Deprecate MeanModelWorkflow in favor of OSPSuite.ReportingFramework

R/mean-model-workflow.R

@@ -29,20 +29,12 @@ MeanModelWorkflow <- R6::R6Class(
     #' @param ... input parameters inherited from R6 class object `Workflow`.
     #' @return A new `MeanModelWorkflow` object
     initialize = function(...) {
-      super$initialize(...)
-      logCatch({
-        self$simulate <- loadSimulateTask(self)
-        self$calculatePKParameters <- loadCalculatePKParametersTask(self)
-        self$calculateSensitivity <- loadCalculateSensitivityTask(self)
-
-        self$plotTimeProfilesAndResiduals <- loadPlotTimeProfilesAndResidualsTask(self)
-        self$plotMassBalance <- loadPlotMassBalanceTask(self)
-        self$plotAbsorption <- loadPlotAbsorptionTask(self)
-        self$plotPKParameters <- loadPlotPKParametersTask(self)
-        self$plotSensitivity <- loadPlotSensitivityTask(self)
-
-        self$taskNames <- enum(self$getAllTasks())
-      })
+      stop(
+        "MeanModelWorkflow is no longer available. ",
+        "Please use OSPSuite.ReportingFramework instead. ",
+        "For more information, visit: https://github.com/Open-Systems-Pharmacology/OSPSuite.ReportingFramework",
+        call. = FALSE
+      )
     },
 
     #' @description

tests/testthat/test-absorption.R

@@ -1,5 +1,8 @@
 context("Run workflow with absorption task")
 
+# MeanModelWorkflow is deprecated, skip all tests in this file
+skip("MeanModelWorkflow is deprecated")
+
 simulationFile <- getTestDataFilePath("input-data/Larson 2013 8-18y meal.pkml")
 
 # Output reference absorption time profiles

tests/testthat/test-lloq.R

@@ -4,6 +4,9 @@ library(ospsuite.reportingengine)
 
 context("Observed Data in plot time profile task")
 
+# MeanModelWorkflow is deprecated, skip all tests in this file
+skip("MeanModelWorkflow is deprecated")
+
 # Input files and structures for comparisons
 simulationFile <- getTestDataFilePath("input-data/MiniModel2.pkml")
 

tests/testthat/test-mass-balance.R

@@ -1,5 +1,8 @@
 context("Run workflow with mass balance task")
 
+# MeanModelWorkflow is deprecated, skip all tests in this file
+skip("MeanModelWorkflow is deprecated")
+
 simulationFile <- getTestDataFilePath("input-data/Larson 2013 8-18y meal.pkml")
 
 # Output reference absorption time profiles

tests/testthat/test-mean-model-gof.R

@@ -1,5 +1,8 @@
 context("Run mean model workflows with Time Profiles and Residuals task")
 
+# MeanModelWorkflow is deprecated, skip all tests in this file
+skip("MeanModelWorkflow is deprecated")
+
 simulationFile <- getTestDataFilePath("input-data/MiniModel2.pkml")
 dataFile <- getTestDataFilePath("input-data/SimpleData.nmdat")
 dictFile <- getTestDataFilePath("input-data/tpDictionary.csv")

tests/testthat/test-mean-pk-parameters.R

@@ -1,4 +1,8 @@
 context("Run workflows with PK parameters task")
+
+# MeanModelWorkflow is deprecated, skip all tests in this file
+skip("MeanModelWorkflow is deprecated")
+
 # Get test data
 simulationFile <- getTestDataFilePath("input-data/MiniModel2.pkml")
 

tests/testthat/test-sensitivity.R

@@ -1,4 +1,8 @@
 context("Run workflows with Sensitivity tasks")
+
+# MeanModelWorkflow is deprecated, skip all tests in this file
+skip("MeanModelWorkflow is deprecated")
+
 # Get test data
 removeAllUserDefinedPKParameters()
 simulationFile <- getTestDataFilePath("input-data/MiniModel2.pkml")

tests/testthat/test-tasks-in-workflow.R

@@ -13,6 +13,9 @@ popSimSet <- PopulationSimulationSet$new(
   populationFile = getTestDataFilePath("input-data/Pop500_p1p2p3.csv")
 )
 
+# MeanModelWorkflow is deprecated, skip tests that use it
+skip("MeanModelWorkflow is deprecated")
+
 mWorkflow <- MeanModelWorkflow$new(
   simulationSets = meanSimSet,
   workflowFolder = meanTestFolder

tests/testthat/test-workflow-structure.R

@@ -33,19 +33,15 @@ test_that("Workflows initialization creates appropriate folder and logs, and war
     simulationFile = getTestDataFilePath("input-data/MiniModel2.pkml"),
     populationFile = "test.csv"
   )
-  # Dummy simulation set for the example
-  expect_output(mWorkflow <- MeanModelWorkflow$new(
-    simulationSets = simSet,
-    workflowFolder = testFolder
-  ))
-
-  expect_true(testFolder %in% list.files())
-  expect_true("log-info.txt" %in% list.files(testFolder))
-  expect_false("log-debug.txt" %in% list.files(testFolder))
-  expect_false("log-error.txt" %in% list.files(testFolder))
-
-  # Make sure testFolder is not there
-  unlink(testFolder, recursive = TRUE)
+
+  # MeanModelWorkflow is deprecated and should throw an error
+  expect_error(
+    MeanModelWorkflow$new(
+      simulationSets = simSet,
+      workflowFolder = testFolder
+    ),
+    "MeanModelWorkflow is no longer available"
+  )
 
   # Dummy simulation set for the example
   expect_output(pWorkflow <- PopulationWorkflow$new(