Package ubic.gemma.rest

Class PlatformsWebService

java.lang.Object

ubic.gemma.rest.PlatformsWebService

@Service
@Path("/platforms")
public class PlatformsWebService
extends Object

RESTful interface for platforms.

Author:

tesarst

Constructor Summary

Constructors

Constructor	Description
PlatformsWebService()	Required by spring
PlatformsWebService(GeneService geneService, ArrayDesignService arrayDesignService, CompositeSequenceService compositeSequenceService, ArrayDesignAnnotationService annotationFileService, PlatformArgService arrayDesignArgService, CompositeSequenceArgService probeArgService)	Constructor for service autowiring

Method Summary

Modifier and Type	Method	Description
FilteredAndPaginatedResponseDataObject<ArrayDesignValueObject>	getBlacklistedPlatforms(FilterArg<ArrayDesign> filter, SortArg<ArrayDesign> sort, OffsetArg offset, LimitArg limit)
ResponseDataObject<Long>	getNumberOfPlatforms(FilterArg<ArrayDesign> filter)
javax.ws.rs.core.Response	getPlatformAnnotations(PlatformArg<?> platformArg)	Retrieves the annotation file for the given platform.
PaginatedResponseDataObject<ExpressionExperimentValueObject>	getPlatformDatasets(PlatformArg<?> platformArg, OffsetArg offset, LimitArg limit)	Retrieves experiments in the given platform.
FilteredAndPaginatedResponseDataObject<CompositeSequenceValueObject>	getPlatformElement(PlatformArg<?> platformArg, CompositeSequenceArrayArg probesArg, OffsetArg offset, LimitArg limit)	Retrieves composite sequences (elements) of the given platform.
FilteredAndPaginatedResponseDataObject<GeneValueObject>	getPlatformElementGenes(PlatformArg<?> platformArg, CompositeSequenceArg<?> probeArg, OffsetArg offset, LimitArg limit)	Retrieves the genes on the given platform element.
PaginatedResponseDataObject<CompositeSequenceValueObject>	getPlatformElements(PlatformArg<?> platformArg, OffsetArg offset, LimitArg limit)	Retrieves the composite sequences (elements) for the given platform.
FilteredAndPaginatedResponseDataObject<ArrayDesignValueObject>	getPlatforms(FilterArg<ArrayDesign> filter, OffsetArg offset, LimitArg limit, SortArg<ArrayDesign> sort)
FilteredAndPaginatedResponseDataObject<ArrayDesignValueObject>	getPlatformsByIds(PlatformArrayArg platformsArg, FilterArg<ArrayDesign> filter, OffsetArg offset, LimitArg limit, SortArg<ArrayDesign> sort)	Retrieves all datasets matching the given identifiers.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PlatformsWebService

public PlatformsWebService()

Required by spring

PlatformsWebService

@Autowired
public PlatformsWebService(GeneService geneService,
                           ArrayDesignService arrayDesignService,
                           CompositeSequenceService compositeSequenceService,
                           ArrayDesignAnnotationService annotationFileService,
                           PlatformArgService arrayDesignArgService,
                           CompositeSequenceArgService probeArgService)

Constructor for service autowiring

Method Detail

getPlatforms

@GET
@Produces("application/json")
public FilteredAndPaginatedResponseDataObject<ArrayDesignValueObject> getPlatforms(@QueryParam("filter") @DefaultValue("")
                                                                                   FilterArg<ArrayDesign> filter,
                                                                                   @QueryParam("offset") @DefaultValue("0")
                                                                                   OffsetArg offset,
                                                                                   @QueryParam("limit") @DefaultValue("20")
                                                                                   LimitArg limit,
                                                                                   @QueryParam("sort") @DefaultValue("+id")
                                                                                   SortArg<ArrayDesign> sort)

getNumberOfPlatforms

@GET
@Path("/count")
@Produces("application/json")
public ResponseDataObject<Long> getNumberOfPlatforms(@QueryParam("filter") @DefaultValue("")
                                                     FilterArg<ArrayDesign> filter)

getPlatformsByIds

@GET
@Path("/{platform}")
@Produces("application/json")
public FilteredAndPaginatedResponseDataObject<ArrayDesignValueObject> getPlatformsByIds(@PathParam("platform")
                                                                                        PlatformArrayArg platformsArg,
                                                                                        @QueryParam("filter") @DefaultValue("")
                                                                                        FilterArg<ArrayDesign> filter,
                                                                                        @QueryParam("offset") @DefaultValue("0")
                                                                                        OffsetArg offset,
                                                                                        @QueryParam("limit") @DefaultValue("20")
                                                                                        LimitArg limit,
                                                                                        @QueryParam("sort") @DefaultValue("+id")
                                                                                        SortArg<ArrayDesign> sort)

Retrieves all datasets matching the given identifiers.

Parameters:

platformsArg - a list of identifiers, separated by commas (','). Identifiers can either be the ExpressionExperiment ID or its short name (e.g. GSE1234). Retrieval by ID is more efficient.

Only datasets that user has access to will be available.

