Sean I was able to serialize cas to json . the issue was with old uima libraries were used.
On Thu, Jan 26, 2017 at 1:05 AM, shahid ashraf <sha...@trialx.com> wrote: > Question 3 was in the Context to below MRCONSO query. > grep -m 100 'everolimus 2.5 MG' MRCONSO.RRF > C2920402|ENG|P|L9444011|PF|S11732016|Y|A18087431|3277625| > 998188||RXNORM|SCDC|998188|everolimus 2.5 MG|0|N|4352| > C2920403|ENG|P|L9440907|PF|S11732014|N|A24007275|6361783| > 998189||RXNORM|PSN|998189|everolimus 2.5 MG Oral Tablet|0|N|4352| > C2920403|ENG|P|L9440907|PF|S11732014|Y|A18086252|3277626| > 998189||RXNORM|SCD|998189|everolimus 2.5 MG Oral Tablet|0|N|4352| > C2920404|ENG|P|L9444010|PF|S11732015|Y|A18089772|3277627| > 998190||RXNORM|SBDC|998190|everolimus 2.5 MG [Afinitor]|0|N|4096| > C2920405|ENG|P|L9442487|PF|S11732013|Y|A18083986|3277628| > 998191||RXNORM|SBD|998191|everolimus 2.5 MG Oral Tablet > [Afinitor]|0|N|4352| > in above we see all these in RXNORM not in fast dictionary. > > Is that Dictionary -Gui filter based on *Term Types* -- > https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ > RXNORM/stats.html > So can we control that ... ? > > Also i was thinking to generate the json output from web-client: > } else if ("json".equalsIgnoreCase(format)) { > response.setContentType("application/json"); > ByteArrayOutputStream output = new ByteArrayOutputStream(); > // XiCasSerializer.serialize(jcas.getCas(), output); > JsonCasSerializer.jsonSerialize(jcas.getCas(), output); > sb.append(output.toString()); > output.close(); > > > Pom.xml > > <dependency> > <groupId>org.apache.uima</groupId> > <artifactId>uimaj-core</artifactId> > <version>2.4.0</version> > </dependency> > <dependency> > <groupId>org.apache.uima</groupId> > <artifactId>uimafit-core</artifactId> > <version>2.1.0</version> > </dependency> > <!-- https://mvnrepository.com/artifact/org.apache.uima/uimaj-json --> > <dependency> > <groupId>org.apache.uima</groupId> > <artifactId>uimaj-json</artifactId> > <version>2.9.0</version> > </dependency> > > > Getting the following error: > > > WARNING] Error for /DemoServlet > java.lang.NoClassDefFoundError: org/apache/uima/cas/impl/ > CasSerializerSupport > at org.apache.uima.json.JsonCasSerializer.<init>( > JsonCasSerializer.java:155) > at org.apache.uima.json.JsonCasSerializer.jsonSerialize( > JsonCasSerializer.java:255) > at org.apache.uima.json.JsonCasSerializer.jsonSerialize( > JsonCasSerializer.java:206) > at org.apache.ctakes.web.client.servlet.DemoServlet. > formatResults(DemoServlet.java:149) > at org.apache.ctakes.web.client.servlet.DemoServlet.doPost( > DemoServlet.java:92) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:707) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:790) > at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:800) > at org.eclipse.jetty.servlet.ServletHandler.doHandle( > ServletHandler.java:587) > at org.eclipse.jetty.server.handler.ScopedHandler.handle( > ScopedHandler.java:143) > at org.eclipse.jetty.security.SecurityHandler.handle( > SecurityHandler.java:577) > at org.eclipse.jetty.server.session.SessionHandler. > doHandle(SessionHandler.java:223) > at org.eclipse.jetty.server.handler.ContextHandler. > doHandle(ContextHandler.java:1125) > at org.eclipse.jetty.servlet.ServletHandler.doScope( > ServletHandler.java:515) > at org.eclipse.jetty.server.session.SessionHandler. > doScope(SessionHandler.java:185) > at org.eclipse.jetty.server.handler.ContextHandler. > doScope(ContextHandler.java:1059) > at org.eclipse.jetty.server.handler.ScopedHandler.handle( > ScopedHandler.java:141) > at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle( > ContextHandlerCollection.java:215) > at org.eclipse.jetty.server.handler.HandlerCollection. > handle(HandlerCollection.java:110) > at org.eclipse.jetty.server.handler.HandlerWrapper.handle( > HandlerWrapper.java:97) > at org.eclipse.jetty.server.Server.handle(Server.java:497) > at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:313) > at org.eclipse.jetty.server.HttpConnection.onFillable( > HttpConnection.java:248) > at org.eclipse.jetty.io.AbstractConnection$2.run( > AbstractConnection.java:540) > at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob( > QueuedThreadPool.java:626) > at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run( > QueuedThreadPool.java:546) > at java.lang.Thread.run(Thread.java:745) > > > On Thu, Jan 26, 2017 at 12:30 AM, Finan, Sean < > sean.fi...