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 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:544) > > at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526) > > ... > > On Wed, Feb 4, 2015 at 8:32 AM, Lingren, Todd > 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 directo
RE: Question about the pipeline
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 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:544) > > at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526) > > ... > > On Wed, Feb 4, 2015 at 8:32 AM, Lingren, Todd > 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 no
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 > 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:544) > > > > at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526) > > > > ... > > > > On Wed, Feb 4, 2015 at 8:32 AM, Lingren, Todd > > 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,
RE: Question about the pipeline
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 > > 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 > > > > 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
