R/synapseUtil.R

In PNNL-CompBio/amlresistancenetworks: Calculates networks that lead to AML resistance to drugs

## This package uses the synapse web platform at http://synapse.org
# you must first register and update your config

##we use the synapse python client and reticulate

##

#####Synapse python client wrapper files



#condaenv="C:\\Users\\gosl241\\OneDrive - PNNL\\Documents\\GitHub\\amlresistancenetworks\\renv\\python\\r-reticulate\\"

#' Logs into Synapse using local information
#' @import reticulate
#' @return Synapse login python entity
#' @export
synapseLogin<-function(){
  library(reticulate)
 # reticulate::use_condaenv(condaenv)
  syn=reticulate::import('synapseclient')
  sync=syn$login()
  return(sync)
}

#' Synapse store
#' @import reticulate
#' @param path to file
#' @param parentId of folder to store
#' @export
synapseStore<-function(path,parentId){
 # library(reticulate)
 # reticulate::use_condaenv(condaenv)

  synapse=reticulate::import('synapseclient')
  sync=synapse$login()
  sync$store(synapse$File(path,parentId=parentId))
}


#' Synapse table store
#' REQUIRES PANDAS ON YOUR PYTHON PATH
#' @param table to store on synapse
#' @param tabname name of table
#' @param parentId id of project
#' @import reticulate
#' @export
synTableStore<-function(tab,tabname,parentId='syn22128879'){
  #we have to first write the table to a file, then build it and store it
  library(reticulate)
  print(head(tab))
  fpath=write.table(tab,file='tmp.csv',sep=',',quote=T,row.names = FALSE)
#  reticulate::use_condaenv(condaenv)
  synapse=reticulate::import('synapseclient')

  tab<-synapse$build_table(tabname,parentId,'tmp.csv')
  sync=synapse$login()
  sync$store(tab)

}


#'synTableUpdate
#'Removes all rows from table and replaces
#'@param table
#'@param synapse id of table to replace
#'@import reticulate
#'@export
synTableUpdate<-function(tab,synid){
  library(reticulate)
  print(head(tab))
 # reticulate::use_condaenv(condaenv)
  synapse=reticulate::import('synapseclient')
  fpath=write.table(tab,file='tmp.csv',sep=',',row.names = FALSE,quote=FALSE)
  ntab = synapse$Table(synid,'tmp.csv')
  
  syn=synapse$login()
  rows = syn$tableQuery(paste("select * from",synid))
  syn$delete(rows)
  syn$store(ntab)
  
}

#' query synapse table
#' This is how you get data from the project
#' @param tableid
#' @export
querySynapseTable<-function(tableid){
  syn=synapseLogin()
  res<-syn$tableQuery(paste('select * from',tableid))$asDataFrame()
 # if('Gene'%in%names(res))
#    res$Gene<-unlist(res$Gene)
#  if('site'%in%names(res))
#    res$site<-unlist(res$site)
  return(res)
}