Discussion: Using HTML VIEWERS to debug protocols

Author: Mike Cherry

Protocol Requirements: Pipeline Pilot 8 or later

PP8 introduced DESIGN MODE to help developers build and test protocols by allowing 'real-time' visualization of your data as it progresses down a pipe. I am sure though that many protocol developers (myself included) still use HTML VIEWERS to inspect data when building and debugging protocols. There are though scenarios where the data presented to you by the HTML VIEWER may not be what you expected or all that it seems. The attached protocol demonstrates four different issues with using html viewers to inspect you data:

     1.     automatic removal of additional whitespace/formatting characters.

     2.     presentation of date formats.

     3.     depiction of molecules with no coordinates.

     4.     hierarchical data not shown

In such scenarios it is worthwhile using an alternate means to inspect your data, DESIGN MODE for example or perhaps the NOTEPAD VIEWER, DATA RECORD TREE VIEWER or EXCEL VIEWER, to ensure you know what data you are working with. It may save you valuable time and unnecessarily banging your head against the wall.