fnndsc/pl-topologicalcopy repository overview

python topologicalcopy.py
        [-h] [--help]
        [--json]
        [--man]
        [--meta]
        [--savejson <DIR>]
        [-v <level>] [--verbosity <level>]
        [--version]
        <outputDir>
        [--plugininstances <instances>]
        [-f <filter>] [--filter <filter>]
        [-g] [--groupByInstance]

.. code::

        [-h] [--help]
        If specified, show help message and exit.

        [--json]
        If specified, show json representation of app and exit.

        [--man]
        If specified, print (this) man page and exit.

        [--meta]
        If specified, print plugin meta data and exit.

        [--savejson <DIR>]
        If specified, save json representation file to DIR and exit.

        [-v <level>] [--verbosity <level>]
        Verbosity level for app. Not used currently.

        [--version]
        If specified, print version number and exit.

        [--plugininstances <instances>]
        If specified, it's a string representing a comma-separated list of plugin
        instance ids.

        [-f <filter>] [--filter <filter>]
        If specified, it's a string representing a comma-separated list of regular
        expressions.

        [-g] [--groupByInstance]
        If specified then an output directory is created for each input plugin instance
        within this plugin app's output path


Getting inline help is:

.. code:: bash

    docker run --rm fnndsc/pl-topologicalcopy topologicalcopy --man

Run
~~~

You need you need to specify the output directory using the `-v` flag to `docker run`.


.. code:: bash

    docker run --rm -u $(id -u) -v $(pwd)/out:/outgoing      \
        fnndsc/pl-topologicalcopy topologicalcopy /outgoing


Development
-----------

Build the Docker container:

.. code:: bash

    docker build -t local/pl-topologicalcopy .

Run unit tests:

.. code:: bash

    docker run --rm local/pl-topologicalcopy nosetests

Examples
--------

This example will copy all files in the output directories of plugin instances with id 1,3
and 7 that have `.dcm` extension. Note: This is a utility 'ts' plugin that only works in
the context of the ChRIS platform.

.. code:: bash

    docker run --rm -v $(pwd)/out:/outgoing fnndsc/pl-topologicalcopy    \
    topologicalcopy /outgoing --plugininstances "1,3,7" --filter "\.dcm$,\.dcm$,\.dcm$"


.. image:: https://raw.githubusercontent.com/FNNDSC/cookiecutter-chrisapp/master/doc/assets/badge/light.png
    :target: https://chrisstore.co