Merge pull request #285 from InstituteforDiseaseModeling/charles/issu…

…e201

pacehrh/R/pace_lint.R

@@ -18,6 +18,7 @@
 #' @param outputFile Results output file. If NULL, results are printed to the console.
 #' @param scenarioSheet Name of the sheet with scenario details. Default = "Scenarios".
 #' @param seasonalityOffsetsSheet Name of the sheet with per-task seasonality offset details. Default = "SeasonalityOffsets"
+#' @param noDate Suppress date stamp from output. Default = FALSE.
 #'
 #' @return Error code.
 #' 0 = Success
@@ -33,7 +34,8 @@
 CheckInputExcelFileFormat <- function(inputFile = NULL,
                                       outputFile = NULL,
                                       scenarioSheet = "Scenarios",
-                                      seasonalityOffsetsSheet = "SeasonalityOffsets") {
+                                      seasonalityOffsetsSheet = "SeasonalityOffsets",
+                                      noDate = FALSE) {
 
   # This is a wrapper function that controls whether report output is directed
   # to the console or a file. The real action is in the called function:
@@ -46,19 +48,23 @@ CheckInputExcelFileFormat <- function(inputFile = NULL,
   }
 
   if (is.null(outputFile)){
-    errcode <- .checkInputExcelFileFormat(inputFile, scenarioSheet, seasonalityOffsetsSheet)
+    errcode <- .checkInputExcelFileFormat(inputFile, scenarioSheet, seasonalityOffsetsSheet, noDate)
   } else {
     withr::with_output_sink(outputFile, code = {
-      errcode <- .checkInputExcelFileFormat(inputFile, scenarioSheet, seasonalityOffsetsSheet)
+      errcode <- .checkInputExcelFileFormat(inputFile, scenarioSheet, seasonalityOffsetsSheet, noDate)
     })
   }
 
   return(errcode)
 }
 
-.checkInputExcelFileFormat <- function(inputFile, scenarioSheet, seasonalityOffsetsSheet){
+.checkInputExcelFileFormat <- function(inputFile, scenarioSheet, seasonalityOffsetsSheet, noDate){
   .catLine()
-  .catLine(date())
+
+  if (!noDate){
+    .catLine(date())
+  }
+
   .catLine("Input file = ", inputFile)
 
