Merge pull request #523 from Gilead-BioStats/fix-434

Fix #434 - return correct `bStatus`
Gilead-BioStats · Jun 7, 2022 · 00f6a93 · 00f6a93
2 parents 94214d6 + 84d0661
commit 00f6a93
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Showing 2 changed files with 46 additions and 30 deletions.
diff --git a/R/util-RunAssessment.R b/R/util-RunAssessment.R
@@ -41,42 +41,46 @@ RunAssessment <- function(lAssessment, lData, lMapping, lTags = NULL, bQuiet = F
   lAssessment$lChecks <- list()
   lAssessment$bStatus <- TRUE
 
-  # Run through each step in lAssessment$workflow
-  stepCount <- 1
-  for (step in lAssessment$workflow) {
-    if (!bQuiet) cli::cli_h2(paste0("Workflow Step ", stepCount, " of ", length(lAssessment$workflow), ": `", step$name, "`"))
-    if (lAssessment$bStatus) {
-      result <- gsm::RunStep(
-        lStep = step,
-        lMapping = lMapping,
-        lData = lAssessment$lData,
-        lTags = c(lTags, lAssessment$tags),
-        bQuiet = bQuiet
-      )
+  if(exists("workflow", where = lAssessment)) {
+    # Run through each step in lAssessment$workflow
+    stepCount <- 1
+    for (step in lAssessment$workflow) {
+      if (!bQuiet) cli::cli_h2(paste0("Workflow Step ", stepCount, " of ", length(lAssessment$workflow), ": `", step$name, "`"))
+      if (lAssessment$bStatus) {
+        result <- gsm::RunStep(
+          lStep = step,
+          lMapping = lMapping,
+          lData = lAssessment$lData,
+          lTags = c(lTags, lAssessment$tags),
+          bQuiet = bQuiet
+        )
 
-      lAssessment$checks[[stepCount]] <- result$lChecks
-      names(lAssessment$checks)[[stepCount]] <- step$name
-      lAssessment$bStatus <- result$lChecks$status
-      if (result$lChecks$status) {
-        cli::cli_alert_success("{.fn {step$name}} Successful")
-      } else {
-        cli::cli_alert_warning("{.fn {step$name}} Failed - Skipping remaining steps")
-      }
+        lAssessment$checks[[stepCount]] <- result$lChecks
+        names(lAssessment$checks)[[stepCount]] <- step$name
+        lAssessment$bStatus <- result$lChecks$status
+        if (result$lChecks$status) {
+          cli::cli_alert_success("{.fn {step$name}} Successful")
+        } else {
+          cli::cli_alert_warning("{.fn {step$name}} Failed - Skipping remaining steps")
+        }
 
-      if (stringr::str_detect(step$output, "^df")) {
-        cli::cli_text("Saving {step$output} to `lAssessment$lData`")
-        lAssessment$lData[[step$output]] <- result$df
+        if (stringr::str_detect(step$output, "^df")) {
+          cli::cli_text("Saving {step$output} to `lAssessment$lData`")
+          lAssessment$lData[[step$output]] <- result$df
+        } else {
+          cli::cli_text("Saving {step$output} to `lAssessment`")
+          lAssessment[[step$output]] <- result
+        }
       } else {
-        cli::cli_text("Saving {step$output} to `lAssessment`")
-        lAssessment[[step$output]] <- result
+        cli::cli_text("Skipping {.fn {step$name}} ...")
       }
-    } else {
-      cli::cli_text("Skipping {.fn {step$name}} ...")
-    }
 
-    stepCount <- stepCount + 1
+      stepCount <- stepCount + 1
+    }
+  } else {
+    cli::cli_alert_warning("Workflow not found for {lAssessment$name} assessment - Skipping remaining steps")
+    lAssessment$bStatus <- FALSE
   }
 
-
   return(lAssessment)
 }
diff --git a/tests/testthat/test_Study_Assess.R b/tests/testthat/test_Study_Assess.R
@@ -222,3 +222,15 @@ test_that("lSubjFilters with 0 rows returns NULL", {
 
   expect_null(tmp)
 })
+
+test_that("correct bStatus is returned when workflow is missing", {
+
+  custom_assessments <- MakeAssessmentList()
+  custom_assessments$ie$workflow <- NULL
+  result <- Study_Assess(
+    lData = lData,
+    lAssessments = custom_assessments
+    )
+
+  expect_false(result$ie$bStatus)
+})