Package org.intermine.objectstore

Interface ObjectStoreWriter

All Superinterfaces:

ObjectStore

All Known Subinterfaces:

IntegrationWriter

All Known Implementing Classes:

IntegrationWriterAbstractImpl, IntegrationWriterDataTrackingImpl, ObjectStoreWriterInterMineImpl

public interface ObjectStoreWriter
extends ObjectStore

Store, update, and delete objects

Author:

Mark Woodbridge

Field Summary

Fields inherited from interface org.intermine.objectstore.ObjectStore

SEQUENCE_IGNORE

Method Summary

Modifier and Type	Method	Description
void	abortTransaction()	Request that the ObjectStoreWriter aborts and closes the transaction
void	addAllToBag(ObjectStoreBag osb, java.util.Collection<java.lang.Integer> coll)	Adds a collection of elements to an ObjectStoreBag.
void	addToBag(ObjectStoreBag osb, java.lang.Integer element)	Adds an element to an ObjectStoreBag.
void	addToBagFromQuery(ObjectStoreBag osb, Query q)	Adds elements to an ObjectStoreBag from the results of a Query.
void	addToCollection(java.lang.Integer hasId, java.lang.Class<?> clazz, java.lang.String fieldName, java.lang.Integer hadId)	Place an object in a many-to-many collection of another object.
void	batchCommitTransaction()	Request that the ObjectStoreWriter commits and closes the transaction and then opens a new one, without guaranteeing that the operation is finished before this method returns.
void	beginTransaction()	Request that the ObjectStoreWriter begins a transaction
void	close()	Closes the connection associated with this ObjectStoreWriter
void	commitTransaction()	Request that the ObjectStoreWriter commits and closes the transaction
void	delete(InterMineObject o)	Delete an object from this ObjectStore
void	delete(QueryClass qc, Constraint c)	Deletes a set of objects from this ObjectStore.
ObjectStore	getObjectStore()	Retrieve this Writer's ObjectStore.
boolean	isInTransaction()	Check whether the ObjectStoreWriter is performing a transaction
void	removeAllFromBag(ObjectStoreBag osb, java.util.Collection<java.lang.Integer> coll)	Removes a collection of elements from an ObjectStoreBag.
void	removeFromBag(ObjectStoreBag osb, java.lang.Integer element)	Removes an element from an ObjectStoreBag.
void	replaceClob(Clob clob, java.lang.String text)	Replaces the contents of the given Clob with the given String.
void	store(java.lang.Object o)	Store an object in this ObjectStore.

Methods inherited from interface org.intermine.objectstore.ObjectStore

cacheObjectById, count, createClob, createObjectStoreBag, estimate, execute, execute, execute, executeSingleton, executeSingleton, flushObjectById, getComponentsForQuery, getMaxLimit, getMaxOffset, getMaxTime, getModel, getNewWriter, getObjectByExample, getObjectById, getObjectById, getObjectsByExample, getObjectsByIds, getSequence, getSerial, invalidateObjectById, isMultiConnection, pilferObjectById, prefetchObjectById

Method Detail

getObjectStore

ObjectStore getObjectStore()

Retrieve this Writer's ObjectStore. This ObjectStoreWriter is a read-write extension to the read-only ObjectStore. This ObjectStoreWriter uses a single database connection in order to allow proper transaction support - use the ObjectStore for general read-only access.

Returns:

the ObjectStore

store

void store(java.lang.Object o)
    throws ObjectStoreException

Store an object in this ObjectStore. If the ID of this object is not set, it will be set to a previously unused value. If the ID matches the ID of an object already in the objectstore, then an update operation is performed - otherwise a store operation is performed.
Attributes and references of the stored object will be set to those of the provided object. Collections of the stored object will contain the union of the contents of any pre-existing stored object, and the contents of the provided object. There is currently no way to remove entries from a collection of a stored object.
Any objects referred to by this object will have their ID set in a similar way to this object. This object will be stored with references and collections using those IDs, however those objects will not be stored themselves. Therefore, the objectstore will be inconsistent until those objects are also stored.
If bidirectional relationships are not consistent in the objects being stored, then the behaviour of the store method is not defined. Specifically, one-to-one relationships must be stored on both sides. For example, if A has a relationship with B1 in the database, and we store a new A that has a relationship with B2, then we must also store B2 with a relationship back to A (to complete the relationship), and store B1 (to completely break the old relationship),

Parameters:

o - the object to store

Throws:

ObjectStoreException - if an error occurs during storage of the object

delete

void delete(InterMineObject o)
     throws ObjectStoreException

Delete an object from this ObjectStore

Parameters:

o - the object to delete

Throws:

ObjectStoreException - if an error occurs during deletion of the object

delete

void delete(QueryClass qc,
            Constraint c)
     throws ObjectStoreException

Deletes a set of objects from this ObjectStore.

