Hi Sean, I am not trying to run it with multiple threads and in fact, I haven't changed the code for the JdbcRareWordDictionary class. The changes are done in the customDictionary.xml file only.
The issue comes when I am running it in a docker container. I did not encounter this issue on my local machine. Attaching logs file. Regards Chahal Arora Software Engineer Raxa On Wed, Dec 27, 2017 at 8:30 PM, Finan, Sean < [email protected]> wrote: > Hi Chahal Arora, > > That is odd - I have never seen that message. Are you trying to run with > multiple threads? Like most of ctakes, that class was designed to be run > in a single thread. There are thread-safe wrappers that can be used if > needed, but they should not be relied upon for speed increases. > > Sean > > -----Original Message----- > From: Chahal Arora [mailto:[email protected]] > Sent: Wednesday, December 27, 2017 7:53 AM > To: [email protected] > Subject: Re: Custom Dictionary connected to mysql [EXTERNAL] > > Hi Gandhi, Sean, and James > > Thank you all for your help. > > It ran fine but after some time, I started getting the following error- > > ERROR JdbcRareWordDictionary - No operations allowed after statement > closed. > > The class giving the issue is - > https://urldefense.proofpoint.com/v2/url?u=https-3A__github. > com_apache_ctakes_blob_bed6cca07743e30aec40aae30af1738a0ba1a93d_ctakes- > 2Ddictionary-2Dlookup-2Dfast_src_main_java_org_apache_ > ctakes_dictionary_lookup2_dictionary_JdbcRareWordDictionary.java&d= > DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m= > VOGRYBwYyG1zdYg5tgQm1oZ7uLNttyQdSvc7jDT9SV0&s= > 4USoFHxgktikbJUwVl1joy0LisnxFzv6M8HGQnlaRVg&e= > > It looks like the statement is getting closed by a thread and another > thread is trying to use it. > > mysqlUrl entred - jdbc:mysql:// > 127.0.0.1:3306/umlstest?useUnicode=true&characterEncoding=utf8& > useSSL=false& > > Is there a MySQL setting I need to change or the code in > JdbcRareWordDictionary.java like creating a connection pool? > > Regards > Chahal Arora > > Regards > Chahal Arora > Software Engineer > Raxa > > On Sat, Dec 23, 2017 at 8:08 AM, James Masanz <[email protected]> > wrote: > > > one advantage of having the database entries be lower-case is > performance. > > > > since a dictionary in a database is typically significantly larger > > than a BSV file dictionary, it is advantageous to lower case the > > database dictionary entries just once. > > > > > > On Thu, Dec 21, 2017 at 4:17 PM, Chahal Arora <[email protected]> > > wrote: > > > > > Hi Sean, > > > > > > I wanted the lookup to be case insensitive. Also wanted to go away > > > with > > the > > > restriction of putting enteries in lowercase in database like the > > > way it was working with BSV. > > > > > > But if lowercase enteries are expected in database then I guess > > > modifying database will work for me. > > > > > > On Fri, 22 Dec 2017 at 12:46 AM, Finan, Sean < > > > [email protected]> wrote: > > > > > > > Do you want your lookup to be case sensitive? If so then new code > > would > > > > be required. The lookup is case insensitive because it does > > > > expect the dictionary/database to contain only lowercase entries. > > > > If you are ok > > > with > > > > the case insensitivity then I propose that you modify your database. > > > > Sean > > > > > > > > > > > > -----Original Message----- > > > > From: Gandhi Rajan Natarajan > > > > [mailto:[email protected]] > > > > Sent: Thursday, December 21, 2017 11:06 AM > > > > To: [email protected] > > > > Subject: RE: Custom Dictionary connected to mysql [EXTERNAL] > > > > > > > > I feel Sean and Tim will be the right persons to answer this. > > > > > > > > > > > > > > > > Regards, > > > > > > > > Gandhi > > > > > > > > > > > > > > > > -----Original Message----- > > > > > > > > From: Chahal Arora [mailto:[email protected]] > > > > > > > > Sent: Thursday, December 21, 2017 7:32 PM > > > > > > > > To: [email protected] > > > > > > > > Subject: Re: Custom Dictionary connected to mysql > > > > > > > > > > > > > > > > Hi Gandhi, Thank you for your help. It's working now. In the > > > > customDictionary.xml, I changed > > > > org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictio > > > > nary > > > to > > > > org.apache.ctakes.dictionary.lookup2.dictionary. > > > UmlsJdbcRareWordDictionary > > > > > > > > and > > > > org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory to > org.apache.ctakes.dictionary.lookup2.concept.UmlsJdbcConceptFactory. > > For > > > > single word term, this worked without any change, but for a > > > > multi-word term, this was returning empty results. When I > > > > debugged, I