See <https://builds.apache.org/job/ctakes-trunk-compiletest/875/changes>

Changes:

[seanfinan] Adding ProcessDir.piper
Refactoring

[seanfinan] Adding ctakes-examples-res with sample notes
Copy notes to resources/ directory for binary build

[seanfinan] FilesInDirectoryCollectionReader now uses FileLocator to access 
resources in source
Adding Example that reads files from a directory using PipelineBuilder
moved ctakes-examples/data/ to a ctakes-examples-res module
Added all other sample notes in ctakes project to the ctakes-examples-res module
   TODO refactor all test and sample code in ctakes to use ctakes-examples-res 
sample notes

------------------------------------------
[...truncated 3600 lines...]
A         ctakes-ytex-res/src/main/resources/org/apache/ctakes
AU        ctakes-ytex-res/src/main/resources/org/apache/ctakes/ctakes_logo.jpg
A         ctakes-ytex-res/src/main/resources/org/apache/ctakes/jdl
A         ctakes-ytex-res/src/main/resources/org/apache/ctakes/jdl/xdl.xsd
A         ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel-sim.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/simSvcBeanRefContext.xml
A         ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima
A         ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/NamedEntityRegex.hbm.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/SegmentRegex.hbm.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/Document.hbm.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-dao.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-mapper.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima.hbm.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/annotators
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/annotators/negex_triggers.txt
A         ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/tools
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/tools/docanalyzer
AU        
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/tools/docanalyzer/icon.gif
AU        
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/tools/docanalyzer/icon.psd
AU        
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/tools/docanalyzer/logo.gif
AU        
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/tools/docanalyzer/logo.psd
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex-umls.properties
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel.xml
A         ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/dictionary
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/dictionary/lookup
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_SNOMED.template.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_stem_SNOMED.template.xml
A         ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/negex
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/negex/negex_triggers.txt
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/negex/negex_triggers_orig.txt
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex-default.properties
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel.hbm.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.orcl.example
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mssql.example
A         ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/conceptGraph
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.template.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/conceptGraph/sct-msh-csp-aod.template.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/conceptGraph/sct-umls.template.xml
A         ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search.mysql.properties
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-kernel-simweb.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search-msh.mysql.properties
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search-sct.mysql.properties
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-security.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-ws.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search.mssql.properties
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search.orcl.properties
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-web.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/messages.properties
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-datasource.xml
A         ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/umls
A         ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/umls/model
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/umls/model/FWord.hbm.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/umls/model/UMLS.hbm.template.xml
A         ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernel
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernel/ehcache.xml
A         ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernel/model
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernel/model/KernelEvaluation.hbm.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernel/model/ClassifierEvaluation.hbm.xml
A         
ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mysql.example
A         ctakes-ytex-res/src/main/resources/ehcache.xml
A         ctakes-ytex-res/src/test
A         ctakes-ytex-res/src/test/resources
A         ctakes-ytex-res/src/test/resources/org
A         ctakes-ytex-res/src/test/resources/org/apache
A         ctakes-ytex-res/src/test/resources/org/apache/ctakes
A         ctakes-ytex-res/src/test/resources/org/apache/ctakes/ytex
A         ctakes-ytex-res/src/test/resources/org/apache/ctakes/ytex/dictionary
A         
ctakes-ytex-res/src/test/resources/org/apache/ctakes/ytex/dictionary/lookup
A         ctakes-ytex-res/pom.xml
A         ctakes-clinical-pipeline
A         ctakes-clinical-pipeline/LICENSE
A         ctakes-clinical-pipeline/src
A         ctakes-clinical-pipeline/src/main
A         ctakes-clinical-pipeline/src/main/java
A         ctakes-clinical-pipeline/src/main/java/org
A         ctakes-clinical-pipeline/src/main/java/org/apache
A         ctakes-clinical-pipeline/src/main/java/org/apache/ctakes
A         
ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline
AU        
ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
A         
ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime
AU        
ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java
AU        
ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfCUIsGenerator.java
A         
ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae
A         
ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java
A         
ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java
A         ctakes-clinical-pipeline/src/test
A         ctakes-clinical-pipeline/src/test/data
A         ctakes-clinical-pipeline/src/test/data/output
A         ctakes-clinical-pipeline/src/test/data/output/NotesIIST_RTF.DTD
A         
ctakes-clinical-pipeline/src/test/data/output/testpatient_cn_1.xml.included.xml
