Todd,
This seems to be the same issue some others are having, as first pointed
out by Steve Bethard in an earlier thread. I believe the issue stems
from the fact that "jcasgen" (the UIMA tool that generates source code
from type system files) is part of the maven build pipeline. You should
be able to work around it by disabling "Build projects automatically" in
eclipse but this is obviously not a great solution. Steve has posted a
fix but it has not been integrated because we're still trying to figure
out why this issue only affects some setups (now that I understand it,
it is surprising that it doesn't affect some people). If you want to
try his fix you can find it here:
https://issues.apache.org/jira/browse/CTAKES-65
Thanks
Tim Miller
On 10/19/2012 09:31 AM, Lingren, Todd wrote:
I downloaded a fresh build of Eclipse 4.2 (my development environment is in
Helios), installed Subversive SVN, Maven SCM handler, M2E connector,
And then followed the eclipse instructions here:
http://incubator.apache.org/ctakes/source.html
When I try to launch the CPE GUID (clinical pipeline), eclipse launches a box
'building workspace' which never completes and looks like it just cycles around
several times, with Build workspace, Launching... Refreshing workspace. And so
on.
Any idea on what I must have done wrong?
Todd Lingren
Biomedical Informatics
Cincinnati Children's Hospital
-----Original Message-----
From: Chen, Pei [mailto:[email protected]]
Sent: Thursday, October 18, 2012 1:45 PM
To: [email protected]
Subject: RE: latest build instructions
Drafted the source code build instructions on the web site (please feel free to
update it as you see fit):
http://incubator.apache.org/ctakes/source.html
-I think the vi and emacs developers will also appreciate the CLI option which
wasn't previously available -End users should just be able to download the
bin.zip/tar.zip, unzip and run bin/startctakesCVD.bat/sh.
There are still some outstanding bugs to be fixed, but hopefully we'll create a
Release Candidate for review shortly.
Also, the release process:
http://incubator.apache.org/ctakes/ctakes-release-guide.html (which will most
likely be updated after our first release).
Thanks,
Pei
-----Original Message-----
From: Chen, Pei [mailto:[email protected]]
Sent: Wednesday, October 17, 2012 6:58 PM
To: [email protected]
Subject: RE: latest build instructions
That worked like a charm. You rock Steve!
The changes have been committed.
-----Original Message-----
From: Steven Bethard [mailto:[email protected]]
Sent: Wednesday, October 17, 2012 4:36 PM
To: [email protected]
Subject: Re: latest build instructions
On Oct 17, 2012, at 10:39 AM, "Wu, Stephen T., Ph.D."
<[email protected]> wrote:
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?
You certainly need to compile after every time you change the code.
Otherwise you won't see your changes.
To avoid having to run `mvn install` before you run the CVD/CPE, you
could change the ctakes-clinical-pipeline/pom.xml to include
something
like:
<profile>
<id>runCPE</id>
<activation>
<property>
<name>runCPE</name>
</property>
</activation>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-
plugin</artifactId>
<version>1.2.1</version>
<executions>
<execution>
<!-- depends
on other modules being on classpath -->
<phase>compile</phase>
<goals>
<goal>java</goal>
</goals>
</execution>
</executions>
<configuration>
<mainClass>org.apache.uima.tools.cpm.CpmFrame</mainClass>
</configuration>
</plugin>
</plugins>
</build>
</profile>
That's different from what's in there now. In particular, it uses
exec:java, not exec:exec, and it links the CpmFrame to the compile
phase whenever the runCPE profile is active. You can then run this,
from the root of the cTAKES checkout as:
$ mvn -PrunCPE compile
That will only recompile anything that has changed in any of the
cTAKES projects, and then run the CPE. No need to install - Maven
will collect the classpath automatically from the target/classes
directories in the various projects.
Depending on what you load in the CPE, you may need more memory. In
that case, you'll want to set your MAVEN_OPTS environment variable
before you run the command above. In bash, you could do something like:
$ MAVEN_OPTS="-Xmx1g" mvn -PrunCPE compile
Steve
