BYOC_ID: 44535 Refactor A&E

R/process_extract_ae.R

@@ -12,7 +12,12 @@
 #' @return the final data as a [tibble][tibble::tibble-package].
 #' @export
 #' @family process extracts
-process_extract_ae <- function(data, year, write_to_disk = TRUE) {
+process_extract_ae <- function(data,
+                               year,
+                               write_to_disk = TRUE,
+                               BYOC_MODE = FALSE,
+                               run_id = NA,
+                               run_date_time = NA) {
   # Only run for a single year
   stopifnot(length(year) == 1L)
 
@@ -221,6 +226,29 @@ process_extract_ae <- function(data, year, write_to_disk = TRUE) {
       cup_pathway = "CUP Pathway Name"
     )
 
+  # ----------------------------------------------------------------------------
+
+  # denodo_connect_cup <- get_denodo_connection()
+  #
+  # c_year_cup <- convert_fyyear_to_year(check_year_format(year))
+  #
+  # ae_cup_file <- dplyr::tbl(
+  #   denodo_connect_cup,
+  #   dbplyr::in_schema("sdl", "sdl_ae_cup_source_placeholder") # TO-DO: Placeholder for data path in denodo
+  # ) %>%
+  #   dplyr::filter(year == !!c_year_cup) %>% # TO-DO: Placeholder for the variable to filter by year
+  #   dplyr::select( # TO-DO: Placeholder variables
+  #     record_keydate1 = "ED Arrival Date",
+  #     keytime1 = "ED Arrival Time",
+  #     record_keydate2 = "ED Discharge Date",
+  #     keytime2 = "ED Discharge Time",
+  #     case_ref_number = "ED Case Reference Number [C]",
+  #     cup_marker = "CUP Marker",
+  #     cup_pathway = "CUP Pathway Name"
+  #   ) %>%
+  #   dplyr::collect()
+  # ----------------------------------------------------------------------------
+
 
   # Data Cleaning---------------------------------------
 
@@ -254,7 +282,13 @@ process_extract_ae <- function(data, year, write_to_disk = TRUE) {
     )
 
   ae_processed <- matched_ae_data %>%
+    dplyr::mutate(
+      run_id = run_id,
+      run_date_time = run_date_time
+    ) %>%
     dplyr::select(
+      "run_id",
+      "run_date_time",
       "year",
       "recid",
       "smrtype",
@@ -310,7 +344,8 @@ 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", BYOC_MODE = BYOC_MODE),
+      BYOC_MODE = BYOC_MODE,
       group_id = 3356 # sourcedev owner
     )
   }

