all unit tests use test database (but they are still slow...)

annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java

@@ -57,7 +57,7 @@ import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
 @Transactional(value = "txManager")
 @Rollback(false)
 @ContextConfiguration(locations = { //
-		"/dataSource.xml", //
+		"/test-dataSource.xml", //
 		"/applicationContext-annotation.xml", //
 		"/applicationContext-persist.xml", //
 		"/test-applicationContext.xml", //

converter-SBGNML/pom.xml

@@ -95,6 +95,15 @@
 			<artifactId>commons-cli</artifactId>
 	    <version>${commons-cli.version}</version>
 		</dependency>
+
+	<!-- Test db definition -->
+    <dependency>
+			<groupId>lcsb.mapviewer</groupId>
+			<artifactId>persist</artifactId>
+			<version>1.0</version>
+      <type>test-jar</type>
+      <scope>test</scope>
+    </dependency>		
 				
 	</dependencies>
 </project>
\ No newline at end of file

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java

@@ -20,7 +20,8 @@ import lcsb.mapviewer.persist.DbUtils;
 import lcsb.mapviewer.persist.dao.map.ModelDao;
 
 @Transactional(value = "txManager")
-@ContextConfiguration(locations = { "/applicationContext-persist.xml", //
+@ContextConfiguration(locations = { "/test-dataSource.xml", //
+		"/applicationContext-persist.xml", //
 		"/test-applicationContext.xml",//
 })
 @RunWith(SpringJUnit4ClassRunner.class)

model/src/main/java/lcsb/mapviewer/model/map/graph/DataMining.java

@@ -43,13 +43,13 @@ public class DataMining implements Serializable {
 	@Id
 	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	@Column(name = "idDb", unique = true, nullable = false)
-	private Integer						id;
+	private int								id;
 
 	/**
 	 * For which element this entry was created.
 	 */
 	@ManyToOne(optional = false)
-	private Element							element;
+	private Element						element;
 
 	/**
 	 * List of the suggested connection.

model/src/main/java/lcsb/mapviewer/model/user/User.java

@@ -40,7 +40,7 @@ public class User implements Serializable, DbObject {
 	@Id
 	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	@Column(name = "idDb", unique = true, nullable = false)
-	private Integer							 id;
+	private int									 id;
 
 	/**
 	 * User login.

model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java

@@ -38,13 +38,13 @@ public class UserAnnotationSchema implements Serializable {
 	/**
 	 * 
 	 */
-	private static final long									serialVersionUID				= 1L;
+	private static final long									 serialVersionUID				 = 1L;
 
 	/**
 	 * Default class logger.
 	 */
 	@Transient
-	private final transient Logger						 logger									= Logger.getLogger(UserAnnotationSchema.class);
+	private final transient Logger						 logger									 = Logger.getLogger(UserAnnotationSchema.class);
 
 	/**
 	 * Unique identifier in the database.
@@ -52,7 +52,7 @@ public class UserAnnotationSchema implements Serializable {
 	@Id
 	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	@Column(name = "idDb", unique = true, nullable = false)
-	private Integer														id;
+	private int																 id;
 
 	/**
 	 * {@link User} for which annotation schema is defined.
@@ -63,18 +63,18 @@ public class UserAnnotationSchema implements Serializable {
 	/**
 	 * Should the miriam types be validated?
 	 */
-	private Boolean														validateMiriamTypes		 = false;
+	private Boolean														 validateMiriamTypes		 = false;
 
 	/**
 	 * Should map be visualized as sbgn?
 	 */
-	private Boolean														sbgnFormat							= false;
+	private Boolean														 sbgnFormat							 = false;
 
 	/**
 	 * Should the default view be network (if not then it will be pathways and
 	 * compartments)?
 	 */
-	private Boolean														networkLayoutAsDefault	= false;
+	private Boolean														 networkLayoutAsDefault	 = false;
 
 	/**
 	 * List of class annotators for specific object types.
@@ -82,7 +82,7 @@ public class UserAnnotationSchema implements Serializable {
 	@Cascade({ CascadeType.ALL })
 	@OneToMany(mappedBy = "annotationSchema")
 	@OrderBy("id")
-	private List<UserClassAnnotators>					classAnnotators				 = new ArrayList<UserClassAnnotators>();
+	private List<UserClassAnnotators>					 classAnnotators				 = new ArrayList<UserClassAnnotators>();
 
