fix some issues preventing the docker container from starting

[PeterHindes]

No description provided.

[PeterHindes]

fixes this issue

[Gonza10V]

The docker image is now building but there is a check that is running for over 3 hours and one failed. Is this expected?

[cjmyers]

This is definitely a problem

[PeterHindes]

the test failed because it expects the container to have its own health check instead of having it in docker compose, I will add it back and it should pass

[PeterHindes]

@cl117 This is now ready for merging. Please review and approve if it looks good.

[Copilot]

Pull Request Overview

This PR ensures the Docker container can start properly by persisting the Git revision before removing the .git folder, adding error handling around SPARQL updates, and switching to a curl-based healthcheck in the Dockerfile.

• Delegate setting revision to a pre-build script (gitrevupdate.js) and shell helper (saveconfig.sh)
• Add .catch handlers in updateQueryJson and deleteStaggered to log and propagate SPARQL errors
• Update Dockerfile to install curl, run revision save, remove old healthcheck script, and define a built-in Docker HEALTHCHECK

Reviewed Changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
synbiohub.js	Removed gitRevision import and inline config.set('revision', ...) to defer to the new script
lib/sparql/sparql.js	Wrapped updateQueryJson and deleteStaggered calls with catch handlers for logging errors
lib/config.js	Removed stray whitespace
gitrevupdate.js	Added CLI script to fetch current Git SHA and write it to the config
docker/saveconfig.sh	New shell helper to invoke gitrevupdate.js during Docker build
docker/healthcheck.js	Removed JS-based healthcheck in favor of Dockerfile HEALTHCHECK
docker/Dockerfile	Installed curl, ran saveconfig.sh, removed the Git folder, and updated HEALTHCHECK/ENTRYPOINT

Comments suppressed due to low confidence (3)

lib/sparql/sparql.js:64

• [nitpick] Directly using console.error can bypass the centralized logging system. Consider replacing these calls with the project's logger.error to keep log output consistent and configurable.

    .then(parseResult)

docker/Dockerfile:8

• [nitpick] This RUN adds an extra layer. To reduce image size and simplify the build, consider combining it with the preceding apk add or the saveconfig.sh invocation into a single RUN statement.

RUN git config --global url."https://".insteadOf git://

[cjmyers]

Docker is failing to build

[PeterHindes]

I would have to check the docs, but this might not fail on 404 etc

[PeterHindes]

never mind it does, this should work just fine

[cjmyers]

@PeterHindes Is this PR still need to be kept open? It is still failing.