I renamed apache-ctakes-3.1.0-SNAPSHOT-bin.zip to jar and created a jar
containing the contents of ctakes-dictionary-lookup\resources and put them on
the classpath. When I don't add the resources jar I get an error because it
can't find those files. Once I get past that, I get a
java.lang.IllegalArgumentException: URI is not hierarchical exception, full
stack trace below. I saw some posts from 2012
(http://ctakes.markmail.org/search/?q=URI+is+not+hierarchical#query:URI%20is%20not%20hierarchical+page:1+mid:yaqtqzbylwdyy35n+state:results)
where you wrote about a similar problem. Any suggestions on why this happens?
2013-08-28 16:41:51,692 ERROR core.SolrCore -
org.apache.solr.common.SolrException: processing error URI is not hierarchical.
id=file:/C:/Users/jvogel/Documents/data/uima_tests/drug%20name%20test%20v1.txt,
text="George Washington was aspirin exposed to butenafine hydrochloride which
is a more complex drug refer..."
at
org.apache.solr.uima.processor.UIMAUpdateRequestProcessor.processAdd(UIMAUpdateRequestProcessor.java:118)
at
org.apache.solr.update.processor.UpdateRequestProcessor.processAdd(UpdateRequestProcessor.java:51)
at
com.lucid.update.FieldMappingProcessor.processAdd(FieldMappingUpdateProcessorFactory.java:98)
at
org.apache.solr.update.processor.LogUpdateProcessor.processAdd(LogUpdateProcessorFactory.java:100)
at
org.apache.solr.handler.loader.XMLLoader.processUpdate(XMLLoader.java:246)
at
org.apache.solr.handler.loader.XMLLoader.load(XMLLoader.java:173)
at
org.apache.solr.handler.UpdateRequestHandler$1.load(UpdateRequestHandler.java:92)
at
org.apache.solr.handler.ContentStreamHandlerBase.handleRequestBody(ContentStreamHandlerBase.java:74)
at
org.apache.solr.handler.RequestHandlerBase.handleRequest(RequestHandlerBase.java:135)
at org.apache.solr.core.SolrCore.execute(SolrCore.java:1816)
at
org.apache.solr.servlet.SolrDispatchFilter.execute(SolrDispatchFilter.java:448)
at
org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:269)
at
com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:163)
at
com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:58)
at
com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPipeline.java:118)
at
com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:113)
at
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1337)
at
org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:484)
at
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:119)
at
org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:524)
at
org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:233)
at
org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1065)
at
org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:413)
at
org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:192)
at
org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:999)
at
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:117)
at
org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:250)
at
org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:149)
at
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:111)
at org.eclipse.jetty.server.Server.handle(Server.java:351)
at
org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:454)
at
org.eclipse.jetty.server.BlockingHttpConnection.handleRequest(BlockingHttpConnection.java:47)
at
org.eclipse.jetty.server.AbstractHttpConnection.content(AbstractHttpConnection.java:900)
at
org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(AbstractHttpConnection.java:954)
at
org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:952)
at
org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:230)
at
org.eclipse.jetty.server.BlockingHttpConnection.handle(BlockingHttpConnection.java:66)
at
org.eclipse.jetty.server.bio.SocketConnector$ConnectorEndPoint.run(SocketConnector.java:254)
at
org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:599)
at
org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:534)
at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.IllegalArgumentException: URI is not hierarchical
at java.io.File.<init>(Unknown Source)
at
org.apache.ctakes.core.resource.FileResourceImpl.load(FileResourceImpl.java:44)
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)
at
org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:146)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:122)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:267)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:361)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:267)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:335)
at
org.apache.lucene.analysis.uima.ae.BasicAEProvider.getAE(BasicAEProvider.java:73)
at
org.apache.solr.uima.processor.UIMAUpdateRequestProcessor.processText(UIMAUpdateRequestProcessor.java:155)
at
org.apache.solr.uima.processor.UIMAUpdateRequestProcessor.processAdd(UIMAUpdateRequestProcessor.java:80)
... 40 more
From: Pei Chen [mailto:[email protected]]
Sent: Wednesday, August 28, 2013 11:43 AM
To: [email protected]
Subject: Re: Package for use with Solr
One can download the binaries which has all of the jars and resources. Of if
you build from source, you can run $mvn package which will generate a
convenience zip with all of the jars and transitive dependencies and resources
neatly packaged inside ctakes-dist/target/.
Hope that helps-
Pei
On Tue, Aug 27, 2013 at 6:07 PM, Vogel, James
<[email protected]<mailto:[email protected]>> wrote:
I'm not yet planning on SolrCAS because I'm not familiar with it yet. First I
just want to use the UIMAUpdateRequestProcessor to map the results from
specific fields into solr. I'm currently stuck on how to create jar(s) that
contain all the things under the *-res folders to work around the following
error:
Caused by: java.io.FileNotFoundException:
org\apache\ctakes\dependency\parser\models\lemmatizer\dictionary-1.3.1.jar (The
system cannot find the path specified)
I'm not familiar with maven. The jars I created via the maven assembly command
only contain the classes. Is there a maven command to create a ctakes jar(s)
that contains all the components (classes, xmls, dictionaries, etc.)?
From: Chen, Pei
[mailto:[email protected]<mailto:[email protected]>]
Sent: Tuesday, August 27, 2013 9:58 AM
To: [email protected]<mailto:[email protected]>
Subject: RE: Package for use with Solr
Hi James,
I believe the process of deploying a primitive annotator should be the same as
an aggregate pipeline that contains a fixed flow...
I presume you would like to append something like the SolrCAS cas consumer at
the end of the pipeline?
--Pei
From: Vogel, James
[mailto:[email protected]<mailto:[email protected]>]
Sent: Tuesday, August 27, 2013 7:09 AM
To: [email protected]<mailto:[email protected]>
Subject: Package for use with Solr
Any guidance on how to package all the components needed for the ctakes
clinical pipeline AggregatePlaintextUMLSProcessor so that it can be deployed as
part of another application? I'd like to deploy it to be run by the
UIMAUpdateRequestProcessor as part of solr document indexing. I know how to
package a single UIMA annotator by just referencing the .xml file and putting
the jar on the class path for Solr. I don't know how to do the same for all of
the components in the pipeline.
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of the individual to whom it is addressed, and may contain information that is
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