Check scripts are in snake case (#793)

* Update `get_boxi_extract_path` for DN/CMH data * Remove extra function * Update documentation * change `get_boxi_extract_path` to snake_case * change `get_source_extract_path` to snake_case * Update documentation * Update targets with snake_case * Fix typo * Style code --------- Co-authored-by: Jennit07 <[email protected]> Co-authored-by: James McMahon <[email protected]> Co-authored-by: Megan McNicol <[email protected]> Co-authored-by: SwiftySalmon <[email protected]>
Public-Health-Scotland · Sep 26, 2023 · b1a7e56 · b1a7e56
1 parent 85f9702
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diff --git a/R/create_individual_file.R b/R/create_individual_file.R
@@ -750,7 +750,7 @@ join_slf_lookup_vars <- function(individual_file,
 join_sc_client <- function(
     individual_file,
     year,
-    sc_client = read_file(get_source_extract_path(year, "Client")),
+    sc_client = read_file(get_source_extract_path(year, "client")),
     sc_demographics = read_file(get_sc_demog_lookup_path(),
       col_select = c("sending_location", "social_care_id", "chi")
     )) {

diff --git a/R/get_boxi_extract_path.R b/R/get_boxi_extract_path.R
@@ -13,23 +13,23 @@
 get_boxi_extract_path <- function(
     year,
     type = c(
-      "AE",
-      "AE_CUP",
-      "Acute",
-      "CMH",
-      "Deaths",
-      "DN",
-      "GP_OoH-c",
-      "GP_OoH-d",
-      "GP_OoH-o",
-      "Homelessness",
-      "Maternity",
-      "MH",
-      "Outpatients"
+      "ae",
+      "ae_cup",
+      "acute",
+      "cmh",
+      "deaths",
+      "dn",
+      "gp_ooh-c",
+      "gp_ooh-d",
+      "gp_ooh-o",
+      "homelessness",
+      "maternity",
+      "mh",
+      "outpatients"
     )) {
   type <- match.arg(type)
 
-  if (type %in% c("DN", "CMH")) {
+  if (type %in% c("dn", "cmh")) {
     dir <- fs::path(get_slf_dir(), "Archived_data")
   } else {
     dir <- get_year_dir(year, extracts_dir = TRUE)
@@ -41,19 +41,19 @@ get_boxi_extract_path <- function(
 
   file_name <- dplyr::case_match(
     type,
-    "AE" ~ "A&E-episode-level-extract",
-    "AE_CUP" ~ "A&E-UCD-CUP-extract",
-    "Acute" ~ "Acute-episode-level-extract",
-    "CMH" ~ "Community-MH-contact-level-extract",
-    "DN" ~ "District-Nursing-contact-level-extract",
-    "GP_OoH-c" ~ "GP-OoH-consultations-extract",
-    "GP_OoH-d" ~ "GP-OoH-diagnosis-extract",
-    "GP_OoH-o" ~ "GP-OoH-outcomes-extract",
-    "Homelessness" ~ "Homelessness-extract",
-    "Maternity" ~ "Maternity-episode-level-extract",
-    "MH" ~ "Mental-Health-episode-level-extract",
-    "Deaths" ~ "NRS-death-registrations-extract",
-    "Outpatients" ~ "Outpatients-episode-level-extract"
+    "ae" ~ "a&e-episode-level-extract",
+    "ae_cup" ~ "a&e-ucd-cup-extract",
+    "acute" ~ "acute-episode-level-extract",
+    "cmh" ~ "community-mh-contact-level-extract",
+    "dn" ~ "district-nursing-contact-level-extract",
+    "gp_ooh-c" ~ "gp-ooh-consultations-extract",
+    "gp_ooh-d" ~ "gp-ooh-diagnosis-extract",
+    "gp_ooh-o" ~ "gp-ooh-outcomes-extract",
+    "homelessness" ~ "homelessness-extract",
+    "maternity" ~ "maternity-episode-level-extract",
+    "mh" ~ "mental-health-episode-level-extract",
+    "deaths" ~ "nrs-death-registrations-extract",
+    "outpatients" ~ "outpatients-episode-level-extract"
   )
 
