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Posted to dev@ctakes.apache.org by "Tol O." <to...@gmail.com> on 2015/02/03 00:52:38 UTC
Re: Question about the pipeline
Maite Meseure Hugues <me...@...> 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.
Re: Question about the pipeline
Posted by Maite Meseure Hugues <me...@gmail.com>.
Thanks all for your replies, now I am able to run CmdLineCpeRunner.java and
RunCPE.java from the cmd line, there were some classpath config to do.
On Thu, Feb 5, 2015 at 2:24 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Hi Maite,
>
> If you can run the cpe gui using the script in bin/ , try specifying the
> descriptor for that:
>
> runctakesCPE -desc pathToXml
>
> If that runs then try copying the runctakesCPE to something like
> runctakesCLI and change the last line of the file to call CmdLineCpeRunner
> instead of CpmFrame.
>
> Sean
>
> p.s. check the last line of runctakesCPE script that you are using and
> make sure that it passes arguments: %* for Windows or $@ for unix/linux
>
> -----Original Message-----
> From: Maite Meseure Hugues [mailto:meseure.maite@gmail.com]
> Sent: Thursday, February 05, 2015 9:42 AM
> To: dev@ctakes.apache.org
> Subject: Re: Question about the pipeline
>
> Yes, it does but only in Eclipse, not in command line even though I am in
> the good directory. I have to look at the classpath more in details
> probably.
> Thanks for your replies.
>
> On Thu, Feb 5, 2015 at 8:08 AM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> > 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
> > <To...@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:54
> > > 4)
> > >
> > > at
> > > sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526
> > > )
> > >
> > > .......
> > >
> > > On Wed, Feb 4, 2015 at 8:32 AM, Lingren, Todd
> > > <To...@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 <me...@...> 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
> >
>
>
>
> --
> --
> Maïté Meseure Hugues
>
--
--
Maïté Meseure Hugues
RE: Question about the pipeline
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Maite,
If you can run the cpe gui using the script in bin/ , try specifying the descriptor for that:
runctakesCPE -desc pathToXml
If that runs then try copying the runctakesCPE to something like runctakesCLI and change the last line of the file to call CmdLineCpeRunner instead of CpmFrame.
Sean
p.s. check the last line of runctakesCPE script that you are using and make sure that it passes arguments: %* for Windows or $@ for unix/linux
-----Original Message-----
From: Maite Meseure Hugues [mailto:meseure.maite@gmail.com]
Sent: Thursday, February 05, 2015 9:42 AM
To: dev@ctakes.apache.org
Subject: Re: Question about the pipeline
Yes, it does but only in Eclipse, not in command line even though I am in the good directory. I have to look at the classpath more in details probably.
Thanks for your replies.
On Thu, Feb 5, 2015 at 8:08 AM, Finan, Sean < Sean.Finan@childrens.harvard.edu> wrote:
> 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
> <To...@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:54
> > 4)
> >
> > at
> > sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526
> > )
> >
> > .......
> >
> > On Wed, Feb 4, 2015 at 8:32 AM, Lingren, Todd
> > <To...@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 <me...@...> 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
>
--
--
Maïté Meseure Hugues
Re: Question about the pipeline
Posted by Maite Meseure Hugues <me...@gmail.com>.
Yes, it does but only in Eclipse, not in command line even though I am in
the good directory. I have to look at the classpath more in details
probably.
Thanks for your replies.
On Thu, Feb 5, 2015 at 8:08 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> 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 <To...@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 <To...@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 <me...@...> 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
>
--
--
Maïté Meseure Hugues
RE: Question about the pipeline
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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 <To...@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 <To...@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 <me...@...> 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
Re: Question about the pipeline
Posted by Maite Meseure Hugues <me...@gmail.com>.
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 <To...@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 <To...@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 <me...@...> 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
RE: Question about the pipeline
Posted by "Lingren, Todd" <To...@cchmc.org>.
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 <To...@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 <me...@...> 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
Re: Question about the pipeline
Posted by Maite Meseure Hugues <me...@gmail.com>.
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 <To...@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 <me...@...> 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
RE: Question about the pipeline
Posted by "Lingren, Todd" <To...@cchmc.org>.
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 <me...@...> 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
Re: Question about the pipeline
Posted by Maite Meseure Hugues <me...@gmail.com>.
Oh yes my apologies, I mixed RunCPE that takes the cpe.xml and
BagofCuisGenerator that takes input and output directories in arguments.
Thanks for the pointer on CmlLineCpeRunner, I hadn't seen that.
On Tue, Feb 3, 2015 at 1:47 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> 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 <me...@...> 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
RE: Question about the pipeline
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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 <me...@...> 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
Re: Question about the pipeline
Posted by Maite Meseure Hugues <me...@gmail.com>.
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 <me...@...> 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
RE: Question about the pipeline
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Tol,
> Essentially, I want to know how to set up the cTAKES objects correctly into a pipeline in a Java programs, so that medical texts are annotated, like the GUI is doing. I would really appreciate any hints or how to accomplish this.
Looking at your embedded code I think that you've got the general idea of how to do everything. Perhaps you are wondering how to create custom pipelines by programmatically adding chosen processors?
Tim Miller made a great addition (imo) to the cTakes code with the org.apache.ctakes.clinicalpipeline. ClinicalPipelineFactory class. Perhaps you can take a look at that and see if it helps?
Sean
-----Original Message-----
From: Tol O. [mailto:toltox@gmail.com]
Sent: Tuesday, February 03, 2015 7:35 PM
To: dev@ctakes.apache.org
Subject: Re: Question about the pipeline
>
Sean,
Thank you for the detailed reply.
