org.molgenis.data.annotation.core.entity.impl.framework

Class AbstractAnnotator

java.lang.Object

org.molgenis.data.annotation.core.entity.impl.framework.QueryAnnotatorImpl

org.molgenis.data.annotation.core.entity.impl.framework.AbstractAnnotator

All Implemented Interfaces:

Annotator, EntityAnnotator

public abstract class AbstractAnnotator
extends QueryAnnotatorImpl
implements EntityAnnotator

The most standard implementation of an EntityAnnotator that first creates a query, queries the resource, then filters the results using a ResultFilter and then copies the resulting attributes to the annotated Entity.

Constructor Summary

Constructors

Constructor and Description
AbstractAnnotator(String sourceRepositoryName, AnnotatorInfo info, QueryCreator queryCreator, ResultFilter resultFilter, DataService dataService, Resources resources, CmdLineAnnotatorSettingsConfigurer cmdLineAnnotatorSettingsConfigurer)

Method Summary

Modifier and Type	Method and Description
List<Attribute>	getRequiredAttributes()
protected Object	getResourceAttributeValue(Attribute attr, Entity entity) Get the resource attribute value for one of this annotator's output attributes.
protected void	processQueryResults(Entity entity, Iterable<Entity> annotationSourceEntities, boolean updateMode) Processes the query results.

Methods inherited from class org.molgenis.data.annotation.core.entity.impl.framework.QueryAnnotatorImpl

annotateEntity, getAnnotatorAttributes, getCmdLineAnnotatorSettingsConfigurer, getInfo, sourceExists

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.molgenis.data.annotation.core.entity.EntityAnnotator

annotateEntity, getCmdLineAnnotatorSettingsConfigurer, sourceExists

Methods inherited from interface org.molgenis.data.annotation.core.entity.Annotator

createAnnotatorAttributes, getAnnotatorAttributes, getInfo

Constructor Detail

AbstractAnnotator

public AbstractAnnotator(String sourceRepositoryName,
                         AnnotatorInfo info,
                         QueryCreator queryCreator,
                         ResultFilter resultFilter,
                         DataService dataService,
                         Resources resources,
                         CmdLineAnnotatorSettingsConfigurer cmdLineAnnotatorSettingsConfigurer)

Method Detail

processQueryResults

protected void processQueryResults(Entity entity,
                                   Iterable<Entity> annotationSourceEntities,
                                   boolean updateMode)

Description copied from class: QueryAnnotatorImpl

Processes the query results.

Specified by:

processQueryResults in class QueryAnnotatorImpl

Parameters:

entity - the input entity that is being annotated

annotationSourceEntities - the entities resulting from the query on the annotation source

getResourceAttributeValue

protected Object getResourceAttributeValue(Attribute attr,
                                           Entity entity)

Get the resource attribute value for one of this annotator's output attributes.

Parameters:

attr - the name of the output attribute

entity - the current entity

Returns:

the value of the attribute to copy from the resource entity

getRequiredAttributes

public List<Attribute> getRequiredAttributes()

Specified by:

getRequiredAttributes in interface EntityAnnotator

Overrides:

getRequiredAttributes in class QueryAnnotatorImpl

Returns:

the List that must be present in the source entity.