kliko 0.3

Scientific Compute Container Spec Parser

About

KLIKO is a sSpecification, validator and parser for the Scientific Compute Container specification. KLIKO is written in Python.

Installation

$ python setup.py install

or:

$ pip install kliko

Usage

import kliko

schema_string = open('examples/kliko.yml', 'r').read()
parameters = open('examples/parameters.json', 'r').read()
schema = kliko.validate_kliko(schema_string)

kliko.validate_parameters(parameters, schema)

The specification

• All is based on standard docker containers

• Container mush have a CMD specified, which would be the main program of the container. It should not require arguments.

• logging should be written to STDOUT and STDERR.

• We define two types of compute containers, split IO and joined IO containers.

• For split IO Input files will be mounted read only into /input. Output file should be written to /output, which will be mounted by the host.

• For joined IO containers input & output is the /work folder which will be mounted RW.

• parameters for the computation will be given when the container is raun in the form of a file in json format called parameters.json in /input

• Which parameters the container will accept should be defined in a yaml file /kliko.yml

• The kliko.yml file should follow the schema defined in kliko/schema.yml.

• an example parameters definition file can be found in examples/form.yml

• fields with type file will enable supply of custom input files. these will be put in the /input folder.

Example

There is an example in examples/form.yml

Django

In kliko.django_form there is a function that can automatically generate a Django form from a parsed parameter definition file. This is used by RODRIGUES to render a form inside a website which then can be used to schedule a parameterized container.

https://github.com/ska-sa/rodrigues/

This requires django-form-utils.

https://pypi.python.org/pypi/django-form-utils

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