├── .gitignore ├── LICENSE.txt ├── README.md ├── aggregate-container ├── Dockerfile ├── GenerateDeploymentDescriptors.java ├── Logging.properties ├── deploy.sh ├── deployAsyncService.sh └── desc │ ├── aggregateDeploymentDescriptor.xml │ ├── docker-fast-dictionary.xml │ ├── docker-mist.xml │ ├── docker-writer.xml │ ├── nodeidDeploymentDescriptor.xml │ ├── remoteFull.xml │ └── remoteNoDeid.xml ├── amq-broker ├── Dockerfile ├── bin │ └── env ├── conf │ ├── activemq-nojournal.xml │ ├── credentials-enc.properties │ ├── credentials.properties │ ├── log4j.properties │ └── logging.properties └── startBroker.sh ├── bin ├── launch-N-aws-instances.sh ├── launch_cluster.py ├── runAggregateContainer.sh ├── runBrokerContainer.sh ├── runFilereaderContainer.sh ├── runMistContainer.sh ├── runMongoContainer.sh ├── runPipelineContainer.sh ├── runReaderContainer.sh ├── runRemoteAsyncAE.sh ├── runWriterContainer.sh ├── stop_cluster.py └── terminate_cluster.py ├── ctakes-as-pipeline ├── DefaultDictionaryLookupSpec.xml ├── DeidAwareTermConsumer.java ├── Dockerfile ├── IgnorableSectionAnnotator.java ├── Logging.properties ├── MultipleDictionaryLookupSpecExample.xml ├── UmlsLookupAnnotator.xml ├── deploy.sh ├── deployAsyncService.sh ├── desc │ ├── NonIgnorableSegmentAnnotator.xml │ ├── deploymentDescriptor.xml │ ├── dictionaryPipeline.xml │ └── nodeidPipeline.xml ├── log4j-1.2.17.jar ├── lookup-descriptor-template.xml └── wrapper.sh ├── desc ├── FilesInDirectoryCollectionReader.xml ├── TypeSystem.xml ├── docker-fast-dictionary.xml ├── docker-mist.xml ├── docker-writer.xml ├── i2b2CollectionReader.xml ├── localDeploymentDescriptor.xml ├── localDeploymentDescriptorNoDeid.xml ├── remoteFull.xml ├── remoteMist.xml └── remoteNoDeid.xml ├── env_file_sample.txt ├── example.config.txt ├── file-reader ├── Dockerfile ├── Logging.properties ├── XmlFixingFilesInDirectoryCollectionReader.java ├── deploy.sh ├── desc │ ├── FilesInDirectoryCollectionReader.xml │ ├── docker-fast-dictionary.xml │ ├── docker-mist.xml │ ├── docker-writer.xml │ ├── localDeploymentDescriptor.xml │ └── remoteFull.xml └── runRemoteAsyncAE.sh ├── i2b2-reader ├── CreateDbReaderDescriptor.java ├── Dockerfile ├── Logging.properties ├── MemReleaseI2b2CollectionReader.java ├── deploy.sh ├── desc │ ├── docker-fast-dictionary.xml │ ├── docker-mist.xml │ ├── docker-writer.xml │ ├── localDeploymentDescriptor.xml │ └── remoteFull.xml └── runRemoteAsyncAE.sh ├── i2b2-writer ├── AbstractJdbcWriter.java ├── CreateDbWriterDescriptor.java ├── Dockerfile ├── I2b2JdbcWriter.java ├── I2b2ReadyFileWriter.java ├── Logging.properties ├── commons-io-2.2.jar ├── commons-lang-2.6.jar ├── commons-logging-1.1.1.jar ├── ctakes-core-4.0.0.jar ├── ctakes-type-system-4.0.0.jar ├── deploy.sh ├── deployAsyncService.sh ├── desc │ ├── deploymentDescriptor.xml │ ├── i2b2ReadyFileWriter.xml │ └── i2b2Writer.xml ├── log4j-1.2.17.jar ├── spring-beans-3.1.2.RELEASE.jar ├── spring-core-3.1.2.RELEASE.jar └── 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