R/loadEntity.R

In Sage-Bionetworks/rSynapseClientRewrite: Synapse R Client from Sage Bionetworks

## Load Entity Objects
## 
## Author: Matthew D. Furia <matt.furia@sagebase.org>
###############################################################################

setMethod(
  f = "loadEntity",
  signature = "character",
  definition = function(entity){
    entity <- getEntity(entity)
    loadEntity(entity)
  }
)

setMethod(
  f = "loadEntity",
  signature = "numeric",
  definition = function(entity){
    loadEntity(as.character(entity))
  }
)
#
#setMethod(
#  f = ".loadSageBioPacket",
#  signature = "SynapseEntity",
#  definition = function(entity){
#    stop("Only Layer entities can be loaded from SageBioCurated format")
#  }
#)
#
#setMethod(
#  f = ".loadSageBioPacket",
#  signature = "PhenotypeLayer",
#  definition = function(entity){
#    if(is.null(annotValue(entity, "format")) || annotValue(entity, "format") != "sageBioCurated")
#      stop("Unable to load Phenotype layers that are not in SageBioCurated format using this function.")
#    
#    if(length(entity@location@files) == 0)
#      entity <- downloadEntity(entity)
#    
#    files <- file.path(entity@location@cacheDir, entity@location@files)
#    
#    ## look in phenotype directory for 
#    indx <- grep("/phenotype/phenotype.txt$",files)
#    d <- read.delim(files[indx], as.is=T)
#    
#    indx <- grep("/phenotype/description.txt$", files)
#    desc <- read.delim(files[indx], as.is=T)
#    
#    indx <- grep("individuals.txt", files)
#    indiv <- read.delim(files[indx], as.is=T)
#    
#    ## TODO fix this hack after demo
#    names(d)[1] <- "individual_id"
#    names(indiv)[1] <- "individual_id"
#    
#    ## return the data as an annotated data frame
#    rownames(d) <- d[,1]
#    d <- d[,-1]
#    rownames(desc) <- desc[,1]
#    desc <- desc[,-1]
#    names(desc)[names(desc) == "description"] <- "labelDescription"
#    objects <- new.env()
#    objects$phenotypes <- new("AnnotatedDataFrame", data = d, varMetadata = desc)
#    objects
#  }
#)
#
#setMethod(
#  f = "loadEntity",
#  signature = "ExpressionLayer",
#  definition = function(entity){
#    if(length(entity$files) == 0L)
#      entity <- downloadEntity(entity)
#    if(is.null(annotValue(entity, "format"))){
#      oldClass <- class(entity)
#      class(entity) <- "Layer"
#      entity <- loadEntity(entity)
#      class(entity) <- oldClass
#    } else if(tolower(annotValue(entity,"format")) %in% c("cel", "geo")){
#      cel.files <- list.celfiles(entity$cacheDir, full.names=TRUE)
#      cdfs <- sapply(cel.files, whatcdf) 
#      expression <- lapply(unique(cdfs), function(cdf){
#          ReadAffy(filenames=names(which(cdfs==cdf)))
#        }
#      )
#      names(expression) <- unique(cdfs)
#      entity <- addObject(entity, expression, unlist = FALSE)
#    } else
#      cat("No functionality to handle that kind of format yet - objects not loaded\n")
#    entity
#  }
#)
#
#
#setMethod(
#  f = "loadEntity",
#  signature = "Code",
#  definition = function(entity){
#    if(length(entity@location@files) == 0)
#      entity <- downloadEntity(entity)
#    entity@location@objects <- new.env()
#    
#    indx <- grep("\\.r$", tolower(entity$files))
#    if(!is.null(propertyValue(entity, "id"))){
#      setPackageName(sprintf("entity%s", propertyValue(entity, "id")), env = entity@location@objects)
#    }else{
#      setPackageName(sprintf("code%s", propertyValue(entity, "name")), env = entity@location@objects)
#    }
#    tryCatch(
#      lapply(entity$files[indx],
#        function(f){
#          f <- file.path(entity$cacheDir, f)
#          sys.source(f, env = entity@location@objects)
#        }
#      ),
#      error = function(e){
#        warning(e)
#      }
#    )
#    entity
#  }
#)
#
#setMethod(
#  f = "loadEntity",
#  signature = "GithubCode",
#  definition = function(entity){
#    if(length(entity@location@files) == 0)
#      entity <- downloadEntity(entity)
#    entity@location@objects <- new.env()
#    
#    indx <- grep("\\.r$", tolower(entity$files))
#    if(!is.null(propertyValue(entity, "id"))){
#      setPackageName(sprintf("entity%s", propertyValue(entity, "id")), env = entity@location@objects)
#    }else{
#      setPackageName(sprintf("code%s", propertyValue(entity, "name")), env = entity@location@objects)
#    }
#    tryCatch(
#      lapply(entity$files[indx],
#        function(f){
#          f <- file.path(entity$cacheDir, f)
#          sys.source(f, env = entity@location@objects)
#        }
#      ),
#      error = function(e){
#        warning(e)
#      }
#    )
#    entity
#  }
#)

setMethod(
  f = "loadEntity",
  signature = "SynapseEntity",
  definition = function(entity){
    getEntity(entity)
  }
)