ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Harpreet Khanduja <hsk5...@rit.edu>
Subject Re: query
Date Thu, 19 Jun 2014 21:39:27 GMT
Hello Pei,

No problem. It was my pleasure.

Now, umls part is working.
Thank you so much for your help.
I really appreciate it.

Harpreet


On Thu, Jun 19, 2014 at 10:22 AM, Pei Chen <chenpei@apache.org> wrote:

> Harpreet,
> There was a typo/incorrect path in one of the xml descriptors.
> Fixed in r1603885.
> Thanks again for testing out trunk...
> --Pei
>
>
> On Wed, Jun 18, 2014 at 8:31 PM, Harpreet Khanduja <hsk5004@rit.edu>
> wrote:
>
> > Hello Pei,
> >
> > It didn't work for me.
> > If it works for you,
> > please let me know.
> >
> > Thank you,
> > Harpreet
> >
> >
> >
> > On Wed, Jun 18, 2014 at 8:02 PM, Pei Chen <chenpei@apache.org> wrote:
> >
> > > Harpreet,
> > > looks like resources just made it to the maven central mirrors.  But I
> > > didn't not get a chance to try it out or fully test it yet.
> > > If you would like to give it a whirl, you can update
> > > ctakes-dictionary-lookup-res/pom.xml to use the latest.
> > > If EclipseIDE doesn't unpack the resources automatically to
> > target/classes,
> > > you can force it to run mvn clean compile.
> > >
> > >  <!-- cTAKES Resources -->
> > >
> > >  <dependency>
> > >
> > >  <groupId>net.sourceforge.ctakesresources</groupId>
> > >
> > >  <artifactId>ctakes-resources-umls2011ab</artifactId>
> > >
> > >  <version>3.1.3</version>
> > >
> > >  </dependency>
> > >
> > >  <dependency>
> > >
> > >  <groupId>net.sourceforge.ctakesresources</groupId>
> > >
> > >  <artifactId>ctakes-resources-rxnorm-hsqldb-2011ab</artifactId>
> > >
> > >  <version>3.1.3</version>
> > >
> > >  </dependency>
> > >
> > >  <dependency>
> > >
> > >  <groupId>net.sourceforge.ctakesresources</groupId>
> > >
> > >  <artifactId>ctakes-resources-orangebook-hsqldb</artifactId>
> > >
> > >  <version>3.1.3</version>
> > >
> > >  </dependency>
> > >
> > >
> > > On Wed, Jun 18, 2014 at 6:58 PM, Harpreet Khanduja <hsk5004@rit.edu>
> > > wrote:
> > >
> > > > Hello Pei,
> > > >   Are you able to use trunk now?
> > > >
> > > > Thank you,
> > > > Harpreet
> > > >
> > > >
> > > > On Wed, Jun 18, 2014 at 12:47 PM, Harpreet Khanduja <
> hsk5004@g.rit.edu
> > >
> > > > wrote:
> > > >
> > > > > Hello Pei,
> > > > >
> > > > > Thank you so much for helping.
> > > > >
> > > > >
> > > > > Harpreet
> > > > >
> > > > >
> > > > > On Wed, Jun 18, 2014 at 11:08 AM, Pei Chen <chenpei@apache.org>
> > wrote:
> > > > >
> > > > >> Harpreet,
> > > > >> I just did a fresh checkout of trunk and could recreate the error.
> >  I
> > > > >> think
> > > > >> I see the issue- the orangebook hsqldb resource is empty on maven
> > > > central.
> > > > >>  I'm hoping to fix that up today.
> > > > >>
> > > > >> --Pei
> > > > >>
> > > > >>
> > > > >> On Tue, Jun 17, 2014 at 6:22 PM, Harpreet Khanduja <
> hsk5004@rit.edu
> > >
> > > > >> wrote:
> > > > >>
> > > > >> > Hello Pei,
> > > > >> >
> > > > >> > I also ran from cmd line same exception
> > > > >> > and I checked pom.xml file on this location.
