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Schema for describing bash command-line tools

Project description

Boutiques
=========

.. image:: https://zenodo.org/badge/32616811.svg
:target: https://zenodo.org/badge/latestdoi/32616811
.. image:: https://img.shields.io/pypi/v/boutiques.svg
:target: https://pypi.python.org/pypi/boutiques
.. image:: https://img.shields.io/pypi/pyversions/boutiques.svg
:target: https://pypi.python.org/pypi/boutiques
.. image:: https://travis-ci.org/boutiques/boutiques.svg?branch=develop
:target: https://travis-ci.org/boutiques/boutiques
.. image:: https://coveralls.io/repos/github/boutiques/boutiques/badge.svg?branch=develop
:target: https://coveralls.io/github/boutiques/boutiques?branch=develop

Boutiques is a cross-platform descriptive command-line framework for
applications.

The Power of Boutiques Tools
============================

While the Boutiques framework enables a descriptive representation of
command-line utilities and informs users of their usage, the Boutiques
Python tool provides users with functionality to perform a variety of
operations on these descriptors.

Installation
------------

Simple! Just open your favourite terminal and type:

::

$ pip install boutiques

Alongside installing the Boutiques package, this will also ensure the
dependencies are installed: ``simplejson``, ``jsonschema``,
``requests``, and ``pytest``.

Command-Line API
----------------

The command-line API for Boutiques can be accessed through your new
favourite command, ***``bosh``***. The Boutiques Shell (``bosh``)
provides an access point to all of the tools wrapped within Boutiques
and has some ``--help`` text to keep you moving forward if you feel like
you’re getting stuck. Let’s consider a few common use-cases…

Search For Tools
~~~~~~~~~~~~~~~~

Perhaps someone has already described the tool you are looking for and
you could reuse their work. For instance, if you are looking for a tool
from the FSL suite, try:

$ bosh search fsl

Search returns a list of identifiers for tools matching your query. You
can use these identifiers in any ``bosh`` command transparently. Even
better, these identifiers are `Digital Object
Identifiers <https://www.doi.org>`__ hosted on
`Zenodo <https://zenodo.org/>`__, they will never change and can’t be
deleted!

Import Your Tool
~~~~~~~~~~~~~~~~

If you’re in the lucky set of people with a Boutiques descriptor from a
previous schema iteration (such as ``0.4``), or you have a `BIDS
app <http://bids-apps.neuroimaging.io>`__, you can easily make yourself
a descriptor from the command-line. For instance, let’s say you have a
BIDS app at ``/awesome/app/``, you would run:

::

$ bosh import bids descriptor.json /awesome/app/

Very exciting, you now have a Boutiques descriptor for your app! If you
aren’t in one of those unique cases, unfortunately you’ll still need to
generate your descriptor by hand according to the
`schema <./tools/python/boutiques/schema/descriptor.schema.json>`__.

Create a New Descriptor
~~~~~~~~~~~~~~~~~~~~~~~

There are two additional ways to get you started with creating Boutiques
descriptors, both wrapped up in the “create” module of Boutiques. First,
if you just want an example descriptor that shows many of the properties
you can later set in Boutiques, you should use the command line
interface:

::

$ bosh create my-new-descriptor.json

However, if you want a bit more of a head start and your tool is built
in Python using the ``argparse`` library, we can help more! In the
Python script with your argparser defined, simply add the following
lines to get yourself a minimal corresponding descriptor:

::

import boutiques.creator as bc
newDescriptor = bc.CreateDescriptor(myparser, execname="/command/to/run/exec")
newDescriptor.save("my-new-descriptor.json")

There are additional custom arguments which can be supplied to this
script, such as tags for your tool. It is also worth noting that no
interpretation of output files is attempted by this tool, so your
descriptor could certainly be enhanced by addind these and other
features available through Boutiques, such as tests, tags, error codes,
groups, and container images.

Once you’ve created your descriptor this way you can translate your
arguments to a Boutiques-style invocation using the following code block
on runtime:

::

args = myparser.parse_args()
invoc = newDescriptor.createInvocation(args)

# Then, if you want to save them to a file...
import json
with open('my-inputs.json', 'w') as fhandle:
fhandle.write(json.dumps(invoc, indent=4))

Validation
~~~~~~~~~~

You just created a Boutiques descriptor (compliant with the
`schema <./tools/python/boutiques/schema/descriptor.schema.json>`__, of
course) named ``descriptor.json`` - Congratulations! Now, you need to
quickly validate it to make sure that you didn’t accidentally break any
rules in this definition (like requiring a “flag” input). You can
validate your schema like this:

::

$ bosh validate descriptor.json

Depending on the status of your descriptor, ``bosh`` will either tell
you it’s A-OK or tell you where the problems are and what you should
fix. If you want to know more about some extra options packed into this
validator, you can check them with ``bosh validate -h``, as one may
expect.

