There is a current limitation where the resources need to be unpacked... (Lucene doesn't like the indexes being inside the compressed jar's.) Try unpacking the resources and adding resources to your classpath... --Pei
On Wed, Aug 28, 2013 at 12:59 PM, Vogel, James <[email protected]>wrote: > 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]> > 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]] > *Sent:* Tuesday, August 27, 2013 9:58 AM > *To:* [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]] > *Sent:* Tuesday, August 27, 2013 7:09 AM > *To:* [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.**** > > **** > ------------------------------ > > IMPORTANT WARNING: Information contained in this email is intended for the > use of the individual to whom it is addressed, and may contain information > that is privileged, confidential, and exempt from disclosure under > applicable law. If you are not the intended recipient, or the employee or > agent responsible for delivering the message to the intended recipient, you > are hereby notified that any dissemination, distribution, or copying of > this communication is STRICTLY FORBIDDEN. If you have received this > communication in error, please notify us immediately by return email and > delete this document. Thank you.**** > > ** ** > ------------------------------ > > IMPORTANT WARNING: Information contained in this email is intended for the > use of the individual to whom it is addressed, and may contain information > that is privileged, confidential, and exempt from disclosure under > applicable law. If you are not the intended recipient, or the employee or > agent responsible for delivering the message to the intended recipient, you > are hereby notified that any dissemination, distribution, or copying of > this communication is STRICTLY FORBIDDEN. If you have received this > communication in error, please notify us immediately by return email and > delete this document. Thank you.**** > > ** ** > > ------------------------------ > IMPORTANT WARNING: Information contained in this email is intended for the > use of the individual to whom it is addressed, and may contain information > that is privileged, confidential, and exempt from disclosure under > applicable law. If you are not the intended recipient, or the employee or > agent responsible for delivering the message to the intended recipient, you > are hereby notified that any dissemination, distribution, or copying of > this communication is STRICTLY FORBIDDEN. If you have received this > communication in error, please notify us immediately by return email and > delete this document. Thank you. >