   # Create a place for the criticalChecks() functions to write some return

pacehrh/tests/testthat/_snaps/pace_lint.md

@@ -0,0 +1,185 @@
+# Lint: basic
+
+    Code
+      errCode <- pacehrh::CheckInputExcelFileFormat(noDate = TRUE)
+    Output
+      
+      Input file = ../../config/model_inputs.xlsx
+      Sheet references from scenarios ... OK
+      No duplicate tasks in seasonality offsets table ... OK
+      The following tasks in the scenario offsets table are not used in task values sheets ...
+      - TV_Comprehensive : OK
+      * TV_Basic : FH.MN.D.3
+      * TV_Basic : FH.MN.D.5
+      * TV_Basic : FH.MN.D.4
+      * TV_Basic : FH.MN.PNC.8
+      * TV_Merged : FH.MN.ANC.2
+      * TV_Merged : FH.MN.D.3
+      * TV_Merged : FH.MN.D.5
+      * TV_Merged : FH.MN.D.4
+      * TV_Merged : FH.MN.PNC.8
+      * TV_Merged : FH.MN.21A
+      * TV_Merged : FH.Ntr.68
+      * TV_Merged : FH.MN.21
+      * TV_Merged : FH.MN.22
+      * TV_Merged : DPC.Mlr.103A
+      * TV_Merged : DPC.Mlr.103B
+      * TV_Merged : DPC.Mlr.103C
+      * TV_Merged : DPC.Mlr.104A
+      * TV_Merged : DPC.Mlr.104B
+      The following tasks are duplicated in task values sheets ...
+      - TV_Comprehensive : OK
+      - TV_Basic : OK
+      - TV_Merged : OK
+      The following numeric columns contain non-numeric values ...
+      - TV_Comprehensive : OK
+      - TV_Basic : OK
+      - TV_Merged : OK
+      The following seasonality curves aren't normalized to 1 ...
+      - TV_Comprehensive : OK
+      Test results: 0-0-1-0-0-0
+
+---
+
+    Code
+      errCode <- pacehrh::CheckInputExcelFileFormat(noDate = TRUE)
+    Output
+      
+      Input file = ./bad_config/model_inputs-malformed.xlsx
+      The following sheets referenced by scenarios do not exist ...
+      * NotASheet
+      * AlsoNotASheet
+      The following tasks are duplicated in the seasonality offsets table ...
+      * DPC.TB.1
+      * DPC.M.2ChTP
+      The following tasks in the scenario offsets table are not used in task values sheets ...
+      * TaskValues : DPC.M.2
+      * TaskValues : NotATaskID
+      * TEST_TaskValues_1 : FH.MC.1
+      * TEST_TaskValues_1 : FH.MC.2
+      * TEST_TaskValues_1 : FH.MC.3
+      * TEST_TaskValues_1 : FH.MC.4
+      * TEST_TaskValues_1 : FH.MC.5
+      * TEST_TaskValues_1 : FH.Im.1
+      * TEST_TaskValues_1 : FH.Im.2
+      * TEST_TaskValues_1 : FH.Im.3
+      * TEST_TaskValues_1 : FH.Im.4
+      * TEST_TaskValues_1 : FH.N.1
+      * TEST_TaskValues_1 : FH.N.2
+      * TEST_TaskValues_1 : FH.N.3
+      * TEST_TaskValues_1 : FH.N.4
+      * TEST_TaskValues_1 : DPC.M.1AdTP
+      * TEST_TaskValues_1 : DPC.M.1ChTP
+      * TEST_TaskValues_1 : DPC.M.1neg
+      * TEST_TaskValues_1 : DPC.M.2AdTP
+      * TEST_TaskValues_1 : DPC.M.2ChTP
+      * TEST_TaskValues_1 : DPC.M.2
+      * TEST_TaskValues_1 : DPC.TB.1
+      * TEST_TaskValues_1 : DPC.TB.2
+      * TEST_TaskValues_1 : DPC.TB.3
+      * TEST_TaskValues_1 : NotATaskID
+      The following tasks are duplicated in task values sheets ...
+      * TaskValues : FH.MC.1
+      * TaskValues : FH.MC.2
+      * TaskValues : FH.MC.3
+      * TaskValues : FH.MC.4
+      * TaskValues : FH.MC.5
+      * TaskValues : FH.MC.6
+      * TaskValues : FH.MC.7
+      * TaskValues : FH.MC.8
+      * TaskValues : FH.Im.1
+      * TaskValues : FH.Im.2
+      * TaskValues : FH.Im.3
+      * TaskValues : FH.Im.4
+      * TaskValues : FH.Im.5
+      * TaskValues : FH.N.1
+      * TaskValues : FH.N.2
+      * TaskValues : FH.N.3
+      * TaskValues : FH.N.4
+      * TaskValues : Travel
+      * TaskValues : Administration
+      * TaskValues : Record keeping
+      * TaskValues : MHH
+      * TaskValues : DPC.TB.1
+      * TaskValues : DPC.TB.2
+      * TaskValues : DPC.TB.3
+      * TaskValues : DPC.M.1AdTP
+      * TaskValues : DPC.M.2AdTP
+      * TaskValues : DPC.M.1ChTP
+      * TaskValues : DPC.M.2ChTP
+      * TaskValues : DPC.M.1neg
+      * TaskValues : DPC.M.3
+      * TaskValues : DPC.FA.1
+      * TaskValues : DPC.H.1
+      * TaskValues : DPC.H.2
+      * TaskValues : DPC.CVD.1
+      * TaskValues : DPC.D.1
+      * TaskValues : DPC.D.2
+      * TaskValues : DPC.MH.2
+      * TaskValues : DPC.MH.3
+      * TaskValues : DPC.NTD.3
+      * TaskValues : DPC.HIV.1
+      * TaskValues : DPC.HIV.3
+      * TaskValues : DPC.HIV.2
+      * TaskValues : FH.FP.1A
+      * TaskValues : FH.FP.1B
+      * TaskValues : FH.FP.1C
+      * TaskValues : FH.FP.1D
+      * TaskValues : FH.FP.2
+      * TaskValues : FH.FP.3
+      * TaskValues : FH.FP.4
+      * TaskValues : FH.FP.5
+      * TaskValues : FH.FP.6
+      - TEST_TaskValues_1 : OK
+      The following numeric columns contain non-numeric values ...
+      - TaskValues : OK
+      * TEST_TaskValues_1 : StartingRateInPop
+      * TEST_TaskValues_1 : RateMultiplier
+      The following seasonality curves aren't normalized to 1 ...
+      * TaskValues : Malnutrition (12)
+      * TaskValues : TB (11.948)
+      * TEST_TaskValues_1 : Malnutrition (12)
+      * TEST_TaskValues_1 : TB (11.948)
+      Test results: 1-1-1-1-1-1
+
+# Lint: bad scenario sheet name
+
+    Code
+      errCode <- pacehrh::CheckInputExcelFileFormat(scenarioSheet = "notasheet",
+        noDate = TRUE)
+    Output
+      
+      Input file = ../../config/model_inputs.xlsx
+      notasheet sheet could not be found
+
+# Lint: bad seasonality offsets sheet name
+
+    Code
+      errCode <- pacehrh::CheckInputExcelFileFormat(seasonalityOffsetsSheet = "notasheet",
+        noDate = TRUE)
+    Output
+      
+      Input file = ../../config/model_inputs.xlsx
+      notasheet sheet could not be found
+
+# Lint: non-existent input file
+
+    Code
+      errCode <- pacehrh::CheckInputExcelFileFormat(inputFile = "notafile", noDate = TRUE)
+    Output
+      
+      Input file = notafile
+      notafile not found
+
+---
+
+    Code
+      errCode <- pacehrh::CheckInputExcelFileFormat(inputFile = "globalconfig.json",
+        noDate = TRUE)
+    Output
+      
+      Input file = globalconfig.json
+      globalconfig.json could not be read
+      Error message: Error: Can't establish that the input is either xls or xlsx.
+      
+

