Merge branch 'release/1.28.0'

Author: pbchase

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: redcapcustodian
 Type: Package
 Title: Data automation for R-centric workflows with a nod towards REDCap
-Version: 1.27.0
+Version: 1.28.0
 Authors@R: c(
   person("Philip", "Chase",
         email = "pbc@ufl.edu",

NEWS.md

@@ -1,3 +1,7 @@
+# redcapcustodian 1.28.0 (released 2025-02-20)
+- Update get_hipaa_disclosure_log_from_ehr_fhir_logs() (@pbchase, #176)
+- Add redcap_ehr_settings values to the disclosures (@saipavan10-git, #172, #175)
+
 # redcapcustodian 1.27.0 (released 2024-12-11)
 - Allow multiple EHR IDs in get_hipaa_disclosure_log_from_ehr_fhir_logs() (@pbchase, #173, #174)
 - Include dependency setup in gh-action for tests (@saipavan10-git, #171)

R/get_hipaa_disclosure_log_from_ehr_fhir_logs.R

@@ -4,9 +4,12 @@
 #' given a DBI connection object to the REDCap database and some optional
 #' parameters to narrow the returned result.
 #'
+#' Optionally filter the data with the data range `[start_date, end_date)`.
+#'
 #' @param conn a DBI connection object to the REDCap database
 #' @param ehr_id a vector of REDCap EHR_IDs for the EHR(s) of interest (optional)
 #' @param start_date The first date from which we should return results (optional)
+#' @param end_date The last date (non-inclusive) from which we should return results (optional)
 #'
 #' @return A dataframe suitable for generating a HIPAA disclosure log
 #' @export
@@ -29,7 +32,8 @@
 get_hipaa_disclosure_log_from_ehr_fhir_logs <- function(
     conn,
     ehr_id = NA_real_,
-    start_date = as.Date(NA)) {
+    start_date = as.Date(NA),
+    end_date = as.Date(NA)) {
 
   # rename parameters for local use
   ehr_id_local <- ehr_id
@@ -56,13 +60,23 @@ 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$created_at >= start_date) |>
+    dplyr::filter(is.na(end_date) | .data$created_at < end_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 +87,10 @@ 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",

VERSION

@@ -1 +1 @@
-1.27.0
+1.28.0

man/get_hipaa_disclosure_log_from_ehr_fhir_logs.Rd

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 2cfe0968-c181-4bdc-a53a-43442dbeb736
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

redcapcustodian.Rproj

@@ -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/make_hipaa_disclosure_log_test_data.R

@@ -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:")
@@ -25,33 +26,43 @@ testthat::test_that("get_hipaa_disclosure_log_from_ehr_fhir_logs works", {
     head(n = 30) |>
     dplyr::collect() |>
     dplyr::mutate(
-      ehr_id = sample(1:3, n(), replace = TRUE),
-      created_at = seq.Date(from = Sys.Date() - 10, to = Sys.Date(), length.out = n())
+      ehr_id = sample(1:3, dplyr::n(), replace = TRUE),
+      created_at = seq.Date(from = Sys.Date() - 10, to = Sys.Date(), length.out = dplyr::n())
     )
 
   # Write the mutated data back to the database
-  duckdb_register(conn, "redcap_ehr_fhir_logs", redcap_ehr_fhir_logs)
+  duckdb::duckdb_register(conn, "redcap_ehr_fhir_logs", redcap_ehr_fhir_logs)
 
   # 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)
 
   testthat::expect_contains(names(result), required_names)
   testthat::expect_gt(nrow(result), 0)
   testthat::expect_equal(
     nrow(result),
-    result |> distinct(disclosure_date, fhir_id, mrn, project_irb_number, username) |> nrow()
+    result |> dplyr::distinct(disclosure_date, fhir_id, mrn, project_irb_number, username) |> nrow()
   )
 
   result_filtered_ehr_id <- get_hipaa_disclosure_log_from_ehr_fhir_logs(conn, ehr_id = 1)
   testthat::expect_true(all(result_filtered_ehr_id$ehr_id == 1))
 
   start_date <- Sys.Date() - 5
-  result_filtered_date <- get_hipaa_disclosure_log_from_ehr_fhir_logs(conn, start_date = start_date)
-  testthat::expect_true(all(result_filtered_date$disclosure_date >= start_date))
+  result_filtered_start_date <- get_hipaa_disclosure_log_from_ehr_fhir_logs(conn, start_date = start_date)
+  testthat::expect_true(all(result_filtered_start_date$disclosure_date >= start_date))
+
+  end_date <- Sys.Date() - 5
+  result_filtered_end_date <- get_hipaa_disclosure_log_from_ehr_fhir_logs(conn, end_date = end_date)
+  testthat::expect_true(all(result_filtered_end_date$disclosure_date < end_date))
+
+  start_date <- Sys.Date() - 7
+  end_date <- Sys.Date() - 5
+  result_filtered_start_and_end_date <- get_hipaa_disclosure_log_from_ehr_fhir_logs(conn, start_date = start_date, end_date = end_date)
+  testthat::expect_true(all(result_filtered_start_and_end_date$disclosure_date >= start_date))
+  testthat::expect_true(all(result_filtered_start_and_end_date$disclosure_date < end_date))
 
   result_combined_filters <- get_hipaa_disclosure_log_from_ehr_fhir_logs(conn, ehr_id = 2, start_date = start_date)
   testthat::expect_true(all(result_combined_filters$ehr_id == 2))