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Posted to dev@ctakes.apache.org by "Bleeker, Troy C." <Bl...@mayo.edu> on 2013/02/16 00:24:01 UTC
User running CPE error
Following the user instructions as they currently are (download bin from here http://www.apache.org/dist/incubator/ctakes/) :
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+User+Guide
Gave me an error about a missing file when trying to runctakesCPE.bat.
Can anyone else reproduce that?
Thanks
Troy Bleeker * Senior Business Analyst CBAP(r) * Biomedical Statistics and Informatics
Phone: 507-293-1574 * Fax: 507-284-0360 * bleeker.troy@mayo.edu
Mayo Clinic * 200 First Street SW * Rochester, MN 55905 * www.mayoclinic.org
RE: User running CPE error
Posted by "Masanz, James J." <Ma...@mayo.edu>.
I don't see an attached image. Maybe that's not important, if this will give an answer:
I updated the User Guide to tell people to get the input file from
https://svn.apache.org/repos/asf/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-clinical-pipeline/src/test/data/testpatient_cn_1.xml (for now)
I created a JIRA issue so that file gets put back into binary distributions in the future.
FYI, when using the CPE GUI, I am in the habit of using File->Clear a lot to avoid being surprised by leftover input fields or values.
When you want to post an image, it's best to upload the image somewhere and post the URL to it instead of attaching.
-- James
> -----Original Message-----
> From: ctakes-dev-return-1241-Masanz.James=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1241-
> Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of Bleeker, Troy
> C.
> Sent: Monday, February 18, 2013 3:20 PM
> To: 'ctakes-dev@incubator.apache.org'
> Subject: RE: User running CPE error
>
> Wait, I see now. If I load test_plaintext.xml then I will get the error
> I reported. If I load test1.xml then I don't. So CPE (on Windows)
> remembers the last CPE descriptor to be loaded (even if I delete my
> entire cTAKES install and do it again). On a clean system that won't be
> true so we can ignore that given that the documentation now points to an
> XML file that will load.
>
> However even though it "loads into CPE", it does not run. I can load up
> this:
> <cTAKES_HOME>/desc/ctakes-clinical-
> pipeline/desc/collection_processing_engine/test1.xml
> but when I click the play button to run the processing I get the
> attached error. I'm not sure what the input data location and output
> location should be.
>
> Thanks
> Troy
>
> -----Original Message-----
> From: Bleeker, Troy C.
> Sent: Monday, February 18, 2013 9:18 AM
> To: ctakes-dev@incubator.apache.org
> Subject: RE: User running CPE error
>
> Sorry. I should have been more specific. Those XML files are not
> involved yet.
>
> After obtaining the binary files and merging in the resources I run the
> command runctakesCPE.bat and I get the error in the attached picture.
> <cTAKES_HOME>/desc/ctakes-clinical-pipeline/ctakes-core/collection-
> reader/FilesInDirectoryCollectionReader.xml
> does not exist.
>
> Thanks
> Troy
> -----Original Message-----
> From: ctakes-dev-return-1226-Bleeker.Troy=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1226-
> Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
> Sent: Friday, February 15, 2013 7:14 PM
> To: ctakes-dev@incubator.apache.org
> Subject: RE: User running CPE error
>
> Hi Troy,
> I updated the documentation to use text1.xml instead of
> test_plaintext.xml for demo/sample purposes.
> <cTAKES_HOME>/desc/ctakes-clinical-
> pipeline/desc/collection_processing_engine/test1.xml
>
> --Pei
>
> ________________________________________
> From: Bleeker, Troy C. [Bleeker.Troy@mayo.edu]
> Sent: Friday, February 15, 2013 7:09 PM
> To: ctakes-dev@incubator.apache.org
> Subject: User running CPE error
>
> Following the user instructions as they currently are (download bin from
> here http://www.apache.org/dist/incubator/ctakes/) :
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+User+Guide
>
> Gave me an error about a missing file when trying to runctakesCPE.bat.
> Can anyone else reproduce that?
>
> Thanks
> Troy Bleeker * Senior Business Analyst CBAP(r) * Biomedical Statistics
> and Informatics
> Phone: 507-293-1574 * Fax: 507-284-0360 * bleeker.troy@mayo.edu Mayo
> Clinic * 200 First Street SW * Rochester, MN 55905 * www.mayoclinic.org
RE: User running CPE error
Posted by "Bleeker, Troy C." <Bl...@mayo.edu>.
Wait, I see now. If I load test_plaintext.xml then I will get the error I reported. If I load test1.xml then I don't. So CPE (on Windows) remembers the last CPE descriptor to be loaded (even if I delete my entire cTAKES install and do it again). On a clean system that won't be true so we can ignore that given that the documentation now points to an XML file that will load.
However even though it "loads into CPE", it does not run. I can load up this:
<cTAKES_HOME>/desc/ctakes-clinical-pipeline/desc/collection_processing_engine/test1.xml
but when I click the play button to run the processing I get the attached error. I'm not sure what the input data location and output location should be.
