Hi Dima,
I believe this is related to the path of LVG. You can try coping the LVG data
folder to the same directory (This is at least how I've gotten around it) when
running a compiled jar. You can also search the mailing list for additional
discussion on this issue.
Thanks,
Brandon
-Or
Looks to me like a missing environment variable..
++
Chris Mattmann, Ph.D.
Chief Architect
Instrument Software and Science Data Systems Section (398)
NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
Office: 168-519, Mailstop: 168
Hi Chris,
Sorry, could you please clarify which environment variable I am missing?
Thanks,
Dima
> On Jun 28, 2016, at 09:49, Mattmann, Chris A (3980)
> wrote:
>
> Looks to me like a missing environment variable..
>
> ++
> Chris
Brandon, thank you.
I just did a quick mailing archive search and it looks like this is known
issue, which presumably was fixed a while ago:
http://mail-archives.apache.org/mod_mbox/ctakes-dev/201510.mbox/%3cd8f818ba-50fd-4a08-95ea-4e841ff6f...@childrens.harvard.edu%3E
Thanks again,
Dima
> On
Hi Dima,
In Apache OODT, when we do environment variable replacement on a URI,
e.g., file://[SOME_ENV]/path, if $SOME_ENV isn’t defined, you get that
error like you had below so that was the source of my suggestion sorry
for not clarifying.
Cheers,
Chris
+
Thanks, Chris.
I didn’t realize cTAKES was relying on environment variables for locating
resources. Do you know which environment variable might be the issue?
Thanks again for your help,
Dima
> On Jun 28, 2016, at 10:26, Mattmann, Chris A (3980)
> wrote:
>
> Hi Dima,
>
> In Apache OODT, wh
Hi Dima,
Might be a red herring - I am not 100% positive that there is an env
var in cTAKES that you are missing just that in the past when I’ve
had that same bug (in another project), that was the cause. You may
try looking for URIs in config file in which the property isn’t being
resolved or it
Dima
Although I'm not an expert, I don't think Ctakes relies on any Environment
variables a priori, unless you have a Ctakes extensions that has added a
dependency. Depending on your error you may need to look in AE or
TypeSystem definition files or in the uimafit types.txt file where search
path
On second thought... This might be useful
http://stackoverflow.com/questions/18055189/why-my-uri-is-not-hierarchical
On 6/28/16, 9:24 AM, "Abramowitsch, Peter"
wrote:
>Dima
>
>Although I'm not an expert, I don't think Ctakes relies on any Environment
>variables a priori, unless you have a Cta
Hi Dima,
Where did you get that class? I don't have UmlsLookupPipeline or the package
org.apache.ctakes.pipelines.
If you want to run from command-line I highly recommend that you use the
PiperFileRunner class in core.pipeline.
To run the clinical pipeline use cli parameters:
-p DefaultFastPi
Hi Sean,
The pipeline I am trying to run is this:
https://github.com/dmitriydligach/ctakes-misc/blob/master/src/main/java/org/apache/ctakes/pipelines/UmlsLookupPipeline.java
(This is the UmlsLookupPipeline class).
It runs fine in Eclipse but fails when I run from command line.
I will look into
ing.
Let me know what happens with the piper approach.
Sean
-Original Message-
From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
Sent: Friday, April 14, 2017 12:47 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Hi Sean,
The pipeline I am trying to run is this:
Hi Sean,
Thanks again for providing this information — the piper approach looks very
promising.
So I gave it a try, but it didn’t quite work. As you suggested, I am trying to
run the PiperFileRunner class in core.pipelines. I give it the following
parameters:
-p
/Users/Dima/Loyola/Workspaces
[mailto:ddlig...@luc.edu]
> Sent: Friday, April 14, 2017 12:47 PM
> To: dev@ctakes.apache.org
> Subject: Re: URI is not hierarchical
>
> Hi Sean,
>
>
>
> The pipeline I am trying to run is this:
>
directory and what is your classpath?
Thanks,
Sean
-Original Message-
From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
Sent: Wednesday, April 26, 2017 12:16 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Hi Sean,
Thanks again for providing this information — the piper
m: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
Sent: Wednesday, April 26, 2017 12:18 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
As I said in my previous email, the piper approach looks very promising.
However many of us probably still have lots of existing uimaFIT pipelin
du]
> Sent: Wednesday, April 26, 2017 12:16 PM
> To: dev@ctakes.apache.org
> Subject: Re: URI is not hierarchical
>
> Hi Sean,
>
>
>
> Thanks again for providing this information — the piper approach looks very
> promising.
>
>
>
> So I gave it a
a fix that worked for me. Since then I cannot duplicate it.
>
> Sean
>
> -Original Message-
> From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
> Sent: Wednesday, April 26, 2017 12:18 PM
> To: dev@ctakes.apache.org
> Subject: Re: URI is not hierarchical
>
> A
-Original Message-
From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
Sent: Wednesday, April 26, 2017 12:18 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
As I said in my previous email, the piper approach looks very promising.
However many of us probably still have lots of
sn't doing anything.