> > > > >> > https://svn.apache.org/repos/asf/ctakes/trunk
> > > > >> > The version mentioned in the file is 3.1.1.
> > > > >> > .
> > > > >> >
> > > > >> > Could you please tell me about the resources directory problem
> > > which I
> > > > >> > mentioned in the last email?
> > > > >> >
> > > > >> > Thank you so much for your time.
> > > > >> >
> > > > >> > Harpreet
> > > > >> >
> > > > >> >
> > > > >> >
> > > > >> >
> > > > >> > On Tue, Jun 17, 2014 at 5:45 PM, Chen, Pei <
> > > > >> Pei.Chen@childrens.harvard.edu
> > > > >> > >
> > > > >> > wrote:
> > > > >> >
> > > > >> > > If this is trunk, Can you do an 'svn update' to ensure
you
> have
> > > the
> > > > >> > latest?
> > > > >> > > If this is trunk you won't need to do a separate download-
> maven
> > > > >> should
> > > > >> > > download and unpack it automatically for you.
> > > > >> > > Also try the command line alternative:
> > > > >> > > 'mvn -PrunCVD compile' from the root dir. Let me know.
> > > > >> > >
> > > > >> > >
> > > > >> > > Sent from my iPhone
> > > > >> > >
> > > > >> > > > On Jun 17, 2014, at 5:37 PM, "Harpreet Khanduja"
<
> > > hsk5004@rit.edu
> > > > >
> > > > >> > > wrote:
> > > > >> > > >
> > > > >> > > > Pei,
> > > > >> > > >
> > > > >> > > >  Thank you for the quick reply.
> > > > >> > > >  I am using CVD GUI within eclipse which is under
> > > > >> > > >> ctakes-clinical-pipeline project..
> > > > >> > > >> resources
> > > > >> > > >> launch
> > > > >> > > > UIMA_CVD---clinical_documents_pipeline.launch.
> > > > >> > > >
> > > > >> > > >  I am using ctakes 3.1.1 and resouces also 3.1
> > > > >> > > >
> > > > >> > > > I used this link for svn :
> > > > >> > https://svn.apache.org/repos/asf/ctakes/trunk
> > > > >> > > > when I downloaded ctakes using Eclipse.
> > > > >> > > >
> > > > >> > > > isn't this svn for ctakes 3.1.1?
> > > > >> > > >
> > > > >> > > > Thank you,
> > > > >> > > >
> > > > >> > > > Harpreet
> > > > >> > > >
> > > > >> > > >
> > > > >> > > >> On Tue, Jun 17, 2014 at 5:29 PM, Pei Chen
<
> > chenpei@apache.org>
> > > > >> wrote:
> > > > >> > > >>
> > > > >> > > >> Harpreet,
> > > > >> > > >> Are you using the CVD GUI? or within Eclipse
IDE?
> > > > >> > > >> Also which version cTAKES are you using? trunk?
> > > > >> > > >> --Pei
> > > > >> > > >>
> > > > >> > > >>
> > > > >> > > >> On Tue, Jun 17, 2014 at 5:13 PM, Harpreet
Khanduja <
> > > > >> hsk5004@rit.edu>
> > > > >> > > >> wrote:
> > > > >> > > >>
> > > > >> > > >>> Hello Pei,
> > > > >> > > >>>  I would really appreciate if you could
help me again.
> > > > >> > > >>>  After talking to you and reading other
email archives. I
> > have
> > > > >> done
> > > > >> > > >> almost
> > > > >> > > >>> everything I could, but I am not able
to use
> > > > >> > > >>> AggregatePlainTextUMLSProcessor.xml using
> > > > >> > > >>> UIMA_CVD----clinical-pipeline.launch.
> > > > >> > > >>>
> > > > >> > > >>>  Just to be sure.
