SiLeBAT/FSK-Lab

File `ParametricModelTest.java` has 373 lines of code (exceeds 250 allowed). Consider refactoring.
/*******************************************************************************
 * Copyright (c) 2015 Federal Institute for Risk Assessment (BfR), Germany
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 *
 * Contributors:
 *     Department Biological Safety - BfR
 *******************************************************************************/
package de.bund.bfr.knime.pmm.common;
 
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
 
import org.jdom2.DataConversionException;
import org.jdom2.Element;
import org.junit.Test;
 
`ParametricModelTest` has 23 methods (exceeds 20 allowed). Consider refactoring.
@SuppressWarnings("static-method")
public class ParametricModelTest {
 
    @Test
    public void testEmptyConstructor() {
        final ParametricModel model = new ParametricModel();
 
        assertTrue(Double.isNaN(model.getRss()));
        assertTrue(Double.isNaN(model.getRsquared()));
        assertTrue(Double.isNaN(model.getRms()));
        assertTrue(Double.isNaN(model.getAic()));
        assertTrue(Double.isNaN(model.getBic()));
        assertNull(model.fittedModelName);
        assertNull(model.isChecked);
        assertNull(model.qualityScore);
        assertNull(model.comment);
        assertTrue(model.modelId < 0);
        assertTrue(model.estModelId < 0);
        assertTrue(model.globalModelId < 0);
        assertEquals(0, model.getEstModelLit().size());
        assertEquals(0, model.getModelLit().size());
        assertEquals(0, model.getIndependent().size());
        assertEquals(0, model.getParameter().size());
    }
 
    /**
     * Test constructor with modelName, formula, depXml, level, modelId and
     * estModelId.
     */
Method `testConstructor2` has 26 lines of code (exceeds 25 allowed). Consider refactoring.
    @Test
    public void testConstructor2() {
 
        final DepXml dep = new DepXml("dep");
 
        final ParametricModel model = new ParametricModel("modelName", "formula", dep, 0, 1, 2);
 
        assertEquals("modelName", model.modelName);
        assertEquals("formula", model.getFormula());
        assertEquals("dep", model.getDepXml().name);
        assertEquals(0, model.getLevel());
        assertEquals(1, model.modelId);
        assertEquals(2, model.estModelId);
 
        assertNull(model.modelDbUuid);
        assertNull(model.estimatedModelDbUuid);
        assertNull(model.modelClass);
        assertEquals(0, model.condId);
        assertTrue(model.warning.isEmpty());
        assertTrue(Double.isNaN(model.getRss()));
        assertTrue(Double.isNaN(model.getRsquared()));
        assertTrue(Double.isNaN(model.getRms()));
        assertTrue(Double.isNaN(model.getAic()));
        assertTrue(Double.isNaN(model.getBic()));
        assertNull(model.isChecked);
        assertNull(model.qualityScore);
        assertNull(model.comment);
        assertTrue(model.globalModelId < 0);
        assertEquals(0, model.getEstModelLit().size());
        assertEquals(0, model.getModelLit().size());
        assertEquals(0, model.getIndependent().size());
        assertEquals(0, model.getParameter().size());
    }
 
Similar blocks of code found in 3 locations. Consider refactoring.
    @Test
    public void testAic() {
        final ParametricModel model = new ParametricModel();
 
        // Empty constructor assigns Double#NAN to aic
        assertTrue(Double.isNaN(model.getAic()));
        assertFalse(model.hasAic());
 
        // Change AIC
        model.setAic(0.5);
        assertEquals(0.5, model.getAic(), .0);
        assertTrue(model.hasAic());
 
        // Unset AIC
        model.setAic(null);
        assertTrue(Double.isNaN(model.getAic()));
        assertFalse(model.hasAic());
    }
 
Similar blocks of code found in 3 locations. Consider refactoring.
    @Test
    public void testBic() {
        final ParametricModel model = new ParametricModel();
 
