Backend_service

Backend service serving as connection between frontend and Solr index.

Description and format of input and output:

https://docs.google.com/document/d/1czwoaHn0FKB0dRzv5Bz-3w-UIRnX_SXm6OeIiee7ff8/edit

Some input examples:

For /nb_translator:

{"query":{

"description": "(Schizophrenia AND (RestingStateImaging OR RestingStateImagingProtocol)) AND NeurocognitiveTest", "expression": {"and":[ { "and": [ { "or": ["RestingStateImaging", "RestingStateImagingProtocol"] }, "Schizophrenia" ] }, "NeurocognitiveTest" ]} }, "max_res": 3, "min_score": 0.0 }

For /article:

{"pmid": 30098853, "terms": ["Schizophrenia", "NoKnownDisorder"]}

Start service on Sterling

Currently, only the Python webapp is configured for deployment to Sterling. The image can be built and pushed to Harbor (see RENCI wiki for setup) with:

Replace VERSIONTAG with the semver version

docker build . -t containers.renci.org/neurobridges/backend-service:VERSIONTAG
docker push containers.renci.org/neurobridges/backend-service:VERSIONTAG

Note that if you're running the container locally to test, you need to be on the RENCI VPN so the app can access the Solr database

The chart can be configured in the /kubernetes folder, using the values.yaml file. To install or upgrade the chart:

helm install backend-service kubernetes -n neurobridges
helm upgrade backend-service kubernetes -n neurobridges

If you update the application, build a new image, change the image.tag value to the newest tag, and run the helm upgrade command above.

Start backend service

These files are stored in the virtual machine owned by RENCI, be sure to connect to RENCI vpn before going through the following procedure:

ssh neurobridges-ml.edc.renci.org

Go to projects/neurobridges/backend_service, then

Start and stop Solr index serving for the backend:

For starting, enter a new screen (for long-term processes):

screen -S solr

run the following command:

/projects/neurobridges/backend_service/solr-8.11.1/bin/solr start

For terminating, run the following command:

screen -r solr /projects/neurobridges/backend_service/solr-8.11.1/bin/solr stop

Start flask service:

For starting, enter a new screen (for long-term processes):

screen -S article

cd to the flask_service directory

cd /projects/neurobridges/backend_service/flask_service

run the following command:

python /projects/neurobridges/backend_service/flask_service/article_server.py

For terminating, go back to the screen (screen -r article):

Ctrl + C