pl-pacscopy

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

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

pip install pacscopy

and run with

pacscopy.py --man /tmp /tmp

to get inline help. To copy from one directory to another, simply do

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

docker run --rm -v $(pwd)/out:/outgoing                             \
        fnndsc/pl-pacscopy pacscopy.py                              \

Thus, getting inline help is:

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.

mkdir out
docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
        fnndsc/pl-pacscopy pacscopy.py                              \
        --dir dataset/MPRAGE                                        \
        /outgoing