 	/**
 	 * List of valid annotations for given object type.
@@ -90,7 +90,7 @@ public class UserAnnotationSchema implements Serializable {
 	@Cascade({ CascadeType.ALL })
 	@OneToMany(mappedBy = "annotationSchema")
 	@OrderBy("id")
-	private List<UserClassValidAnnotations>		classValidAnnotators		= new ArrayList<UserClassValidAnnotations>();
+	private List<UserClassValidAnnotations>		 classValidAnnotators		 = new ArrayList<UserClassValidAnnotations>();
 
 	/**
 	 * List of required annotations for given object type.
@@ -321,7 +321,8 @@ public class UserAnnotationSchema implements Serializable {
 	}
 
 	/**
-	 * @param sbgnFormat the sbgnFormat to set
+	 * @param sbgnFormat
+	 *          the sbgnFormat to set
 	 * @see #sbgnFormat
 	 */
 	public void setSbgnFormat(Boolean sbgnFormat) {
@@ -337,7 +338,8 @@ public class UserAnnotationSchema implements Serializable {
 	}
 
 	/**
-	 * @param networkLayoutAsDefault the networkLayoutAsDefault to set
+	 * @param networkLayoutAsDefault
+	 *          the networkLayoutAsDefault to set
 	 * @see #networkLayoutAsDefault
 	 */
 	public void setNetworkLayoutAsDefault(Boolean networkLayoutAsDefault) {

model/src/main/java/lcsb/mapviewer/model/user/UserClassAnnotators.java

@@ -32,7 +32,7 @@ public class UserClassAnnotators implements Serializable {
 	/**
 	 * 
 	 */
-	private static final long	serialVersionUID	= 1L;
+	private static final long		 serialVersionUID	= 1L;
 
 	/**
 	 * Unique identifier in the database.
@@ -40,19 +40,19 @@ public class UserClassAnnotators implements Serializable {
 	@Id
 	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	@Column(name = "idDb", unique = true, nullable = false)
-	private Integer								id;
+	private int									 id;
 
 	/**
 	 * {@link UserAnnotationSchema} that defines which user is using this set of
 	 * annotators.
 	 */
 	@ManyToOne
-	private UserAnnotationSchema	annotationSchema;
+	private UserAnnotationSchema annotationSchema;
 
 	/**
 	 * Class for which this set of annotators is defined.
 	 */
-	private String								className;
+	private String							 className;
 
 	/**
 	 * List of strings defining set of annotators (canonical class names).
@@ -61,7 +61,7 @@ public class UserClassAnnotators implements Serializable {
 	@CollectionTable(name = "class_annotator_annotators_table", joinColumns = @JoinColumn(name = "class_annotator_iddb"))
 	@IndexColumn(name = "idx")
 	@Column(name = "annotator_name")
-	private List<String>					annotators	= new ArrayList<String>();
+	private List<String>				 annotators				= new ArrayList<String>();
 
 	/**
 	 * Default constructor.

model/src/main/java/lcsb/mapviewer/model/user/UserClassRequiredAnnotations.java

@@ -52,7 +52,7 @@ public class UserClassRequiredAnnotations implements Serializable {
 	@Id
 	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	@Column(name = "idDb", unique = true, nullable = false)
-	private Integer								 id;
+	private int										 id;
 
 	/**
 	 * {@link UserAnnotationSchema} in which this set of required

model/src/main/java/lcsb/mapviewer/model/user/UserClassValidAnnotations.java

@@ -35,7 +35,7 @@ public class UserClassValidAnnotations implements Serializable {
 	/**
 	 * 
 	 */
-	private static final long	serialVersionUID	= 1L;
+	private static final long		 serialVersionUID	= 1L;
 
 	/**
 	 * Unique identifier in the database.
@@ -43,19 +43,19 @@ public class UserClassValidAnnotations implements Serializable {
 	@Id
 	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	@Column(name = "idDb", unique = true, nullable = false)
-	private Integer								id;
+	private int									 id;
 
 	/**
 	 * {@link UserAnnotationSchema} in which this set of valid {@link MiriamType
 	 * annotations} is used.
 	 */
 	@ManyToOne
-	private UserAnnotationSchema	annotationSchema;
+	private UserAnnotationSchema annotationSchema;
 
 	/**
 	 * Name of the class for which this set is defined.
 	 */
-	private String								className;
+	private String							 className;
 
