Stratigraphic Units Knowledge Platform

Includes ontology, graph database, API.

Getting started

Spinning up infrastructure

Bring up the GraphDB instance

$ ./startup-graphdb.sh --local-build

Bring up the GDS

$ docker-compose -f docker-compose.gds.yml up -d --build

Bring up the REST API and Explorer app

If need be, edit the explorer_app/.env file and update the REACT_APP_STRATNAMES_API_ENDPOINT or REACT_APP_GDS_TO_URL_PREFIX. If only testing the REST API - ignore this bit. REACT_APP_STRATNAMES_API_ENDPOINT should point to a resolvable stratnames REST API endpoint (with the actual API because your browser will be resolving the URL at client side). REACT_APP_GDS_TO_URL_PREFIX similarly will need to point to the GDS instance resolvable at client side, so use an IP that will work.

Then run the following to bring up the REST API and explorer app.

$ docker-compose -f docker-compose.api.yml up -d --build

Test the deployment using

$ ./check-deployment.sh

Bring down the infrastructure

$ docker-compose -f docker-compose.api.yml -f docker-compose.gds.yml -f docker-compose.yml down -v

GraphDB deployment

Pre-requisites

docker
docker-compose

Start the GraphDB instance

Add your RDF files in strat_graph_data. This will then be loaded into the GraphDB instance

$ ./startup-graphdb.sh --local-build

The GraphDB will be available at http://localhost:7200. If you would like to change the port, edit .env and the PORT environment variable.

Running graphdb in remote-build mode

You can run graphdb in remote build mode, which means running the download-data.sh script to populate the data directory to load into graphDB at build time. By default it downloads the Pizza OWL ontology.

$ ./startup.sh --remote-build

To specify your own download-data.sh script, you can map that into the docker container. Edit the docker-compose.yml file to add that in like so (last line in the example below) in the volumes section.

   volumes:
      - "/tmp:/tmp"
      - "graphdb_data:${GRAPHDB_HOME}"
      - "./strat_graph_data:${GRAPHDB_SOURCE}"
      - "./custom-download-data.sh:/app/download-data.sh"

Geometry Data Service

$ docker-compose -f docker-compose.gds.yml up -d --build

Add your spatial layers in /gds/load_spatial_data/ or configure and modify gds/load_spatial_data/entrypoint.sh to download your spatial layers and load it into PostGIS.

The current GDS is configured to load the Strat Relations Geojson dataset.

To bring down the GDS, run the following:

$ docker-compose -f docker-compose.gds.yml down -v

Environment variables

Modify GDS_PORT in .env to specify which port GDS should be deployed to.

Modify docker-compose.gds.yml to update default settings for the DB credentials or specify those values in .env

"GSDB_DBNAME=${GSDB_DBNAME:-gis}"
"GSDB_HOSTNAME=${GSDB_HOSTNAME:-db}"
"GSDB_PORT=${GSDB_PORT:-5432}"
"GSDB_USER=${GSDB_USER:-jon}"
"GSDB_PASS=${GSDB_PASS:-jon}"
"GSDB_CLIENT_MAX_CONN_POOL=${GSDB_CLIENT_MAX_CONN_POOL:-30}"

REST API

Bring up the REST API

$ docker-compose -f docker-compose.api.yml up -d --build

Configure .env to bind the GEOM_DATA_SVC_ENDPOINT variable to the desired GDS instance. The default is a local deployment at http://gds:3000

vjf/strat-ontology-graph-API