found that > > the > > > > issue was coming at code below in DefaultJCasTermAnnotator class > > > > line > > > 103- > > > > if ( hitTokens[ hit ].equals(allTokens.get( i ).getText() ) || > > hitTokens[ > > > > hit ].equals( allTokens.get( i ).getVariant() ) ); This was > > > > happening > > due > > > > to the difference in string case. The input string is converted to > > > > lowercase, but the string from MySQL database is not converted. > > > > Right > > > now I > > > > have to put all terms in my database in lower case to make it > > > > work. Do > > > you > > > > know any configuration so that I don't have to deal with the case > > > > issue without changing DefaultJCasTermAnnotator file? When using > > > > BSV file, I > > am > > > > getting lower case sting for both input and term. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Regards > > > > > > > > Chahal Arora > > > > > > > > Software Engineer > > > > > > > > Raxa > > > > > > > > > > > > > > > > On Tue, Dec 19, 2017 at 11:23 PM, Gandhi Rajan Natarajan < > > > > [email protected]> wrote: > > > > > > > > > > > > > > > > > Hi Chahal, > > > > > > > > > > > > > > > > > > Looking at the error trace: > > > > > > > > > ‘javax.servlet.ServletException,java.io.IOException > > > > > > > > > 19 Dec 2017 17:56:01 INFO RequestMappingHandlerAdapter - > > > > > Looking for > > > > > > > > > @ControllerAdvice: WebApplicationContext for namespace > > > > > > > > > 'ctakes-rest-service-servlet'’ > > > > > > > > > > > > > > > > > > It looks like you are trying to mix match codes from both > > > > > > > > > ctakes-rest-service and ctakes-web-rest module I guess. > > > > > > > > > Ctakes-rest-service module is obsolete now and request you to > > consider > > > > > > > > > only ctakes-web-rest module in > > > > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github. > > > com_GoTeamEpsilon_ctakes-2Drest-2D&d=DwIGaQ&c=qS4goWBT7poplM69zy_ > > > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc > > pKGd4f7d4gTao&m= > > > FqnIF6F3Z8G6N9y2xdT6hsGRUtI9Gkcio-84DqbbEJM&s=6B-VtVwKMYDaxqmRYJgeUq > > > - > > > 3W2oT9wb6XDlnckfJ9rU&e= > > > > > > > > > service/tree/master/ctakes-web-rest > > > > > > > > > > > > > > > > > > Regards, > > > > > > > > > Gandhi > > > > > > > > > > > > > > > > > > From: Chahal Arora [mailto:[email protected]] > > > > > > > > > Sent: Tuesday, December 19, 2017 8:20 PM > > > > > > > > > To: [email protected] > > > > > > > > > Subject: Re: Custom Dictionary connected to mysql > > > > > > > > > > > > > > > > > > Hi Gandhi, > > > > > > > > > > > > > > > > > > With updated customDictionary.xml all errors were gone. > > > > > > > > > > > > > > > > > > I am not sure about the schema of the tables used. I have taken > > > > > > > > > reference from JdbcRareWordDictionary.java - > > > > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github. > > > com_apache_&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r > > > = fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m= > > > FqnIF6F3Z8G6N9y2xdT6hsGRUtI9Gkcio-84DqbbEJM&s=JLcnqVyhD1PRoXduqLRON_ > > > SkVHeLv0q7doqV6RSn-7A&e= > > > > > > > > > ctakes/blob/trunk/ctakes-dictionary-lookup-fast/src/ > > > > > > > > > main/java/org/apache/ctakes/dictionary/lookup2/dictionary/ > > > > > > > > > JdbcRareWordDictionary.java and JdbcConceptFactory.java - > > > > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github. > > > com_apache_ctakes_blob_trunk_ctakes-2D&d=DwIGaQ&c=qS4goWBT7poplM69zy > > > _ 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc > > pKGd4f7d4gTao&m= > > > FqnIF6F3Z8G6N9y2xdT6hsGRUtI9Gkcio-84DqbbEJM&s=cfygw3v7SDiH3Wjz_ > > > VepLVO006NEJBCH79qO3sHBlm4&e= > > > > > > > > > dictionary-lookup-fast/src/main/java/org/apache/ctakes/ > > > > > > > > > dictionary/lookup2/concept/JdbcConceptFactory.java > > > > > > > > > > > > > > > > > > I am using the ctakes-rest-web server and getting all the > > > > > annotation > > > > > > > > > array as empty in the result json. > > > > > > > > > > > > > > > > > > Attached tomcat logs again. > > > > > > > > > > > > > > > > > > Regards > > > > > > > > > Chahal Arora > > > > > > > > > Software Engineer > > > > > > > > > Raxa > > > > > > > > > > > > > > > > > > On Tue, Dec 19, 2017 at 6:44 PM, Gandhi Rajan Natarajan < > > > > > > > > > [email protected]<mailto:Gandhi.Natarajan@ > > arisglobal.com > > > > > > > > > >> > > > > > > > > > wrote: > > > > > > > > > Not able to see any tomcat logs attached. > > > > > > > > > > > > > > > > > > Do you see any errors in tomcat console? > > > > > > > > > > > > > > > > > > Regards, > > > > > > > > > Gandhi > > > > > > > > > > > > > > > > > > From: Chahal Arora [mailto:[email protected]<mailto: > > > > > > > > > [email protected]>] > > > > > > > > > Sent: Tuesday, December 19, 2017 6:09 PM > > > > > > > > > To: [email protected]<mailto:[email protected]> > > > > > > > > > Subject: Re: Custom Dictionary connected to mysql > > > > > > > > > > > > > > > > > > Hi, > > > > > > > > > > > > > > > > > > I have updated the customDictionary.xml and all the erros have > > > > > gone > > > > > > > > > but still not getting any result. I am attaching the latest > > > > > > > > > customDictionary.xml and tomcat logs file. