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 > >>> > >>
