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 class	AnnotationsWebService.AnnotationSearchResultValueObject

Constructor Summary

Constructors

Constructor	Description
AnnotationsWebService()	Required by spring
AnnotationsWebService(OntologyService ontologyService, SearchService searchService, CharacteristicService characteristicService, ExpressionExperimentService expressionExperimentService, DatasetArgService datasetArgService, TaxonArgService taxonArgService)	Constructor for service autowiring

Method Summary

Modifier and Type	Method	Description
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<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<ExpressionExperimentValueObject>	searchDatasets(StringArrayArg query, FilterArg<ExpressionExperiment> filterArg, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sortArg)	Does a search for datasets containing characteristics matching the given string.
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	searchDatasetsByQueryInPath(StringArrayArg query, FilterArg<ExpressionExperiment> filterArg, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sortArg)
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	searchTaxonDatasets(TaxonArg<?> taxonArg, StringArrayArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort)	Same as searchDatasets(StringArrayArg, FilterArg, OffsetArg, LimitArg, SortArg) but also filters by taxon.
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	searchTaxonDatasetsByQueryInPath(TaxonArg<?> taxonArg, StringArrayArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<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(OntologyService ontologyService,
 SearchService searchService,
 CharacteristicService characteristicService,
 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.

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<ExpressionExperimentValueObject> searchDatasets(@QueryParam("query") @DefaultValue("")
 StringArrayArg query,
 @QueryParam("filter") @DefaultValue("")
 FilterArg<ExpressionExperiment> filterArg,
 @QueryParam("offset") @DefaultValue("0")
 OffsetArg offset,
 @QueryParam("limit") @DefaultValue("20")
 LimitArg limit,
 @QueryParam("sort") @DefaultValue("+id")
 SortArg<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<ExpressionExperimentValueObject> searchDatasetsByQueryInPath(@PathParam("query") @DefaultValue("")
 StringArrayArg query,
 @QueryParam("filter") @DefaultValue("")
 FilterArg<ExpressionExperiment> filterArg,
 @QueryParam("offset") @DefaultValue("0")
 OffsetArg offset,
 @QueryParam("limit") @DefaultValue("20")
 LimitArg limit,
 @QueryParam("sort") @DefaultValue("+id")
 SortArg<ExpressionExperiment> sortArg)

searchTaxonDatasets

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

See Also:

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