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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: Question about the pipeline
Date Thu, 05 Feb 2015 14:08:53 GMT
Hi Maite,

Without more information I can't venture a guess as to a cause of the error.  If RunCPE works
then why not use that?  They are practically identical.

Sean
________________________________________
From: Maite Meseure Hugues [meseure.maite@gmail.com]
Sent: Thursday, February 05, 2015 8:51 AM
To: dev@ctakes.apache.org
Subject: Re: Question about the pipeline

I see. In my case, I am using the CPE descriptor saved from the GUI for
CmdLineCpeRunner as said Sean. I've selected
AggregatePlaintextProcessor.xml as AE but I have this error:

"Couldn't initialize processing engine.

  Initialization of CAS Processor with name "AggregatePlaintextProcessor"
failed. "

Meanwhile, RunCPE.java works properly with the same descriptor in Eclipse.
Does anyone have an idea?

On Wed, Feb 4, 2015 at 12:56 PM, Lingren, Todd <Todd.Lingren@cchmc.org>
wrote:

> Hi Maite,
> For each patient in my list, I create a new FilesToFiles CPE xml using
> some sed commands on the template original.
>
> Specifically, here's the command line argument (I'm on linux).
>
> CTAKES_HOME=...
> java -cp $CTAKES_HOME/lib/*:$CTAKES_HOME/desc/:$CTAKES_HOME/resources/
> -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx2048M
> CmdLineCpeRunner FilesToFiles_patient_cui.xml > outputfile.txt
>
> I don't think it matters, but I'm using the cTAKES 3.1.0 version.
>
>
> Todd Lingren
> Biomedical Informatics
> Cincinnati Children’s Hospital
> Todd.Lingren@cchmc.org
> 513-803-9032
>
>
> -----Original Message-----
> From: Maite Meseure Hugues [mailto:meseure.maite@gmail.com]
> Sent: Wednesday, February 04, 2015 12:59 PM
> To: dev@ctakes.apache.org
> Subject: Re: Question about the pipeline
>
> Interesting, Todd thank you and how do you use CMdLineCpeRunner basically?
> Because I tested in cmd line with:
>
> java org.apache.ctakes.core.cpe.CmdLineCpeRunner [path-to-my-cpe.xml]
>
> but here is that I've got:
>
>
> Exception in thread "main" java.lang.NoClassDefFoundError:
> org/apache/uima/util/InvalidXMLException
>
> at java.lang.Class.getDeclaredMethods0(Native Method)
>
> at java.lang.Class.privateGetDeclaredMethods(Class.java:2693)
>
> at java.lang.Class.privateGetMethodRecursive(Class.java:3040)
>
> at java.lang.Class.getMethod0(Class.java:3010)
>
> at java.lang.Class.getMethod(Class.java:1776)
>
> at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
>
> at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
>
> .......
>
> On Wed, Feb 4, 2015 at 8:32 AM, Lingren, Todd <Todd.Lingren@cchmc.org>
> wrote:
>
> > Sean and Maite,
> > FWIW, I use CmdLineCpeRunner frequently. I employ it with a bash
> > script to automatically create a new xml file based on the subfolder
> > names contained in the target directory. So in our HPC, it spawns a
> > new job for each subfolder (which may have between 5 and 2500 notes).
> >
> > Todd Lingren
> > Biomedical Informatics
> > Cincinnati Children’s Hospital
> > Todd.Lingren@cchmc.org
> > 513-803-9032
> >
> >
> > -----Original Message-----
> > From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> > Sent: Tuesday, February 03, 2015 2:47 PM
> > To: dev@ctakes.apache.org
> > Subject: RE: Question about the pipeline
> >
> > Hi Maite,
> >
> > RunCPE is a good find, and if it fits your bil hten you should use it.
> > But it (if you mean the yTex class) doesn't take input and output
> > directories from the command line.  It does take the path to a CPE.xml
> > file.  There is a cTakes (non-yTex) equivalent named CmdLineCpeRunner.
> > Either one of them should print a usage if you run it without arguments.
> > As the CmdLineCpeRunner indicates, you can create a cpe .xml file with
> > the cpe gui.  Basically, start the cpe gui, select your input
> > (reader), output
> > (writer) and pipeline (ae) in the gui and then save the cpe descriptor
> > (via the menubar).  You can exit the gui and run either one of the cmd
> > line utilities with the path to that cpe .xml descriptor as the argument.
> > Please note: sometimes you have to explicitly type ".xml" in the
> > filename when saving with the cpe gui.  If you run with the cpe gui
> > and then exit it should automatically ask you if you want to save the
> cpe .xml descriptor.
> > Anyway, once you have the .xml file you can always edit the input and
> > output paths in that file to change your run parameters.
> >
> > Sean
> >
> > -----Original Message-----
> > From: Maite Meseure Hugues [mailto:meseure.maite@gmail.com]
> > Sent: Tuesday, February 03, 2015 9:01 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: Question about the pipeline
> >
> > Thanks a lot Sean for your detailed reply. I've also found RunCPE.java
> > that allows to put the input and outpur directories in arguments in
> > the environment and do the same job than the CPE-GUI -at least in
> > Eclipse, I haven't managed to run it via the command line yet.
