iRobot Client

Basic iRobot client to interact with the iRobot HTTP API. The client has a Common Workflow Language wrapper for integration with Arvados and other applications if needed.

Getting Started

These instructions will get you a copy of the project up and running on your local machine or in a Docker container for development and testing purposes.

Prerequisites

What things you need to install the software:

• python 3.6

Installing

From GitHub:

git clone https://github.com/wtsi-hgi/irobot-client.git
cd irobot-client
python setup.py install

Alternatively in a Docker container but without test resources (CANNOT run the cwl inside the irobot-client container):

docker run -it mercury/irobot-client

Check that the iRobot-Client works:

The best way to check the client works without connecting to the irobot server is to run a docker container with the Bissell image from dockerhub.

mkdir testdir
irobotclient http://localhost:5000/test.cram testdir --arvados_token testtoken -f

The above command should download two files (test.cram and it's associated index file: test.cram.crai) to the testdir folder.

Usage

Command line interface

usage: irobotclient [options] INPUT_FILE OUTPUT_DIR

Command line interface for iRobot HTTP requests

positional arguments:
  input_file            path and name of input file
  output_dir            path of output directory

optional arguments:
  -h, --help            show this help message and exit
  -u URL, --url URL     Use this tag if no irobot URL is set as an environment variable {IROBOT_URL}. URL scheme, domain and port for irobot. EXAMPLE: http://irobot:5000/
  --arvados_token ARVADOS_TOKEN
                        Arvados authentication token; if not supplied here it will be sourced from the environment {ARVADOS_TOKEN} or default to an
  --basic_username BASIC_USERNAME
                        Basic authentication username; if not supplied here it will be sourced from the environment {BASIC_USERNAME} then, failing that, current system user
  --basic_password BASIC_PASSWORD
                        Basic authentication password; if not supplied here it will be sourced from the environment {BASIC_PASSWORD}
  -f, --force           force overwrite output file if it already exists
  --no_index            Do not download index files for CRAM/BAM files
  -o, --override_url    Override a URL set in the IROBOT_URL environment 
                        variable"

Common Workflow Language (CWL)

The below commands run the cwl wrapper passing in the example YAML file defining program argument values.

cd cwl
pip install -r cwl_requirements.txt
cwl-runner cwl_wrapper.cwl config_example.yml

If the Bissell container is up and running, the above command should return a test_text.txt file to your working directory. To specify a different output directory use the cwl-runner --outdir OUTDIR option.

Deployment

Values required for the client can be passed in as arguments on the command line, a YAML file when using CWL, or the following can be set as environment variables:

IROBOT_URL      -   URL scheme, domain and port for irobot. EXAMPLE: http://irobot:5000/
ARVADOS_TOKEN   -   Arvados authentication token
BASIC_USERNAME  -   Basic authentication username
BASIC_PASSWORD  -   Basic authentication password

Running the tests

• TODO: Update unittests
• TODO: Create automated test script for cwl
• TODO: Explain how to run the automated tests for this system

And coding style tests

• TODO: This project follows the unittest and PEP8 coding style.

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

• Elizabeth Weatherill

See also the list of contributors who participated in this project.

License

This project is licensed under the GNU General Public License - see the LICENSE.md file for details

Acknowledgments

• Chris Harrison - iRobot developer
• Colin Nolan - Code reviewer
• Josh Randall - Team lead and Bissell author
• Billie Thompson - README template
• Stack Overflow