Hello, I currently inherited an existing Apache cTakes Pipeline Application from a previous developer who is no longer with the parent organization I am supporting in the Molecular Genetics space. The organization has a built and runnable code, running on a scheduled basis in production. Separately, in a Development environment we are wanting to address defects, add new features, and also address security exceptions and vulnerabilities which we can later QA and roll into Production.
At the moment in Development we are experiencing an error in trying to run our Apache cTakes pipeline with the same sources and binaries taken from prod. Both Dev and Prod are using Maven 3.9.8 for building and JDK 8 for build and execution. The specific error (some info redacted for sensitivity , some for brevity) is: Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of CAS Processor with name "XYZ Aggregate Engine" failed. Caused by: org.apache.uima.resource.ResourceInitializationException: Initalization of annotator class "com.xyz.XyzSetenceRegexAnnotator" failed. (Descriptor: file:/opt/xyzapp/scripts/resources/cTakes/desc/XyzSetenceRegexAnnotator.xml) ... 8 more Caused by: org.springframework.beans.factory.access.BootstrapException: Unable to initialize group definition. Group resource name [classpath* org/apache/ctakes/ytex/uima/beanRefContext.xml]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name "ytexApplicationContext" defined in URL [jar: /opt/xyzapp/nlp/nlp-c-takes/apache-ctakes-4.00.1-src/ctakes-distribution/target/apache-ctakes-4.0.0.1-jar-with-dependencies.jar!/org/apache/ytex/uima/beanRefContext.xml]: Instantiation of bean failed .... Unable to locate Spring NamespaceHandler for XML schema namespace [http://www.springframework.org/schema/aop] offending resource: class path resource [org/apache/ctakes/ytex/beans-kernel.xml] ...41 more ... To execute I run: Java -cp "/opt/xyzapp/scripts/resources/*:/opt/xyzapp/nlp/nlp-c-takes/apache-ctakes-4.0.0.1-src/ctakes-distribution/target/* -Dorg.apache-ctakes.ytex.conceptGraphDir='pwd' org.xyz.pipeline.RunCPE /opt/xyzapp/scripts/resources/cTakes/CPEDescriptor.xml I experience this error, if I take the apache-ctakes-4.0.0.1-jar-with-dependencies.jar from Prod where the pipeline is successfully running and place it in the target dir, and I also experience it if I build in the development environment, and use the apache-ctakes-4.0.0.1-jar-with-dependencies.jar produced in this target directory. I am also evaluating if the Production shell scripts used for setting environment variables, paths, and the Java class path is the same ( which I suspect is not). If anyone can provide me with more clues or advice on this, I would greatly appreciate it. The cTakes portion of this application and pipeline is 1 of 4x separate applications, and if we are able to run/build cTakes we will be able to proceed with maintaining the application portfolio. Thanks, Ryan