> > > > >> > > >>>  The resources folder that from <
> > > > >> > > >>
> > > > >> > >
> > > > >> >
> > > > >>
> > > >
> > >
> >
> http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.1.0.zip/download
> > > > >> > > >>> url
> > > > >> > > >>>  is used to replace the resources folder
which is already
> > > inside
> > > > >> > > >>> ctakes/ctakes-dictionary-lookup/ -- directory
>  or
> > > > >> > > >>>         ctakes/ctakes-dictionary-lookup-res/source/main/
> --
> > > > >> > directory.
> > > > >> > > >>>
> > > > >> > > >>> And then which directory is used as a
classpath to
> > > > >> > > >>> ctakes-clinical-pipeline project.
> > > > >> > > >>>
> > > > >> > > >>> I still get the same exception that I
was getting
> earlier. I
> > > > >> looked
> > > > >> > > into
> > > > >> > > >>> the exception deeply and I found that
the exception is
> > thrown
> > > > >> > > >>> while creating a connection object ( iv_conn
) in
> > > > >> > > >>> JdbcConnectionResourceImpl.java (   line
109 or 110 )
> which
> > is
> > > > >> inside
> > > > >> > > >>>                      ctakes- core/
> > > > >> > > >>>> src/main/java
> > > > >> > > >>>> org.apache.ctakes.core.resource
> > > > >> > > >>>
>  package.
> > > > >> > > >>>
> > > > >> > > >>> Thank you very much.
> > > > >> > > >>> Harpreet
> > > > >> > > >>>
> > > > >> > > >>>
> > > > >> > > >>> On Wed, Jun 11, 2014 at 4:33 PM, Chen,
Pei <
> > > > >> > > >> Pei.Chen@childrens.harvard.edu
> > > > >> > > >>> wrote:
> > > > >> > > >>>
> > > > >> > > >>>> Harpreet,
> > > > >> > > >>>> Just curious- is maven able to connect
to the internet
> > (maven
> > > > >> > central
> > > > >> > > >>>> repositories)? i.e. did you have to
set your
> > > ~/.m2/settings.xml
> > > > >> with
> > > > >> > > >>> proxy
> > > > >> > > >>>> info if behind a firewall?
> > > > >> > > >>>> If it was an intermittent issue, you
can try clearing out
> > the
> > > > >> local
> > > > >> > > >>>> ~/.m2/repository?
> > > > >> > > >>>> --Pei
> > > > >> > > >>>>
> > > > >> > > >>>>> -----Original Message-----
> > > > >> > > >>>>> From: Harpreet Khanduja [mailto:hsk5004@rit.edu]
> > > > >> > > >>>>> Sent: Wednesday, June 11, 2014
3:54 PM
> > > > >> > > >>>>> To: dev@ctakes.apache.org
> > > > >> > > >>>>> Subject: Re: query
> > > > >> > > >>>>>
> > > > >> > > >>>>> Pei,
> > > > >> > > >>>>>   I had provided the classpath
=
> > > > >> ctakes-dictionay-look-up/resources
> > > > >> > > >> to
> > > > >> > > >>>> all the
> > > > >> > > >>>>> projects in ctakes.
> > > > >> > > >>>>>   as it says in the documentation
but there was nothing
> > > inside
> > > > >> my
> > > > >> > > >>> target
> > > > >> > > >>>>> folder in ctakes-clinical-pipeline
directory.
> > > > >> > > >>>>>   So, then I ran maven compile
and I got following
> error.
