Improve atlas build

.github/workflows/docker-build-push.yaml

@@ -361,33 +361,27 @@ jobs:
         env:
           CI: ${{ matrix.NPM != 'bun' }}
           NODE_AUTH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      # Atlas3 sub-plugins (network/notebook-plugin/results-viewer/strategus/studies) live
-      # in the trex-notebook submodule at plugins/atlas/trex-notebook and are unpublished;
+      # Atlas3 sub-plugins (network/notebook-plugin/strategus/studies) live in the
+      # trex-notebook submodule at plugins/atlas/trex-notebook and are unpublished;
       # build them from source so plugins/atlas's file: deps resolve during its
       # install/postinstall. This is a second checkout of trex-notebook, pinned to the
       # restructured monorepo; plugins/ui/libs/react-notebook stays on the older
       # single-package commit that the portal's webr-notebook builds against.
+      # results-viewer is NOT built here: it is consumed prebuilt from GitHub
+      # Packages (@ohdsi/results-viewer) with its WebR/shinylive runtime included,
+      # so no R toolchain is needed on this runner.
       - name: Build Atlas sub-plugins (trex-notebook submodule)
         if: ${{ matrix.ATLAS }}
         env:
           CI: "true"
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           NODE_AUTH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          # results-viewer's shinylive export (scripts/build-atlas.sh) needs a full R +
-          # renv toolchain — renv.lock pins 132 packages, several with compiled deps
-          # (V8, Rcpp, RSQLite), which is too heavy/slow to provision on this shared,
-          # already disk-constrained matrix runner. Skip it here rather than flake the
-          # whole build_plugins job; SKIP_SHINYLIVE is the same escape hatch
-          # scripts/build-atlas.sh honors locally. Until a dedicated R-provisioned
-          # runner/step exists, the shinylive bundle (and thus
-          # /atlas/plugins/results-viewer/shinylive/) is absent from CI-built images.
-          SKIP_SHINYLIVE: "1"
         run: |
           SUB=plugins/atlas/trex-notebook/plugins
           # notebook-plugin bundles the notebook app's source, which imports webr.
           ( cd "$SUB/notebook" && npm install )
           # Prefer build:pkg (targets dist/); the plain build targets the sibyl dev host.
-          for p in network notebook-plugin results-viewer strategus studies; do
+          for p in network notebook-plugin strategus studies; do
             ( cd "$SUB/$p" && npm install \
               && npm run "$(node -e "process.stdout.write(require('./package.json').scripts['build:pkg'] ? 'build:pkg' : 'build')")" )
           done

plugins/atlas/package.json

@@ -19,7 +19,7 @@
     "@ohdsi/network-plugin": "file:./trex-notebook/plugins/network",
     "@ohdsi/notebook-plugin": "file:./trex-notebook/plugins/notebook-plugin",
     "@ohdsi/pythia-plugin": "0.1.0-develop.14.gf8bbfc7",
-    "@ohdsi/results-viewer": "file:./trex-notebook/plugins/results-viewer",
+    "@ohdsi/results-viewer": "0.2.0-20260721005526.g6593d88",
     "@ohdsi/strategus-plugin": "file:./trex-notebook/plugins/strategus",
     "@ohdsi/studies-plugin": "file:./trex-notebook/plugins/studies",
     "react": "^18.2.0",

scripts/build-atlas.sh

@@ -3,9 +3,11 @@
 # tarball into services/trex/plugin-artifacts/ so the trex image bakes it in via the
 # existing plugin-artifacts extract step. Reproducible counterpart to the CI atlas job.
 #
-# The sub-plugins (network, notebook-plugin, results-viewer, strategus, studies) live in
-# the trex-notebook submodule (plugins/atlas/trex-notebook) and are not published, so
+# The sub-plugins (network, notebook-plugin, strategus, studies) live in the
+# trex-notebook submodule (plugins/atlas/trex-notebook) and are not published, so
 # they are built from source here; plugins/atlas references them via file: deps.
+# results-viewer is consumed prebuilt from GitHub Packages (@ohdsi/results-viewer)
+# with its WebR/shinylive runtime included, so no R toolchain is needed here.
 #
 # Requires a GitHub token with read:packages (public @ohdsi/atlas3, @ohdsi/atlas-ui,
 # @ohdsi/pythia-* still need auth on GitHub Packages). Reads GITHUB_TOKEN or, locally,
@@ -26,7 +28,7 @@ ATLAS_DIR="plugins/atlas"
 ARTIFACTS_DIR="services/trex/plugin-artifacts"
 
 # Atlas3 sub-plugins built from the submodule (dir name under $PLUGIN_DIR).
-SUBPLUGINS=(network notebook-plugin results-viewer strategus studies)
+SUBPLUGINS=(network notebook-plugin strategus studies)
 
 : "${GITHUB_TOKEN:=$(gh auth token 2>/dev/null || true)}"
 if [ -z "${GITHUB_TOKEN}" ]; then
@@ -47,23 +49,8 @@ if printf '%s\n' "${SUBPLUGINS[@]}" | grep -qx notebook-plugin; then
   ( cd "$PLUGIN_DIR/notebook" && npm install )
 fi
 
-build_results_viewer_shinylive() {
-  local dir="$PLUGIN_DIR/results-viewer"
-  if ! command -v Rscript >/dev/null 2>&1; then
-    echo "[build-atlas] WARN: Rscript not found; results-viewer shinylive export skipped." >&2
-    [ "${SKIP_SHINYLIVE:-0}" = "1" ] && return 0
-    echo "[build-atlas] ERROR: R toolchain required for the results-viewer viewer. Install R + shinylive, or set SKIP_SHINYLIVE=1 to build without it." >&2
-    exit 1
-  fi
-  echo "[build-atlas] Building results-viewer shinylive export (R)..."
-  ( cd "$dir" && Rscript scripts/build-shim-packages.R && Rscript scripts/build-shinylive-export.R )
-}
-
 for p in "${SUBPLUGINS[@]}"; do
   echo "[build-atlas] Building sub-plugin: $p"
-  if [ "$p" = "results-viewer" ]; then
-    build_results_viewer_shinylive
-  fi
   # Prefer build:pkg (targets dist/); the plain build targets the sibyl dev host.
   ( cd "$PLUGIN_DIR/$p" && npm install \
     && npm run "$(node -e "process.stdout.write(require('./package.json').scripts['build:pkg'] ? 'build:pkg' : 'build')")" )