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Posted to dev@ctakes.apache.org by "Monogyiou, Eugenia" <Eu...@nttdata.com> on 2021/01/08 15:43:45 UTC
Running PiperGui produces No Analysis Component found for
ContextDependentTokenizerAnnotator error
Hello,
Sean is probably very busy with the release so if anyone else could please provide any guidance on the below would very much appreciated as I am working on a tight deadline at the moment :(
I switched recently to Intellij and I no longer encountering all the weird maven plugin errors produced with Eclipse - however I have not been able to run the Gui successfully yet.
1. I got the code from the latest trunk and I do not seem to have any password/ username to remove from any xml files (am I missing something?) I have set an environment variable with the api key
2. I run the PiperRunnerGui by navigating to \ctakes-gui\src\main\java\org\apache\ctakes\gui\pipeline\PiperRunnerGui , right-click and run successfully (no run configuration set)
3. I navigate to \ctakes-clinical-pipeline-res\src\main\resources\org\apache\ctakes\clinical\pipeline\ and I load the DefaultFastPipeline.piper
4. First of all I had to copy here all the required subPipe files in the directory before the file was load successfully - I am not sure this is default behaviour or I am missing config
5. and then when I attempted to run, it failed immediately with org.apache.uima.resource.ResourceInitializationException: MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for ContextDependentTokenizerAnnotator
Adding dependencies to the clinical pipeline and/or ctakes-gui pom file did not help.
Many sincere thanks in advance,
Kind Regards,
Eugenia Monogyiou | NTT Data UK
Consulting & IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG
Mob: +44 (0)7971623683 Email: eugenia.monogyiou@nttdata.com<ma...@nttdata.com>
Disclaimer: This email and any attachments are sent in strictest confidence for the sole use of the addressee and may contain legally privileged, confidential, and proprietary data. If you are not the intended recipient, please advise the sender by replying promptly to this email and then delete and destroy this email and any attachments without any further use, copying or forwarding.
RE: Running PiperGui produces No Analysis Component found for
ContextDependentTokenizerAnnotator error [EXTERNAL]
Posted by "Monogyiou, Eugenia" <Eu...@nttdata.com>.
Yes this worked like a charm and I should have updated this thread : classpath of ctakes-examples works perfectly!
And for historical reasons to say that the submitter Gui works just fine without any of the weird Maven plugin issues that were coming up all the time in Eclipse.
Thank you !
Kind Regards,
Eugenia Monogyiou | NTT Data UK
Consulting & IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG
Mob: +44 (0)7971623683 Email: eugenia.monogyiou@nttdata.com
-----Original Message-----
From: Finan, Sean <Se...@childrens.harvard.edu>
Sent: 13 January 2021 15:53
To: dev@ctakes.apache.org
Subject: Re: Running PiperGui produces No Analysis Component found for ContextDependentTokenizerAnnotator error [EXTERNAL]
Hi Eugenia,
In intellij you can easily run any class containing a main(..) method with a simple right-click as you have done. In a single module project this works just fine. However, in a multi-module project like ctakes intellij may not know to use the entire classpath necessary for the class execution.
After the right-click Intellilj probably made a run configuration named after the class. Go into "Run > Edit Configurations ..." in the top/main menubar (or elsewhere). There you should see a list of available configurations on the left. One should be in grey font and named after the class - in this case PiperRunnerGui. On the right side you should see a bunch of parameters that you can play with.
I always use -Xmx3G in my VM options. For the PiperRunnerGui ( "cTAKES Piper File Submitter" ) you shouldn't need any program arguments. However, you should set the "Use classpath of module" to "ctakes-examples". ctakes-examples has the classpath for all of the ctakes modules within its classpath and I use it for pretty much every ctakes run configuration that I have.
Click "Ok" at the bottom and clicking "run" in the menubar or elsewhere should run using the correct classpath.
You can also run the "Piper File Submitter" gui through a maven profile, but that is a different story.