Parameters:

qc - a QueryClass for the class of objects to delete. The class given in the query class must not inherit from org.intermine.model.InterMineObject.

c - a Constraint based on the QueryClass to filter the objects to delete, or null to delete all objects

Throws:

ObjectStoreException - if an error occurs while deleting the objects

addToCollection

void addToCollection(java.lang.Integer hasId,
                     java.lang.Class<?> clazz,
                     java.lang.String fieldName,
                     java.lang.Integer hadId)
              throws ObjectStoreException

Place an object in a many-to-many collection of another object. This method provides a way to place an object into a collection in another object without having either object loaded in memory. Only the IDs of the two objects are required, along with the name of the collection.

Parameters:

hasId - the ID of the object that has the collection

clazz - the class of the object that has the collection

fieldName - the name of the collection

hadId - the ID of the object to place in the collection

Throws:

ObjectStoreException - if a problem occurs

addToBag

void addToBag(ObjectStoreBag osb,
              java.lang.Integer element)
       throws ObjectStoreException

Adds an element to an ObjectStoreBag.

Parameters:

osb - an ObjectStoreBag

element - an Integer to add to the bag

Throws:

ObjectStoreException - if an error occurs

addAllToBag

void addAllToBag(ObjectStoreBag osb,
                 java.util.Collection<java.lang.Integer> coll)
          throws ObjectStoreException

Adds a collection of elements to an ObjectStoreBag.

Parameters:

osb - an ObjectStoreBag

coll - a Collection of Integers

Throws:

ObjectStoreException - if an error occurs

removeFromBag

void removeFromBag(ObjectStoreBag osb,
                   java.lang.Integer element)
            throws ObjectStoreException

Removes an element from an ObjectStoreBag.

Parameters:

osb - an ObjectStoreBag

element - an Integer to add to the bag

Throws:

ObjectStoreException - if an error occurs

removeAllFromBag

void removeAllFromBag(ObjectStoreBag osb,
                      java.util.Collection<java.lang.Integer> coll)
               throws ObjectStoreException

Removes a collection of elements from an ObjectStoreBag.

Parameters:

osb - an ObjectStoreBag

coll - a Collection of Integers

Throws:

ObjectStoreException - if an error occurs

addToBagFromQuery

void addToBagFromQuery(ObjectStoreBag osb,
                       Query q)
                throws ObjectStoreException

Adds elements to an ObjectStoreBag from the results of a Query. The data may not be loaded into Java, so this is a performance improvement method. For example, in SQL this method may issue a command like "INSERT INTO bag SELECT ...".

Parameters:

osb - an ObjectStoreBag

q - an objectstore Query, which contains only one result column, which is a suitable type for insertion into the given bag

Throws:

ObjectStoreException - if something goes wrong

replaceClob

void replaceClob(Clob clob,
                 java.lang.String text)
          throws ObjectStoreException

Replaces the contents of the given Clob with the given String.

Parameters:

clob - the Clob to write to

text - the text to write to the Clob

Throws:

ObjectStoreException - if something goes wrong

isInTransaction

boolean isInTransaction()
                 throws ObjectStoreException

Check whether the ObjectStoreWriter is performing a transaction

Returns:

true if in a transaction, false otherwise

Throws:

ObjectStoreException - if an error occurs

beginTransaction

void beginTransaction()
               throws ObjectStoreException

Request that the ObjectStoreWriter begins a transaction

Throws:

ObjectStoreException - if a transaction is in progress, or is aborted

commitTransaction

void commitTransaction()
                throws ObjectStoreException

Request that the ObjectStoreWriter commits and closes the transaction

Throws:

ObjectStoreException - if a transaction is not in progress, or is aborted

abortTransaction

void abortTransaction()
               throws ObjectStoreException

Request that the ObjectStoreWriter aborts and closes the transaction

Throws:

ObjectStoreException - if a transaction is not in progress

batchCommitTransaction

void batchCommitTransaction()
                     throws ObjectStoreException

Request that the ObjectStoreWriter commits and closes the transaction and then opens a new one, without guaranteeing that the operation is finished before this method returns. Note that writes that are made AFTER this method may be treated as if they were BEFORE this method and be committed in the transaction.

Throws:

ObjectStoreException - if an error occurs

close

void close()
    throws ObjectStoreException

Closes the connection associated with this ObjectStoreWriter

Throws:

ObjectStoreException - if something goes wrong