org.molgenis.data.annotation.impl

Class EbiServiceAnnotator

java.lang.Object

org.molgenis.data.annotation.AbstractRepositoryAnnotator

org.molgenis.data.annotation.impl.EbiServiceAnnotator

All Implemented Interfaces:

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

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

This class calls the EBI CHeMBL webservice with a uniprot ID. The webservice returns a map with information on the submitted protein ID.

EBI returns: {target={targetType, chemblId, geneNames, description, compoundCount, bioactivityCount, proteinAccession, synonyms, organism, preferredName}}

Version:

EBI: database version 17, prepared on 29th August 2013

Author:

mdehaan

Field Summary

Fields

Modifier and Type	Field and Description
static String	NAME
static String	UNIPROT_ID

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

ANNOTATOR_PREFIX

Constructor Summary

Constructors

Constructor and Description
EbiServiceAnnotator()
EbiServiceAnnotator(org.apache.http.client.HttpClient client)

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

UNIPROT_ID

public static final String UNIPROT_ID

See Also:

Constant Field Values

NAME

public static final String NAME

See Also:

Constant Field Values

Constructor Detail

EbiServiceAnnotator

public EbiServiceAnnotator()

EbiServiceAnnotator

public EbiServiceAnnotator(org.apache.http.client.HttpClient client)

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