Package ubic.gemma.rest.util.args

Class DatasetArgService

java.lang.Object
ubic.gemma.rest.util.args.AbstractEntityArgService<ubic.gemma.model.expression.experiment.ExpressionExperiment,ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService>
ubic.gemma.rest.util.args.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 Details

    • 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 Details

    • getEntityId

      @Nullable public Long getEntityId(DatasetArg<?> datasetArg)
      Retrieve an ID for a given dataset argument.

    • 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, javax.ws.rs.ServiceUnavailableException
      Description copied from interface: EntityArgService
      Obtain a Filters from a filter argument.
      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 - if the argument is malformed
      javax.ws.rs.ServiceUnavailableException

    • getFilters

      public ubic.gemma.persistence.util.Filters getFilters(FilterArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> filterArg, @Nullable Collection<OntologyTerm> mentionedTerms, @Nullable Collection<OntologyTerm> inferredTerms) throws javax.ws.rs.ServiceUnavailableException
      Throws:
      javax.ws.rs.ServiceUnavailableException

    • getFilters

      public ubic.gemma.persistence.util.Filters getFilters(FilterArg<ubic.gemma.model.expression.experiment.ExpressionExperiment> filterArg, @Nullable Collection<OntologyTerm> mentionedTerms, @Nullable Collection<OntologyTerm> inferredTerms, long timeout, TimeUnit timeUnit) throws TimeoutException
      Throws:
      TimeoutException

    • getResultsForSearchQuery

      public List<ubic.gemma.core.search.SearchResult<ubic.gemma.model.expression.experiment.ExpressionExperiment>> getResultsForSearchQuery(QueryArg query, @Nullable ubic.gemma.core.search.Highlighter highlighter, @Nullable Collection<Throwable> queryWarnings) throws javax.ws.rs.BadRequestException, javax.ws.rs.ServiceUnavailableException, javax.ws.rs.InternalServerErrorException
      Obtain the search results for a given query and highlighter.
      Parameters:
      highlighter - a highlighter to use for the query or null to ignore
      queryWarnings - a collection that will receive warnings regarding the full-text query
      Throws:
      javax.ws.rs.BadRequestException - if the query is empty
      javax.ws.rs.ServiceUnavailableException - if the search times out
      javax.ws.rs.InternalServerErrorException - for any other search-related exceptions

    • getIdsForSearchQuery

      public Set<Long> getIdsForSearchQuery(QueryArg query, Map<Long,Double> scoreById, @Nullable Collection<Throwable> queryWarnings)
      Shortcut for extracting the result IDs and scores from getResultsForSearchQuery(QueryArg, Highlighter, Collection).
      See Also:

    • getIdsForSearchQuery

      public Set<Long> getIdsForSearchQuery(QueryArg query, @Nullable Collection<Throwable> queryWarnings)
      Shortcut for extracting the result IDs from getResultsForSearchQuery(QueryArg, Highlighter, Collection).
      See Also:

    • 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.

    • getSamples

      public List<ubic.gemma.model.expression.bioAssay.BioAssayValueObject> getSamples(DatasetArg<?> datasetArg, ubic.gemma.model.common.quantitationtype.QuantitationType qt)
      Obtain a collection of BioAssays that represent the experiments samples for a particular quantitation type.

    • getAnnotations

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

    • getSubSets

      public List<ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet> getSubSets(DatasetArg<?> datasetArg)

    • getSubSet

      public ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet getSubSet(DatasetArg<?> datasetArg, Long subSetId)

    • getSubSetGroupIds

      public List<Long> getSubSetGroupIds(DatasetArg<?> datasetArg, ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet subset)

    • getSubSetsGroupIds

      public Map<ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet,List<Long>> getSubSetsGroupIds(DatasetArg<?> datasetArg)

    • getSubSetSamples

      public List<ubic.gemma.model.expression.bioAssay.BioAssayValueObject> getSubSetSamples(DatasetArg<?> datasetArg, Long subSetId)

    • getPreferredQuantitationType

      public ubic.gemma.model.common.quantitationtype.QuantitationType getPreferredQuantitationType(DatasetArg<?> datasetArg)

    • getPublications

      public List<ubic.gemma.model.common.description.BibliographicReferenceValueObject> getPublications(DatasetArg<?> datasetArg)

    • populateOutliers

      public void populateOutliers(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, Collection<ubic.gemma.model.expression.bioAssay.BioAssayValueObject> bioAssayValueObjects)