Re: Trying to install dictionary [EXTERNAL]

["Finan, Sean" <Se...@childrens.harvard.edu>]

Hi Don,

Oh yes - the file extension ".script" is a bit misleading.  You don't need to execute anything.

We really gloss over it here https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide
but basically:

Copy the contents of the .zip file so that they are in the ctakes resources/org/apache/ctakes/dictionary/lookup/fast/ directory.

Sean
________________________________________
From: Don Flinn <fl...@alum.mit.edu>
Sent: Friday, March 9, 2018 2:10 AM
To: dev@ctakes.apache.org
Subject: Trying to install dictionary [EXTERNAL]

I'm using cTakes dev and am attempting to install the
org/apache/ctakes/dictionary/lookup/fast dictionary, but can not find the
instructions.  I've downloaded sno_rx_16ab.zip.  There is a script in the
zip file.  Where are the how to instructions?   Do I just blindly run the
script?  I do have my environment variables set up.

Thanks for any advice
Don

Re: Trying to install dictionary [EXTERNAL]

[Don Flinn <fl...@alum.mit.edu>]

Sean,

Thank you for the info on the dictionary.   The next problem  is with the
LVG properties.  I'm receiving the following errors:
** Configuration Error: file:\C:\apache-ctakes-4.0.
0Dev\ctakes\ctakes-lvg-res\target\classes\org\apache\
ctakes\lvg\data\config\lvg.properties (The filename, directory name, or
volume label syntax is incorrect)
** Error: problem of opening/reading config file:
'file:\C:\apache-ctakes-4.0.0Dev\ctakes\ctakes-lvg-res\
target\classes\org\apache\ctakes\lvg\data\config\lvg.properties'. Use -x
option to specify the config file path.
** Configuration Error: file:\C:\apache-ctakes-4.0.
0Dev\ctakes\ctakes-lvg-res\target\classes\org\apache\
ctakes\lvg\data\config\lvg.properties (The filename, directory name, or
volume label syntax is incorrect)
** Error: problem of opening/reading config file:
'file:\C:\apache-ctakes-4.0.0Dev\ctakes\ctakes-lvg-res\
target\classes\org\apache\ctakes\lvg\data\config\lvg.properties'. Use -x
option to specify the config file path.

The properties file is in the right place but the something is wrong with
the syntax.  I'm not sure what it needs or how to feed it.  As the docs
said this is necessary to run at a reasonable pace.  My first run of
ClinicalPipelineFactory.java took multiple hours.  Thankfully subsequent
runs went reasonably fast.

What do I need to add to or modify lvg.properties.  Again a pointer to
documentation would be appreciated.

I also had problems with the batch file but I'm more interested in the java
code.  The problem output there was:

Mar 12, 2018 5:00:33 PM org.apache.uima.util.MessageReport
decreasingWithTrace(51)
WARNING: Message count: 1; Feature
org.apache.ctakes.typesystem.type.textsem.Predicate:relations is marked
multipleReferencesAllowed=false, but it has multiple references.  These
will be serialized in duplicate. Message count indicates messages skipped
to avoid potential flooding. Set FINE logging level for stacktrace.
Mar 12, 2018 5:00:33 PM org.apache.uima.util.MessageReport
decreasingWithTrace(51)
WARNING: Message count: 2; Feature
org.apache.ctakes.typesystem.type.textsem.Predicate:relations is marked
multipleReferencesAllowed=false, but it has multiple references.  These
will be serialized in duplicate. Message count indicates messages skipped
to avoid potential flooding. Set FINE logging level for stacktrace.
Mar 12, 2018 5:00:33 PM org.apache.uima.util.MessageReport
decreasingWithTrace(51)
WARNING: Message count: 4; Feature
org.apache.ctakes.typesystem.type.textsem.Predicate:relations is marked
multipleReferencesAllowed=false, but it has multiple references.  These
will be serialized in duplicate. Message count indicates messages skipped
to avoid potential flooding. Set FINE logging level for stacktrace.
Mar 12, 2018 5:00:33 PM org.apache.uima.util.MessageReport
decreasingWithTrace(51)
WARNING: Message count: 8; Feature
org.apache.ctakes.typesystem.type.textsem.Predicate:relations is marked
multipleReferencesAllowed=false, but it has multiple references.  These
will be serialized in duplicate. Message count indicates messages skipped
to avoid potential flooding. Set FINE logging level for stacktrace.

Thanks
Don


On Fri, Mar 9, 2018 at 9:13 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Hi Don,
>
> Oh yes - the file extension ".script" is a bit misleading.  You don't need
> to execute anything.
>
> We really gloss over it here https://cwiki.apache.org/
> confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide
> but basically:
>
> Copy the contents of the .zip file so that they are in the ctakes
> resources/org/apache/ctakes/dictionary/lookup/fast/ directory.
>
> Sean
> ________________________________________
> From: Don Flinn <fl...@alum.mit.edu>
> Sent: Friday, March 9, 2018 2:10 AM
> To: dev@ctakes.apache.org
> Subject: Trying to install dictionary [EXTERNAL]
>
> I'm using cTakes dev and am attempting to install the
> org/apache/ctakes/dictionary/lookup/fast dictionary, but can not find the
> instructions.  I've downloaded sno_rx_16ab.zip.  There is a script in the
> zip file.  Where are the how to instructions?   Do I just blindly run the
> script?  I do have my environment variables set up.
>
> Thanks for any advice
> Don
>