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From "Lingren, Todd" <Todd.Ling...@cchmc.org>
Subject RE: Question about the pipeline
Date Wed, 04 Feb 2015 18:56:40 GMT
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
>



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 Maïté Meseure Hugues
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