Merge pull request #557 from OuhscBbmc/dev

add cron example

R/helpers-testing.R

@@ -9,19 +9,23 @@ retrieve_credential_testing <- function(
     if(Sys.getenv("redcapr_test_server") != "") {
       Sys.getenv("redcapr_test_server")
     } else {
+      # nocov start
       message("The test server was not explicitly set, so defaulting to 'dev-2'.")
       "dev-2"
+      # nocov end
     }
   checkmate::assert_character(server_instance , any.missing = FALSE, min.chars = 2, max.chars = 50)
 
   # This line avoids a warning from the package check.
   projects <- project_id <- instance <- tag <- NULL
 
   if (!requireNamespace("yaml", quietly = TRUE)) {
+    # nocov start
     stop(
       "Package `yaml` must be installed to use this function.",
       call. = FALSE
     )
+    # nocov end
   }
   d_map <-
     system.file("misc/project-redirection.yml", package = "REDCapR") |>
@@ -40,18 +44,20 @@ retrieve_credential_testing <- function(
     dplyr::filter(tag      == project_tag)
 
   if (nrow(d_map) == 0L) {
-    stop("A credential mapping entry does not exist for the desired arguments.")
+    stop("A credential mapping entry does not exist for the desired arguments.") # nocov
   }
 
   path_credential <- system.file(d_map$credential_file, package = "REDCapR")
   if (!base::file.exists(path_credential)) {
+    # nocov start
     stop(
       "The credential file `",
       d_map$credential_file,
       "` associated with the `",
       server_instance,
       "` does not exist on this machine."
     )
+    # nocov end
   }
 
   retrieve_credential_local(
@@ -67,19 +73,23 @@ retrieve_plugins <- function(plugin_name) {
     if(Sys.getenv("redcapr_test_server") != "") {
       Sys.getenv("redcapr_test_server")
     } else {
+      # nocov start
       message("The test server was not explicitly set for plugins, so defaulting to 'dev-2'.")
       "dev-2"
+      # nocov end
     }
   checkmate::assert_character(server_instance , any.missing = FALSE, min.chars = 2, max.chars = 50)
 
   # This line avoids a warning from the package check.
   plugins <- instance <- tag <- project_tag <- NULL
 
   if (!requireNamespace("yaml", quietly = TRUE)) {
+    # nocov start
     stop(
       "Package `yaml` must be installed to use this function.",
       call. = FALSE
     )
+    # nocov end
   }
   d_map <-
     system.file("misc/plugin-redirection.yml", package = "REDCapR") |>
@@ -98,7 +108,7 @@ retrieve_plugins <- function(plugin_name) {
     dplyr::filter(tag      == plugin_name)
 
   if (nrow(d_map) == 0L) {
-    stop("A plugin mapping entry does not exist for the desired arguments.")
+    stop("A plugin mapping entry does not exist for the desired arguments.") # nocov
   }
 
   d_map |>

utility/cron-example.R

@@ -0,0 +1,28 @@
+# Simplified script incorporating a cron job & REDCapR
+# Adapted from https://heds.nz/posts/automate-r-reporting-linux-cron/
+message("==============================")
+message(paste0(Sys.time(), " Starting cron job...\n"))
+
+uri   <- "https://redcap-dev-2.ouhsc.edu/redcap/api/"
+
+message("---- simple project --------------------------")
+token_1 <- "9A068C425B1341D69E83064A2D273A70"
+REDCapR::redcap_metadata_read(redcap_uri=uri, token=token_1)
+
+message("---- repeating measures project w/ environmental token --------------------------")
+Sys.setenv(REDCAP_KIRA_SGM_KEY = "77842BD8C18D3408819A21DD0154CCF4")
+token_3 <- Sys.getenv("REDCAP_KIRA_SGM_KEY")
+REDCapR::redcap_metadata_read(redcap_uri=uri, token=token_3)
+
+message("---- longitudinal project w/ stored token--------------------------")
+path <- system.file("misc/dev-2.credentials", package = "REDCapR")
+# message(path)
+message("Credential file exists: ", fs::file_exists(path))
+credential <- REDCapR::retrieve_credential_local(path, 34L)
+# message(credential)
+REDCapR::redcap_metadata_read(redcap_uri=credential$redcap_uri, token=credential$token)
+
+message("------------------------------")
+message(paste0(Sys.time(), " Finished running utility/cron-example.R.\n"))
+
+# * * * * * Rscript ~/redcap/REDCapR/utility/cron-example.R >> ~/redcap/REDCapR/utility/cron-example.log 2>&1