Re: Setting the Lvg Resources Location in lvg.properties

[James Masanz]

No.  I think that when the database was converted to be compatible with the
more recent hsqlb, the conversion program lost the readonly attribute.
I'll fix that. Thanks for letting everyone know it's working now for you
and what needs to be done.


On Sep 29, 2017 5:27 PM, "Michael Trepanier"  wrote:

> Taking the resources out of my fat jar resolved this issue. I should add
> that as I'm running this pipeline in Spark I had to set the related HSQLDBs
> to read-only to permit simultaneous reads. Is there any reason they are not
> set to read-only to begin with?
>
> Mike
>
> On Thu, Sep 28, 2017 at 6:27 PM, James Masanz 
> wrote:
>
>>
>> I would expect that if you copy the LVG resources out of your UberJar, it
>> should resolve the issue.
>> Modifying the lvg.properties file generally causes problems.
>> Following the hints in the 30/Jul/17 23:06 update to CTAKES-445
>>   should work without
>> your having to modify the lvg.properties file.
>>
>> I haven't tested the patch to CTAKES-445
>>  myself yet so I don't
>> know whether it takes care of the problem in this case. I do know that the
>> ctakes-lvg code does a change directory (cd)  to where it expects the LVG
>> resources to be, or at least that's what it used to do when I last looked
>> at it.  I suspect trying to cd into a jar is the problem you are seeing.
>> I'll have to revisit that when I look at that patch.
>>
>> -- James
>>
>>
>>
>> On Tue, Sep 26, 2017 at 5:53 PM, Michael Trepanier 
>> wrote:
>>
>>> I am attempting to run cTAKES from an executable UberJar. While the fast
>>> pipeline seems to run correctly (in terms of producing an output), when
>>> stepping through the LvgAnnotator related steps, cTAKES produces the below
>>> error.
>>>
>>> 26 Sep 2017 22:47:01  INFO LvgAnnotator - URL for lvg.properties 
>>> =file:/home/mike/ctakes-assembly-4.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
>>> 26 Sep 2017 22:47:01  INFO SentenceDetector - Sentence detector model file: 
>>> org/apache/ctakes/core/sentdetect/sd-med-model.zip
>>> 26 Sep 2017 22:47:01  INFO TokenizerAnnotatorPTB - Initializing 
>>> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
>>> 26 Sep 2017 22:47:01  INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg 
>>> with config file = 
>>> jar:file:/home/mike/ctakes-assembly-4.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
>>> 26 Sep 2017 22:47:01  INFO LvgCmdApiResourceImpl -   config file absolute 
>>> path = 
>>> /home/mike/jar:file:/home/mike/ctakes-assembly-4.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
>>> 26 Sep 2017 22:47:01  INFO LvgCmdApiResourceImpl - cwd = /home/mike
>>> 26 Sep 2017 22:47:01  INFO LvgCmdApiResourceImpl - cd 
>>> jar:file:/home/mike/ctakes-assembly-4.0.jar!/org/apache/ctakes/lvg/
>>> ** Configuration Error: 
>>> jar:file:/home/mike/ctakes-assembly-4.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
>>>  (No such file or directory)
>>> ** Error: problem of opening/reading config file: 
>>> 'jar:file:/home/mike/ctakes-assembly-4.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties'.
>>>  Use -x option to specify the config file path.
>>> ** Configuration Error: 
>>> jar:file:/home/mike/ctakes-assembly-4.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
>>>  (No such file or directory)
>>> ** Error: problem of opening/reading config file: 
>>> 'jar:file:/home/mike/ctakes-assembly-4.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties'.
>>>  Use -x option to specify the config file path.
>>>
>>> Would taking the additional cTAKES resources out of the UberJar resolve
>>> this issue? And if so, can I use the lvg.properties file to set where these
>>> resources should be?
>>>
>>> Note, as mentioned before, this error does not cause cTAKES to crash; I
>>> am just worried it may be impacting the output. As well, I have implemented
>>> the patch outlined at https://issues.apache.org/jira/browse/CTAKES-445
>>>
>>>
>>> Regards,
>>>
>>> Mike
>>>
>>> --
>>> [image: MetiStream Logo - 500]
>>> Mike Trepanier| Big Data Engineer | MetiStream, Inc. |
>>> m...@metistream.com | 845 - 270 - 3129 <(845)%20270-3129> (m) |
>>> www.metistream.com
>>>
>>
>>
>
>
> --
> [image: MetiStream Logo - 500]
> Mike Trepanier| Big Data Engineer | MetiStream, Inc. |
> m...@metistream.com | 845 - 270 - 3129 <(845)%20270-3129> (m) |
> www.metistream.com
>

Re: Setting the Lvg Resources Location in lvg.properties

[Michael Trepanier]

Taking the resources out of my fat jar resolved this issue. I should add
that as I'm running this pipeline in Spark I had to set the related HSQLDBs
to read-only to permit simultaneous reads. Is there any reason they are not
set to read-only to begin with?

