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/***********************************************************************************************************************
*
* blueBill Mobile - open source birdwatching
* ==========================================
*
* Copyright (C) 2009, 2010 by Tidalwave s.a.s. (http://www.tidalwave.it)
* http://bluebill.tidalwave.it/mobile/
*
***********************************************************************************************************************
*
* 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.
*
***********************************************************************************************************************
*
* $Id: Clements2008Importer.java,v d3b28eab0cdd 2010/08/01 20:17:04 fabrizio $
*
**********************************************************************************************************************/
package it.tidalwave.bluebill.taxonomy.birds.clements;
import it.tidalwave.util.logging.Logger;
import javax.annotation.Nonnull;
import java.util.Locale;
import java.util.Scanner;
import java.util.regex.MatchResult;
import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.InputStreamReader;
import org.openrdf.elmo.Entity;
import org.openrdf.repository.Repository;
import it.tidalwave.bluebill.taxonomy.Taxonomy;
import it.tidalwave.bluebill.taxonomy.TaxonomyConcept;
import it.tidalwave.bluebill.taxonomy.birds.BirdTaxonomyImporter;
import it.tidalwave.bluebill.taxonomy.birds.DisplayNameInitializer;
import it.tidalwave.openrdf.elmo.RDFUtils;
import it.tidalwave.util.EmptyInitializer;
import java.io.InputStream;
import java.util.zip.GZIPInputStream;
import static it.tidalwave.bluebill.taxonomy.elmo.ElmoTaxonomyVocabulary.*;
/***********************************************************************************************************************
*
* @author Fabrizio Giudici
* @version $Id: Clements2008Importer.java,v d3b28eab0cdd 2010/08/01 20:17:04 fabrizio $
*
**********************************************************************************************************************/
public class Clements2008Importer extends BirdTaxonomyImporter
{
private static final String CLASS = Clements2008Importer.class.getName();
private static final Logger logger = Logger.getLogger(CLASS);
/*******************************************************************************************************************
*
*
******************************************************************************************************************/
@Nonnull
public Taxonomy run (@Nonnull final Repository repository,
@Nonnull final String taxonomyName)
throws Exception
{
itisCodeMap.initialize();
init(repository);
final String root = ID_TAXONOMY_PREFIX + "Clements/2008";
final Taxonomy taxonomy = taxonomyManager.createTaxonomy("Clements 2008", root, repository);
final String avesId = ID_TAXONOMY_PREFIX + "Clements/2008" + "/Animalia/Chordata/Aves";
final TaxonomyConcept aves = taxonomy.createTopConcept("Aves", avesId);
setType(aves, classType);
final InputStream is = new GZIPInputStream(getClass().getResourceAsStream(sourceResourceName));
final BufferedReader br = new BufferedReader(new InputStreamReader(is, "UTF-8"));
br.readLine();
br.readLine();
br.readLine();
String previousEnglishName = "";
for (;;)
{
final String s = br.readLine();
if (s == null)
{
break;
}
// System.err.println(s);
final Scanner scanner = new Scanner(s).useDelimiter("\\$");
final int sort = scanner.nextInt();
scanner.next(); // page
final String categoryName = scanner.next();
final String scientificName = scanner.next();
String englishName = scanner.next();
if ("".equals(englishName))
{
englishName = previousEnglishName;
}
if (!categoryName.equals("species") && !categoryName.equals("subspecies") && !categoryName.equals("group"))
{
continue;
}
final String range = scanner.next(); // range
final String orderName = scanner.next();
String familyNameWithEnglishName = scanner.next();
if (familyNameWithEnglishName.equals("Tyranni Incertae Sedis"))
{
familyNameWithEnglishName += " (" + familyNameWithEnglishName + ")";
}
final Scanner scanner2 = new Scanner(scientificName).useDelimiter(" ");
final String genusName = scanner2.next();
final String speciesName = scanner2.next();
final String subSpeciesName = scanner2.hasNext() ? scanner2.next() : null;
final Scanner scanner3 = new Scanner(familyNameWithEnglishName);
scanner3.findInLine("(\\w*) \\((\\w*)"); // e.g. "Struthionidae (Ostrich)"
MatchResult result = null;
try
{
result = scanner3.match();
}
catch (IllegalStateException e)
{
throw new RuntimeException(familyNameWithEnglishName, e);
}
final String familyName = result.group(1);
final String familyEnglishName = result.group(2);
logger.info("%d %s %s %s %s %s %s %s", sort, categoryName, englishName, orderName, familyName, genusName, speciesName, subSpeciesName);
//
// FIXME: some names contains / and note between [...] - I don't know how to handle them
//
if ((subSpeciesName != null) && (subSpeciesName.contains("/") || subSpeciesName.contains("[")))
{
brokenSpecies.add(scientificName + " / " + englishName);
continue;
}
previousEnglishName = englishName;
String path = "/Animalia/Chordata/Aves";
path += "/" + orderName;
final TaxonomyConcept order = findOrCreateSubConcept(aves, orderName, root, path, orderType, EmptyInitializer.instance());
path += "/" + familyName;
final TaxonomyConcept family = findOrCreateSubConcept(order, familyName, root, path, familyType, EmptyInitializer.instance());
// FIXME: errato, set the name only if it is created now
RDFUtils.setDisplayName(family.as(Entity.class), familyEnglishName, Locale.ENGLISH);
path += "/" + genusName;
final TaxonomyConcept genus = findOrCreateSubConcept(family, genusName, root, path, genusType, EmptyInitializer.instance());
path += "/" + speciesName;
final TaxonomyConcept species = findOrCreateSubConcept(genus, speciesName, root, path, speciesType, new DisplayNameInitializer(englishName));
if (subSpeciesName != null)
{
path += "/" + subSpeciesName;
try
{
findOrCreateSubConcept(species, subSpeciesName, root, path, subSpeciesType, new DisplayNameInitializer(englishName));
}
catch (RuntimeException e)
{
brokenSpecies.add(path + ": " + e);
throw e;
}
}
}
br.close();
taxonUniqueIdManager.close();
return taxonomy;
}
}
