Spring hibernate mongodb (#432)

* hibernate 5, spring 5, mongo driver 4

* migration to new mongodb java api to support all mongodb versions

magma-api/pom.xml

@@ -17,7 +17,7 @@
   <parent>
     <groupId>org.obiba.magma</groupId>
     <artifactId>magma</artifactId>
-    <version>3.1-SNAPSHOT</version>
+    <version>4.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

magma-beans/pom.xml

@@ -17,7 +17,7 @@
   <parent>
     <groupId>org.obiba.magma</groupId>
     <artifactId>magma</artifactId>
-    <version>3.1-SNAPSHOT</version>
+    <version>4.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

magma-crypt/pom.xml

@@ -17,7 +17,7 @@
   <parent>
     <groupId>org.obiba.magma</groupId>
     <artifactId>magma</artifactId>
-    <version>3.1-SNAPSHOT</version>
+    <version>4.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

magma-data-generator/pom.xml

@@ -17,7 +17,7 @@
   <parent>
     <groupId>org.obiba.magma</groupId>
     <artifactId>magma</artifactId>
-    <version>3.1-SNAPSHOT</version>
+    <version>4.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

magma-datasource-csv/pom.xml

@@ -17,7 +17,7 @@
   <parent>
     <groupId>org.obiba.magma</groupId>
     <artifactId>magma</artifactId>
-    <version>3.1-SNAPSHOT</version>
+    <version>4.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

magma-datasource-excel/pom.xml

@@ -17,7 +17,7 @@
   <parent>
     <groupId>org.obiba.magma</groupId>
     <artifactId>magma</artifactId>
-    <version>3.1-SNAPSHOT</version>
+    <version>4.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

magma-datasource-fs/pom.xml

@@ -17,7 +17,7 @@
   <parent>
     <groupId>org.obiba.magma</groupId>
     <artifactId>magma</artifactId>
-    <version>3.1-SNAPSHOT</version>
+    <version>4.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

magma-datasource-hibernate/pom.xml

@@ -17,7 +17,7 @@
   <parent>
     <groupId>org.obiba.magma</groupId>
     <artifactId>magma</artifactId>
-    <version>3.1-SNAPSHOT</version>
+    <version>4.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

magma-datasource-hibernate/src/main/java/org/obiba/magma/datasource/hibernate/HibernateDatasource.java

@@ -105,8 +105,10 @@ public ValueTableWriter createWriter(@NotNull String tableName, @NotNull String
       } else {
         // Create table transaction.
         ValueTableState valueTableState = new ValueTableState(tableName, entityType, getDatasourceState());
-        getSessionFactory().getCurrentSession().save(valueTableState);
-        getSessionFactory().getCurrentSession().refresh(valueTableState); //OPAL-2635
+        Session session = getSessionFactory().getCurrentSession();
+        session.save(valueTableState);
+        session.flush();
+        session.refresh(valueTableState); //OPAL-2635
         // Create a transaction for a new table
         valueTableTransaction = newTableTransaction(new HibernateValueTable(this, valueTableState), true);
       }
@@ -227,8 +229,10 @@ protected void onInitialise() {
     // If datasource not persisted, create the persisted DatasourceState.
     if(datasourceState == null) {
       datasourceState = new DatasourceState(getName());
-      sessionFactory.getCurrentSession().save(datasourceState);
-      sessionFactory.getCurrentSession().refresh(datasourceState); //OPAL-2635
+      Session session = sessionFactory.getCurrentSession();
+      session.save(datasourceState);
+      session.flush();
+      session.refresh(datasourceState); //OPAL-2635
     } else {
       // If already persisted, load the persisted attributes for that datasource.
       for(AttributeState attribute : datasourceState.getAttributes()) {

magma-datasource-hibernate/src/main/java/org/obiba/magma/datasource/hibernate/HibernateValueTableWriter.java

@@ -81,8 +81,8 @@ class HibernateValueTableWriter implements ValueTableWriter {
 
     session = valueTable.getDatasource().getSessionFactory().getCurrentSession();
     valueSourceFactory = new HibernateVariableValueSourceFactory(valueTable);
-    if(session.getFlushMode() != FlushMode.MANUAL) {
-      session.setFlushMode(FlushMode.MANUAL);
+    if(session.getHibernateFlushMode() != FlushMode.MANUAL) {
+      session.setHibernateFlushMode(FlushMode.MANUAL);
     }
 
     context = valueTable.createContext();
@@ -261,6 +261,7 @@ private HibernateValueSetWriter(@NotNull VariableEntity entity) {
         state = new ValueSetState(valueTable.getValueTableState(), variableEntityState);
         // Persists the ValueSet
         session.save(state);
+        session.flush();
         session.refresh(state); //OPAL-2635
         values = Maps.newHashMap();
         isNewValueSet = true;

magma-datasource-hibernate/src/main/java/org/obiba/magma/datasource/hibernate/cfg/MagmaDialectResolver.java

@@ -9,29 +9,41 @@
  */
 package org.obiba.magma.datasource.hibernate.cfg;
 
