Migrate local analysis replay to jaspSyntax by FBartos · Pull Request #79 · jasp-stats/jaspTools

FBartos · 2026-05-14T12:04:31Z

Summary

remove the local .jasp option/dataset/QML bridge code and delegate native semantics to jaspSyntax
split analysisOptions() into saved, QML-bound runnable options and analysisRuntimeOptions() for backend/runtime inspection
route runAnalysis() through jaspBase::runWrappedAnalysis() with explicit source module/QML provenance and reject already-prepared runtime options
add subprocess isolation for native/log-heavy bridge work and keep state files on the native callback contract
decode JSON result text via jaspSyntax::decodeAnalysisResults() and delegate result-state figure decoding to public jaspBase::decodeJaspResultState()
update generated test scaffolding and table expectations for the native encoded-token naming contract

Why

jaspTools should not own Desktop/QML/native option semantics. This PR turns it back into the orchestration layer: it asks jaspSyntax to prepare Desktop-faithful options and asks jaspBase to replay analyses with source-module context. That removes the parallel parser/encoder drift that made local replay fragile.

The last local semantic leak was state-figure decoding: jaspTools walked state$figures and called jaspBase:::decodeplot() directly. That has now moved behind jaspBase::decodeJaspResultState(), leaving jaspTools responsible only for reading the state payload and passing it to the owning package.

Related PRs

jaspSyntax: Add native bridge APIs for JASP replay jaspSyntax#7 provides the native .jasp, QML, dataset, and result-decoding bridge APIs used here.
jaspSyntax: Decode embedded column names in analysis results jaspSyntax#8 decodes embedded encoded names in result strings/footnotes.
jaspBase: Support source-module wrapped analysis replay jaspBase#204 supports source-module runWrappedAnalysis() replay, standalone state callbacks, R-facing result object decoding, and decodeJaspResultState().
jasp-desktop: Update jaspBase for decoded result objects jasp-desktop#6235 updates Desktop to the matching jaspBase result-object/state decoding commit.
jaspDescriptives: Fix Pareto count variable visibility binding jaspDescriptives#500 fixes the QML visibility blocker that keeps real Descriptives replay available as integration coverage.

Verification

Rscript -e "pkgload::load_all('C:/JASP-Packages/jaspTools', quiet = TRUE); testthat::test_dir('tests/testthat', reporter = 'summary')"
Rscript -e "pkgload::load_all('C:/JASP-Packages/jasp-desktop/Engine/jaspBase', quiet = TRUE); testthat::test_dir('tests/testthat', reporter = 'summary')"
git diff --check

vandenman

Still need to actually run this, but some feedback below. The subprocesses idea looks interesting and has potential, but the current implementation looks a little fragile. Also, subprocesses are nice in theory but can make errors much harder to debug.

vandenman · 2026-05-14T12:12:55Z

 #'
 #' @export analysisOptions
-analysisOptions <- function(source) {
+analysisOptions <- function(source, modulePath = NULL) {


Isn't this always clear from context? E.g., when running jaspdescriptives it's clear that that is also always the module path?

Mostly yes, and the default path still does that inference from module.dirs / the active module context. I kept modulePath as an optional provenance override because .jasp files record module identity/version, not the local source checkout path. That matters for source-branch replay, generated tests, and multi-module archives; normal module workflows should not need to pass it.

vandenman · 2026-05-14T12:13:39Z

+
+  modulePath <- .modulePathForAnalysisName(analysis, modulePath)
+  options <- jaspSyntax::readDefaultAnalysisOptions(
+    modulePath = modulePath,


Or is this the reason for the above? Still think we could infer the module path automatically?

Yes, this is the reason for the optional argument. The implementation still infers when modulePath = NULL; explicit modulePath only pins the source checkout or disambiguates a named module/analysis path collection. I kept this as orchestration/provenance, not extra QML semantics in jaspTools.

vandenman · 2026-05-14T12:15:14Z

-  rFuncLocExpr <- paste0("\\{[^\\{\\}]*func:\\s*", name, "[^\\{\\}]*\\}")
-  if (!grepl(rFuncLocExpr, fileContents))
-    stop("Could not locate qml file for R function ", name, " in inst/qml directory and did not find the R function in inst/Description.qml to look for an alternative name for the qml file")
+analysisOptionsFromQMLFileSubprocess <- function(analysis, modulePath = NULL) {


Why do we use subprocesses? That feels a little over engineered? I mean not a bad idea to be able to run tests in parallel in the future, but don't think that is your motivation right now?

