using cTAKES to parse clinical documents

Question

I am trying to figure out how to run the Clinical Document Pipeline from Java. I have a set of clinical documents as plain texts. I want to parse these documents and extract a list of that is in document doc_ID, there is CUI with frequency of freq. I spent several days installing cTAKES and looking for a solution. I narrow it down to ClinicalPipelineWithUmls.java where gets a test and runs SimplePipeline with a AnaylisisEngineDescription. Here is a part of the code:

String documentText = "Text of document to test goes here, such as the following. No edema, some soreness, denies pain.";
InputStream inStream = InputStreamCollectionReader.convertToByteArrayInputStream(documentText);
CollectionReader collectionReader = InputStreamCollectionReader.getCollectionReader(inStream);
AnalysisEngineDescription pipelineIncludingUmlsDictionaries = AnalysisEngineFactory.createAnalysisEngineDescription(
            "desc/analysis_engine/AggregatePlaintextUMLSProcessor");
AnalysisEngineDescription xWriter = AnalysisEngineFactory.createPrimitiveDescription(
            XWriter.class,
            XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
            AssertionConst.evalOutputDir,
            XWriter.PARAM_XML_SCHEME_NAME,
            XWriter.XMI,
            XWriter.PARAM_FILE_NAMER_CLASS_NAME,
            CtakesFileNamer.class.getName());
SimplePipeline.runPipeline(collectionReader, pipelineIncludingUmlsDictionaries, xWriter);
System.out.println("Done at " + new Date());

The problem is it can not find "InputStreamCollectionReader". I searched for it but no success so far! Would you please give me a hint or show some directions? thanks for any help!

Answer 1

Is there any particular reason why you want to use InputStreamCollectionReader? Otherwise, there are examples on how to use TextReader here.