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 ###################################################################### -- GitLab