 	/**
 	 * List of annotations that are valid.
@@ -65,7 +65,7 @@ public class UserClassValidAnnotations implements Serializable {
 	@Column(name = "miriam_type_name", nullable = false)
 	@IndexColumn(name = "idx")
 	@Enumerated(EnumType.STRING)
-	private List<MiriamType>			validMiriamTypes	= new ArrayList<MiriamType>();
+	private List<MiriamType>		 validMiriamTypes	= new ArrayList<MiriamType>();
 
 	/**
 	 * Default constructor.

persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java

@@ -56,7 +56,7 @@ import lcsb.mapviewer.persist.dao.user.UserDao;
 
 @Transactional(value = "txManager")
 @Rollback(true)
-@ContextConfiguration(locations = { "/dataSource.xml", "/applicationContext-persist.xml", "/test-applicationContext.xml" })
+@ContextConfiguration(locations = { "/test-dataSource.xml", "/applicationContext-persist.xml", "/test-applicationContext.xml" })
 @RunWith(SpringJUnit4ClassRunner.class)
 public abstract class PersistTestFunctions {
 	private Logger						 logger	 = Logger.getLogger(PersistTestFunctions.class);

persist/src/test/resources/db.properties

-database.uri=jdbc:postgresql://localhost:5432/map_viewer_test
\ No newline at end of file

persist/src/test/resources/dataSource.xml → persist/src/test/resources/test-dataSource.xml

@@ -12,14 +12,14 @@
 		http://www.springframework.org/schema/context 
 		http://www.springframework.org/schema/context/spring-context-4.0.xsd">
 
-	<context:property-placeholder location="classpath:db.properties" />
+	<context:property-placeholder location="classpath:test-db.properties" />
 				 
 <!-- Data Source Declaration -->
 	 <bean id="DataSource" class="org.springframework.jdbc.datasource.DriverManagerDataSource" >
 		<property name="driverClassName" value="org.postgresql.Driver" />
 		<property name="url" value="${database.uri}" />
-		<property name="username" value="map_viewer" />
-		<property name="password" value="123qweasdzxc" /> 
+		<property name="username" value="${database.username}" />
+		<property name="password" value="${database.password}" /> 
 	 </bean>
 	 
 	 <jdbc:initialize-database data-source="DataSource">

persist/src/test/resources/test-db.properties

+database.uri=jdbc:postgresql://localhost:5432/map_viewer_test
+database.username=map_viewer
+database.password=123qweasdzxc

reactome/pom.xml

@@ -83,6 +83,15 @@
 			<artifactId>spring-faces</artifactId>
 			<version>${springframework.webflow.version}</version>
 		</dependency>
+
+	<!-- Test db definition -->
+    <dependency>
+			<groupId>lcsb.mapviewer</groupId>
+			<artifactId>persist</artifactId>
+			<version>1.0</version>
+      <type>test-jar</type>
+      <scope>test</scope>
+    </dependency>		
 	
 	</dependencies>
 	

reactome/src/test/java/lcsb/mapviewer/reactome/ReactomeTestFunctions.java

@@ -51,26 +51,27 @@ import org.xml.sax.SAXException;
 
 @Transactional(value = "txManager")
 @Rollback(false)
-@ContextConfiguration(locations = { "/applicationContext-annotation.xml", //
+@ContextConfiguration(locations = { "/test-dataSource.xml", //
+		"/applicationContext-annotation.xml", //
 		"/applicationContext-reactome.xml", //
 		"/applicationContext-persist.xml", //
 		"/test-applicationContext.xml", //
 })
 @RunWith(SpringJUnit4ClassRunner.class)
 public abstract class ReactomeTestFunctions {
-	private Logger																	logger	= Logger.getLogger(ReactomeTestFunctions.class);
+	private Logger																 logger	= Logger.getLogger(ReactomeTestFunctions.class);
 
 	@Autowired
-	protected PermanentDatabaseLevelCacheInterface	cache;
+	protected PermanentDatabaseLevelCacheInterface cache;
 
 	@Autowired
-	protected DataSourceUpdater											rc;
+	protected DataSourceUpdater										 rc;
 
 	@Autowired
-	protected DbUtils																dbUtils;
+	protected DbUtils															 dbUtils;
 
 	@Autowired
-	protected ReactomeQueryUtil											rcu;
+	protected ReactomeQueryUtil										 rcu;
 
 	protected String readFile(String file) throws IOException {
 		StringBuilder stringBuilder = new StringBuilder();
@@ -132,7 +133,7 @@ public abstract class ReactomeTestFunctions {
 		return doc;
 	}
 
