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From Pei Chen <chen...@apache.org>
Subject Re: Package for use with Solr
Date Thu, 05 Sep 2013 14:38:59 GMT
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 <JVogel@activehealth.net> 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:Pei.Chen@childrens.harvard.edu]
>
> Sent: Thursday, August 29, 2013 5:57 PM
> To: <user@ctakes.apache.org>
> Cc: user@ctakes.apache.org
>
> 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" <JVogel@activehealth.net> 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:Pei.Chen@childrens.harvard.edu]
> Sent: Thursday, August 29, 2013 5:43 PM
> To: user@ctakes.apache.org
> 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:JVogel@activehealth.net]
> Sent: Thursday, August 29, 2013 5:37 PM
> To: user@ctakes.apache.org
> 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:chenpei@apache.org]
> Sent: Wednesday, August 28, 2013 1:43 PM
> To: user@ctakes.apache.org
> 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 <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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>
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>
>
> ________________________________
>
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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
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> in error, please notify us immediately by return email and delete this
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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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> 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
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> 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
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