Is there something special about where org\apache\ctakes\typesystem\types\TypeSystem.xml needs to be placed relative to the other files in the binary distribution? I put a 'resources' folder on the path containing org\apache\ctakes\typesystem\types\TypeSystem.xml but it isn't being found.
From: Pei Chen [mailto:[email protected]] Sent: Wednesday, August 28, 2013 1:43 PM To: [email protected] Subject: Re: Package for use with Solr 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]<mailto:[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]<mailto:[email protected]>] Sent: Wednesday, August 28, 2013 11:43 AM To: [email protected]<mailto:[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. ________________________________ 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. 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