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From Pei Chen <chen...@apache.org>
Subject Re: Package for use with Solr
Date Wed, 28 Aug 2013 17:42:50 GMT
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 <JVogel@activehealth.net>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:chenpei@apache.org]
> *Sent:* Wednesday, August 28, 2013 11:43 AM
> *To:* user@ctakes.apache.org
> *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 <JVogel@activehealth.net>
> 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:Pei.Chen@childrens.harvard.edu]
> *Sent:* Tuesday, August 27, 2013 9:58 AM
> *To:* user@ctakes.apache.org
> *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:JVogel@activehealth.net]
> *Sent:* Tuesday, August 27, 2013 7:09 AM
> *To:* user@ctakes.apache.org
> *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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> ** **
>  ------------------------------
>
> 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
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> ** **
>
> ------------------------------
> 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
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> agent responsible for delivering the message to the intended recipient, you
> are hereby notified that any dissemination, distribution, or copying of
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