org.molgenis.data.annotation.impl

Class ClinVarServiceAnnotator

java.lang.Object

org.molgenis.data.annotation.AbstractRepositoryAnnotator

org.molgenis.data.annotation.LocusAnnotator

org.molgenis.data.annotation.VariantAnnotator

org.molgenis.data.annotation.impl.ClinVarServiceAnnotator

All Implemented Interfaces:

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

@Component(value="clinvarService")
public class ClinVarServiceAnnotator
extends VariantAnnotator

Field Summary

Fields

Modifier and Type	Field and Description
static String	ALLELEID
static String	ASSEMBLY
static String	CLINICALSIGNIFICANCE
static String	CLINVAR_CHROMOSOME
static String	CLINVAR_FILE_LOCATION_PROPERTY
static String	CYTOGENETIC
static String	GENE_NAME
static String	GENEID
static String	GENESYMBOL
static String	GUIDELINES
static String	HGVS_C
static String	HGVS_P
static String	LASTEVALUATED
static String	NSV_DBVAR
static String	NUMBERSUBMITTERS
static String	ORIGIN
static String	OTHERIDS
static String	PHENOTYPEIDS
static String	RCVACCESSION
static String	REVIEWSTATUS
static String	RS_DBSNP
static String	START
static String	STOP
static String	TESTEDINGTR
static String	TYPE
static String	VARIANTIDS

Fields inherited from class org.molgenis.data.annotation.VariantAnnotator

ALTERNATIVE, REFERENCE

Fields inherited from class org.molgenis.data.annotation.LocusAnnotator

CHROMOSOME, POSITION

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

ANNOTATOR_PREFIX

Constructor Summary

Constructors

Constructor and Description
ClinVarServiceAnnotator(MolgenisSettings molgenisSettings, AnnotationService annotatorService, ClinvarDataProvider clinvarDataProvider)

Method Summary

Modifier and Type	Method and Description
List<Entity>	annotateEntity(Entity entity)
protected boolean	annotationDataExists() Checks if folder and files that were set with a runtime property actually exist, or if a webservice can be reached
EntityMetaData	getOutputMetaData()
String	getSimpleName()
void	onApplicationEvent(org.springframework.context.event.ContextRefreshedEvent event)

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

getInputMetaData

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

annotate, canAnnotate, getFullName

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

Field Detail

CLINVAR_FILE_LOCATION_PROPERTY

public static final String CLINVAR_FILE_LOCATION_PROPERTY

See Also:

Constant Field Values

ALLELEID

public static final String ALLELEID

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Constant Field Values

TYPE

public static final String TYPE

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Constant Field Values

GENE_NAME

public static final String GENE_NAME

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Constant Field Values

GENEID

public static final String GENEID

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Constant Field Values

GENESYMBOL

public static final String GENESYMBOL

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Constant Field Values

CLINICALSIGNIFICANCE

public static final String CLINICALSIGNIFICANCE

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Constant Field Values

RS_DBSNP

public static final String RS_DBSNP

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Constant Field Values

NSV_DBVAR

public static final String NSV_DBVAR

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Constant Field Values

RCVACCESSION

public static final String RCVACCESSION

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Constant Field Values

TESTEDINGTR

public static final String TESTEDINGTR

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Constant Field Values

PHENOTYPEIDS

public static final String PHENOTYPEIDS

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Constant Field Values

ORIGIN

public static final String ORIGIN

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Constant Field Values

ASSEMBLY

public static final String ASSEMBLY

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Constant Field Values

CLINVAR_CHROMOSOME

public static final String CLINVAR_CHROMOSOME

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Constant Field Values

START

public static final String START

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Constant Field Values

STOP

public static final String STOP

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Constant Field Values

CYTOGENETIC

public static final String CYTOGENETIC

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Constant Field Values

REVIEWSTATUS

public static final String REVIEWSTATUS

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Constant Field Values

HGVS_C

public static final String HGVS_C

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Constant Field Values

HGVS_P

public static final String HGVS_P

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Constant Field Values

NUMBERSUBMITTERS

public static final String NUMBERSUBMITTERS

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Constant Field Values

LASTEVALUATED

public static final String LASTEVALUATED

See Also:

Constant Field Values

GUIDELINES

public static final String GUIDELINES

See Also:

Constant Field Values

OTHERIDS

public static final String OTHERIDS

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Constant Field Values

VARIANTIDS

public static final String VARIANTIDS

See Also:

Constant Field Values

Constructor Detail

ClinVarServiceAnnotator

@Autowired
public ClinVarServiceAnnotator(MolgenisSettings molgenisSettings,
                                          AnnotationService annotatorService,
                                          ClinvarDataProvider clinvarDataProvider)
                                   throws IOException

Throws:

IOException

Method Detail

onApplicationEvent

public void onApplicationEvent(org.springframework.context.event.ContextRefreshedEvent event)

Specified by:

onApplicationEvent in interface org.springframework.context.ApplicationListener<org.springframework.context.event.ContextRefreshedEvent>

Overrides:

onApplicationEvent in class AbstractRepositoryAnnotator

getSimpleName

public String getSimpleName()

annotationDataExists

protected 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)
                            throws IOException,
                                   InterruptedException

Specified by:

annotateEntity in class AbstractRepositoryAnnotator

Throws:

IOException

InterruptedException

getOutputMetaData

public EntityMetaData getOutputMetaData()