Package org.intermine.api.query

Class QueryExecutor

java.lang.Object

org.intermine.api.query.QueryExecutor

Direct Known Subclasses:

PathQueryExecutor, WebResultsExecutor

public abstract class QueryExecutor
extends java.lang.Object

Common superclass of query executors that holds cache of pathToQueryNode maps per query. This cache is not just for performance, if a query hits the results cache a different pathToQueryNode map needs to be used because QueryNodes are not equals() to one another even if they represent the same class/field.

Author:

Richard Smith

Field Summary

Fields

Modifier and Type	Field	Description
protected BagManager	bagManager
protected BagQueryRunner	bagQueryRunner
protected ObjectStore	os
protected Profile	profile	The profile to use to find bags from.
protected static java.util.Map<Query,java.util.Map<java.lang.String,QuerySelectable>>	queryToPathToQueryNode	A cache of pathToQueryNode maps that is shared between subclasses of QueryExecutor.
protected int	summaryBatchSize

Constructor Summary

Constructors

Constructor	Description
QueryExecutor()

Method Summary

Modifier and Type	Method	Description
int	count(PathQuery pathQuery)	Take a query and return the results row count.
abstract Query	makeQuery(PathQuery pathQuery)	Make an InterMine Query object from a PathQuery.
Query	makeSummaryQuery(PathQuery pathQuery, java.lang.String summaryPath)
Query	makeSummaryQuery(PathQuery pathQuery, java.lang.String summaryPath, boolean asOccurrances)	Creates a query that returns the summary for a column in a PathQuery.
Query	makeSummaryQuery(PathQuery pq, java.lang.String summaryPath, java.lang.String filterTerm, boolean asOccurrances)	Creates a query that returns the summary for a column in a PathQuery, applying a filter at the database level.
Results	summariseQuery(PathQuery pathQuery, java.lang.String summaryPath)
Results	summariseQuery(PathQuery pathQuery, java.lang.String summaryPath, boolean asOccurrances)	Returns the results for a summary for a column in a PathQuery.
Results	summariseQuery(PathQuery pq, java.lang.String summaryPath, java.lang.String filterTerm, boolean asOccurrances)	Summarise a query.
int	uniqueColumnValues(PathQuery pq, java.lang.String path)	Get the the total number of unique column values for a given path in the context of a given query.
void	updateQueryToPathToQueryNode(Query q, java.util.Map<java.lang.String,QuerySelectable> pathToQueryNode)	Update the map to query queryToPathToQueryNode

Methods inherited from class java.lang.Object

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

Field Detail

queryToPathToQueryNode

protected static java.util.Map<Query,java.util.Map<java.lang.String,QuerySelectable>> queryToPathToQueryNode

A cache of pathToQueryNode maps that is shared between subclasses of QueryExecutor. The maps are needed to link paths in path queries to objects in the underlying ObjectStore results.

summaryBatchSize

protected int summaryBatchSize

profile

protected Profile profile

The profile to use to find bags from.

bagManager

protected BagManager bagManager

bagQueryRunner

protected BagQueryRunner bagQueryRunner

os

protected ObjectStore os

Constructor Detail

QueryExecutor

public QueryExecutor()

Method Detail

makeSummaryQuery

public Query makeSummaryQuery(PathQuery pathQuery,
                              java.lang.String summaryPath,
                              boolean asOccurrances)
                       throws ObjectStoreException

Creates a query that returns the summary for a column in a PathQuery. The format of the results is as follows:

• For non-numeric types:
1. The item
2. The count of occurrences of this item
• For numeric types:
1. Minimum Value
2. Maximum Value
3. Average
4. Standard Deviation

Parameters:

pathQuery - the query to convert

summaryPath - the column to summarise

asOccurrances - If true, will only return the list of values and their counts.

Returns:

an IQL Query object

Throws:

ObjectStoreException - if there is a problem creating the query

makeSummaryQuery

public Query makeSummaryQuery(PathQuery pathQuery,
                              java.lang.String summaryPath)
                       throws ObjectStoreException

Parameters:

pathQuery - the query to summarise

summaryPath - the column to summarise

Returns:

a Results object with varying styles of data

Throws:

ObjectStoreException - if there is a problem creating the query

makeSummaryQuery

public Query makeSummaryQuery(PathQuery pq,
                              java.lang.String summaryPath,
                              java.lang.String filterTerm,
                              boolean asOccurrances)
                       throws ObjectStoreException

Creates a query that returns the summary for a column in a PathQuery, applying a filter at the database level.

Parameters:

filterTerm - what to filter by

asOccurrances - If true, will only return the list of values and their counts.

pq - the query to convert

summaryPath - the column to summarise

Returns:

an IQL Query object

Throws:

ObjectStoreException - if there is a problem creating the query

summariseQuery

public Results summariseQuery(PathQuery pathQuery,
                              java.lang.String summaryPath,
                              boolean asOccurrances)
                       throws ObjectStoreException

Returns the results for a summary for a column in a PathQuery. The format of the results is as follows:

• For non-numeric types:
1. The item
2. The count of occurrences of this item
• For numeric types:
1. Minimum Value
2. Maximum Value
3. Average
4. Standard Deviation

Parameters:

pathQuery - the query to summarise

summaryPath - the column to summarise

asOccurrances - If true, will only return the list of values and their counts.

Returns:

a Results object with varying styles of data

Throws:

ObjectStoreException - if there is a problem summarising

summariseQuery

public Results summariseQuery(PathQuery pathQuery,
                              java.lang.String summaryPath)
                       throws ObjectStoreException

Parameters:

pathQuery - The query to execute.

summaryPath - The path whose unique column value count we want.

Returns:

A set of results.

Throws:

ObjectStoreException - If there is a problem making the query.

summariseQuery

public Results summariseQuery(PathQuery pq,
                              java.lang.String summaryPath,
                              java.lang.String filterTerm,
                              boolean asOccurrances)
                       throws ObjectStoreException

Summarise a query.

Parameters:

pq - The query to summarise

summaryPath - The path of the query to focus on.

filterTerm - An optional term to further filter by.

asOccurrances - If true, will only return the list of values and their counts.

Returns:

A set of results.

Throws:

ObjectStoreException - in case of Ragnarok.

count

public int count(PathQuery pathQuery)
          throws ObjectStoreException

Take a query and return the results row count.

Parameters:

pathQuery - the query to count

Returns:

the number of rows returned

Throws:

ObjectStoreException - if there is a problem counting the query

uniqueColumnValues

public int uniqueColumnValues(PathQuery pq,
                              java.lang.String path)
                       throws ObjectStoreException

Get the the total number of unique column values for a given path in the context of a given query. eg:

   int count = ex.uniqueColumnValues(pq, "Gene.symbol");
 

Parameters:

pq - The query to execute.

path - The path whose unique column value count we want.

Returns:

The number of different values this path can have.

Throws:

ObjectStoreException - If there is a problem making the query.

makeQuery

public abstract Query makeQuery(PathQuery pathQuery)
                         throws ObjectStoreException

Make an InterMine Query object from a PathQuery.

Parameters:

pathQuery - The path query.

Returns:

The internal Query representation.

Throws:

ObjectStoreException - If there is a problem making the query.

updateQueryToPathToQueryNode

public void updateQueryToPathToQueryNode(Query q,
                                         java.util.Map<java.lang.String,QuerySelectable> pathToQueryNode)

Update the map to query queryToPathToQueryNode

Parameters:

q - The query.

pathToQueryNode - the pathToQueryNode