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)