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Regards > > > > > > > > > Chahal Arora > > > > > > > > > Software Engineer > > > > > > > > > Raxa > > > > > > > > > > > > > > > > > > On Tue, Dec 19, 2017 at 5:45 PM, Chahal Arora > > > > > <[email protected] > > > > > > > > > <mailto:[email protected]><mailto:[email protected]<mail > > > > > to:c > > > > > > > > > [email protected]>>> wrote: > > > > > > > > > Hi All, > > > > > > > > > > > > > > > > > > I was working on moving the terms from custom dictionary BSV > > > > > file to > > > > > > > > > MySQL database in LabValueFinder. I am able to connect to the > > database > > > > > > > > > but not sure about the database schema. > > > > > > > > > > > > > > > > > > Is there an example available where the custom dictionary is > > connected > > > > > > > > > to mysql database instead of a bsv file or hsql database? > > > > > > > > > > > > > > > > > > Attached is the customDictionary.xml file that I am using. > > > > > > > > > > > > > > > > > > > > > > > > > > > Regards > > > > > > > > > Chahal Arora > > > > > > > > > Software Engineer > > > > > > > > > Raxa > > > > > > > > > > > > > > > > > > This email and any files transmitted with it are confidential > > > > > and > > > > > > > > > intended solely for the use of the individual or entity to whom > > > > > they > > > are > > > > addressed. > > > > > > > > > If you are not the named addressee you should not disseminate, > > > > > > > > > distribute or copy this e-mail. Please notify the sender or > > > > > system > > > > > > > > > manager by email immediately if you have received this e-mail by > > > > > > > > > mistake and delete this e-mail from your system. If you are not > > > > > the > > > > > > > > > intended recipient you are notified that disclosing, copying, > > > > > > > > > distributing or taking any action in reliance on the contents of > > > > > this > > > > > > > > > information is strictly prohibited and against the law. > > > > > > > > > > > > > > > > > > This email and any files transmitted with it are confidential > > > > > and > > > > > > > > > intended solely for the use of the individual or entity to whom > > > > > they > > > are > > > > addressed. > > > > > > > > > If you are not the named addressee you should not disseminate, > > > > > > > > > distribute or copy this e-mail. Please notify the sender or > > > > > system > > > > > > > > > manager by email immediately if you have received this e-mail by > > > > > > > > > mistake and delete this e-mail from your system. If you are not > > > > > the > > > > > > > > > intended recipient you are notified that disclosing, copying, > > > > > > > > > distributing or taking any action in reliance on the contents of > > > > > this > > > > > > > > > information is strictly prohibited and against the law. > > > > > > > > > > > > > > > > > This email and any files transmitted with it are confidential and > > > intended > > > > solely for the use of the individual or entity to whom they are > > > addressed. > > > > If you are not the named addressee you should not disseminate, > > distribute > > > > or copy this e-mail. Please notify the sender or system manager by > > email > > > > immediately if you have received this e-mail by mistake and delete > > > > this e-mail from your system. If you are not the intended > > > > recipient you are notified that disclosing, copying, distributing > > > > or taking any action in reliance on the contents of this > > > > information is strictly prohibited and against the law. > > > > > > > > -- > > > Regards > > > Chahal Arora > > > Software Engineer > > > Raxa > > > > > >