A         ctakes-clinical-pipeline/src/test/data/testpatient_cn_1.xml
A         ctakes-clinical-pipeline/src/test/data/testpatient_cn_2.xml
A         ctakes-clinical-pipeline/src/test/data/plaintext
A         
ctakes-clinical-pipeline/src/test/data/plaintext/testpatient_plaintext_1.txt
A         
ctakes-clinical-pipeline/src/test/data/plaintext/testpatient_plaintext_2.txt
A         ctakes-clinical-pipeline/src/test/data/plaintext/sample_note_plaintext
A         ctakes-clinical-pipeline/data
A         ctakes-clinical-pipeline/data/input
A         ctakes-clinical-pipeline/data/output
A         ctakes-clinical-pipeline/pom.xml
A         ctakes-clinical-pipeline/resources
A         ctakes-clinical-pipeline/resources/launch
AU        
ctakes-clinical-pipeline/resources/launch/UIMA_CPE_GUI--clinical_documents_pipeline.launch
AU        
ctakes-clinical-pipeline/resources/launch/UIMA_CVD--clinical_documents_pipeline.launch
A         ctakes-clinical-pipeline/SystemArchitectureOverview.txt
A         ctakes-clinical-pipeline/README
A         ctakes-clinical-pipeline/desc
A         ctakes-clinical-pipeline/desc/analysis_engine
A         ctakes-clinical-pipeline/desc/analysis_engine/auto
A         ctakes-clinical-pipeline/desc/analysis_engine/auto/defaultPipeline.xml
A         ctakes-clinical-pipeline/desc/analysis_engine/MaxLookupWindows.xml
A         ctakes-clinical-pipeline/desc/analysis_engine/NegationAnnotator.xml
A         
ctakes-clinical-pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml
A         
ctakes-clinical-pipeline/desc/analysis_engine/AggregateCdaProcessor.xml
AU        
ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml
A         
ctakes-clinical-pipeline/desc/analysis_engine/AggregateCdaUMLSProcessor.xml
A         
ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor.xml
A         
ctakes-clinical-pipeline/desc/analysis_engine/CuisOnlyPlaintextUMLSProcessor.xml
A         
ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml
A         ctakes-clinical-pipeline/desc/analysis_engine/NP2LookupWindow.xml
A         ctakes-clinical-pipeline/desc/analysis_engine/assertion_training_steps
A         
ctakes-clinical-pipeline/desc/analysis_engine/assertion_training_steps/AggregatePlaintextUMLSProcessor__no_dictionary_no_assertion.xml
A         
ctakes-clinical-pipeline/desc/analysis_engine/SimpleSegmentAnnotator.xml
A         
ctakes-clinical-pipeline/desc/analysis_engine/LookupWindowAnnotator.xml
A         ctakes-clinical-pipeline/desc/collection_processing_engine
A         
ctakes-clinical-pipeline/desc/collection_processing_engine/test_plaintext.xml
A         ctakes-clinical-pipeline/desc/collection_processing_engine/test1.xml
A         
ctakes-clinical-pipeline/desc/collection_processing_engine/assertion_training_steps
A         
ctakes-clinical-pipeline/desc/collection_processing_engine/assertion_training_steps/process_gold_assertion_data.xml
A         
ctakes-clinical-pipeline/desc/collection_processing_engine/test_cda.xml
A         ctakes-constituency-parser
A         ctakes-constituency-parser/conf
A         ctakes-constituency-parser/doc
A         ctakes-constituency-parser/scripts
A         ctakes-constituency-parser/scripts/groovy
AU        ctakes-constituency-parser/scripts/groovy/parser.groovy
A         ctakes-constituency-parser/src
A         ctakes-constituency-parser/src/main
A         ctakes-constituency-parser/src/main/java
A         ctakes-constituency-parser/src/main/java/org
A         ctakes-constituency-parser/src/main/java/org/apache
A         ctakes-constituency-parser/src/main/java/org/apache/ctakes
A         
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency
A         
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser
A         
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae
A         
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ParserEvaluationAnnotator.java
A         
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java
A         
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java
A         
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/uima
A         
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/uima/co
A         
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/uima/co/ParserTreeWriterConsumer.java
A         
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ParserWrapper.java
A         
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util
A         
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/AnnotationTreeUtils.java
A         
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/TreeUtils.java
AU        
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/CommandLineParserUtil.java
A         
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/treekernel
A         
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/treekernel/TreeExtractor.java
A         
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/treekernel/TreeKernel.java
A         ctakes-constituency-parser/src/main/resources
A         ctakes-constituency-parser/src/main/resources/org
A         ctakes-constituency-parser/src/main/resources/org/apache
A         ctakes-constituency-parser/src/main/resources/org/apache/ctakes
A         
ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency
A         
ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser
A         
ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/types
A         
ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml
A         ctakes-constituency-parser/data
A         ctakes-constituency-parser/data/test
A         ctakes-constituency-parser/data/test/testfakenote.txt
A         ctakes-constituency-parser/data/test/output
A         ctakes-constituency-parser/data/test/output/testfakenote.xml
A         ctakes-constituency-parser/pom.xml
A         ctakes-constituency-parser/resources
A         ctakes-constituency-parser/resources/launch
AU        ctakes-constituency-parser/resources/launch/UIMA_CPE--Constituency 
Parser.launch
AU        ctakes-constituency-parser/resources/launch/UIMA_CVD--Constituency 
Parser.launch
A         ctakes-constituency-parser/README
A         ctakes-constituency-parser/desc
A         ctakes-constituency-parser/desc/analysis_engine
A         
ctakes-constituency-parser/desc/analysis_engine/ParserEvaluatorAnnotator.xml
A         
ctakes-constituency-parser/desc/analysis_engine/AggregateParsingProcessor.xml
A         ctakes-constituency-parser/desc/ConstituencyParserAnnotator.xml
A         ctakes-constituency-parser/desc/collection_processing_engine
A         
ctakes-constituency-parser/desc/collection_processing_engine/ParsingCPE.xml
A         ctakes-constituency-parser/desc/cas_consumer
A         
ctakes-constituency-parser/desc/cas_consumer/ParseTreeWriterConsumer.xml
A         ctakes-constituency-parser/metadata
A         ctakes-constituency-parser/metadata/install.xml
A         ctakes-constituency-parser/LICENSE
 U        .
At revision 1765003

