org.oncoblocks.centromere.mongodb.test.MongoImportTests.java Source code

Introduction

Here is the source code for org.oncoblocks.centromere.mongodb.test.MongoImportTests.java

Source

/*
 * 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.mongodb.test;

import com.mongodb.Mongo;
import org.junit.Before;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TemporaryFolder;
import org.junit.runner.RunWith;
import org.oncoblocks.centromere.core.dataimport.RepositoryRecordWriter;
import org.oncoblocks.centromere.mongodb.MongoCredentials;
import org.oncoblocks.centromere.mongodb.MongoImportTempFileImporter;
import org.oncoblocks.centromere.mongodb.MongoImportTempFileWriter;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.data.mongodb.core.MongoTemplate;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.util.Assert;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.util.ArrayList;
import java.util.List;

/**
 * @author woemler
 */

@RunWith(SpringJUnit4ClassRunner.class)
@ContextConfiguration(classes = { TestMongoConfig.class })
public class MongoImportTests {

    @Autowired
    private EntrezGeneRepository repository;
    @Autowired
    private MongoTemplate mongoTemplate;
    @Autowired
    private Mongo mongo;
    @Autowired
    private Environment env;
    @Rule
    public TemporaryFolder temporaryFolder = new TemporaryFolder();
    private final String geneInfoPath = ClassLoader.getSystemClassLoader().getResource("Homo_sapiens.gene_info")
            .getPath();
    private File tempFile;
    private List<EntrezGene> genes;

    @Before
    public void setup() throws Exception {
        tempFile = temporaryFolder.newFile();
        genes = new ArrayList<>();
        GeneInfoReader geneInfoReader = new GeneInfoReader();
        try {
            geneInfoReader.open(geneInfoPath);
            EntrezGene gene = geneInfoReader.readRecord();
            while (gene != null) {
                genes.add(gene);
                gene = geneInfoReader.readRecord();
            }
        } catch (Exception e) {
            e.printStackTrace();
        } finally {
            geneInfoReader.close();
        }
    }

    @Test
    public void repositoryWriterTest() throws Exception {
        repository.deleteAll();
        RepositoryRecordWriter<EntrezGene> writer = new RepositoryRecordWriter<>(repository);
        for (EntrezGene gene : genes) {
            writer.writeRecord(gene);
        }
        List<EntrezGene> geneList = repository.findAll();
        Assert.notNull(geneList);
        Assert.notEmpty(geneList);
        Assert.isTrue(geneList.size() == 5);
    }

    @Test
    public void tempWriterTest() throws Exception {
        MongoImportTempFileWriter<EntrezGene> geneWriter = new MongoImportTempFileWriter<>(mongoTemplate);
        try {
            geneWriter.open(tempFile.getAbsolutePath());
            for (EntrezGene gene : genes) {
                geneWriter.writeRecord(gene);
            }
        } catch (Exception e) {
            e.printStackTrace();
        } finally {
            if (geneWriter != null)
                geneWriter.close();
        }
        Assert.isTrue(tempFile.canRead());
        boolean flag = false;
        BufferedReader reader = null;
        try {
            reader = new BufferedReader(new FileReader(tempFile));
            String line = reader.readLine();
            while (line != null) {
                Assert.notNull(line);
                System.out.println(line);
                line = reader.readLine();
            }
            flag = true;
        } finally {
            if (reader != null)
                reader.close();
        }
        Assert.isTrue(flag);
    }

    @Test
    public void mongoImportTest() throws Exception {
        this.tempWriterTest();
        repository.deleteAll();
        StringBuilder stringBuilder = new StringBuilder();
        BufferedReader bufferedReader = null;
        try {
            bufferedReader = new BufferedReader(new FileReader(tempFile));
            String line = bufferedReader.readLine();
            while (line != null) {
                stringBuilder.append(line);
                line = bufferedReader.readLine();
            }
        } catch (Exception e) {
            e.printStackTrace();
        } finally {
            if (bufferedReader != null) {
                bufferedReader.close();
            }
        }
        String content = stringBuilder.toString();
        Assert.notNull(content);
        System.out.print(content);

        MongoCredentials credentials = new MongoCredentials();
        credentials.setDatabase(env.getRequiredProperty("mongo.name"));
        credentials.setHost(mongo.getAddress().getHost());
        credentials.setPort(String.valueOf(mongo.getAddress().getPort()));
        MongoImportTempFileImporter importer = new MongoImportTempFileImporter(credentials, "genes");
        importer.importFile(tempFile.getAbsolutePath());
        List<EntrezGene> genes = repository.findAll();
        Assert.notNull(genes);
        Assert.notEmpty(genes);
    }

}