Agreed for analysisOptions(). I removed the jaspTools subprocess path there; QML defaults now call jaspSyntax::readDefaultAnalysisOptions() directly. The .jasp extraction isolation remains in jaspSyntax, where the native bridge state is owned.

vandenman · 2026-05-14T12:17:32Z


-      return(list(value = value, types = typesStructure))
-    }
+`%||%` <- function(x, y) {


This exists in base R already since R 4.5.0 or so, so maybe use that one instead (and definitely avoid shadowing that one otherwise).

Agreed. I removed the custom %||% helper so we do not shadow base R. The only remaining use case was a label fallback, now handled by a named internal helper.

vandenman · 2026-05-14T12:21:12Z

+
+.jaspToolsLaunchSubprocess <- function(scriptPath, inputPath, outputPath, logPath) {
+  rscript <- file.path(R.home("bin"), if (.Platform$OS.type == "windows") "Rscript.exe" else "Rscript")
+  system2(


Yeah so if we really want this we should consider mirai or processx rather than doing it "manually".

Agreed. I replaced the manual Rscript/system2 runner with callr, which uses processx underneath. I kept subprocess containment only for runAnalysis(): while checking this against jaspMixedModels, direct in-process replay of the Larks and Owls GLMM still crashes R with access violation 0xC0000005, so the child process is currently protecting the parent/test session from native crashes rather than preparing for parallelism.

vandenman · 2026-05-14T12:21:58Z

+
+.jaspToolsSubprocessScript <- function(resultLines, saveLines,
+                                       beforeResultLines = character(0),
+                                       statusExpression = "inherits(result, 'jaspTools.subprocessError')") {


This much code as a string seems very prone to breakage and hard to debug?

Agreed. The long generated child script is gone. The child process now runs normal internal R functions via callr, so the code is easier to debug and covered like ordinary R code.

vandenman · 2026-05-14T12:23:43Z

+  if (!is.character(x) || length(x) == 0L)
+    return(x)
+
+  tokenPattern <- "(JaspColumn_[[:alnum:]_]+_Encoded|jaspColumn[0-9]+)"


Is this still necessary? Decoding is handled by jasp Syntax?

Agreed. I removed canonicalizeJaspColumnTokens() and the compatibility test around native/legacy encoded tokens. Runtime result decoding is handled by jaspSyntax::decodeAnalysisResults(); expect_equal_tables() now compares strings literally again.

vandenman · 2026-05-14T12:26:56Z

+runAnalysisSubprocessScript <- function() {
+  .jaspToolsSubprocessScript(
+    beforeResultLines = "warnings <- character(0)",
+    resultLines = c(


Same stuff about very long code as text

Agreed. The long code-as-text path in runAnalysis() is gone as part of the callr refactor.

FBartos · 2026-05-14T13:07:28Z

Pushed follow-up commit e464286 addressing the review pass.

Summary:

kept modulePath as an optional source-checkout/provenance override, while preserving automatic inference for the normal module workflow;
removed the analysisOptions() subprocess path entirely;
replaced the manual Rscript/string-script runner with callr for runAnalysis() crash containment only;
removed the custom %||% helper to avoid shadowing base R;
removed canonicalizeJaspColumnTokens() because result decoding belongs to jaspSyntax.

Verification:

focused jaspTools bridge tests pass: test-analysisOptions.R, test-expect-equal-tables.R, test-rbridge-shim.R, test-jaspSyntax-lifecycle.R;
git diff --check passes;
checked the jaspMixedModels Larks and Owls GLMM path: options and dataset extraction succeed, but direct in-process runAnalysis() still hard-crashes R with access violation 0xC0000005; the new callr path contains that crash and reports a parent-side subprocess failure instead of taking down the session.

FBartos · 2026-05-14T14:36:05Z

Follow-up from the jaspMixedModels replay crash reported against jaspTools::runAnalysis():

I reproduced the failure through this PR's public path, but the fix belongs in the lower bridge layer and was pushed to the linked jaspSyntax PR:

jaspSyntax PR: Add native bridge APIs for JASP replay jaspSyntax#7
Fix commit: 79258ee Preserve JASP replay provenance
Detailed root-cause/verification note: Add native bridge APIs for JASP replay jaspSyntax#7 (comment)

No new jaspTools patch was needed. The important behavior is that jaspTools::extractDatasetFromJASPFile() now receives a data frame with .jasp provenance from jaspSyntax; when runAnalysis() preloads it, jaspSyntax::loadAnalysisDataset() reuses the saved .jasp archive as the native dataset source. That preserves Desktop column typing for real replay instead of forcing jaspTools to know or reconstruct QML/data semantics.

