From 1d15b92049296ef719ffac0c18cb2e8ee67f87e7 Mon Sep 17 00:00:00 2001
From: Thomas  OBADIA <thomas.obadia@pasteur.fr>
Date: Thu, 17 Oct 2024 14:35:59 +0200
Subject: [PATCH] Add a step to both 01_INVENTORY and 02_OBSERVATIONAL database
 dumping scripts to write the raw output to an external file.

---
 .../INVENTORY_01_dump_REDCap_database.R       | 25 +++++++++++++++++++
 .../OBSERVATIONAL_01_dump_REDCap_database.R   | 25 +++++++++++++++++++
 2 files changed, 50 insertions(+)

diff --git a/01_INVENTORY/INVENTORY_01_dump_REDCap_database.R b/01_INVENTORY/INVENTORY_01_dump_REDCap_database.R
index b98612f..5531059 100644
--- a/01_INVENTORY/INVENTORY_01_dump_REDCap_database.R
+++ b/01_INVENTORY/INVENTORY_01_dump_REDCap_database.R
@@ -135,6 +135,31 @@ if (!DATA_EXTRACT_IS_RECENT) {
 
 
 
+######################################################################
+### WRITE RAW DATA TO OUTPUT DIRECTORY
+######################################################################
+## Name of output file
+INVENTORY_OUT_01_FILENAME <- paste0("INVENTORY_OUT_01_raw_data", 
+                                    "_country-", 
+                                    paste(unique(dat_inventory_raw$country), collapse = "-"), 
+                                    "_timestamp-", 
+                                    strftime(Sys.time(), format = "%Y%m%d_%H%M%S"), 
+                                    ".csv")
+
+## Write to output file
+write.table(dat_inventory_raw, 
+            file      = paste0("./01_INVENTORY/outputs/", 
+                               INVENTORY_OUT_01_FILENAME), 
+            sep       = ",", 
+            dec       = ".", 
+            quote     = TRUE, 
+            col.names = TRUE, 
+            row.names = FALSE)
+
+
+
+
+
 ######################################################################
 ### UPDATE DATA_EXTRACT_IS_RECENT
 ######################################################################
diff --git a/02_OBSERVATIONAL/OBSERVATIONAL_01_dump_REDCap_database.R b/02_OBSERVATIONAL/OBSERVATIONAL_01_dump_REDCap_database.R
index 98b17d8..68dc807 100644
--- a/02_OBSERVATIONAL/OBSERVATIONAL_01_dump_REDCap_database.R
+++ b/02_OBSERVATIONAL/OBSERVATIONAL_01_dump_REDCap_database.R
@@ -107,6 +107,31 @@ if (!DATA_EXTRACT_IS_RECENT) {
 
 
 
+######################################################################
+### WRITE RAW DATA TO OUTPUT DIRECTORY
+######################################################################
+## Name of output file
+OBSERVATIONAL_OUT_01_FILENAME <- paste0("OBSERVATIONAL_OUT_01_raw_data", 
+                                        "_country-", 
+                                        paste(unique(dat_observational_raw$country), collapse = "-"), 
+                                        "_timestamp-", 
+                                        strftime(Sys.time(), format = "%Y%m%d_%H%M%S"), 
+                                        ".csv")
+
+## Write to output file
+write.table(dat_observational_raw, 
+            file      = paste0("./02_OBSERVATIONAL/outputs/", 
+                               OBSERVATIONAL_OUT_01_FILENAME), 
+            sep       = ",", 
+            dec       = ".", 
+            quote     = TRUE, 
+            col.names = TRUE, 
+            row.names = FALSE)
+
+
+
+
+
 ######################################################################
 ### UPDATE DATA_EXTRACT_IS_RECENT
 ######################################################################
-- 
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