Merge pull request #175 from saipavan10-git/add_ehr_details

Add ehr details

Author: pbchase

R/get_hipaa_disclosure_log_from_ehr_fhir_logs.R

@@ -56,13 +56,22 @@ get_hipaa_disclosure_log_from_ehr_fhir_logs <- function(
       "project_irb_number"
     )
 
+  redcap_ehr_settings <- dplyr::tbl(conn, "redcap_ehr_settings") |>
+    dplyr::select(
+      "ehr_id",
+      "ehr_name",
+      "fhir_base_url",
+      "patient_identifier_string"
+    )
+
   disclosures <-
     dplyr::tbl(conn, "redcap_ehr_fhir_logs") |>
     dplyr::filter(.data$resource_type == "Patient" & .data$mrn != "") |>
     dplyr::filter(is.na(start_date) | .data$created_at >= start_date) |>
     dplyr::filter(ehr_id_is_na | .data$ehr_id %in% ehr_id_local) |>
     dplyr::left_join(user_information, by = c("user_id" = "ui_id")) |>
     dplyr::left_join(projects, by = c("project_id")) |>
+    dplyr::left_join(redcap_ehr_settings, by = c("ehr_id")) |>
     dplyr::collect() |>
     dplyr::mutate(disclosure_date = lubridate::floor_date(.data$created_at, unit = "day")) |>
     dplyr::select(-c("id", "created_at")) |>
@@ -73,6 +82,10 @@ get_hipaa_disclosure_log_from_ehr_fhir_logs <- function(
       "disclosure_date",
       "fhir_id",
       "mrn",
+      "ehr_id",
+      "ehr_name",
+      "fhir_base_url",
+      "patient_identifier_string",
       "project_irb_number",
       "project_pi_firstname",
       "project_pi_mi",

tests/testthat/hipaa_disclosure_log/make_hipaa_disclosure_log_test_data.R

@@ -49,10 +49,25 @@ redcap_projects <- dplyr::tbl(conn, "redcap_projects") |>
   ) |>
   collect()
 
+redcap_ehr_settings <- dplyr::tbl(rc_conn, "redcap_ehr_settings") |>
+  dplyr::select(
+    "ehr_id",
+    "ehr_name",
+    "fhir_base_url",
+    "patient_identifier_string"
+  ) |>
+  collect() |>
+  dplyr::mutate(
+    ehr_name = "ehrnameEHRName",
+    fhir_base_url = "https://fhir.example.com",
+    patient_identifier_string = "mrnaabbccc"
+  )
+
 # Save our test tables
 test_tables <- c(
   "redcap_ehr_fhir_logs",
   "redcap_user_information",
-  "redcap_projects"
+  "redcap_projects",
+  "redcap_ehr_settings"
 )
 purrr::walk(test_tables, write_rds_to_test_dir, "hipaa_disclosure_log")

tests/testthat/hipaa_disclosure_log/redcap_ehr_settings.rds

@@ -12,7 +12,8 @@ testthat::test_that("get_hipaa_disclosure_log_from_ehr_fhir_logs works", {
   test_tables <- c(
     "redcap_ehr_fhir_logs",
     "redcap_user_information",
-    "redcap_projects"
+    "redcap_projects",
+    "redcap_ehr_settings"
   )
 
   conn <- DBI::dbConnect(duckdb::duckdb(), dbdir = ":memory:")
@@ -34,8 +35,8 @@ testthat::test_that("get_hipaa_disclosure_log_from_ehr_fhir_logs works", {
 
   # Required column names
   required_names <- c(
-    "disclosure_date", "fhir_id", "mrn", "project_irb_number"
-  )
+  "disclosure_date", "fhir_id", "mrn", "project_irb_number",
+  "ehr_id", "ehr_name", "fhir_base_url", "patient_identifier_string")
 
   result <- get_hipaa_disclosure_log_from_ehr_fhir_logs(conn)