecord.getVARIANT_CLASSIFICATION(),
                        annotator.getUrlForRecord(record, isoformOverride), annotationErrorMessage);
        }
    }
    // print summary statistics and save error messages to file if applicable
    printSummaryStatistics(failedAnnotations, failedNullHgvspAnnotations, snpAndIndelVariants,
            failedServerAnnotations);
    if (errorReportLocation != null) {
        saveErrorMessagesToFile(errorMessages);
    }
    ec.put("mutation_header", new ArrayList(header));
}

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