23 Dec 2017 17:46:34 INFO AbstractJCasTermAnnotator - Finished processing 23 Dec 2017 17:46:34 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:http-nio-8089-exec-10 23 Dec 2017 17:46:34 INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:http-nio-8089-exec-10 23 Dec 2017 17:46:34 INFO ClearNLPSemanticRoleLabelerAE - Starting processing ... 23 Dec 2017 17:46:34 INFO ClearNLPSemanticRoleLabelerAE - Finished processing 23 Dec 2017 17:46:34 INFO CleartkAnalysisEngine - Assigning Attributes ... 23 Dec 2017 17:46:34 INFO CleartkAnalysisEngine - Finished Assigning Attributes 23 Dec 2017 17:46:34 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 23 Dec 2017 17:46:34 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 23 Dec 2017 17:46:34 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 23 Dec 2017 17:46:34 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 23 Dec 2017 17:46:34 INFO AbstractJCasTermAnnotator - Finished processing 23 Dec 2017 17:46:34 INFO LabValueFinder - Associating Labs with values ... 23 Dec 2017 17:46:34 INFO LabValueFinder - Finished. 23 Dec 2017 17:46:34 INFO DrugMentionAnnotator - process(JCas) mentionName -> SignSymptomMention part -> BLOOD PRESSURE -- 9,23 24 Dec 2017 09:58:10 INFO SentenceDetector - Starting processing. 24 Dec 2017 09:58:10 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 24 Dec 2017 09:58:10 INFO ContextDependentTokenizerAnnotator - process(JCas) 24 Dec 2017 09:58:10 INFO POSTagger - process(JCas) 24 Dec 2017 09:58:10 INFO Chunker - process(JCas) 24 Dec 2017 09:58:10 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 09:58:10 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 09:58:10 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 09:58:10 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 09:58:10 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:http-nio-8089-exec-6 24 Dec 2017 09:58:10 INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:http-nio-8089-exec-6 24 Dec 2017 09:58:10 INFO ClearNLPSemanticRoleLabelerAE - Starting processing ... 24 Dec 2017 09:58:10 INFO ClearNLPSemanticRoleLabelerAE - Finished processing 24 Dec 2017 09:58:10 INFO CleartkAnalysisEngine - Assigning Attributes ... 24 Dec 2017 09:58:10 INFO CleartkAnalysisEngine - Finished Assigning Attributes 24 Dec 2017 09:58:10 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 09:58:10 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 09:58:10 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 09:58:10 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 09:58:10 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 09:58:10 INFO LabValueFinder - Associating Labs with values ... 24 Dec 2017 09:58:10 INFO LabValueFinder - Finished. 24 Dec 2017 09:58:10 INFO DrugMentionAnnotator - process(JCas) mentionName -> SignSymptomMention part -> BLOOD PRESSURE -- 9,23 24 Dec 2017 10:24:55 INFO SentenceDetector - Starting processing. 24 Dec 2017 10:24:55 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 24 Dec 2017 10:24:55 INFO ContextDependentTokenizerAnnotator - process(JCas) 24 Dec 2017 10:24:55 INFO POSTagger - process(JCas) 24 Dec 2017 10:24:55 INFO Chunker - process(JCas) 24 Dec 2017 10:24:55 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 10:24:55 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 10:24:55 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 10:24:55 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 10:24:55 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:http-nio-8089-exec-4 24 Dec 2017 10:24:55 INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:http-nio-8089-exec-4 24 Dec 2017 10:24:55 INFO ClearNLPSemanticRoleLabelerAE - Starting processing ... 24 Dec 2017 10:24:55 INFO ClearNLPSemanticRoleLabelerAE - Finished processing 24 Dec 2017 10:24:55 INFO CleartkAnalysisEngine - Assigning Attributes ... 24 Dec 2017 10:24:55 INFO CleartkAnalysisEngine - Finished Assigning Attributes 24 Dec 2017 10:24:55 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 10:24:55 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 10:24:55 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 10:24:55 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 10:24:55 INFO LabValueFinder - Associating Labs with values ... 24 Dec 2017 10:24:55 INFO LabValueFinder - Finished. 24 Dec 2017 10:24:55 INFO DrugMentionAnnotator - process(JCas) mentionName -> SignSymptomMention part -> BLOOD PRESSURE -- 0,14 24 Dec 2017 10:25:24 INFO SentenceDetector - Starting processing. 24 Dec 2017 10:25:24 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 24 Dec 2017 10:25:24 INFO ContextDependentTokenizerAnnotator - process(JCas) 24 Dec 2017 10:25:24 INFO POSTagger - process(JCas) 24 Dec 2017 10:25:24 INFO Chunker - process(JCas) 24 Dec 2017 10:25:24 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 10:25:24 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 10:25:24 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 10:25:24 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 10:25:24 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:http-nio-8089-exec-6 24 Dec 2017 10:25:24 INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:http-nio-8089-exec-6 24 Dec 2017 10:25:24 INFO ClearNLPSemanticRoleLabelerAE - Starting processing ... 