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Posted to dev@ctakes.apache.org by "Ying, Jun" <JY...@mgh.harvard.edu> on 2014/12/03 04:28:47 UTC
Asking help for always unsuccessful AE load
Dear Sir/Madam,
When I Load some AE in cTakes like "SimulatedProdSmokingTAE.xml", It always jump the Exception "java.lang.illegalArgumentException: URl is not hierarchical". Why it happens? How to fix it.
Thanks.
[X]
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RE: Asking help for always unsuccessful AE load
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Jun,
Do AE pipelines that do not use the Smoking Status module work?
I think that Smoking Status configuration (via binary install) might be broken in the last several versions. I thought that I had submitted a Jira long, long ago, but right now I can't find it so maybe my memory is playing games. I have gotten the module to work, but it took hours to find and fix the problems. If you can get other AEs to run then let me know and I'll try to find my working setup and diff it with the cTakes install tomorrow. If I remember correctly I had to move (unpack) some things from lib/ jars to resources/ and change a path or two in the desc/ xmls.
Sean
From: Kim Ebert [mailto:kim.ebert@perfectsearchcorp.com]
Sent: Wednesday, December 03, 2014 10:52 AM
To: dev@ctakes.apache.org
Subject: Re: Asking help for always unsuccessful AE load
Hi Jun,
I know this has been a problem in some versions. What version are you using? Could you try this out on the latest release candidate to see if it is still an issue?
Thanks,
[IMAT Solutions]<http://imatsolutions.com>
Kim Ebert
Software Engineer
[Office:]801.669.7342
kim.ebert@imatsolutions.com<ma...@imatsolutions.com>
On 12/02/2014 08:28 PM, Ying, Jun wrote:
Dear Sir/Madam,
When I Load some AE in cTakes like "SimulatedProdSmokingTAE.xml", It always jump the Exception "java.lang.illegalArgumentException: URl is not hierarchical". Why it happens? How to fix it.
Thanks.
[X]
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: Asking help for always unsuccessful AE load
Posted by Kim Ebert <ki...@perfectsearchcorp.com>.
Hi Jun,
I know this has been a problem in some versions. What version are you
using? Could you try this out on the latest release candidate to see if
it is still an issue?
Thanks,
IMAT Solutions <http://imatsolutions.com>
Kim Ebert
Software Engineer
Office: 801.669.7342
kim.ebert@imatsolutions.com <ma...@imatsolutions.com>
On 12/02/2014 08:28 PM, Ying, Jun wrote:
> Dear Sir/Madam,
> When I Load some AE in cTakes like "SimulatedProdSmokingTAE.xml", It always jump the Exception "java.lang.illegalArgumentException: URl is not hierarchical". Why it happens? How to fix it.
> Thanks.
>
> [X]
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.
>
Re: Asking help for always unsuccessful AE load
Posted by David Kincaid <ki...@gmail.com>.
This problem is coming from the LvgAnnotator. The issue is with the
lvg.properties file. The annotation engine is trying to find its
lvg.properties file in the classpath. This file is part of the cTAKES
resources bundle, so should be installed under
$CTAKES_HOME/resources/org/apache/ctakes/lvg/data/config. Unfortunately
this file also exists inside the jar file ctakes-lvg-res-3.2.0.jar as well.
So if you have that jar file on your classpath and it comes before the
CTAKES_HOME/resources/... then you'll get this error. In my case the
ctakes-lvg-res-3.2.0.jar file was being pulled into my project by Maven.
My stack trace looked like this:
java.lang.IllegalArgumentException: URI is not hierarchical
at java.io.File.<init>(File.java:418)
at
org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiResourceImpl.java:65)
and the URI it was using for the file was:
jar:file:/home/davek/.m2/repository/org/apache/ctakes/ctakes-lvg-res/3.2.0/ctakes-lvg-res-3.2.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
I fixed it by making sure that the cTAKES resources were in the classpath
before the dependent jar files (I use IntelliJ for development).
Hope that helps others when they search the archives since this issue seems
to come up quite a bit.
- Dave
On Tue, Dec 2, 2014 at 9:36 PM, Chen, Pei <Pe...@childrens.harvard.edu>
wrote:
> Jun,
> Which version of cTAKES are you using. Also- how are you running ctakes-
> via the binary artifacts or from a dev env such as eclipse ide?
>
> Sent from my iPhone
>
> > On Dec 2, 2014, at 10:33 PM, Ying, Jun <JY...@mgh.harvard.edu> wrote:
> >
> > Dear Sir/Madam,
> > When I Load some AE in cTakes like "SimulatedProdSmokingTAE.xml", It
> always jump the Exception "java.lang.illegalArgumentException: URl is not
> hierarchical". Why it happens? How to fix it.
> > Thanks.
> >
> > [X]
> >
> >
> > The information in this e-mail is intended only for the person to whom
> it is
> > addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> > contains patient information, please contact the Partners Compliance
> HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> > but does not contain patient information, please contact the sender and
> properly
> > dispose of the e-mail.
>
Re: Asking help for always unsuccessful AE load
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Jun,
Which version of cTAKES are you using. Also- how are you running ctakes- via the binary artifacts or from a dev env such as eclipse ide?
Sent from my iPhone
> On Dec 2, 2014, at 10:33 PM, Ying, Jun <JY...@mgh.harvard.edu> wrote:
>
> Dear Sir/Madam,
> When I Load some AE in cTakes like "SimulatedProdSmokingTAE.xml", It always jump the Exception "java.lang.illegalArgumentException: URl is not hierarchical". Why it happens? How to fix it.
> Thanks.
>
> [X]
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.