diff --git a/R/mean-model-workflow.R b/R/mean-model-workflow.R index fded21a6..f3988eab 100644 --- a/R/mean-model-workflow.R +++ b/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 diff --git a/tests/testthat/test-absorption.R b/tests/testthat/test-absorption.R index b3f94b28..9cde98b0 100644 --- a/tests/testthat/test-absorption.R +++ b/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 diff --git a/tests/testthat/test-lloq.R b/tests/testthat/test-lloq.R index 4fffaf57..71338338 100644 --- a/tests/testthat/test-lloq.R +++ b/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") diff --git a/tests/testthat/test-mass-balance.R b/tests/testthat/test-mass-balance.R index 999addd7..cbe8c586 100644 --- a/tests/testthat/test-mass-balance.R +++ b/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 diff --git a/tests/testthat/test-mean-model-gof.R b/tests/testthat/test-mean-model-gof.R index 01534243..7e403509 100644 --- a/tests/testthat/test-mean-model-gof.R +++ b/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") diff --git a/tests/testthat/test-mean-pk-parameters.R b/tests/testthat/test-mean-pk-parameters.R index 7b64037f..53f72971 100644 --- a/tests/testthat/test-mean-pk-parameters.R +++ b/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") diff --git a/tests/testthat/test-sensitivity.R b/tests/testthat/test-sensitivity.R index accc7483..6d77dd67 100644 --- a/tests/testthat/test-sensitivity.R +++ b/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") diff --git a/tests/testthat/test-tasks-in-workflow.R b/tests/testthat/test-tasks-in-workflow.R index 2dddf2de..b83cbae6 100644 --- a/tests/testthat/test-tasks-in-workflow.R +++ b/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$new( simulationSets = meanSimSet, workflowFolder = meanTestFolder diff --git a/tests/testthat/test-workflow-structure.R b/tests/testthat/test-workflow-structure.R index 35127808..d77e2b4d 100644 --- a/tests/testthat/test-workflow-structure.R +++ b/tests/testthat/test-workflow-structure.R @@ -33,19 +33,15 @@ test_that("Workflows initialization creates appropriate folder and logs, and war simulationFile = getTestDataFilePath("input-data/MiniModel2.pkml"), populationFile = "test.csv" ) - # Dummy simulation set for the example - expect_output(mWorkflow <- MeanModelWorkflow$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(