org.hupo.psi.mi.psicquic.ws.IndexBasedPsicquicRestServiceTest.java Source code

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Here is the source code for org.hupo.psi.mi.psicquic.ws.IndexBasedPsicquicRestServiceTest.java

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/**
 * Copyright 2009 The European Bioinformatics Institute, and others.
 *
 * 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.hupo.psi.mi.psicquic.ws;

import org.apache.commons.lang.StringUtils;
import org.apache.cxf.jaxrs.impl.ResponseImpl;
import org.hupo.psi.mi.psicquic.ws.config.PsicquicConfig;
import org.hupo.psi.mi.psicquic.ws.utils.PsicquicStreamingOutput;
import org.junit.AfterClass;
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
import org.springframework.context.support.ClassPathXmlApplicationContext;
import psidev.psi.mi.search.Searcher;

import javax.ws.rs.core.GenericEntity;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.util.zip.GZIPInputStream;

/**
 * @author Bruno Aranda (baranda@ebi.ac.uk)
 * @version $Id$
 */
public class IndexBasedPsicquicRestServiceTest {

    private static IndexBasedPsicquicRestService service;

    @BeforeClass
    public static void beforeClass() throws Exception {
        File indexDir = new File("target", "brca-mitab.index");

        Searcher.buildIndex(indexDir,
                IndexBasedPsicquicServiceTest.class.getResourceAsStream("/META-INF/brca2.mitab.txt"), true, true);
        Searcher.buildIndex(indexDir,
                IndexBasedPsicquicServiceTest.class.getResourceAsStream("/META-INF/400.mitab.txt"), false, true);

        ClassPathXmlApplicationContext context = new ClassPathXmlApplicationContext(
                new String[] { "/META-INF/beans.spring.test.xml" });
        PsicquicConfig config = (PsicquicConfig) context.getBean("psicquicConfig");
        config.setIndexDirectory(indexDir.toString());

        service = (IndexBasedPsicquicRestService) context.getBean("indexBasedPsicquicRestService");
    }

    @AfterClass
    public static void afterClass() throws Exception {
        service = null;
    }

    @Test
    public void testGetByQuery() throws Exception {
        ResponseImpl response = (ResponseImpl) service.getByQuery("FANCD1", "tab25", "0", "200", "n");

        System.out.println(response.getEntity());
        PsicquicStreamingOutput pso = ((GenericEntity<PsicquicStreamingOutput>) response.getEntity()).getEntity();

        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        pso.write(baos);

        Assert.assertEquals(12, baos.toString().split("\n").length);
    }

    @Test
    public void testGetByQuery_maxResults() throws Exception {
        ResponseImpl response = (ResponseImpl) service.getByQuery("FANCD1", "tab25", "0", "3", "n");

        PsicquicStreamingOutput pso = ((GenericEntity<PsicquicStreamingOutput>) response.getEntity()).getEntity();

        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        pso.write(baos);

        Assert.assertEquals(3, baos.toString().split("\n").length);
    }

    @Test
    public void testGetByQuery_maxResults_nolimit() throws Exception {
        ResponseImpl response = (ResponseImpl) service.getByQuery("FANCD1", "tab25", "0",
                String.valueOf(Integer.MAX_VALUE), "n");

        PsicquicStreamingOutput pso = ((GenericEntity<PsicquicStreamingOutput>) response.getEntity()).getEntity();

        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        pso.write(baos);

        Assert.assertEquals(12, baos.toString().split("\n").length);
    }

    @Test
    public void testGetByQuery_maxResults_above200() throws Exception {
        ResponseImpl response = (ResponseImpl) service.getByQuery("*", "tab25", "0", "305", "n");

        PsicquicStreamingOutput pso = ((GenericEntity<PsicquicStreamingOutput>) response.getEntity()).getEntity();

        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        pso.write(baos);

        Assert.assertEquals(305, baos.toString().split("\n").length);
    }

    @Test
    public void testGetByQuery_maxResults_above400() throws Exception {
        ResponseImpl response = (ResponseImpl) service.getByQuery("*", "tab25", "0", "405", "n");

        PsicquicStreamingOutput pso = ((GenericEntity<PsicquicStreamingOutput>) response.getEntity()).getEntity();

        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        pso.write(baos);

        Assert.assertEquals(405, baos.toString().split("\n").length);
    }

    @Test
    public void testGetByQuery_firstResult_above200() throws Exception {
        ResponseImpl response = (ResponseImpl) service.getByQuery("*", "tab25", "150", "255", "n");

        PsicquicStreamingOutput pso = ((GenericEntity<PsicquicStreamingOutput>) response.getEntity()).getEntity();

        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        pso.write(baos);

        Assert.assertEquals(255, baos.toString().split("\n").length);
    }

    @Test
    public void testGetByQuery_firstResult_above200_max() throws Exception {
        ResponseImpl response = (ResponseImpl) service.getByQuery("*", "tab25", "250", "500", "n");

        PsicquicStreamingOutput pso = ((GenericEntity<PsicquicStreamingOutput>) response.getEntity()).getEntity();

        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        pso.write(baos);

        Assert.assertEquals(163, baos.toString().split("\n").length);
    }

    @Test
    public void testGetByQuery_bin() throws Exception {
        ResponseImpl response = (ResponseImpl) service.getByQuery("FANCD1", "tab25-bin", "0",
                String.valueOf(Integer.MAX_VALUE), "n");

        PsicquicStreamingOutput pso = ((GenericEntity<PsicquicStreamingOutput>) response.getEntity()).getEntity();

        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        pso.write(baos);

        // gunzip the output
        ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray());
        GZIPInputStream gzipInputStream = new GZIPInputStream(bais);

        ByteArrayOutputStream mitabOut = new ByteArrayOutputStream();

        byte[] buf = new byte[1024];
        int len;
        while ((len = gzipInputStream.read(buf)) > 0)
            mitabOut.write(buf, 0, len);

        gzipInputStream.close();
        mitabOut.close();

        Assert.assertEquals(12, mitabOut.toString().split("\n").length);
    }

    @Test
    public void testGetByQuery_biopax() throws Exception {
        ResponseImpl response = (ResponseImpl) service.getByQuery("FANCD1", "biopax", "0", "5", "n");

        final String output = ((GenericEntity<String>) response.getEntity()).getEntity();
        Assert.assertEquals(5, StringUtils.countMatches(output, "<j.0:MolecularInteraction "));
    }
}