From 67b5beed229ee5f39f3792c32866d1bf25dae950 Mon Sep 17 00:00:00 2001
From: Thomas OBADIA <thomas.obadia@pasteur.fr>
Date: Thu, 17 Oct 2024 15:08:42 +0200
Subject: [PATCH] Make the global variables about outdated data extracts
(DATA_EXTRACT_IS_RECENT and DATA_EXTRACT_TS) project-dependent, i.e. named
differently across sub-directories. Also, a bunch of cleaning in indentation.
---
01_INVENTORY/INVENTORY_00_R_environment.R | 2 +-
01_INVENTORY/INVENTORY_00_R_functions.R | 4 ++--
.../INVENTORY_01_dump_REDCap_database.R | 20 +++++++++----------
...NTORY_02_list_all_inventory_participants.R | 10 +++++-----
.../INVENTORY_03_list_all_inventory_houses.R | 10 +++++-----
...NVENTORY_04_display_summary_demographics.R | 4 ++--
.../OBSERVATIONAL_00_R_environment.R | 2 +-
.../OBSERVATIONAL_01_dump_REDCap_database.R | 20 +++++++++----------
8 files changed, 36 insertions(+), 36 deletions(-)
diff --git a/01_INVENTORY/INVENTORY_00_R_environment.R b/01_INVENTORY/INVENTORY_00_R_environment.R
index d4ff8ec..6d65f64 100644
--- a/01_INVENTORY/INVENTORY_00_R_environment.R
+++ b/01_INVENTORY/INVENTORY_00_R_environment.R
@@ -58,7 +58,7 @@ DATA_SOURCE_REDCAP_AHRI_INV <- TRUE
## if a REDCap extract should be conducted again
# - TRUE : data is recent enough, don't dump
# - FALSE: new extract is necessary (default)
-DATA_EXTRACT_IS_RECENT <- FALSE
+DATA_EXTRACT_IS_RECENT_INV <- FALSE
## Date at which the last extract was done. Defaults to Epoch time
## in the R Environment file, so that a new dump is always done after
diff --git a/01_INVENTORY/INVENTORY_00_R_functions.R b/01_INVENTORY/INVENTORY_00_R_functions.R
index 86b0df2..9cd9c3f 100644
--- a/01_INVENTORY/INVENTORY_00_R_functions.R
+++ b/01_INVENTORY/INVENTORY_00_R_functions.R
@@ -161,8 +161,8 @@ get_group_subset <- function(x, country_f, clusterid_f, sex_f, agey_cat_f, n_tar
# Global flags necessary for that function
GOOGLE_VALID_MAP_TYPES <- c("terrain", "satellite", "roadmap", "hybrid")
STADIA_BASEMAP_TYPES <- c("stamen_terrain", "stamen_toner", "stamen_toner_lite",
- "stamen_watercolor", "alidade_smooth", "alidade_smooth_dark",
- "outdoors")
+ "stamen_watercolor", "alidade_smooth", "alidade_smooth_dark",
+ "outdoors")
STADIA_BACKGROUND_LAYERGROUP_TYPES <- c("stamen_terrain_background", "stamen_toner_background")
STADIA_TRANSPARENT_LAYERGROUP_TYPES <- c("stamen_terrain_labels", "stamen_terrain_lines",
"stamen_toner_labels", "stamen_toner_lines")
diff --git a/01_INVENTORY/INVENTORY_01_dump_REDCap_database.R b/01_INVENTORY/INVENTORY_01_dump_REDCap_database.R
index 5531059..6ba3730 100644
--- a/01_INVENTORY/INVENTORY_01_dump_REDCap_database.R
+++ b/01_INVENTORY/INVENTORY_01_dump_REDCap_database.R
@@ -59,17 +59,17 @@ RCON_INVENTORY <- list("IPP" = RCON_IPP_INVENTORY,
