org.molgenis.data.annotation.impl

Class ClinicalGenomicsDatabaseServiceAnnotator

java.lang.Object

org.molgenis.data.annotation.AbstractRepositoryAnnotator

org.molgenis.data.annotation.LocusAnnotator

org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator

All Implemented Interfaces:

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

@Component(value="CgdService")
public class ClinicalGenomicsDatabaseServiceAnnotator
extends LocusAnnotator

Field Summary

Fields

Modifier and Type	Field and Description
static String	ALLELIC_CONDITIONS
static String	CGD_AGE_GROUP
static String	CGD_CONDITION
static String	CGD_FILE_LOCATION
static String	CGD_GENERALIZED_INHERITANCE
static String	CGD_INHERITANCE
static String	COMMENTS
static String	ENTREZ_GENE_ID
static String	GENE
static String	HGNC_ID
static String	INTERVENTION_CATEGORIES
static String	INTERVENTION_RATIONALE
static String	MANIFESTATION_CATEGORIES
static String	REFERENCES

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
ClinicalGenomicsDatabaseServiceAnnotator(File cgdFileLocation, File inputVcfFile, File outputVCFFile)
ClinicalGenomicsDatabaseServiceAnnotator(MolgenisSettings molgenisSettings, AnnotationService annotationService, HgncLocationsProvider hgncLocationsProvider, CgdDataProvider cgdDataProvider)

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	getOutputMetaData()
String	getSimpleName()
void	onApplicationEvent(org.springframework.context.event.ContextRefreshedEvent event)

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

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

REFERENCES

public static final String REFERENCES

See Also:

Constant Field Values

INTERVENTION_RATIONALE

public static final String INTERVENTION_RATIONALE

See Also:

Constant Field Values

COMMENTS

public static final String COMMENTS

See Also:

Constant Field Values

INTERVENTION_CATEGORIES

public static final String INTERVENTION_CATEGORIES

See Also:

Constant Field Values

MANIFESTATION_CATEGORIES

public static final String MANIFESTATION_CATEGORIES

See Also:

Constant Field Values

ALLELIC_CONDITIONS

public static final String ALLELIC_CONDITIONS

See Also:

Constant Field Values

ENTREZ_GENE_ID

public static final String ENTREZ_GENE_ID

See Also:

Constant Field Values

GENE

public static final String GENE

See Also:

Constant Field Values

HGNC_ID

public static final String HGNC_ID

See Also:

Constant Field Values

CGD_FILE_LOCATION

public static final String CGD_FILE_LOCATION

See Also:

Constant Field Values

CGD_CONDITION

public static final String CGD_CONDITION

See Also:

Constant Field Values

CGD_AGE_GROUP

public static final String CGD_AGE_GROUP

See Also:

Constant Field Values

CGD_INHERITANCE

public static final String CGD_INHERITANCE

See Also:

Constant Field Values

CGD_GENERALIZED_INHERITANCE

public static final String CGD_GENERALIZED_INHERITANCE

See Also:

Constant Field Values

Constructor Detail

ClinicalGenomicsDatabaseServiceAnnotator

@Autowired
public ClinicalGenomicsDatabaseServiceAnnotator(MolgenisSettings molgenisSettings,
                                                           AnnotationService annotationService,
                                                           HgncLocationsProvider hgncLocationsProvider,
                                                           CgdDataProvider cgdDataProvider)
                                                    throws IOException

Throws:

IOException

ClinicalGenomicsDatabaseServiceAnnotator

public ClinicalGenomicsDatabaseServiceAnnotator(File cgdFileLocation,
                                                File inputVcfFile,
                                                File outputVCFFile)
                                         throws Exception

Throws:

Exception

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

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)
                            throws IOException

Specified by:

annotateEntity in class AbstractRepositoryAnnotator

Throws:

IOException

getOutputMetaData

public EntityMetaData getOutputMetaData()