org.cbioportal.annotation.pipeline.TestConfiguration.java Source code

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Here is the source code for org.cbioportal.annotation.pipeline.TestConfiguration.java

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/*
 * Copyright (c) 2016 Memorial Sloan-Kettering Cancer Center.
 *
 * This library is distributed in the hope that it will be useful, but WITHOUT
 * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
 * FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder
 * is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no
 * obligations to provide maintenance, support, updates, enhancements or
 * modifications. In no event shall Memorial Sloan-Kettering Cancer Center be
 * liable to any party for direct, indirect, special, incidental or
 * consequential damages, including lost profits, arising out of the use of this
 * software and its documentation, even if Memorial Sloan-Kettering Cancer
 * Center has been advised of the possibility of such damage.
 */

/*
 * This file is part of cBioPortal CMO-Pipelines.
 *
 * cBioPortal is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Affero General Public License for more details.
 *
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
*/
package org.cbioportal.annotation.pipeline;

import org.cbioportal.models.AnnotatedRecord;
import org.springframework.batch.core.*;
import org.springframework.batch.core.configuration.annotation.*;
import org.springframework.batch.item.*;
import org.springframework.batch.test.JobLauncherTestUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.boot.autoconfigure.EnableAutoConfiguration;
import org.springframework.context.annotation.*;
import org.springframework.test.context.TestPropertySource;

/**
 *
 * @author heinsz
 */

@Configuration
@EnableAutoConfiguration
@Import(BatchConfiguration.class)
@TestPropertySource("classpath:application.properties")
public class TestConfiguration {

    public static final String ANNOTATION_JOB_TEST = "annotationJobTest";

    @Autowired
    public JobBuilderFactory jobBuilderFactory;

    @Autowired
    public StepBuilderFactory stepBuilderFactory;

    @Bean
    public JobLauncherTestUtils jobLauncherTestUtils() {
        JobLauncherTestUtils jobLauncherTestUtils = new JobLauncherTestUtils();
        jobLauncherTestUtils.setJob(annotationJob());
        return new JobLauncherTestUtils();
    }

    @Value("${chunk}")
    private String chunk;

    @Bean
    public Job annotationJob() {
        return jobBuilderFactory.get(ANNOTATION_JOB_TEST).start(step()).build();
    }

    @Bean
    public Step step() {
        return stepBuilderFactory.get("step").<AnnotatedRecord, String>chunk(Integer.parseInt(chunk))
                .reader(reader()).processor(processor()).writer(writer()).build();
    }

    @Bean
    @StepScope
    public ItemStreamReader<AnnotatedRecord> reader() {
        return new MutationRecordReader();
    }

    @Bean
    public MutationRecordProcessor processor() {
        return new MutationRecordProcessor();
    }

    @Bean
    @StepScope
    public ItemStreamWriter<String> writer() {
        return new MutationRecordWriter();
    }
}