implement reporting system

[chrisgorgo]

After pipeline execution or even when it is still running user would like to be able to have a quick glance on what where the outputs of the intermediate stages. An online reporting system could provide with such information. A simple solution would consist of generating an auto updating html page (similar to FSL approach).

[satra]

going to start working on it.

[chrisgorgo]

Can we brainstorm on the architecture first?

[chrisgorgo]

Ok let me share my thoughts on the topic here.

Goals

1. Be able to quickly verify if the nodes produced expected results.
2. Produce custom reports.

Architecture

Each node will produce a report in its working dir (pdf or html - presentation should be separated from the content). There will be a generic method for generating those that will include:

• inputs
• stderr, stdout
• parsed outputs (volumes will be converted into images, text files will be included)

This method can be overridden to achieve specific functionality such as plotting results (for example for motion correction) or adding *.m files for matlab based nodes.

A simple html interface can be made to access those mini reports. Imaging the grapviz plots in which you can click on the nodes to access detailed information. Also updating the report while the pipeline is still running would be very useful (imaging nodes colour coded with regards to their status: finished, failed, not yet started, running).

[mwaskom]

I like all of Chris's ideas, although I think that we should provide some way to separate reporting about the pipeline operation (ie when the node is done, stdout/err, etc) from the reporting about the data (ie motion correction plots, sliced images of activation, etc.) For the latter, it would be ideal just to have a keyword arg to the node constructor that says "report=True", which will probably require the underlying interface to have some sort of reporting API that says "here's the outputs I generate that should go into a report".

[chrisgorgo]

Sphinx might be a good framework for generating html and pdf reports http://sphinx.pocoo.org/

[chrisgorgo]

Kudos to Satra for creating the barebones. We need to remember to add error reporting in the future.