Package org.intermine.dataloader

Class IntegrationWriterDataTrackingImpl

java.lang.Object

org.intermine.dataloader.IntegrationWriterAbstractImpl

org.intermine.dataloader.IntegrationWriterDataTrackingImpl

All Implemented Interfaces:

IntegrationWriter, ObjectStore, ObjectStoreWriter

public class IntegrationWriterDataTrackingImpl
extends IntegrationWriterAbstractImpl

Priority-based implementation of IntegrationWriter. Allows field values to be chosen according to the relative priorities of the data sources that originated them.

Author:

Matthew Wakeling, Andrew Varley

Field Summary

Fields

Modifier and Type	Field	Description
protected DataTracker	dataTracker
protected IntPresentSet	duplicateObjects	This is a list of the objects in the destination database that we have written to as a non-skeleton more than once.
protected boolean	isDuplicates
protected PriorityConfig	priorityConfig
protected IntPresentSet	pureObjects	This is a list of the objects that did not merge with anything from a previous data source
protected IntPresentSet	skeletons
protected java.util.Set<java.lang.Class<?>>	trackerMissingClasses
protected IntPresentSet	writtenObjects	This is a list of the objects in the destination database that we have written to as a non-skeleton.

Fields inherited from class org.intermine.dataloader.IntegrationWriterAbstractImpl

beof, dbIdsStored, eof, FROM_DB, idMap, idMapOps, ignoreDuplicates, lastSource, osw, seenBrokenOneToMany, SKELETON, SOURCE, timeSpentRecursing

Fields inherited from interface org.intermine.objectstore.ObjectStore

SEQUENCE_IGNORE

Constructor Summary

Constructors

Constructor	Description
IntegrationWriterDataTrackingImpl(ObjectStoreWriter osw, DataTracker dataTracker)	Constructs a new instance of IntegrationWriterDataTrackingImpl.
IntegrationWriterDataTrackingImpl(ObjectStoreWriter osw, DataTracker dataTracker, java.util.Set<java.lang.Class<?>> trackerMissingClasses)	Constructs a new instance of IntegrationWriterDataTrackingImpl.

Method Summary

Modifier and Type	Method	Description
void	close()	Closes the connection associated with this ObjectStoreWriter
boolean	doTrackerFor(java.lang.Class<?> c)	Returns true if the given class is NOT a subclass of any of the classes in trackerMissingClasses.
DataTracker	getDataTracker()	Returns the data tracker being used.
static IntegrationWriterDataTrackingImpl	getInstance(java.lang.String osAlias, java.util.Properties props)	Creates a new instance of this class, given the properties defining it.
protected static IntegrationWriterDataTrackingImpl	getInstance(java.lang.String osAlias, java.util.Properties props, java.lang.Class<? extends IntegrationWriterDataTrackingImpl> iwClass, java.lang.Class<? extends DataTracker> trackerClass)	Creates a new IntegrationWriter instance of the specified class and with a specified DataTracker class plus properties.
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	reset()	Resets the IntegrationWriter, clearing the id map and the hints
protected InterMineObject	store(FastPathObject nimo, Source source, Source skelSource, int type)	Stores the given object in the objectstore.

Methods inherited from class org.intermine.dataloader.IntegrationWriterAbstractImpl

abortTransaction, addAllToBag, addToBag, addToBagFromQuery, addToCollection, assignMapping, batchCommitTransaction, beginTransaction, cacheObjectById, commitTransaction, copyField, count, createClob, createObjectStoreBag, delete, delete, estimate, execute, execute, execute, executeSingleton, executeSingleton, flushObjectById, getBaseEof, getComponentsForQuery, getEof, getEquivalentObjects, getMaxLimit, getMaxOffset, getMaxTime, getModel, getNewWriter, getObjectByExample, getObjectById, getObjectById, getObjectsByExample, getObjectsByIds, getObjectStore, getObjectStoreWriter, getSequence, getSerial, invalidateObjectById, isInTransaction, isMultiConnection, pilferObjectById, prefetchObjectById, removeAllFromBag, removeFromBag, replaceClob, setEof, setIgnoreDuplicates, store, store