24 Dec 2017 10:25:24 INFO ClearNLPSemanticRoleLabelerAE - Finished processing 24 Dec 2017 10:25:24 INFO CleartkAnalysisEngine - Assigning Attributes ... 24 Dec 2017 10:25:24 INFO CleartkAnalysisEngine - Finished Assigning Attributes 24 Dec 2017 10:25:24 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 10:25:24 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 10:25:24 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 10:25:24 INFO LabValueFinder - Associating Labs with values ... 24 Dec 2017 10:25:24 INFO LabValueFinder - Finished. 24 Dec 2017 10:25:24 INFO DrugMentionAnnotator - process(JCas) mentionName -> SignSymptomMention part -> CONSCIOUS -- 0,9 24 Dec 2017 10:25:58 INFO SentenceDetector - Starting processing. 24 Dec 2017 10:25:58 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 24 Dec 2017 10:25:58 INFO ContextDependentTokenizerAnnotator - process(JCas) 24 Dec 2017 10:25:58 INFO POSTagger - process(JCas) 24 Dec 2017 10:25:58 INFO Chunker - process(JCas) 24 Dec 2017 10:25:58 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 10:25:58 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 10:25:58 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 10:25:58 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 10:25:58 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:http-nio-8089-exec-8 24 Dec 2017 10:25:58 INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:http-nio-8089-exec-8 24 Dec 2017 10:25:58 INFO ClearNLPSemanticRoleLabelerAE - Starting processing ... 24 Dec 2017 10:25:58 INFO ClearNLPSemanticRoleLabelerAE - Finished processing 24 Dec 2017 10:25:58 INFO CleartkAnalysisEngine - Assigning Attributes ... 24 Dec 2017 10:25:58 INFO CleartkAnalysisEngine - Finished Assigning Attributes 24 Dec 2017 10:25:58 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 10:25:58 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 10:25:58 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 10:25:58 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 10:25:58 INFO LabValueFinder - Associating Labs with values ... 24 Dec 2017 10:25:58 INFO LabValueFinder - Finished. 24 Dec 2017 10:25:58 INFO DrugMentionAnnotator - process(JCas) mentionName -> SignSymptomMention part -> BLOOD PRESSURE -- 0,14 24 Dec 2017 10:31:12 INFO SentenceDetector - Starting processing. 24 Dec 2017 10:31:12 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 24 Dec 2017 10:31:12 INFO ContextDependentTokenizerAnnotator - process(JCas) 24 Dec 2017 10:31:12 INFO POSTagger - process(JCas) 24 Dec 2017 10:31:12 INFO Chunker - process(JCas) 24 Dec 2017 10:31:12 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 10:31:12 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 10:31:12 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 10:31:12 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 10:31:12 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:http-nio-8089-exec-6 24 Dec 2017 10:31:12 INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:http-nio-8089-exec-6 24 Dec 2017 10:31:12 INFO ClearNLPSemanticRoleLabelerAE - Starting processing ... 24 Dec 2017 10:31:12 INFO ClearNLPSemanticRoleLabelerAE - Finished processing 24 Dec 2017 10:31:12 INFO CleartkAnalysisEngine - Assigning Attributes ... 24 Dec 2017 10:31:12 INFO CleartkAnalysisEngine - Finished Assigning Attributes 24 Dec 2017 10:31:12 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 10:31:12 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 10:31:12 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 10:31:12 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 10:31:12 INFO LabValueFinder - Associating Labs with values ... 24 Dec 2017 10:31:12 INFO LabValueFinder - Finished. 24 Dec 2017 10:31:12 INFO DrugMentionAnnotator - process(JCas) mentionName -> SignSymptomMention part -> BLOOD PRESSURE -- 0,14 24 Dec 2017 10:36:19 INFO SentenceDetector - Starting processing. 24 Dec 2017 10:36:19 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 24 Dec 2017 10:36:19 INFO ContextDependentTokenizerAnnotator - process(JCas) 24 Dec 2017 10:36:19 INFO POSTagger - process(JCas) 24 Dec 2017 10:36:19 INFO Chunker - process(JCas) 24 Dec 2017 10:36:19 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 10:36:19 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 10:36:19 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 10:36:19 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 10:36:19 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:http-nio-8089-exec-10 24 Dec 2017 10:36:19 INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:http-nio-8089-exec-10 24 Dec 2017 10:36:19 INFO ClearNLPSemanticRoleLabelerAE - Starting processing ... 