overture/score repository overview

⁠SCORe Client

SCORe Client for the SCORe storage system.

⁠Libraries

The storage client is comprised of the following components:

• Spring Boot⁠
• Spring Security⁠
• Spring Security OAuth⁠
• AWS SDK⁠
• JavaFS⁠
• HTSJDK⁠

⁠Build

To compile, test and package the module, execute the following from the root of the repository:

mvn -am -pl score/score-core

⁠Run

bin/score-client upload —manifest manifest.txt

⁠Docker image Usage

An example usage of the container which will download a remote file (with associated index file) having object-id 5b845b9a-3dcd-59ef-9f56-9a99396e988f to /tmp on the docker host machine in "bundle" layout. The files will be written with ownership set to the current user (/usr/bin/id -u) and group (/usr/bin/id -g)

# Get latest image
pull overture/score

# Publish token
export ACCESSTOKEN=<access token from https://dcc.icgc.org>

# Make life easy for usage
alias score-client="docker run -it --rm  -u $(id -u):$(id -g) -e ACCESSTOKEN -v /tmp:/data score-client 
bin/score-client"

# Usage with an example object-id from https://dcc.icgc.org
score-client download --object-id 5b845b9a-3dcd-59ef-9f56-9a99396e988f --output-dir /data --output-layout bundle

⁠Develop

The following will allow a developer to hit against production from the Eclipse IDE

⁠Entry Point

bio.overture.score.client.ClientMain

⁠VM Arguments

-Dspring.config.location=src/main/conf/
-Dspring.profiles.active=prod
-Dclient.strictSsl=true
-Dclient.upload.serviceHostname=<host>
-DaccessToken=<token>

⁠Program Arguments

score-client upload --manifest src/test/resources/fixtures/upload/manifest.txt

⁠HTTP Logging

To enable logging of request bodies and headers, append the following to the command line:

--logging.level.org.apache.http=DEBUG