R/s3_parse_methods.R

In moj-analytical-services/s3tools: Tools to help explore Amazon S3

assign_s3_file_class <- function(path){
  file_ext <- tools::file_ext(path)
  attr(path, "class") <- file_ext
  return(path)
}


#' Read data from s3 with automatic processing 
#' 
#' Currently supports csv, tsv, xls, and xlsx files. 
#'
#' @param path path to the s3 file bucket/folder/file.csv 
#' @param ...  arguemtns passed to read.csv or read_excel. 
#'
#' @return dataframe
#'
#' @examples s3tools::s3_path_to_full_df("alpha-test-team/mpg.csv")
#' @examples s3tools::s3_path_to_preview_df("alpha-test-team/mpg.csv")
s3_path_to_df <- function(s3_path, ...){
  s3_path <- assign_s3_file_class(s3_path)
  UseMethod("s3_path_to_df", s3_path)
}

s3_path_to_df.default <- function(path, ...){
  message('s3tools cannot parse this file automatically')
  message('If you want to specify your own reading function see s3tools::read_using()')
  message('or use the file path provided by this function')
  file_location <- s3_download_temp_file(path, ...)
  message(paste0('your file is available at: ', file_location))
  message(paste0("\'", file_location, "'"), execute = FALSE)
  file_location
}

s3_path_to_df.csv <- function(path, ..., head) {
  message('using csv (or similar) method, reading directly to R supported')
  
  p <- separate_bucket_path(path)
  credentials <- suppressMessages(get_credentials())
  if (head) {
    suppressMessages(refresh(credentials))
    ob <- aws.s3::get_object(p$object, p$bucket,  headers = list(Range='bytes=0-12000'), check_region=TRUE)
    df <- read.csv(text = rawToChar(ob), stringsAsFactors = FALSE)
    df <- head(df)
  } else {
    suppressMessages(refresh(credentials))
    ob <- aws.s3::get_object(p$object, p$bucket, check_region=TRUE)
    df <- read.csv(text = rawToChar(ob), stringsAsFactors = FALSE)
  }
  
  df
  
}

s3_path_to_df.tsv <- function(path, ...){
  s3_path_to_df.csv(path, ..., head)
}


s3_path_to_df.xlsx <- function(path, ..., head){
  
  if(is.logical(head) && head){
    message('Preview not supported for Excel files')
  }
  file_location <- s3_download_temp_file(path)
  message(paste0('Temp file saved to: ', file_location))
  
  df <- tryCatch({
          readxl::read_excel(path=file_location, ...)
          },
          error= function(cond){
             message("Attempted to read file using the readxl package, but it is not installed or the file could not be parsed")
             message("You can install this package by running install.packages('readxl')")
             
             stop("Cannot read file, stopping", call.=FALSE)
             })
  
  df
  
}

s3_path_to_df.xls <- function(path, ...){
  s3_path_to_df.xlsx(path, ...)
}

s3_path_to_df.sas7bdat <- function(path, ..., head){
  
  if(is.logical(head) && head){
    message('Preview not supported for sas files')
  }
  file_location <- s3_download_temp_file(path)
  message(paste0('Temp file saved to: ', file_location))
  
  df <- tryCatch({
    haven::read_sas(file_location, ...)
  },
  error= function(cond){
    message("Attempted to read file using the haven package, but it is not installed or the file could not be parsed  ")
    message("You can install this package by running install.packages('haven')")
    
    stop("Cannot read file, stopping", call.=FALSE)
  })
  
  df
  
}

s3_path_to_df.sav <- function(path, ..., head){
  
  if(is.logical(head) && head){
    message('Preview not supported for spss files')
  }
  file_location <- s3_download_temp_file(path)
  message(paste0('Temp file saved to: ', file_location))
  
  df <- tryCatch({
    haven::read_spss(file_location, ...)
  },
  error= function(cond){
    message("Attempted to read file using the haven package, but it is not installed or the file could not be parsed  ")
    message("You can install this package by running install.packages('haven')")
    
    stop("Cannot read file, stopping")
  })
  
  df
  
}


s3_path_to_df.dta <- function(path, ..., head){
  
  if(is.logical(head) && head){
    message('Preview not supported for stata .dat files')
  }
  file_location <- s3_download_temp_file(path)
  message(paste0('Temp file saved to: ', file_location))
  
  df <- tryCatch({
    haven::read_stata(file_location, ...)
  },
  error= function(cond){
    message("Attempted to read file using the haven package, but it is not installed or the file could not be parsed")
    message("You can install this package by running install.packages('haven')")
    
    stop("Cannot read file, stopping", call.=FALSE)
  })
  
  df
  
}


s3_download_temp_file <- function(path, ...){
  p <- separate_bucket_path(path)
  credentials <- suppressMessages(s3tools:::get_credentials())
  suppressMessages(refresh(credentials))
  file_ext <- paste('.', tools::file_ext(p$object), sep='')
  file_name <- tempfile(fileext = file_ext)
  file_location <- aws.s3:::save_object(object = p$object, bucket = p$bucket, file=file_name, check_region=TRUE)
  return(file_location)
}