@childrens.harvard.edu> wrote: > >> Hi Shahid, answers are below. >> >> >> >> >I am seeing few more FP like MEN : >> >> >SENTENCE: MEN >> >> NN >> >> |======| >> >> Disorder >> >> C0027662 >> >> |======| >> >> Drug >> >> C0127527 >> >> >> >> MEN is an abbreviation for Multiple Endocrine Neoplasia (Disorder C0027662). >> In is also an abbreviation for the antibiotic Menogaril (Drug C0127527). >> Strictly speaking, these are not false positives. There is a lot of effort >> in the nlp community, including by ctakes contributors, on word sense >> disambiguation (WSD) that would improve mapping of words such as “men”. >> >> >> >> >Where as it could have been matched to : >> >> >Meta Mapping (1000): >> >> > 1000 C0025266:Men (Male population group) >> >> >> >> Ctakes uses a set of semantic types for lookup. Population Group (T098) >> is not one of them. By default ctakes focuses on clinically-relevant >> terms. If you create a custom dictionary you can add semantic types like >> Population Group. >> >> >> >> > 2) Also is there any way round to match based on spelling mistakes. >> like >> >> >advill ==> advil >> >> >neplasm ==> neoplasm >> >> >> >> Spell correction is another thing that ctakes does not focus upon. There >> are many approaches and a module could be created to handle spelling. >> >> >> >> >3) Can we all concepts from MRCONSO into fast matching dictionary. >> >> >> >> Yes, using the dictionary gui select all vocabulary sources and all >> semantic types. Get ready for a big database and you may need to bump up >> your memory allocation for ctakes. >> >> >> >> Sean >> >> >> >> >> >> >> >> >> >> On Wed, Jan 25, 2017 at 10:12 PM, Finan, Sean < >> sean.fi...@childrens.harvard.edu> wrote: >> >> Hi Shahid, >> >> >> >> I tested LVG on “levels” and it didn’t produce an equivalent singular >> form. I don’t know of any special lvg parameters that will toggle this on >> and off – as far as I know it should always attempt it for nouns. Because >> this may happen quite a bit I started thinking on an alternative solution … >> but may not get to it for a while and when I do I’ll still need to run some >> tests to make sure it works. >> >> >> >> Andrey Kurdumov recently made an update for ctakes to use LVG 2016 >> (cheers!). The current version is fairly old and the 2016 may very well >> perform better. I have pasted his email below. >> >> >> >> As I promise, I udpate cTakes to support LVG version 2016 year. >> >> >> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__github. >> com_kant2002_cTakes&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J >> ZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao >> &m=RdfyvGDEhgrlIGv4Ue0X6DViLFyykHEokJgGzgoG5Vs&s=IJWxluJDIVh >> ugnzWsfRl0TzL0LWzW6_kunc_GRJVew4&e= >> >> >> >> Please take a look. >> >> In the github following modifications to current version of cTakes >> >> - Removed two large files to make project fit GitHub restrictions. >> >> - Some very small cleanup which placed in separate commit. >> >> - Some fixes to ytex related tests, that's was required for me to pass >> mvn install command. >> >> >> >> Assumptions: >> >> - User should update ctakesnormx and other databases from HSQLdb 1.8 to >> HSQLDB 2.3.4 >> >> >> >> >> >> >> >> *From:* shahid ashraf [mailto:sha...@trialx.com] >> *Sent:* Wednesday, January 25, 2017 2:11 AM >> >> >> *To:* Finan, Sean >> *Cc:* dev@ctakes.apache.org; kant2...@googlemail.com; pratik agarwal >> *Subject:* Re: Ctakes Dictionary Gui >> >> >> >> Thanks sean for this insightful information. This is of great help.(i am >> newbie to ctakes and also come from python background.) >> >> I tested on the Fast version. Is it so that ctakes LVG is not currently >> adding plurals to the terms. Because in logs i see that LVG is being setup >> before processing the docs in CVD. >> >> I guess below logs show ctakes is using LVG: >> >> >> >> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - Loading NLM Norm and >> Lvg with config file = /Users/shahid/projects/workspa >> ce/ctakes/ctakes-dictionary-lookup/resources/org/apache/ >> ctakes/lvg/data/config/lvg.properties >> >> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - config file absolute >> path = /Users/shahid/projects/workspace/ctakes/ctakes-dictionary- >> lookup/resources/org/apache/ctakes/lvg/data/config/lvg.properties >> >> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - cwd = >> /Users/shahid/projects/workspace/ctakes/ctakes-clinical-pipeline >> >> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - cd >> /Users/shahid/projects/workspace/ctakes/ctakes-dictionary- >> lookup/resources/org/apache/ctakes/lvg/ >> >> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - cd >> /Users/shahid/projects/workspace/ctakes/ctakes-clinical-pipeline >> >> 25 Jan 2017 12:31:40 INFO ClearNLPDependencyParserAE - using Morphy >> analysis? true >> >> Loading configuration. >> >> Loading feature templates. >> >> Loading lexica. >> >> Loading model: >> >> ............................................................ >> ............................ >> >> 25 Jan 2017 12:31:54 INFO Chunker - Chunker model file: >> org/apache/ctakes/chunker/models/chunker-model.zip >> >> 25 Jan 2017 12:31:55 INFO ContextDependentTokenizerAnnotator - Finite >> state machines loaded. >> >> 25 Jan 2017 12:31:55 INFO ConstituencyParser - Initializing parser... >> >> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using left , right scope >> sizes: 7 , 7 >> >> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using scope order: >> LEFT,RIGHT >> >> 25 Jan 2017 12:31:59 INFO ContextAnnotator - SCOPE ORDER: [1, 3] >> >> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using context analyzer: >> org.apache.ctakes.necontexts.negation.NegationContextAnalyzer >> >> 25 Jan 2017 12:31:59 INFO NegationContextAnalyzer - initBoundaryData() >> called for ContextInitializer >> >> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using context consumer: >> org.apache.ctakes.necontexts.negation.NegationContextHitConsumer >> >> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using lookup window type: >> org.apache.ctakes.typesystem.type.textspan.Sentence >> >> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using focus type: >> org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation >> >> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using context type: >> org.apache.ctakes.typesystem.type.syntax.BaseToken >> >> 25 Jan 2017 12:31:59 INFO DrugMentionAnnotator - Finite state machines >> loaded. >> >> 25 Jan 2017 12:31:59 INFO POSTagger - POS tagger model file: >> org/apache/ctakes/postagger/models/mayo-pos.zip >> >> 25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Using dictionary >> lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence >> >> 25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Exclusion tagset >> loaded: CC CD EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN VBP >> VBZ WDT WP WPS WRB >> >> 25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Using minimum term >> text span: 3 >> >> 25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Using Dictionary >> Descriptor: org/apache/ctakes/dictionary/lookup/fast/custom_appliedvocab >> .xml >> >> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - Parsing >> dictionary specifications: >> >> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - saxBuilder had >> build doc >> >> FILEPATH: [Document: No DOCTYPE declaration, Root is [Element: >> <lookupSpecification/>]] >> >> 25 Jan 2017 12:32:00 INFO JdbcRareWordDictionary - Connected to cui and >> term table CUI_TERMS >> >> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - >> RareWordDictionary parseDictionaries Done... >> >> [Element: <conceptFactories/>] >> >> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - Started >> parseConceptFactories... >> >> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - Started >> parseConceptFactories... Collection >> >> >> >> Also in FASTAGGREGATE PIPELINE Desc i see >> >> <flowConstraints> >> >> <fixedFlow> >> >> <node>SimpleSegmentAnnotator</node> >> >> <node>SentenceDetectorAnnotator</node> >> >> <node>TokenizerAnnotator</node> >> >> * <node>LvgAnnotator</node>* >> >> <node>ContextDependentTokenizerAnnotator</node> >> >> <node>POSTagger</node> >> >> <!-- <node>ClearPOSTagger</node> --> >> >> <node>Chunker</node> >> >> <node>AdjustNounPhraseToIncludeFollowingNP</node> >> >> <node>AdjustNounPhraseToIncludeFollowingPPNP</node> >> >> <node>LookupWindowAnnotator</node> >> >> <node>DictionaryLookupAnnotatorDB</node> >> >> <node>DependencyParser</node> >> >> ... >> >> </fixedFlow> >> >> >> >> >> >> Is there any setting that will let LVG generate plurals. >> >> >> >> On Wed, Jan 25, 2017 at 1:08 AM, Finan, Sean < >> sean.fi...