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From "Vogel, James" <JVo...@activehealth.net>
Subject RE: Package for use with Solr
Date Thu, 05 Sep 2013 13:37:52 GMT
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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto:chenpei@apache.org>]
Sent: Wednesday, August 28, 2013 11:43 AM
To: user@ctakes.apache.org<mailto: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<mailto: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<mailto:Pei.Chen@childrens.harvard.edu>]
Sent: Tuesday, August 27, 2013 9:58 AM
To: user@ctakes.apache.org<mailto: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<mailto:JVogel@activehealth.net>]
Sent: Tuesday, August 27, 2013 7:09 AM
To: user@ctakes.apache.org<mailto: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
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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
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