README.rst

pl-statsmodels

Table of Contents

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

Abstract

An application that fit OLS model on the inputs and present results in output. Idea users of this tool includes doctors, healthcare professionals or anyone familiar with the ChRIS project

Description

statsmodels_tool is a ChRIS ds-type application that takes in images as files and produces text.

Usage

docker run --rm fnndsc/pl-statsmodels statsmodels_tool
    [-h|--help]
    [--json] [--man] [--meta]
    [--savejson <DIR>]
    [-v|--verbosity <level>]
    [--version]
    [--columns] <columnsForOLS>
    <inputDir> <outputDir>

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.

[--columns]
[REQUIRED] Columns to be used as input for OLS. Refer: https://www.statsmodels.org/devel/gettingstarted.html for more information.

Getting inline help is:

docker run --rm fnndsc/pl-statsmodels statsmodels_tool --man

Run

You need to specify input and output directories using the -v flag to docker run.

docker run --rm -u $(id -u)                                             \
    -v $(pwd)/test_input:/incoming -v $(pwd)/test_output:/outgoing      \
    fnndsc/pl-statsmodels statsmodels_tool                              \
    --columns "Lottery ~ Literacy + Wealth + Region"                    \
    /incoming /outgoing

Development

Build the Docker container:

docker build --tag pl-statsmodels -f ./Dockerfile

Run unit tests:

docker run --rm pl-statsmodels nosetests

Examples

Running docker container:

docker run --rm -u $(id -u) -v $(pwd)/test_input:/incoming -v $(pwd)/test_output:/outgoing local/pl-statsmodels statsmodels_tool --columns "Lottery ~ Literacy + Wealth + Region" /incoming /outgoing