R/read_extract_ae.R

@@ -4,89 +4,67 @@
 #'
 #' @export
 #'
-read_extract_ae <- function(
-  year,
-  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"),
-      "DAT Date" = readr::col_date(format = "%Y/%m/%d %T"),
-      "anon_chi" = readr::col_character(),
-      "Pat Date Of Birth [C]" = readr::col_date(format = "%Y/%m/%d %T"),
-      "Pat Gender Code" = readr::col_double(),
-      "NHS Board of Residence Code - current" = readr::col_character(),
-      "Treatment NHS Board Code - current" = readr::col_character(),
-      "Treatment Location Code" = readr::col_character(),
-      "GP Practice Code" = readr::col_character(),
-      "Council Area Code" = readr::col_character(),
-      "Postcode (epi) [C]" = readr::col_character(),
-      "Postcode (CHI) [C]" = readr::col_character(),
-      "HSCP of Residence Code - current" = readr::col_character(),
-      "Arrival Time" = readr::col_time(""),
-      "DAT Time" = readr::col_time(""),
-      "Arrival Mode Code" = readr::col_character(),
-      "Referral Source Code" = readr::col_character(),
-      "Attendance Category Code" = readr::col_character(),
-      "Discharge Destination Code" = readr::col_character(),
-      "Patient Flow Code" = readr::col_double(),
-      "Place of Incident Code" = readr::col_character(),
-      "Reason for Wait Code" = readr::col_character(),
-      "Disease 1 Code" = readr::col_character(),
-      "Disease 2 Code" = readr::col_character(),
-      "Disease 3 Code" = readr::col_character(),
-      "Bodily Location Of Injury Code" = readr::col_character(),
-      "Alcohol Involved Code" = readr::col_character(),
-      "Alcohol Related Admission" = readr::col_character(),
-      "Substance Misuse Related Admission" = readr::col_character(),
-      "Falls Related Admission" = readr::col_character(),
-      "Self Harm Related Admission" = readr::col_character(),
-      "Total Net Costs" = readr::col_double(),
-      "Age at Midpoint of Financial Year" = readr::col_double(),
-      "Case Reference Number" = readr::col_character(),
-      "Significant Facility Code" = readr::col_character(),
-      "Community Hospital Flag" = readr::col_character(),
-    )
+read_extract_ae <- function(year,
+                            denodo_connect, # TO-DO: will be hardcoded to denodo_connect = get_denodo_connection()
+                            file_path = get_boxi_extract_path(year = year, type = "ae", BYOC_MODE),
+                            BYOC_MODE) {
+  year <- check_year_format(year, format = "fyyear")
+  c_year <- convert_fyyear_to_year(year)
+
+  # Specify years available for running
+  if (file_path == get_dummy_boxi_extract_path(BYOC_MODE = BYOC_MODE)) {
+    return(tibble::tibble())
+  }
+
+  # Read Extract
+  extract_ae <- dplyr::tbl(
+    denodo_connect,
+    dbplyr::in_schema("sdl", "sdl_ae2_episode_level_source")
   ) %>%
-    # rename variables
-    dplyr::rename(
-      record_keydate1 = "Arrival Date",
-      record_keydate2 = "DAT Date",
-      dob = "Pat Date Of Birth [C]",
-      postcode_epi = "Postcode (epi) [C]",
-      postcode_chi = "Postcode (CHI) [C]",
-      age = "Age at Midpoint of Financial Year",
-      ae_alcohol = "Alcohol Involved Code",
-      alcohol_adm = "Alcohol Related Admission",
-      ae_arrivalmode = "Arrival Mode Code",
-      keytime1 = "Arrival Time",
-      ae_attendcat = "Attendance Category Code",
-      ae_bodyloc = "Bodily Location Of Injury Code",
-      lca = "Council Area Code",
-      ae_disdest = "Discharge Destination Code",
-      keytime2 = "DAT Time",
-      diag1 = "Disease 1 Code",
-      diag2 = "Disease 2 Code",
-      diag3 = "Disease 3 Code",
-      falls_adm = "Falls Related Admission",
-      gpprac = "GP Practice Code",
-      hscp = "HSCP of Residence Code - current",
-      hbrescode = "NHS Board of Residence Code - current",
-      hbtreatcode = "Treatment NHS Board Code - current",
-      anon_chi = "anon_chi",
-      gender = "Pat Gender Code",
-      ae_patflow = "Patient Flow Code",
-      ae_placeinc = "Place of Incident Code",
-      ae_reasonwait = "Reason for Wait Code",
-      refsource = "Referral Source Code",
-      selfharm_adm = "Self Harm Related Admission",
-      submis_adm = "Substance Misuse Related Admission",
-      sigfac = "Significant Facility Code",
-      cost_total_net = "Total Net Costs",
-      location = "Treatment Location Code",
-      case_ref_number = "Case Reference Number",
-      commhosp = "Community Hospital Flag"
-    )
+    dplyr::filter(
+      financial_year == !!c_year & # TO-DO: check assumption that arrival_financial_year == financial_year
+        (significant_facility_code == "32" | is.na(significant_facility_code))
+    ) %>%
+    dplyr::select(
+      record_keydate1 = "arrival_date",
+      record_keydate2 = "dat_date",
+      keytime1 = "arrival_time",
+      keytime2 = "dat_time",
+      chi = "patient_chi",
+      gender = "patient_sex",
+      dob = "patient_dob",
+      gpprac = "gp_practice_code",
+      lca = "council_area_code",
+      hscp = "hscp_of_residence_code_curr",
+      location = "treatment_location_code",
+      hbrescode = "nhs_board_of_residence_code_curr",
+      hbtreatcode = "treatment_nhs_board_code_curr",
+      diag1 = "disease_1_code",
+      diag2 = "disease_2_code",
+      diag3 = "disease_3_code",
+      ae_arrivalmode = "arrival_mode_code",
+      refsource = "referral_source_code",
+      sigfac = "significant_facility_code",
+      ae_attendcat = "attendance_category_code",
+      ae_disdest = "discharge_destination_code",
+      ae_patflow = "patient_flow_code",
+      ae_placeinc = "place_of_incident_code",
+      ae_reasonwait = "reason_for_wait_code",
+      ae_bodyloc = "bodily_location_of_injury_code",
+      ae_alcohol = "alcohol_involved_code",
+      alcohol_adm = "alcohol_related_admission",
+      submis_adm = "substance_misuse_related_admission",
+      falls_adm = "falls_related_admission",
+      selfharm_adm = "self_harm_related_admission",
+      cost_total_net = "total_net_cost",
+      age = "age_at_midpoint_of_financial_year",
+      case_ref_number = "care_reference_number", # TO-DO: needs to be renamed by NSS from care to case?
+      postcode_epi = "postcode_epi",
+      postcode_chi = "postcode_chi",
+      commhosp = "community_hospital_flag"
+    ) %>%
+    dplyr::collect() %>%
+    slfhelper::get_anon_chi("chi")
 
   return(extract_ae)
 }