Piper File Submitter

Introduction

Piper Files contain cTAKES pipelines in a simple flat file format. They can be run via command line using the bin/runPiperFile script. If you are running from a development environment (checked out trunk from SVN) they can also be run using the Piper File Submitter GUI. The GUI allows the user to enter and save command line parameters, making any future re-run of a piper file quick and easy.

Step-by-step guide

1. Open the Piper File Submitter GUI ... execute bin/runPiperSubmitter

• The window will be mostly empty as no pipeline has been configured.
• There are simple instructions in the panel at the bottom.
  
  
  

2. Load a Piper File using the Open Piper File button. (Blue folder with blue gear)

• The contents of the selected piper file will appear in the panel on the right.
• In the image below the Default Clinical Pipeline was selected.
• If the piper loads additional piper files they can be viewed by selecting labeled tabs.
  
  
  

3. Enter command line parameter values in the table on the left.

• The rightmost column contains a button that can open a file chooser for convenience.
• The LookupXml (-l) parameter can be left empty to use the default lookup dictionary for Named Entity Recognition.
• If your run parameters have previously been saved, load the CLI (.piper_cli) value file. (Crate with blue contents)
  
  
  

4. Save your parameter values with the Save CLI Values button. (Crate with green arrow)
5. Click Run Piper File to run the pipeline with the current parameter values. (Green circle with runner)

• The status bar will indicate the progress of the run.

• The main gui will turn grey while the job is running.
  
  
  

• When working directly from code, run using the PiperRunnerGui class in the ctakes-gui module.

Related articles

• Piper Files
• Default Clinical Pipeline
• Simple Pipeline Fabricator