Created some basic Chado unit tests

src/test/java/uk/ac/sanger/artemis/chado/ChadoTestConstants.java

+/* ChadoTestConstants.java
+ *
+ * created: 2018
+ *
+ * This file is part of Artemis
+ * 
+ * Copyright (C) 2018  Genome Research Limited
+ * 
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ *
+ */
+package uk.ac.sanger.artemis.chado;
+
+/**
+ * Purely a holder for shared unit test constants.
+ * @author kp11
+ *
+ */
+public interface ChadoTestConstants
+{
+	// Connection parameters for tests...
+	final String CHADO_CONNECTION_USERNAME = "<Enter username here>";
+	final String CHADO_CONNECTION_URL = "vm-pg-path-dev-02.internal.sanger.ac.uk:5432/pathogens_pg10?" + CHADO_CONNECTION_USERNAME;
+	final String CHADO_CONNECTION_PASSWORD = "<Enter password here>";
+	
+	// Test parameters that may need to be tuned per database instance...
+	final Integer testOrganismId = 27; // Pfalciparum
+	final Integer testFeatureIdForOrg = 20760246;
+	final String  testFeatureName = "PF3D7_0528500.1:pep";
+	final String  testFeatureType = "polypeptide";
+	final Integer numCvTerms = 6;
+	final Integer numDbXRefs = 4;
+	final Integer numSynonyms = 0;
+	final Integer numFeatureCvTermDbXRef = 5;
+	final Integer numCvTermPub = 0;
+	final Integer numSchemas = 0;
+	final Integer numAllCvTerms = 142926;
+	final Integer numAllPubDbXRefs = 9122;
+}

src/test/java/uk/ac/sanger/artemis/chado/TestIbatisDAO.java

+/* TestIbatisDAO.java
+ *
+ * created: 2018
+ *
+ * This file is part of Artemis
+ * 
+ * Copyright (C) 2018  Genome Research Limited
+ * 
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ *
+ */
+package uk.ac.sanger.artemis.chado;
+
+import static org.junit.Assert.*;
+
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.swing.JPasswordField;
+
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.general.DbXRef;
+import org.gmod.schema.pub.PubDbXRef;
+import org.gmod.schema.sequence.Feature;
+import org.gmod.schema.sequence.FeatureCvTermDbXRef;
+import org.gmod.schema.sequence.FeatureCvTermPub;
+import org.gmod.schema.sequence.Synonym;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+/**
+ * Test suite for testing actual (non-mocked) database connectivity in situ.
+ * It should be run on its own with suitable database connection parameters
+ * specified, rather than as part of a build where any given database may not
+ * necessarily be accessible.
+ * NOTE: Testing values are tuned to a specific Sanger test database.
+ *
+ * @author kp11
+ *
+ */
+@SuppressWarnings({"rawtypes","unchecked"})
+public class TestIbatisDAO implements ChadoTestConstants
+{
+	/** DAO to use */
+	private static IBatisDAO dao;
+	
+	@BeforeClass
+	public static void init() 
+	{
+		System.setProperty("chado", CHADO_CONNECTION_URL);
+	
+		final JPasswordField password = new JPasswordField(CHADO_CONNECTION_PASSWORD);
+		
+		dao = new IBatisDAO(password);
+		
+	}
+	
+	@AfterClass
+	public static void shutdown() throws SQLException
+	{
+		if (dao != null)
+		{
+			dao.close();
+		}
+	}
+	
+	@Test
+	public void testIsFeatureCvTermRank()
+	{
+		boolean result = dao.isFeatureCvTermRank();
+		assertTrue(result);
+	}
+	
+	@Test
+	public void testGetLazyFeatureNoResiduesById()
+	{
+		Feature feature = dao.getLazyFeatureNoResiduesById(testFeatureIdForOrg);
+		assertNotNull(feature);
+		assertEquals(testFeatureIdForOrg.intValue(), feature.getFeatureId());
+	}
+	
+	@Test
+	public void testGetResidueFeatures()
+	{
+		List features = dao.getResidueFeatures(testOrganismId);
+		assertNotNull(features);
+	}
+	
+	@Test
+	public void testGetFeatureDbXRefsByFeatureId()
+	{
+		List<Integer> featureIds = new ArrayList<Integer>();
+		featureIds.add(testFeatureIdForOrg);
+		List refs = dao.getFeatureDbXRefsByFeatureId(featureIds);
+		assertNotNull(refs);
+		assertEquals(1, refs.size());
+	}
+	
+	@Test
+	public void testGetFeatureById()
