Hi,
I have an abstract class PDBElement and two concrete subclasses Residue and Atom which inherits of it.
These are my mapping files:
Code:
<?xml version="1.0"?>
<!DOCTYPE hibernate-mapping PUBLIC
"-//Hibernate/Hibernate Mapping DTD 3.0//EN"
"http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
<hibernate-mapping>
<class name="org.mmb.model.PDBElement" table="PDBElement" abstract="true">
<id name="pdbElementId">
<generator class="native"/>
</id>
<many-to-one name="pdbEntry" class="org.mmb.model.PDBEntry" column="idCode"/>
<property name="model"/>
</class>
</hibernate-mapping>
Code:
<?xml version="1.0"?>
<!DOCTYPE hibernate-mapping PUBLIC
"-//Hibernate/Hibernate Mapping DTD 3.0//EN"
"http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
<hibernate-mapping>
<joined-subclass name="org.mmb.model.Atom" extends="org.mmb.model.PDBElement" table="Atom">
<key column="pdbElementId"/>
<property name="name"/>
<property name="serial"/>
<property name="altLoc"/>
<property name="tempFactor"/>
<property name="element"/>
<many-to-one name="residue" class="org.mmb.model.Residue" column="residueId"/>
</joined-subclass>
</hibernate-mapping>
Code:
<?xml version="1.0"?>
<!DOCTYPE hibernate-mapping PUBLIC
"-//Hibernate/Hibernate Mapping DTD 3.0//EN"
"http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
<hibernate-mapping>
<joined-subclass name="org.mmb.model.Residue" extends="org.mmb.model.PDBElement" table="Residue">
<key column="pdbElementId"/>
<property name="resName"/>
<property name="chainId"/>
<property name="resSeq"/>
<property name="insertionCode" column="iCode"/>
</joined-subclass>
</hibernate-mapping>
When the database is consistent with this structure then there is no problem. By consistent I mean that if it exists a row in table PDBElement then it must exist another one in any of the two concrete tables (Residue or Atom). If the database is not consistent (there is a row in PDBElement but there is no concrete instance) I begin to have problems. I know that the point should be to avoid having this inconsistent situation, but the database is accessed for so many applications (some of them out of my own control) and I would need to shield my application of these kind of problems.
For example, I have another entity (PDBEntry) with the following mapping file:
Code:
<?xml version="1.0"?>
<!DOCTYPE hibernate-mapping PUBLIC
"-//Hibernate/Hibernate Mapping DTD 3.0//EN"
"http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
<hibernate-mapping>
<class name="org.mmb.model.PDBEntry" table="entries">
<id name="idCode" type="string"/>
<set name="simulations" inverse="true">
<key column="pdbCode"/>
<one-to-many class="org.mmb.model.Simulation"/>
</set>
<set name="pdbElements" inverse="true">
<key column="idCode"/>
<one-to-many class="org.mmb.model.PDBElement"/>
</set>
<map name="dataSets" table="entries_DataSet">
<key column="pdbCode" not-null="true"/>
<map-key formula="dataSetId" type="string"/>
<many-to-many class="org.mmb.model.DataSet" column="dataSetId"/>
</map>
<property name="header"/>
<property name="ascDate"/>
<property name="compound"/>
<property name="source"/>
<property name="autors"/>
<property name="resolution"/>
<property name="expType"/>
<property name="type"/>
<property name="hetnam"/>
</class>
</hibernate-mapping>
When I try to execute the following code:
Code:
...
PDBEntry entry = ...
entry.getPdbElements();
...
where
Code:
public Set<PDBElement> getPdbElements()
{
return pdbElements;
}
then I get the following stack error:
Code:
[java] org.hibernate.InstantiationException: Cannot instantiate abstract class or interface: org.mmb.model.PDBElement
[java] at org.hibernate.tuple.PojoInstantiator.instantiate(PojoInstantiator.java:79)
[java] at org.hibernate.tuple.PojoInstantiator.instantiate(PojoInstantiator.java:106)
[java] at org.hibernate.tuple.AbstractEntityTuplizer.instantiate(AbstractEntityTuplizer.java:344)
[java] at org.hibernate.persister.entity.AbstractEntityPersister.instantiate(AbstractEntityPersister.java:3272)
[java] at org.hibernate.impl.SessionImpl.instantiate(SessionImpl.java:1239)
[java] at org.hibernate.impl.SessionImpl.instantiate(SessionImpl.java:1228)
[java] at org.hibernate.loader.Loader.instanceNotYetLoaded(Loader.java:1291)
[java] at org.hibernate.loader.Loader.getRow(Loader.java:1197)
[java] at org.hibernate.loader.Loader.getRowFromResultSet(Loader.java:569)
[java] at org.hibernate.loader.Loader.doQuery(Loader.java:689)
[java] at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224)
[java] at org.hibernate.loader.Loader.loadCollection(Loader.java:1919)
[java] at org.hibernate.loader.collection.CollectionLoader.initialize(CollectionLoader.java:36)
[java] at org.hibernate.persister.collection.AbstractCollectionPersister.initialize(AbstractCollectionPersister.java:520)
[java] at org.hibernate.event.def.DefaultInitializeCollectionEventListener.onInitializeCollection(DefaultInitializeCollectionEventListener.java:60)
[java] at org.hibernate.impl.SessionImpl.initializeCollection(SessionImpl.java:1676)
[java] at org.hibernate.collection.AbstractPersistentCollection.initialize(AbstractPersistentCollection.java:344)
[java] at org.hibernate.collection.AbstractPersistentCollection.read(AbstractPersistentCollection.java:86)
[java] at org.hibernate.collection.PersistentSet.iterator(PersistentSet.java:138)
[java] at org.mmb.model.database.DatabaseConnector.deletePDBElementsByPDBId(DatabaseConnector.java:430)
[java] at org.mmb.model.database.PDBParserHelper.startElement(PDBParserHelper.java:136)
[java] at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)
[java] at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source)
[java] at org.apache.xerces.impl.XMLNSDocumentScannerImpl$NSContentDispatcher.scanRootElementHook(Unknown Source)
[java] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
[java] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
[java] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
[java] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
[java] at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
[java] at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
[java] at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
[java] at javax.xml.parsers.SAXParser.parse(SAXParser.java:198)
[java] at org.mmb.model.database.PDBParser.populatePDBElements(PDBParser.java:190)
[java] at org.mmb.model.database.PDBParser.main(PDBParser.java:260)
Any idea to solve the problem? I've tried some things but I got no success and I'm beginning to get crazy :-P
Thanks
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