> >
> > On Mon, Feb 2, 2015 at 7:12 PM, Finan, Sean <
> > Sean.Finan@childrens.harvard.edu> wrote:
> >
> > > Hi Tol (and Maite),
> > >
> > > I'm not entirely certain that I understand the question, but here is
> > > an attempt to help.  If I'm oversimplifying then I apologize.
> > >
> > > I think that ExampleAggregatePipeline is intended to represent a
> > > very simple single-note pipeline and that custom code could be
> > > produced by using it as an example.
> > >
> > > If you want to process texts in a directory, you can find with a web
> > > search plenty of ways to list files in a directory and read text
> > > from files.
> > > org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader
> > > might be what you used in the CPE, and you can certainly peruse the
> > > code and take what you need.  Or, if you decide to write a simple
> > > diy, here is one
> > > possibility:
> > >
> > > Static public Collection<File> getFilesInDir( final File directory )
{
> > >    final Collection<File> fileList = new ArrayList<>();
> > >    final File[] fileList = directory.listFiles();
> > >    if ( fileList == null ) {
> > >       System.err.println( "please check the directory " +
> > > directory.getAbsolutePath() );
> > >       System.exit( 1 );
> > >    }
> > >     for ( final File file : directory.listFiles() ) {
> > >         if ( file.canRead() ) {
> > >             fileList.add( file );
> > >         }
> > >     }
> > > }
> > >
> > > Static public String getTextInFile( final File file ) throws
> IOException
> > > {   -- or handle ioE herein
> > >    final Path nioPath = file.toPath();
> > >    return new String( Files.readAllBytes( nioPath ) ); }
> > >
> > > Static public void main( String ... args ) {
> > >    If ( args[0].isEmpty() ) {
> > >       System.out.println( "Enter a directory path" );
> > >       System.exit( 0 );
> > >    }
> > >    Final Collection<File> files = getFilesInDir( new File( args[0] );
> > >    For ( File file : files ) {
> > >       Final String note = getTextInFile( file );
> > >       ---  Insert here code a' la ExampleAggregatePipeline  ---
> > >       ---  swap out the writer in ExampleAggregatePipeline with
> > > CasIOUtil method (below)  ---
> > >    }
> > > }
> > >
> > > I must admit that I have never directly used it, but there is an xmi
> > > file writing method in org.apache.uima.fit.util.CasIOUtil named
> > > writeXmi( JCas jCas, File file ).  You could give this a try and see
> > > if it produces the type of output that you want.  The same utility
> > > class has a writeXCas(..) method.
> > >
> > >
> > > If the above has absolutely nothing to do with your needs then
> > > please send me a bulleted list of items, example workflow, etc. and
> > > I'll see if I can be of service.
> > >
> > > Oh, and I wrote the above code freehand, so MS Outlook is adding
> > > capital letters, etc.  If you cut and paste you'll need to change
> > > that
> > > - plus I haven't run/compiled, so there might be a typo or missed
> > > exception or something.  Or it may not work (in which case I'll
> > > throw in a little more effort).
> > >
> > > Sean
> > >
> > >
> > > -----Original Message-----
> > > From: Tol O. [mailto:toltox@gmail.com]
> > > Sent: Monday, February 02, 2015 6:56 PM
> > > To: dev@ctakes.apache.org
> > > Subject: Re: Question about the pipeline
> > >
> > > Maite Meseure Hugues <meseure.maite@...> writes:
> > >
> > > >
> > > > Hello all,
> > > >
> > > > Thank you for your preceding answers.
> > > > I have a few questions regarding the pipeline example to run
> > > > cTakes programmatically.
> > > > I am running ExampleAggregatePipeline.java with
> > > > ExampleHelloWorldAnnotator but I would like to know how I can
> > > > change it to run my data, as the CPE where we can choose the
> > > > directory of our
> > > data.
> > > > My second question is about the xml output generated with the CPE,
> > > > can I get the same xml output in using the example pipeline? and How?
> > > > Thanks for your time.
> > >
> > >
> > > I would like to ask the same question. After successfully setting up
> > > CTAKES following the Developers Guide I would also like to use a
> > > modified ExampleAggregatePipeline to output a CAS file identical to
> > > the output obtained by the CPE or the CVD when following the Users
> Guide.
> > >
> > > This would be a great help for developers as a starting class to be
> > > able to programmatically obtain an annotated file based on a
> > > plaintext or XML input, same as through the two GUIs.
> > >
> > > Right now I am reading through the Component Use Guide to replicate
> > > the CPE or the CVD tutorial with the test input, but it is a bit
> > overwhelming.
> > >
> > > Any pointers or suggestions would be really appreciated.
> > >
> > > Tol O.
> > >
> > >
> >
> >
> > --
> > --
> >  Maïté Meseure Hugues
> >
>
>
>
> --
> --
>  Maïté Meseure Hugues
>



--
--
 Maïté Meseure Hugues

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