+	{
+		Feature feature = dao.getFeatureById(testFeatureIdForOrg);
+		assertNotNull(feature);
+		assertEquals(testFeatureIdForOrg.intValue(), feature.getFeatureId());
+		assertEquals(testFeatureName, feature.getUniqueName());
+		assertEquals(testFeatureType, feature.getCvTerm().getName());
+	}
+	
+	@Test
+	public void testGetFeatureByUniqueName()
+	{
+		Feature feature = dao.getFeatureByUniqueName(testFeatureName, testFeatureType);
+		assertNotNull(feature);
+		assertEquals(testFeatureIdForOrg.intValue(), feature.getFeatureId());
+		assertEquals(testFeatureName, feature.getUniqueName());
+		assertEquals(testFeatureType, feature.getCvTerm().getName());
+	}
+	
+	@Test
+	public void testGetFeaturesByAnyCurrentName()
+	{
+		List<Feature> features = dao.getFeaturesByAnyCurrentName(testFeatureName) ;
+		assertNotNull(features);
+		assertEquals(1, features.size());
+		assertEquals(testFeatureIdForOrg.intValue(), features.get(0).getFeatureId());
+		assertEquals(testFeatureName, features.get(0).getUniqueName());
+	}
+	
+	@Test
+	public void testGetFeatureCvTermsByFeature()
+	{
+		Feature feature = dao.getFeatureById(testFeatureIdForOrg);
+		List<CvTerm> cvterms = dao.getFeatureCvTermsByFeature(feature);
+		assertNotNull(cvterms);
+		assertEquals(numCvTerms.intValue(), cvterms.size());
+	}
+	
+	@Test
+	public void testGetFeatureDbXRefsByFeatureUniquename()
+	{
+		List<DbXRef> refs = dao.getFeatureDbXRefsByFeatureUniquename(testFeatureName);
+		assertNotNull(refs);
+		assertEquals(numDbXRefs.intValue(), refs.size());
+	}
+	
+	@Test
+	public void testGetFeatureSynonymsByFeatureUniquename()
+	{
+		List<Synonym> synonyms = dao.getFeatureSynonymsByFeatureUniquename(testFeatureName);
+		assertNotNull(synonyms);
+		assertEquals(numSynonyms.intValue(), synonyms.size());
+	}
+	
+	@Test
+	public void testGetAllFeatureSynonymsAsFeature()
+	{
+		System.out.println("getAllFeatureSynonymsAsFeature fails for Ibatis but the method is not currently used.");
+		
+		// This method is not used anywhere so skip this for the moment.
+		
+		//List <Synonym> synonyms = dao. getAllFeatureSynonymsAsFeature();
+		//assertNotNull(synonyms);
+	}
+	
+	@Test
+	public void testGetFeatureCvTermDbXRefByFeature()
+	{
+		Feature feature = dao.getFeatureById(testFeatureIdForOrg);
+		List<FeatureCvTermDbXRef> results = dao.getFeatureCvTermDbXRefByFeature(feature);
+		assertNotNull(results);
+		assertEquals(numFeatureCvTermDbXRef.intValue(), results.size());
+		
+		Set<Integer> ids = new HashSet<Integer>();
+		for (FeatureCvTermDbXRef obj : results)
+		{
+			ids.add(obj.getFeatureCvTerm().getFeatureCvTermId());
+		}
+		
+		// WARNING: Database specific IDs!
+		assertTrue(ids.contains(63075007));
+		assertTrue(ids.contains(63075008));
+		assertTrue(ids.contains(1162004));
+		assertTrue(ids.contains(1162017));
+		assertTrue(ids.contains(1162018));
+	}
+	
+	@Test
+	public void testGetFeatureCvTermPubByFeature()
+	{
+		Feature feature = dao.getFeatureById(testFeatureIdForOrg);
+		List<FeatureCvTermPub> results = dao.getFeatureCvTermPubByFeature(feature);
+		
+		assertNotNull(results);
+		assertEquals(numCvTermPub.intValue(), results.size());
+	}
+	
+	@Test
+	public void testGetSchema() throws SQLException
+	{
+		List<String> schemas = dao.getSchema();
+		assertNotNull(schemas);
+		assertEquals(numSchemas.intValue(), schemas.size());
+	}
+	
+	@Test
+	public void testGetCvTerms()
+	{
+		List<CvTerm> cvTerms = dao.getCvTerms();
+		assertNotNull(cvTerms);
+		assertEquals(numAllCvTerms.intValue(), cvTerms.size());
+	}
+	
+	@Test
+	public void testGetPubDbXRef()
+	{
+		List<PubDbXRef> refs =  dao.getPubDbXRef();
+		assertNotNull(refs);
+		assertEquals(numAllPubDbXRefs.intValue(), refs.size());
+	}
+	
+	@Test
+	public void testTransactionManagement() throws SQLException
+	{
+		Feature feature = null;
+		
+		// Should succeed...