Sean
________________________________________
From: Monogyiou, Eugenia <Eu...@nttdata.com>
Sent: Friday, January 8, 2021 10:43 AM
To: dev@ctakes.apache.org
Subject: Running PiperGui produces No Analysis Component found for ContextDependentTokenizerAnnotator error [EXTERNAL]
* External Email - Caution *
Hello,
Sean is probably very busy with the release so if anyone else could please provide any guidance on the below would very much appreciated as I am working on a tight deadline at the moment :(
I switched recently to Intellij and I no longer encountering all the weird maven plugin errors produced with Eclipse - however I have not been able to run the Gui successfully yet.
1. I got the code from the latest trunk and I do not seem to have any password/ username to remove from any xml files (am I missing something?) I have set an environment variable with the api key
2. I run the PiperRunnerGui by navigating to \ctakes-gui\src\main\java\org\apache\ctakes\gui\pipeline\PiperRunnerGui , right-click and run successfully (no run configuration set)
3. I navigate to \ctakes-clinical-pipeline-res\src\main\resources\org\apache\ctakes\clinical\pipeline\ and I load the DefaultFastPipeline.piper
4. First of all I had to copy here all the required subPipe files in the directory before the file was load successfully - I am not sure this is default behaviour or I am missing config
5. and then when I attempted to run, it failed immediately with org.apache.uima.resource.ResourceInitializationException: MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for ContextDependentTokenizerAnnotator
Adding dependencies to the clinical pipeline and/or ctakes-gui pom file did not help.
Many sincere thanks in advance,
Kind Regards,
Eugenia Monogyiou | NTT Data UK
Consulting & IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG
Mob: +44 (0)7971623683 Email: eugenia.monogyiou@nttdata.com<ma...@nttdata.com>
Disclaimer: This email and any attachments are sent in strictest confidence for the sole use of the addressee and may contain legally privileged, confidential, and proprietary data. If you are not the intended recipient, please advise the sender by replying promptly to this email and then delete and destroy this email and any attachments without any further use, copying or forwarding.
Disclaimer: This email and any attachments are sent in strictest confidence for the sole use of the addressee and may contain legally privileged, confidential, and proprietary data. If you are not the intended recipient, please advise the sender by replying promptly to this email and then delete and destroy this email and any attachments without any further use, copying or forwarding.
Re: Running PiperGui produces No Analysis Component found for
ContextDependentTokenizerAnnotator error [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Eugenia,
In intellij you can easily run any class containing a main(..) method with a simple right-click as you have done. In a single module project this works just fine. However, in a multi-module project like ctakes intellij may not know to use the entire classpath necessary for the class execution.
After the right-click Intellilj probably made a run configuration named after the class. Go into "Run > Edit Configurations ..." in the top/main menubar (or elsewhere). There you should see a list of available configurations on the left. One should be in grey font and named after the class - in this case PiperRunnerGui. On the right side you should see a bunch of parameters that you can play with.
I always use -Xmx3G in my VM options. For the PiperRunnerGui ( "cTAKES Piper File Submitter" ) you shouldn't need any program arguments. However, you should set the "Use classpath of module" to "ctakes-examples". ctakes-examples has the classpath for all of the ctakes modules within its classpath and I use it for pretty much every ctakes run configuration that I have.
Click "Ok" at the bottom and clicking "run" in the menubar or elsewhere should run using the correct classpath.
You can also run the "Piper File Submitter" gui through a maven profile, but that is a different story.
Sean
________________________________________
From: Monogyiou, Eugenia <Eu...@nttdata.com>
Sent: Friday, January 8, 2021 10:43 AM
To: dev@ctakes.apache.org
Subject: Running PiperGui produces No Analysis Component found for ContextDependentTokenizerAnnotator error [EXTERNAL]
* External Email - Caution *
Hello,
Sean is probably very busy with the release so if anyone else could please provide any guidance on the below would very much appreciated as I am working on a tight deadline at the moment :(
I switched recently to Intellij and I no longer encountering all the weird maven plugin errors produced with Eclipse - however I have not been able to run the Gui successfully yet.
