ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcherTest.java Source code

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Here is the source code for ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcherTest.java

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/*
 * The Gemma project
 *
 * Copyright (c) 2006 University of British Columbia
 *
 * 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 ubic.gemma.core.loader.entrez.pubmed;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import ubic.gemma.model.common.description.BibliographicReference;

import java.io.IOException;
import java.text.SimpleDateFormat;

import static org.junit.Assert.*;

/**
 * @author pavlidis
 */
public class PubMedXMLFetcherTest {
    private static final Log log = LogFactory.getLog(PubMedXMLFetcherTest.class.getName());
    private PubMedXMLFetcher pmf;

    @Test
    public final void testRetrieveByHTTP() {
        try {
            BibliographicReference br = pmf.retrieveByHTTP(15173114);

            assertNotNull(br);

            assertEquals("Lee, Homin K; Hsu, Amy K; Sajdak, Jon; Qin, Jie; Pavlidis, Paul", br.getAuthorList());
            assertEquals("Genome Res", br.getPublication());
            assertEquals("Coexpression analysis of human genes across many microarray data sets.", br.getTitle());

            SimpleDateFormat f = new SimpleDateFormat("mm/HH/MM/dd/yyyy");
            assertEquals("00/00/06/01/2004", f.format(br.getPublicationDate()));
        } catch (RuntimeException e) {
            this.checkCause(e);
        }
    }

    @Test
    public final void testRetrieveByHTTP2() {
        try {
            BibliographicReference br = pmf.retrieveByHTTP(24850731);

            assertNotNull(br);

            assertEquals(
                    "Iwata-Yoshikawa, Naoko; Uda, Akihiko; Suzuki, Tadaki; Tsunetsugu-Yokota, Yasuko; Sato, Yuko; "
                            + "Morikawa, Shigeru; Tashiro, Masato; Sata, Tetsutaro; Hasegawa, Hideki; Nagata, Noriyo",
                    br.getAuthorList());
            assertEquals("J Virol", br.getPublication());

        } catch (RuntimeException e) {
            this.checkCause(e);
        }
    }

    /*
     * 23865096 is a NCBI bookshelf article, not a paper
     */
    @Test
    public final void testRetrieveByHTTPBookshelf() {
        try {
            BibliographicReference br = pmf.retrieveByHTTP(23865096);

            assertNotNull(br);

            assertEquals("Tatton-Brown, Katrina; Rahman, Nazneen", br.getAuthorList());

            assertEquals("GeneReviews", br.getPublication().substring(0, "GeneReviews".length()));
            assertEquals("EZH2-Related Overgrowth", br.getTitle());

            SimpleDateFormat f = new SimpleDateFormat("yyyy");
            assertEquals("2013", f.format(br.getPublicationDate()));
        } catch (RuntimeException e) {
            this.checkCause(e);
        }
    }

    @Test
    public final void testRetrieveByHTTPNotFound() {
        try {
            BibliographicReference br = pmf.retrieveByHTTP(1517311444);
            assertNull(br);
        } catch (RuntimeException e) {
            this.checkCause(e);
        }
    }

    @Before
    public void setUp() {
        pmf = new PubMedXMLFetcher();
    }

    @After
    public void tearDown() {
        pmf = null;
    }

    private void checkCause(RuntimeException e) {
        if (e.getCause() instanceof java.net.ConnectException) {
            PubMedXMLFetcherTest.log.warn("Test skipped due to connection exception");
        } else if (e.getCause() instanceof java.net.UnknownHostException) {
            PubMedXMLFetcherTest.log.warn("Test skipped due to unknown host exception");
        } else if (e.getCause() instanceof IOException && e.getMessage().contains("503")) {
            PubMedXMLFetcherTest.log.warn("Test skipped due to a 503 error from NCBI");
        } else if (e.getCause() instanceof IOException && e.getMessage().contains("502")) {
            PubMedXMLFetcherTest.log.warn("Test skipped due to a 502 error from NCBI");
        } else {
            throw (e);
        }
    }
}