See <https://builds.apache.org/job/ctakes-trunk-compiletest/1101/display/redirect?page=changes>
Changes: [seanfinan] DocumentIDAnnotationUtil can now fetch idPrefix, useful for patient id NumberedSuffixComparator to compare text and number strings logically - "abc1" < "abc10" Add patient package for multi-document patient handling AbstractPatientConsumer processes when patients are complete PatientNoteCollector AE sends patient document cas to a cache PatientNoteStore caches documents into views in a common patient cas PatientViewUtil utilities for fetching cas views and view names. Could be named "CasViewUtil" and moved MentionClusterCoreferenceAnnotator added notYetProcess() for Tim to review PatientMentionClusterCoreferencer extends AbstractPatientConsumer and delegates to MentionClusterCoreferenceAnnotator ------------------------------------------ [...truncated 320.51 KB...] A ctakes-relation-extractor/src/test A ctakes-relation-extractor/src/test/java A ctakes-relation-extractor/src/test/java/org A ctakes-relation-extractor/src/test/java/org/apache A ctakes-relation-extractor/src/test/java/org/apache/ctakes A ctakes-relation-extractor/src/test/java/org/apache/ctakes/relationextractor A ctakes-relation-extractor/src/test/java/org/apache/ctakes/relationextractor/ae AU ctakes-relation-extractor/src/test/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotatorsTest.java AU ctakes-relation-extractor/src/test/java/org/apache/ctakes/relationextractor/ae/NamedEntityFeaturesExtractorTest.java A ctakes-relation-extractor/docs A ctakes-relation-extractor/docs/knowtator.txt A ctakes-relation-extractor/docs/readme.txt A ctakes-relation-extractor/docs/todo.txt A ctakes-relation-extractor/pom.xml A ctakes-relation-extractor/resources A ctakes-relation-extractor/resources/launch AU ctakes-relation-extractor/resources/launch/UIMA_CVD--relation-extractor.launch AU ctakes-relation-extractor/resources/launch/UIMA_CPE--relation-extractor.launch A ctakes-relation-extractor/desc A ctakes-relation-extractor/desc/analysis_engine A ctakes-relation-extractor/desc/analysis_engine/LocationOfRelationExtractorAnnotator.xml A ctakes-relation-extractor/desc/analysis_engine/DegreeOfRelationExtractorAnnotator.xml A ctakes-relation-extractor/desc/analysis_engine/ModifierExtractorAnnotator.xml AU ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml AU ctakes-relation-extractor/desc/analysis_engine/RelationExtractorPreprocessor.xml A ctakes-relation-extractor/desc/analysis_engine/RemoteDictionary.xml A 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ctakes-preprocessor/src/main/java/edu/mayo A ctakes-preprocessor/src/main/java/edu/mayo/bmi A ctakes-preprocessor/src/main/java/edu/mayo/bmi/uima A ctakes-preprocessor/src/main/java/org A ctakes-preprocessor/src/main/java/org/apache A ctakes-preprocessor/src/main/java/org/apache/ctakes A ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor A ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/Annotation.java A ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/IntegerRange.java A ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/ClinicalNotePreProcessor.java A ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/DocumentMetaData.java A ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/test A ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/test/TestDriver.java A ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/DTDloader.java A ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/SegmentMetaData.java A ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/Utility.java A ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/ae A ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/ae/CdaCasInitializer.java A ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/PreProcessor.java A ctakes-preprocessor/src/main/resources A ctakes-preprocessor/src/main/resources/org A ctakes-preprocessor/src/main/resources/org/apache A ctakes-preprocessor/src/main/resources/org/apache/ctakes A ctakes-preprocessor/src/main/resources/org/apache/ctakes/preprocessor A ctakes-preprocessor/src/main/resources/org/apache/ctakes/preprocessor/cda A ctakes-preprocessor/src/main/resources/org/apache/ctakes/preprocessor/cda/NotesIIST_RTF.DTD A ctakes-preprocessor/src/main/resources/org/apache/ctakes/preprocessor/tokenizer A 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ctakes-smoking-status/desc/analysis_engine/ResolutionAnnotator.xml AU ctakes-smoking-status/desc/analysis_engine/PcsClassifierAnnotator_libsvm.xml AU ctakes-smoking-status/desc/analysis_engine/ExternalBaseAggregateTAE.xml AU ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE.xml AU ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml AU ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.xml AU ctakes-smoking-status/desc/analysis_engine/NonsmokerDictionaryLookupAnnotator.xml AU ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml AU ctakes-smoking-status/desc/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml AU ctakes-smoking-status/desc/analysis_engine/ArtificialSentenceAnnotator.xml AU ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step1.xml AU ctakes-smoking-status/desc/analysis_engine/Sentence.xml AU ctakes-smoking-status/desc/analysis_engine/ExternalBaseAggregateTAE_CDA.xml AU ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE_CDA.xml AU ctakes-smoking-status/desc/analysis_engine/SentenceAdjuster.xml A ctakes-smoking-status/desc/collection_processing_engine AU ctakes-smoking-status/desc/collection_processing_engine/Sample_SmokingStatus_output_flatfile.xml AU ctakes-smoking-status/desc/collection_processing_engine/Sample_SmokingStatus_output_cda.xml A ctakes-smoking-status/metadata AU ctakes-smoking-status/metadata/PEAR.properties AU ctakes-smoking-status/metadata/setenv.txt AU ctakes-smoking-status/metadata/install.xml AU ctakes-smoking-status/LICENSE A ctakes-smoking-status/src A ctakes-smoking-status/src/main A ctakes-smoking-status/src/main/java A ctakes-smoking-status/src/main/java/org A ctakes-smoking-status/src/main/java/org/apache A ctakes-smoking-status/src/main/java/org/apache/ctakes A ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus A ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup A ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae AU ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/NonSmokerNamedEntityLookupConsumerImpl.java AU ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/SmokerNamedEntityLookupConsumerImpl.java AU ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/UnknownSmokerNamedEntityLookupConsumerImpl.java A ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/patientLevel AU ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/patientLevel/PatientLevelSmokingStatus.java A ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/util AU ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/util/ClassifiableEntry.java AU ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/util/TruthValue.java A ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/i2b2 A ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context AU ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/NamedEntityContextAnalyzer.java A ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/negation AU ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/negation/NegationContextAnalyzer.java A ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/machine AU ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/machine/NegationFSM.java A ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae AU ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ClassifiableEntries.java AU ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/PcsClassifierAnnotator_libsvm.java AU ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/KuRuleBasedClassifierAnnotator.java AU ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/SentenceAdjuster.java AU ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ResolutionAnnotator.java A ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/cc AU ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/cc/RecordResolutionCasConsumer.java AU ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/Const.java A ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil AU ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.java A ctakes-smoking-status/src/main/resources A ctakes-smoking-status/src/main/resources/org A ctakes-smoking-status/src/main/resources/org/apache A ctakes-smoking-status/src/main/resources/org/apache/ctakes A ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus A ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types A ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml A ctakes-smoking-status/data A ctakes-smoking-status/data/test A ctakes-smoking-status/data/test/output AU ctakes-smoking-status/data/test/output/record_resolution.txt AU ctakes-smoking-status/data/test/doc1_07543210_sample_past_smoker.txt AU ctakes-smoking-status/data/test/doc2_07543210_sample_past_smoker.txt A ctakes-smoking-status/data/test/cda A ctakes-smoking-status/data/test/cda/testpatient_cn_1.xml AU ctakes-smoking-status/data/test/doc1_07543210_sample_unknown.txt AU ctakes-smoking-status/data/test/doc1_07543210_sample_current.txt AU ctakes-smoking-status/data/test/doc2_07543210_sample_current.txt A ctakes-smoking-status/launch AU ctakes-smoking-status/launch/UIMA_CPE_GUI--Smokin_Status.launch AU ctakes-smoking-status/launch/UIMA CPE GUI (SmokingStatus).launch AU ctakes-smoking-status/launch/UIMA CAS Visual Debugger (Smoking Status).launch A ctakes-smoking-status/pom.xml AU ctakes-smoking-status/README A ctakes-assertion-zoner-res A ctakes-assertion-zoner-res/src A ctakes-assertion-zoner-res/src/test A ctakes-assertion-zoner-res/src/main A ctakes-assertion-zoner-res/src/main/resources A ctakes-assertion-zoner-res/src/main/resources/META-INF A ctakes-assertion-zoner-res/src/main/resources/META-INF/org.apache.uima.fit A ctakes-assertion-zoner-res/src/main/resources/META-INF/org.apache.uima.fit/types.txt A ctakes-assertion-zoner-res/src/main/resources/org A ctakes-assertion-zoner-res/src/main/resources/org/mitre A ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts A ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima A ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.xml.bak A ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/mayo_sections.xml A ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.04162012.xml A ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.xml.bak2 A ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.06162011.xml A ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.xml A ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.out.xml A ctakes-assertion-zoner-res/pom.xml A ctakes-assertion-zoner-res/LICENSE U . At revision 1809920 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@76e412b9:H27: hudson.remoting.ProxyException: hudson.maven.MavenModuleSetBuild$MavenExecutionException: org.apache.maven.project.ProjectBuildingException: Some problems were encountered while processing the POMs: [ERROR] Child module <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-scaleout> of <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/pom.xml> does not exist @ at hudson.FilePath.act(FilePath.java:993) at hudson.FilePath.act(FilePath.java:975) at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.parsePoms(MavenModuleSetBuild.java:985) at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.doRun(MavenModuleSetBuild.java:690) at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:490) at hudson.model.Run.execute(Run.java:1735) at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:542) at hudson.model.ResourceController.execute(ResourceController.java:97) at hudson.model.Executor.run(Executor.java:405) Caused by: hudson.remoting.ProxyException: hudson.maven.MavenModuleSetBuild$MavenExecutionException: org.apache.maven.project.ProjectBuildingException: Some problems were encountered while processing the POMs: [ERROR] Child module <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-scaleout> of <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/pom.xml> does not exist @ at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1389) at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1123) at hudson.FilePath$FileCallableWrapper.call(FilePath.java:2739) at hudson.remoting.UserRequest.perform(UserRequest.java:153) at hudson.remoting.UserRequest.perform(UserRequest.java:50) at hudson.remoting.Request$2.run(Request.java:336) at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:68) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:748) at ......remote call to H27(Native Method) at hudson.remoting.Channel.attachCallSiteStackTrace(Channel.java:1545) at hudson.remoting.UserResponse.retrieve(UserRequest.java:253) at hudson.remoting.Channel.call(Channel.java:830) at hudson.FilePath.act(FilePath.java:986) ... 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-scaleout> 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$PomParser.invoke(MavenModuleSetBuild.java:1326) at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1123) at hudson.FilePath$FileCallableWrapper.call(FilePath.java:2739) at hudson.remoting.UserRequest.perform(UserRequest.java:153) at hudson.remoting.UserRequest.perform(UserRequest.java:50) at hudson.remoting.Request$2.run(Request.java:336) at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:68) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:748)
