Package ubic.gemma.rest

Class AnnotationsWebService

  • @Service
@Path("/annotations")
public class AnnotationsWebService
extends Object
    RESTful interface for annotations.
    Author:
    tesarst

    • Constructor Detail

      • 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 Detail

      • getAnnotationsChildren

        @GET
@Path("/children")
@Produces("application/json")
public 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.

      • 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)