See <https://builds.apache.org/job/ctakes-trunk-package/475/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 [seanfinan] Add AttributesCleartkSubPipe.piper refactor other .piper files to use it [seanfinan] Added extraction/copy of TypeSystem.xml to the resources/ directory for binary packages. Necessary to use the CVD. Added * extensions to copy for README* etc. [dligach] added region-based data printer ------------------------------------------ Started by an SCM change [EnvInject] - Loading node environment variables. Building remotely on ubuntu-eu2 (Ubuntu ubuntu ubuntu-eu docker) in workspace <https://builds.apache.org/job/ctakes-trunk-package/ws/> Cleaning up <https://builds.apache.org/job/ctakes-trunk-package/ws/.> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/resources> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-context-tokenizer/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-dependency-parser/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-side-effect-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex-web/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-dictionary-lookup-fast/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-coreference/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-dependency-parser-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-clinical-pipeline-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-relation-extractor-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-chunker/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-dictionary-lookup-fast-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-drug-ner-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-drug-ner/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-smoking-status/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ne-contexts/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-pos-tagger/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-coreference-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion-zoner/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-clinical-pipeline/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-type-system/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-dictionary-lookup-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-core-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-lvg/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-pos-tagger-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-relation-extractor/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-chunker-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-core/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-smoking-status-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-regression-test/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-examples/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-dictionary-lookup/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex-uima/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-lvg-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-distribution/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion-zoner-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-template-filler/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-utils/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ne-contexts-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-constituency-parser/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-side-effect/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-preprocessor/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-constituency-parser-res/target> Updating http://svn.apache.org/repos/asf/ctakes/trunk at revision '2016-10-15T11:42:46.475 +0000' U ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper U ctakes-distribution/src/main/assembly/bin.xml U pom.xml A ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/pipeline A ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/pipeline/AttributesCleartkSubPipe.piper A ctakes-examples-res A ctakes-examples-res/src A ctakes-examples-res/src/main A ctakes-examples-res/src/main/resources A ctakes-examples-res/src/main/resources/org A ctakes-examples-res/src/main/resources/org/apache A ctakes-examples-res/src/main/resources/org/apache/ctakes A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/dr_nutritious_2.txt A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/shark_bite.txt A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/mother_goose A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/mother_goose/README A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/mother_goose/OneMistyMoistyMorning.txt A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-DVT_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_AAA_Leak_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_FebrileSez_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_PVD_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_LaborProgressNote_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-DVT.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_PROMCheck_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_Gen_Abscess_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-AAA_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_MVAPrego_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_IUD_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/GenSurg_UmbilicalHernia_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_RoutBirthNote_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_HysterectomyAndBSO_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_Dysphagia_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_FollowUp_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/right_knee_arthroscopy A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/claudication A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_past_smoker.txt A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc2_07543210_sample_past_smoker.txt A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_unknown.txt A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_current.txt A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc2_07543210_sample_current.txt A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/SampleInputRadiologyNotes.txt A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/pain_no_swelling.txt A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/cda A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/cda/testpatient_cn_1.xml A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/cda/testpatient_cn_2.xml A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/dr_nutritious_1.txt A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/edge_cases_plaintext_1.txt D ctakes-examples/data D ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPipeline.piper D ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldCuiPipeline.piper D ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.piper D ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPropsPipeline.piper D ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldAssertPropsPipeline.piper A ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkProps.piper A ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldProps.piper A ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldAssertProps.piper A ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorld.piper A ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldCui.piper A ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/ProcessDir.piper U ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsPiperRunner.java A ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirBuilderRunner.java U ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPiperRunner.java U ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiPiperRunner.java A ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirPiperRunner.java U ctakes-examples/pom.xml U ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventEventRelPrinter.java U ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java At revision 1765036 Parsing POMs ERROR: Failed to parse POMs java.io.IOException: remote file operation failed: <https://builds.apache.org/job/ctakes-trunk-package/ws/> at hudson.remoting.Channel@1b735c02:ubuntu-eu2: hudson.remoting.ProxyException: hudson.maven.MavenModuleSetBuild$MavenExecutionException: org.apache.maven.project.ProjectBuildingException: Some problems were encountered while processing the POMs: [ERROR] Child module <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-examples-res/pom.xml> of <https://builds.apache.org/job/ctakes-trunk-package/ws/pom.xml> does not exist @ at hudson.FilePath.act(FilePath.java:1014) at hudson.FilePath.act(FilePath.java:996) at hudson.maven.MavenModuleSetBuild$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$MavenExecutionException: org.apache.maven.project.ProjectBuildingException: Some problems were encountered while processing the POMs: [ERROR] Child module <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-examples-res/pom.xml> of <https://builds.apache.org/job/ctakes-trunk-package/ws/pom.xml> does not exist @ at hudson.maven.MavenModuleSetBuild$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 ubuntu-eu2(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-package/ws/ctakes-examples-res/pom.xml> of <https://builds.apache.org/job/ctakes-trunk-package/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)