James,
Ensure that dir is in your classpath. To test out the theory, try
making that path an {absolute_path} instead of res.Note, if you're trying to run this under a servlet container, the webapp could have a different class loader than the container. On Thu, Sep 5, 2013 at 9:37 AM, Vogel, James <[email protected]> wrote: > hsqldb is throwing java.sql.SQLException: File input/output error: > java.io.IOException: Stream closed at the following code in > JdbcConnectionResourceImpl. load: > > > > iv_conn = DriverManager.getConnection( > > urlStr, > > username, > > password); > > > > urlStr is: > jdbc:hsqldb:res:org/apache/ctakes/dictionary/lookup/umls2011ab/umls > > username is: SA > > password is: blank > > > > That path is expanded as regular files along with the other resources off of > my default directory and on the classpath. Is there something special about > the placement of the hsqldb files or something I need to do to enable use of > hsqldb? > > > > Exception details: > > > > Caused by: org.apache.uima.resource.ResourceInitializationException > > at > org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:130) > > at > org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:611) > > at > org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:450) > > at > org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:182) > > 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:123) > > 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:269) > > at > org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387) > > at > org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:255) > > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:429) > > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:373) > > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:186) > > 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:269) > > at > org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354) > > 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 > > Caused by: java.sql.SQLException: File input/output error: > java.io.IOException: Stream closed > > at org.hsqldb.jdbc.Util.sqlException(Unknown Source) > > at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source) > > at org.hsqldb.jdbcDriver.getConnection(Unknown Source) > > at org.hsqldb.jdbcDriver.connect(Unknown Source) > > at java.sql.DriverManager.getConnection(Unknown Source) > > at java.sql.DriverManager.getConnection(Unknown Source) > > at > org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:109) > > ... 60 more > > > > From: Chen, Pei [mailto:[email protected]] > > Sent: Thursday, August 29, 2013 5:57 PM > To: <[email protected]> > Cc: [email protected] > > Subject: Re: Package for use with Solr > > > > Sorry if i was unclear- i meant Only resources need to be unpacked. > What was the full stack trace? > > > Sent from my iPhone > > > On Aug 29, 2013, at 5:52 PM, "Vogel, James" <[email protected]> wrote: > > I do, including ctakes-type-system-3.0.0-incubating.jar. I thought you said > that the xml files needed to be unpacked rather than just in jars so I was > assuming the reason it wasn’t being found had to do with that. > > > > From: Chen, Pei [mailto:[email protected]] > Sent: Thursday, August 29, 2013 5:43 PM > To: [email protected] > Subject: RE: Package for use with Solr > > > > James, > > Do you have all of the ctakes jars in your classpath? > > i.e: > > ctakes-type-system-{version}.jar in your classpath? > > > > --Pei > > > > > > From: Vogel, James [mailto:[email protected]] > Sent: Thursday, August 29, 2013 5:37 PM > To: [email protected] > Subject: RE: Package for use with Solr > > > > 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]> > 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. > > > > > > ________________________________ > > 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.
