List of usage examples for org.springframework.batch.item.file FlatFileItemReader setResource
@Override public void setResource(Resource resource)
From source file:org.cbioportal.annotation.pipeline.MutationRecordReader.java
@Override public void open(ExecutionContext ec) throws ItemStreamException { processComments(ec);//from www. ja va 2 s .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.springframework.batch.admin.sample.LeadRandomizer.java
@Test public void testLeads() throws Exception { FlatFileItemReader<FieldSet> reader = new FlatFileItemReader<FieldSet>(); reader.setResource(new ClassPathResource("/data/test.txt")); DefaultLineMapper<FieldSet> lineMapper = new DefaultLineMapper<FieldSet>(); lineMapper.setLineTokenizer(new DelimitedLineTokenizer()); lineMapper.setFieldSetMapper(new PassThroughFieldSetMapper()); reader.setLinesToSkip(1);/*from w w w .j a va 2s . c o m*/ final List<String> headers = new ArrayList<String>(); reader.setSkippedLinesCallback(new LineCallbackHandler() { public void handleLine(String line) { headers.add(line); } }); reader.setLineMapper(lineMapper); reader.open(new ExecutionContext()); List<FieldSet> list = new ArrayList<FieldSet>(); FieldSet item = reader.read(); while (item != null) { list.add(item); item = reader.read(); } assertEquals(7, list.size()); FlatFileItemWriter<FieldSet> writer = new FlatFileItemWriter<FieldSet>(); FileSystemResource resource = new FileSystemResource("target/output/output.txt"); FileUtils.deleteQuietly(resource.getFile()); writer.setResource(resource); writer.setHeaderCallback(new FlatFileHeaderCallback() { public void writeHeader(Writer writer) throws IOException { for (String header : headers) { writer.write(header); } } }); writer.setLineAggregator(new DelimitedLineAggregator<FieldSet>()); writer.open(new ExecutionContext()); String[] names = getFields(list, 1); String[] country = getFields(list, 2); String[] products = getFields(list, 3); double[] amounts = getMinMax(list, 4); NumberFormat formatter = new DecimalFormat("#.##"); int count = 20; for (int i = 0; i < 100; i++) { List<FieldSet> items = new ArrayList<FieldSet>(); for (FieldSet fieldSet : list) { String[] values = fieldSet.getValues(); values[0] = "" + (count++); values[1] = choose(names); values[2] = choose(country); values[3] = choose(products); values[4] = formatter.format(random(amounts)); items.add(new DefaultFieldSet(values)); } writer.write(items); } writer.close(); }
From source file:org.springframework.batch.item.file.builder.FlatFileItemReaderBuilder.java
/** * Builds the {@link FlatFileItemReader}. * * @return a {@link FlatFileItemReader}//from ww w . j a v a2s. co m * @throws Exception */ public FlatFileItemReader<T> build() throws Exception { if (this.saveState) { Assert.state(StringUtils.hasText(this.name), "A name is required when saveSate is set to true."); } if (this.resource == null) { logger.debug("The resource is null. This is only a valid scenario when " + "injecting it later as in when using the MultiResourceItemReader"); } Assert.notNull(this.recordSeparatorPolicy, "A RecordSeparatorPolicy is required."); int validatorValue = this.tokenizerValidator.intValue(); Assert.state(validatorValue == 1 || validatorValue == 2 || validatorValue == 4, "Only one LineTokenizer option may be configured"); FlatFileItemReader<T> reader = new FlatFileItemReader<>(); if (StringUtils.hasText(this.name)) { reader.setName(this.name); } reader.setResource(this.resource); if (this.lineMapper != null) { reader.setLineMapper(this.lineMapper); } else { DefaultLineMapper<T> lineMapper = new DefaultLineMapper<>(); if (this.lineTokenizer != null && this.fieldSetMapper != null) { lineMapper.setLineTokenizer(this.lineTokenizer); } else if (this.fixedLengthBuilder != null) { lineMapper.setLineTokenizer(this.fixedLengthBuilder.build()); } else if (this.delimitedBuilder != null) { lineMapper.setLineTokenizer(this.delimitedBuilder.build()); } else { throw new IllegalStateException("No LineTokenizer implementation was provided."); } if (this.targetType != null || StringUtils.hasText(this.prototypeBeanName)) { BeanWrapperFieldSetMapper<T> mapper = new BeanWrapperFieldSetMapper<>(); mapper.setTargetType(this.targetType); mapper.setPrototypeBeanName(this.prototypeBeanName); mapper.setStrict(this.beanMapperStrict); mapper.setBeanFactory(this.beanFactory); mapper.setDistanceLimit(this.distanceLimit); mapper.setCustomEditors(this.customEditors); mapper.afterPropertiesSet(); lineMapper.setFieldSetMapper(mapper); } else if (this.fieldSetMapper != null) { lineMapper.setFieldSetMapper(this.fieldSetMapper); } else { throw new IllegalStateException("No FieldSetMapper implementation was provided."); } reader.setLineMapper(lineMapper); } reader.setLinesToSkip(this.linesToSkip); if (!this.comments.isEmpty()) { reader.setComments(this.comments.toArray(new String[this.comments.size()])); } reader.setSkippedLinesCallback(this.skippedLinesCallback); reader.setRecordSeparatorPolicy(this.recordSeparatorPolicy); reader.setMaxItemCount(this.maxItemCount); reader.setSaveState(this.saveState); reader.setStrict(this.strict); return reader; }