Improve atlas build - #8
Merged
Merged
Conversation
The publish workflow ran npm ci + build:pkg on a plain Node runner, where shinylive-export/ (gitignored) never exists, and vite's copy step silently skips it — so a published package would be a JS shell with no viewer runtime. - Dockerfile: add a scratch rv-runtime stage exposing the r-builder outputs (shinylive-export/ + r-packages/) for local-output extraction. - publish-results-viewer.yml: build that stage (gha-cached) and stage its outputs into the package before build:pkg; auth npm ci (@ohdsi/atlas-ui requires a token even for reads). - prepublishOnly guard: refuse to publish a dist/ missing the shinylive runtime or the shim r-packages.
p-hoffmann
changed the title
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
The publish workflow built the package on a plain Node runner where
shinylive-export/(gitignored) never exists; vite's copy step silently skips it, so a published package would have been a JS shell with no viewer runtime.Dockerfile: newrv-runtimescratch stage exposing ther-builderoutputs (shinylive-export/+r-packages/) for--output type=localextraction.publish-results-viewer.yml: build that stage (gha-cached — cache hit unless the R inputs changed) and stage its outputs into the package beforebuild:pkg;npm cinow getsNODE_AUTH_TOKEN(@ohdsi/atlas-ui 401s without it).prepublishOnlyguard: refuses to publish adist/missing the shinylive runtime or shim r-packages, so a runtime-less package can never publish again.Resulting package: ~152 MB
dist/withshinylive/+r-packages/folded in — the exact shape d2e's atlas postinstall copies to/atlas/plugins/results-viewer/. After merge, dispatch the workflow (or tagresults-viewer-v*) to publish the first version; OHDSI/d2e then switches itsfile:dep to the published package and drops the R toolchain requirement from its atlas build (companion PR in d2e).