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fnndsc/pl-simpledsapp_moc

By fnndsc

•Updated over 7 years ago

A test ChRIS DS-type app for the Massachusetts Open Cloud remote computing environment.

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fnndsc/pl-simpledsapp_moc repository overview

⁠pl-simpledsapp_moc

.. image:: https://badge.fury.io/py/simpledsapp_moc.svg⁠ :target: https://badge.fury.io/py/simpledsapp_moc⁠

.. image:: https://travis-ci.org/FNNDSC/simpledsapp_moc.svg?branch=master⁠ :target: https://travis-ci.org/FNNDSC/simpledsapp_moc⁠

.. image:: https://img.shields.io/badge/python-3.5%2B-blue.svg⁠ :target: https://badge.fury.io/py/pl-simpledsapp_moc⁠

.. contents:: Table of Contents

⁠Abstract

A simple DS type ChRIS application specifically created for the Massachusetts Open Cloud remote computing environment.

⁠Synopsis

.. code::

python simpledsapp_moc.py                                       \
    [--prefix <filePrefixString>]                               \
    [--sleepLength <sleepLength>]                               \
    [--ignoreInputDir]                                          \
    [-v <level>] [--verbosity <level>]                          \
    [--version]                                                 \
    [--man]                                                     \
    [--meta]                                                    \
    <inputDir>
    <outputDir>

⁠Description

simpledsapp_moc.py is a ChRIS-based application that basically does an explicit copy of each file in an input directory to the output directory, prefixing an optional string to each filename.

⁠Agruments

.. code::

[--prefix <prefixString>]
If specified, a prefix string to append to each file copied.

[--sleepLength <sleepLength>]
If specified, sleep for <sleepLength> seconds before starting script processing. This is to simulate a possibly long running  process.

[--ignoreInputDir] 
If specified, ignore the input directory. Simply write a single json  file to the output dir that is a timestamp. Useful if the input  directory contains large nested file trees.

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

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

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

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

⁠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 simpledsapp_moc

and run with

.. code:: bash

    simpledsapp_moc.py --man /tmp /tmp

to get inline help. The app should also understand being called with only two positional arguments

.. code:: bash

    simpledsapp_moc.py /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-simpledsapp_moc simpledsapp_moc.py                \

Thus, getting inline help is:

.. code:: bash

mkdir in out && chmod 777 out
docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
        fnndsc/pl-simpledsapp_moc simpledsapp_moc.py                \
        --man                                                       \
        /incoming /outgoing

⁠Examples

Tag summary

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Digest

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Last updated

over 7 years ago

docker pull fnndsc/pl-simpledsapp_moc