Package org.intermine.objectstore.translating

Class ObjectStoreTranslatingImpl

java.lang.Object

org.intermine.objectstore.ObjectStoreAbstractImpl

org.intermine.objectstore.translating.ObjectStoreTranslatingImpl

All Implemented Interfaces:

ObjectStore

public class ObjectStoreTranslatingImpl
extends ObjectStoreAbstractImpl

ObjectStore that transparently translates incoming queries and outgoing objects

Author:

Andrew Varley, Mark Woodbridge

Field Summary

Fields inherited from class org.intermine.objectstore.ObjectStoreAbstractImpl

cache, getObjectHits, getObjectOps, getObjectPrefetches, maxLimit, maxOffset, maxQueryParseTime, maxTime, model, rand, sequenceKeys, sequenceNumber

Fields inherited from interface org.intermine.objectstore.ObjectStore

SEQUENCE_IGNORE

Constructor Summary

Constructors

Constructor	Description
ObjectStoreTranslatingImpl(Model model, ObjectStore os, Translator translator)	Constructor

Method Summary

Modifier and Type	Method	Description
int	count(Query q, java.util.Map<java.lang.Object,java.lang.Integer> sequence)	Counts the number of rows the query will produce
ResultsInfo	estimate(Query q)	Explain a Query (give estimate for execution time and number of rows).
java.util.List<ResultsRow<java.lang.Object>>	execute(Query q, int start, int limit, boolean optimise, boolean explain, java.util.Map<java.lang.Object,java.lang.Integer> sequence)	Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
java.util.Set<java.lang.Object>	getComponentsForQuery(Query q)	Returns a Set of independent components that affect the results of the given Query.
static ObjectStoreTranslatingImpl	getInstance(java.lang.String osAlias, java.util.Properties props)	Gets an ObjectStore for the given underlying properties.
<T extends InterMineObject> T	getObjectByExample(T o, java.util.Set<java.lang.String> fieldNames)	Return an object from the objectstore that has the fields mentioned in the list set to the same values as the fields in the provided example object.
<T extends InterMineObject> java.util.Collection<T>	getObjectsByExample(T o, java.util.Set<java.lang.String> fs)	Return an object from the objectstore that has the fields mentioned in the list set to the same values as the fields in the provided example object.
java.lang.Integer	getSerial()	Gets an ID number which is unique in the database.
Translator	getTranslator()	Return the Translator that was passed to the constructor.
InterMineObject	internalGetObjectById(java.lang.Integer id, java.lang.Class<? extends InterMineObject> clazz)	Internal service method for getObjectById.
boolean	isMultiConnection()	Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.

Methods inherited from class org.intermine.objectstore.ObjectStoreAbstractImpl

cacheObjectById, changeSequence, checkSequence, checkStartLimit, createClob, createObjectStoreBag, execute, execute, executeSingleton, executeSingleton, flushObjectById, getMaxLimit, getMaxOffset, getMaxQueryParseTime, getMaxTime, getModel, getModelFromClasspath, getNewWriter, getObjectById, getObjectById, getObjectsByIds, getSequence, invalidateObjectById, pilferObjectById, prefetchObjectById

Methods inherited from class java.lang.Object

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

Constructor Detail

ObjectStoreTranslatingImpl

public ObjectStoreTranslatingImpl(Model model,
                                  ObjectStore os,
                                  Translator translator)

Constructor

Parameters:

model - the Model that this ObjectStore appears to use

os - the underlying ObjectStore

translator - the Translator used to translate queries and objects

Method Detail

getInstance

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

Gets an ObjectStore for the given underlying properties.

Parameters:

osAlias - the alias of this objectstore

props - the properties used to configure the objectstore

Returns:

the ObjectStore

Throws:

java.lang.IllegalArgumentException - if props or model are invalid

ObjectStoreException - if there is any problem with the instance

getTranslator

public Translator getTranslator()

Return the Translator that was passed to the constructor.

Returns:

the Translator

execute

public java.util.List<ResultsRow<java.lang.Object>> execute(Query q,
                                                            int start,
                                                            int limit,
                                                            boolean optimise,
                                                            boolean explain,
                                                            java.util.Map<java.lang.Object,java.lang.Integer> sequence)
                                                     throws ObjectStoreException

Execute a Query on this ObjectStore, asking for a certain range of rows to be returned. This will usually only be called by the Results object returned from execute(Query q).

