org.oncoblocks.centromere.core.test.DataImportTests.java Source code

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Here is the source code for org.oncoblocks.centromere.core.test.DataImportTests.java

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/*
 * Copyright 2016 William Oemler, Blueprint Medicines
 *
 * 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 org.oncoblocks.centromere.core.test;

import com.fasterxml.jackson.databind.ObjectMapper;
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.oncoblocks.centromere.core.dataimport.RepositoryRecordUpdater;
import org.oncoblocks.centromere.core.dataimport.RepositoryRecordWriter;
import org.oncoblocks.centromere.core.dataimport.BasicImportOptions;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.util.Assert;
import org.springframework.validation.BeanPropertyBindingResult;
import org.springframework.validation.ObjectError;
import org.springframework.validation.Validator;

import java.util.ArrayList;
import java.util.List;

import static org.junit.Assert.fail;

/**
 * @author woemler
 */

@RunWith(SpringJUnit4ClassRunner.class)
@ContextConfiguration(classes = { TestConfig.class })
public class DataImportTests {

    @Autowired
    private Validator validator;
    private final String geneInfoPath = ClassLoader.getSystemClassLoader().getResource("Homo_sapiens.gene_info")
            .getPath();
    private final String importJobJsonFilePath = ClassLoader.getSystemClassLoader()
            .getResource("example_import.json").getPath();
    @Autowired
    private GeneInfoProcessor processor;
    @Autowired
    private TestRepository testRepository;
    @Autowired
    private ApplicationContext applicationContext;
    @Autowired
    private BasicImportOptions defaultImportOptions;
    private static final ObjectMapper mapper = new ObjectMapper();

    @Before
    public void setup() throws Exception {
        testRepository.deleteAll();
        testRepository.insert(EntrezGene.createDummyData());
    }

    @Test
    public void geneInfoReaderTest() throws Exception {
        GeneInfoReader reader = new GeneInfoReader();
        List<EntrezGene> genes = new ArrayList<>();
        try {
            reader.open(geneInfoPath);
            EntrezGene gene = reader.readRecord();
            while (gene != null) {
                genes.add(gene);
                gene = reader.readRecord();
            }
        } finally {
            reader.close();
        }
        Assert.notEmpty(genes);
        Assert.isTrue(genes.size() == 5);
        Assert.isTrue(genes.get(4).getEntrezGeneId().equals(10L));
    }

    @Test
    public void validationTest() throws Exception {
        EntrezGene gene = new EntrezGene();
        BeanPropertyBindingResult bindingResult = new BeanPropertyBindingResult(gene, gene.getClass().getName());
        validator.validate(gene, bindingResult);
        if (bindingResult.hasErrors()) {
            for (ObjectError error : bindingResult.getAllErrors()) {
                System.out.println(error.toString());
            }
        } else {
            fail("Validation did not catch missing field.");
        }
    }

    @Test
    public void recordWriterTest() throws Exception {
        testRepository.deleteAll();
        Assert.isTrue(testRepository.count() == 0);
        RepositoryRecordWriter<EntrezGene> writer = new RepositoryRecordWriter<>(testRepository);
        for (EntrezGene gene : EntrezGene.createDummyData()) {
            writer.writeRecord(gene);
        }
        Assert.isTrue(testRepository.count() == 5);
    }

    @Test
    public void recordUpdaterTest() throws Exception {
        RepositoryRecordUpdater<EntrezGene, Long> updater = new RepositoryRecordUpdater<>(testRepository);
        EntrezGene gene = testRepository.findOne(1L);
        Assert.isTrue("GeneA".equals(gene.getPrimaryGeneSymbol()));
        gene.setPrimaryGeneSymbol("GeneX");
        updater.writeRecord(gene);
        gene = testRepository.findOne(1L);
        Assert.isTrue("GeneX".equals(gene.getPrimaryGeneSymbol()));
    }

    @Test
    public void recordProcessorTest() throws Exception {
        testRepository.deleteAll();
        System.out.println(String.format("There are %d records in the test repository.", testRepository.count()));
        Assert.isTrue(testRepository.count() == 0);
        processor.setImportOptions(defaultImportOptions);
        processor.run(geneInfoPath);
        Assert.isTrue(testRepository.count() == 5);
        EntrezGene gene = testRepository.findOne(1L);
        Assert.notNull(gene);
        Assert.isTrue(gene.getId() == 1L);
        System.out.println(String.format("There are %d records in the test repository.", testRepository.count()));
        System.out.println(gene.toString());
    }

}