combine data

This script combines the continent-level data files produced by setfinder into single, global-level files.

The following files are combined and created:

• basin.json
• cycle_passes.json
• hivdisets.json
• metrosets.json
• passes.json
• reach_node.json
• reaches.json
• s3_list.json
• sicsets.json

Files are written out to directory referenced by 'datadir' command line argument.

installation

Build a Docker image: docker build -t combine .

execution

Command line arguments:

• -c: Path to continent JSON file
• -d: Path to directory that contains datagen output data
• -x: Indicate the datagen output continent-level JSON files should be deleted

Execute a Docker container:

# Docker run command
docker run --rm --name combiner -v /mnt/combiner:/data combiner:latest -c /data/continent.json -d /data/datagen_output -x

deployment

There is a script to deploy the Docker container image and Terraform AWS infrastructure found in the deploy directory.

Script to deploy Terraform and Docker image AWS infrastructure

REQUIRES:

• jq (https://jqlang.github.io/jq/)
• docker (https://docs.docker.com/desktop/) > version Docker 1.5
• AWS CLI (https://docs.aws.amazon.com/cli/latest/userguide/getting-started-install.html)
• Terraform (https://developer.hashicorp.com/terraform/tutorials/aws-get-started/install-cli)

Command line arguments:

[1] registry: Registry URI [2] repository: Name of repository to create [3] prefix: Prefix to use for AWS resources associated with environment deploying to [4] s3_state_bucket: Name of the S3 bucket to store Terraform state in (no need for s3:// prefix) [5] profile: Name of profile used to authenticate AWS CLI commands

Example usage: ``./deploy.sh "account-id.dkr.ecr.region.amazonaws.com" "container-image-name" "prefix-for-environment" "s3-state-bucket-name" "confluence-named-profile"`

Note: Run the script from the deploy directory.