From 4949538c1106112e6f79ee763cd0945cf56e070a Mon Sep 17 00:00:00 2001
From: hhunterzinck <haley.hunterzinck@sagebase.org>
Date: Mon, 4 Oct 2021 15:32:50 +0000
Subject: [PATCH] check on date time formats in site upload

---
 ...04_michele_vicc_panc_upload_date_formats.R | 63 +++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 2021-10-04_michele_vicc_panc_upload_date_formats.R

diff --git a/2021-10-04_michele_vicc_panc_upload_date_formats.R b/2021-10-04_michele_vicc_panc_upload_date_formats.R
new file mode 100644
index 0000000..57a9947
--- /dev/null
+++ b/2021-10-04_michele_vicc_panc_upload_date_formats.R
@@ -0,0 +1,63 @@
+# Description: Check date formats marked as incorrect in the QA report.  
+# Author: Haley Hunter-Zinck
+# Date: 2021-10-04
+
+# setup ----------------------------
+
+tic = as.double(Sys.time())
+
+library(glue)
+library(dplyr)
+library(synapser)
+synLogin()
+
+# synapse
+synid_file_vicc_panc <- "syn25541702"
+
+# functions ----------------------------
+
+get_synapse_entity_data_in_csv <- function(synapse_id, 
+                                           version = NA,
+                                           sep = ",", 
+                                           na.strings = c("NA"), 
+                                           header = T) {
+  
+  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 = F,
+                   header = header)
+  return(data)
+}
+
+# read ----------------------------
+
+data_curr <- get_synapse_entity_data_in_csv(synid_file_vicc_panc, version = 3)
+data_prev <- get_synapse_entity_data_in_csv(synid_file_vicc_panc, version = 2)
+
+# main ----------------------------
+
+column_names <- c("qa_full_date", "curation_dt", "pt_start_time", "drugs_stop_time")
+
+print("Current version date formats:")
+for (column_name in column_names) {
+  print(column_name)
+  print(head(data_curr[[column_name]][data_curr[[column_name]] != ""]))
+  print("-----")
+}
+
+print("Previous version date formats:")
+for (column_name in column_names) {
+  print(column_name)
+  print(head(data_curr[[column_name]][data_curr[[column_name]] != ""]))
+  print("-----")
+}
+
+# close out ----------------------------
+
+toc = as.double(Sys.time())
+print(glue("Runtime: {round(toc - tic)} s"))