Mike

On Thu, Sep 28, 2017 at 6:27 PM, James Masanz 
wrote:

>
> I would expect that if you copy the LVG resources out of your UberJar, it
> should resolve the issue.
> Modifying the lvg.properties file generally causes problems.
> Following the hints in the 30/Jul/17 23:06 update to CTAKES-445
>   should work without
> your having to modify the lvg.properties file.
>
> I haven't tested the patch to CTAKES-445
>  myself yet so I don't
> know whether it takes care of the problem in this case. I do know that the
> ctakes-lvg code does a change directory (cd)  to where it expects the LVG
> resources to be, or at least that's what it used to do when I last looked
> at it.  I suspect trying to cd into a jar is the problem you are seeing.
> I'll have to revisit that when I look at that patch.
>
> -- James
>
>
>
> On Tue, Sep 26, 2017 at 5:53 PM, Michael Trepanier 
> wrote:
>
>> I am attempting to run cTAKES from an executable UberJar. While the fast
>> pipeline seems to run correctly (in terms of producing an output), when
>> stepping through the LvgAnnotator related steps, cTAKES produces the below
>> error.
>>
>> 26 Sep 2017 22:47:01  INFO LvgAnnotator - URL for lvg.properties 
>> =file:/home/mike/ctakes-assembly-4.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
>> 26 Sep 2017 22:47:01  INFO SentenceDetector - Sentence detector model file: 
>> org/apache/ctakes/core/sentdetect/sd-med-model.zip
>> 26 Sep 2017 22:47:01  INFO TokenizerAnnotatorPTB - Initializing 
>> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
>> 26 Sep 2017 22:47:01  INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg 
>> with config file = 
>> jar:file:/home/mike/ctakes-assembly-4.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
>> 26 Sep 2017 22:47:01  INFO LvgCmdApiResourceImpl -   config file absolute 
>> path = 
>> /home/mike/jar:file:/home/mike/ctakes-assembly-4.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
>> 26 Sep 2017 22:47:01  INFO LvgCmdApiResourceImpl - cwd = /home/mike
>> 26 Sep 2017 22:47:01  INFO LvgCmdApiResourceImpl - cd 
>> jar:file:/home/mike/ctakes-assembly-4.0.jar!/org/apache/ctakes/lvg/
>> ** Configuration Error: 
>> jar:file:/home/mike/ctakes-assembly-4.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
>>  (No such file or directory)
>> ** Error: problem of opening/reading config file: 
>> 'jar:file:/home/mike/ctakes-assembly-4.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties'.
>>  Use -x option to specify the config file path.
>> ** Configuration Error: 
>> jar:file:/home/mike/ctakes-assembly-4.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
>>  (No such file or directory)
>> ** Error: problem of opening/reading config file: 
>> 'jar:file:/home/mike/ctakes-assembly-4.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties'.
>>  Use -x option to specify the config file path.
>>
>> Would taking the additional cTAKES resources out of the UberJar resolve
>> this issue? And if so, can I use the lvg.properties file to set where these
>> resources should be?
>>
>> Note, as mentioned before, this error does not cause cTAKES to crash; I
>> am just worried it may be impacting the output. As well, I have implemented
>> the patch outlined at https://issues.apache.org/jira/browse/CTAKES-445
>>
>>
>> Regards,
>>
>> Mike
>>
>> --
>> [image: MetiStream Logo - 500]
>> Mike Trepanier| Big Data Engineer | MetiStream, Inc. |
>> m...@metistream.com | 845 - 270 - 3129 <(845)%20270-3129> (m) |
>> www.metistream.com
>>
>
>


-- 
[image: MetiStream Logo - 500]
Mike Trepanier| Big Data Engineer | MetiStream, Inc. |  m...@metistream.com |
845 - 270 - 3129 (m) | www.metistream.com