24 Dec 2017 10:36:19 INFO ClearNLPSemanticRoleLabelerAE - Finished processing 24 Dec 2017 10:36:19 INFO CleartkAnalysisEngine - Assigning Attributes ... 24 Dec 2017 10:36:19 INFO CleartkAnalysisEngine - Finished Assigning Attributes 24 Dec 2017 10:36:19 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 10:36:19 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 10:36:19 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 10:36:19 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 10:36:19 INFO LabValueFinder - Associating Labs with values ... 24 Dec 2017 10:36:19 INFO LabValueFinder - Finished. 24 Dec 2017 10:36:19 INFO DrugMentionAnnotator - process(JCas) mentionName -> SignSymptomMention part -> BLOOD PRESSURE -- 0,14 24 Dec 2017 10:36:50 INFO SentenceDetector - Starting processing. 24 Dec 2017 10:36:50 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 24 Dec 2017 10:36:50 INFO ContextDependentTokenizerAnnotator - process(JCas) 24 Dec 2017 10:36:50 INFO POSTagger - process(JCas) 24 Dec 2017 10:36:50 INFO Chunker - process(JCas) 24 Dec 2017 10:36:50 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 10:36:50 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 10:36:50 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 10:36:50 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 10:36:50 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:http-nio-8089-exec-1 24 Dec 2017 10:36:50 INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:http-nio-8089-exec-1 24 Dec 2017 10:36:50 INFO ClearNLPSemanticRoleLabelerAE - Starting processing ... 24 Dec 2017 10:36:50 INFO ClearNLPSemanticRoleLabelerAE - Finished processing 24 Dec 2017 10:36:50 INFO CleartkAnalysisEngine - Assigning Attributes ... 24 Dec 2017 10:36:50 INFO CleartkAnalysisEngine - Finished Assigning Attributes 24 Dec 2017 10:36:50 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 10:36:50 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 10:36:50 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 10:36:50 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 10:36:50 INFO LabValueFinder - Associating Labs with values ... 24 Dec 2017 10:36:50 INFO LabValueFinder - Finished. 24 Dec 2017 10:36:50 INFO DrugMentionAnnotator - process(JCas) mentionName -> SignSymptomMention part -> BLOOD PRESSURE -- 0,14 24 Dec 2017 11:24:58 INFO SentenceDetector - Starting processing. 24 Dec 2017 11:24:58 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 24 Dec 2017 11:24:58 INFO ContextDependentTokenizerAnnotator - process(JCas) 24 Dec 2017 11:24:58 INFO POSTagger - process(JCas) 24 Dec 2017 11:24:58 INFO Chunker - process(JCas) 24 Dec 2017 11:24:58 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 11:24:58 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 11:24:58 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 11:24:58 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 11:24:58 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:http-nio-8089-exec-4 24 Dec 2017 11:24:58 INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:http-nio-8089-exec-4 24 Dec 2017 11:24:58 INFO ClearNLPSemanticRoleLabelerAE - Starting processing ... 24 Dec 2017 11:24:58 INFO ClearNLPSemanticRoleLabelerAE - Finished processing 24 Dec 2017 11:24:58 INFO CleartkAnalysisEngine - Assigning Attributes ... 24 Dec 2017 11:24:58 INFO CleartkAnalysisEngine - Finished Assigning Attributes 24 Dec 2017 11:24:58 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 11:24:58 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 11:24:58 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 11:24:58 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 11:24:58 INFO LabValueFinder - Associating Labs with values ... 24 Dec 2017 11:24:58 INFO LabValueFinder - Finished. 24 Dec 2017 11:24:58 INFO DrugMentionAnnotator - process(JCas) mentionName -> SignSymptomMention part -> BLOOD PRESSURE -- 0,14 24 Dec 2017 11:51:33 INFO SentenceDetector - Starting processing. 