Thanks
Troy
-----Original Message-----
From: Bleeker, Troy C.
Sent: Monday, February 18, 2013 9:18 AM
To: ctakes-dev@incubator.apache.org
Subject: RE: User running CPE error
Sorry. I should have been more specific. Those XML files are not involved yet.
After obtaining the binary files and merging in the resources I run the command runctakesCPE.bat and I get the error in the attached picture.
<cTAKES_HOME>/desc/ctakes-clinical-pipeline/ctakes-core/collection-reader/FilesInDirectoryCollectionReader.xml
does not exist.
Thanks
Troy
-----Original Message-----
From: ctakes-dev-return-1226-Bleeker.Troy=mayo.edu@incubator.apache.org [mailto:ctakes-dev-return-1226-Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
Sent: Friday, February 15, 2013 7:14 PM
To: ctakes-dev@incubator.apache.org
Subject: RE: User running CPE error
Hi Troy,
I updated the documentation to use text1.xml instead of test_plaintext.xml for demo/sample purposes.
<cTAKES_HOME>/desc/ctakes-clinical-pipeline/desc/collection_processing_engine/test1.xml
--Pei
________________________________________
From: Bleeker, Troy C. [Bleeker.Troy@mayo.edu]
Sent: Friday, February 15, 2013 7:09 PM
To: ctakes-dev@incubator.apache.org
Subject: User running CPE error
Following the user instructions as they currently are (download bin from here http://www.apache.org/dist/incubator/ctakes/) :
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+User+Guide
Gave me an error about a missing file when trying to runctakesCPE.bat.
Can anyone else reproduce that?
Thanks
Troy Bleeker * Senior Business Analyst CBAP(r) * Biomedical Statistics and Informatics
Phone: 507-293-1574 * Fax: 507-284-0360 * bleeker.troy@mayo.edu Mayo Clinic * 200 First Street SW * Rochester, MN 55905 * www.mayoclinic.org
RE: User running CPE error
Posted by "Bleeker, Troy C." <Bl...@mayo.edu>.
Sorry. I should have been more specific. Those XML files are not involved yet.
After obtaining the binary files and merging in the resources I run the command
runctakesCPE.bat
and I get the error in the attached picture.
<cTAKES_HOME>/desc/ctakes-clinical-pipeline/ctakes-core/collection-reader/FilesInDirectoryCollectionReader.xml
does not exist.
Thanks
Troy
-----Original Message-----
From: ctakes-dev-return-1226-Bleeker.Troy=mayo.edu@incubator.apache.org [mailto:ctakes-dev-return-1226-Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
Sent: Friday, February 15, 2013 7:14 PM
To: ctakes-dev@incubator.apache.org
Subject: RE: User running CPE error
Hi Troy,
I updated the documentation to use text1.xml instead of test_plaintext.xml for demo/sample purposes.
<cTAKES_HOME>/desc/ctakes-clinical-pipeline/desc/collection_processing_engine/test1.xml
--Pei
________________________________________
From: Bleeker, Troy C. [Bleeker.Troy@mayo.edu]
Sent: Friday, February 15, 2013 7:09 PM
To: ctakes-dev@incubator.apache.org
Subject: User running CPE error
Following the user instructions as they currently are (download bin from here http://www.apache.org/dist/incubator/ctakes/) :
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+User+Guide
Gave me an error about a missing file when trying to runctakesCPE.bat.
Can anyone else reproduce that?
Thanks
Troy Bleeker * Senior Business Analyst CBAP(r) * Biomedical Statistics and Informatics
Phone: 507-293-1574 * Fax: 507-284-0360 * bleeker.troy@mayo.edu Mayo Clinic * 200 First Street SW * Rochester, MN 55905 * www.mayoclinic.org
RE: User running CPE error
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Hi Troy,
I updated the documentation to use text1.xml instead of test_plaintext.xml for demo/sample purposes.
<cTAKES_HOME>/desc/ctakes-clinical-pipeline/desc/collection_processing_engine/test1.xml
--Pei
________________________________________
From: Bleeker, Troy C. [Bleeker.Troy@mayo.edu]
Sent: Friday, February 15, 2013 7:09 PM
To: ctakes-dev@incubator.apache.org
Subject: User running CPE error
Following the user instructions as they currently are (download bin from here http://www.apache.org/dist/incubator/ctakes/) :
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+User+Guide
Gave me an error about a missing file when trying to runctakesCPE.bat.
Can anyone else reproduce that?
Thanks
Troy Bleeker * Senior Business Analyst CBAP(r) * Biomedical Statistics and Informatics
Phone: 507-293-1574 * Fax: 507-284-0360 * bleeker.troy@mayo.edu
Mayo Clinic * 200 First Street SW * Rochester, MN 55905 * www.mayoclinic.org