As you mentioned, I had to revert the capital letters from your Outlook, and also, if somebody else wants to use the code and cannot get it to run: the getFilesInDir method needs to return the populated Collection<File> fileList, the variable final File[] fileList and its usage should be renamed to something else (as the variable name already exists) and the main method needs to throw an IOException.
I think these were all the changes I made so that the txt files from a folder are added to the collection, many thanks again.
What I am looking to do is also what the description in "ExampleAggregatePipeline" says, "running a pipeline programatically w/o uima xml descriptor xml files". This is accomplished by what I understand the uimaFIT classes, so that AEs can be defined in Java, added to a Pipeline and directly run.
The uimaFIT page gives a nice Java snippet that uses uimaFIT in a similar way as the cTAKES example, I pasted the few Java lines below at [1].
https://urldefense.proofpoint.com/v2/url?u=http-3A__uima.apache.org_d_uimafit-2Dcurrent_tools.uimafit.book.html-23ugr.tools.uimafit.introduction&d=BQICAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=uhPMXYD_U8cpnenfJCFigx00DCavTuwRGY-irX80FfU&s=4s5P35eByjHcLHM6WEp5jmjquPc-wynEgjBWnY6I6Pg&e=
I would like to use cTAKES in my own Java programs such that, just like the ExampleAggregatePipeline, uimaFIT can be used create and run a cTAKES pipeline to annotate medical texts. Then, I could also output the result in CAS files, just like the CVD GUI is doing. This would allow to directly be able to add or modify my own AnalysisEngines.
Essentially, I want to know how to set up the cTAKES objects correctly into a pipeline in a Java programs, so that medical texts are annotated, like the GUI is doing. I would really appreciate any hints or how to accomplish this.
Following your code example to read the files the outlined idea is:
for ( File file : files ) {
Final String note = getTextInFile( file );
JCas jCas = JCasFactory.createJCas();
jCas.setDocumentText(note);
// 1. create the AnalysisEngines for tokenizer, tagger and other cTAKES components etc. to annotate medical texts
// 2. runPipeline(jCas, ...);
}
[1]
The code snippet from uimaFIT:
JCas jCas = JCasFactory.createJCas();
jCas.setDocumentText("some text");
AnalysisEngine tokenizer = createEngine(MyTokenizer.class);
AnalysisEngine tagger = createEngine(MyTagger.class);
runPipeline(jCas, tokenizer, tagger);
for(Token token : iterate(jCas, Token.class)){
System.out.println(token.getTag());
}
Tol O.
Finan, Sean <Se...@...> writes:
>
> 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@...]
> Sent: Monday, February 02, 2015 6:56 PM
> To: dev@...
> Subject: Re: Question about the pipeline
>
> Maite Meseure Hugues <meseure.maite <at> ...> 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.
>
>
Re: Question about the pipeline
Posted by "Tol O." <to...@gmail.com>.
>
Sean,
Thank you for the detailed reply.
As you mentioned, I had to revert the capital letters from your Outlook, and
also, if somebody else wants to use the code and cannot get it to run: the
getFilesInDir method needs to return the populated Collection<File>
fileList, the variable final File[] fileList and its usage should be renamed
to something else (as the variable name already exists) and the main method
needs to throw an IOException.
I think these were all the changes I made so that the txt files from a
folder are added to the collection, many thanks again.
What I am looking to do is also what the description in
"ExampleAggregatePipeline" says, "running a pipeline programatically w/o
uima xml descriptor xml files". This is accomplished by what I understand
the uimaFIT classes, so that AEs can be defined in Java, added to a Pipeline
and directly run.
The uimaFIT page gives a nice Java snippet that uses uimaFIT in a similar
way as the cTAKES example, I pasted the few Java lines below at [1].
http://uima.apache.org/d/uimafit-current/tools.uimafit.book.html#ugr.tools.uimafit.introduction
I would like to use cTAKES in my own Java programs such that, just like the
ExampleAggregatePipeline, uimaFIT can be used create and run a cTAKES
pipeline to annotate medical texts. Then, I could also output the result in
CAS files, just like the CVD GUI is doing. This would allow to directly be
able to add or modify my own AnalysisEngines.
Essentially, I want to know how to set up the cTAKES objects correctly into
a pipeline in a Java programs, so that medical texts are annotated, like the
GUI is doing. I would really appreciate any hints or how to accomplish this.
Following your code example to read the files the outlined idea is:
for ( File file : files ) {
Final String note = getTextInFile( file );
JCas jCas = JCasFactory.createJCas();
jCas.setDocumentText(note);
// 1. create the AnalysisEngines for tokenizer, tagger and other
cTAKES components etc. to annotate medical texts
// 2. runPipeline(jCas, ...);
}
[1]
The code snippet from uimaFIT:
JCas jCas = JCasFactory.createJCas();
jCas.setDocumentText("some text");
AnalysisEngine tokenizer = createEngine(MyTokenizer.class);
AnalysisEngine tagger = createEngine(MyTagger.class);
runPipeline(jCas, tokenizer, tagger);
for(Token token : iterate(jCas, Token.class)){
System.out.println(token.getTag());
}
Tol O.
Finan, Sean <Se...@...> writes:
>
> 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@...]
> Sent: Monday, February 02, 2015 6:56 PM
> To: dev@...
> Subject: Re: Question about the pipeline
>
> Maite Meseure Hugues <meseure.maite <at> ...> 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.
>
>
RE: Question about the pipeline
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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 <me...@...> 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.