        // Empty constructor assigns Double#NAN to aic
        assertTrue(Double.isNaN(model.getBic()));
        assertFalse(model.hasBic());
 
        // Change Bic
        model.setBic(0.5);
        assertEquals(0.5, model.getBic(), .0);
        assertTrue(model.hasBic());
 
        // Unset Bic
        model.setBic(null);
        assertTrue(Double.isNaN(model.getBic()));
        assertFalse(model.hasBic());
    }
 
Similar blocks of code found in 3 locations. Consider refactoring.
    @Test
    public void testRMS() {
        final ParametricModel model = new ParametricModel();
 
        // Empty constructor assigns Double#NAN to aic
        assertTrue(Double.isNaN(model.getRms()));
        assertFalse(model.hasRms());
 
        // Change Rms
        model.setRms(0.5);
        assertEquals(0.5, model.getRms(), .0);
        assertTrue(model.hasRms());
 
        // Unset Rms
        model.setRms(null);
        assertTrue(Double.isNaN(model.getRms()));
        assertFalse(model.hasRms());
    }
 
    @Test(expected = PmmException.class)
    public void testSetRmsInfinite() {
        final ParametricModel model = new ParametricModel();
        model.setRms(Double.POSITIVE_INFINITY);
    }
 
    @Test(expected = PmmException.class)
    public void testSetRmsNegative() {
        final ParametricModel model = new ParametricModel();
        model.setRms(-1.0);
    }
 
    @Test
    public void testRss() {
        final ParametricModel model = new ParametricModel();
 
        // Empty constructor assigns Double.NAN to rss
        assertTrue(Double.isNaN(model.getRss()));
 
        // Check change
        model.setRss(0.5);
        assertEquals(0.5, model.getRss(), .0);
    }
 
    @Test
    public void testRssNull() {
        final ParametricModel model = new ParametricModel();
        model.setRss(null);
        assertTrue(Double.isNaN(model.getRss()));
    }
 
    @Test(expected = PmmException.class)
    public void testRssInfinite() {
        final ParametricModel model = new ParametricModel();
        model.setRss(Double.POSITIVE_INFINITY);
    }
 
    @Test(expected = PmmException.class)
    public void testRssNegative() {
        final ParametricModel model = new ParametricModel();
        model.setRss(-1.0);
    }
 
    @Test
    public void testRSquared() {
        final ParametricModel model = new ParametricModel();
 
        // Empty constructor assigns Double.NaN
        assertTrue(Double.isNaN(model.getRsquared()));
 
        // Check change
        model.setRsquared(0.7);
        assertEquals(0.7, model.getRsquared(), .0);
 
        // Null is replaced with Double.NaN
        model.setRsquared(null);
        assertTrue(Double.isNaN(model.getRsquared()));
    }
 
    @Test(expected = PmmException.class)
    public void testSetRsquaredException() {
        final ParametricModel model = new ParametricModel();
        model.setRsquared(2.0);
    }
 
    @Test
    public void testDependent() {
        final ParametricModel model = new ParametricModel();
 
        // Empty constructor assigns null
        assertNull(model.getDepXml());
 
        // When the dep is not set the getters return null
        assertNull(model.getDepVar());
        assertNull(model.getDepDescription());
        assertNull(model.getDepCategory());
        assertNull(model.getDepUnit());
 
        // Setters ignore null
        model.setDepVar(null);
        assertNull(model.getDepVar());
 
        model.setDepDescription(null);
        assertNull(model.getDepDescription());
 
        model.setDepCategory(null);
        assertNull(model.getDepCategory());
 
        model.setDepUnit(null);
        assertNull(model.getDepUnit());
 
        model.setDepXml(new DepXml("lalala"));
        assertEquals("lalala", model.getDepXml().name);
 
        model.setDepVar("Atreus");
        assertEquals("Atreus", model.getDepVar());
 
        model.setDepDescription("Boy");
        assertEquals("Boy", model.getDepDescription());
 
        model.setDepCategory("Nordic god");
        assertEquals("Nordic god", model.getDepCategory());
 
        model.setDepUnit("Half Kratos");
        assertEquals("Half Kratos", model.getDepUnit());
    }
 