> > > > >> > > >>>>>
> > > > >> > > >>>>>
> > > > >> > > >>>>> [ERROR] Failed to execute goal
on project
> > > > >> ctakes-clinical-pipeline:
> > > > >> > > >>>> Could not
> > > > >> > > >>>>> resolve dependencies for project
> > > > >> > > >>>>>
> > > org.apache.ctakes:ctakes-clinical-pipeline:jar:3.1.2-SNAPSHOT:
> > > > >> > Failed
> > > > >> > > >>> to
> > > > >> > > >>>>> collect dependencies for
> > > > >> > > >>> [org.apache.ctakes:ctakes-type-system:jar:3.1.2-
> > > > >> > > >>>>> SNAPSHOT (compile),
> > > > >> > org.apache.ctakes:ctakes-core:jar:3.1.2-SNAPSHOT
> > > > >> > > >>>>> (compile),
> > org.apache.ctakes:ctakes-utils:jar:3.1.2-SNAPSHOT
> > > > >> > > >> (compile),
> > > > >> > > >>>>> jdom:jdom:jar:1.0 (compile), junit:junit:jar:4.10
> (test),
> > > > >> > > >>>>>
> > > org.apache.ctakes:ctakes-context-tokenizer:jar:3.1.2-SNAPSHOT
> > > > >> > > >>> (compile),
> > > > >> > > >>>>>
> > > org.apache.ctakes:ctakes-dictionary-lookup:jar:3.1.2-SNAPSHOT
> > > > >> > > >>> (compile),
> > > > >> > > >>>>> org.apache.ctakes:ctakes-preprocessor:jar:3.1.2-SNAPSHOT
> > > > >> (compile),
> > > > >> > > >>>>> org.apache.ctakes:ctakes-lvg:jar:3.1.2-SNAPSHOT
> (compile),
> > > > >> > > >>>>> org.apache.ctakes:ctakes-chunker:jar:3.1.2-SNAPSHOT
> > > (compile),
> > > > >> > > >>>>> org.apache.ctakes:ctakes-ne-contexts:jar:3.1.2-SNAPSHOT
> > > > >> (compile),
> > > > >> > > >>>>> org.apache.ctakes:ctakes-pos-tagger:jar:3.1.2-SNAPSHOT
> > > > >> (compile),
> > > > >> > > >>>>> org.apache.ctakes:ctakes-assertion:jar:3.1.2-SNAPSHOT
> > > > (compile),
> > > > >> > > >>>>>
> > > org.apache.ctakes:ctakes-dependency-parser:jar:3.1.2-SNAPSHOT
> > > > >> > > >>> (compile),
> > > > >> > > >>>>>
> > > > >> org.apache.ctakes:ctakes-dependency-parser-res:jar:3.1.2-SNAPSHOT
> > > > >> > > >>>>> (compile),
> > org.apache.ctakes:ctakes-ytex:jar:3.1.2-SNAPSHOT
> > > > >> > > >> (compile),
> > > > >> > > >>>>> org.apache.ctakes:ctakes-ytex-res:jar:3.1.2-SNAPSHOT
> > > > (compile),
> > > > >> > > >>>>> org.apache.ctakes:ctakes-ytex-uima:jar:3.1.2-SNAPSHOT
> > > > >> (compile)]:
> > > > >> > > >>> Failed
> > > > >> > > >>>>> to read artifact descriptor for
> > > > >> > > >>>>> org.apache.ctakes:ctakes-type-system:jar:3.1.2-SNAPSHOT:
> > > > >> Failure to
> > > > >> > > >>> find
> > > > >> > > >>>>> org.apache.ctakes:ctakes:pom:3.1.2-SNAPSHOT
in
> > > > >> > > >>>>> http://repository.apache.org/snapshots
was cached in
> the
> > > > local
> > > > >> > > >>>> repository,
> > > > >> > > >>>>> resolution will not be reattempted
until the update
> > interval
> > > > of
> > > > >> > > >>>>> apache.snapshots has elapsed or
updates are forced ->
> > [Help
> > > 1]
> > > > >> > > >> [ERROR]
> > > > >> > > >>>>>
> > > > >> > > >>>>>
> > > > >> > > >>>>>
> > > > >> > > >>>>> On Wed, Jun 11, 2014 at 2:17 PM,
Chen, Pei
> > > > >> > > >>>>> <Pei.Chen@childrens.harvard.edu>
> > > > >> > > >>>>> wrote:
> > > > >> > > >>>>>
> > > > >> > > >>>>>> Harpreet,
> > > > >> > > >>>>>> I had a closer look at your
log file and it looks like
> > you
> > > > were
> > > > >> > > >>>>>> actually trying to run it
from Eclipse IDE?