### DUMP DATABASE
######################################################################
## Check if data needs to be extracted again
-DATA_EXTRACT_IS_RECENT <- as.logical(difftime(time1 = Sys.Date(),
- time2 = as.Date(ifelse(exists("DATA_EXTRACT_TS"), DATA_EXTRACT_TS, DATA_EXTRACT_TS_DEFAULT)),
- units = "days") <= DATA_EXTRACT_EXPIRY_TIME_D)
+DATA_EXTRACT_IS_RECENT_INV <- as.logical(difftime(time1 = Sys.Date(),
+ time2 = as.Date(ifelse(exists("DATA_EXTRACT_TS_INV"), DATA_EXTRACT_TS_INV, DATA_EXTRACT_TS_DEFAULT)),
+ units = "days") <= DATA_EXTRACT_EXPIRY_TIME_D)
## Use the exportRecordsTyped method from package redcapAPI
-if (!DATA_EXTRACT_IS_RECENT) {
+if (!DATA_EXTRACT_IS_RECENT_INV) {
# Initialize empty element for raw data
dat_inventory_raw <- list()
for (RCON in names(RCON_INVENTORY)) {
- cat("Extracting data from RCON element: ",
+ cat("Extracting data from RCON_INVENTORY element: ",
RCON,
"...\n",
sep = "")
@@ -128,7 +128,7 @@ if (!DATA_EXTRACT_IS_RECENT) {
bind_rows()
## Update timestamp of extract
- DATA_EXTRACT_TS <- Sys.Date()
+ DATA_EXTRACT_TS_INV <- Sys.Date()
}
@@ -161,8 +161,8 @@ write.table(dat_inventory_raw,
######################################################################
-### UPDATE DATA_EXTRACT_IS_RECENT
+### UPDATE DATA_EXTRACT_IS_RECENT_INV
######################################################################
-DATA_EXTRACT_IS_RECENT <- as.logical(difftime(time1 = Sys.Date(),
- time2 = as.Date(ifelse(exists("DATA_EXTRACT_TS"), DATA_EXTRACT_TS, DATA_EXTRACT_TS_DEFAULT)),
- units = "days") <= DATA_EXTRACT_EXPIRY_TIME_D)
+DATA_EXTRACT_IS_RECENT_INV <- as.logical(difftime(time1 = Sys.Date(),
+ time2 = as.Date(ifelse(exists("DATA_EXTRACT_TS_INV"), DATA_EXTRACT_TS_INV, DATA_EXTRACT_TS_DEFAULT)),
+ units = "days") <= DATA_EXTRACT_EXPIRY_TIME_D)
diff --git a/01_INVENTORY/INVENTORY_02_list_all_inventory_participants.R b/01_INVENTORY/INVENTORY_02_list_all_inventory_participants.R
index e92e884..3cd117c 100644
--- a/01_INVENTORY/INVENTORY_02_list_all_inventory_participants.R
+++ b/01_INVENTORY/INVENTORY_02_list_all_inventory_participants.R
@@ -16,7 +16,7 @@
######################################################################
### SOURCE THE DATABASE
######################################################################
-if (!exists("DATA_EXTRACT_IS_RECENT") || !DATA_EXTRACT_IS_RECENT) {
+if (!exists("DATA_EXTRACT_IS_RECENT_INV") || !DATA_EXTRACT_IS_RECENT_INV) {
cat("Database is outdated and will be dumped again.\n")
source("./01_INVENTORY/INVENTORY_01_dump_REDCap_database.R")
}
@@ -127,8 +127,8 @@ rm(INVENTORY_OUT_02_FILENAME)
######################################################################
-### UPDATE DATA_EXTRACT_IS_RECENT
+### UPDATE DATA_EXTRACT_IS_RECENT_INV
######################################################################