Parameters:

q - the Query to execute

start - the start row

limit - the maximum number of rows to return

optimise - true if it is expected that optimising the query will improve performance

explain - true if the ObjectStore should enforce maximum query running time constraints

sequence - an object representing the state of the database corresponding to when the action that resulted in this execute was started. This number must match the ObjectStore's internal sequence number or a DataChangedException is thrown. The sequence number is incremented each time the data in the objectstore is changed

Returns:

a List of ResultRows

Throws:

ObjectStoreException - if an error occurs during the running of the Query

estimate

public ResultsInfo estimate(Query q)
                     throws ObjectStoreException

Explain a Query (give estimate for execution time and number of rows).

Parameters:

q - the query to estimate rows for

Returns:

parsed results of EXPLAIN

Throws:

ObjectStoreException - if an error occurs explaining the query

count

public int count(Query q,
                 java.util.Map<java.lang.Object,java.lang.Integer> sequence)
          throws ObjectStoreException

Counts the number of rows the query will produce

Parameters:

q - InterMine Query on which to count rows

sequence - an object representing the state of the database corresponding to when the action that resulted in this execute was started. This number must match the ObjectStore's internal sequence number or a DataChangedException is thrown. The sequence number is incremented each time the data in the objectstore is changed

Returns:

the number of rows that will be produced by query

Throws:

ObjectStoreException - if an error occurs counting the query

getObjectByExample

public <T extends InterMineObject> T getObjectByExample(T o,
                                                        java.util.Set<java.lang.String> fieldNames)

Description copied from interface: ObjectStore

Return an object from the objectstore that has the fields mentioned in the list set to the same values as the fields in the provided example object. If there are no objects in the objectstore like that, then this method returns null. If there are more than one object, then this method throws an IllegalArgumentException.

Specified by:

getObjectByExample in interface ObjectStore

Overrides:

getObjectByExample in class ObjectStoreAbstractImpl

Type Parameters:

T - The actual type to return.

Parameters:

o - an example object

fieldNames - a Set of fieldnames

Returns:

an InterMineObject from the objectstore, or null if none fits

getObjectsByExample

public <T extends InterMineObject> java.util.Collection<T> getObjectsByExample(T o,
                                                                               java.util.Set<java.lang.String> fs)

Description copied from interface: ObjectStore

Return an object from the objectstore that has the fields mentioned in the list set to the same values as the fields in the provided example object. If there are no objects in the objectstore like that, then this method returns null. If there are more than one object, then this method throws an IllegalArgumentException.

Specified by:

getObjectsByExample in interface ObjectStore

Overrides:

getObjectsByExample in class ObjectStoreAbstractImpl

Type Parameters:

T - The actual type to return.

Parameters:

o - an example object

fs - a Set of fieldnames

Returns:

zero or more InterMineObjects from the objectstore

isMultiConnection

public boolean isMultiConnection()

Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made. Note that ALL Objectstore must be multi-threading safe. If this method returns true, then the ObjectStore probably handles multiple connections to the database. The Results class uses this to work out whether or not to do prefetching.

Returns:

true if one should do multiple simultaneous operations

getComponentsForQuery

public java.util.Set<java.lang.Object> getComponentsForQuery(Query q)

Returns a Set of independent components that affect the results of the given Query.

Specified by:

getComponentsForQuery in interface ObjectStore

Specified by:

getComponentsForQuery in class ObjectStoreAbstractImpl

Parameters:

q - a Query

Returns:

a Set of objects

internalGetObjectById

public InterMineObject internalGetObjectById(java.lang.Integer id,
                                             java.lang.Class<? extends InterMineObject> clazz)
                                      throws ObjectStoreException

Internal service method for getObjectById.

Overrides:

internalGetObjectById in class ObjectStoreAbstractImpl

Parameters:

id - the ID of the object to get

clazz - a class of the object

Returns:

an object from the database

Throws:

ObjectStoreException - if an error occurs during the running of the Query

getSerial

public java.lang.Integer getSerial()
                            throws ObjectStoreException

Gets an ID number which is unique in the database.

Returns:

an Integer

Throws:

ObjectStoreException - if a problem occurs