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Add option to not run simulations when converting snapshots #1488

Merged
merged 17 commits into from
Sep 23, 2024
+215 −511
Merged

Add option to not run simulations when converting snapshots #1488

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17e1381
update core files
Felixmil Sep 13, 2024
fad9a0a
Add argument to run simulations or not during conversion
Felixmil Sep 13, 2024
9f231bb
fix typo
Felixmil Sep 13, 2024
d933676
🤖 Update Core Files.
github-actions[bot] Sep 13, 2024
b0374f8
update the json for consistency
rwmcintosh Sep 13, 2024
f19430d
temporary disable core files updates in github actions
Felixmil Sep 13, 2024
41af041
update core files manually
Felixmil Sep 13, 2024
f7efa7e
manually update core files
Felixmil Sep 13, 2024
684b096
add details
Felixmil Sep 13, 2024
c0264dd
Add test for RunSimulations argument
Felixmil Sep 13, 2024
f079d3f
Restore core files update during github workflow
Felixmil Sep 16, 2024
42ee414
Manually update Core files
Felixmil Sep 16, 2024
ab86cd2
fix pluralization
Felixmil Sep 16, 2024
7caa968
print whole error if message could not be extracted
Felixmil Sep 23, 2024
ba6d736
🤖 Update Core Files.
github-actions[bot] Sep 23, 2024
88706a9
fix typo
Felixmil Sep 23, 2024
65b4179
Merge branch 'convert-snapshot-dont-run-simulations' of https://githu…
Felixmil Sep 23, 2024
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27 changes: 24 additions & 3 deletions R/snapshots.R
View file
Original file line number Diff line number Diff line change
@@ -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]*")
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Some error messages won't have a message line of format "Message: *". In this case str_extract() returns in NA resulting in

Error in `convertSnapshot()`:
! NA
✖ An error occured while converting files

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Good catch, I added an if case to handle this.


if (is.na(message){
message <- e
})