> > > > >> > > >>>>>> If so, just ensure that the
resources do exist in the
> > > > >> classpath.
> > > > >> > > >>>>>> If it's within eclipse ide,
the plugin should download
> > and
> > > > >> unpack
> > > > >> > > >> the
> > > > >> > > >>>>>> umls dictionaries automatically
actually. (you can
> check
> > > the
> > > > >> below
> > > > >> > > >> to
> > > > >> > > >>>>>> ensure it exists
> > > > >> > > >>>>>>
> > > > target/classes/org/apache/ctakes/dictionary/lookup/umls2011ab/)
> > > > >> > > >>>>>> You can also try running 'mvn
clean compile' from the
> > > command
> > > > >> line
> > > > >> > > >> as
> > > > >> > > >>>>> well.
> > > > >> > > >>>>>>
> > > > >> > > >>>>>>
> > > > >> > > >>>>>>
> > > > >> > > >>>>>>> -----Original Message-----
> > > > >> > > >>>>>>> From: Harpreet Khanduja
[mailto:hsk5004@rit.edu]
> > > > >> > > >>>>>>> Sent: Wednesday, June
11, 2014 2:09 PM
> > > > >> > > >>>>>>> To: dev@ctakes.apache.org
> > > > >> > > >>>>>>> Subject: Re: query
> > > > >> > > >>>>>>>
> > > > >> > > >>>>>>> Hello,
> > > > >> > > >>>>>>>   Thanks for the reply,
but I have already done that
> > and I
> > > > >> made
> > > > >> > > >>>>>>> sure
> > > > >> > > >>>>>> that
> > > > >> > > >>>>>>>   these resources are
there all over again.
> > > > >> > > >>>>>>>
> > > > >> > > >>>>>>> Harpreet
> > > > >> > > >>>>>>>
> > > > >> > > >>>>>>>
> > > > >> > > >>>>>>>
> > > > >> > > >>>>>>> On Wed, Jun 11, 2014 at
1:49 PM, Pei Chen <
> > > > chenpei@apache.org
> > > > >> >
> > > > >> > > >>>>> wrote:
> > > > >> > > >>>>>>>
> > > > >> > > >>>>>>>> Harpreet,
> > > > >> > > >>>>>>>> Ensure that you have
downloaded the dictionaries
> (umls)
> > > per
> > > > >> > > >>>>>>>> download
> > > > >> > > >>>>>>> page:
> > > > >> > > >>>>>>>> http://ctakes.apache.org/downloads.cgi
> > > > >> > > >>>>>>>> Resources
> > > > >> > > >>>>>>>>
> > > > >> > > >>>>>>>> Resources are required
to run most of cTAKES. They
> are
> > > > >> > > >> available
> > > > >> > > >>>>>>>> for download from
SourceForge:
> > > ctakes-resources-3.1.0.zip <
> > > > >> > > >>>
> > > > >>
> http://sourceforge.net/projects/ctakesresources/files/ctakes-resou
> > > > >> > > >>>>>>>> rces
> > > > >> > > >>>>>>>> -3.1.0.zip/download
> > > > >> > > >>>>>>>> .
> > > > >> > > >>>>>>>>
> > > > >> > > >>>>>>>> Please download, unzip
and add/merge the contents to
> > the
> > > > >> > > >> existing
> > > > >> > > >>>>>>>> resources directory.
Follow the User
> > > > >> > > >>>>>>>> <https://cwiki.apache.org/confluence/x/oxAHAg>
> > > > >> > > >>>>>>>> or Developer <
> > > https://cwiki.apache.org/confluence/x/nxAHAg
> > > > >
> > > > >> > > >>>>>>>> Install Guide to direct
you through the installation
> > > > process.
