LONI Student Project Fall 2013: Module Creation Utility

LONI Pipeline (http://pipeline.loni.usc.edu/, devpipeline@loni.usc.edu)

LONI Pipeline is a workflow management and processing application primarily aimed at neuroimaging researchers. Users can quickly create workflows that take advantage of all the neuroimaging and genomics computing tools.

Main Features

- Graphical workflows

- Client-server model with various grid support

- Predefined workflow library  

Pipeline Basics

- Data source, data sink

- Module: the executable with parameters

- Connections

Project Description: Module Creation Utility

In this project, you will implement an utility feature to create Pipeline modules based on executable’s manual/help file. We are interested in executable’s description, as well as its parameter arguments. For each parameter argument, we want to know its name and description, type (string or file), flag, whether it’s input or output, if it is optional, and so on. After parsing, the utility should output to a CSV format that we will provide, so that it will be converted to Pipeline modules.

Sample input (manual/hep) for the utility

Sample output (CSV) file, visualized for easy readability

The utility should be able to recognize commonly used manual formats and parse them automatically. When unknown formats are given to the utility, it should provide an easy to use interface (e.g. drag & drop, highlight) to assist user manually parse a few parameters. Then it should be able to generalize and complete the parsing on its own.