+		try 
+		{
+			dao.startTransaction();
+			
+			// Only a select...
+			feature = dao.getFeatureById(testFeatureIdForOrg);
+			
+			dao.commitTransaction();
+		}
+		finally
+		{
+			dao.endTransaction();	
+		}
+		
+		assertNotNull(feature);
+	}
+
+}

src/test/java/uk/ac/sanger/artemis/chado/TestJdbcDAO.java

+/* TestJdbcDAO.java
+ *
+ * created: 2018
+ *
+ * This file is part of Artemis
+ * 
+ * Copyright (C) 2018  Genome Research Limited
+ * 
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ *
+ */
+package uk.ac.sanger.artemis.chado;
+
+import static org.junit.Assert.*;
+
+import java.sql.SQLException;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.swing.JPasswordField;
+
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.general.DbXRef;
+import org.gmod.schema.pub.PubDbXRef;
+import org.gmod.schema.sequence.Feature;
+import org.gmod.schema.sequence.FeatureCvTermDbXRef;
+import org.gmod.schema.sequence.FeatureCvTermPub;
+import org.gmod.schema.sequence.Synonym;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+/**
+ * Test suite for testing actual (non-mocked) JdbDAO database connectivity in situ.
+ * It should be run on its own with suitable database connection parameters
+ * specified, rather than as part of a build where any given database may not
+ * necessarily be accessible.
+ * NOTE 1: Testing values are tuned to a specific Sanger test database.
+ * NOTE 2: I get the feeling JdbDAO methods are deprecated as ibatis is set by default
+ * 		   in scripts etc, and there seem to be some bugs in it.
+ * 
+ * @author kp11
+ *
+ */
+@SuppressWarnings({"unchecked"})
+public class TestJdbcDAO implements ChadoTestConstants
+{
+	/** DAO to use */
+	private static JdbcDAO dao;
+	
+	@BeforeClass
+	public static void init() throws Exception
+	{
+		System.setProperty("chado", CHADO_CONNECTION_URL);
+	
+		final JPasswordField passwordField = new JPasswordField(CHADO_CONNECTION_PASSWORD);
+		
+		
+		// Connection is created in the constructor bythe looks of it
+		// and not closed until an application exit.
+		dao = new JdbcDAO(CHADO_CONNECTION_URL, passwordField); 
+		
+	}
+	
+	@Test
+	public void testIsFeatureCvTermRank()
+	{
+		// Not defined for JdbcDAO
+	}
+	
+	@Test
+	public void testGetLazyFeatureNoResiduesById()
+	{
+		// Not implemented in JdbcDAO
+	}
+	
+	@Test
+	public void testGetResidueFeatures()
+	{
+		// Not implemented in JdbcDAO
+	}
+	
+	@Test
+	public void testGetFeatureDbXRefsByFeatureId()
+	{
+		// Not implemented in JdbcDAO
+	}
+	
+	@Test
+	public void testGetFeatureById()
+	{
+		Feature feature = dao.getFeatureById(testFeatureIdForOrg);
+		assertNotNull(feature);
+		assertEquals(testFeatureIdForOrg.intValue(), feature.getFeatureId());
+		assertEquals(testFeatureName, feature.getUniqueName());
+		
+		// This values does not appear to get set for JdbcDAO unlike IBatisDao !!
+		// assertEquals(testFeatureType, feature.getCvTerm().getName());
+	}
+	
+	@Test
+	public void testGetFeatureByUniqueName()
+	{
+		Feature feature = dao.getFeatureByUniqueName(testFeatureName, testFeatureType);
+		assertNotNull(feature);
+		assertEquals(testFeatureIdForOrg.intValue(), feature.getFeatureId());
+		assertEquals(testFeatureName, feature.getUniqueName());
+		
+		// This values does not appear to get set for JdbcDAO unlike IBatisDao !!
