/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created at 08 Aug 2017
 */

package org.biojava.nbio.ontology;

import junit.framework.TestCase;
import org.biojava.nbio.ontology.io.OboParser;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.Set;

import static org.biojava.nbio.ontology.obo.OboFileHandler.NAMESPACE;

public class TestParseOBO extends TestCase {

	private static final Logger logger = LoggerFactory.getLogger(TestParseOBO.class);

	public void testNamespace(){

		String testTermEntry = "\n[Term]\n" +
                "id: SO:0000691\n" +
                "name: cleaved_initiator_methionine \n" +
                "namespace: sequence\n" +
                "alt_id: BS:00067\n" +
                "def: \"The initiator methionine that has been cleaved from a mature polypeptide sequence.\" [EBIBS:GAR]\n" +
                "subset: biosapiens\n" +
                "synonym: \"cleaved initiator methionine\" EXACT []\n" +
                "synonym: \"init_met\" RELATED [uniprot:feature_type]\n" +
                "synonym: \"initiator methionine\" RELATED []\n" +
                "is_a: SO:0100011 ! cleaved_peptide_region\n\n";

        OboParser parser = new OboParser();

		try {


            InputStream inStream = new ByteArrayInputStream(testTermEntry.getBytes());

			assertNotNull(inStream);

			BufferedReader oboFile = new BufferedReader ( new InputStreamReader ( inStream ) );

			Ontology ontology;

			ontology = parser.parseOBO(oboFile, "so-xp/subsets/biosapiens",
                    "snippet from biosapiens protein feature ontology");
			Set<Term> keys = ontology.getTerms();

			assertTrue(keys.size() > 1);
			assertTrue(ontology.getTerm("SO:0000691").getAnnotation().containsProperty(NAMESPACE));
            assertEquals("sequence",ontology.getTerm("SO:0000691").getAnnotation().getProperty(NAMESPACE));

		} catch (Exception e) {
			// TODO Auto-generated catch block
			logger.error("Exception: ", e);
			fail(e.getMessage());
		}
	}
}

/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created at 08 Aug 2017
 */

package org.biojava.nbio.ontology;

import junit.framework.TestCase;
import org.biojava.nbio.ontology.io.OboParser;

import java.io.*;
import java.text.ParseException;
import java.util.Set;

import static org.biojava.nbio.ontology.obo.OboFileHandler.NAMESPACE;

public class TestParseOBO extends TestCase {

	public void testNamespace() throws IOException, ParseException {

		String testTermEntry = "\n[Term]\n" +
                "id: SO:0000691\n" +
                "name: cleaved_initiator_methionine \n" +
                "namespace: sequence\n" +
                "alt_id: BS:00067\n" +
                "def: \"The initiator methionine that has been cleaved from a mature polypeptide sequence.\" [EBIBS:GAR]\n" +
                "subset: biosapiens\n" +
                "synonym: \"cleaved initiator methionine\" EXACT []\n" +
                "synonym: \"init_met\" RELATED [uniprot:feature_type]\n" +
                "synonym: \"initiator methionine\" RELATED []\n" +
                "is_a: SO:0100011 ! cleaved_peptide_region\n\n";

        OboParser parser = new OboParser();
        InputStream inStream = new ByteArrayInputStream(testTermEntry.getBytes());

		assertNotNull(inStream);

		BufferedReader oboFile = new BufferedReader ( new InputStreamReader ( inStream ) );
		Ontology ontology = parser.parseOBO(oboFile, "so-xp/subsets/biosapiens",
                    "snippet from biosapiens protein feature ontology");
		Set<Term> keys = ontology.getTerms();

		assertTrue(keys.size() > 1);
		assertTrue(ontology.getTerm("SO:0000691").getAnnotation().containsProperty(NAMESPACE));
        assertEquals("sequence",ontology.getTerm("SO:0000691").getAnnotation().getProperty(NAMESPACE));
	}
}

throw exception instead of fail