mvmr plugin

Migrated from the legacy mvmr_container wrapper in nodes-io. One directory = one plugin family = one git-able unit. Panel-free family: MVMR needs no reference data bundles, so the manifest declares no [[panels]] (the loader documents mvmr as a legitimately panel-free family).

Layout

• manifest.toml — node kind mvmr: params, ports, image provenance
• scripts/mvmr.R — the execution script (R, run by Rscript), referenced relatively and inlined by the loader at startup
• Dockerfile — pinned official MVMR 0.4.8 image build (rocker/r-ver 4.5.1 base, upstream source tarball at revision bceaa38)
• test_mvmr.sh — image baseline: builds the image and smoke-tests the official package against fixtures/rawdat_mvmr.csv
• fixtures/ — vendored test data for the image baseline

Install

Development checkout at /mnt/projects/node-plugins/mvmr; the runtime loads every subdirectory with a manifest.toml from the plugins root (~/.autonomics/plugins, or AUTONOMICS_PLUGIN_ROOT, or the explicit plugins_root argument of build_default_registry_with_container_execution).

Migration parity

The golden test (autonomics repo, crates/container-plugin/tests/mvmr_migration.rs) compares the compiled ContainerCommandSpec against the legacy Rust wrapper's contract: image, outputs, timeout, and artifact prefix are asserted directly; the script is asserted on semantic markers. Structural deltas, all deliberate:

• Kind rename: mvmr_container → mvmr (plugin convention drops the _container suffix); artifact_prefix follows the kind (/artifacts/mvmr, legacy default was /artifacts/mvmr_container). DAG specs referencing the old kind must be regenerated.
• Params via env: the legacy wrapper baked every parameter into the R program with Rust string-building (empty env); the plugin renders MVMR_* env values and the script reads them with Sys.getenv. String arrays (beta_xg, sebeta_xg) render space-joined and are rebuilt with strsplit; booleans render true/false and convert with as.logical; optional params render as empty strings and test with nzchar. Column access uses data[[name]] (identical to the legacy data$name codegen, robust to non-syntactic names).
• Diagnostic dispatch: strength/strhet/pleiotropy/qhet stay booleans; the legacy compile-time choice between the upstream call and NULL became a script-side if (flag) MVMR::… else NULL. Result-slot semantics are unchanged (assigning NULL drops the slot, exactly like the legacy emitted result$x <- NULL).
• gencov is gone as a param: the legacy field was #[schemars(skip)], had to be zero, and the R code ignored its value (gencov <- 0 or phenocov_mvmr). The plugin derives gencov from pcor presence only, which is everything the legacy path supported.
• pcor serialization (DSL gap): the v0 param vocabulary has no number-matrix type, so the legacy nested-array pcor travels as a row-major serialized string (rows ;-separated, entries ,- separated, e.g. 1,0.25;0.25,1). The script rebuilds the exact legacy matrix(..., byrow = TRUE) construction and re-implements the legacy validation (square, finite, symmetric, unit diagonal, and qhet requires a pcor matrix). Replace with a structured param type once container-plugin grows one.
• Validation moved into the container: legacy validate() ran at DAG build time; its checks (non-empty columns, equal-length exposure vectors, pcor shape) now run at the top of the script with the same failure messages. beta_xg/sebeta_xg equal-length and qhet ⇒ pcor are cross-field rules the DSL cannot express (requires gates bools only), so they live in the script.
• Output port labels: legacy ports were unlabeled; manifest ports always carry labels, and both file stems are mvmr, so the outputs declare explicit result / log labels.
• Everything numerical — format_mvmr input construction, the upstream ivw_mvmr / strength_mvmr / strhet_mvmr / pleiotropy_mvmr / qhet_mvmr / phenocov_mvmr calls, the sink/print log epilogue, saveRDS output, and the output file names (mvmr.RDS, mvmr.log) — is byte-faithful to the legacy program.