Example usage for org.springframework.batch.item ItemStreamException ItemStreamException

List of usage examples for org.springframework.batch.item ItemStreamException ItemStreamException

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Introduction

In this page you can find the example usage for org.springframework.batch.item ItemStreamException ItemStreamException.

Prototype

public ItemStreamException(Throwable nested)

Source Link

Document

Constructs a new instance with a nested exception and empty message.

Usage

From source file:es.fcs.batch.integration.chunk.MyChunkMessageChannelItemWriter.java

public void open(ExecutionContext executionContext) throws ItemStreamException {
    if (executionContext.containsKey(EXPECTED)) {
        localState.open(executionContext.getInt(EXPECTED), executionContext.getInt(ACTUAL));
        if (!waitForResults()) {
            throw new ItemStreamException("Timed out waiting for back log on open");
        }/*from   ww w . j a  va2s  .c  om*/
    }
}

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

private void processComments(ExecutionContext ec) {
    List<String> comments = new ArrayList<>();
    String sequencedSamples = "";
    BufferedReader reader = null;
    try {//w  w  w .j  a  va2s  .c  o  m
        reader = new BufferedReader(new FileReader(filename));
        String line;
        while ((line = reader.readLine()) != null) {
            if (line.startsWith("#")) {
                comments.add(line);
            } else {
                // no more comments, go on processing
                break;
            }
        }
        reader.close();
    } catch (Exception e) {
        throw new ItemStreamException(e);
    }

    // Add comments to the config for the writer to access later
    ec.put("commentLines", comments);
}

From source file:egovframework.rte.bat.core.item.file.EgovPartitionFlatFileItemWriter.java

/**
 * state? ?  ??  position? /* ww w  .j  a  va  2  s.c  om*/
 * @see ItemStream#update(ExecutionContext)
 */
public void update(ExecutionContext executionContext) {
    if (state == null) {
        throw new ItemStreamException("ItemStream not open or already closed.");
    }

    Assert.notNull(executionContext, "ExecutionContext must not be null");

    if (saveState) {

        try {

            executionContext.putLong(getKey(RESTART_DATA_NAME), state.position());
        } catch (IOException e) {
            throw new ItemStreamException("ItemStream does not return current position properly", e);
        }

        executionContext.putLong(getKey(WRITTEN_STATISTICS_NAME), state.linesWritten);
    }
}

From source file:me.andpay.ti.spring.batch.FlatFileItemWriter.java

/**
 * @see ItemStream#update(ExecutionContext)
 *//*from   w w w  .  j  ava2s .  c o m*/
public void update(ExecutionContext executionContext) {
    if (state == null) {
        throw new ItemStreamException("ItemStream not open or already closed.");
    }

    Assert.notNull(executionContext, "ExecutionContext must not be null");

    if (saveState) {

        try {
            executionContext.putLong(getKey(RESTART_DATA_NAME), state.position());
        } catch (IOException e) {
            throw new ItemStreamException("ItemStream does not return current position properly", e);
        }

        executionContext.putLong(getKey(WRITTEN_STATISTICS_NAME), state.linesWritten);
    }
}

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

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

    processComments(ec);/* w  ww. j  ava 2s  .  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));
}

From source file:org.geoserver.backuprestore.writer.CatalogFileWriter.java

/**
 * @throws Exception//from  w w  w  . j  ava  2s .c  o  m
 * @see ItemStream#update(ExecutionContext)
 */
@Override
public void update(ExecutionContext executionContext) {
    super.update(executionContext);
    if (state == null) {
        throw new ItemStreamException("ItemStream not open or already closed.");
    }

    Assert.notNull(executionContext, "ExecutionContext must not be null");

    if (saveState) {
        try {
            executionContext.putLong(getExecutionContextKey(RESTART_DATA_NAME), state.position());
        } catch (IOException e) {
            logValidationExceptions((T) null,
                    new ItemStreamException("ItemStream does not return current position properly", e));
        }

        executionContext.putLong(getExecutionContextKey(WRITTEN_STATISTICS_NAME), state.linesWritten);
    }
}

From source file:org.springframework.batch.item.file.FlatFileItemWriter.java

/**
 * @see ItemStream#update(ExecutionContext)
 *///ww w .j a  va 2s . com
@Override
public void update(ExecutionContext executionContext) {
    super.update(executionContext);
    if (state == null) {
        throw new ItemStreamException("ItemStream not open or already closed.");
    }

    Assert.notNull(executionContext, "ExecutionContext must not be null");

    if (saveState) {

        try {
            executionContext.putLong(getExecutionContextKey(RESTART_DATA_NAME), state.position());
        } catch (IOException e) {
            throw new ItemStreamException("ItemStream does not return current position properly", e);
        }

        executionContext.putLong(getExecutionContextKey(WRITTEN_STATISTICS_NAME), state.linesWritten);
    }
}

From source file:org.springframework.batch.jsr.item.CheckpointSupport.java

@Override
public void open(ExecutionContext executionContext) throws ItemStreamException {
    try {/*from w  w  w  . j  ava2  s  .c  o  m*/
        String executionContextKey = getExecutionContextKey(checkpointKey);
        Serializable checkpoint = (Serializable) executionContext.get(executionContextKey);
        doOpen(checkpoint);
    } catch (Exception e) {
        throw new ItemStreamException(e);
    }
}

From source file:org.springframework.batch.jsr.item.CheckpointSupport.java

@Override
public void update(ExecutionContext executionContext) throws ItemStreamException {
    try {/*from   w  w w.  j  a va  2 s  . c o  m*/
        executionContext.put(getExecutionContextKey(checkpointKey), deepCopy(doCheckpoint()));
    } catch (Exception e) {
        throw new ItemStreamException(e);
    }
}

From source file:org.springframework.batch.jsr.item.CheckpointSupport.java

@Override
public void close() throws ItemStreamException {
    try {//from  w  ww. j a  v a 2  s  . co m
        doClose();
    } catch (Exception e) {
        throw new ItemStreamException(e);
    }
}