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

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Here is the source code for ubic.gemma.core.loader.entrez.pubmed.PubMedSearchTest.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.Test;
import ubic.gemma.model.common.description.BibliographicReference;

import java.io.IOException;
import java.util.Collection;
import java.util.HashSet;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;

/**
 * @author pavlidis
 */
public class PubMedSearchTest {

    private static final Log log = LogFactory.getLog(PubMedSearchTest.class.getName());

    /*
     * Test method for 'ubic.gemma.core.loader.entrez.pubmed.PubMedSearch.searchAndRetriveByHTTP(Collection<String>)'
     */
    @Test
    public void testSearchAndRetrieveByHTTP() throws Exception {
        try {
            PubMedSearch pms = new PubMedSearch();
            Collection<String> searchTerms = new HashSet<>();
            searchTerms.add("brain");
            searchTerms.add("hippocampus");
            searchTerms.add("habenula");
            searchTerms.add("glucose");
            Collection<BibliographicReference> actualResult = pms.searchAndRetrieveByHTTP(searchTerms);
            assertTrue("Expected at least 5 results, got " + actualResult.size(), actualResult.size() >= 5);
            /*
             * at least, this was the result on 4/2008.
             */
        } catch (java.net.UnknownHostException e) {
            PubMedSearchTest.log.warn("Test skipped due to unknown host exception");
        } catch (java.io.IOException e) {
            if (e.getMessage().contains("503") || e.getMessage().contains("502")) {
                PubMedSearchTest.log.warn("Test skipped due to a 50X error from NCBI");
                return;
            }
            throw e;
        }
    }

    /*
     * Test method for 'ubic.gemma.core.loader.entrez.pubmed.PubMedSearch.searchAndRetriveByHTTP(Collection<String>)'
     */
    @Test
    public void testSearchAndRetrieveByHTTPInChunks() throws Exception {
        try {
            PubMedSearch pms = new PubMedSearch();
            Collection<String> searchTerms = new HashSet<>();
            searchTerms.add("brain");
            searchTerms.add("hippocampus");
            searchTerms.add("habenula");
            Collection<BibliographicReference> actualResult = pms.searchAndRetrieveByHTTP(searchTerms);
            /*
             * at least, this was the result on 4/2008.
             */
            assertTrue("Expected at least 10, got " + actualResult.size(), actualResult.size() >= 10);
        } catch (java.net.UnknownHostException e) {
            PubMedSearchTest.log.warn("Test skipped due to unknown host exception");
        } catch (java.io.IOException e) {
            this.checkCause(e);
        }

    }

    @Test
    public void testSearchAndRetrieveIdByHTTPBookshelf() throws Exception {
        try {
            PubMedSearch pms = new PubMedSearch();
            Collection<String> searchTerms = new HashSet<>();
            searchTerms.add("23865096");
            Collection<BibliographicReference> actualResult = pms.searchAndRetrieveIdByHTTP(searchTerms);
            assertEquals(1, actualResult.size());
        } catch (java.net.UnknownHostException e) {
            PubMedSearchTest.log.warn("Test skipped due to unknown host exception");
        } catch (java.io.IOException e) {
            this.checkCause(e);
        }
    }

    @Test
    public void testSearchAndRetrievIdsByHTTP() throws Exception {
        try {
            PubMedSearch pms = new PubMedSearch();
            Collection<String> searchTerms = new HashSet<>();
            searchTerms.add("brain");
            searchTerms.add("hippocampus");
            searchTerms.add("habenula");
            searchTerms.add("glucose");
            Collection<String> actualResult = pms.searchAndRetrieveIdsByHTTP(searchTerms);
            assertTrue("Expect at least 5 results, got " + actualResult.size(), actualResult.size() >= 5);
            /*
             * at least, this was the result on 4/2008.
             */
        } catch (java.net.UnknownHostException e) {
            PubMedSearchTest.log.warn("Test skipped due to unknown host exception");
        } catch (java.io.IOException e) {
            this.checkCause(e);
        }
    }

    private void checkCause(java.io.IOException e) throws IOException {
        if (e.getMessage().contains("503") || e.getMessage().contains("502")) {
            PubMedSearchTest.log.warn("Test skipped due to a 50x from NCBI");
            return;
        }
        throw e;
    }
}