   boxi_extract_path_csv_gz <- fs::path(

diff --git a/R/get_source_extract_path.R b/R/get_source_extract_path.R
@@ -10,28 +10,28 @@
 #' @export
 #'
 #' @family extract file paths
-get_source_extract_path <- function(
-    year,
-    type = c(
-      "Acute",
-      "AE",
-      "AT",
-      "CH",
-      "Client",
-      "CMH",
-      "DD",
-      "Deaths",
-      "DN",
-      "GPOoH",
-      "HC",
-      "Homelessness",
-      "Maternity",
-      "MH",
-      "Outpatients",
-      "PIS",
-      "SDS"
-    ),
-    ...) {
+get_source_extract_path <- function(year,
+                                    type = c(
+                                      "acute",
+                                      "ae",
+                                      "at",
+                                      "ch",
+                                      "client",
+                                      "cmh",
+                                      "dd",
+                                      "deaths",
+                                      "dn",
+                                      "gp_ooh",
+                                      "hc",
+                                      "homelessness",
+                                      "maternity",
+                                      "mh",
+                                      "outpatients",
+                                      "pis",
+                                      "sds"
+                                    ),
+                                    ...) {
+
   if (year %in% type) {
     cli::cli_abort("{.val {year}} was supplied to the {.arg year} argument.")
   }
@@ -46,24 +46,26 @@ get_source_extract_path <- function(
 
   file_name <- dplyr::case_match(
     type,
-    "Acute" ~ "acute_for_source",
-    "AE" ~ "a_and_e_for_source",
-    "AT" ~ "alarms-telecare-for-source",
-    "CH" ~ "care_home_for_source",
-    "CMH" ~ "cmh_for_source",
-    "Client" ~ "client_for_source",
-    "DD" ~ "delayed_discharge_for_source",
-    "Deaths" ~ "deaths_for_source",
-    "DN" ~ "district_nursing_for_source",
-    "GPOoH" ~ "gp_ooh_for_source",
-    "HC" ~ "home_care_for_source",
-    "Homelessness" ~ "homelessness_for_source",
-    "Maternity" ~ "maternity_for_source",
-    "MH" ~ "mental_health_for_source",
-    "Outpatients" ~ "outpatients_for_source",
-    "PIS" ~ "prescribing_for_source",
-    "SDS" ~ "sds_for_source"
-  ) %>%
+    "acute" ~ "acute_for_source",
+    "ae" ~ "a_and_e_for_source",
+    "at" ~ "alarms-telecare-for-source",
+    "ch" ~ "care_home_for_source",
+    "cmh" ~ "cmh_for_source",
+    "client" ~ "client_for_source",
+    "dd" ~ "delayed_discharge_for_source",
+    "deaths" ~ "deaths_for_source",
+    "dn" ~ "district_nursing_for_source",
+    "gp_ooh" ~ "gp_ooh_for_source",
+    "hc" ~ "home_care_for_source",
+    "homelessness" ~ "homelessness_for_source",
+    "maternity" ~ "maternity_for_source",
+    "mh" ~ "mental_health_for_source",
+    "dd" ~ "dd_for_source",
+    "outpatients" ~ "outpatients_for_source",
+    "pis" ~ "prescribing_file_for_source",
+    "sds" ~ "sds-for-source"
+  )
+ %>%
     stringr::str_glue("-{year}.parquet")
 
   source_extract_path <- get_file_path(

diff --git a/R/link_delayed_discharge_eps.R b/R/link_delayed_discharge_eps.R
@@ -11,7 +11,7 @@
 link_delayed_discharge_eps <- function(
     episode_file,
     year,
-    dd_data = read_file(get_source_extract_path(year, "DD"))) {
+    dd_data = read_file(get_source_extract_path(year, "dd"))) {
   episode_file <- episode_file %>%
     dplyr::mutate(
       # remember to revoke the cij_end_date with dummy_cij_end

diff --git a/R/process_extract_acute.R b/R/process_extract_acute.R
@@ -113,7 +113,7 @@ process_extract_acute <- function(data, year, write_to_disk = TRUE) {
   if (write_to_disk) {
     write_file(
       acute_processed,
-      get_source_extract_path(year, "Acute", check_mode = "write")
+      get_source_extract_path(year, "acute", check_mode = "write")
     )
   }
 

diff --git a/R/process_extract_ae.R b/R/process_extract_ae.R
@@ -192,7 +192,7 @@ process_extract_ae <- function(data, year, write_to_disk = TRUE) {
   # Read in data---------------------------------------
 
