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

Class QueryAnnotatorImpl

java.lang.Object

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

All Implemented Interfaces:

Annotator, EntityAnnotator

Direct Known Subclasses:

AbstractAnnotator

public abstract class QueryAnnotatorImpl
extends Object
implements EntityAnnotator

Base class for any EntityAnnotator that uses a QueryCreator to query the DataService or Resources. It leaves it up to concrete implementations how they wish to process the results by implementing processQueryResults(Entity, Iterable, boolean).

See AbstractAnnotator for the most standard implementation of processQueryResults(Entity, Iterable, boolean).

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
List<Entity>	annotateEntity(Entity entity, boolean updateMode) Annotates a single entity.
List<Attribute>	getAnnotatorAttributes() Be aware that several calls to this function will give you the same auto identifiers every time
CmdLineAnnotatorSettingsConfigurer	getCmdLineAnnotatorSettingsConfigurer()
AnnotatorInfo	getInfo()
List<Attribute>	getRequiredAttributes()
protected abstract void	processQueryResults(Entity inputEntity, Iterable<Entity> annotationSourceEntities, boolean updateMode) Processes the query results.
boolean	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.Annotator

createAnnotatorAttributes

Constructor Detail

QueryAnnotatorImpl

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

Method Detail

getInfo

public AnnotatorInfo getInfo()

Specified by:

getInfo in interface Annotator

Returns:

AnnotatorInfo for the Annotator

getAnnotatorAttributes

public List<Attribute> getAnnotatorAttributes()

Description copied from interface: Annotator

Be aware that several calls to this function will give you the same auto identifiers every time

Specified by:

getAnnotatorAttributes in interface Annotator

Returns:

List of Attribute for the attributes that get added by this Annotator

sourceExists

public boolean sourceExists()

Specified by:

sourceExists in interface EntityAnnotator

Returns:

Indication if the required source repository is present in the dataService

getRequiredAttributes

public List<Attribute> getRequiredAttributes()

Specified by:

getRequiredAttributes in interface EntityAnnotator

Returns:

the List that must be present in the source entity.

annotateEntity

public List<Entity> annotateEntity(Entity entity,
                                   boolean updateMode)

Description copied from interface: EntityAnnotator

Annotates a single entity.

Specified by:

annotateEntity in interface EntityAnnotator

Parameters:

entity - the entity to annotate

updateMode - boolean indicating if existing annotations should be updated

Returns:

Iterable for the annotated data

getCmdLineAnnotatorSettingsConfigurer

public CmdLineAnnotatorSettingsConfigurer getCmdLineAnnotatorSettingsConfigurer()

Specified by:

getCmdLineAnnotatorSettingsConfigurer in interface EntityAnnotator

processQueryResults

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

Processes the query results.

Parameters:

inputEntity - the input entity that is being annotated

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