pl-topologicalcopy

Table of Contents

• Abstract
• Description
• Usage
  • Arguments
  • Run
• Development
• Examples

Abstract

A plugin ts app to copy filtered output directories from many input plugin instances.

Description

topologicalcopy is a ChRIS-based application to copy filtered output directories from a list of input plugin instances.

Usage

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

Arguments

[-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:

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.

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

Development

Build the Docker container:

docker build -t local/pl-topologicalcopy .

Run unit tests:

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.

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