> > > > >> > > >>>>>>>>
> > > > >> > > >>>>>>>>
> > > > >> > > >>>>>>>> On Wed, Jun 11, 2014
at 1:45 PM, Harpreet Khanduja
> > > > >> > > >>>>>>>> <hsk5004@rit.edu>
> > > > >> > > >>>>>>>> wrote:
> > > > >> > > >>>>>>>>
> > > > >> > > >>>>>>>>> Hello,
> > > > >> > > >>>>>>>>>  I am trying to
use ctakes as a developer. I am not
> > able
> > > > to
> > > > >> > > >>> use
> > > > >> > > >>>>>>>>> UMLS resources
when I run
> > > > >> > > >>>>>>>>>  the AEs which
use UMLS Dictionary.
> > > > >> > > >>>>>>>>>  I have signed
up on the UMLS website and I am using
> > the
> > > > >> > > >>>>>>>>> correct email
> > > > >> > > >>>>>>>> and
> > > > >> > > >>>>>>>>> password.
> > > > >> > > >>>>>>>>>  I have specified
username and password in
> > > > >> > > >>>>>>>>>
> > > > >> > > >>>>>>>>>   Dictionary Lookup:
> > > <cTAKES_HOME>/desc/ctakes-dictionary-
> > > > >> > > >>>>>
> > > lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml*
> > > > >> > > >>>>>>>>>
> > > > >> > > >>>>>>>>>
> > > > >> > > >>>>>>>>>  But I keep getting
the exception. I would really
> > > > appreciate
> > > > >> > > >>>>>>>>> any help on this.
> > > > >> > > >>>>>>>>>
> > > > >> > > >>>>>>>>> OUTPUT THAT I
GET  on running
> > > > >> > > >>>>> AggregatePlaintextUMLSProcessor.xml
:
> > > > >> > > >>>>>>>>>
> > > > >> > > >>>>>>>>>
> > > > >> > > >>>>>>>>>  log4j: reset
attribute= "false".
> > > > >> > > >>>>>>>>> log4j: Threshold
="null".
> > > > >> > > >>>>>>>>> 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].
> > > > >> > > >>>>>>>>> 11 Jun 2014 13:07:01
 INFO TokenizerAnnotatorPTB -
> > > > >> > > >> Initializing
> > > > >> > > >>>>>>>>> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> > > > >> > > >>>>>>>>> 11 Jun 2014 13:07:01
 INFO POSTagger - POS tagger
> > model
> > > > >> file:
> > > > >> > > >>>>>>>>> org/apache/ctakes/postagger/models/mayo-pos.zip
> > > > >> > > >>>>>>>>> 11 Jun 2014 13:07:01
 INFO
> > > > >> > > >> ContextDependentTokenizerAnnotator -
> > > > >> > > >>>>>>>>> Finite state machines
loaded.
> > > > >> > > >>>>>>>>> 11 Jun 2014 13:07:01
 INFO Chunker - Chunker model
> > file:
> > > > >> > > >>>>>>>>> org/apache/ctakes/chunker/models/chunker-model.zip
> > > > >> > > >>>>>>>>> 11 Jun 2014 13:07:03
 INFO SentenceDetector -
> Sentence
> > > > >> > > >> detector
> > > > >> > > >>>>>>>>> model
> > > > >> > > >>>>>>>> file:
> > > > >> > > >>>>>>>>> org/apache/ctakes/core/sentdetect/sd-med-model.zip
> > > > >> > > >>>>>>>>> 11 Jun 2014 13:07:03
 INFO LvgCmdApiResourceImpl -
> > > Loading
> > > > >> > > >> NLM
> > > > >> > > >>>>>>>>> Norm and
> > > > >> > > >>>>>>>> Lvg
> > > > >> > > >>>>>>>>> with config file
=
> > > > >> > > >>>>>>>>
> > D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-
> > > > >> > > >>>>>>> lookup\resourc
> > > > >> > > >>>>>>>> es\org\apache\ctakes\lvg\data\config\lvg.properties
> > > > >> > > >>>>>>>>> 11 Jun 2014 13:07:03
 INFO LvgCmdApiResourceImpl -
> > > > config
> > > > >> > > >>> file
> > > > >> > > >>>>>> absolute
> > > > >> > > >>>>>>>>> path =
> > > > >> > > >>>>>>>>
> > D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-
> > > > >> > > >>>>>>> lookup\resourc
> > > > >> > > >>>>>>>> es\org\apache\ctakes\lvg\data\config\lvg.properties
> > > > >> > > >>>>>>>>> 11 Jun 2014 13:07:03
 INFO LvgCmdApiResourceImpl -
> > cwd =
> > > > >> > > >>
> > D:\workspaces\workspace_cTakes\ctakes\ctakes-clinical-pipeline
> > > > >> > > >>>>>>>>> 11 Jun 2014 13:07:03
 INFO LvgCmdApiResourceImpl -
> cd
> > > > >> > > >>>>>>>>
> > D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-
> > > > >> > > >>>>>>> lookup\resourc
> > > > >> > > >>>>>>>> es\org\apache\ctakes\lvg\
> > > > >> > > >>>>>>>>> 11 Jun 2014 13:07:03
 INFO LvgCmdApiResourceImpl -
> cd
> > > > >> > > >>
> > D:\workspaces\workspace_cTakes\ctakes\ctakes-clinical-pipeline
