Contains a set of functions for interacting with the Synapse REST services.

Help topics

  • AccessControlList
    AccessControlList Constructor
  • Activity
    Activity Constructor
  • annotationNames
    annotationNames
  • annotations(annotationValues, annotationValues<-, annotValue, annotValue<-, deleteAnnotation)
    Entity Annotations
  • annotations-methods(annotations,SynapseEntity-method)
    Methods for Function
  • annotationValues<--methods(annotationValues<-,SynapseAnnotation,list-method, annotationValues<-,SynapseEntity,list-method)
    Methods for Function
  • annotationValues-methods(annotationValues,SynapseAnnotation-method, annotationValues,SynapseEntity-method)
    ~~ Methods for Function
  • annotValue<--methods(annotValue<-,SynapseAnnotation,character,character-method, annotValue<-,SynapseAnnotation,character,integer-method, annotValue<-,SynapseAnnotation,character,logical-method, annotValue<-,SynapseAnnotation,character,numeric-method, annotValue<-,SynapseEntity,character,character-method, annotValue<-,SynapseEntity,character,integer-method, annotValue<-,SynapseEntity,character,logical-method, annotValue<-,SynapseEntity,character,numeric-method)
    Methods for Function
  • annotValue-methods(annotValue,SynapseAnnotation,character-method, annotValue,SynapseEntity,character-method)
    Methods for Function
  • as.list
    as.list
  • as.tableColumns
    as.tableColumns
  • Create Entity Access Control List(synCreateEntityACL)
    Create Entity Access Control List
  • deleteAnnotation-methods(deleteAnnotation,SynapseAnnotation,character-method, deleteAnnotation,SynapseEntity,character-method)
    ~~ Methods for Function
  • Delete Entity Access Control List(synDeleteEntityACL)
    Delete Entity Access Control List
  • deleteProperty-methods(deleteProperty,SynapseAnnotation,character-method, deleteProperty,SynapseEntity,character-method)
    ~~ Methods for Function
  • Evaluation
    Evaluation Constructor
  • executed
  • executed<--methods(executed<-)
  • File
    Synapse File Constructor
  • Folder
    Synapse Folder Constructor
  • generatedBy
    generatedBy
  • generatedBy<--methods(generatedBy<-)
    generatedBy<-
  • getActivity-methods(getActivity)
    getActivity
  • Get Entity Access Control List(synGetEntityACL)
    Get Entity Access Control List
  • getFileLocation
    getFileLocation
  • getParentEntity-methods(getParentEntity,SynapseEntity-method)
    ~~ Methods for Function
  • hmacSecretKey
    hmacSecretKey
  • length
    length
  • names
    names
  • onWeb
    View an Entity's Synapse Web Page
  • onWeb-methods(onWeb,SynapseEntity-method)
    ~~ Methods for Function
  • Project
    Synapse Project Constructor
  • properties(propertyValue<-, propertyValue, propertyValues<-, propertyValues, deleteProperty)
    Functions for Manipulating Entity Properties
  • properties-methods(properties,SynapseAnnotation-method, properties,SynapseEntity-method)
    ~~ Methods for Function
  • propertyNames
    propertyNames
  • propertyValue<--methods(propertyValue<-,SynapseAnnotation,character-method, propertyValue<-,SynapseAnnotation,integer-method, propertyValue<-,SynapseAnnotation,logical-method, propertyValue<-,SynapseAnnotation,numeric-method, propertyValue<-,SynapseEntity,character-method)
    ~~ Methods for Function
  • propertyValue-methods(propertyValue,SynapseAnnotation,character-method, propertyValue,SynapseEntity,character-method)
    ~~ Methods for Function
  • propertyValues<--methods(propertyValues<-,SynapseAnnotation,list-method, propertyValues<-,SynapseEntity,list-method)
    ~~ Methods for Function
  • propertyValues-methods(propertyValues,SynapseAnnotation-method, propertyValues,SynapseEntity-method)
    ~~ Methods for Function
  • QueryResult(fetch, collect, collectAll)
    Retrieve Query Results
  • ResourceAccess
    ResourceAccess Constructor
  • Row
    Row Constructor
  • RowReference
    RowReference Constructor
  • RowReferenceSet
    RowReferenceSet Constructor
  • sendMessage
    sendMessage
  • sessionToken(refreshSessionToken)
    Refresh the Auth Service Session Token
  • setApiCredentials
    setApiCredentials
  • setPackageName
    setPackageName
  • Settings
    Settings Constructor
  • SubmissionQuota
    SubmissionQuota Constructor
  • SubmissionStatus
    Constructor for SubmissionStatus
  • submit
    submit
  • synAddColumn
    synAddColumn
  • synAnnot
    synAnnot
  • synapseAuthServiceEndpoint(synapseRepoServiceEndpoint, synapseFileServiceEndpoint, synapsePortalEndpoint, synapseResetEndpoints)
