Thank you both. I just deleted everything and redownloaded in order to make
sure all files were transferred properly. I downloaded ctakes version 3.2.2,
and resources version 3.2.1.1.
As outlined in the User Guide, I moved the temp resources download to the
apache folder, overwriting the previous resources folder. I confirmed that
there is a folder
/apache-ctakes-3.2.2/resources/org/apache/ctakes/dictionary/lookup/fast
When trying to load an UMLS AE (Aggregate Plain Text), this that I get the
error message:
“org.apache.uima.resource.ResourceInitializationException: initialization of
annotator class
“org.apache.ctakes.assertio.medfacts.cleartk.HistoryCleartkAnalysisEngine”
failed.”
Here is the terminal output:
27 Sep 2016 13:58:32 INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip
27 Sep 2016 13:58:33 INFO ContextDependentTokenizerAnnotator - Finite state
machines loaded.
27 Sep 2016 13:58:33 INFO ConstituencyParser - Initializing parser...
SFGH-0H0DHJW-DT:apache-ctakes-3.2.2 mgianfrancesco$ bin/runctakesCVD.sh
log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressAppender] additivity to [false].
log4j: Level value for ProgressAppender is [INFO].
log4j: ProgressAppender level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m].
log4j: Adding appender named [noEolAppender] to category [ProgressAppender].
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressDone] additivity to [false].
log4j: Level value for ProgressDone is [INFO].
log4j: ProgressDone level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m%n].
log4j: Adding appender named [eolAppender] to category [ProgressDone].
log4j: Level value for root is [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss} %5p
%c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
27 Sep 2016 14:03:29 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg
with config file =
/Users/mgianfrancesco/Desktop/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/data/config/lvg.properties
27 Sep 2016 14:03:30 INFO LvgCmdApiResourceImpl - config file absolute path
=
/Users/mgianfrancesco/Desktop/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/data/config/lvg.properties
27 Sep 2016 14:03:30 INFO LvgCmdApiResourceImpl - cwd =
/Users/mgianfrancesco/Desktop/apache-ctakes-3.2.2
27 Sep 2016 14:03:30 INFO LvgCmdApiResourceImpl - cd
/Users/mgianfrancesco/Desktop/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/
27 Sep 2016 14:03:30 INFO LvgCmdApiResourceImpl - cd
/Users/mgianfrancesco/Desktop/apache-ctakes-3.2.2
27 Sep 2016 14:03:30 INFO ClearNLPDependencyParserAE - using Morphy analysis?
true
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
27 Sep 2016 14:03:42 INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip
27 Sep 2016 14:03:44 INFO ContextDependentTokenizerAnnotator - Finite state
machines loaded.
27 Sep 2016 14:03:44 INFO ConstituencyParser - Initializing parser...
From: Bandeep Singh <[email protected]<mailto:[email protected]>>
Reply-To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Date: Tuesday, September 27, 2016 at 1:21 PM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: Trouble loading AE
If you are trying to run the AggregatePlaintextFastUMLSProcessor.xml as
described by the User guide , my best guess is that you are missing the folder
/apache-ctakes-3.2.2/resources/org/apache/ctakes/dictionary/fast
On Tue, Sep 27, 2016 at 1:09 PM, Bandeep Singh
<[email protected]<mailto:[email protected]>> wrote:
Can you share the complete stack trace (error logs). And may be we will know
what is going on.
On Tue, Sep 27, 2016 at 12:47 PM, Gianfrancesco, Milena
<[email protected]<mailto:[email protected]>> wrote:
Thanks, yes, so I am getting this error message in response to loading the AE
even though resources have been downloaded as specified in the User Manuel. Any
other thoughts as to why this may be occurring? Do any of the files within the
resources folder need to be modified before loading?
From: Bandeep Singh <[email protected]<mailto:[email protected]>>
Reply-To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Date: Tuesday, September 27, 2016 at 11:55 AM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: Trouble loading AE
Hi Milena,
I am referring to the same resources mentioned in the User Install Guide doc.
-Bandeep
On Tue, Sep 27, 2016 at 11:05 AM, Gianfrancesco, Milena
<[email protected]<mailto:[email protected]>> wrote:
Hi Bandeep,
I downloaded resources as instructed in the User Install Guide and copied them
into the resources folder. Is that what you are referring to? Or it there
another set of UMLS resources to be downloaded? There didn’t appear to be so in
the link.
Thanks
From: Bandeep Singh <[email protected]<mailto:[email protected]>>
Reply-To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Date: Wednesday, September 21, 2016 at 3:54 PM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: Trouble loading AE
Hi,
Glad that it worked !
I think resources are missing in your cTakes installation.
Did you download the UMLS resources separately from
https://sourceforge.net/projects/ctakesresources/files/?source=navbar
And You have to put these resources under org/apache/ctakes/dictionary/
Hope that Helps !
Bandeep
On Wed, Sep 21, 2016 at 3:45 PM, Gianfrancesco, Milena
<[email protected]<mailto:[email protected]>> wrote:
Thanks, Bandeep. That seems to have solved that issue, but now when I try to
load AE I get an error message popup that states:
"org.apache.uima.resource.ResourceInitializationException". I'm not sure what
this means? It only happens when I try to load the AEs that utilize UMLS.
Thanks in advance.
________________________________
From: Bandeep Singh [[email protected]<mailto:[email protected]>]
Sent: Tuesday, September 13, 2016 5:24 PM
To: [email protected]<mailto:[email protected]>
Subject: Re: Trouble loading AE
Hi Milena,
It looks like a classic example of Java version mismatch. One of the
dependencies of cTakes is Java 8
Please make sure you have JAVA SDK installed and not JRE. I have OpenJDK 8
running on my system and cTakes runs fine on my system.
-Bandeep
On Tue, Sep 13, 2016 at 2:32 PM, Gianfrancesco, Milena
<[email protected]<mailto:[email protected]>> wrote:
Hello,
I have just installed cTakes and followed instructions in the 3.2 User Install
Guide. However, I am unable to load an AE. I have a UMLS user name and
password, and have updated the appropriate scripts as outlined in the User
Guide, yet I get this error when trying to load any AE (even the non-UMLS ones):
Exception in thread "AWT-EventQueue-0" java.lang.UnsupportedClassVersionError:
org/apache/ctakes/dependency/parser/ae/ClearNLPDependencyParserAE : Unsupported
major.minor version 51.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)
at java.lang.ClassLoader.defineClass(ClassLoader.java:621)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
…… + more
I have double checked that I have the latest Java software. Any idea what
could be causing this error?
Thank you!
Milena
