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.fi...@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.ma...@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.fi...@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.ma...@gmail.com] > > Sent: Thursday, February 05, 2015 8:51 AM > > To: dev@ctakes.apache.org > > Subject: Re: Question about the pipeline > > > > I see. In my case, I am using the CPE descriptor saved from the GUI > > for CmdLineCpeRunner as said Sean. I've selected > > AggregatePlaintextProcessor.xml as AE but I have this error: > > > > "Couldn't initialize processing engine. > > > > Initialization of CAS Processor with name "AggregatePlaintextProcessor" > > failed. " > > > > Meanwhile, RunCPE.java works properly with the same descriptor in > Eclipse. > > Does anyone have an idea? > > > > On Wed, Feb 4, 2015 at 12:56 PM, Lingren, Todd > > <todd.ling...@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.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:54 > > > 4) > > > > > > 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 > > > > > > > > > > > -- > > -- > > Maïté Meseure Hugues > > > > > > -- > -- > Maïté Meseure Hugues > -- -- Maïté Meseure Hugues