24 Dec 2017 11:51:33 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 24 Dec 2017 11:51:33 INFO ContextDependentTokenizerAnnotator - process(JCas) 24 Dec 2017 11:51:33 INFO POSTagger - process(JCas) 24 Dec 2017 11:51:33 INFO Chunker - process(JCas) 24 Dec 2017 11:51:33 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 11:51:33 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 11:51:33 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 11:51:33 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 11:51:33 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:http-nio-8089-exec-1 24 Dec 2017 11:51:33 INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:http-nio-8089-exec-1 24 Dec 2017 11:51:33 INFO ClearNLPSemanticRoleLabelerAE - Starting processing ... 24 Dec 2017 11:51:33 INFO ClearNLPSemanticRoleLabelerAE - Finished processing 24 Dec 2017 11:51:33 INFO CleartkAnalysisEngine - Assigning Attributes ... 24 Dec 2017 11:51:33 INFO CleartkAnalysisEngine - Finished Assigning Attributes 24 Dec 2017 11:51:33 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 11:51:33 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 11:51:33 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 11:51:33 INFO LabValueFinder - Associating Labs with values ... 24 Dec 2017 11:51:33 INFO LabValueFinder - Finished. 24 Dec 2017 11:51:33 INFO DrugMentionAnnotator - process(JCas) 24 Dec 2017 11:51:47 INFO SentenceDetector - Starting processing. 24 Dec 2017 11:51:47 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 24 Dec 2017 11:51:47 INFO ContextDependentTokenizerAnnotator - process(JCas) 24 Dec 2017 11:51:47 INFO POSTagger - process(JCas) 24 Dec 2017 11:51:47 INFO Chunker - process(JCas) 24 Dec 2017 11:51:47 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 11:51:47 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 11:51:47 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 11:51:47 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 11:51:47 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:http-nio-8089-exec-3 24 Dec 2017 11:51:47 INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:http-nio-8089-exec-3 24 Dec 2017 11:51:47 INFO ClearNLPSemanticRoleLabelerAE - Starting processing ... 24 Dec 2017 11:51:47 INFO ClearNLPSemanticRoleLabelerAE - Finished processing 24 Dec 2017 11:51:47 INFO CleartkAnalysisEngine - Assigning Attributes ... 24 Dec 2017 11:51:47 INFO CleartkAnalysisEngine - Finished Assigning Attributes 24 Dec 2017 11:51:47 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 11:51:47 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 11:51:47 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 11:51:47 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 11:51:47 INFO LabValueFinder - Associating Labs with values ... 24 Dec 2017 11:51:47 INFO LabValueFinder - Finished. 24 Dec 2017 11:51:47 INFO DrugMentionAnnotator - process(JCas) mentionName -> SignSymptomMention part -> BLOOD PRESSURE -- 0,14 24 Dec 2017 12:45:12 INFO SentenceDetector - Starting processing. 24 Dec 2017 12:45:12 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 24 Dec 2017 12:45:12 INFO ContextDependentTokenizerAnnotator - process(JCas) 24 Dec 2017 12:45:12 INFO POSTagger - process(JCas) 24 Dec 2017 12:45:12 INFO Chunker - process(JCas) 24 Dec 2017 12:45:12 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 12:45:12 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 12:45:12 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 12:45:12 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 12:45:12 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:http-nio-8089-exec-8 24 Dec 2017 12:45:12 INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:http-nio-8089-exec-8 24 Dec 2017 12:45:12 INFO ClearNLPSemanticRoleLabelerAE - Starting processing ... 24 Dec 2017 12:45:12 INFO ClearNLPSemanticRoleLabelerAE - Finished processing 24 Dec 2017 12:45:12 INFO CleartkAnalysisEngine - Assigning Attributes ... 24 Dec 2017 12:45:12 INFO CleartkAnalysisEngine - Finished Assigning Attributes 24 Dec 2017 12:45:12 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 12:45:12 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 12:45:12 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 12:45:12 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 12:45:12 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 12:45:12 INFO LabValueFinder - Associating Labs with values ... 24 Dec 2017 12:45:12 INFO LabValueFinder - Finished. 24 Dec 2017 12:45:12 INFO DrugMentionAnnotator - process(JCas) mentionName -> SignSymptomMention part -> BLOOD PRESSURE -- 9,23 24 Dec 2017 12:47:24 INFO SentenceDetector - Starting processing. 