    Synapse Endpoints
  • synapseCacheDir
    Synapse Local File Cache Directory
  • synapseClient-package(synapseClient)
    Synapse Client
  • SynapseEntity(Study, Code, Data, Preview, ExpressionData, GenotypeData, PhenotypeData, RObject)
    DEPRECATED Entity Constructors
  • SynapseEntityMethods(addFile-methods, addFile,CachedLocation,character,character-method, addFile,LocationOwner,character,missing-method, addFile,LocationOwner,character,character-method, addFile, deleteFile, moveFile, addObject-methods, addObject,SynapseLocationOwner,ANY-method, addObject,SynapseLocationOwner,data.frame-method, addObject,SynapseLocationOwner,list-method, addObject, deleteObject, getObject, listObjects, renameObject, getEntity, getEntity-methods, getEntity,character-method, getEntity,list-method, getEntity,numeric-method, getEntity,SynapseEntity-method, deleteFile-methods, deleteFile,FileCache,character-method, deleteFile,SynapseLocationOwner,character-method, deleteEntity-methods, deleteEntity,character-method, deleteEntity,list-method, deleteEntity,numeric-method, deleteEntity,SynapseEntity-method, deleteObject-methods, deleteObject,SynapseLocationOwner,character-method, moveFile-methods, moveFile,FileCache-method, moveFile,SynapseLocationOwner-method, getObject-methods, getObject,SynapseLocationOwner,character-method, renameObject-methods, renameObject,SynapseLocationOwner,character,character-method, storeEntity-methods, storeEntity,SynapseLocationOwner-method, storeEntity,SynapseEntity-method, createEntity, deleteEntity, updateEntity, storeEntity, storeEntityFiles, storeEntityObjects, downloadEntity, loadEntity, getParentEntity, createEntity-methods, createEntity,SynapseLocationOwner-method, createEntity,SynapseEntity-method, updateEntity-methods, updateEntity,SynapseLocationOwner-method, updateEntity,SynapseEntity-method, downloadEntity-methods, downloadEntity,character-method, downloadEntity,SynapseLocationOwner-method, downloadEntity,numeric-method, downloadEntity,SynapseEntity-method, loadEntity-methods, loadEntity,character-method, loadEntity,SynapseLocationOwner-method, loadEntity,numeric-method)
    DEPRECATED Entity Methods
  • synapseExecute
    Execute Code and Upload Results to Synapse
  • synapseGet(synapsePost, synapseDelete, synapsePut, .synapsePostPut, .synapseGetDelete)
    Synapse REST
  • synapseLogin(synapseLogout, invalidateAPIKey)
    Authentication
  • synapseQuery(synQuery)
    Query The Synapse API
  • synDelete
    synDelete
  • synDeleteRows
    synDeleteRows
  • synDownloadTableColumns
    synDownloadTableColumns
  • synGet
    Retrieve an object from Synapse
  • synGetActivity
    synGetActivity
  • synGetAnnotation
    synGetAnnotation
  • synGetAnnotations
    synGetAnnotations
  • synGetColumns
    synGetColumns
  • synGetEndpoints
    synGetEndpoints
  • synGetEvaluation(synGetEvaluationByContentSource)
    synGetEvaluation
  • synGetOwnSubmissions
    synGetOwnSubmissions
  • synGetParticipants
    synGetParticipants
  • synGetProperties
    synGetProperties
  • synGetProperty
    synGetProperty
  • synGetSubmission
    synGetSubmission
  • synGetSubmissions
    synGetSubmissions
  • synGetSubmissionStatus
    synGetSubmissionStatus
  • synGetUserProfile
    synGetUserProfile
  • synGetWiki
    synGetWiki
  • synGetWikiHeaders
    synGetWikiHeaders
  • synRemoveColumn
    synRemoveColumn
  • synRestGET(synRestPOST, synRestPUT, synRestDELETE)
    Synapse REST Functions
  • synSetAnnotation
    synSetAnnotation
  • synSetAnnotations
    synSetAnnotations
  • synSetEndpoints
    synSetEndpoints
  • synSetProperties
    synSetProperties
  • synSetProperty
    synSetProperty
  • synStore
    Store an object in Synapse
  • synTableQuery
    synTableQuery
  • Table
    Table Constructor
  • TableColumn
    TableColumn Constructor
  • TableRowSet
    TableRowSet Constructor
  • TableSchema
    TableSchema Constructor
  • touOnWeb
    View the Synapse Terms of Use as a Web Page
  • TypedList(as.ResourceAccessList, as.SelectColumnList, as.RowList, as.RowReferenceList)
  • TypedList(as.ResourceAccessList, as.SelectColumnList, as.RowList, as.RowReferenceList)
  • Update Entity Access Control List(synUpdateEntityACL)
    Update Entity Access Control List
  • used
  • used<--methods(used<-)
  • UserProfile
    Constructor for UserProfile
  • WikiHeader
    Constructor for WikiHeader
  • WikiPage
    Constructor for WikiPage

Vignettes

Dependencies

  • Depends: methods
  • Imports: rjson, RCurl, tools, digest, utils
  • Suggests: RUnit, rGithubClient, Rsftp

Authors