I tried adding the NegexAnnotator to my pipeline and after 11 documents were
successfully processed, the 12th fails consistently with
ConcurrentModificationException. I am using the default configuration for the
annotator. Has anyone else encountered this? I'm running ctakes 4.0.0 on
Windows 7
whether you see that relation type?
Tim
On Tue, 2018-03-20 at 18:08 +, Mullane, Sean *HS wrote:
> It seems Liam’s email account is dead. Can anyone else can shed light
> on this?
>
> From: Mullane, Sean *HS
> Sent: Tuesday, March 20, 2018 2:03 PM
> To: 'Liam Bui'; user
It seems Liam’s email account is dead. Can anyone else can shed light on this?
From: Mullane, Sean *HS
Sent: Tuesday, March 20, 2018 2:03 PM
To: 'Liam Bui'; user@ctakes.apache.org
Subject: RE: Extract relation among entities in cTAKES
Liam,
Can you share your descriptor file? I am also trying
iguator, I think.
Sean
From: Schenk, Gundolf [mailto:gundolf.sch...@ucsf.edu]
Sent: Tuesday, March 06, 2018 12:43 PM
To: Mullane, Sean *HS; user@ctakes.apache.org
Subject: Re: YTEX installation
Hi,
Here is my modified clinical pipeline with DBConsumer added at the end:
apache-ctakes-4.0.0> cat
pplicationContext]; root of factory hierarchy
05 Mar 2018 22:36:01 ERROR PiperFileRunner - Initialization of annotator class
"org.apache.ctakes.ytex.uima.annotators.DBConsumer" failed. (Descriptor:
)
Seems to me that some classes were not found?
Is my $CLASSPATH correct?
> echo $CLASSPATH
/mnt/apache-ctakes-4.0.0/desc/:/mnt/apach
should just see logs in the
CLI. You would only see file-based logs if you use a fileAppender appender.
These are also set within the log4j.xml file.
Sean
From: Schenk, Gundolf [mailto:gundolf.sch...@ucsf.edu]
Sent: Monday, March 05, 2018 5:25 PM
To: Mullane, Sean *HS; user@ctakes.apache.org
Subject
Subject: Re: YTEX installation
Yes, step 7) of the YTEX install instructions worked successfully. Which
environment variables need to be set?
I have (manually) sourced ~/ctakes.profile, which sets $CTAKES_HOME and
$CLASSPATH. What else should I check?
Cheers,
Gundolf.
From: "Mullane, Sea
Have you done step 7 listed here? (
https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation )
If so, maybe check that your environment variables are set correctly.
From: Schenk, Gundolf [mailto:gundolf.sch...@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS
Have you set the references to your database in the ytex.properties file? This
is necessary so that ctakes knows how to connect to the database.
Sean
From: Schenk, Gundolf [mailto:gundolf.sch...@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org
Subject: Re: YTEX
Hello all,
I have noticed a common theme in our notes where a list of conditions are
listed with yes/no indicators, like this:
Hyperlipidemia: Yes
Hypercholesterolemia: Yes
Chronic Renal Insufficiency: N/A
Chronic Renal Failure on Dialysis: No
Acute Renal Failure: Yes
Family History of
to work through
the Weka issue if we don't have any good alternatives.
Thanks,
Sean
From: Alan Simmons <alan.simm...@tempus.com>
Sent: Tuesday, November 22, 2016 2:43 PM
To: Mullane, Sean *HS
Cc: user@ctakes.apache.org
Subject: Re: ytex
Sean,
Your exception me
Alan,
Have you had any luck getting past this issue? I am getting similar errors
trying to install YTEX on Windows 7. I tried downgrading to jdk1.7.0_71 but am
still getting a NoClassDefFoundException when running the ant script
setup-build.xml. The error message I get in setup.out is:
Hi All,
I am trying to parse the xml of the AggregatePlaintextFastUMLSProcessor.xml
pipeline file from cTAKES 3.2.2. It seems that the xml namespace resource is no
longer available, which is causing problems for the parser I am using. I can
work around this but it could be an issue for others.
Enders 144.1
Boston, MA 02115
Tel: (617) 919-2972
Fax: (617) 730-0817
Harvard Scholar: http://scholar.harvard.edu/guergana_k_savova/biocv
From: Mullane, Sean *HS [mailto:sp...@hscmail.mcc.virginia.edu]
Sent: Friday, June 24, 2016 5:04 PM
To: 'user@ctakes.apache.org'
<user@ctakes.apache.
There was some mention previously (June 2015, I think) on the mailing list
about the next release of cTAKES including improved temporal relation
extraction. Can anyone share information about what improvements or new
features will be included and when the release is expected?
Thanks,
Sean
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