> > > > >> > > >>>>>>>>> 11 Jun 2014 13:07:04
 INFO
> JdbcConnectionResourceImpl
> > -
> > > > >> > > >>>>>>>>> Connection established
to:
> > > > >> > > >>>
> > > jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/umls2011ab/
> > > > >> > > >>>>>>>>> umls
> > > > >> > > >>>>>>>>> Exception in thread
"main"
> > > > >> > > >>>>>>>>>
> > org.apache.uima.resource.ResourceInitializationException
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>
> > > > >>
> org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(Jdbc
> > > > >> > > >>>>>>> Co
> > > > >> > > >>>>>>>> nnectionResourceImpl.java:130)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>>>
> > > > >> >
> > org.apache.uima.resource.impl.ResourceManager_impl.registerResource(
> > > > >> > > >>>>>>> Re
> > > > >> > > >>>>>>>> sourceManager_impl.java:603)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>
> > > > org.apache.uima.resource.impl.ResourceManager_impl.initializeExter
> > > > >> > > >>>>>>>> nalR
> > > > >> > > >>>>>>>> esources(ResourceManager_impl.java:442)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>
> > > > org.apache.uima.resource.Resource_ImplBase.initialize(Resource_Imp
> > > > >> > > >>>>>>>> lBas
> > > > >> > > >>>>>>>> e.java:153)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>
> > > > org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initia
> > > > >> > > >>>>>>>> lize
> > > > >> > > >>>>>>>> (AnalysisEngineImplBase.java:157)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>
> > > > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> > > > >> > > >>>>>>>> init
> > > > >> > > >>>>>>>> ialize(PrimitiveAnalysisEngine_impl.java:123)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>>>
> > > > >> >
> > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Anal
> > > > >> > > >>>>>>> ys
> > > > >> > > >>>>>>>> isEngineFactory_impl.java:94)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>>>
> > > > >> >
> > org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
> > > > >> > > >>>>>>> om
> > > > >> > > >>>>>>>> positeResourceFactory_impl.java:62)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>>>
> > > > >> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:
> > > > >> > > >>>>>>> 269
> > > > >> > > >>>>>>>>> )
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>>>
> > > > >> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework
> > > > >> > > >>>>>>> .java
> > > > >> > > >>>>>>>> :387)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>
> > > > >>
> > org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:
> > > > >> > > >>>>>>>> 254)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>
> > > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> > > > >> > > >>>>>>>> init
> > > > >> > > >>>>>>>> ASB(AggregateAnalysisEngine_impl.java:431)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>
> > > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> > > > >> > > >>>>>>>> init
> > > > >> > > >>>
> > > > ializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:37
> > > > >> > > >>>>>>>> 5)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>
> > > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> > > > >> > > >>>>>>>> init
> > > > >> > > >>>>>>>> ialize(AggregateAnalysisEngine_impl.java:185)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>>>
> > > > >> >
> > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Anal
> > > > >> > > >>>>>>> ys
> > > > >> > > >>>>>>>> isEngineFactory_impl.java:94)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>>>
> > > > >> >
> > org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
> > > > >> > > >>>>>>> om
> > > > >> > > >>>>>>>> positeResourceFactory_impl.java:62)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>>>
> > > > >> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:
