[ENH] Move to Docker multistage builds

[rmanaem]

• Closes Setup Docker multi-stage builds for env runtime changes #433

Changes proposed in this pull request:

• Added ENV variables with placeholder values to the Dockerfile
  • these values are meant to be replaced every time a container starts up
• Added entrypoint script that replaces placeholder values
  • entrypoint won't let container start unless required .env variables are provided

Other note: plan is to release from this PR

NOTE: If this pull request is to be released, the release label must be applied once the review process is done to avoid the local and remote from going out of sync as a consequence of the bump version workflow run

Checklist

This section is for the PR reviewer

• PR has an interpretable title with a prefix ([ENH], [FIX], [REF], [TST], [CI], [MNT], [INF], [MODEL], [DOC]) (see our Contributing Guidelines for more info)
• PR has a label for the release changelog or skip-release (to be applied by maintainers only)
• PR links to GitHub issue with mention Closes #XXXX
• Tests pass
• Checks pass
• If the PR changes the participant-level and/or the dataset-level result file, the query-tool-results files in the neurobagel_examples repo have been regenerated

For new features:

• Tests have been added

For bug fixes:

• There is at least one test that would fail under the original bug conditions.

Summary by Sourcery

Switch the base image to node:20-alpine and copy the built files to an nginx:alpine image. Inject a custom plausible link to the docker container at runtime using environment variables.

Build:

• Use a multi-stage build to reduce the final image size.

Deployment:

• Add an entrypoint script to inject a custom plausible link if the PLAUSIBLE_DOMAIN and PLAUSIBLE_SRC environment variables are set.

Summary by Sourcery

Update the Dockerfile to use a multi-stage build, switching to node:20-alpine for building and nginx:alpine for serving. Implement dynamic injection of environment variables at runtime via an entrypoint script, enabling customization of plausible link, authentication settings, and other configurations.

Build:

• Use a multi-stage build to reduce the final image size.

Deployment:

• Add an entrypoint script to inject environment variables at runtime.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request modifies the Dockerfile to enable the injection of a custom plausible link at runtime using environment variables. It also introduces an entrypoint script to handle the replacement of placeholder values in the built application.

Sequence diagram for container startup and environment variable injection

sequenceDiagram
    participant User
    participant Container
    participant Entrypoint
    participant Files
    User->>Container: Start container with env vars
    Container->>Entrypoint: Execute entrypoint.sh
    Entrypoint->>Entrypoint: Check required env vars
    alt Missing NB_API_QUERY_URL
        Entrypoint-->>Container: Exit with error
    else All required vars present
        Entrypoint->>Files: Replace placeholders in JS/HTML
        Files-->>Entrypoint: Files updated
        Entrypoint->>Container: Start Nginx
    end

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Flow diagram for environment variable processing

flowchart TD
    A[Start Container] --> B{Check NB_API_QUERY_URL}
    B -->|Not Set| C[Exit with Error]
    B -->|Set| D[Process Files]
    D --> E[Replace API URL]
    E --> F[Replace Auth Settings]
    F --> G[Replace Client ID]
    G --> H[Replace Chatbot Settings]
    H --> I[Replace Base Path]
    I --> J[Replace Header Script]
    J --> K[Start Nginx]
    K --> L[End]

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File-Level Changes

Change	Details	Files
Modified the Dockerfile to use a multi-stage build process and include environment variables for runtime configuration.	Switched the base image from node:20 to node:20-alpine for the build stage. Added a new stage using nginx:alpine as the base image. Copied the built application from the build stage to the nginx stage. Added ENV variables with placeholder values for runtime configuration. Exposed port 80 instead of 5173.	Dockerfile
Added an entrypoint script to replace placeholder values in the built application with environment variables.	Created a new entrypoint.sh script. The script checks if the required environment variables are set. The script uses sed to replace placeholder values in .js and .html files with the values of the environment variables. The script executes the command passed to it after the replacements are done.	entrypoint.sh
Added a placeholder for the plausible script in the index.html file.	Added a placeholder comment <!-- REPLACE_ME_NB_QUERY_HEADER_SCRIPT_REPLACE_ME --> in index.html to inject the plausible script.	index.html

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#433	Implement multi-stage Docker builds to reduce image size and container startup time	✅
#433	Provide a way to configure .env variables at runtime that replace default values in the built app	✅
#433	Create a process to search-replace specific place-holder strings after the app is built	✅

Possibly linked issues

• Setup Docker multi-stage builds for env runtime changes #433: The PR closes the issue by allowing the plausible link to be configurable at runtime, effectively addressing the original concern of having a hardcoded link.

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[surchs]

@sourcery-ai review

[rmanaem]

Thanks for addressing this @surchs! 🧑‍🍳

[rmanaem]

Don't forget to add a PR label and a release label before merging.

[alyssadai]

For some reason it looks like this PR didn't trigger a release as expected...not sure why ☹️