Simulate Execution
~~~~~~~~~~~~~~~~~~

Now that you’ve got a valid descriptor, you need to make sure it is
actually describing *your* tool and command-line. One of the easiest
ways to do this is by simulating inputs for fake executions of your
tool. You can do this using the ``exec`` function in ``bosh``:

::

$ bosh exec simulate descriptor.json -r -n 5

You just simulated 5 sets of random inputs which were dumped to our
terminal for you to validate. If anything seems fishy, you can update
your descriptor and ensure you’re describing the command-line you want.
If you had a particular set of inputs in mind, you could pass them in
with the ``-i`` flag rather than using the ``-r`` and ``-n`` flags.
Again, as I’m sure you’ve guessed, you can learn more here with
``bosh exec simulate -h``.

Launch Your Tool
~~~~~~~~~~~~~~~~

Your descriptor has now been vetted both by the validator and simulation
to describe meaningful command-lines for your tool - now it’s time to
put it to work! You can also use the ``exec`` function to launch an
analysis, provided you’ve described your inputs in ``invocation.json``
with the matching key-value pairs as in your descriptor (this is called
the ``invocationSchema``, which you can also generate and learn about
with ``bosh invocation``). One catch: we assume you have
`Docker <https://docker.com>`__ or
`Singularity <https://singularity.lbl.gov>`__ installed. A fair
assumption, nowadays? We hope so:

::

$ bosh exec launch descriptor.json invocation.json

You just launched your tool! You should be seeing outputs to your
terminal, and by default your current working directory will be mounted
to the container. You can mount more volumes with ``-v`` (consistent
with Docker), and see what other options are available, such as
switching users in the container, through the usual help menu,
``bosh exec launch -h``.

Test Your Tool
~~~~~~~~~~~~~~

You may now want to write a test for your descriptor, so that everyone
using it could check that it produces correct results. This can be done
by extending the tool descriptor with a ``tests`` property. For
instance, the description below would test if the execution of the
specified invocation returns with exit code 0 and produces a file in
output ``logfile`` with the right MD5 hash.

::

"tests": [
{
"name": "test1",
"invocation": {
"config_num": 4,
"enum_input": "val1",
"file_input": "/tests/image.nii.gz",
"list_int_input": [
1,
2,
3
],
"str_input": [
"foo",
"bar"
]
},
"assertions": {
"exit-code": 0,
"output-files": [
{
"id": "logfile",
"md5-reference": "0868f0b9bf25d4e6a611be8f02a880b5"
}
]
}
}
]

You can then test your descriptor by simply typing:

::

$ bosh test descriptor.json

Evaluate Your Usage
~~~~~~~~~~~~~~~~~~~

If you’ve been using your tool and forget what exactly that output file
will be named, or if it’s optional, but find re-reading the descriptor a
bit cumbersome, you should just evaluate your invocation! If we wanted
to check the location of our output corresponding to the id
``my_batmobile``, or which of our inputs are numbers and optional, we
could do the following two queries, respectively:

::

$ bosh evaluate descriptor.json invocation.json output-files/id=my_batmobile inputs/type=Number,optional=True
[{"my_batmobile": "/the/batcave/batmobile.car"}, {"bad_guys": "0", "times_saved_gotham": "5000"}]

Publish Your Tool
~~~~~~~~~~~~~~~~~

Congratulations on successfully running your analysis! So excited about
your tool, you now want to share this descriptor with the world. This is
the step which requires our GitHub libraries for Python which you got in
the installation above - we’re going to make a fork of the
`NeuroLinks <https://brainhack101.github.io/neurolinks>`__ repository,
add your tool, and get everying queued up for you to submit a Pull
Request back with the brand new addition. There is a fair bit of
metadata we’ll collect here, but the basics will be run with the
following, assuming your descriptor lives in a Git-repo available at
``/utility/belt/``, your name is ``Batman``, and your tool lives at the
url ``http://thebatcave.io`` (sorry to anyone who owns this url…):

::

$ bosh publish /utility/belt/ Batman http://thebatcave.io

Your tool is now being shared in a packaged and fully described fashion,
making it easier than ever to reproduce and extend your work! As always,
learn more about this feature with ``bosh publish -h``.

Python API
----------

Now that you’ve spent all that time learning the command-line API, we’ve
got some good news for you: you already know the Python API, too. The
interfaces are entirely consistent with those exposed on the
command-line, so you just need to do the following, to say, validate
your schema:

::

> import boutiques
> boutiques.validate('descriptor.json')

Whether you’re working from the shell or a Python script, ``bosh`` will
treat you exactly the same.

Contributing
============

Excited by the project and want to get involved?! *Please* check out our
`contributing guide <./CONTRIBUTING.md>`__, and look through the
`issues <https://github.com/boutiques/boutiques/issues/>`__ (in
particular, those tagged with
“`beginner <https://github.com/boutiques/boutiques/issues?utf8=%E2%9C%93&q=is%3Aissue%20is%3Aopen%20label%3Abeginner>`__”)
to start seeing where you can lend a hand. We look forward to approving
your amazing contributions!

.. |DOI| image:: https://zenodo.org/badge/32616811.svg
:target: https://zenodo.org/badge/latestdoi/32616811
.. |PyPI| image:: https://img.shields.io/pypi/v/boutiques.svg
:target: https://pypi.python.org/pypi/boutiques
.. |PyPI| image:: https://img.shields.io/pypi/pyversions/boutiques.svg
:target: https://pypi.python.org/pypi/boutiques
.. |Build Status| image:: https://travis-ci.org/boutiques/boutiques.svg?branch=develop
:target: https://travis-ci.org/boutiques/boutiques
.. |Coverage Status| image:: https://coveralls.io/repos/github/boutiques/boutiques/badge.svg?branch=develop
:target: https://coveralls.io/github/boutiques/boutiques?branch=develop


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