diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java b/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
index a155631f38d2cfc47a562f3909b1dab0208bd79c..cad5977a4cb5118f7eaceff87cd6e50f04042bd3 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
@@ -60,6 +60,8 @@ import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
"/applicationContext-annotation.xml", //
"/applicationContext-persist.xml", //
"/test-applicationContext.xml", //
+ "/test-applicationContext.xml", //
+ "/dataSource.xml", //
})
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class AnnotationTestFunctions extends AbstractTransactionalJUnit4SpringContextTests {
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java
index 66b52bba704f5b30c80582230cc5bf9f1e0124a7..c98a7c7b0094e0509ea67d57e6b168a4ac2b8c87 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java
@@ -22,6 +22,8 @@ import lcsb.mapviewer.persist.dao.map.ModelDao;
@Transactional(value = "txManager")
@ContextConfiguration(locations = { "/applicationContext-persist.xml", //
"/test-applicationContext.xml",//
+ "/dataSource.xml", //
+
})
@RunWith(SpringJUnit4ClassRunner.class)
public class DbSerializationTest {
diff --git a/persist/.classpath b/persist/.classpath
index 62d4b8e4723486982a42cd5dd2b44363281a0bd8..08d7a50f5bdeedd3895bec12935a95bb700fbf77 100644
--- a/persist/.classpath
+++ b/persist/.classpath
@@ -1,37 +1,37 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" output="target/classes" path="src/main/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="src" output="target/test-classes" path="src/test/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- <attribute name="org.eclipse.jst.component.nondependency" value=""/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" output="target/classes" path="src/main/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/test-classes" path="src/test/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ <attribute name="org.eclipse.jst.component.nondependency" value=""/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
diff --git a/persist/src/main/resources/applicationContext-persist.xml b/persist/src/main/resources/applicationContext-persist.xml
index 896e204ca1ca0b1a64eb6b4ba1dc01905591c689..b459702a7a5076281cd6cd5ca476dbb3d2bcc3cf 100644
--- a/persist/src/main/resources/applicationContext-persist.xml
+++ b/persist/src/main/resources/applicationContext-persist.xml
@@ -8,28 +8,14 @@
http://www.springframework.org/schema/tx/spring-tx-4.0.xsd
http://www.springframework.org/schema/context
http://www.springframework.org/schema/context/spring-context-4.0.xsd">
-
-<!-- Data Source Declaration -->
- <bean id="DataSource" class="com.mchange.v2.c3p0.ComboPooledDataSource" destroy-method="close">
- <property name="driverClass" value="org.postgresql.Driver" />
- <property name="jdbcUrl" value="jdbc:postgresql://localhost:5432/map_viewer" />
- <property name="user" value="map_viewer" />
- <property name="password" value="123qweasdzxc" />
- <property name="maxPoolSize" value="100" />
- <property name="maxStatements" value="5" />
- <property name="minPoolSize" value="5" />
- </bean>
-
-
- <bean id="BaseDao" class="lcsb.mapviewer.persist.dao.BaseDao" abstract="true">
- </bean>
+
+ <bean id="BaseDao" class="lcsb.mapviewer.persist.dao.BaseDao" abstract="true"/>
<bean id="UserDao" class="lcsb.mapviewer.persist.dao.user.UserDao" parent="BaseDao"/>
<bean id="PrivilegeDao" class="lcsb.mapviewer.persist.dao.user.PrivilegeDao" parent="BaseDao"/>
<bean id="LogDao" class="lcsb.mapviewer.persist.dao.log.LogDao" parent="BaseDao"/>
-
<bean id="BigFileEntryDao" class="lcsb.mapviewer.persist.dao.cache.BigFileEntryDao" parent="BaseDao"/>
<bean id="UploadedFileEntryDao" class="lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao" parent="BaseDao"/>
