Check if Synapse-listed MD5 matches locally calculated MD5 by downloading files with client

check_md5.R

library(synapser)
synLogin()

ids <- synTableQuery("select id from syn23664752")$asDataFrame()

md5_fail <- "syn45353855" # a known file with a bad md5 in filehandle

ids_testing <- c(md5_fail, ids$id)
  
res <- lapply(ids_testing[1:2], function(x){
  message(glue::glue("{which(ids_testing==x)} of {length(ids_testing)}:{x}"))
  res = tryCatch({
    boo <- synGet(x)$path
    res <- 'md5 match'
    
    #need to delete file to avoid clogging instance after check 
    if (file.exists(boo)) {
      #Delete file if it exists
      message(glue::glue("deleting {x}"))
      file.remove(boo)
    }
    
    res
  }, error = function(e) {
    #assume that if synapse returns an error it is an md5 mismatch error
    res <- "md5 mismatch"
  })
})

 
res_df <- dplyr::bind_cols(tibble::as_tibble_col(ids_testing, column_name = "synapse_id"),
                           tibble::as_tibble_col(res, column_name = "md5_passed"))