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 <https://issues.apache.org/jira/browse/CTAKES-445> should work without your having to modify the lvg.properties file.
I haven't tested the patch to CTAKES-445 <https://issues.apache.org/jira/browse/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 <[email protected]> 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. | > [email protected] | 845 - 270 - 3129 <(845)%20270-3129> (m) | > www.metistream.com >