-Original Message-
From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
Sent: Wednesday, April 26, 2017 12:46 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
I am definitely still seeing the “URI is not hierarchical” issue. Here’s a
piece of informa
y rate, the code works but I think that something is missing from your
> configuration.
> Since it is a personal development environment you are kind of on your own.
> Good luck,
> Sean
>
> P.S. Get rid of the ctakes-resources-umls2011ab artifact in your pom. It
> isn't doin
> > At any rate, the code works but I think that something is missing from
> your configuration.
> > Since it is a personal development environment you are kind of on your
> own.
> > Good luck,
> > Sean
> >
> > P.S. Get rid of the ctakes-resources-umls2011ab ar
, April 28, 2017 12:28 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Going back to your original email, I notice cTAKES is referencing
lvg.properties as being within a jar
14 Apr 2017 11:04:24 INFO LvgAnnotator - URL for lvg.properties
=file:/home/dima/.m2/repository/net/s
[mailto:masanz.ja...@gmail.com]
Sent: Friday, April 28, 2017 12:28 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Going back to your original email, I notice cTAKES is referencing
lvg.properties
as being within a jar
14 Apr 2017 11:04:24 INFO LvgAnnotator - URL for lvg.properties
sqldb port of lvg2008 is not working.
>>>
>>> Caused by: org.hsqldb.HsqlException: error in script file line: 61
>> C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\
>> org\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read
>> beyond end
x27;t take too much kludge. Flw.
Sean
-Original Message-
From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
Sent: Friday, April 28, 2017 1:52 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Hi Sean,
My goal is just to run the pipelines in ctakes-misc on a remote server. I
ata\HSqlDb\lvg2008 java.io.IOException: read
>> beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX '3198299
>> 60557 3198299 53129 0 0 0 0 1210464']
>> >
>> > Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException:
>> read beyond
[mailto:masanz.ja...@gmail.com]
Sent: Friday, April 28, 2017 5:31 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Hi Dima,
Just to let you know I am taking a look at this. More later, if not today,
then tomorrow. FYI here is where I'm at so far.
I checked out a fresh copy
nly happens if the pipeline includes dictionary lookup. For
>>> instance, this one fails:
>>>>
>>>>
>>>>
>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
>>> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_
>>> org
Leak_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19
> >>> VascSurg_FollowUp_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19
> >>> VascSurg_PVD_1.rtf.xmi
> >>>> -rwxrwx---+ 1 A
Domain Users 340626 Apr 26 14:19
>> >>> Peds_Dysphagia_1.rtf.xmi
>> >>>> -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19
>> >>> Peds_FebrileSez_1.rtf.xmi
>> >>>> -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 2
-
From: James Masanz [mailto:masanz.ja...@gmail.com]
Sent: Saturday, April 29, 2017 2:00 AM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Hi Dima,
what revision of trunk are you using? I'm getting an error you weren't seeing
so I'm guessing it's because I c
t;I couldn't
> find it here or there or the other place ..." and then thrown a
> FileNotFoundException.
>
>
>
> -Original Message-
> From: James Masanz [mailto:masanz.ja...@gmail.com]
> Sent: Saturday, April 29, 2017 2:00 AM
> To: dev@ctakes.apache.org
&
Users 238984 Apr 26 14:19
>>>>>> OBGYN_Gen_Abscess_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19
>>>>>> OBGYN_HysterectomyAndBSO_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
>>&
dule, and my umls
> >>>>>> credentials in the environment.
> >>>>>>> All database files were found, the pipeline ran, and I got output:
> >>>>>>> total 2448
> >>>>>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
&g
Ok thanks, I found the problem and checked in a fix.
From: James Masanz [mailto:masanz.ja...@gmail.com]
Sent: Saturday, April 29, 2017 10:59 AM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Attached is a snippet of the console messages
On Sat, Apr 29, 2017 at 9:18 AM, Finan
--+ 1 Administrators Domain Users 82308 Apr 26 14:19
>>>>>> OBGYN_HysterectomyAndBSO_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
>>>>>> OBGYN_IUD_1.rtf.xmi
>>>>>>&
box as the
> >>>>>> working directory, ctakes-misc as the classpath module, and my umls
> >>>>>> credentials in the environment.
> >>>>>>> All database files were found, the pipeline ran, and I got output:
> >>>>>>> to
, I
understand that there may be some push back against a manual download.
Sean
-Original Message-
From: James Masanz [mailto:masanz.ja...@gmail.com]
Sent: Tuesday, May 02, 2017 11:14 AM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Where I'm at with avoiding "
: RE: URI is not hierarchical [SUSPICIOUS]
Hi Dima,
Where did you get that class? I don't have UmlsLookupPipeline or the package
org.apache.ctakes.pipelines.
If you want to run from command-line I highly recommend that you use the
PiperFileRunner class in core.pipeline.
To ru
It would be great if we could have a patch that allows lvg to load from
resource from steam. Thanks for looking into that Lewis. Note though- the
physical files requirement may go deeper into lvg code.
Sent from my iPhone
On Oct 15, 2015, at 2:36 AM, Lewis John Mcgibbney
mailto:lewis.mcgibb...
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