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From Kirti Bhamare <kirti.bham...@zsassociates.com>
Subject RE: Need help to build java pipeline to call ctakes
Date Tue, 22 Jul 2014 13:13:45 GMT
Hi Abhishek ,

Thanks for your reply!

I think the one you mentioned is not the automated way, for that you need to run .bat file,
provide input path and all manually.
I want to automate this thing.
I am thinking can I write a java code which will call CVD/ CPE(any one of them) using collection
reader or something.

I am trying like this:

// specify the input directory-
CollectionReader collectionReader = CollectionReaderFactory.createCollectionReaderFromPath(
                                   "desc/ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml",
                                   FilesInDirectoryCollectionReader.PARAM_INPUTDIR,
                                   "resources1")
                       // make sure the model parameters match those used for training
AnalysisEngine relationExtractor = AnalysisEngineFactory.createAnalysisEngineFromPath(
                                   "C:/apache-ctakes-3.1.1/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml");
AnalysisEngine xWriter = AnalysisEngineFactory.createPrimitive(
                        XWriter.class,
                        XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
                        "output");
SimplePipeline.runPipeline(collectionReader, relationExtractor, xWriter);

Is anyone tried out such thing?

Thanks,
Kirti



From: Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in]
Sent: Tuesday, July 22, 2014 6:25 PM
To: user@ctakes.apache.org
Subject: Re: Need help to build java pipeline to call ctakes


*Run it with.
Assuming of course, you're working on Linux. If you're on windows, use the .bat file to run
CPE. When running CPE use the test_plaintext.xml descriptor with suitable processing engine
to process large number of documents. Hope that helps. :)

Abhishek Raj,

Bachelor of Technology,3rd year,

Department of Computer Science and Engineering,

Indian Institute of Technology Ropar.
On Jul 22, 2014 5:05 PM, "Kirti Bhamare" <kirti.bhamare@zsassociates.com<mailto:kirti.bhamare@zsassociates.com>>
wrote:
Hi all,
I am new to apache ctakes. I am able to run clinical pipeline using CVD. I want to automate
this process.
I want to build a java pipeline which will call analysis engine, process the input string(Input
Text may be medical note) and generate the XMI.
I searched a lot but not able to figure out how to use the API’s?
Can anyone help me with this?

Thanks in advance!

Regards,
Kirti



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