Do not combine different identifiers in one query.

getBlacklistedPlatforms

@GET
@Path("/blacklisted")
@Produces("application/json")
@Secured("GROUP_ADMIN")
public FilteredAndPaginatedResponseDataObject<ArrayDesignValueObject> getBlacklistedPlatforms(@QueryParam("filter") @DefaultValue("")
                                                                                              FilterArg<ArrayDesign> filter,
                                                                                              @QueryParam("sort") @DefaultValue("+id")
                                                                                              SortArg<ArrayDesign> sort,
                                                                                              @QueryParam("offset") @DefaultValue("0")
                                                                                              OffsetArg offset,
                                                                                              @QueryParam("limit") @DefaultValue("20")
                                                                                              LimitArg limit)

getPlatformDatasets

@GET
@Path("/{platform}/datasets")
@Produces("application/json")
public PaginatedResponseDataObject<ExpressionExperimentValueObject> getPlatformDatasets(@PathParam("platform")
                                                                                        PlatformArg<?> platformArg,
                                                                                        @QueryParam("offset") @DefaultValue("0")
                                                                                        OffsetArg offset,
                                                                                        @QueryParam("limit") @DefaultValue("20")
                                                                                        LimitArg limit)

Retrieves experiments in the given platform.

Parameters:

platformArg - can either be the ArrayDesign ID or its short name (e.g. "GPL1355" ). Retrieval by ID is more efficient. Only platforms that user has access to will be available.

offset - optional parameter (defaults to 0) skips the specified amount of datasets when retrieving them from the database.

limit - optional parameter (defaults to 20) limits the result to specified amount of datasets. Use 0

getPlatformElements

@GET
@Path("/{platform}/elements")
@Produces("application/json")
public PaginatedResponseDataObject<CompositeSequenceValueObject> getPlatformElements(@PathParam("platform")
                                                                                     PlatformArg<?> platformArg,
                                                                                     @QueryParam("offset") @DefaultValue("0")
                                                                                     OffsetArg offset,
                                                                                     @QueryParam("limit") @DefaultValue("20")
                                                                                     LimitArg limit)

Retrieves the composite sequences (elements) for the given platform.

Parameters:

platformArg - can either be the ArrayDesign ID or its short name (e.g. "GPL1355" ). Retrieval by ID is more efficient. Only platforms that user has access to will be available.

offset - optional parameter (defaults to 0) skips the specified amount of datasets when retrieving them from the database.

limit - optional parameter (defaults to 20) limits the result to specified amount of datasets. Use 0

getPlatformElement

@GET
@Path("/{platform}/elements/{probes}")
@Produces("application/json")
public FilteredAndPaginatedResponseDataObject<CompositeSequenceValueObject> getPlatformElement(@PathParam("platform")
                                                                                               PlatformArg<?> platformArg,
                                                                                               @PathParam("probes")
                                                                                               CompositeSequenceArrayArg probesArg,
                                                                                               @QueryParam("offset") @DefaultValue("0")
                                                                                               OffsetArg offset,
                                                                                               @QueryParam("limit") @DefaultValue("20")
                                                                                               LimitArg limit)

Retrieves composite sequences (elements) of the given platform.

Parameters:

platformArg - can either be the ArrayDesign ID or its short name (e.g. "GPL1355" ). Retrieval by ID is more efficient. Only platforms that user has access to will be available.

probesArg - a list of identifiers, separated by commas (','). Identifiers can either be the CompositeSequence ID or its name (e.g. AFFX_Rat_beta-actin_M_at).

Only elements on platforms that user has access to will be available.

Do not combine different identifiers in one query.

getPlatformElementGenes

@GET
@Path("/{platform}/elements/{probe}/genes")
@Produces("application/json")
public FilteredAndPaginatedResponseDataObject<GeneValueObject> getPlatformElementGenes(@PathParam("platform")
                                                                                       PlatformArg<?> platformArg,
                                                                                       @PathParam("probe")
                                                                                       CompositeSequenceArg<?> probeArg,
                                                                                       @QueryParam("offset") @DefaultValue("0")
                                                                                       OffsetArg offset,
                                                                                       @QueryParam("limit") @DefaultValue("20")
                                                                                       LimitArg limit)

Retrieves the genes on the given platform element.

Parameters:

platformArg - can either be the ArrayDesign ID or its short name (e.g. "GPL1355" ). Retrieval by ID is more efficient. Only platforms that user has access to will be available.

probeArg - the name or ID of the platform element for which the genes should be retrieved. Note that names containing a forward slash are not accepted. Should you need this restriction temporarily lifted, please contact us.

offset - optional parameter (defaults to 0) skips the specified amount of datasets when retrieving them from the database.

limit - optional parameter (defaults to 20) limits the result to specified amount of datasets. Use 0 for no limit.

getPlatformAnnotations

@GET
@Path("/{platform}/annotations")
@Produces("text/tab-separated-values; charset=UTF-8")
public javax.ws.rs.core.Response getPlatformAnnotations(@PathParam("platform")
                                                        PlatformArg<?> platformArg)

Retrieves the annotation file for the given platform.

Parameters:

platformArg - can either be the ArrayDesign ID or its short name (e.g. "GPL1355" ). Retrieval by ID is more efficient. Only platforms that user has access to will be available.

Returns:

the content of the annotation file of the given platform.