Metadata-Version: 1.0
Name: pacscopy
Version: 1.0.2
Summary: copy from (openstorage) to output directory
Home-page: https://github.com/FNNDSC/pl-pacscopy
Author: Rudolph Pienaar
Author-email: rudolph.pienaar@gmail.com
License: MIT
Description: 
        pl-pacscopy
        ===========
        
        .. image:: https://badge.fury.io/py/pacscopy.svg
            :target: https://badge.fury.io/py/pacscopy
        
        .. image:: https://travis-ci.org/FNNDSC/pacscopy.svg?branch=master
            :target: https://travis-ci.org/FNNDSC/pacscopy
        
        .. image:: https://img.shields.io/badge/python-3.5%2B-blue.svg
            :target: https://badge.fury.io/py/pl-pacscopy
        
        .. contents:: Table of Contents
        
        
        Abstract
        --------
        
        ``pacscopy`` is a simple plugin that copies data from open storage to create a new top level ChRIS Feed. It's core utility is in demonstrating how to create a largely trivial FS plugin/app for the ChRIS system.
        
        Synopsis
        --------
        
        .. code::
        
            python pacscopy.py                                              \
                [-v <level>] [--verbosity <level>]                          \
                [-d <dir>] [--dir <dir>]                                    \
                [--version]                                                 \
                [--man]                                                     \
                [--meta]                                                    \
                <outputDir> 
        
        
        Run
        ----
        
        This ``plugin`` can be run in two modes: natively as a python package or as a containerized docker image.
        
        Using PyPI
        ~~~~~~~~~~
        
        To run from PyPI, simply do a 
        
        .. code:: bash
        
            pip install pacscopy
        
        and run with
        
        .. code:: bash
        
            pacscopy.py --man /tmp /tmp
        
        to get inline help. To copy from one directory to another, simply do
        
        .. code:: bash
        
            pacscopy.py --dir /some/input/directory /destination/directory
        
        
        Using ``docker run``
        ~~~~~~~~~~~~~~~~~~~~
        
        To run using ``docker``, be sure to assign an "input" directory to ``/incoming`` and an output directory to ``/outgoing``. *Make sure that the* ``$(pwd)/out`` *directory is world writable!*
        
        Now, prefix all calls with 
        
        .. code:: bash
        
            docker run --rm -v $(pwd)/out:/outgoing                             \
                    fnndsc/pl-pacscopy pacscopy.py                              \
        
        Thus, getting inline help is:
        
        .. code:: bash
        
            docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
                    fnndsc/pl-pacscopy pacscopy.py                              \
                    --man                                                       \
                    /outgoing
        
        Examples
        --------
        
        Copy a directory ``dataset/MPRAGE`` to the output directory. If called from ChRIS, the input directory spec refers to a location in openstorage, otherwise it is interpreted as a system directory spec.
        
        .. code:: bash
        
            mkdir out
            docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
                    fnndsc/pl-pacscopy pacscopy.py                              \
                    --dir dataset/MPRAGE                                        \
                    /outgoing
        
        
        
        
        
        
        
Platform: UNKNOWN