-	private static Map<String, Model>	models	= new HashMap<String, Model>();
+	private static Map<String, Model> models = new HashMap<String, Model>();
 
 	protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
 		if (!fromCache) {
@@ -248,8 +249,9 @@ public abstract class ReactomeTestFunctions {
 
 	protected void waitForRefreshCacheQueueToEmpty() throws InterruptedException {
 		while (cache.refreshIsBusy()) {
-			logger.debug("Waiting for refresh queue to empty. " + cache.getRefreshPendingQueueSize() + " pending. " + cache.getRefreshExecutingTasksSize()
-					+ " tasks are executed.");
+			logger.debug(
+					"Waiting for refresh queue to empty. " + cache.getRefreshPendingQueueSize() + " pending. " + cache.getRefreshExecutingTasksSize()
+							+ " tasks are executed.");
 			Thread.sleep(100);
 		}
 	}

rest-api/pom.xml

@@ -74,6 +74,15 @@
 			<version>${mockito.version}</version>
 			<scope>test</scope>
 		</dependency>
+
+	<!-- Test db definition -->
+    <dependency>
+			<groupId>lcsb.mapviewer</groupId>
+			<artifactId>persist</artifactId>
+			<version>1.0</version>
+      <type>test-jar</type>
+      <scope>test</scope>
+    </dependency>		
   	
 	</dependencies>
 </project>

rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java

@@ -63,8 +63,13 @@ import lcsb.mapviewer.services.view.AuthenticationToken;
 
 @Transactional(value = "txManager")
 @Rollback(true)
-@ContextConfiguration(
-		locations = { "/applicationContext-persist.xml", "/applicationContext-annotation.xml", "/applicationContext-service.xml", "/applicationContext-rest.xml" })
+@ContextConfiguration(locations = { "/test-dataSource.xml", //
+		"/applicationContext-persist.xml", //
+		"/applicationContext-annotation.xml", //
+		"/applicationContext-service.xml", //
+		"/applicationContext-rest.xml", //
+})
+
 @RunWith(SpringJUnit4ClassRunner.class)
 public abstract class RestTestFunctions {
 	private Logger								logger	= Logger.getLogger(RestTestFunctions.class);
@@ -200,9 +205,9 @@ public abstract class RestTestFunctions {
 			complexParams.entry(entry4);
 			complexParams.entry(entry5);
 
-			Model model =parser.createModel(complexParams);
+			Model model = parser.createModel(complexParams);
 			model.setTileSize(256);
-			for (ModelSubmodelConnection connection: model.getSubmodelConnections()) {
+			for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
 				connection.getSubmodel().setTileSize(256);
 			}
 			model.setProject(new Project());

service/pom.xml

@@ -126,6 +126,15 @@
 			<scope>test</scope>
 		</dependency>
 
+	<!-- Test db definition -->
+    <dependency>
+			<groupId>lcsb.mapviewer</groupId>
+			<artifactId>persist</artifactId>
+			<version>1.0</version>
+      <type>test-jar</type>
+      <scope>test</scope>
+    </dependency>		
+
 	</dependencies>
 
 </project>
\ No newline at end of file

service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java

@@ -83,7 +83,11 @@ import lcsb.mapviewer.services.search.db.drug.IDrugService;
 
 @Transactional(value = "txManager")
 @Rollback(false)
-@ContextConfiguration(locations = { "/applicationContext-annotation.xml", "/applicationContext-persist.xml", "/applicationContext-service.xml" })
+@ContextConfiguration(locations = { "/test-dataSource.xml", //
+		"/applicationContext-annotation.xml", //
+		"/applicationContext-persist.xml", //
+		"/applicationContext-service.xml",//
+})
 @RunWith(SpringJUnit4ClassRunner.class)
 public abstract class ServiceTestFunctions {
 	private Logger										 logger	 = Logger.getLogger(ServiceTestFunctions.class);
@@ -178,7 +182,7 @@ public abstract class ServiceTestFunctions {
 	protected ReactionDao							 reactionDao;
 
 	@Autowired
-	protected ElementDao								 aliasDao;
+	protected ElementDao							 aliasDao;
 
 	protected User										 user;
 	protected User										 user2	 = null;

web/pom.xml

@@ -194,6 +194,16 @@
 			<scope>test</scope>
 		</dependency>
 
+	<!-- Test db definition -->
+    <dependency>
+			<groupId>lcsb.mapviewer</groupId>
+			<artifactId>persist</artifactId>
+			<version>1.0</version>
+      <type>test-jar</type>
+      <scope>test</scope>
+    </dependency>		
+
+
 	</dependencies>
 
 <build>