uk.ac.ebi.eva.pipeline.jobs.AggregatedVcfJob.java Source code

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/*
 * Copyright 2015-2016 EMBL - European Bioinformatics Institute
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package uk.ac.ebi.eva.pipeline.jobs;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.core.Job;
import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
import org.springframework.batch.core.job.builder.FlowJobBuilder;
import org.springframework.batch.core.job.builder.JobBuilder;
import org.springframework.batch.core.job.flow.Flow;
import org.springframework.batch.core.launch.support.RunIdIncrementer;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;

import uk.ac.ebi.eva.pipeline.jobs.steps.VariantLoaderStep;

import javax.annotation.PostConstruct;

/**
 *  Complete pipeline workflow for aggregated VCF.
 *  Aggregated statistics are provided in the VCF instead of the genotypes.
 *
 *  transform ---> load --> (optionalAnnotationFlow: variantsAnnotGenerateInput --> (annotationCreate --> annotationLoad))
 *
 *  Steps in () are optional
 */
@Configuration
@EnableBatchProcessing
@Import({ VariantLoaderStep.class, AnnotationJob.class })
public class AggregatedVcfJob extends CommonJobStepInitialization {

    private static final Logger logger = LoggerFactory.getLogger(AggregatedVcfJob.class);

    private static final String jobName = "load-aggregated-vcf";

    //job default settings
    private static final boolean INCLUDE_SAMPLES = false;
    private static final boolean COMPRESS_GENOTYPES = false;
    private static final boolean CALCULATE_STATS = true;
    private static final boolean INCLUDE_STATS = true;

    @PostConstruct
    public void configureDefaultVariantOptions() {
        getJobOptions().configureGenotypesStorage(INCLUDE_SAMPLES, COMPRESS_GENOTYPES);
        getJobOptions().configureStatisticsStorage(CALCULATE_STATS, INCLUDE_STATS);
    }

    @Autowired
    private JobBuilderFactory jobBuilderFactory;
    @Autowired
    private Flow optionalAnnotationFlow;
    @Autowired
    private VariantLoaderStep variantLoaderStep;

    @Bean
    @Qualifier("aggregatedJob")
    public Job aggregatedJob() {
        logger.debug("Building variant aggregated job");

        JobBuilder jobBuilder = jobBuilderFactory.get(jobName).incrementer(new RunIdIncrementer());

        FlowJobBuilder builder = jobBuilder.flow(normalize()).next(load(variantLoaderStep))
                .next(optionalAnnotationFlow).end();

        return builder.build();
    }

}