Thank you, Pei!
After a few more fixes I think I got one of the relation extraction
pipelines to work!
Dima
On 10/17/2012 03:36 PM, Chen, Pei wrote:
FYI:
I reverted the main pom.xml back to use Lucene 3.0.2 instead of 3.5.0.
(whoever needs 3.5.0 will need to work around this until someone rebuilds the
OrangeBook index- JIRA issue #38).
--Pei
-----Original Message-----
From: Wu, Stephen T., Ph.D. [mailto:[email protected]]
Sent: Wednesday, October 17, 2012 12:41 PM
To: [email protected]
Subject: Re: latest build instructions
I get errors when I try what pei suggested, running the standard /ctakes-
clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProces
sor.xml
The stack trace is below. However, if I run it using ctakes-clinical-
pipeline/resources/launch/UIMA_CPE_GUI--clinical_documents_
pipeline.launch
then this doesn't come up, and I instead get problems like JIRA issue #38
(lucene.index.IndexFormatTooOldException)
Do we need to run mvn install (or mvn compile as steve suggests) before a
CVD/CPE, every time we change code? If so, maven gurus, how do we
change that?
stephen
Exception in thread "Thread-7" java.lang.NoClassDefFoundError:
net/openai/util/fsm/State
at
org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnota
tor.ini
tialize(ContextDependentTokenizerAnnotator.java:95)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize
AnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize
(PrimitiveAnalysisEngine_impl.java:156)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analysi
sEngi
neFactory_impl.java:94)
... 22 more
Caused by: java.lang.ClassNotFoundException: net.openai.util.fsm.State
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
... 26 more
On 10/15/12 8:09 PM, "Chen, Pei" <[email protected]> wrote:
It should compile and test fine at minimum. Feel free to update the
instructions.
We can Make the runCVD mvn install optional as the exec scripts needs
the jars and its dependencies to be installed somewhere in order for
it to work. We can revisit the optional scripts after the first
release to see what we want to do with snapshot repos and running scripts
(using the jars and libs).
On Oct 15, 2012, at 6:01 PM, "Steven Bethard"
<[email protected]>
wrote:
On Oct 15, 2012, at 2:52 PM, "Chen, Pei"
<[email protected]>
wrote:
Building and Running from Command Line:
Requirements: svn, java jdk 1.6+, maven 3.0.4+
1) svn co http://svn.apache.org/repos/asf/incubator/ctakes/trunk
2) mvn install
Don't do this. Do `mvn compile` or `mvn test` instead.
The only reason to do `mvn install` is if you do *not* intend to
modify anything in the cTAKES source code, and you *just* want to
depend on the current snapshot of cTAKES in some *other* project.
Otherwise, `mvn install` is almost guaranteed to get your dependencies
out of sync.
3)Optional to run the UIMA CAS Visual Debugger or Collection
Processing Engine GUI:
cd ctakes-clincial-pipeline
mvn exec:exec -PrunCVD
or
mvn exec:exec -PrunCPE
Building and Running from Eclipse IDE:
Requirements: Eclipse IDE 4.2.1+, java jdk 1.6+, subversive plugin
(or svn equivalent with appropriate svn team provider connectors),
m2e plugin (or mvn equivalent) Import Project > Maven > Checkout
Maven Project from SCM
svn: http://svn.apache.org/repos/asf/incubator/ctakes/trunk
Select all projects
Wait until Eclipse downloads and builds all of your projects. The
various build helpers should run jcasgen and builds the projects for
you (there shouldn't be a real need to run mvn install, etc.)
Finish.
-----Original Message-----
From: Coarr, Matt [mailto:[email protected]]
Sent: Monday, October 15, 2012 4:23 PM
To: [email protected]
Subject: latest build instructions
[I already read the thread "Update cTAKES Building and Running
page?" that Pei started 2012-10-10T16:56.]
iWhat are the latest build instructions for command-line and for
eclipse?
I have some changes to commit and need to get my system building
from the latest apache svn code.
I'm catching up on the recent emails about building, maven,
command-line, eclipse, and target users. Lots of discussions going on!
I already have a working copy checked out from svn. And I've seen
(the
yet-to-be-completed) instructions here:
http://incubator.apache.org/ctakes/source.html
(I'd be happy to update this with a quick set of instructions once
I go through the process.)
I'm assuming it's something along the lines of:
* for command-line
- checkout from svn
- run "mvn compile"/"mvn test"/"mvn package"
(I've been using maven for 8+ years and I've always run "mvn
install", but I've been listening to Steve's advice and I'll switch
to these commands :-)
* for eclipse
- checkout from svn
- make sure you have m2e installed
- import the projects into eclipse
- ...trying to figure out what I should be doing hereŠ
Do I just let it build automatically? (In the past I've always
done right click on project -> choose "run as..." -> "mvn install"
but now I know that this is
evil.)
Thanks!
Matt
