Merge pull request #165 from ljwoodley/monitor_job_runs

Monitor failed job runs

Author: pbchase

R/logging.R

@@ -641,7 +641,7 @@ write_info_log_entry <- function(conn, target_db_name, table_written = NULL, df,
 #' @param email_from The email addresses of the sender
 #' @param df_to_email (Optional) A dataframe or a list of dataframes to be included as file attachment(s). If this parameter is used, `file_name` must also be specified.
 #'                    Each dataframe in the list must have a corresponding file name in the `file_name` parameter to ensure a one-to-one match between dataframes and file names.
-#' @param file_name (Optional) A character vector specifying the file name(s) of the attachment(s). Valid file extensions are `.csv`, `.xlsx`, and `.zip`. Each file name must be unique.
+#' @param file_name (Optional) A character vector specifying the file name(s) of the attachment(s). Valid file extensions are `.csv`, `.xlsx`, `.zip` and, `.txt`. Each file name must be unique.
 #' @param ... Additional arguments passed directly to the file writing functions: `write.csv` for CSV files, and `writexl::write_xlsx` for XLSX files.
 #'
 #' @return No returned value. It performs an action by sending an email.
@@ -783,7 +783,7 @@ send_email <-
           }
         }
 
-        if (file_extension == "zip" &&
+        if ((file_extension == "zip" || file_extension == "txt") &&
             !file.copy(file_name[[i]], output_dir, overwrite = TRUE)) {
           stop(paste("Failed to move", file_name[[i]]))
         }

etl/run_etl.R

@@ -0,0 +1,47 @@
+library(redcapcustodian)
+library(dotenv)
+library(callr)
+library(argparse)
+
+set_script_run_time()
+
+parser <- ArgumentParser()
+parser$add_argument("script_name", help="Script to be run")
+parser$add_argument("optional_args", nargs='*', help="Zero or more optional arguments of any type")
+
+if (!interactive()) {
+  args <- parser$parse_args()
+} else {
+  args <- parser$parse_args(
+    c(
+      "study_template/etl/test_failure_alert.R",
+      "test",
+      "another test"
+    )
+  )
+}
+
+script_name <- args$script_name
+optional_args <- args$optional_args
+
+if(!fs::file_exists(script_name)) {
+  stop(sprintf("Specified file, %s, does not exist", script_name))
+}
+
+tryCatch({
+  if (length(optional_args) == 0) {
+    rscript(script = script_name, stderr = "log.txt")
+  } else {
+    rscript(script = script_name, cmdargs = optional_args, stderr = "log.txt")
+  }
+}, error = function(e) {
+  email_body <- "See the attached log for error details."
+  script_path <- paste(basename(getwd()), script_name, sep = "/")
+  email_subject <- paste0("Failed | ", script_path, " | ", format(get_script_run_time(), "%Y-%m-%d"))
+  file_name = "log.txt"
+
+  send_email(email_body = email_body, email_subject = email_subject, file_name = file_name)
+})
+
+
+

etl/test_failure_alert.R

@@ -0,0 +1,11 @@
+print("Hello, example host!")
+
+args <- commandArgs(trailingOnly = TRUE)
+
+# Test that the command line args are read
+print(paste0("This is a ", args[1]))
+print(paste0("This is ", args[2]))
+
+# This will fail as test.csv does not exist.
+read.csv("test.csv")
+

man/send_email.Rd

@@ -0,0 +1,3 @@
+# Test email alert on script failure
+0 0 1 * * root /usr/bin/docker run --rm --env-file /rcc/study_template/.env rcc.site Rscript etl/run_etl.R etl/test_failure_alert.R test "another test"
+

study_template/cron/test_failure_alert

@@ -0,0 +1,47 @@
+library(redcapcustodian)
+library(dotenv)
+library(callr)
+library(argparse)
+
+set_script_run_time()
+
+parser <- ArgumentParser()
+parser$add_argument("script_name", help="Script to be run")
+parser$add_argument("optional_args", nargs='*', help="Zero or more optional arguments of any type")
+
+if (!interactive()) {
+  args <- parser$parse_args()
+} else {
+  args <- parser$parse_args(
+      c(
+        "study_template/etl/test_failure_alert.R",
+        "test",
+        "another test"
+      )
+    )
+}
+
+script_name <- args$script_name
+optional_args <- args$optional_args
+
+if(!fs::file_exists(script_name)) {
+  stop(sprintf("Specified file, %s, does not exist", script_name))
+}
+
+tryCatch({
+  if (length(optional_args) == 0) {
+    rscript(script = script_name, stderr = "log.txt")
+  } else {
+    rscript(script = script_name, cmdargs = optional_args, stderr = "log.txt")
+  }
+}, error = function(e) {
+  email_body <- "See the attached log for error details."
+  script_path <- paste(basename(getwd()), script_name, sep = "/")
+  email_subject <- paste0("Failed | ", script_path, " | ", format(get_script_run_time(), "%Y-%m-%d"))
+  file_name = "log.txt"
+
+  send_email(email_body = email_body, email_subject = email_subject, file_name = file_name)
+})
+
+
+

study_template/etl/run_etl.R

@@ -0,0 +1,11 @@
+print("Hello, example host!")
+
+args <- commandArgs(trailingOnly = TRUE)
+
+# Test that the command line args are read
+print(paste0("This is a ", args[1]))
+print(paste0("This is ", args[2]))
+
+# This will fail as test.csv does not exist.
+read.csv("test.csv")
+