Verified locally with jaspMixedModels/examples/Larks and Owls.jasp: jaspTools::runAnalysis('MixedModelsGLMM', dataset, opts) now returns results,status,typeRequest,state instead of the callr/native crash.

FBartos · 2026-05-14T18:09:52Z

Final cross-repo follow-up from the senior pass: no additional jaspTools code changes were needed here.

The remaining failures were below the orchestration layer:

jaspSyntax needed hardening around module-description parsing, .jasp dataset provenance, strict decoder boundaries, and source-checkout subprocess DLL ordering. Those fixes are in Add native bridge APIs for JASP replay jaspSyntax#7.
Desktop/SyntaxInterface needed native fixes for QGuiApplication argument lifetime and archive-version-aware DB loading. Those fixes are in Expose SyntaxInterface bridge APIs for jaspSyntax jasp-desktop#6221.

With those branches installed together, the reported MixedModels path now completes:

analysisOptions("Larks and Owls.jasp") returns saved options.
extractDatasetFromJASPFile("Larks and Owls.jasp") returns the expected 260 x 9 dataset.
runAnalysis("MixedModelsGLMM", dataset, opts) returns a result list with status = "complete".

This keeps jaspTools as orchestration only, which matches the review direction: QML/native semantics stay in jaspSyntax and Desktop rather than being reimplemented here.

FBartos · 2026-05-14T19:42:43Z

I chased the noisy focused-test warnings through the bridge stack. There are no jaspTools code changes for this follow-up; the fixes landed in the owning layers:

Desktop PR: guards the headless QML layout edge case, adds terminal SyntaxInterface shutdown, and avoids eager parse-only jaspBase/friendly-helper startup.
jaspSyntax PR: calls the terminal shutdown on unload/session exit and fixes Windows DLL bundling order so a rebuilt build/R-Interface/libR-InterfaceNoRInside.dll is not overwritten by a stale build-root DLL.

With those PRs pushed, fresh installed jaspSyntax focused tests are clean for the prior GridLayout, qml:, QThreadStorage, and stack imbalance noise. No orchestration change was needed in jaspTools.

Migrate local analysis replay to jaspSyntax

fd212e4

FBartos requested a review from vandenman May 14, 2026 12:09

vandenman requested changes May 14, 2026

View reviewed changes

Simplify jaspTools bridge subprocess handling

e464286

FBartos added 4 commits May 14, 2026 22:40

Prune stale bridge compatibility code

ef194f2

Align bridge setup and extraction tests

4d3e3fe

Remove machine-specific bridge test paths

039104e

Delegate result state decoding to jaspBase

53dec21

FBartos mentioned this pull request May 26, 2026

Update jaspBase for decoded result objects jasp-stats/jasp-desktop#6235

Open

FBartos added 3 commits May 27, 2026 09:12

Forward quiet flag to wrapped analysis

9dde127

Add runAnalysis verbosity levels

db6ab20

Honor jaspSyntax verbosity defaults

91a1e44

Conversation

FBartos commented May 14, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Summary

Why

Related PRs

Verification

Uh oh!

vandenman left a comment

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

FBartos May 14, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

FBartos May 14, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

FBartos May 14, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

FBartos May 14, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

FBartos May 14, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

FBartos May 14, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

FBartos May 14, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

FBartos May 14, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

FBartos commented May 14, 2026

Uh oh!

FBartos commented May 14, 2026

Uh oh!

FBartos commented May 14, 2026

Uh oh!

FBartos commented May 14, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

FBartos commented May 14, 2026 •

edited

Loading

FBartos May 14, 2026 •

edited

Loading

FBartos May 14, 2026 •

edited

Loading

FBartos May 14, 2026 •

edited

Loading

FBartos May 14, 2026 •

edited

Loading

FBartos May 14, 2026 •

edited

Loading

FBartos May 14, 2026 •

edited

Loading

FBartos May 14, 2026 •

edited

Loading

FBartos May 14, 2026 •

edited

Loading