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.ling...@cchmc.org 513-803-9032 -----Original Message----- From: Maite Meseure Hugues [mailto:meseure.ma...@gmail.com] Sent: Wednesday, February 04, 2015 12:59 PM To: dev@ctakes.apache.org Subject: Re: Question about the pipeline Interesting, Todd thank you and how do you use CMdLineCpeRunner basically? Because I tested in cmd line with: java org.apache.ctakes.core.cpe.CmdLineCpeRunner [path-to-my-cpe.xml] but here is that I've got: Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/uima/util/InvalidXMLException at java.lang.Class.getDeclaredMethods0(Native Method) at java.lang.Class.privateGetDeclaredMethods(Class.java:2693) at java.lang.Class.privateGetMethodRecursive(Class.java:3040) at java.lang.Class.getMethod0(Class.java:3010) at java.lang.Class.getMethod(Class.java:1776) at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544) at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526) ....... On Wed, Feb 4, 2015 at 8:32 AM, Lingren, Todd <todd.ling...@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.ling...@cchmc.org > 513-803-9032 > > > -----Original Message----- > From: Finan, Sean [mailto:sean.fi...@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.ma...@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.fi...@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:tol...@gmail.com] > > Sent: Monday, February 02, 2015 6:56 PM > > To: dev@ctakes.apache.org > > Subject: Re: Question about the pipeline > > > > Maite Meseure Hugues <meseure.maite@...> writes: > > > > > > > > Hello all, > > > > > > Thank you for your preceding answers. > > > I have a few questions regarding the pipeline example to run > > > cTakes programmatically. > > > I am running ExampleAggregatePipeline.java with > > > ExampleHelloWorldAnnotator but I would like to know how I can > > > change it to run my data, as the CPE where we can choose the > > > directory of our > > data. > > > My second question is about the xml output generated with the CPE, > > > can I get the same xml output in using the example pipeline? and How? > > > Thanks for your time. > > > > > > I would like to ask the same question. After successfully setting up > > CTAKES following the Developers Guide I would also like to use a > > modified ExampleAggregatePipeline to output a CAS file identical to > > the output obtained by the CPE or the CVD when following the Users Guide. > > > > This would be a great help for developers as a starting class to be > > able to programmatically obtain an annotated file based on a > > plaintext or XML input, same as through the two GUIs. > > > > Right now I am reading through the Component Use Guide to replicate > > the CPE or the CVD tutorial with the test input, but it is a bit > overwhelming. > > > > Any pointers or suggestions would be really appreciated. > > > > Tol O. > > > > > > > -- > -- > Maïté Meseure Hugues > -- -- Maïté Meseure Hugues