+import org.hibernate.dialect.Database;
 import org.hibernate.dialect.Dialect;
 import org.hibernate.dialect.HSQLDialect;
 import org.hibernate.dialect.MySQL5Dialect;
 import org.hibernate.engine.jdbc.dialect.internal.StandardDialectResolver;
 import org.hibernate.engine.jdbc.dialect.spi.DialectResolutionInfo;
+import org.hibernate.engine.jdbc.dialect.spi.DialectResolver;
 
 /**
  * Ensures usage of InnoDB for MySQL databases and uses custom dialect for HSQLDB, otherwise, fallback to default
  * behavior.
  * <p/>
  * This class is instantiated by Hibernate itself through the {@code hibernate.properties} file.
  */
-public class MagmaDialectResolver extends StandardDialectResolver {
+public class MagmaDialectResolver implements DialectResolver {
 
   private static final long serialVersionUID = 6167226108895659666L;
 
   @Override
   @SuppressWarnings("ChainOfInstanceofChecks")
   public Dialect resolveDialect(DialectResolutionInfo info) {
-    Dialect dialect = super.resolveDialect(info);
+    Dialect dialect = resolveStandardDialect(info);
     if(dialect instanceof MySQL5Dialect) return new MySQL5InnoDbUtf8Dialect();
     if(dialect instanceof HSQLDialect) return new MagmaHSQLDialect();
     return dialect;
   }
 
+  private Dialect resolveStandardDialect(DialectResolutionInfo info) {
+    for ( Database database : Database.values() ) {
+      Dialect dialect = database.resolveDialect( info );
+      if ( dialect != null ) {
+        return dialect;
+      }
+    }
+    return null;
+  }
+
 }

magma-datasource-hibernate/src/main/java/org/obiba/magma/datasource/hibernate/converter/VariableEntityConverter.java

@@ -31,7 +31,7 @@ public VariableEntityState marshal(VariableEntity variableEntity, HibernateMarsh
     if(variableEntityState == null) {
       variableEntityState = new VariableEntityState(variableEntity.getIdentifier(), variableEntity.getType());
       context.getSessionFactory().getCurrentSession().save(variableEntityState);
-      context.getSessionFactory().getCurrentSession().refresh(variableEntityState); //OPAL-2635
+      //context.getSessionFactory().getCurrentSession().refresh(variableEntityState); //OPAL-2635
     }
 
     return variableEntityState;

magma-datasource-hibernate/src/main/java/org/obiba/magma/datasource/hibernate/support/LocalSessionFactoryProvider.java

@@ -10,21 +10,21 @@
 
 package org.obiba.magma.datasource.hibernate.support;
 
-import java.util.Properties;
-
-import javax.annotation.Nullable;
-import javax.sql.DataSource;
-import javax.validation.constraints.NotNull;
-
 import org.hibernate.SessionFactory;
+import org.hibernate.boot.model.naming.ImplicitNamingStrategyLegacyHbmImpl;
 import org.hibernate.cfg.Environment;
-import org.hibernate.cfg.ImprovedNamingStrategy;
+import org.obiba.core.service.impl.hibernate.PhysicalNamingStrategyImpl;
 import org.obiba.magma.Initialisable;
 import org.obiba.magma.MagmaRuntimeException;
 import org.obiba.magma.datasource.hibernate.SessionFactoryProvider;
 import org.obiba.magma.datasource.hibernate.cfg.HibernateConfigurationHelper;
 import org.obiba.magma.datasource.hibernate.cfg.MagmaDialectResolver;
-import org.springframework.orm.hibernate4.LocalSessionFactoryBuilder;
+import org.springframework.orm.hibernate5.LocalSessionFactoryBuilder;
+
+import javax.annotation.Nullable;
+import javax.sql.DataSource;
+import javax.validation.constraints.NotNull;
+import java.util.Properties;
 
 public class LocalSessionFactoryProvider implements SessionFactoryProvider, Initialisable {
 
@@ -53,7 +53,8 @@ public void initialise() {
     // Set some reasonable defaults
     LocalSessionFactoryBuilder builder = new LocalSessionFactoryBuilder(dataSource);
     builder.addAnnotatedClasses(HibernateConfigurationHelper.getAnnotatedTypesAsArray());
-    builder.setNamingStrategy(ImprovedNamingStrategy.INSTANCE);
+    builder.setImplicitNamingStrategy(ImplicitNamingStrategyLegacyHbmImpl.INSTANCE);
+    builder.setPhysicalNamingStrategy(PhysicalNamingStrategyImpl.INSTANCE);
     builder.setProperty(Environment.DIALECT, dialect);
     builder.setProperty(Environment.HBM2DDL_AUTO, "update");
     builder.setProperty(Environment.USE_SECOND_LEVEL_CACHE, "true");

magma-datasource-hibernate/src/main/java/org/obiba/magma/datasource/hibernate/type/ValueHibernateType.java

@@ -10,27 +10,24 @@
 
 package org.obiba.magma.datasource.hibernate.type;
 
