Redwood Client

For Users

End users should use the core-client, which extends this client.

Getting Started

Download the config file and edit it to specify your redwood access token.

wget https://raw.githubusercontent.com/BD2KGenomics/dcc-redwood-client/develop/src/main/conf/application-redwood.properties

Now you can invoke the client (or derived clients) by mounting in the config file as a volume and specifying the REDWOOD_ENDPOINT environment variable:

docker run -it -e REDWOOD_ENDPOINT=<redwood_endpoint> -v $(pwd)/application-redwood.properties:/dcc/dcc-redwood-client/conf/application-redwood.properties -v ~/data:/dcc/data quay.io/ucsc_cgl/redwood-client:1.2.2 bash

Note: you can also specify -e ACCESS_TOKEN=<your-access-token> when you invoke docker run instead of using the config file (as long as you're on a private machine).

Specification

The redwood client is released as the quay.io/ucsc_cgl/redwood-client docker image.

The following commands are exposed (help commands shown):

• upload -h upload a set of files
• download -h download individual files
• redwood-download -h download via manifest
• icgc-storage-client help underlying storage client
• dcc-metadata-client help underlying metadata client

Configuration on the underlying igcg clients can be set via (from highest to lowest precedence):

• /dcc/dcc-redwood-client/conf/application-redwood.properties java properties file
• REDWOOD_PROPERTIES, ACCESS_TOKEN, and REDWOOD_LOG_DIR environment variables
• Java system properties specified in the JAVA_OPTS environment variable

For Developers

Please update the change log to reflect each user-facing change you make

Development

Build docker image with:

./mvnw

(Use the -P prod maven profile for prod builds)

Use dcc-ops to test against a local (dev mode) storage system instance:

docker run --rm -it --net=redwood_internal --link redwood-nginx:storage.redwood.io --link redwood-nginx:metadata.redwood.io -e ACCESS_TOKEN=<access_token> -v ~/data:/dcc/data quay.io/ucsc_cgl/redwood-client:1.2.2-SNAPSHOT bash

Tip: If you're using a local redwood instance and the redwood cli is on your path you can create an access token and launch the client in one line:

docker run --rm -it --net=redwood_internal --link redwood-nginx:storage.redwood.io --link redwood-nginx:metadata.redwood.io -e ACCESS_TOKEN=$(redwood token create) -v ~/data:/dcc/data quay.io/ucsc_cgl/redwood-client:1.2.2-SNAPSHOT bash

Release

• Bump the version number in pom.xml
• Login to quay.io on the command line 'docker login quay.io'
• ./mvnw deploy to build and push the docker image to quay.io
• Update this README to use the latest version number
• Edit the version on the pom.xml to the next_version-SNAPSHOT
• Update the change log (rename the "Unreleased" section, etc.)