Replace more instances of CALYPSO with OMOPCAT (#73)

* Replace more instances of `CALYPSO` with `OMOPCAT` Apparently missed the environment variables last time * Add test for `.check_env()`
SAFEHR-data · Sep 25, 2024 · 3575188 · 3575188
1 parent aead0b4
commit 3575188
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Showing 5 changed files with 15 additions and 11 deletions.
diff --git a/R/run_app.R b/R/run_app.R
@@ -33,7 +33,7 @@ run_app <- function(
 }
 
 .check_env <- function() {
-  required <- "CALYPSO_DATA_PATH"
+  required <- "OMOPCAT_DATA_PATH"
   missing <- required[!required %in% names(Sys.getenv())]
   if (length(missing) > 0) {
     cli::cli_abort("The following environment variables are missing: {.envvar {missing}}")

diff --git a/R/utils_get_data.R b/R/utils_get_data.R
@@ -1,11 +1,11 @@
 #' Should we be using the inst/dev_data?
 #'
-#' Only if we are running as a development server and CALYPSO_DATA_PATH
+#' Only if we are running as a development server and OMOPCAT_DATA_PATH
 #' is not set.
 #'
 #' @noRd
 should_use_dev_data <- function() {
-  golem::app_dev() && Sys.getenv("CALYPSO_DATA_PATH") == ""
+  golem::app_dev() && Sys.getenv("OMOPCAT_DATA_PATH") == ""
 }
 
 
@@ -48,9 +48,9 @@ get_summary_stats <- function() {
 }
 
 .read_parquet_table <- function(table_name) {
-  data_dir <- Sys.getenv("CALYPSO_DATA_PATH")
+  data_dir <- Sys.getenv("OMOPCAT_DATA_PATH")
   if (data_dir == "") {
-    cli::cli_abort("Environment variable {.envvar CALYPSO_DATA_PATH} not set")
+    cli::cli_abort("Environment variable {.envvar OMOPCAT_DATA_PATH} not set")
   }
   if (!dir.exists(data_dir)) {
     cli::cli_abort("Data directory {.file {data_dir}} not found")

diff --git a/deploy/docker-compose.yml b/deploy/docker-compose.yml
@@ -12,7 +12,7 @@ services:
       HTTP_PROXY: ${HTTP_PROXY}
       HTTPS_PROXY: ${HTTPS_PROXY}
       GOLEM_CONFIG_ACTIVE: production
-      CALYPSO_DATA_PATH: /etc/omopcat/data
+      OMOPCAT_DATA_PATH: /etc/omopcat/data
       LOW_FREQUENCY_THRESHOLD: 5
       LOW_FREQUENCY_REPLACEMENT: 2.5
     volumes:

diff --git a/tests/testthat/test-run_app.R b/tests/testthat/test-run_app.R
@@ -0,0 +1,4 @@
+test_that("Env check fails when envvars missing", {
+  withr::local_envvar(OMOPCAT_DATA_PATH = NULL)
+  expect_error(.check_env(), "The following environment variables are missing: `OMOPCAT_DATA_PATH`")
+})
diff --git a/tests/testthat/test-utils_get_data.R b/tests/testthat/test-utils_get_data.R
@@ -20,19 +20,19 @@ test_that("Dev data files are consistent", {
 })
 
 test_that("Data getters fail in production if envvar not set", {
-  withr::local_envvar(GOLEM_CONFIG_ACTIVE = "production", CALYPSO_DATA_PATH = NA)
+  withr::local_envvar(GOLEM_CONFIG_ACTIVE = "production", OMOPCAT_DATA_PATH = NA)
   withr::local_options(list("golem.app.prod" = TRUE))
 
   expect_true(golem::app_prod())
-  expect_error(get_concepts_table(), "Environment variable `CALYPSO_DATA_PATH` not set")
-  expect_error(get_monthly_counts(), "Environment variable `CALYPSO_DATA_PATH` not set")
-  expect_error(get_summary_stats(), "Environment variable `CALYPSO_DATA_PATH` not set")
+  expect_error(get_concepts_table(), "Environment variable `OMOPCAT_DATA_PATH` not set")
+  expect_error(get_monthly_counts(), "Environment variable `OMOPCAT_DATA_PATH` not set")
+  expect_error(get_summary_stats(), "Environment variable `OMOPCAT_DATA_PATH` not set")
 })
 
 test_that("Data getters fail in production if data directory does not exist", {
   withr::local_envvar(c(
     "GOLEM_CONFIG_ACTIVE" = "production",
-    "CALYPSO_DATA_PATH" = "/i/dont/exist"
+    "OMOPCAT_DATA_PATH" = "/i/dont/exist"
   ))
   withr::local_options(list("golem.app.prod" = TRUE))