    @Test
    public void testIndependent() {
        final ParametricModel model = new ParametricModel();
 
        // Empty constructor assigns empty PmmXmlDoc
        assertEquals(0, model.getIndependent().size());
 
        // Check setIndependent
        model.setIndependent(null);
        assertNull(model.getIndependent());
    }
 
Method `testIndependentSetters` has 26 lines of code (exceeds 25 allowed). Consider refactoring.
    @Test
    public void testIndependentSetters() {
        final ParametricModel model = new ParametricModel();
        model.addIndepVar("indep");
 
        // Add a non-independent object. Getters/setters must ignore it.
        model.getIndependent().add(new MatrixXml());
 
        // When the parameter does not exist the setters do nothing.
Define a constant instead of duplicating this literal "aloha" 27 times.
Define a constant instead of duplicating this literal "description" 6 times.
        model.setIndepDescription("aloha", "description");
        model.setIndepMin("aloha", 0.0);
        model.setIndepMax("aloha", 1.0);
        model.setIndepUnit("aloha", "unit");
Define a constant instead of duplicating this literal "category" 6 times.
        model.setIndepCategory("aloha", "category");
 
        // and the getters return null
        assertNull(model.getIndepDescription("aloha"));
        assertNull(model.getIndepMin("aloha"));
        assertNull(model.getIndepMax("aloha"));
        assertNull(model.getIndepUnit("aloha"));
        assertNull(model.getIndepCategory("aloha"));
 
        // Check with existing parameter
        model.addIndepVar("odin");
 
        model.setIndepDescription("odin", "description");
        assertEquals("description", model.getIndepDescription("odin"));
 
        model.setIndepMin("odin", 0.0);
        assertEquals(0.0, model.getIndepMin("odin"), .0);
 
        model.setIndepMax("odin", 1.0);
        assertEquals(1.0, model.getIndepMax("odin"), .0);
 
        model.setIndepUnit("odin", "unit");
        assertEquals("unit", model.getIndepUnit("odin"));
 
        model.setIndepCategory("odin", "category");
        assertEquals("category", model.getIndepCategory("odin"));
 
        assertFalse(model.containsIndep("aloha"));
        assertTrue(model.containsIndep("odin"));
    }
 
    @Test
    public void testParameter() {
        final ParametricModel model = new ParametricModel();
 
        // Empty constructor assigns empty PmmXmlDoc
        assertEquals(0, model.getParameter().size());
 
        // Check setParameter
        model.setParameter(null);
        assertNull(model.getParameter());
    }
 
Method `testParameterSetters` has 39 lines of code (exceeds 25 allowed). Consider refactoring.
    @Test
    public void testParameterSetters() {
        final ParametricModel model = new ParametricModel();
        model.addParam("param", false);
 
        // Add a non-parameter object. Getters/setters must ignore it.
        model.getParameter().add(new AgentXml());
 
        // When the parameter does not exist the setters do nothing
        model.setParamDescription("aloha", "description");
        model.setParamMin("aloha", 0.0);
        model.setParamMax("aloha", 1.0);
        model.setParamUnit("aloha", "unit");
        model.setParamCategory("aloha", "category");
 
        // and the getters return null
        assertNull(model.getParamDescription("aloha"));
        assertNull(model.getParamMin("aloha"));
        assertNull(model.getParamMax("aloha"));
        assertNull(model.getParamUnit("aloha"));
        assertNull(model.getParamCategory("aloha"));
        assertNull(model.getParamIsStart("aloha"));
        assertNull(model.getParamValue("aloha"));
        assertNull(model.getParamError("aloha"));
        assertNull(model.getParamP("aloha"));
        assertNull(model.getParamT("aloha"));
 
