Hello Again,
Ok - I think I've straightened out some version issues (and resolved the
hierarchical URI loading issue) but now I'm having a problem getting Lucene to
behave nicely when resources are on the classpath vs. the buildpath.
An update: I've checked out the latest code - and am pointing to the
AggregatePlaintextUMLSProcessor.xml in the clinical pipeline. Although (to
complicate things a little), I'm NOT building using the checked out code - but
using mvn to add a dependency on clinical pipeline 3.1.0.
I have my old 3.0.1 resources folder which I've clobbered with the 3.1.0
dependencies. After running a few times and picking up "not founds" I've added
enough of the resources from the various checked out 3.1.0 projects into the
resources folder to get up and running. When I run things with the resources
directory on the buildpath everything works as expected. But, when I run with
the resources directory on the classpath instead, I get a FileNotFoundException:
org.apache.uima.resource.ResourceInitializationException
at
org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.java:80)
at
org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)
at
org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
........
Caused by: java.io.FileNotFoundException:
org/apache/ctakes/dictionary/lookup/rxnorm_index
at
org.apache.ctakes.core.resource.FileLocator.locateExplicitly(FileLocator.java:93)
If I look in my resource folder I do in fact have a matching directory that's
populated with a number of files.
Any insight would be much appreciated,
Steve
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-----Original Message-----
From: Steve Hookway [mailto:[email protected]]
Sent: Tuesday, September 10, 2013 9:52 AM
To: [email protected]
Subject: RE: managing ctakes resources on classpath
Hi Pei,
Thanks for the help!
I'm using version 3.0.1 of the resources and am grabbing my dependencies (using
maven central) from ctakes-clinical-pipeline version 3.0.0-incubating. I wound
up hosting versions of zoner,med-facts, and jcarafe myself; I found a ticket
that made it seem like this is fixed in the latest release, but I couldn't get
the stuff from maven central working without adding these dependencies manually.
I'm using: analysisEngine =
AnalysisEngineFactory.createAnalysisEngineFromPath(analysisEnginePath);
And the Path points to the
ctakes-clinical-pipeline\\desc\\analysis_engine\\AggregatePlaintextUMLSProcessor.xml
It's interesting to me that when running from Eclipse adding the resources to
the buildpath vs. classpath makes a difference - I'm not sure what tricks
Eclipse uses here to transfer buildpath entries to the classpath during runtime
(that threats the resources differently)....
Hopefully this is just a configuration problem!
Thanks again for the help,
Steve
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-----Original Message-----
From: Pei Chen [mailto:[email protected]]
Sent: Tuesday, September 10, 2013 9:34 AM
To: [email protected]
Subject: Re: managing ctakes resources on classpath
Hi Steve,
The URI is not hierarchical is most likely caused by the code trying to use the
resources/models, but they are inside a jar instead of unpacked.
-Which version of cTAKES are you using?
-Do you happen to have the resource file name that caused the above?
--Pei
On Mon, Sep 9, 2013 at 9:48 PM, Steve Hookway <[email protected]> wrote:
> Hi all,
>
> I'm trying to integrate ctakes into a webapp and am running into
> issues getting the resources to load correctly. In a standalone
> version of the app, if I add the resources folder to the buildpath (as
> described in the install directions) everything works as expected.
> However, if I add the folder to the project classpath instead, I get a
> URI is not hierarchical exception from FileResourceImpl.load:
>
> java.lang.IllegalArgumentException: URI is not hierarchical
> at java.io.File.<init>(File.java:392)
> at
> org.apache.ctakes.core.resource.FileResourceImpl.load(FileResourceImpl.java:44)
> at
> org.apache.uima.resource.impl.ResourceManager_impl.registerResource(Re
> sourceManager_impl.java:603)
>
> Similarly if I try and run from a webapp - setting up tomcat's
> classpath to include the ctakes resource folder, I get the same URI is
> not hierarchical error. I found this bug report:
> https://issues.apache.org/jira/browse/CTAKES-89 but it suggests
> adding the resource folder to my classpath, which isn't doing the trick.
>
> If you can steer me in the right direction, I'd really appreciate it.
>
> Thanks,
> Steve
>
>
>
>
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>
>
>
