chemscraper-helm-chart

Helm chart for running Chemscraper + YOLO + sscraper + LGAP in a Kubernetes cluster

References

• Source code:
  • Chemscraper: dprl/graphics-extraction
  • YOLO: dprl/yolov8sever
  • Symbolscraper: dprl/symbolscraper-server
  • LGAP: dprl/lgap-parser
• Docker Compose recipe: dprl/dprl-alphasynthesis

PSA: Always check Pod AGE after deploying

You may need to delete the running Pod to trigger a new Pod to be created with the new config.

Local

If you are running Docker + Kubernetes locally on your laptop, you can use the following to run chemscraper locally

To change the existing application in your local cluster, you can use the following command:

$ kubectl config use-context docker-desktop
$ helm upgrade --install chemscraper -n staging . -f values.local.yaml

This will overwrite the configuration of the instance in your local cluster.

You should then be able to access the following URLs:

• Chemscraper: http://chemscraper.backend.localhost/docs
• YOLO: http://yolo.chemscraper.backend.localhost/swagger-ui
• Symbolscraper: http://symbolscraper.chemscraper.backend.localhost/docs
• LGAP: http://lgap.chemscraper.backend.localhost/docs

This example is currently configured to use the NGINX Ingress Controller, but you can adjust values.local.yaml to cahnge the ingress class.

Staging

To change the existing application in the staging namespace, you can use the following command:

$ kubectl config use-context mmli1
$ helm upgrade --install chemscraper -n staging . -f values.staging.yaml

This will overwrite the configuration of the current staging instance.

Swagger UI is available to test each service individually (if desired):

• Chemscraper: https://chemscraper.backend.staging.mmli1.ncsa.illinois.edu/docs
• YOLO: https://yolo.chemscraper.backend.staging.mmli1.ncsa.illinois.edu/swagger-ui
• Symbolscraper: https://symbolscraper.chemscraper.backend.staging.mmli1.ncsa.illinois.edu/docs
• LGAP: https://lgap.chemscraper.backend.staging.mmli1.ncsa.illinois.edu/docs

Production

To change the existing application in the alphasynthesis namespace, you can use the following command:

$ kubectl config use-context mmli1
$ helm upgrade --install chemscraper -n alphasynthesis . -f values.prod.yaml

This will overwrite the configuration of the current production instance.

Swagger UI is available to test each service individually (if desired):

• Chemscraper: https://chemscraper.backend.mmli1.ncsa.illinois.edu/docs
• YOLO: https://yolo.chemscraper.backend.mmli1.ncsa.illinois.edu/swagger-ui
• Symbolscraper: https://symbolscraper.chemscraper.backend.mmli1.ncsa.illinois.edu/docs
• LGAP: https://lgap.chemscraper.backend.mmli1.ncsa.illinois.edu/docs