Package org.intermine.dataloader

Interface IntegrationWriter

All Superinterfaces:

ObjectStore, ObjectStoreWriter

All Known Implementing Classes:

IntegrationWriterAbstractImpl, IntegrationWriterDataTrackingImpl

public interface IntegrationWriter
extends ObjectStoreWriter

Define methods needed to deal with integration when writing to an ObjectStore. To retain O/R mapping independence implementations of this interface should delegate writing to a mapping tool specific implementation of ObjectStoreWriter.

Author:

Richard Smith, Matthew Wakeling

Field Summary

Fields inherited from interface org.intermine.objectstore.ObjectStore

SEQUENCE_IGNORE

Method Summary

Modifier and Type	Method	Description
Source	getMainSource(java.lang.String name, java.lang.String type)	Converts a string describing the data source into a Source object suitable for passing to the store method as the main source.
Source	getSkeletonSource(java.lang.String name, java.lang.String type)	Converts a string describing the data source into a Source object suitable for passing to the store method as the skeleton source.
void	setIgnoreDuplicates(boolean ignoreDuplicates)	Tell this IntegrationWriter whether to ignore duplicate objects from the same source.
void	store(FastPathObject o, Source source, Source skelSource)	Stores the given object in the 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

Methods inherited from interface org.intermine.objectstore.ObjectStoreWriter

abortTransaction, addAllToBag, addToBag, addToBagFromQuery, addToCollection, batchCommitTransaction, beginTransaction, close, commitTransaction, delete, delete, getObjectStore, isInTransaction, removeAllFromBag, removeFromBag, replaceClob, store

Method Detail

store

void store(FastPathObject o,
           Source source,
           Source skelSource)
    throws ObjectStoreException

Stores the given object in the objectstore. To update an objectstore with data in the form of an interconnected graph of objects, call this method on each of the objects in that structure. This method will take care of merging objects, and resolving field priority issues.

Parameters:

o - the object to store

source - the data Source to which to attribute the data

skelSource - the data Source to which to attribute skeleton data

Throws:

ObjectStoreException - if an error occurs in the underlying objectstore

getMainSource

Source getMainSource(java.lang.String name,
                     java.lang.String type)
              throws ObjectStoreException

Converts a string describing the data source into a Source object suitable for passing to the store method as the main source.

Parameters:

name - the name of the data source

type - the source type

Returns:

a Source

Throws:

ObjectStoreException - if something goes wrong

getSkeletonSource

Source getSkeletonSource(java.lang.String name,
                         java.lang.String type)
                  throws ObjectStoreException

Converts a string describing the data source into a Source object suitable for passing to the store method as the skeleton source.

Parameters:

name - the name of the data source

type - the source type

Returns:

a skeleton Source

Throws:

ObjectStoreException - if something goes wrong

setIgnoreDuplicates

void setIgnoreDuplicates(boolean ignoreDuplicates)

Tell this IntegrationWriter whether to ignore duplicate objects from the same source. ALL DUPLICATES OF THE OBJECT MUST HAVE THE SAME FIELDS FILLED IN WITH THE SAME DATA. Data that differs between copies will result in undefined behaviour as so what data will appear in the destination database. Data that differs in primary keys may result in an exception being thrown during data loading. Note that setting a field to null differs from another copy with the field set to a value.

Parameters:

ignoreDuplicates - the value of ignoreDuplicates