        // Check with existing parameter
Define a constant instead of duplicating this literal "Baldur" 20 times.
        model.addParam("Baldur", true);
 
        model.setParamDescription("Baldur", "description");
        assertEquals("description", model.getParamDescription("Baldur"));
 
        model.setParamMin("Baldur", 0.0);
        assertEquals(0.0, model.getParamMin("Baldur"), .0);
 
        model.setParamMax("Baldur", 1.0);
        assertEquals(1.0, model.getParamMax("Baldur"), .0);
 
        model.setParamUnit("Baldur", "unit");
        assertEquals("unit", model.getParamUnit("Baldur"));
 
        model.setParamCategory("Baldur", "category");
        assertEquals("category", model.getParamCategory("Baldur"));
 
        model.setParamIsStart("Baldur", false);
        assertFalse(model.getParamIsStart("Baldur"));
 
        model.setParamValue("Baldur", 1.0);
        assertEquals(1.0, model.getParamValue("Baldur"), .0);
 
        model.setParamError("Baldur", 0.5);
        assertEquals(0.5, model.getParamError("Baldur"), .0);
 
        assertNull(model.getParamP("Baldur"));
        assertNull(model.getParamT("Baldur"));
 
        assertFalse(model.containsParam("aloha"));
        assertTrue(model.containsParam("Baldur"));
    }
 
Similar blocks of code found in 2 locations. Consider refactoring.
    @Test
    public void testModelLiterature() {
 
        final ParametricModel model = new ParametricModel();
        assertEquals(0, model.getModelLit().size());
 
        model.setMLit(new PmmXmlDoc(new MatrixXml()));
        assertEquals(1, model.getModelLit().size());
 
        final LiteratureItem item = new LiteratureItem("author", 0, "title", "abstractText", "journal", "volume", "issue", 0,
                0, "website", 0, "comment");
        model.addModelLit(item);
        assertEquals(2, model.getModelLit().size());
 
        model.removeModelLits();
        assertEquals(0, model.getModelLit().size());
    }
 
Similar blocks of code found in 2 locations. Consider refactoring.
    @Test
    public void testEstimatedModelLiterature() {
 
        final ParametricModel model = new ParametricModel();
        assertEquals(0, model.getEstModelLit().size());
 
        model.setEstLit(new PmmXmlDoc(new MatrixXml()));
        assertEquals(1, model.getEstModelLit().size());
 
        final LiteratureItem item = new LiteratureItem("author", 0, "title", "abstractText", "journal", "volume", "issue", 0,
                0, "website", 0, "comment");
        model.addEstModelLit(item);
        assertEquals(2, model.getEstModelLit().size());
 
        model.removeEstModelLits();
        assertEquals(0, model.getEstModelLit().size());
    }
 
Method `testToXmlElement` has 46 lines of code (exceeds 25 allowed). Consider refactoring.
    @Test
    public void testToXmlElement() throws DataConversionException {
 
        Element element = new ParametricModel().toXmlElement();
        assertEquals("ParametricModel", element.getName());
 
