check duke files

2022-04-12_michelle_mg_file_errors.R

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+# Description: Get details on MG file errors.
+# Author: Haley Hunter-Zinck
+# Date: 2022-04-012
+
+# setup ----------------------------
+
+tic = as.double(Sys.time())
+
+library(glue)
+library(dplyr)
+library(synapser)
+
+# synapse
+synid_file_cli <- "syn17023617"
+
+# parameters
+valid_seq_dates <- c("Jan", "Apr", "Jul", "Oct")
+
+# functions ----------------------------
+
+#' Download and load data stored in csv or other delimited format on Synapse
+#' into an R data frame.
+#' 
+#' @param synapse_id Synapse ID
+#' @version Version of the Synapse entity to download.  NA will load current
+#' version
+#' @param set Delimiter for file
+#' @param na.strings Vector of strings to be read in as NA values
+#' @param header TRUE if the file contains a header row; FALSE otherwise.
+#' @param check_names TRUE if column names should be modified for compatibility 
+#' with R upon reading; FALSE otherwise.
+#' @param comment.char character designating comment lines to ignore
+#' @return data frame
+get_synapse_entity_data_in_csv <- function(synapse_id, 
+                                           version = NA,
+                                           sep = ",", 
+                                           na.strings = c("NA"), 
+                                           header = T,
+                                           check_names = F,
+                                           comment.char = "#",
+                                           colClasses = "character") {
+
+  if (is.na(version)) {
+    entity <- synGet(synapse_id)
+  } else {
+    entity <- synGet(synapse_id, version = version)
+  }
+
+  data <- read.csv(entity$path, stringsAsFactors = F, 
+                   na.strings = na.strings, sep = sep, check.names = check_names,
+                   header = header, comment.char = comment.char, colClasses = colClasses)
+  return(data)
+}
+
+# synapse login --------------------
+
+synLogin()
+
+# read ----------------------------
+
+data <- get_synapse_entity_data_in_csv(synid_file_cli, sep = "\t")
+
+# main ----------------------------
+
+# invalid SEQ_DATE
+n_invalid_month <- data %>% 
+  filter(!is.element(substr(SEQ_DATE, 1, 3), valid_seq_dates)) %>%
+  count()
+n_year_four <- data %>%
+  filter(grepl(pattern = "[A-z]{3}-[0-9]{4}", x = SEQ_DATE)) %>%
+  count()
+n_year_two <- data %>%
+  filter(grepl(pattern = "[A-z]{3}-[0-9]{2}", x = SEQ_DATE)) %>%
+  count()
+
+# invalid oncotree code
+record_invalid_oncotree <- unlist(data %>% 
+  filter(ONCOTREE_CODE == "") %>%
+  select(PATIENT_ID))
+
+# report -----------------------------
+
+print(glue("Number of invalid months in SEQ_DATE: {n_invalid_month}"))
+print(glue("Number of four digit (valid) years in SEQ_DATE: {n_year_four}"))
+print(glue("Number of two digit (invalid) years in SEQ_DATE: {n_year_two}"))
+print(glue("Record(s) with blank (invalid) OncoTree codes: {paste0(record_invalid_oncotree, collapse = ',')}"))
+
+# close out ----------------------------
+
+toc = as.double(Sys.time())
+print(glue("Runtime: {round(toc - tic)} s"))