<bean id="ConfigurationDao" class="lcsb.mapviewer.persist.dao.ConfigurationDao" parent="BaseDao"/>
@@ -200,8 +186,6 @@
<prop key="hibernate.dialect">org.hibernate.dialect.PostgreSQLDialect</prop>
<!--<prop key="hibernate.show_sql">true</prop>-->
<!--<prop key="hibernate.current_session_context_class">thread</prop>-->
-
- <!--<prop key="hibernate.hbm2ddl.auto">create</prop> -->
</props>
</property>
</bean>
@@ -220,27 +204,4 @@
<bean id="PasswordEncoder" class="org.springframework.security.authentication.encoding.Md5PasswordEncoder"/>
-<!-- These beans are responsible for statistics (used for debuging) -->
-<!--
- <bean id="hibernateStatisticsMBean" class="org.hibernate.jmx.StatisticsService">
- <property name="statisticsEnabled" value="true" />
- <property name="sessionFactory" value="#{SessionFactory}" />
- </bean>
-
- <bean id="mbeanServer" class="org.springframework.jmx.support.MBeanServerFactoryBean">
- <property name="locateExistingServerIfPossible" value="true" />
- </bean>
-
- <bean id="jmxExporter" class="org.springframework.jmx.export.MBeanExporter"
- lazy-init="false">
- <property name="server" ref="mbeanServer" />
- <property name="registrationBehaviorName" value="REGISTRATION_REPLACE_EXISTING"/>
- <property name="beans">
- <map>
- <entry key="yourkey:name=hibernateStatistics" value-ref="hibernateStatisticsMBean" />
- </map>
- </property>
- </bean>
--->
-
</beans>
diff --git a/persist/src/main/resources/dataSource.xml b/persist/src/main/resources/dataSource.xml
new file mode 100644
index 0000000000000000000000000000000000000000..e6551f4fb1e63988a4faaceb069c69fe2fb7de07
--- /dev/null
+++ b/persist/src/main/resources/dataSource.xml
@@ -0,0 +1,25 @@
+<beans xmlns="http://www.springframework.org/schema/beans"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:tx="http://www.springframework.org/schema/tx"
+ xmlns:context="http://www.springframework.org/schema/context"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans-4.0.xsd
+ http://www.springframework.org/schema/tx
+ http://www.springframework.org/schema/tx/spring-tx-4.0.xsd
+ http://www.springframework.org/schema/context
+ http://www.springframework.org/schema/context/spring-context-4.0.xsd">
+
+ <context:property-placeholder location="classpath:db.properties" />
+
+<!-- Data Source Declaration -->
+ <bean id="DataSource" class="com.mchange.v2.c3p0.ComboPooledDataSource" destroy-method="close">
+ <property name="driverClass" value="org.postgresql.Driver" />
+ <property name="jdbcUrl" value="${database.uri}" />
+ <property name="user" value="${database.username}" />
+ <property name="password" value="${database.password}" />
+ <property name="maxPoolSize" value="100" />
+ <property name="maxStatements" value="5" />
+ <property name="minPoolSize" value="5" />
+ </bean>
+
+</beans>
diff --git a/persist/src/main/resources/db.properties b/persist/src/main/resources/db.properties
new file mode 100644
index 0000000000000000000000000000000000000000..e1edfb39acf73ef0ad8d928ba01941bb4d87ac72
--- /dev/null
+++ b/persist/src/main/resources/db.properties
@@ -0,0 +1,3 @@
+database.uri=jdbc:postgresql://localhost:5432/map_viewer
+database.username=map_viewer
+database.password=123qweasdzxc
\ No newline at end of file
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java b/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java
index 494cdbda1c133287c00a6db01947ff660f73a1d8..03b6cad1942c420382e0e165f6ef8e59029c6a58 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java
@@ -56,7 +56,10 @@ import lcsb.mapviewer.persist.dao.user.UserDao;
@Transactional(value = "txManager")
@Rollback(true)
-@ContextConfiguration(locations = { "/applicationContext-persist.xml", "/test-applicationContext.xml" })
+@ContextConfiguration(locations = { "/applicationContext-persist.xml", //
+ "/test-applicationContext.xml", //
