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

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Here is the source code for uk.ac.ebi.eva.pipeline.jobs.PopulationStatisticsJob.java

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/*
 * Copyright 2015 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.BatchStatus;
import org.springframework.batch.core.Job;
import org.springframework.batch.core.Step;
import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
import org.springframework.batch.core.job.builder.FlowBuilder;
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.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;

import uk.ac.ebi.eva.pipeline.jobs.deciders.SkipStepDecider;
import uk.ac.ebi.eva.pipeline.jobs.steps.PopulationStatisticsGeneratorStep;
import uk.ac.ebi.eva.pipeline.jobs.steps.PopulationStatisticsLoaderStep;

/**
 * Configuration to run a full Statistics job: variantStatsFlow: statsCreate --> statsLoad
 *
 */
@Configuration
@EnableBatchProcessing
@Import({ PopulationStatisticsGeneratorStep.class, PopulationStatisticsLoaderStep.class })
public class PopulationStatisticsJob extends CommonJobStepInitialization {

    private static final Logger logger = LoggerFactory.getLogger(PopulationStatisticsJob.class);
    private static final String jobName = "calculate-statistics";
    public static final String SKIP_STATS = "statistics.skip";
    public static final String CALCULATE_STATISTICS = "Calculate statistics";
    public static final String LOAD_STATISTICS = "Load statistics";
    private static final String STATS_FLOW = "statsFlow";

    @Autowired
    private JobBuilderFactory jobBuilderFactory;

    @Autowired
    private PopulationStatisticsGeneratorStep populationStatisticsGeneratorStep;

    @Autowired
    private PopulationStatisticsLoaderStep populationStatisticsLoaderStep;

    @Bean
    public Job variantStatisticsJob() {
        JobBuilder jobBuilder = jobBuilderFactory.get(jobName).incrementer(new RunIdIncrementer());

        return jobBuilder.start(optionalStatisticsFlow()).build().build();
    }

    @Bean
    public Flow optionalStatisticsFlow() {
        SkipStepDecider statisticsSkipStepDecider = new SkipStepDecider(getPipelineOptions(), SKIP_STATS);

        return new FlowBuilder<Flow>(STATS_FLOW).start(statisticsSkipStepDecider).on(SkipStepDecider.DO_STEP)
                .to(statsCreate()).next(statsLoad()).from(statisticsSkipStepDecider).on(SkipStepDecider.SKIP_STEP)
                .end(BatchStatus.COMPLETED.toString()).build();
    }

    private Step statsCreate() {
        return generateStep(CALCULATE_STATISTICS, populationStatisticsGeneratorStep);
    }

    private Step statsLoad() {
        return generateStep(LOAD_STATISTICS, populationStatisticsLoaderStep);
    }
}