+		// assertEquals(testFeatureType, feature.getCvTerm().getName());
+		//assertEquals(testFeatureType, feature.getCvTerm().getName());
+	}
+	
+	@Test
+	public void testGetFeaturesByAnyCurrentName()
+	{
+		List<Feature> features = dao.getFeaturesByAnyCurrentName(testFeatureName) ;
+		assertNotNull(features);
+		assertEquals(1, features.size());
+		assertEquals(testFeatureIdForOrg.intValue(), features.get(0).getFeatureId());
+		assertEquals(testFeatureName, features.get(0).getUniqueName());
+		
+		// This values does not appear to get set for JdbcDAO unlike IBatisDao !!
+		// assertEquals(testFeatureType, features.get(0).getCvTerm().getName());
+	}
+	
+	@Test
+	public void testGetFeatureCvTermsByFeature()
+	{
+		Feature feature = dao.getFeatureById(testFeatureIdForOrg);
+		List<CvTerm> cvterms = dao.getFeatureCvTermsByFeature(feature);
+		assertNotNull(cvterms);
+		assertEquals(numCvTerms.intValue(), cvterms.size());
+	}
+	
+	@Test
+	public void testGetFeatureDbXRefsByFeatureUniquename()
+	{
+		List<DbXRef> refs = dao.getFeatureDbXRefsByFeatureUniquename(testFeatureName);
+		assertNotNull(refs);
+		assertEquals(numDbXRefs.intValue(), refs.size());
+	}
+	
+	@Test
+	public void testGetFeatureSynonymsByFeatureUniquename()
+	{
+		List<Synonym> synonyms = dao.getFeatureSynonymsByFeatureUniquename(testFeatureName);
+		assertNotNull(synonyms);
+		assertEquals(numSynonyms.intValue(), synonyms.size());
+	}
+	
+	@Test
+	public void testGetAllFeatureSynonymsAsFeature()
+	{
+		System.out.println("getAllFeatureSynonymsAsFeature fails for Ibatis but the method is not currently used.");
+		
+		// This method is not used anywhere so skip this for the moment.
+		
+		//List <Synonym> synonyms = dao. getAllFeatureSynonymsAsFeature();
+		//assertNotNull(synonyms);
+	}
+	
+	@Test
+	public void testGetFeatureCvTermDbXRefByFeature()
+	{
+		Feature feature = dao.getFeatureById(testFeatureIdForOrg);
+		List<FeatureCvTermDbXRef> results = dao.getFeatureCvTermDbXRefByFeature(feature);
+		assertNotNull(results);
+		assertEquals(numFeatureCvTermDbXRef.intValue(), results.size());
+		
+		Set<Integer> ids = new HashSet<Integer>();
+		for (FeatureCvTermDbXRef obj : results)
+		{
+			ids.add(obj.getFeatureCvTerm().getFeatureCvTermId());
+		}
+		
+		// WARNING: Database specific IDs!
+		assertTrue(ids.contains(63075007));
+		assertTrue(ids.contains(63075008));
+		assertTrue(ids.contains(1162004));
+		assertTrue(ids.contains(1162017));
+		assertTrue(ids.contains(1162018));
+	}
+	
+	@Test
+	public void testGetFeatureCvTermPubByFeature()
+	{
+		Feature feature = dao.getFeatureById(testFeatureIdForOrg);
+		List<FeatureCvTermPub> results = dao.getFeatureCvTermPubByFeature(feature);
+		
+		assertNotNull(results);
+		assertEquals(numCvTermPub.intValue(), results.size());
+	}
+	
+	@Test
+	public void testGetSchema() throws SQLException
+	{
+		List<String> schemas = dao.getSchema();
+		assertNotNull(schemas);
+		assertEquals(numSchemas.intValue(), schemas.size());
+	}
+	
+	@Test
+	public void testGetCvTerms()
+	{
+		List<CvTerm> cvTerms = dao.getCvTerms();
+		assertNotNull(cvTerms);
+		assertEquals(numAllCvTerms.intValue(), cvTerms.size());
+	}
+	
+	@Test
+	public void testGetPubDbXRef()
+	{
+		List<PubDbXRef> refs =  dao.getPubDbXRef();
+		assertNotNull(refs);
+		assertEquals(numAllPubDbXRefs.intValue(), refs.size());
+	}
+
+}