Package org.intermine.dataloader

Class BaseEquivalentObjectFetcher

java.lang.Object

org.intermine.dataloader.BaseEquivalentObjectFetcher

All Implemented Interfaces:

EquivalentObjectFetcher

Direct Known Subclasses:

HintingFetcher

public class BaseEquivalentObjectFetcher
extends java.lang.Object
implements EquivalentObjectFetcher

Class providing methods to look up equivalent objects by primary key in a production objectstore.

Author:

Matthew Wakeling

Field Summary

Fields

Modifier and Type	Field	Description
protected IntToIntMap	idMap
protected ObjectStore	lookupOs
protected Model	model
protected java.util.Map<java.lang.Class<? extends InterMineObject>,java.lang.Integer>	summaryCallCounts
protected java.util.Map<java.lang.Class<? extends InterMineObject>,java.lang.Integer>	summaryCounts
protected java.util.Map<java.lang.Class<? extends InterMineObject>,java.lang.Long>	summaryTimes

Constructor Summary

Constructors

Constructor	Description
BaseEquivalentObjectFetcher(Model model, IntToIntMap idMap, ObjectStore lookupOs)	Constructor for this EquivalentObjectFetcher.

Method Summary

Modifier and Type	Method	Description
void	close(Source source)	Close method - prints out summary data.
java.util.Set<Query>	createPKQueriesForClass(InterMineObject obj, Source source, boolean queryNulls, ClassDescriptor cld)	Generates a query that searches for all objects in the database equivalent to a given example object, considering only one of it's classes.
Query	createPKQuery(InterMineObject obj, Source source, boolean queryNulls)	Generates a query that searches for all objects in the database equivalent to a given example object according to the primary keys defined for the given source.
void	createPKQueryForPK(InterMineObject obj, boolean queryNulls, ClassDescriptor cld, PrimaryKey pk, Source source, java.util.Set<Query> returnSet)	Adds a Query to handle a primary key to a Set.
IntToIntMap	getIdMap()	Returns the IdMap used.
ObjectStore	getLookupOs()	Returns the objectstore that contains the equivalent objects.
Model	getModel()	Returns the Model used.
protected java.lang.StringBuffer	getSummary(Source source)	Returns a StringBuffer containing summary information.
java.util.Set<InterMineObject>	queryEquivalentObjects(InterMineObject obj, Source source)	Returns a Set of objects that are equivalent to the given object, according to the primary keys defined by the given Source.

Methods inherited from class java.lang.Object

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

Field Detail

model

protected Model model

idMap

protected IntToIntMap idMap

lookupOs

protected ObjectStore lookupOs

summaryTimes

protected java.util.Map<java.lang.Class<? extends InterMineObject>,java.lang.Long> summaryTimes

summaryCounts

protected java.util.Map<java.lang.Class<? extends InterMineObject>,java.lang.Integer> summaryCounts

summaryCallCounts

protected java.util.Map<java.lang.Class<? extends InterMineObject>,java.lang.Integer> summaryCallCounts

Constructor Detail

BaseEquivalentObjectFetcher

public BaseEquivalentObjectFetcher(Model model,
                                   IntToIntMap idMap,
                                   ObjectStore lookupOs)

Constructor for this EquivalentObjectFetcher.

Parameters:

model - a Model

idMap - an IntToIntMap from source IDs to destination IDs

lookupOs - an ObjectStore for the production database

Method Detail

getModel

public Model getModel()

Returns the Model used.

Returns:

a Model

getIdMap

public IntToIntMap getIdMap()

Returns the IdMap used.

Returns:

an IntToIntMap

getLookupOs

public ObjectStore getLookupOs()

Returns the objectstore that contains the equivalent objects.

Returns:

an ObjectStore

close

public void close(Source source)

Close method - prints out summary data.

Parameters:

source - the Source used

getSummary

protected java.lang.StringBuffer getSummary(Source source)

Returns a StringBuffer containing summary information.

Parameters:

source - the Source used

Returns:

a StringBuffer

queryEquivalentObjects

public java.util.Set<InterMineObject> queryEquivalentObjects(InterMineObject obj,
                                                             Source source)
                                                      throws ObjectStoreException

Returns a Set of objects that are equivalent to the given object, according to the primary keys defined by the given Source.

Specified by:

queryEquivalentObjects in interface EquivalentObjectFetcher

Parameters:

obj - the Object to look for

source - the data Source

Returns:

a Set of InterMineObjects

Throws:

ObjectStoreException - if an error occurs

createPKQuery

public Query createPKQuery(InterMineObject obj,
                           Source source,
                           boolean queryNulls)
                    throws MetaDataException

Generates a query that searches for all objects in the database equivalent to a given example object according to the primary keys defined for the given source.

Specified by:

createPKQuery in interface EquivalentObjectFetcher

Parameters:

obj - the Object to take as an example

source - the Source database

queryNulls - if true allow primary keys to contain null values if the template obj has nulls. If false the Query will constrain only those keys that have a value in the template obj

Returns:

a new Query (or null if all the primary keys from obj contain a null)

Throws:

MetaDataException - if anything goes wrong

createPKQueriesForClass

public java.util.Set<Query> createPKQueriesForClass(InterMineObject obj,
                                                    Source source,
                                                    boolean queryNulls,
                                                    ClassDescriptor cld)
                                             throws MetaDataException

Generates a query that searches for all objects in the database equivalent to a given example object, considering only one of it's classes.

Specified by:

createPKQueriesForClass in interface EquivalentObjectFetcher

Parameters:

obj - the Object to take as an example

source - the Source database

queryNulls - if true allow primary keys to contain null values if the template obj has nulls. If false the Query will constrain only those keys that have a value in the template obj

cld - one of the classes that obj is. Only primary keys for this classes will be considered

Returns:

a new Query (or null if all the primary keys from obj contain a null)

Throws:

MetaDataException - if anything goes wrong

createPKQueryForPK

public void createPKQueryForPK(InterMineObject obj,
                               boolean queryNulls,
                               ClassDescriptor cld,
                               PrimaryKey pk,
                               Source source,
                               java.util.Set<Query> returnSet)
                        throws MetaDataException

Adds a Query to handle a primary key to a Set.

Parameters:

obj - an InterMineObject

queryNulls - true to make null a valid value, false to make null ignore the key

cld - the ClassDescriptor for the key

pk - the PrimaryKey

source - the Source of the object

returnSet - the Set to which the Query will be added

Throws:

MetaDataException - if something goes wrong