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From Pei Chen <chen...@apache.org>
Subject Re: Package for use with Solr
Date Thu, 05 Sep 2013 18:39:51 GMT
James,
Also- If you plan to run this in the same JVM process as Solr or other
multithreaded webapp setup-
be sure to look out for Jira CTAKES-151 [1]
https://issues.apache.org/jira/browse/CTAKES-151

On Thu, Sep 5, 2013 at 10:38 AM, Pei Chen <chenpei@apache.org> wrote:
> 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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>>
>>
>>
>>
>> ________________________________
>>
>> IMPORTANT WARNING: Information contained in this email is intended for the
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>>
>>
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>> IMPORTANT WARNING: Information contained in this email is intended for the
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>> use of the individual to whom it is addressed, and may contain information
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