-DATA_EXTRACT_IS_RECENT <- as.logical(difftime(time1 = Sys.Date(),
- time2 = as.Date(ifelse(exists("DATA_EXTRACT_TS"), DATA_EXTRACT_TS, DATA_EXTRACT_TS_DEFAULT)),
- units = "days") <= DATA_EXTRACT_EXPIRY_TIME_D)
+DATA_EXTRACT_IS_RECENT_INV <- as.logical(difftime(time1 = Sys.Date(),
+ time2 = as.Date(ifelse(exists("DATA_EXTRACT_TS_INV"), DATA_EXTRACT_TS_INV, DATA_EXTRACT_TS_DEFAULT)),
+ units = "days") <= DATA_EXTRACT_EXPIRY_TIME_D)
diff --git a/01_INVENTORY/INVENTORY_03_list_all_inventory_houses.R b/01_INVENTORY/INVENTORY_03_list_all_inventory_houses.R
index 49c6ee4..ae71f68 100644
--- a/01_INVENTORY/INVENTORY_03_list_all_inventory_houses.R
+++ b/01_INVENTORY/INVENTORY_03_list_all_inventory_houses.R
@@ -15,7 +15,7 @@
######################################################################
### SOURCE THE DATABASE
######################################################################
-if (!exists("DATA_EXTRACT_IS_RECENT") || !DATA_EXTRACT_IS_RECENT) {
+if (!exists("DATA_EXTRACT_IS_RECENT_INV") || !DATA_EXTRACT_IS_RECENT_INV) {
cat("Database is outdated and will be dumped again.\n")
source("./01_INVENTORY/INVENTORY_01_dump_REDCap_database.R")
}
@@ -87,8 +87,8 @@ rm(INVENTORY_OUT_03_FILENAME)
######################################################################
-### UPDATE DATA_EXTRACT_IS_RECENT
+### UPDATE DATA_EXTRACT_IS_RECENT_INV
######################################################################
-DATA_EXTRACT_IS_RECENT <- as.logical(difftime(time1 = Sys.Date(),
- time2 = as.Date(ifelse(exists("DATA_EXTRACT_TS"), DATA_EXTRACT_TS, DATA_EXTRACT_TS_DEFAULT)),
- units = "days") <= DATA_EXTRACT_EXPIRY_TIME_D)
+DATA_EXTRACT_IS_RECENT_INV <- as.logical(difftime(time1 = Sys.Date(),
+ time2 = as.Date(ifelse(exists("DATA_EXTRACT_TS_INV"), DATA_EXTRACT_TS_INV, DATA_EXTRACT_TS_DEFAULT)),
+ units = "days") <= DATA_EXTRACT_EXPIRY_TIME_D)
diff --git a/01_INVENTORY/INVENTORY_04_display_summary_demographics.R b/01_INVENTORY/INVENTORY_04_display_summary_demographics.R
index 2ce2f88..5ea093c 100644
--- a/01_INVENTORY/INVENTORY_04_display_summary_demographics.R
+++ b/01_INVENTORY/INVENTORY_04_display_summary_demographics.R
@@ -251,8 +251,8 @@ for (country in names(gps_data_range)) {
# Pass list of plots for current page to cowplot::plot_grid()
gps_map_panels[[country]][[pg]] <- cowplot::plot_grid(plotlist = gps_maps[[country]][page_clusterids],
- nrow = MAP_PLOT_PANEL_LAYOUT_NROW,
- ncol = MAP_PLOT_PANEL_LAYOUT_NCOL)
+ nrow = MAP_PLOT_PANEL_LAYOUT_NROW,
+ ncol = MAP_PLOT_PANEL_LAYOUT_NCOL)
# Also print the panel version of the plot
print(gps_map_panels[[country]][[pg]])
diff --git a/02_OBSERVATIONAL/OBSERVATIONAL_00_R_environment.R b/02_OBSERVATIONAL/OBSERVATIONAL_00_R_environment.R
index 4402f6b..59bdeb3 100644