        assertTrue(element.getAttributeValue("M_DB_UID").isEmpty());
        assertTrue(element.getAttributeValue("EM_DB_UID").isEmpty());
        assertTrue(element.getAttributeValue("ModelName").isEmpty());
        assertTrue(element.getAttributeValue("ModelClass").isEmpty());
        assertTrue(element.getAttributeValue("FittedModelName").isEmpty());
        assertEquals(0, element.getAttribute("Level").getIntValue());
        assertTrue(element.getAttribute("ModelCatalogId").getIntValue() < 0);
        assertTrue(element.getAttribute("EstModelId").getIntValue() < 0);
        assertTrue(element.getAttribute("GlobalModelId").getIntValue() < 0);
        assertEquals(0, element.getAttribute("CondId").getIntValue());
        assertTrue(Double.isNaN(element.getAttribute("RSS").getDoubleValue()));
        assertTrue(Double.isNaN(element.getAttribute("RMS").getDoubleValue()));
        assertEquals(Double.NaN, element.getAttribute("AIC").getDoubleValue(), .0);
        assertEquals(Double.NaN, element.getAttribute("BIC").getDoubleValue(), .0);
        assertTrue(Double.isNaN(element.getAttribute("AIC").getDoubleValue()));
        assertTrue(Double.isNaN(element.getAttribute("BIC").getDoubleValue()));
        assertTrue(element.getAttributeValue("ModelChecked").isEmpty());
        assertTrue(element.getAttributeValue("ModelComment").isEmpty());
        assertTrue(element.getAttributeValue("ModelQualityScore").isEmpty());
        assertTrue(Double.isNaN(element.getAttribute("Rsquared").getDoubleValue()));
        assertNotNull(element.getChild("Formula"));
        assertTrue(element.getChild("ParameterXml").getChildren().isEmpty());
        assertTrue(element.getChild("IndependentXml").getChildren().isEmpty());
        assertNull(element.getChild("DependentXml"));
        assertTrue(element.getChild("ModelLiterature").getChildren().isEmpty());
        assertTrue(element.getChild("EstimatedModelLiterature").getChildren().isEmpty());
 
        final ParametricModel model = new ParametricModel();
        model.modelDbUuid = "";
        model.estimatedModelDbUuid = "";
        model.modelName = "model name";
        model.fittedModelName = "fitted model";
        model.isChecked = true;
        model.comment = "Comment";
        model.qualityScore = 0;
        model.setDepXml(new DepXml("dep"));
 
        element = model.toXmlElement();
 
        assertTrue(element.getAttributeValue("M_DB_UID").isEmpty());
        assertTrue(element.getAttributeValue("EM_DB_UID").isEmpty());
        assertEquals("model name", element.getAttributeValue("ModelName"));
        assertEquals("fitted model", element.getAttributeValue("FittedModelName"));
        assertTrue(element.getAttribute("ModelChecked").getBooleanValue());
        assertEquals("Comment", element.getAttributeValue("ModelComment"));
        assertEquals(0, element.getAttribute("ModelQualityScore").getIntValue());
        assertNotNull(element.getChild("DependentXml"));
    }
 
    @Test
    public void testGetCatModel() {
        final ParametricModel model = new ParametricModel();
        model.modelId = 0;
        model.modelName = "Model name";
        model.setFormula("2+2");
        model.modelClass = 9001;
        model.modelDbUuid = "id";
 
        final CatalogModelXml catModel = (CatalogModelXml) model.getCatModel().get(0);
        assertEquals(0, catModel.id.intValue());
        assertEquals("Model name", catModel.name);
        assertEquals("2+2", catModel.formula);
        assertEquals(9001, catModel.modelClass.intValue());
        assertNull(catModel.comment);
        assertEquals("id", catModel.dbuuid);
    }
 
    @Test
    public void testGetEstModel() {
        final ParametricModel model = new ParametricModel();
        model.estModelId = 0;
        model.fittedModelName = "name";
        model.setRss(null);
        model.setRms(null);
        model.setRsquared(null);
        model.setAic(null);
        model.setBic(null);
        model.isChecked = true;
        model.qualityScore = 0;
        model.estimatedModelDbUuid = "id";
 
        final EstModelXml estimatedModel = (EstModelXml) model.getEstModel().get(0);
        assertEquals(0, estimatedModel.id.intValue());
        assertEquals("name", estimatedModel.name);
        assertNull(estimatedModel.sse);
        assertTrue(Double.isNaN(estimatedModel.rms));
        assertTrue(Double.isNaN(estimatedModel.r2));
        assertTrue(Double.isNaN(estimatedModel.aic));
        assertTrue(Double.isNaN(estimatedModel.bic));
        assertNull(estimatedModel.dof);
        assertTrue(estimatedModel.checked);
        assertEquals(0, estimatedModel.qualityScore.intValue());
        assertEquals("id", estimatedModel.dbuuid);
    }
}