pacehrh/tests/testthat/test-pace_lint.R

@@ -6,61 +6,68 @@ withr::local_dir("..")
 test_that("Lint: basic", {
   e <- pacehrh:::GPE
   local_vars("inputExcelFile", envir = e)
-  e$inputExcelFile <- "./config/model_inputs.xlsx"
-
+  e$inputExcelFile <- "../../config/model_inputs.xlsx"
   outFile = "lintout_01_clean.txt"
+
+  # Check that linting produces an output file
   errCode <- pacehrh::CheckInputExcelFileFormat(outputFile = outFile)
   testthat::expect_true(file.exists(outFile))
+
+  if (file.exists(outFile)){
+    file.remove(outFile)
+  }
+
+  # Check that linting output is stable
+  testthat::expect_snapshot({
+    errCode <- pacehrh::CheckInputExcelFileFormat(noDate = TRUE)
+  })
 })
 
 # Basic operation: use default config file and scenario tab, redirect output to a file
 test_that("Lint: basic", {
   e <- pacehrh:::GPE
   local_vars("inputExcelFile", envir = e)
   e$inputExcelFile <- "./bad_config/model_inputs-malformed.xlsx"
-
-  outFile = "lintout_01_dirty.txt"
-  errCode <- pacehrh::CheckInputExcelFileFormat(outputFile = outFile)
-  testthat::expect_true(file.exists(outFile))
+  testthat::expect_snapshot({
+    errCode <- pacehrh::CheckInputExcelFileFormat(noDate = TRUE)
+  })
 })
 
 # Bad name for the scenarios sheet
-test_that("Lint: bad scenario steet name", {
+test_that("Lint: bad scenario sheet name", {
   e <- pacehrh:::GPE
   local_vars("inputExcelFile", envir = e)
-  e$inputExcelFile <- "./simple_config/model_inputs.xlsx"
-
-  outFile = "lintout_02.txt"
-  errCode <- pacehrh::CheckInputExcelFileFormat(outputFile = outFile, scenarioSheet = "notasheet")
-  testthat::expect_true(file.exists(outFile))
+  e$inputExcelFile <- "../../config/model_inputs.xlsx"
+  testthat::expect_snapshot({
+    errCode <- pacehrh::CheckInputExcelFileFormat(scenarioSheet = "notasheet", noDate = TRUE)
+  })
   testthat::expect_equal(errCode, pacehrh:::.errScenarioSheetNotFound)
 })
 
 # Bad name for the seasonality offsets sheet
 test_that("Lint: bad seasonality offsets sheet name", {
   e <- pacehrh:::GPE
   local_vars("inputExcelFile", envir = e)
-  e$inputExcelFile <- "./simple_config/model_inputs.xlsx"
-
-  outFile = "lintout_05.txt"
-  errCode <- pacehrh::CheckInputExcelFileFormat(outputFile = outFile, seasonalityOffsetsSheet = "notasheet")
-  testthat::expect_true(file.exists(outFile))
+  e$inputExcelFile <- "../../config/model_inputs.xlsx"
+  testthat::expect_snapshot({
+    errCode <- pacehrh::CheckInputExcelFileFormat(seasonalityOffsetsSheet = "notasheet", noDate = TRUE)
+  })
   testthat::expect_equal(errCode, pacehrh:::.errSeasonalityOffsetSheetNotFound)
 })
 
 # Bad name for the input file
 test_that("Lint: non-existent input file", {
-  outFile = "lintout_03.txt"
-  errCode <- pacehrh::CheckInputExcelFileFormat(inputFile = "notafile", outputFile = outFile)
-  testthat::expect_true(file.exists(outFile))
+  testthat::expect_snapshot({
+    errCode <- pacehrh::CheckInputExcelFileFormat(inputFile = "notafile", noDate = TRUE)
+  })
   testthat::expect_equal(errCode, pacehrh:::.errInputFileNotFound)
 })
 
 # Valid input file name, but not an Excel file
 test_that("Lint: non-existent input file", {
-  outFile = "lintout_04.txt"
-  errCode <- pacehrh::CheckInputExcelFileFormat(inputFile = "globalconfig.json", outputFile = outFile)
-  testthat::expect_true(file.exists(outFile))
+  testthat::expect_snapshot({
+    errCode <- pacehrh::CheckInputExcelFileFormat(inputFile = "globalconfig.json", noDate = TRUE)
+  })
   testthat::expect_equal(errCode, pacehrh:::.errInputFileNotReadable)
 })