org.molgenis.omx.xgap.db

Class VariantJpaMapper

java.lang.Object

org.molgenis.framework.db.AbstractMapper<E>

org.molgenis.framework.db.jpa.AbstractJpaMapper<Variant>

org.molgenis.omx.xgap.db.VariantJpaMapper

All Implemented Interfaces:

Mapper<Variant>

public class VariantJpaMapper
extends AbstractJpaMapper<Variant>

Field Summary

Fields inherited from class org.molgenis.framework.db.AbstractMapper

BATCH_SIZE

Constructor Summary

Constructors

Constructor and Description
VariantJpaMapper(Database db)

Method Summary

Methods

Modifier and Type	Method and Description
Variant	create()
void	create(Variant entity) This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object
String	createFindSqlInclRules(QueryRule[] rules)
List<Variant>	createList(int size) Return EMPTY list of given allocated size
void	destroy(Variant variant)
void	edit(Variant variant)
int	executeAdd(List<? extends Variant> entities)
int	executeRemove(List<? extends Variant> entities)
int	executeUpdate(List<? extends Variant> entities)
FieldType	getFieldType(String fieldName)
String	getTableFieldName(String fieldName)
void	prepareFileAttachements(List<Variant> entities, File baseDir)
void	resolveForeignKeys(List<Variant> entities)
boolean	saveFileAttachements(List<Variant> entities, File baseDir)

Methods inherited from class org.molgenis.framework.db.jpa.AbstractJpaMapper

count, find, findById, getEntityClass, getEntityManager, removeMrefs, storeMrefs

Methods inherited from class org.molgenis.framework.db.AbstractMapper

add, add, getDatabase, remove, remove, update, update

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

VariantJpaMapper

public VariantJpaMapper(Database db)

Method Detail

createFindSqlInclRules

public String createFindSqlInclRules(QueryRule[] rules)
                              throws DatabaseException

Specified by:

createFindSqlInclRules in interface Mapper<Variant>

Specified by:

createFindSqlInclRules in class AbstractJpaMapper<Variant>

Throws:

DatabaseException

create

public void create(Variant entity)
            throws DatabaseException

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

Throws:

DatabaseException

destroy

public void destroy(Variant variant)
             throws DatabaseException

Throws:

DatabaseException

edit

public void edit(Variant variant)
          throws DatabaseException

Throws:

DatabaseException

executeAdd

public int executeAdd(List<? extends Variant> entities)
               throws DatabaseException

Specified by:

executeAdd in interface Mapper<Variant>

Specified by:

executeAdd in class AbstractMapper<Variant>

Throws:

DatabaseException

executeUpdate

public int executeUpdate(List<? extends Variant> entities)
                  throws DatabaseException

Specified by:

executeUpdate in interface Mapper<Variant>

Specified by:

executeUpdate in class AbstractMapper<Variant>

Throws:

DatabaseException

executeRemove

public int executeRemove(List<? extends Variant> entities)
                  throws DatabaseException

Specified by:

executeRemove in interface Mapper<Variant>

Specified by:

executeRemove in class AbstractMapper<Variant>

Throws:

DatabaseException

getTableFieldName

public String getTableFieldName(String fieldName)

Specified by:

getTableFieldName in interface Mapper<Variant>

Specified by:

getTableFieldName in class AbstractJpaMapper<Variant>

createList

public List<Variant> createList(int size)

Return EMPTY list of given allocated size

Specified by:

createList in interface Mapper<Variant>

Specified by:

createList in class AbstractMapper<Variant>

Parameters:

i - initial capacity of returned EMPTY list

Returns:

an EMPTY list with initial capacity given by size

create

public Variant create()

Specified by:

create in interface Mapper<Variant>

Specified by:

create in class AbstractJpaMapper<Variant>

resolveForeignKeys

public void resolveForeignKeys(List<Variant> entities)
                        throws DatabaseException,
                               ParseException

Specified by:

resolveForeignKeys in interface Mapper<Variant>

Specified by:

resolveForeignKeys in class AbstractJpaMapper<Variant>

Throws:

DatabaseException

ParseException

getFieldType

public FieldType getFieldType(String fieldName)

Specified by:

getFieldType in interface Mapper<Variant>

Specified by:

getFieldType in class AbstractJpaMapper<Variant>

prepareFileAttachements

public void prepareFileAttachements(List<Variant> entities,
                           File baseDir)
                             throws IOException

Specified by:

prepareFileAttachements in class AbstractMapper<Variant>

Throws:

IOException

saveFileAttachements

public boolean saveFileAttachements(List<Variant> entities,
                           File baseDir)
                             throws IOException

Specified by:

saveFileAttachements in class AbstractMapper<Variant>

Throws:

IOException