Hi Carolina, If you are using a binary installation of ctakes 4.0.0 and editing an examples piper in the root resources/ directory then you may have a problem such as you describe. There is an unwanted ctakes-examples-res.jar in the lib/ directory that contain copies of all the example pipers, and those pipers are loaded instead of the ones in resources/ You can delete the ctakes-examples-res.jar in lib/ and try again.
When you start writing your own piper files you should probably also start using the PiperFileRunner class. Or the Piper File Submitter GUI. https://cwiki.apache.org/confluence/display/CTAKES/Piper+Files Here is a template for an annotator. public class MyAnnotator extends JCasAnnotator_ImplBase { public void initialize( UimaContext context ) throws ResourceInitializationException { super.initialize( context ); // My initialization code. } public void process( JCas jcas ) throws AnalysisEngineProcessException { // My process code. } } The JCas is the main data object passed through the pipeline. You can find information on JCas on the web, but it can be overwhelming. The two primary get() style methods are 1. org.apache.uima.fit.util.JCasUtil.select( jcas, [type class] ) http://uima.apache.org/d/uimafit-current/api/org/apache/uima/fit/util/JCasUtil.html 2. org.apache.ctakes.core.util.OntologyConceptUtil. *(..) http://ctakes.apache.org/apidocs/4.0.0/org/apache/ctakes/core/util/OntologyConceptUtil.html If you are a developer (you are writing your own java class), then I highly recommend checking out the ctakes trunk repository and looking at existing annotators. svn co https://svn.apache.org/repos/asf/ctakes/trunk/ Within the code are the various ctakes modules, and almost all of them have a package named "ae" containing annotators. Sean ________________________________________ From: Cervantes, Carolina <ccervant...@luc.edu> Sent: Wednesday, December 4, 2019 2:13 PM To: dev@ctakes.apache.org Subject: Adding Java Class to Piper File [EXTERNAL] Warning: Email originated outside Boston Children's. Don't click links/attachments unless you know sender & content seems safe. ********************************************************************** Hello, I have been attempting to add a custom java class into a .piper file which can extract CUIs. I have been focused on adding this class to the HelloWorldCui.piper file and I am then running the class HelloWorldCuiPiperRunner via the terminal. While I have been tinkering with the HelloWorldCui.piper file, I have run into two main issues: 1. Modifications to the .piper file are not reflected while running the HelloWorldCuiPiperRunner via terminal (or IntelliJ). I have tried to add code to include the class file, after not having luck with this, I began to comment out other parts of the .piper file to observe the effects. I commented out integral pieces of the HelloWorldCui.piper file (the lines containing 'load DictionarySubPipe.piper' and 'collectCuis'). After running HelloWorldPiperRunner with the aforementioned lines commented out, the behavior is exactly the same. I have ensured that the changes to the .piper file were saved, have cleaned and compiled, and have run this on another machine. Is this the correct way to modify and use piper files? 2. What is the correct way to add a java file to a pipeline? Best, Carolina
