uk.ac.ebi.microarray.zooma.retrieval
Class CompositeOntologyTermRetriever

java.lang.Object
  uk.ac.ebi.microarray.zooma.retrieval.CompositeOntologyTermRetriever

All Implemented Interfaces:

OntologyTermRetriever

public class CompositeOntologyTermRetriever
extends java.lang.Object
implements OntologyTermRetriever

An ontology term retriever that is a composite of a list of ontology term retrievers. Retrieval queries are delegated to each retriever and responses pooled.

Author:

Tony Burdett

Constructor Summary

CompositeOntologyTermRetriever(java.util.List<OntologyTermRetriever> retrievers)

CompositeOntologyTermRetriever(OntologyTermRetriever... retrievers)

Method Summary

java.util.Collection<OntologyMappingContext>	fetchMappingContexts(Value value, uk.ac.ebi.ontocat.OntologyTerm term) Returns the set of unique contexts retrieved from each retriever encapsulated by this composite retriever.
java.util.Collection<uk.ac.ebi.ontocat.OntologyTerm>	fetchTerms(Value value) Returns a set of unique terms retrieved from each retriever encapsulated by this composite retriever.
java.util.List<OntologyTermRetriever>	getOntologyTermRetrievers()
protected java.util.concurrent.ExecutorService	getService()
void	setOntologyTermRetrievers(java.util.List<OntologyTermRetriever> retrievers)

Methods inherited from class java.lang.Object

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

Constructor Detail

CompositeOntologyTermRetriever

public CompositeOntologyTermRetriever(OntologyTermRetriever... retrievers)

CompositeOntologyTermRetriever

public CompositeOntologyTermRetriever(java.util.List<OntologyTermRetriever> retrievers)

Method Detail

setOntologyTermRetrievers

public void setOntologyTermRetrievers(java.util.List<OntologyTermRetriever> retrievers)

getOntologyTermRetrievers

public java.util.List<OntologyTermRetriever> getOntologyTermRetrievers()

getService

protected java.util.concurrent.ExecutorService getService()

fetchTerms

public java.util.Collection<uk.ac.ebi.ontocat.OntologyTerm> fetchTerms(Value value)
                                                                throws java.io.IOException

Returns a set of unique terms retrieved from each retriever encapsulated by this composite retriever. This returns only unique results - if terms acquired from separate sources satisfy Object.equals(Object) then the duplication is ignored. However, two terms being equal does not necessarily imply that the context in which they are used is also equal.

Specified by:

fetchTerms in interface OntologyTermRetriever

Parameters:

value - the text description to search for

Returns:

the collection of unique terms from all retrievers backing this composite

Throws:

java.io.IOException - if an error occurred retrieving terms from any of the backing datasources

fetchMappingContexts

public java.util.Collection<OntologyMappingContext> fetchMappingContexts(Value value,
                                                                         uk.ac.ebi.ontocat.OntologyTerm term)
                                                                  throws java.io.IOException

Returns the set of unique contexts retrieved from each retriever encapsulated by this composite retriever. This returns only unique results - if contexts acquired from separate sources satisfy Object.equals(Object) then the duplication is ignored. Be aware that the same term may be applied in different contexts in the same datasource, let alone different ones, so there are no guarantees that this returns a single result.

Specified by:

fetchMappingContexts in interface OntologyTermRetriever

Parameters:

value - the text description to search for

term - the term that is mapped to this description - usually, retrieved by OntologyTermRetriever.fetchTerms(uk.ac.ebi.microarray.zooma.lang.Value) first

Returns:

term the term to acquire the contexts

Throws:

java.io.IOException - if an error occurred retrieving terms from any of the backing datasources