diff --git a/R/snapshots.R b/R/snapshots.R index 9c1db5a7..85a28d20 100644 --- a/R/snapshots.R +++ b/R/snapshots.R @@ -95,6 +95,8 @@ runSimulationsFromSnapshot <- function(..., output = ".", exportCSV = TRUE, expo #' @param ... character strings, path to files or a directory containing files to convert #' @param format, character string, target format either "snapshot" or "project". #' @param output character string, path to the output directory where to write the converted files +#' @param runSimulations logical, whether to run simulations during conversion (default = FALSE). +#' Only when converting from snapshot to project. #' #' @return NULL #' @export @@ -104,7 +106,7 @@ runSimulationsFromSnapshot <- function(..., output = ".", exportCSV = TRUE, expo #' convertSnapshot("path/to/snapshot.json", format = "project") #' convertSnapshot("path/to/project.pksim5", format = "snapshot") #' } -convertSnapshot <- function(..., format, output = ".") { +convertSnapshot <- function(..., format, output = ".", runSimulations = FALSE) { rlang::arg_match(arg = format, values = c("snapshot", "project")) initPKSim() @@ -115,6 +117,12 @@ convertSnapshot <- function(..., format, output = ".") { SnapshotRunOptions$set(name = "InputFolder", value = temp_dir) SnapshotRunOptions$set(name = "OutputFolder", value = normalizePath(output)) + if (isTRUE(runSimulations)) { + SnapshotRunOptions$set(name = "RunSimulations", value = TRUE) + } else { + SnapshotRunOptions$set(name = "RunSimulations", value = FALSE) + } + if (format == "project") { SnapshotRunOptions$set("ExportMode", 0L) nfiles <- length(list.files(temp_dir, pattern = ".json")) @@ -124,12 +132,25 @@ convertSnapshot <- function(..., format, output = ".") { } cli::cli_process_start( - msg = "Converting {nfiles} files{?s} to {format} format", + msg = "Converting {nfiles} file{?s} to {format} format", msg_done = "Conversion completed", msg_failed = "An error occured while converting files" ) - rSharp::callStatic("PKSim.R.Api", "RunSnapshot", SnapshotRunOptions) + tryCatch( + { + invisible(rSharp::callStatic("PKSim.R.Api", "RunSnapshot", SnapshotRunOptions)) + }, + error = function(e) { + message <- stringr::str_extract(as.character(e), "(?<=Message: )[^\\n]*") + + if (is.na(message)){ + message <- e + } + + cli::cli_abort(message = message, call = rlang::caller_env(n = 4)) + } + ) } diff --git a/inst/lib/ConsoleApp.deps.json b/inst/lib/ConsoleApp.deps.json index 87bb55b0..5494d979 100644 --- a/inst/lib/ConsoleApp.deps.json +++ b/inst/lib/ConsoleApp.deps.json @@ -9,10 +9,10 @@ "ConsoleApp/1.0.0": { "dependencies": { "OSPSuite.FuncParser.Ubuntu22": "4.0.0.59", - "OSPSuite.R": "12.0.313", + "OSPSuite.R": "12.0.317", "OSPSuite.SimModel.Ubuntu22": "4.0.0.59", "OSPSuite.SimModelSolver_CVODES.Ubuntu22": "4.1.0.9", - "PKSim.R": "12.0.328" + "PKSim.R": "12.0.338" }, "runtime": { "ConsoleApp.dll": {} @@ -374,36 +374,36 @@ } } }, - "OSPSuite.Assets/12.0.313": { + "OSPSuite.Assets/12.0.317": { "dependencies": { 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in container", - "CurveOptions": { - "Color": "#FF00FF", - "LegendIndex": 1, - "LineStyle": "Dash" - } - }, - { - "Name": "Simulation - IV + Weibull - Default tolerance-Generic_compound-Skin-Intracellular-Concentration", - "X": "Time", - "Y": "Simulation - IV + Weibull - Default tolerance|Organism|Skin|Intracellular|Generic_compound|Concentration in container", - "CurveOptions": { - "Color": "#008000", - "LegendIndex": 2, - "LineStyle": "Dash" - } - } - ], - "Name": "Simulation Comparison - Default tolerance", - "FontAndSize": { - "Fonts": { - "AxisSize": 10, - "LegendSize": 8, - "TitleSize": 16, - "DescriptionSize": 12, - "OriginSize": 8, - "FontFamilyName": "Microsoft Sans Serif", - "WatermarkSize": 32 - } - }, - "Settings": { - "SideMarginsEnabled": true, - "LegendPosition": "RightInside", - "BackColor": "#FFFFFF", - "DiagramBackColor": "#FFFFFF" - } - } + "HasResults": false } ] } \ No newline at end of file diff --git a/tests/testthat/test-snapshots.R b/tests/testthat/test-snapshots.R index f4614fcb..60981c42 100644 --- a/tests/testthat/test-snapshots.R +++ b/tests/testthat/test-snapshots.R @@ -40,6 +40,15 @@ test_that("Convert project to snapshot works", { expect_length(list.files(temp_dir, pattern = ".json"), 1) }) +test_that("RunSimulations argument is supported", { + path <- getTestDataFilePath("test_snapshot.json") + temp_dir <- withr::local_tempdir() + expect_no_error({ + convertSnapshot(path, output = temp_dir, format = "project", runSimulations = TRUE) + convertSnapshot(path, output = temp_dir, format = "project", runSimulations = FALSE) + }) +}) + test_that("gather files handles one file path", { # create a temporary file temp_file <- withr::local_tempfile(fileext = ".json", lines = "content")