   ae_cup_file <- read_file(
-    path = get_boxi_extract_path(year, "AE_CUP"),
+    path = get_boxi_extract_path(year, "ae_cup),
     col_type = readr::cols(
       "ED Arrival Date" = readr::col_date(format = "%Y/%m/%d %T"),
       "ED Arrival Time" = readr::col_time(""),
@@ -292,11 +292,12 @@ process_extract_ae <- function(data, year, write_to_disk = TRUE) {
     )
 
   if (write_to_disk) {
+
     write_file(
       ae_processed,
-      get_source_extract_path(year, "AE", check_mode = "write")
+      get_source_extract_path(year, "ae", check_mode = "write")
     )
-  }
+ }
 
   return(ae_processed)
 }
diff --git a/R/process_extract_alarms_telecare.R b/R/process_extract_alarms_telecare.R
@@ -64,7 +64,7 @@ process_extract_alarms_telecare <- function(
   if (write_to_disk) {
     at_data %>%
       write_file(
-        get_source_extract_path(year, type = "AT", check_mode = "write")
+        get_source_extract_path(year, type = "at", check_mode = "write")
       )
   }
 

diff --git a/R/process_extract_care_home.R b/R/process_extract_care_home.R
@@ -143,7 +143,7 @@ process_extract_care_home <- function(
   if (write_to_disk) {
     write_file(
       ch_processed,
-      get_source_extract_path(year, type = "CH", check_mode = "write")
+      get_source_extract_path(year, type = "ch", check_mode = "write")
     )
   }
 

diff --git a/R/process_extract_cmh.R b/R/process_extract_cmh.R
@@ -73,7 +73,7 @@ process_extract_cmh <- function(data,
   if (write_to_disk) {
     write_file(
       cmh_processed,
-      get_source_extract_path(year, "CMH", check_mode = "write")
+      get_source_extract_path(year, "cmh", check_mode = "write")
     )
   }
 

diff --git a/R/process_extract_delayed_discharges.R b/R/process_extract_delayed_discharges.R
@@ -110,7 +110,7 @@ process_extract_delayed_discharges <- function(
   if (write_to_disk) {
     write_file(
       dd_final,
-      get_source_extract_path(year, "DD", check_mode = "write")
+      get_source_extract_path(year, "dd", check_mode = "write")
     )
   }
 

diff --git a/R/process_extract_district_nursing.R b/R/process_extract_district_nursing.R
@@ -135,7 +135,7 @@ process_extract_district_nursing <- function(
 
   if (write_to_disk) {
     dn_episodes %>%
-      write_file(get_source_extract_path(year, "DN", check_mode = "write"))
+      write_file(get_source_extract_path(year, "dn", check_mode = "write"))
   }
 
   return(dn_episodes)

diff --git a/R/process_extract_gp_ooh.R b/R/process_extract_gp_ooh.R
@@ -127,7 +127,7 @@ process_extract_gp_ooh <- function(year, data_list, write_to_disk = TRUE) {
 
   if (write_to_disk) {
     final_data %>%
-      write_file(get_source_extract_path(year, "GPOoH", check_mode = "write"))
+      write_file(get_source_extract_path(year, "gp_ooh", check_mode = "write"))
   }
 
   return(final_data)

diff --git a/R/process_extract_home_care.R b/R/process_extract_home_care.R
@@ -104,7 +104,7 @@ process_extract_home_care <- function(
   if (write_to_disk) {
     write_file(
       hc_processed,
-      get_source_extract_path(year, type = "HC", check_mode = "write")
+      get_source_extract_path(year, type = "hc", check_mode = "write")
     )
   }
 

diff --git a/R/process_extract_maternity.R b/R/process_extract_maternity.R
@@ -112,7 +112,7 @@ process_extract_maternity <- function(data, year, write_to_disk = TRUE) {
   if (write_to_disk) {
     write_file(
       maternity_processed,
-      get_source_extract_path(year, "Maternity", check_mode = "write")
+      get_source_extract_path(year, "maternity", check_mode = "write")
     )
   }
 

diff --git a/R/process_extract_mental_health.R b/R/process_extract_mental_health.R
@@ -117,7 +117,7 @@ process_extract_mental_health <- function(data, year, write_to_disk = TRUE) {
   if (write_to_disk) {
     write_file(
       mh_processed,
-      get_source_extract_path(year, "MH", check_mode = "write")
+      get_source_extract_path(year, "mh", check_mode = "write")
     )
   }
 

diff --git a/R/process_extract_nrs_deaths.R b/R/process_extract_nrs_deaths.R
@@ -27,7 +27,7 @@ process_extract_nrs_deaths <- function(data, year, write_to_disk = TRUE) {
 
