copy from (openstorage) to output directory
Project description
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
Project details
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