Use no-email-list (#68)

* Add log output sink for dev
* Add no-email check
* Refactor into wrapper fun for easier testing
* Add unit test
* Update README
* Ignore logs

.gitignore

@@ -0,0 +1 @@
+**/*.log

monitor_annotations/README.md

@@ -8,9 +8,9 @@ It does the following:
 - How each studyFileView is checked:
     - If no files, don't do anything
     - If files present, check for core required annotations (e.g. `assay`)
-- Make list of the subset of files without required annotations
+- Reference which folders have files without required annotations
 - Get user id(s) who uploaded the data
-- Send email to user with list of files
+- Send email to user with folders referenced
 
 
 ### Secrets and env vars
@@ -42,6 +42,11 @@ DIGEST_SUBSCRIBERS=1111111;2222222
 
 ### Testing Notes
 
+#### With Docker image
+
 - Build the image with e.g. `docker build -t ghcr.io/nfosi/jobs-monitor-annotations .` (or pull current/pre-build image if available)
 - Create an envfile `envfile-monitor-anno` as above and run `docker run --env-file envfile-monitor-anno ghcr.io/nf-osi/jobs-monitor-annotations`
 
+#### Unit tests
+
+- See tests in `tests` folder

monitor_annotations/helpers.R

@@ -229,4 +229,40 @@ make_active_study_reminder_list <- function(study_tab_id, fileview_tab_id) {
   return(reminder_list_by_study)
 }
 
+#' Send reminder messages
+#'
+#' @param todo The "todo" list, which is generated by `make_active_study_reminder_list`
+#' @param dcc_user DCC account
+#' @param test_user Test user account, which may be different from DCC user. Only used in test mode.
+#' @param no_email_list_users List of users to skip emails
+#' @param sleep_interval Number of seconds to wait between emails (throttling).
+send_message_list <- function(todo,
+                              dcc_user = NULL,
+                              test_user = NULL,
+                              no_email_list_users = NULL,
+                              dry_run = TRUE,
+                              sleep_interval = 6) {
 
+  for(project in names(todo)) {
+    for(user in names(todo[[project]][["naf"]]) ) {
+      # Check user against no-email-list
+      if(user %in% no_email_list_users) {
+
+        message("Skipping reminder for: ", user)
+
+      } else {
+
+        email_re_annotation(recipient = user,
+                            list = todo[[project]][["naf"]][[user]],
+                            type = "folder",
+                            project = project,
+                            test_user = test_user,
+                            dcc = dcc_user,
+                            dry_run = dry_run)
+        cat("\nEmail composed for:", user, "\n")
+        Sys.sleep(sleep_interval)
+
+      }
+    }
+  }
+}

monitor_annotations/monitor_annotations.R

@@ -9,7 +9,7 @@ library(httr)
 # Check whether running as DEV, TEST or PROD, with DEV being default and catch-all. Behavior for:
 # PROD = Send emails to actual users
 # TEST = Send emails to nf-osi-service (3421893)
-# DEV = Print emails to stout
+# DEV = Print emails to stout and save in messages.log only
 PROFILE <- switch(Sys.getenv("PROFILE"),
                   PROD = "PROD",
                   TEST = "TEST",
@@ -26,12 +26,14 @@ TEST_USER <- as.character(Sys.getenv("TEST_USER"))
 
 if(PROFILE == "TEST" && TEST_USER == "") error("For PROFILE=TEST you must set TEST_USER=xxx")
 
-DRY_RUN <- if(PROFILE == "DEV") TRUE else FALSE 
-SLEEP_INTERVAL <- 6 # seconds
+DRY_RUN <- if(PROFILE == "DEV") TRUE else FALSE
 
-# Input/target tables
+# Reference tables
 study_tab_id <- 'syn16787123'
 fileview_tab_id <- 'syn16858331'
+no_email_list <- 'syn51907919'
+
+no_email_list_users <- as.character(unlist(table_query(no_email_list, columns = "user"), use.names = FALSE))
 
 # Define job
 schedule <- if(Sys.getenv("SCHEDULE") != "") paste(Sys.getenv("SCHEDULE"), "-") else ""
@@ -47,20 +49,13 @@ try({
     withCallingHandlers(
     {
       todo <- make_active_study_reminder_list(study_tab_id, fileview_tab_id)
-      for(project in names(todo)) {
-        for(user in names(todo[[project]][["naf"]]) ) {
-          TEST_USER <- if(PROFILE == "TEST") TEST_USER else NULL
-          email_re_annotation(recipient = user, 
-                              list = todo[[project]][["naf"]][[user]],
-                              type = "folder",
-                              project = project,
-                              test_user = TEST_USER,
-                              dcc = DCC_USER,
-                              dry_run = DRY_RUN)
-          cat("Email composed for:", user, "\n")
-          Sys.sleep(SLEEP_INTERVAL)
-        }
-      }
+      if(DRY_RUN) sink("messages.log", append = TRUE, split = TRUE)
+      send_message_list(todo,
+                        dcc_user = DCC_USER,
+                        test_user = TEST_USER,
+                        no_email_list_users = no_email_list_users,
+                        dry_run = DRY_RUN)
+      sink()
 
     }, 
     warning = function(w) handleWarning(w, "main"),

monitor_annotations/tests/unit_tests.R

@@ -0,0 +1,18 @@
+source("../helpers.R")
+
+mock_reminder_list <- list(
+  syn123 = list(`naf` = list(`3423450` = c("folderA", "folderB"), `3421893` = "folderC")),
+  syn456 = list(`naf` = list(`3434950` = c("folderA")))
+)
+
+mock_no_email_list <- c("3421893")
+
+testthat::test_that("Confirms that 3421893 is skipped", {
+
+  testthat::expect_message(send_message_list(todo = mock_reminder_list, 
+                                             no_email_list_users = mock_no_email_list, 
+                                             dry_run = TRUE,
+                                             sleep_interval = 0),
+                           "Skipping reminder for: 3421893")
+  }
+)