cli::cli_abort(message = message, call = rlang::caller_env(n = 4))
}
)
}


360 changes: 180 additions & 180 deletions inst/lib/ConsoleApp.deps.json
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330 changes: 2 additions & 328 deletions tests/data/test_snapshot.json
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Original file line number Diff line number Diff line change
@@ -364,74 +364,7 @@
}
}
],
"HasResults": true,
"IndividualAnalyses": [
{
"Axes": [
{
"Unit": "h",
"Dimension": "Time",
"Type": "X",
"GridLines": false,
"Visible": true,
"DefaultColor": "#FFFFFF",
"DefaultLineStyle": "None",
"Scaling": "Linear",
"NumberMode": "Normal"
},
{
"Unit": "µmol/l",
"Dimension": "Concentration (molar)",
"Type": "Y",
"GridLines": false,
"Visible": true,
"DefaultColor": "#FFFFFF",
"DefaultLineStyle": "Solid",
"Scaling": "Log",
"NumberMode": "Normal"
}
],
"Curves": [
{
"Name": "Generic_compound-Venous Blood-Plasma-Concentration",
"X": "Time",
"Y": "Simulation - IV + Weibull - Default tolerance|Organism|VenousBlood|Plasma|Generic_compound|Concentration in container",
"CurveOptions": {
"Color": "#FF0000",
"LegendIndex": 1
}
},
{
"Name": "Generic_compound-Skin-Intracellular-Concentration",
"X": "Time",
"Y": "Simulation - IV + Weibull - Default tolerance|Organism|Skin|Intracellular|Generic_compound|Concentration in container",
"CurveOptions": {
"Color": "#0000FF",
"LegendIndex": 2
}
}
],
"Name": "Time Profile Analysis",
"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"
},
"OriginText": "Comparison advanced admin with weibull\nSimulation - IV + Weibull - Default tolerance\n2024-08-30 09:51"
}
]
"HasResults": false
},
{
"Name": "Simulation - IV only - Default tolerance",
@@ -511,266 +444,7 @@
}
}
],
"HasResults": true,
"IndividualAnalyses": [
{
"Axes": [
{
"Unit": "h",
"Dimension": "Time",
"Type": "X",
"GridLines": false,
"Visible": true,
"DefaultColor": "#FFFFFF",
"DefaultLineStyle": "None",
"Scaling": "Linear",
"NumberMode": "Normal"
},
{
"Unit": "µmol/l",
"Dimension": "Concentration (molar)",
"Type": "Y",
"GridLines": false,
"Visible": true,
"DefaultColor": "#FFFFFF",
"DefaultLineStyle": "Solid",
"Scaling": "Log",
"NumberMode": "Normal"
}
],
"Curves": [
{
"Name": "Generic_compound-Skin-Intracellular-Concentration",
"X": "Time",
"Y": "Simulation - IV only - Default tolerance|Organism|Skin|Intracellular|Generic_compound|Concentration in container",
"CurveOptions": {
"Color": "#FF0000",
"LegendIndex": 1
}
},
{
"Name": "Generic_compound-Venous Blood-Plasma-Concentration",
"X": "Time",
"Y": "Simulation - IV only - Default tolerance|Organism|VenousBlood|Plasma|Generic_compound|Concentration in container",
"CurveOptions": {
"Color": "#0000FF",
"LegendIndex": 2
}
}
],
"Name": "Time Profile Analysis",
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}
},
"Settings": {
"SideMarginsEnabled": true,
"LegendPosition": "RightInside",
"BackColor": "#FFFFFF",
"DiagramBackColor": "#FFFFFF"
},
"OriginText": "Comparison advanced admin with weibull\nSimulation - IV only - Default tolerance\n2024-08-30 09:51"
}
]
}
],
"SimulationComparisons": [
{
"Name": "Simulation Comparison - Tolerance reduced",
"Simulations": [
"Simulation - IV + Weibull - Tolerance reduced",
"Simulation - IV only - Tolerance reduced"
],
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"NumberMode": "Normal"
},
{
"Unit": "µmol/l",
"Dimension": "Concentration (molar)",
"Type": "Y",
"GridLines": false,
"Visible": true,
"Min": 5.034298E-07,
"Max": 0.3479374,
"DefaultColor": "#FFFFFF",
"DefaultLineStyle": "Solid",
"Scaling": "Log",
"NumberMode": "Normal"
}
],
"Curves": [
{
"Name": "Simulation - IV only-Generic_compound-Venous Blood-Plasma-Concentration",
"X": "Time",
"Y": "Simulation - IV only - Tolerance reduced|Organism|VenousBlood|Plasma|Generic_compound|Concentration in container",
"CurveOptions": {
"Color": "#800080",
"LegendIndex": 2
}
},
{
"Name": "Simulation - IV only-Generic_compound-Skin-Intracellular-Concentration",
"X": "Time",
"Y": "Simulation - IV only - Tolerance reduced|Organism|Skin|Intracellular|Generic_compound|Concentration in container",
"CurveOptions": {
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},
{
"Name": "Simulation - IV + Weibull-Generic_compound-Venous Blood-Plasma-Concentration",
"X": "Time",
"Y": "Simulation - IV + Weibull - Tolerance reduced|Organism|VenousBlood|Plasma|Generic_compound|Concentration in container",
"CurveOptions": {
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"LegendIndex": 1,
"LineStyle": "Dash"
}
},
{
"Name": "Simulation - IV + Weibull-Generic_compound-Skin-Intracellular-Concentration",
"X": "Time",
"Y": "Simulation - IV + Weibull - Tolerance reduced|Organism|Skin|Intracellular|Generic_compound|Concentration in container",
"CurveOptions": {
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"Name": "Simulation Comparison - Tolerance reduced",
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"DescriptionSize": 12,
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}
},
"Settings": {
"SideMarginsEnabled": true,
"LegendPosition": "RightInside",
"BackColor": "#FFFFFF",
"DiagramBackColor": "#FFFFFF"
}
}
},
{
"Name": "Simulation Comparison - Default tolerance",
"Simulations": [
"Simulation - IV only - Default tolerance",
"Simulation - IV + Weibull - Default tolerance"
],
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"Curves": [
{
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"X": "Time",
"Y": "Simulation - IV only - Default tolerance|Organism|Skin|Intracellular|Generic_compound|Concentration in container",
"CurveOptions": {
"Color": "#0000FF",
"LegendIndex": 1
}
},
{
"Name": "Simulation - IV only - Default tolerance-Generic_compound-Venous Blood-Plasma-Concentration",
"X": "Time",
"Y": "Simulation - IV only - Default tolerance|Organism|VenousBlood|Plasma|Generic_compound|Concentration in container",
"CurveOptions": {
"Color": "#800080",
"LegendIndex": 2
}
},
{
"Name": "Simulation - IV + Weibull - Default tolerance-Generic_compound-Venous Blood-Plasma-Concentration",
"X": "Time",
"Y": "Simulation - IV + Weibull - Default tolerance|Organism|VenousBlood|Plasma|Generic_compound|Concentration 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"
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}
],
"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
}
]
}
9 changes: 9 additions & 0 deletions tests/testthat/test-snapshots.R
View file
Original file line number Diff line number Diff line change
@@ -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")