SDFileReaderTest.java

/*
 * MX Cheminformatics Tools for Java
 * 
 * Copyright (c) 2007, 2008 Metamolecular, LLC
 * 
 * http://metamolecular.com
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package com.chemhack.jsMolEditor.client.test;

import com.chemhack.jsMolEditor.client.io.mdl.SDFileReader;
import com.chemhack.jsMolEditor.client.model.Molecule;
import com.google.gwt.junit.client.GWTTestCase;

import java.util.Arrays;
import java.util.List;


/**
 * @author Richard L. Apodaca <rapodaca at metamolecular.com>
 */
public class SDFileReaderTest extends GWTTestCase {
    private SDFileReader reader;
    private String[] keys =
            {
                    "PUBCHEM_COMPOUND_CID", "PUBCHEM_COMPOUND_CANONICALIZED", "PUBCHEM_CACTVS_COMPLEXITY", "PUBCHEM_CACTVS_HBOND_ACCEPTOR", "PUBCHEM_CACTVS_HBOND_DONOR", "PUBCHEM_CACTVS_ROTATABLE_BOND", "PUBCHEM_CACTVS_SUBSKEYS", "PUBCHEM_IUPAC_OPENEYE_NAME", "PUBCHEM_IUPAC_CAS_NAME", "PUBCHEM_IUPAC_NAME", "PUBCHEM_IUPAC_SYSTEMATIC_NAME", "PUBCHEM_IUPAC_TRADITIONAL_NAME", "PUBCHEM_NIST_INCHI", "PUBCHEM_EXACT_MASS", "PUBCHEM_MOLECULAR_FORMULA", "PUBCHEM_MOLECULAR_WEIGHT", "PUBCHEM_OPENEYE_CAN_SMILES", "PUBCHEM_OPENEYE_ISO_SMILES", "PUBCHEM_CACTVS_TPSA", "PUBCHEM_MONOISOTOPIC_WEIGHT", "PUBCHEM_TOTAL_CHARGE", "PUBCHEM_HEAVY_ATOM_COUNT", "PUBCHEM_ATOM_DEF_STEREO_COUNT", "PUBCHEM_ATOM_UDEF_STEREO_COUNT", "PUBCHEM_BOND_DEF_STEREO_COUNT", "PUBCHEM_BOND_UDEF_STEREO_COUNT", "PUBCHEM_ISOTOPIC_ATOM_COUNT", "PUBCHEM_COMPONENT_COUNT", "PUBCHEM_CACTVS_TAUTO_COUNT", "PUBCHEM_BONDANNOTATIONS"
            };

    public String getModuleName() {
        return "com.chemhack.jsMolEditor.Editor";
    }


    @Override
    protected void gwtSetUp() throws Exception {
        String fileContent="";
        reader = new SDFileReader("../resources/pubchem_sample_33.sdf");
    }

    @Override
    protected void gwtTearDown() throws Exception {
        reader.close();
    }

    public void testItShouldIterateOverEveryRecord() {
        int count = 0;

        while (reader.hasNextRecord()) {
            reader.nextRecord();

            count++;
        }

        assertEquals(33, count);
    }

    public void testItShoudReadAllKeysInTheFirstRecord() {
        reader.nextRecord();

        for (String key : keys) {
            assertFalse("".equals(reader.getData(key)));
        }
    }

    public void testItShouldFetchAllKeysForTheFirstRecord() {
        reader.nextRecord();

        List<String> fields = reader.getKeys();

        assertEquals(Arrays.asList(keys), fields);
    }

    public void testItShouldReturnAnEmptyStringWhenKeyNotFound() {
        reader.nextRecord();

        assertEquals("", reader.getData("PUBCHEM_FOO_BAR"));
    }

    public void testItShouldThrowIllegalStateExceptionIfGetDataCalledBeforeNextRecord() {
        try {
            reader.getData("PUBCHEM_FOO_BAR");

            fail();
        }
        catch (IllegalStateException e) {
            assertTrue(true);
        }
    }

    public void testItShouldThrowIllegalStateExceptionIfGetMoleculeCalledBeforeNextRecord() {
        try {
            reader.getMolecule();

            fail();
        }
        catch (IllegalStateException e) {
            assertTrue(true);
        }
    }

//    It makes no sence as SDFileReader load file content directly
//    
//    public void testItShouldThrowIOExceptionWhenCreatedFromANonexistentFile() {
//        try {
//            new SDFileReader("bar.sdf");
//
//            fail();
//        }
//        catch (IOException ignore) {
//            assertTrue(true);
//        }
//    }

    public void testItShouldLoadAMoleculeForEveryRecord() {
        while (reader.hasNextRecord()) {
            reader.nextRecord();

            Molecule molecule = reader.getMolecule();

            assertFalse(molecule.countAtoms() == 0);
        }
    }

    public void testItShouldLoadAVirtualizedHydrogenMoleculeForEveryRecord() {
        while (reader.hasNextRecord()) {
            reader.nextRecord();

            Molecule molecule = reader.getMolecule(true);

            assertFalse(molecule.countAtoms() == 0);
        }
    }
}