Package ubic.gemma.rest

Class AnnotationsWebService

java.lang.Object

ubic.gemma.rest.AnnotationsWebService

@Service
@Path("/annotations")
public class AnnotationsWebService
extends Object

RESTful interface for annotations.

Author:

tesarst

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static final class	AnnotationsWebService.AnnotationSearchResultValueObject
static final class	AnnotationsWebService.OntologyTermSimpleValueObject
static final class	AnnotationsWebService.OntologyTermValueObject

Constructor Summary

Constructors

Constructor	Description
AnnotationsWebService()	Required by spring
AnnotationsWebService(ubic.gemma.core.ontology.OntologyService ontologyService, ubic.gemma.core.search.SearchService searchService, ubic.gemma.persistence.service.common.description.CharacteristicService characteristicService, ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService expressionExperimentService, DatasetArgService datasetArgService, TaxonArgService taxonArgService)	Constructor for service autowiring

Method Summary

Modifier and Type	Method	Description
ResponseDataObject<List<AnnotationsWebService.OntologyTermSimpleValueObject>>	getAnnotationCategories()	List the ontology categories allowed for use in characteristics.
ResponseDataObject<List<AnnotationsWebService.OntologyTermSimpleValueObject>>	getAnnotationPredicates()	List the ontology predicates allowed for use in statements.
ResponseDataObject<List<AnnotationsWebService.AnnotationSearchResultValueObject>>	getAnnotationsChildren(String termUri, boolean direct)	Obtain the children of a given annotation.
ResponseDataObject<List<AnnotationsWebService.AnnotationSearchResultValueObject>>	getAnnotationsParents(String termUri, boolean direct)
ResponseDataObject<AnnotationsWebService.OntologyTermValueObject>	getAnnotationTerm(String termUri)	Look up an ontology term by its URI.
ResponseDataObject<List<AnnotationsWebService.AnnotationSearchResultValueObject>>	searchAnnotations(StringArrayArg query)	Does a search for annotation tags based on the given string.
ResponseDataObject<List<AnnotationsWebService.AnnotationSearchResultValueObject>>	searchAnnotationsByPathQuery(StringArrayArg query)
QueriedAndFilteredAndPaginatedResponseDataObject<ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject>	searchDatasets(StringArrayArg query, FilterArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> filterArg, OffsetArg offset, LimitArg limit, SortArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> sortArg)	Does a search for datasets containing characteristics matching the given string.
QueriedAndFilteredAndPaginatedResponseDataObject<ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject>	searchDatasetsByQueryInPath(StringArrayArg query, FilterArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> filterArg, OffsetArg offset, LimitArg limit, SortArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> sortArg)
QueriedAndFilteredAndPaginatedResponseDataObject<ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject>	searchTaxonDatasets(TaxonArg<?> taxonArg, StringArrayArg query, FilterArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> sort)	Same as searchDatasets(StringArrayArg, FilterArg, OffsetArg, LimitArg, SortArg) but also filters by taxon.
QueriedAndFilteredAndPaginatedResponseDataObject<ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject>	searchTaxonDatasetsByQueryInPath(TaxonArg<?> taxonArg, StringArrayArg query, FilterArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> sort)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

AnnotationsWebService

public AnnotationsWebService()

Required by spring

AnnotationsWebService

@Autowired
public AnnotationsWebService(ubic.gemma.core.ontology.OntologyService ontologyService,
 ubic.gemma.core.search.SearchService searchService,
 ubic.gemma.persistence.service.common.description.CharacteristicService characteristicService,
 ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService expressionExperimentService,
 DatasetArgService datasetArgService,
 TaxonArgService taxonArgService)

Constructor for service autowiring

Method Details

getAnnotationsParents

@GET
@Path("/parents")
@Produces("application/json")
public ResponseDataObject<List<AnnotationsWebService.AnnotationSearchResultValueObject>> getAnnotationsParents(@QueryParam("uri")
 String termUri,
 @QueryParam("direct") @DefaultValue("false")
 boolean direct)

getAnnotationsChildren

@GET
@Path("/children")
@Produces("application/json")
public ResponseDataObject<List<AnnotationsWebService.AnnotationSearchResultValueObject>> getAnnotationsChildren(@QueryParam("uri")
 String termUri,
 @QueryParam("direct") @DefaultValue("false")
 boolean direct)

Obtain the children of a given annotation.