24 Dec 2017 12:47:24 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 24 Dec 2017 12:47:24 INFO ContextDependentTokenizerAnnotator - process(JCas) 24 Dec 2017 12:47:24 INFO POSTagger - process(JCas) 24 Dec 2017 12:47:24 INFO Chunker - process(JCas) 24 Dec 2017 12:47:24 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 12:47:24 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 12:47:24 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 12:47:24 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 12:47:24 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:http-nio-8089-exec-1 24 Dec 2017 12:47:24 INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:http-nio-8089-exec-1 24 Dec 2017 12:47:24 INFO ClearNLPSemanticRoleLabelerAE - Starting processing ... 24 Dec 2017 12:47:24 INFO ClearNLPSemanticRoleLabelerAE - Finished processing 24 Dec 2017 12:47:24 INFO CleartkAnalysisEngine - Assigning Attributes ... 24 Dec 2017 12:47:24 INFO CleartkAnalysisEngine - Finished Assigning Attributes 24 Dec 2017 12:47:24 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 12:47:24 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 12:47:24 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 12:47:24 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 12:47:24 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 12:47:24 INFO LabValueFinder - Associating Labs with values ... 24 Dec 2017 12:47:24 INFO LabValueFinder - Finished. 24 Dec 2017 12:47:24 INFO DrugMentionAnnotator - process(JCas) mentionName -> SignSymptomMention part -> BLOOD PRESSURE -- 9,23 24 Dec 2017 12:50:18 INFO SentenceDetector - Starting processing. 24 Dec 2017 12:50:18 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 24 Dec 2017 12:50:18 INFO ContextDependentTokenizerAnnotator - process(JCas) 24 Dec 2017 12:50:18 INFO POSTagger - process(JCas) 24 Dec 2017 12:50:18 INFO Chunker - process(JCas) 24 Dec 2017 12:50:18 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 12:50:18 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 12:50:18 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 12:50:18 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 12:50:18 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:http-nio-8089-exec-4 24 Dec 2017 12:50:18 INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:http-nio-8089-exec-4 24 Dec 2017 12:50:18 INFO ClearNLPSemanticRoleLabelerAE - Starting processing ... 24 Dec 2017 12:50:18 INFO ClearNLPSemanticRoleLabelerAE - Finished processing 24 Dec 2017 12:50:18 INFO CleartkAnalysisEngine - Assigning Attributes ... 24 Dec 2017 12:50:18 INFO CleartkAnalysisEngine - Finished Assigning Attributes 24 Dec 2017 12:50:18 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 12:50:18 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 12:50:18 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 12:50:18 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 12:50:18 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 12:50:18 INFO LabValueFinder - Associating Labs with values ... 24 Dec 2017 12:50:18 INFO LabValueFinder - Finished. 24 Dec 2017 12:50:18 INFO DrugMentionAnnotator - process(JCas) mentionName -> SignSymptomMention part -> BLOOD PRESSURE -- 9,23 24 Dec 2017 12:51:45 INFO SentenceDetector - Starting processing. 24 Dec 2017 12:51:45 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 24 Dec 2017 12:51:45 INFO ContextDependentTokenizerAnnotator - process(JCas) 24 Dec 2017 12:51:45 INFO POSTagger - process(JCas) 24 Dec 2017 12:51:45 INFO Chunker - process(JCas) 24 Dec 2017 12:51:45 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 12:51:45 INFO ChunkAdjuster - process(JCas) 24 Dec 2017 12:51:45 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 12:51:45 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 12:51:45 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:http-nio-8089-exec-8 24 Dec 2017 12:51:45 INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:http-nio-8089-exec-8 24 Dec 2017 12:51:45 INFO ClearNLPSemanticRoleLabelerAE - Starting processing ... 24 Dec 2017 12:51:45 INFO ClearNLPSemanticRoleLabelerAE - Finished processing 24 Dec 2017 12:51:45 INFO CleartkAnalysisEngine - Assigning Attributes ... 24 Dec 2017 12:51:45 INFO CleartkAnalysisEngine - Finished Assigning Attributes 24 Dec 2017 12:51:45 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 24 Dec 2017 12:51:45 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 12:51:45 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 12:51:45 ERROR JdbcRareWordDictionary - No operations allowed after statement closed. 24 Dec 2017 12:51:45 INFO AbstractJCasTermAnnotator - Finished processing 24 Dec 2017 12:51:45 INFO LabValueFinder - Associating Labs with values ... 24 Dec 2017 12:51:45 INFO LabValueFinder - Finished. 24 Dec 2017 12:51:45 INFO DrugMentionAnnotator - process(JCas) mentionName -> SignSymptomMention part -> BLOOD PRESSURE -- 9,23