1. I got the code from the latest trunk and I do not seem to have any password/ username to remove from any xml files (am I missing something?) I have set an environment variable with the api key
2. I run the PiperRunnerGui by navigating to \ctakes-gui\src\main\java\org\apache\ctakes\gui\pipeline\PiperRunnerGui , right-click and run successfully (no run configuration set)
3. I navigate to \ctakes-clinical-pipeline-res\src\main\resources\org\apache\ctakes\clinical\pipeline\ and I load the DefaultFastPipeline.piper
4. First of all I had to copy here all the required subPipe files in the directory before the file was load successfully - I am not sure this is default behaviour or I am missing config
5. and then when I attempted to run, it failed immediately with org.apache.uima.resource.ResourceInitializationException: MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for ContextDependentTokenizerAnnotator
Adding dependencies to the clinical pipeline and/or ctakes-gui pom file did not help.
Many sincere thanks in advance,
Kind Regards,
Eugenia Monogyiou | NTT Data UK
Consulting & IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG
Mob: +44 (0)7971623683 Email: eugenia.monogyiou@nttdata.com<ma...@nttdata.com>
Disclaimer: This email and any attachments are sent in strictest confidence for the sole use of the addressee and may contain legally privileged, confidential, and proprietary data. If you are not the intended recipient, please advise the sender by replying promptly to this email and then delete and destroy this email and any attachments without any further use, copying or forwarding.
Re: Running PiperGui produces No Analysis Component found for
ContextDependentTokenizerAnnotator error
Posted by Peter Abramowitsch <pa...@gmail.com>.
Hi Eugenia
Not sure if Sean has changed this part of the code that I had checked in,
I'm still using my original check-in. So there may be a small alignment
issue if you are using his newer version and my original instructions.
Raising the level of log4j to DEBUG, the UmlsUserValidator module should
report where it is getting the credentials from. So that should show
you if there are any "rogue" credentials that are being read in favor of
your environment variable. Make sure also that the URL fields in those
XML files are also nulled out in case they still contain the old UTS url.
The validator module will supply the correct URL unless you need to
override it.
Let us know the exact value of the variable(s) you are supplying. If, for
instance, you have a left-over UMLSUSER variable and it still has your old
value, that would be a problem. If you do have it, its value must be the
string "umls_api_key" and the password variable would contain the key
itself.
Regards
Peter
On Fri, Jan 8, 2021 at 4:44 PM Monogyiou, Eugenia <
Eugenia.Monogyiou@nttdata.com> wrote:
> Hello,
>
> Sean is probably very busy with the release so if anyone else could please
> provide any guidance on the below would very much appreciated as I am
> working on a tight deadline at the moment :(
>
> I switched recently to Intellij and I no longer encountering all the weird
> maven plugin errors produced with Eclipse - however I have not been able to
> run the Gui successfully yet.
>
> 1. I got the code from the latest trunk and I do not seem to have
> any password/ username to remove from any xml files (am I missing
> something?) I have set an environment variable with the api key
>
> 2. I run the PiperRunnerGui by navigating to
> \ctakes-gui\src\main\java\org\apache\ctakes\gui\pipeline\PiperRunnerGui ,
> right-click and run successfully (no run configuration set)
>
> 3. I navigate to
> \ctakes-clinical-pipeline-res\src\main\resources\org\apache\ctakes\clinical\pipeline\
> and I load the DefaultFastPipeline.piper
>
> 4. First of all I had to copy here all the required subPipe files in
> the directory before the file was load successfully - I am not sure this is
> default behaviour or I am missing config
>
> 5. and then when I attempted to run, it failed immediately with
> org.apache.uima.resource.ResourceInitializationException: MESSAGE
> LOCALIZATION FAILED: Can't find resource for bundle
> java.util.PropertyResourceBundle, key No Analysis Component found for
> ContextDependentTokenizerAnnotator
>
> Adding dependencies to the clinical pipeline and/or ctakes-gui pom file
> did not help.
>
> Many sincere thanks in advance,
>
>
> Kind Regards,
>
> Eugenia Monogyiou | NTT Data UK
> Consulting & IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG
>
> Mob: +44 (0)7971623683 Email: eugenia.monogyiou@nttdata.com<mailto:
> eugenia.monogyiou@nttdata.com>
>
> Disclaimer: This email and any attachments are sent in strictest
> confidence for the sole use of the addressee and may contain legally
> privileged, confidential, and proprietary data. If you are not the intended
> recipient, please advise the sender by replying promptly to this email and
> then delete and destroy this email and any attachments without any further
> use, copying or forwarding.
>