Patch/update handler (#85)

* Close #84

* Lint

update_study_annotations/update_study_annotations.R

@@ -1,12 +1,14 @@
 reticulate::use_virtualenv("/r-reticulate")
 
 library(nfportalutils)
+library(jsonlite)
 library(httr)
 
 # Values -----------------------------------------------------------------------#
 # Extract and use token
 secrets <- jsonlite::fromJSON(Sys.getenv("SCHEDULED_JOB_SECRETS"))
-syn_login(authtoken = secrets[["SYNAPSE_AUTH_TOKEN"]])
+token <- secrets[["SYNAPSE_AUTH_TOKEN"]]
+syn_login(authtoken = token)
 
 # Input/target tables
 study_tab_id <- 'syn52694652'
@@ -21,6 +23,46 @@ job <- list(main = paste(schedule, "update_study_annotations"))
 
 source("https://raw.githubusercontent.com/nf-osi/jobs/764c62a94be9fd4dc2b0e04dd310c07472044faa/utils/slack.R")
 
+
+#' Query with some handling for very long lists
+benefactor_query <- function(ids, portal_fileview) {
+
+  id_lists <- split(ids, ceiling(seq_along(ids)/1000))
+  ben_results <- c()
+  for(i in names(id_lists)) {
+    batch <- paste(sQuote(id_lists[[i]], q = FALSE), collapse = ",")
+    meta <- .syn$tableQuery(glue::glue("select distinct benefactorId from {portal_fileview} where id in ({batch})"))  
+    bens <- unlist(meta$asDataFrame())
+    ben_results <- append(ben_results, bens)
+  }
+  ben_results <- unique(ben_results)
+  paste(ben_results, sep = ", ")
+}
+
+
+handleUpdateError <- function(e, subjob, portal_fileview = portal_fileview_id) {
+
+  if(grepl("Not all of the entities were updated.", e)) {
+    # parse potentially long error string to get ids and failureCodes
+    # error must be accessed as below because of how errors are passed from Python to R
+    e_log <- capture.output(print(e))
+    json_pattern <- "Failed updates: (\\[.*\\])"
+    json_match <- regmatches(e_log, regexpr(json_pattern, e_log, perl = TRUE))
+    json_string <- gsub("'", '"', gsub("Failed updates: ", "", json_match))
+    failed_records <- fromJSON(json_string)
+    reason <- unique(failed_records$failureCode)
+    if(length(reason) == 1L && reason == "UNAUTHORIZED") {
+      needs_review <- benefactor_query(failed_records$entityId, portal_fileview)
+      report[[subjob]] <<- paste0(":warning: ", job[[subjob]], "- Files successfully updated except for those unauthorized. Check\n",
+                                  blockquote(needs_review))
+    } else {
+      report[[subjob]] <<- paste(":x:", job[[subjob]], "failed for some entities for unknown/multiple reasons!")
+    }
+  } else {
+    report[[subjob]] <<- paste(":x:", job[[subjob]], "failed!")
+  }
+}
+
 try({
     withCallingHandlers(
     {
@@ -30,10 +72,11 @@ try({
                                dry_run = FALSE)
     }, 
     message = function(m) handleMessage(m, "main"),
-    error = function(e) handleError(e, "main")
-  )
+    error = function(e) handleUpdateError(e, "main") 
+   )
 })
 
+
 slack_report(report)