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1. Create an empty text file.  The standard file extension for piper files is .piper
2. Set a reader for your pipeline.   To set values to parameters used by the reader class, simply add one or more name=value pairs after the class name.   
   * readFiles is a convenience command.  "readFiles my/data" is equivalent to "reader FileTreeReader InputDirectory=my/data".
3. add annotation engines and cas consumers to your pipeline. To set values to parameters used by the annotation engine class, simply add one or more name=value pairs after the class name. 
4. load common groups of components from another piper file.  See Table 2 for piper files in cTAKES.
   
5. reader, load and add* commands all take class names or file directories as their first parameter.  
   If the class is not in a standard cTAKES module's crae or cc package, or a piper file is not in a standard module's pipeline/ directory then the package or path must be specified for that component / file.
6. Use package to simplify adding multiple pipeline components from a package not standard to cTAKES.
   

   Gliffy Diagram
   chrome min name Use of package

7. Use set to assign a value to a parameter used by following components.
   

   Gliffy Diagram
   name set global value

   
   *A name=value pair on a component line will, for that component, override a set parameter value.

8. cli is a special type of set that sets a parameter to some value entered by the User on a command line.
   

   Gliffy Diagram
   name Use of cli

   * cli can only be used with the PiperFileRunner class, the bin/runPiperFile script or the Piper File Submitter GUI.
   * Reserved parameters unavailable for cli are listed in Table 3.

9. addDescription is a special type of add that utilizes a component's static addDescription(..) method.  

   * Use with care as not all components have such a method.

10. Use addLogged to ensure a component's start and finish time are logged.  This is useful for debugging and profiling some components.

11. Use addLast to ensure that a component, such as a writer, executes at the end of a pipeline.  Multiple components can be added with addLast.
    * writeXmis is a convenience command.  "writeXmis my/output" is equivalent to "add FileTreeXmiWriter OutputDirectory=my/output".
12. name=value pairs can accept comma-delimited arrays:   ArrayParm=this,is,an,array
    * Texts enclosed in quotes are not arrays:  NotArrayParm="this,is,just,text"

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1. To run a piper file from the command line, execute the script bin/runPiperFile -p path/to/piper

2. To run a piper from code use the main(..) method of PiperFileRunner in ctakes-core, or more directly use the PiperFileReader class in ctakes-core.


3. There are examples of piper file use in the ctakes-examples module.

4. A piper file can also be loaded and run by the Simple Pipeline Fabricator GUI and the Piper File Submitter GUI.

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