> > > > >> > > >>>>>>> 269
> > > > >> > > >>>>>>>>> )
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>>>
> > > > >> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework
> > > > >> > > >>>>>>> .java
> > > > >> > > >>>>>>>> :387)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>
> > > > >>
> > org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:
> > > > >> > > >>>>>>>> 254)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>
> > > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> > > > >> > > >>>>>>>> init
> > > > >> > > >>>>>>>> ASB(AggregateAnalysisEngine_impl.java:431)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>
> > > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> > > > >> > > >>>>>>>> init
> > > > >> > > >>>
> > > > ializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:37
> > > > >> > > >>>>>>>> 5)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>
> > > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> > > > >> > > >>>>>>>> init
> > > > >> > > >>>>>>>> ialize(AggregateAnalysisEngine_impl.java:185)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>>>
> > > > >> >
> > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Anal
> > > > >> > > >>>>>>> ys
> > > > >> > > >>>>>>>> isEngineFactory_impl.java:94)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>>>
> > > > >> >
> > org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
> > > > >> > > >>>>>>> om
> > > > >> > > >>>>>>>> positeResourceFactory_impl.java:62)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>>>
> > > > >> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:
> > > > >> > > >>>>>>> 269
> > > > >> > > >>>>>>>>> ) at
> > > > >> > > >>>>>
> > > > >> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:
> > > > >> > > >>>>>>> 314
> > > > >> > > >>>>>>>>> )
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>>>
> > > > >> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework
> > > > >> > > >>>>>>> .java
> > > > >> > > >>>>>>>> :425)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>
> > > > org.uimafit.factory.AnalysisEngineFactory.createAggregate(Analysis
> > > > >> > > >>>>>>>> Engi
> > > > >> > > >>>>>>>> neFactory.java:424)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>
> > > > org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.jav
> > > > >> > > >>>>>>>> a:16
> > > > >> > > >>>>>>>> 5)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>
> > > > org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.jav
> > > > >> > > >>>>>>>> a:19
> > > > >> > > >>>>>>>> 0)
> > > > >> > > >>>>>>>>> at
> > > > >> > > >>>
> > > > org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.main(Cl
> > > > >> > > >>>>>>>> inic
> > > > >> > > >>>>>>>> alPipelineFactory.java:116)
> > > > >> > > >>>>>>>>> Caused by: java.sql.SQLException:
File input/output
> > > error:
> > > > >> > > >>>>>>>>> java.io.IOException:
Stream closed at
> > > > >> > > >>>>>>>>> org.hsqldb.jdbc.Util.sqlException(Unknown
Source) at
> > > > >> > > >>>>>>>>> org.hsqldb.jdbc.jdbcConnection.<init>(Unknown
> Source)
> > at
> > > > >> > > >>>>>>>>> org.hsqldb.jdbcDriver.getConnection(Unknown
Source)
> at
> > > > >> > > >>>>>>>>> org.hsqldb.jdbcDriver.connect(Unknown
Source) at
> > > > >> > > >>>>>>>>> java.sql.DriverManager.getConnection(Unknown
Source)
> > at
> > > > >> > > >>>>>>>>> java.sql.DriverManager.getConnection(Unknown
Source)
> > at
> > > > >> > > >>>
> > > > >>
> org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(Jdbc
> > > > >> > > >>>>>>> Co
> > > > >> > > >>>>>>>> nnectionResourceImpl.java:109)
> > > > >> > > >>>>>>>>> ... 30 more
> > > > >> > > >>
> > > > >> > >
> > > > >> >
> > > > >>
> > > > >
> > > > >
> > > >
> > >
> >
>

Mime
  • Unnamed multipart/alternative (inline, None, 0 bytes)
View raw message