   if (write_to_disk) {
     deaths_clean %>%
-      write_file(get_source_extract_path(year, "Deaths", check_mode = "write"))
+      write_file(get_source_extract_path(year, "deaths", check_mode = "write"))
   }
 
   return(deaths_clean)

diff --git a/R/process_extract_outpatients.R b/R/process_extract_outpatients.R
@@ -87,7 +87,7 @@ process_extract_outpatients <- function(data, year, write_to_disk = TRUE) {
   if (write_to_disk) {
     write_file(
       outpatients_processed,
-      get_source_extract_path(year, "Outpatients", check_mode = "write")
+      get_source_extract_path(year, "outpatients", check_mode = "write")
     )
   }
 

diff --git a/R/process_extract_prescribing.R b/R/process_extract_prescribing.R
@@ -52,7 +52,7 @@ process_extract_prescribing <- function(data, year, write_to_disk = TRUE) {
   if (write_to_disk) {
     write_file(
       pis_clean,
-      get_source_extract_path(year, "PIS", check_mode = "write")
+      get_source_extract_path(year, "pis", check_mode = "write")
     )
   }
 

diff --git a/R/process_extract_sds.R b/R/process_extract_sds.R
@@ -58,7 +58,7 @@ process_extract_sds <- function(
 
   if (write_to_disk) {
     outfile %>%
-      write_file(get_source_extract_path(year, type = "SDS", check_mode = "write"))
+      write_file(get_source_extract_path(year, type = "sds", check_mode = "write"))
   }
 
   return(outfile)

diff --git a/R/process_lookup_deaths.R b/R/process_lookup_deaths.R
@@ -16,7 +16,7 @@
 process_slf_deaths_lookup <- function(
     year,
     nrs_deaths_data = read_file(
-      get_source_extract_path(year, "Deaths"),
+      get_source_extract_path(year, "deaths"),
       col_select = c("chi", "record_keydate1")
     ),
     chi_deaths_data = read_file(get_slf_chi_deaths_path()),

diff --git a/R/process_lookup_sc_client.R b/R/process_lookup_sc_client.R
@@ -124,7 +124,7 @@ process_lookup_sc_client <- function(data, year, write_to_disk = TRUE) {
   if (write_to_disk) {
     write_file(
       sc_client_lookup,
-      get_source_extract_path(year, "Client", check_mode = "write")
+      get_source_extract_path(year, "client", check_mode = "write")
     )
   }
 

diff --git a/R/read_extract_acute.R b/R/read_extract_acute.R
@@ -6,7 +6,7 @@
 #' @return a [tibble][tibble::tibble-package].
 #'
 #' @export
-read_extract_acute <- function(year, file_path = get_boxi_extract_path(year = year, type = "Acute")) {
+read_extract_acute <- function(year, file_path = get_boxi_extract_path(year = year, type = "acute")) {
   # Read BOXI extract
   extract_acute <- read_file(file_path,
     col_type = readr::cols(

diff --git a/R/read_extract_ae.R b/R/read_extract_ae.R
@@ -6,7 +6,7 @@
 #'
 read_extract_ae <- function(
     year,
-    file_path = get_boxi_extract_path(year = year, type = "AE")) {
+    file_path = get_boxi_extract_path(year = year, type = "ae")) {
   extract_ae <- read_file(file_path,
     col_type = readr::cols(
       "Arrival Date" = readr::col_date(format = "%Y/%m/%d %T"),

diff --git a/R/read_extract_cmh.R b/R/read_extract_cmh.R
@@ -5,7 +5,7 @@
 #' @export
 read_extract_cmh <- function(
     year,
-    file_path = get_boxi_extract_path(year = year, type = "CMH")) {
+    file_path = get_boxi_extract_path(year = year, type = "cmh")) {
   # Specify years available for running
   if (file_path == get_dummy_boxi_extract_path()) {
     return(tibble::tibble())

diff --git a/R/read_extract_district_nursing.R b/R/read_extract_district_nursing.R
@@ -5,7 +5,7 @@
 #' @export
 read_extract_district_nursing <- function(
     year,
-    file_path = get_boxi_extract_path(year = year, type = "DN")) {
+    file_path = get_boxi_extract_path(year = year, type = "dn")) {
   if (file_path == get_dummy_boxi_extract_path()) {
     return(tibble::tibble())
   }