+ "/dataSource.xml" //
+ })
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class PersistTestFunctions {
private Logger logger = Logger.getLogger(PersistTestFunctions.class);
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/ReactomeTestFunctions.java b/reactome/src/test/java/lcsb/mapviewer/reactome/ReactomeTestFunctions.java
index 48dbbe2bf51456dbfe18a2bf280d36fc84bfc1c3..8ac8e12415f3623e38d4afc572f873e731e805c5 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/ReactomeTestFunctions.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/ReactomeTestFunctions.java
@@ -55,6 +55,7 @@ import org.xml.sax.SAXException;
"/applicationContext-reactome.xml", //
"/applicationContext-persist.xml", //
"/test-applicationContext.xml", //
+ "/dataSource.xml", //
})
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class ReactomeTestFunctions {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java b/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
index af2f8dcf6120fddefb942ed728c8a84d9e044e8e..504d6a7f6f4d5e20ff32c7197d8f423b86d742a5 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
@@ -63,8 +63,12 @@ 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 = { "/applicationContext-persist.xml", //
+ "/applicationContext-annotation.xml", //
+ "/applicationContext-service.xml", //
+ "/applicationContext-rest.xml", //
+ "/dataSource.xml", //
+})
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class RestTestFunctions {
private Logger logger = Logger.getLogger(RestTestFunctions.class);
@@ -200,9 +204,9 @@ 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());
diff --git a/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java b/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
index 869300e0881027ad3223efc0090c1256d688873c..be7a28143ec317cd966efc6bbf931ad7c175a5d5 100644
--- a/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
+++ b/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 = { "/applicationContext-annotation.xml", //
+ "/applicationContext-persist.xml", //
+ "/applicationContext-service.xml", //
+ "/dataSource.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;
diff --git a/web/src/main/webapp/WEB-INF/web.xml b/web/src/main/webapp/WEB-INF/web.xml
index d794ecf3da612eb4bcb4fb069329c11f3abdf88e..9b6aa5e3e08a46dd5469cc0163928c9c677034eb 100644
--- a/web/src/main/webapp/WEB-INF/web.xml
+++ b/web/src/main/webapp/WEB-INF/web.xml
@@ -18,6 +18,7 @@
classpath:applicationContext-persist.xml
classpath:applicationContext-rest.xml
classpath:applicationContext-service.xml
+ classpath:dataSource.xml
</param-value>
</context-param>
<context-param>
diff --git a/web/src/test/java/lcsb/mapviewer/bean/WebTestFunctions.java b/web/src/test/java/lcsb/mapviewer/bean/WebTestFunctions.java
index 35be8824267f92a04303aa84a0d2cfc5bb5d4968..fccf8ea97ff33d35499ff9af035184565b46f1f5 100644
--- a/web/src/test/java/lcsb/mapviewer/bean/WebTestFunctions.java
+++ b/web/src/test/java/lcsb/mapviewer/bean/WebTestFunctions.java
@@ -86,7 +86,11 @@ import lcsb.mapviewer.services.view.ModelViewFactory;
@Transactional(value = "txManager")
@Rollback(true)
-@ContextConfiguration(locations = { "/applicationContext-persist.xml", "/applicationContext-annotation.xml", "/applicationContext-service.xml" })
+@ContextConfiguration(locations = { "/applicationContext-persist.xml", //
+ "/applicationContext-annotation.xml", //
+ "/applicationContext-service.xml", //
+ "/dataSource.xml", //
+})
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class WebTestFunctions {
private Logger logger = Logger.getLogger(WebTestFunctions.class);
@@ -184,7 +188,7 @@ public abstract class WebTestFunctions {
protected ReactionDao reactionDao;
@Autowired
- protected ElementDao aliasDao;
+ protected ElementDao aliasDao;
@Autowired
protected ModelViewFactory modelViewFactory;