Package ubic.gemma.rest
Class GeneWebService
- java.lang.Object
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- ubic.gemma.rest.GeneWebService
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@Service @Path("/genes") public class GeneWebService extends Object
RESTful interface for genes. Does not have an 'all' endpoint (no use-cases). Most methods also have a taxon-specific counterpart in theTaxaWebService
(useful when using the 'official symbol' identifier, as this class will just return a random taxon homologue).- Author:
- tesarst
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Constructor Summary
Constructors Constructor Description GeneWebService()
Required by springGeneWebService(GeneService geneService, CompositeSequenceService compositeSequenceService, GeneCoexpressionSearchService geneCoexpressionSearchService, GeneArgService geneArgService)
Constructor for service autowiring
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Method Summary
All Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description ResponseDataObject<List<GeneEvidenceValueObject>>
getGeneEvidence(GeneArg<?> geneArg)
Deprecated.ResponseDataObject<List<CoexpressionValueObjectExt>>
getGeneGeneCoexpression(GeneArg<?> geneArg, GeneArg<?> with, LimitArg limit, Integer stringency)
Retrieves the coexpression of two given genes.ResponseDataObject<List<GeneOntologyTermValueObject>>
getGeneGoTerms(GeneArg<?> geneArg)
Retrieves the GO terms of the given gene.ResponseDataObject<List<PhysicalLocationValueObject>>
getGeneLocations(GeneArg<?> geneArg)
Retrieves the physical location of the given gene.FilteredAndPaginatedResponseDataObject<CompositeSequenceValueObject>
getGeneProbes(GeneArg<?> geneArg, OffsetArg offset, LimitArg limit)
Retrieves the probes (composite sequences) with this gene.ResponseDataObject<List<GeneValueObject>>
getGenes(GeneArrayArg genes)
Retrieves all genes matching the identifier.
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Constructor Detail
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GeneWebService
public GeneWebService()
Required by spring
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GeneWebService
@Autowired public GeneWebService(GeneService geneService, CompositeSequenceService compositeSequenceService, GeneCoexpressionSearchService geneCoexpressionSearchService, GeneArgService geneArgService)
Constructor for service autowiring
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Method Detail
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getGenes
@GET @Path("/{genes}") @Produces("application/json") public ResponseDataObject<List<GeneValueObject>> getGenes(@PathParam("genes") GeneArrayArg genes)
Retrieves all genes matching the identifier.- Parameters:
genes
- a list of gene identifiers, separated by commas (','). Identifiers can be one of NCBI ID, Ensembl ID or official symbol. NCBI ID is the most efficient (and guaranteed to be unique) identifier. Official symbol returns a gene homologue on a random taxon.Do not combine different identifiers in one query.
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getGeneEvidence
@GET @Path("/{gene}/evidence") @Produces("application/json") @Deprecated public ResponseDataObject<List<GeneEvidenceValueObject>> getGeneEvidence(@PathParam("gene") GeneArg<?> geneArg)
Deprecated.Retrieves gene evidence for the given gene.- Parameters:
geneArg
- can either be the NCBI ID, Ensembl ID or official symbol. NCBI ID is most efficient (and guaranteed to be unique). Official symbol returns a gene homologue on a random taxon.
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getGeneLocations
@GET @Path("/{gene}/locations") @Produces("application/json") public ResponseDataObject<List<PhysicalLocationValueObject>> getGeneLocations(@PathParam("gene") GeneArg<?> geneArg)
Retrieves the physical location of the given gene.- Parameters:
geneArg
- can either be the NCBI ID, Ensembl ID or official symbol. NCBI ID is most efficient (and guaranteed to be unique). Official symbol returns a gene homologue on a random taxon.
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getGeneProbes
@GET @Path("/{gene}/probes") @Produces("application/json") public FilteredAndPaginatedResponseDataObject<CompositeSequenceValueObject> getGeneProbes(@PathParam("gene") GeneArg<?> geneArg, @QueryParam("offset") @DefaultValue("0") OffsetArg offset, @QueryParam("limit") @DefaultValue("20") LimitArg limit)
Retrieves the probes (composite sequences) with this gene.- Parameters:
geneArg
- can either be the NCBI ID, Ensembl ID or official symbol. NCBI ID is most efficient (and guaranteed to be unique). Official symbol returns a gene homologue on a random taxon.
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getGeneGoTerms
@GET @Path("/{gene}/goTerms") @Produces("application/json") public ResponseDataObject<List<GeneOntologyTermValueObject>> getGeneGoTerms(@PathParam("gene") GeneArg<?> geneArg)
Retrieves the GO terms of the given gene.- Parameters:
geneArg
- can either be the NCBI ID, Ensembl ID or official symbol. NCBI ID is most efficient (and guaranteed to be unique). Official symbol returns a gene homologue on a random taxon.
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getGeneGeneCoexpression
@GET @Path("/{gene}/coexpression") @Produces("application/json") public ResponseDataObject<List<CoexpressionValueObjectExt>> getGeneGeneCoexpression(@PathParam("gene") GeneArg<?> geneArg, @QueryParam("with") GeneArg<?> with, @QueryParam("limit") @DefaultValue("100") LimitArg limit, @QueryParam("stringency") @DefaultValue("1") Integer stringency)
Retrieves the coexpression of two given genes.- Parameters:
geneArg
- can either be the NCBI ID, Ensembl ID or official symbol. NCBI ID is most efficient (and guaranteed to be unique). Official symbol returns a gene homologue on a random taxon.with
- the gene to calculate the coexpression with. Same formatting rules as with the 'geneArg' apply.stringency
- optional parameter controlling the stringency of coexpression search. Defaults to 1.
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