Parsing POMs
ERROR: Failed to parse POMs
java.io.IOException: remote file operation failed: 
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/> at 
hudson.remoting.Channel@153124c:H10: hudson.remoting.ProxyException: 
hudson.maven.MavenModuleSetBuild$MavenExecutionException: 
org.apache.maven.project.ProjectBuildingException: Some problems were 
encountered while processing the POMs:
[ERROR] Child module 
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-examples-res/pom.xml>
 of <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/pom.xml> does 
not exist @ 

        at hudson.FilePath.act(FilePath.java:1014)
        at hudson.FilePath.act(FilePath.java:996)
        at 
hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.parsePoms(MavenModuleSetBuild.java:960)
        at 
hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.doRun(MavenModuleSetBuild.java:679)
        at 
hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:534)
        at hudson.model.Run.execute(Run.java:1741)
        at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:531)
        at hudson.model.ResourceController.execute(ResourceController.java:98)
        at hudson.model.Executor.run(Executor.java:410)
Caused by: hudson.remoting.ProxyException: 
hudson.maven.MavenModuleSetBuild$MavenExecutionException: 
org.apache.maven.project.ProjectBuildingException: Some problems were 
encountered while processing the POMs:
[ERROR] Child module 
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-examples-res/pom.xml>
 of <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/pom.xml> does 
not exist @ 

        at 
hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1364)
        at 
hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1098)
        at hudson.FilePath$FileCallableWrapper.call(FilePath.java:2772)
        at hudson.remoting.UserRequest.perform(UserRequest.java:153)
        at hudson.remoting.UserRequest.perform(UserRequest.java:50)
        at hudson.remoting.Request$2.run(Request.java:332)
        at 
hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:68)
        at java.util.concurrent.FutureTask.run(FutureTask.java:262)
        at 
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at 
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:745)
        at ......remote call to H10(Native Method)
        at hudson.remoting.Channel.attachCallSiteStackTrace(Channel.java:1416)
        at hudson.remoting.UserResponse.retrieve(UserRequest.java:253)
        at hudson.remoting.Channel.call(Channel.java:781)
        at hudson.FilePath.act(FilePath.java:1007)
        ... 8 more
Caused by: hudson.remoting.ProxyException: 
org.apache.maven.project.ProjectBuildingException: Some problems were 
encountered while processing the POMs:
[ERROR] Child module 
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-examples-res/pom.xml>
 of <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/pom.xml> does 
not exist @ 

        at 
org.apache.maven.project.DefaultProjectBuilder.build(DefaultProjectBuilder.java:364)
        at hudson.maven.MavenEmbedder.buildProjects(MavenEmbedder.java:361)
        at hudson.maven.MavenEmbedder.readProjects(MavenEmbedder.java:331)
        at 
hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1301)
        at 
hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1098)
        at hudson.FilePath$FileCallableWrapper.call(FilePath.java:2772)
        at hudson.remoting.UserRequest.perform(UserRequest.java:153)
        at hudson.remoting.UserRequest.perform(UserRequest.java:50)
        at hudson.remoting.Request$2.run(Request.java:332)
        at 
hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:68)
        at java.util.concurrent.FutureTask.run(FutureTask.java:262)
        at 
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at 
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:745)

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