This is plural as we might add support for querying multiple annotations at once in the future.

getAnnotationTerm

@GET
@Path("/term")
@Produces("application/json")
public ResponseDataObject<AnnotationsWebService.OntologyTermValueObject> getAnnotationTerm(@QueryParam("uri")
 String termUri)

Look up an ontology term by its URI.

getAnnotationCategories

@GET
@Path("/categories")
@Produces("application/json")
public ResponseDataObject<List<AnnotationsWebService.OntologyTermSimpleValueObject>> getAnnotationCategories()

List the ontology categories allowed for use in characteristics.

getAnnotationPredicates

@GET
@Path("/predicates")
@Produces("application/json")
public ResponseDataObject<List<AnnotationsWebService.OntologyTermSimpleValueObject>> getAnnotationPredicates()

List the ontology predicates allowed for use in statements.

searchAnnotations

@GET
@Path("/search")
@Produces("application/json")
public ResponseDataObject<List<AnnotationsWebService.AnnotationSearchResultValueObject>> searchAnnotations(@QueryParam("query") @DefaultValue("")
 StringArrayArg query)

Does a search for annotation tags based on the given string.

Parameters:

query - the search query. Either plain text, or an ontology term URI

Returns:

response data object with a collection of found terms, each wrapped in a CharacteristicValueObject.

See Also:

• for better description of the search process.
• for the output object structure.

searchAnnotationsByPathQuery

@GET
@Path("/search/{query}")
@Produces("application/json")
public ResponseDataObject<List<AnnotationsWebService.AnnotationSearchResultValueObject>> searchAnnotationsByPathQuery(@PathParam("query") @DefaultValue("")
 StringArrayArg query)

See Also:

• searchAnnotations(StringArrayArg)

searchDatasets

@GET
@Path("/search/datasets")
@Produces("application/json")
public QueriedAndFilteredAndPaginatedResponseDataObject<ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject> searchDatasets(@QueryParam("query") @DefaultValue("")
 StringArrayArg query,
 @QueryParam("filter") @DefaultValue("")
 FilterArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> filterArg,
 @QueryParam("offset") @DefaultValue("0")
 OffsetArg offset,
 @QueryParam("limit") @DefaultValue("20")
 LimitArg limit,
 @QueryParam("sort") @DefaultValue("+id")
 SortArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> sortArg)

Does a search for datasets containing characteristics matching the given string. If filterArg, offset, limit or sortArg parameters are provided.

Parameters:

query - the search query. Either plain text, or an ontology term URI

Returns:

response data object with a collection of dataset that match the search query.

See Also:

• for better description of the search process.

searchDatasetsByQueryInPath

@GET
@Path("/search/{query}/datasets")
@Produces("application/json")
public QueriedAndFilteredAndPaginatedResponseDataObject<ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject> searchDatasetsByQueryInPath(@PathParam("query") @DefaultValue("")
 StringArrayArg query,
 @QueryParam("filter") @DefaultValue("")
 FilterArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> filterArg,
 @QueryParam("offset") @DefaultValue("0")
 OffsetArg offset,
 @QueryParam("limit") @DefaultValue("20")
 LimitArg limit,
 @QueryParam("sort") @DefaultValue("+id")
 SortArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> sortArg)

searchTaxonDatasets

@GET
@Path("/{taxon}/search/datasets")
@Produces("application/json")
public QueriedAndFilteredAndPaginatedResponseDataObject<ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject> searchTaxonDatasets(@PathParam("taxon")
 TaxonArg<?> taxonArg,
 @QueryParam("query") @DefaultValue("")
 StringArrayArg query,
 @QueryParam("filter") @DefaultValue("")
 FilterArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> filter,
 @QueryParam("offset") @DefaultValue("0")
 OffsetArg offset,
 @QueryParam("limit") @DefaultValue("20")
 LimitArg limit,
 @QueryParam("sort") @DefaultValue("+id")
 SortArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> sort)

Same as searchDatasets(StringArrayArg, FilterArg, OffsetArg, LimitArg, SortArg) but also filters by taxon.

searchTaxonDatasetsByQueryInPath

@GET
@Path("/{taxon}/search/{query}/datasets")
@Produces("application/json")
public QueriedAndFilteredAndPaginatedResponseDataObject<ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject> searchTaxonDatasetsByQueryInPath(@PathParam("taxon")
 TaxonArg<?> taxonArg,
 @PathParam("query") @DefaultValue("")
 StringArrayArg query,
 @QueryParam("filter") @DefaultValue("")
 FilterArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> filter,
 @QueryParam("offset") @DefaultValue("0")
 OffsetArg offset,
 @QueryParam("limit") @DefaultValue("20")
 LimitArg limit,
 @QueryParam("sort") @DefaultValue("+id")
 SortArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> sort)

See Also:

• searchDatasets(StringArrayArg, FilterArg, OffsetArg, LimitArg, SortArg)