org.molgenis.data.annotation.impl

Class CosmicServiceAnnotator

java.lang.Object

org.molgenis.data.annotation.AbstractRepositoryAnnotator

org.molgenis.data.annotation.impl.CosmicServiceAnnotator

All Implemented Interfaces:

EventListener, RepositoryAnnotator, org.springframework.context.ApplicationListener<org.springframework.context.event.ContextRefreshedEvent>

@Component(value="cosmicService")
public class CosmicServiceAnnotator
extends AbstractRepositoryAnnotator
implements RepositoryAnnotator, org.springframework.context.ApplicationListener<org.springframework.context.event.ContextRefreshedEvent>

This class calls the Ensembl webservice with a ensemble ID. The webservice returns a map with information on the somatic variants associated with the gene

Author:

bcharbon

Field Summary

Fields

Modifier and Type	Field and Description
static String	ALT_ALLELES
static String	CONSEQUENCE_TYPE
static String	END
static String	ENSEMBLE_ID
static String	FEATURE_TYPE
static String	ID
static String	NAME
static String	SEQ_REGION_NAME
static String	START
static String	STRAND

Fields inherited from interface org.molgenis.data.annotation.RepositoryAnnotator

ANNOTATOR_PREFIX

Constructor Summary

Constructors

Constructor and Description
CosmicServiceAnnotator()

Method Summary

Modifier and Type	Method and Description
List<Entity>	annotateEntity(Entity entity)
boolean	annotationDataExists() Checks if folder and files that were set with a runtime property actually exist, or if a webservice can be reached
EntityMetaData	getInputMetaData()
EntityMetaData	getOutputMetaData()
String	getSimpleName()

Methods inherited from class org.molgenis.data.annotation.AbstractRepositoryAnnotator

annotate, canAnnotate, getFullName, onApplicationEvent

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.RepositoryAnnotator

annotate, canAnnotate, getDescription, getFullName

Methods inherited from interface org.springframework.context.ApplicationListener

onApplicationEvent

Field Detail

ENSEMBLE_ID

public static final String ENSEMBLE_ID

See Also:

Constant Field Values

NAME

public static final String NAME

See Also:

Constant Field Values

ID

public static final String ID

See Also:

Constant Field Values

FEATURE_TYPE

public static final String FEATURE_TYPE

See Also:

Constant Field Values

ALT_ALLELES

public static final String ALT_ALLELES

See Also:

Constant Field Values

END

public static final String END

See Also:

Constant Field Values

SEQ_REGION_NAME

public static final String SEQ_REGION_NAME

See Also:

Constant Field Values

CONSEQUENCE_TYPE

public static final String CONSEQUENCE_TYPE

See Also:

Constant Field Values

STRAND

public static final String STRAND

See Also:

Constant Field Values

START

public static final String START

See Also:

Constant Field Values

Constructor Detail

CosmicServiceAnnotator

public CosmicServiceAnnotator()

Method Detail

getSimpleName

public String getSimpleName()

Specified by:

getSimpleName in interface RepositoryAnnotator

getInputMetaData

public EntityMetaData getInputMetaData()

Specified by:

getInputMetaData in interface RepositoryAnnotator

annotationDataExists

public boolean annotationDataExists()

Description copied from class: AbstractRepositoryAnnotator

Checks if folder and files that were set with a runtime property actually exist, or if a webservice can be reached

Specified by:

annotationDataExists in class AbstractRepositoryAnnotator

Returns:

boolean

annotateEntity

public List<Entity> annotateEntity(Entity entity)

Specified by:

annotateEntity in class AbstractRepositoryAnnotator

getOutputMetaData

public EntityMetaData getOutputMetaData()

Specified by:

getOutputMetaData in interface RepositoryAnnotator