Merge pull request #176 from pbchase/add_end_date_param

Update get_hipaa_disclosure_log_from_ehr_fhir_logs()

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
@@ -68,6 +72,7 @@ get_hipaa_disclosure_log_from_ehr_fhir_logs <- function(
     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")) |>

redcapcustodian.Rproj

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

tests/testthat/test-get_hipaa_disclosure_log_from_ehr_fhir_logs.R

@@ -26,12 +26,12 @@ 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(
@@ -44,15 +44,25 @@ testthat::test_that("get_hipaa_disclosure_log_from_ehr_fhir_logs works", {
   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))