org.gbif.namefinder.analysis.sciname.SciNameAnalyzerTest.java Source code

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Here is the source code for org.gbif.namefinder.analysis.sciname.SciNameAnalyzerTest.java

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/***************************************************************************
 * Copyright 2010 Global Biodiversity Information Facility Secretariat
 *
 * 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.gbif.namefinder.analysis.sciname;

import org.gbif.utils.file.InputStreamUtils;

import java.io.IOException;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.util.LinkedList;

import org.apache.commons.lang3.StringUtils;
import org.apache.lucene.analysis.TokenStream;
import org.junit.Test;

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

/**
 */
public class SciNameAnalyzerTest {

    private static final InputStreamUtils isu = new InputStreamUtils();

    private TokenStream getTokens(Reader input) throws IOException {
        SciNameAnalyzer ana = new SciNameAnalyzer();
        TokenStream tokens = ana.tokenStream(null, input);
        tokens.reset();
        return tokens;
    }

    @Test
    public void testAbbreviatedNames() throws Exception {
        String text = "A survey of the Abies conifers found in Europe. A. is not a abbreviated genus. A. alba, A. betula, A.picea and Picea picea is something else.";
        Reader input = new StringReader(text);
        LinkedList<String> expected = new LinkedList<String>();
        expected.add("Abies");
        expected.add("Abies alba");
        expected.add("Abies betula");
        expected.add("Abies picea");
        expected.add("Picea picea");

        TokenStream tokens = getTokens(input);
        SciNameIterator iter = new SciNameIterator(tokens);
        for (SciName sn : iter) {
            //      System.out.println(sn);
            assertEquals(expected.poll(), sn.scientificName);
        }
        tokens.end();
        tokens.close();
    }

    /**
     * Test Biebersteiniaceae eFlora example html that proved to have problems with names found across html tags
     * Source: http://www.efloras.org/florataxon.aspx?flora_id=2&taxon_id=20048
     */
    @Test
    public void testBiebersteiniaceae() throws Exception {
        Reader input = new InputStreamReader(isu.classpathStream("sources/biebersteiniaceae/document.txt"),
                "UTF-8");
        TokenStream tokens = getTokens(input);
        SciNameIterator iter = new SciNameIterator(tokens);
        int count = 0;
        for (SciName sn : iter) {
            System.out.println(sn);
            count++;
        }
        System.out.println("Biebersteiniaceae names found: " + count);
        assertTrue(count == 14);
        tokens.end();
        tokens.close();
    }

    /**
     * Test bioline html file taken from http://www.bioline.org.br/abstract?id=fb95003
     */
    @Test
    public void testHtml() throws Exception {
        Reader input = new InputStreamReader(isu.classpathStream("sources/bioline/document.txt"), "UTF-8");
        // input = new InputStreamReader(new FileInputStream(new File("/Users/markus/Desktop/bioline-fb95003.html")), "UTF-8");
        TokenStream tokens = getTokens(input);
        SciNameIterator iter = new SciNameIterator(tokens);
        int count = 0;
        int countMugil = 0;
        for (SciName sn : iter) {
            System.out.println(sn);
            count++;
            if (sn.scientificName.startsWith("Mugil ")) {
                countMugil++;
            }
        }
        System.out.println("BIOLINE names found: " + count);
        assertTrue(count == 49);
        assertTrue(countMugil == 12);
        tokens.end();
        tokens.close();
    }

    @Test
    public void testSimpleText() throws Exception {
        System.out.println(StringUtils.isAllUpperCase("G"));
        System.out.println(StringUtils.isAllUpperCase("G"));
        String text = "Help, Asteraceae or is (Felinia) or Felis (Felinia) foordi found. I can't see any of these famous Abies alba anywhere around here, can you? Maybe this is Potentilla vulgaris L. ? You can't be sure, my dear. Paris is a pretty town too, isn't it? They have big numbers of Passer domesticus subsp. domesticus, the most frequent subspecies of Passer domesticus (Linnaeus, 1758)";
        Reader input = new StringReader(text);
        LinkedList<String> expected = new LinkedList<String>();
        expected.add("Asteraceae");
        expected.add("Felis (Felinia) foordi");
        expected.add("Abies alba");
        expected.add("Potentilla vulgaris");
        expected.add("Passer domesticus subsp. domesticus");
        expected.add("Passer domesticus");
        TokenStream tokens = getTokens(input);
        SciNameIterator iter = new SciNameIterator(tokens);
        for (SciName sn : iter) {
            //      System.out.println(sn);
            assertEquals(expected.poll(), sn.scientificName);
        }
        tokens.end();
        tokens.close();
    }
}