Package ubic.gemma.rest.util.args

Class DatasetArgService

  • All Implemented Interfaces:
    EntityArgService<ubic.gemma.model.expression.experiment.ExpressionExperiment,​ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService>
    @Service
public class DatasetArgService
extends AbstractEntityArgService<ubic.gemma.model.expression.experiment.ExpressionExperiment,​ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService>

    • Constructor Detail

      • DatasetArgService

        @Autowired
public DatasetArgService​(ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService service,
                         ubic.gemma.core.search.SearchService searchService,
                         ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService adService,
                         ubic.gemma.persistence.service.expression.bioAssay.BioAssayService baService,
                         ubic.gemma.core.analysis.preprocess.OutlierDetectionService outlierDetectionService)

    • Method Detail

      • getExcludedUris

        @Nullable
public List<String> getExcludedUris​(@Nullable
                                    StringArrayArg excludedUrisArg,
                                    boolean excludeFreeText,
                                    boolean excludeUncategorizedTerms)
        Obtain a list of exclude URIs from an argument containing excluded URIs.
        Parameters:
        excludedUrisArg - argument containing excluded URIs or null if unspecified
        excludeFreeText - if true, null will be included in the returned list which will result in the exclusion of free-text categories or terms
        Returns:
        null if excludedUrisArg is null and excludeFreeText is false, otherwise a list of excluded URIs

      • getFilters

        public ubic.gemma.persistence.util.Filters getFilters​(FilterArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> filterArg)
                                               throws javax.ws.rs.BadRequestException
        Specified by:
        getFilters in interface EntityArgService<ubic.gemma.model.expression.experiment.ExpressionExperiment,​ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService>
        Overrides:
        getFilters in class AbstractEntityArgService<ubic.gemma.model.expression.experiment.ExpressionExperiment,​ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService>
        Throws:
        javax.ws.rs.BadRequestException

      • getSort

        public ubic.gemma.persistence.util.Sort getSort​(SortArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> sortArg)
                                         throws javax.ws.rs.BadRequestException
        Specified by:
        getSort in interface EntityArgService<ubic.gemma.model.expression.experiment.ExpressionExperiment,​ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService>
        Overrides:
        getSort in class AbstractEntityArgService<ubic.gemma.model.expression.experiment.ExpressionExperiment,​ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService>
        Throws:
        javax.ws.rs.BadRequestException

      • getFilters

        public ubic.gemma.persistence.util.Filters getFilters​(FilterArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> filterArg,
                                                      @Nullable
                                                      Collection<OntologyTerm> mentionedTerm)

      • getResultsForSearchQuery

        public List<ubic.gemma.core.search.SearchResult<ubic.gemma.model.expression.experiment.ExpressionExperiment>> getResultsForSearchQuery​(QueryArg query,
                                                                                                                                       @Nullable
                                                                                                                                       ubic.gemma.core.search.Highlighter highlighter)
                                                                                                                                throws javax.ws.rs.BadRequestException
        Obtain the search results for a given query and highlighter.
        Parameters:
        highlighter - a highlighter to use for the query or null to ignore
        Throws:
        javax.ws.rs.BadRequestException - if the query is empty

      • getIdsForSearchQuery

        public Set<Long> getIdsForSearchQuery​(QueryArg query,
                                      @Nullable
                                      Map<Long,​Double> scoreById)
                               throws javax.ws.rs.BadRequestException
        Obtain a Filter for the result of a ExpressionExperiment search.

        The filter is a restriction over the EE IDs.

        Parameters:
        query - query
        scoreById - if non-null, a destination for storing the scores by result ID
        Throws:
        javax.ws.rs.BadRequestException - if the query is empty

      • getQuantitationTypes

        public Set<ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject> getQuantitationTypes​(DatasetArg<?> arg)
        Retrieve a dataset with quantitation type initialized.

      • getPlatforms

        public List<ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject> getPlatforms​(DatasetArg<?> arg)
        Retrieves the Platforms of the Dataset that this argument represents.
        Returns:
        a collection of Platforms that the dataset represented by this argument is in.

      • getSamples

        public List<ubic.gemma.model.expression.bioAssay.BioAssayValueObject> getSamples​(DatasetArg<?> arg)
        Returns:
        a collection of BioAssays that represent the experiments samples.

      • getAnnotations

        public Set<ubic.gemma.model.common.description.AnnotationValueObject> getAnnotations​(DatasetArg<?> arg)
        Returns:
        a collection of Annotations value objects that represent the experiments annotations.