--- a/02_OBSERVATIONAL/OBSERVATIONAL_00_R_environment.R
+++ b/02_OBSERVATIONAL/OBSERVATIONAL_00_R_environment.R
@@ -58,7 +58,7 @@ DATA_SOURCE_REDCAP_AHRI_OBS <- TRUE
## if a REDCap extract should be conducted again
# - TRUE : data is recent enough, don't dump
# - FALSE: new extract is necessary (default)
-DATA_EXTRACT_IS_RECENT <- FALSE
+DATA_EXTRACT_IS_RECENT_OBS <- FALSE
## Date at which the last extract was done. Defaults to Epoch time
## in the R Environment file, so that a new dump is always done after
diff --git a/02_OBSERVATIONAL/OBSERVATIONAL_01_dump_REDCap_database.R b/02_OBSERVATIONAL/OBSERVATIONAL_01_dump_REDCap_database.R
index 68dc807..496ed91 100644
--- a/02_OBSERVATIONAL/OBSERVATIONAL_01_dump_REDCap_database.R
+++ b/02_OBSERVATIONAL/OBSERVATIONAL_01_dump_REDCap_database.R
@@ -58,17 +58,17 @@ RCON_OBSERVATIONAL <- list("IPP" = RCON_IPP_OBSERVATIONAL,
### DUMP DATABASE
######################################################################
## Check if data needs to be extracted again
-DATA_EXTRACT_IS_RECENT <- as.logical(difftime(time1 = Sys.Date(),
- time2 = as.Date(ifelse(exists("DATA_EXTRACT_TS"), DATA_EXTRACT_TS, DATA_EXTRACT_TS_DEFAULT)),
- units = "days") <= DATA_EXTRACT_EXPIRY_TIME_D)
+DATA_EXTRACT_IS_RECENT_OBS <- as.logical(difftime(time1 = Sys.Date(),
+ time2 = as.Date(ifelse(exists("DATA_EXTRACT_TS_OBS"), DATA_EXTRACT_TS_OBS, DATA_EXTRACT_TS_DEFAULT)),
+ units = "days") <= DATA_EXTRACT_EXPIRY_TIME_D)
## Use the exportRecordsTyped method from package redcapAPI
-if (!DATA_EXTRACT_IS_RECENT) {
+if (!DATA_EXTRACT_IS_RECENT_OBS) {
# Initialize empty element for raw data
dat_observational_raw <- list()
for (RCON in names(RCON_OBSERVATIONAL)) {
- cat("Extracting data from RCON element: ",
+ cat("Extracting data from RCON_OBSERVATIONAL element: ",
RCON,
"...\n",
sep = "")
@@ -100,7 +100,7 @@ if (!DATA_EXTRACT_IS_RECENT) {
bind_rows()
## Update timestamp of extract
- DATA_EXTRACT_TS <- Sys.Date()
+ DATA_EXTRACT_TS_OBS <- Sys.Date()
}
@@ -133,8 +133,8 @@ write.table(dat_observational_raw,
######################################################################
-### UPDATE DATA_EXTRACT_IS_RECENT
+### UPDATE DATA_EXTRACT_IS_RECENT_OBS
######################################################################
-DATA_EXTRACT_IS_RECENT <- as.logical(difftime(time1 = Sys.Date(),
- time2 = as.Date(ifelse(exists("DATA_EXTRACT_TS"), DATA_EXTRACT_TS, DATA_EXTRACT_TS_DEFAULT)),
- units = "days") <= DATA_EXTRACT_EXPIRY_TIME_D)
+DATA_EXTRACT_IS_RECENT_OBS <- as.logical(difftime(time1 = Sys.Date(),
+ time2 = as.Date(ifelse(exists("DATA_EXTRACT_TS_OBS"), DATA_EXTRACT_TS_OBS, DATA_EXTRACT_TS_DEFAULT)),
+ units = "days") <= DATA_EXTRACT_EXPIRY_TIME_D)
--
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