-import java.io.StringReader;
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.sql.Types;
-import java.util.Map;
-
-import javax.annotation.Nullable;
-
-import org.dom4j.Node;
+import com.google.common.base.Strings;
 import org.hibernate.HibernateException;
 import org.hibernate.MappingException;
+import org.hibernate.engine.jdbc.Size;
 import org.hibernate.engine.spi.Mapping;
 import org.hibernate.engine.spi.SessionFactoryImplementor;
-import org.hibernate.engine.spi.SessionImplementor;
-import org.hibernate.metamodel.relational.Size;
+import org.hibernate.engine.spi.SharedSessionContractImplementor;
 import org.hibernate.type.AbstractType;
 import org.obiba.magma.Value;
 import org.obiba.magma.ValueType;
 
-import com.google.common.base.Strings;
+import javax.annotation.Nullable;
+import java.io.StringReader;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.sql.Types;
+import java.util.Map;
 
 /**
  * A Hibernate Type for persisting {@code Value} instances. The strategy uses 3 columns:
@@ -54,28 +51,30 @@ public String getName() {
     return "Value";
   }
 
-  @Override
-  public boolean isDirty(Object old, Object current, boolean[] checkable, SessionImplementor session)
-      throws HibernateException {
-    return !old.equals(current);
-  }
-
   @Override
   public boolean isMutable() {
     // Value instances are immutable
     return false;
   }
 
   @Override
-  public Object nullSafeGet(ResultSet rs, String name, SessionImplementor session, Object owner)
-      throws HibernateException, SQLException {
-    throw new UnsupportedOperationException();
+  public Object replace(Object original, Object target, SharedSessionContractImplementor session, Object owner, Map copyCache) throws HibernateException {
+    return null;
+  }
+
+  @Override
+  public Class<?> getReturnedClass() {
+    return Value.class;
+  }
+
+  @Override
+  public boolean isDirty(Object oldState, Object currentState, boolean[] checkable, SharedSessionContractImplementor session) throws HibernateException {
+    return !oldState.equals(currentState);
   }
 
   @Nullable
   @Override
-  public Object nullSafeGet(ResultSet rs, String[] names, SessionImplementor session, Object owner)
-      throws HibernateException, SQLException {
+  public Object nullSafeGet(ResultSet rs, String[] names, SharedSessionContractImplementor session, Object owner) throws HibernateException, SQLException {
     String valueTypeName = rs.getString(names[0]);
     // Even when the column is NOT NULL, a SELECT statement can return NULL (using a left join for example).
     // When this column is null, we cannot construct a valid {@code Value} instance, so this method returns null
@@ -89,8 +88,12 @@ public Object nullSafeGet(ResultSet rs, String[] names, SessionImplementor sessi
   }
 
   @Override
-  public void nullSafeSet(PreparedStatement st, Object obj, int index, boolean[] settable, SessionImplementor session)
-      throws HibernateException, SQLException {
+  public Object nullSafeGet(ResultSet rs, String name, SharedSessionContractImplementor session, Object owner) throws HibernateException, SQLException {
+    throw new UnsupportedOperationException();
+  }
+
+  @Override
+  public void nullSafeSet(PreparedStatement st, Object obj, int index, boolean[] settable, SharedSessionContractImplementor session) throws HibernateException, SQLException {
     Value value = (Value) obj;
 
     int offset = 0;
@@ -106,38 +109,14 @@ public void nullSafeSet(PreparedStatement st, Object obj, int index, boolean[] s
   }
 
   @Override
-  public void nullSafeSet(PreparedStatement st, Object obj, int index, SessionImplementor session)
-      throws HibernateException, SQLException {
+  public void nullSafeSet(PreparedStatement st, Object obj, int index, SharedSessionContractImplementor session) throws HibernateException, SQLException {
     Value value = (Value) obj;
     st.setString(index, value.getValueType().getName());
     st.setBoolean(index + 1, value.isSequence());
     String stringValue = Strings.nullToEmpty(value.isNull() ? null : value.toString());
     st.setClob(index + 2, new StringReader(stringValue), stringValue.length());
   }
 
-  @Override
-  public Class<?> getReturnedClass() {
-    return Value.class;
-  }
-
-  @Override
-  @SuppressWarnings({ "unchecked", "rawtypes" })
-  public Object replace(Object original, Object target, SessionImplementor session, Object owner, Map copyCache)
-      throws HibernateException {
-    // It is safe to return the original parameter since Value instances are immutable
-    return original;
-  }
-
-  @Override
-  public Object fromXMLNode(Node xml, Mapping factory) throws HibernateException {
-    throw new UnsupportedOperationException();
-  }
-
-  @Override
-  public void setToXMLNode(Node node, Object value, SessionFactoryImplementor factory) throws HibernateException {
-    throw new UnsupportedOperationException();
-  }
-
   @Override
   public int[] sqlTypes(Mapping mapping) throws MappingException {
     return new int[] { Types.VARCHAR, Types.BIT, Types.CLOB };