Methods inherited from class java.lang.Object

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

Field Detail

dataTracker

protected DataTracker dataTracker

trackerMissingClasses

protected java.util.Set<java.lang.Class<?>> trackerMissingClasses

skeletons

protected IntPresentSet skeletons

pureObjects

protected IntPresentSet pureObjects

This is a list of the objects that did not merge with anything from a previous data source

writtenObjects

protected IntPresentSet writtenObjects

This is a list of the objects in the destination database that we have written to as a non-skeleton. This is so that we can notice if we write to a given object twice, given ignoreDuplicates, so we can tell the user if ignoreDuplicates is necessary.

duplicateObjects

protected IntPresentSet duplicateObjects

This is a list of the objects in the destination database that we have written to as a non-skeleton more than once.

isDuplicates

protected boolean isDuplicates

priorityConfig

protected PriorityConfig priorityConfig

Constructor Detail

IntegrationWriterDataTrackingImpl

public IntegrationWriterDataTrackingImpl(ObjectStoreWriter osw,
                                         DataTracker dataTracker)

Constructs a new instance of IntegrationWriterDataTrackingImpl.

Parameters:

osw - an instance of an ObjectStoreWriter, which we can use to access the database

dataTracker - an instance of DataTracker, which we can use to store data tracking information

IntegrationWriterDataTrackingImpl

public IntegrationWriterDataTrackingImpl(ObjectStoreWriter osw,
                                         DataTracker dataTracker,
                                         java.util.Set<java.lang.Class<?>> trackerMissingClasses)

Constructs a new instance of IntegrationWriterDataTrackingImpl.

Parameters:

osw - an instance of an ObjectStoreWriter, which we can use to access the database

dataTracker - an instance of DataTracker, which we can use to store data tracking information

trackerMissingClasses - a Set of classes for which DataTracker data is useless

Method Detail

getInstance

public static IntegrationWriterDataTrackingImpl getInstance(java.lang.String osAlias,
                                                            java.util.Properties props)
                                                     throws ObjectStoreException

Creates a new instance of this class, given the properties defining it.

Parameters:

osAlias - the alias of this objectstore

props - the Properties

Returns:

an instance of this class

Throws:

ObjectStoreException - sometimes

getInstance

protected static IntegrationWriterDataTrackingImpl getInstance(java.lang.String osAlias,
                                                               java.util.Properties props,
                                                               java.lang.Class<? extends IntegrationWriterDataTrackingImpl> iwClass,
                                                               java.lang.Class<? extends DataTracker> trackerClass)
                                                        throws ObjectStoreException

Creates a new IntegrationWriter instance of the specified class and with a specified DataTracker class plus properties.

Parameters:

osAlias - the alias of this objectstore

props - the Properties

iwClass - Class of IntegrationWriter to create - IntegrationWriterDataTrackingImpl or a subclass.

trackerClass - Class of DataTracker to use with IntegrationWriter

Returns:

an instance of this class

Throws:

ObjectStoreException - sometimes

reset

public void reset()

Resets the IntegrationWriter, clearing the id map and the hints

Overrides:

reset in class IntegrationWriterAbstractImpl

getMainSource

public 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.

Parameters:

name - the name of the data source

type - the source type

Returns:

a Source

getSkeletonSource

public 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.

Parameters:

name - the name of the data source

type - the source type

Returns:

a skeleton Source

getDataTracker

public DataTracker getDataTracker()

Returns the data tracker being used.

Returns:

dataTracker

doTrackerFor

public boolean doTrackerFor(java.lang.Class<?> c)

Returns true if the given class is NOT a subclass of any of the classes in trackerMissingClasses.

Parameters:

c - a Class

Returns:

a boolean

store

protected InterMineObject store(FastPathObject nimo,
                                Source source,
                                Source skelSource,
                                int type)
                         throws ObjectStoreException

Stores the given object in the objectstore. This method recurses into the object's fields according to the type variable.

Specified by:

store in class IntegrationWriterAbstractImpl

Parameters:

nimo - the object to store

source - the data Source to which to attribute the data

skelSource - the data Source to which to attribute skeleton data

type - the type of action required, from SOURCE, SKELETON, or FROM_DB

Returns:

the InterMineObject that was written to the database

Throws:

ObjectStoreException - if an error occurs in the underlying objectstore

close

public void close()
           throws ObjectStoreException

Closes the connection associated with this ObjectStoreWriter

Specified by:

close in interface ObjectStoreWriter

Overrides:

close in class IntegrationWriterAbstractImpl

Throws:

ObjectStoreException - if something goes wrong