@childrens.harvard.edu> wrote: >> >> Hi Shahid, >> >> You will definitely find instances where the old dictionary finds terms >> but the fast does not, and vice-versa. The fast lookup uses a more concise >> dictionary, and the concepts that you noted are probably not in it. There >> is another thread between myself and Pratik Agarwal (last week in fact) on >> exactly the topic of drugs identified generically or with dose, route, >> form, etc. That may be why you don’t see everolimus 2.5 mg specifically. >> >> Everolimus is in the dictionary by itself: >> >> sql> select * from cui_terms where text like '%everolimus%'; >> >> CUI RINDEX TCOUNT TEXT RWORD >> >> ------ ------ ------ ---------- ---------- >> >> 541315 0 1 everolimus everolimus >> >> >> >> The reason why everolimus was not identified by itself is because it was >> given the part of speech “DT” (Determiner), which is specified as unwanted >> for lookup. In my test with “… given everolimus 2.5 MG …”: >> >> WordToken >> >> begin >> >> 12 >> >> end >> >> 16 >> >> tokenNumber >> >> 2 >> >> partOfSpeech >> >> VBD >> >> capitalization >> >> 0 >> >> numPosition >> >> 0 >> >> WordToken >> >> begin >> >> 17 >> >> end >> >> 27 >> >> tokenNumber >> >> 3 >> >> partOfSpeech >> >> DT >> >> capitalization >> >> 0 >> >> numPosition >> >> 0 >> >> MeasurementAnnotation >> >> begin >> >> 28 >> >> end >> >> 34 >> >> id >> >> 0 >> >> typeID >> >> 0 >> >> discoveryTechnique >> >> 0 >> >> polarity >> >> 0 >> >> uncertainty >> >> 0 >> >> conditional >> >> false >> >> generic >> >> false >> >> historyOf >> >> 0 >> >> >> >> “DT” normally is assigned to things like “the, a, these” and at some >> point the community decided that words with the DT part of speech should >> not be considered as candidates for dictionary lookup. >> http://www.clips.ua.ac.be/pages/mbsp-tags >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.clips.ua.ac.be_pages_mbsp-2Dtags&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=3k7SCH8Gvj_palkdWwWeKGysBHTV_K5itUG2DE4icAI&s=xwP78R729SFVEwbCNa_af452uzXvIik2Ob4SYQyNPHw&e=> >> >> The default exclusion parts of speech are: >> >> >> “VB,VBD,VBG,VBN,VBP,VBZ,CC,CD,DT,EX,IN,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB” >> >> To change this, set the parameter “exclusionTags” to this string without >> DT. >> >> >> >> As for “higher testosterone levels”, are you running the LVG (Lexical >> Variant Generator) module? “testosterone level” is in the dictionary, but >> the plural “testosterone levels” is not. This is done on purpose to keep >> the database small. The old dictionary may not have the same tactic. >> >> sql> select * from cui_terms where text like 'testosterone level%'; >> >> CUI RINDEX TCOUNT TEXT RWORD >> >> ------ ------ ------ ------------------ ------------ >> >> 523912 0 2 testosterone level testosterone >> >> >> >> The LVG module –should- add the plural as a variant and the lookup module >> will use that variant for lookup. The dictionary module (and others) does >> not stand on its own – its success depends upon the proper output of >> previous modules in the pipeline. When I test with “… higher testosterone >> level …” (without LVG) it does find what you are looking for: >> >> WordToken >> >> begin >> >> 18 >> >> end >> >> 24 >> >> tokenNumber >> >> 4 >> >> partOfSpeech >> >> JJR >> >> capitalization >> >> 0 >> >> numPosition >> >> 0 >> >> ProcedureMention >> >> begin >> >> 25 >> >> end >> >> 43 >> >> id >> >> 0 >> >> codingScheme >> >> SNOMEDCT >> >> code >> >> 104957004 >> >> score >> >> 0.0 >> >> disambiguated >> >> false >> >> cui >> >> C0523912 >> >> tui >> >> T059 >> >> preferredText >> >> Testosterone measurement >> >> typeID >> >> 5 >> >> discoveryTechnique >> >> 1 >> >> polarity >> >> 0 >> >> uncertainty >> >> 0 >> >> conditional >> >> false >> >> generic >> >> false >> >> historyOf >> >> 0 >> >> MedicationMention >> >> begin >> >> 25 >> >> end >> >> 37 >> >> id >> >> 0 >> >> codingScheme >> >> SNOMEDCT >> >> code >> >> 109033004 >> >> score >> >> 0.0 >> >> disambiguated >> >> false >> >> cui >> >> C0039601 >> >> tui >> >> T121 >> >> preferredText >> >> Testosterone >> >> codingScheme >> >> >> >> I just ran through with LVG and LVG does not form “level” from “levels”. >> >> >> >> >> I hope that helps, >> >> Sean >> >> >> >> *From:* shahid ashraf [mailto:sha...@trialx.com] >> *Sent:* Tuesday, January 24, 2017 10:17 AM >> >> >> *To:* Finan, Sean >> *Cc:* dev@ctakes.apache.org; kant2...@googlemail.com; pratik agarwal >> *Subject:* Re: Ctakes Dictionary Gui >> >> >> >> Hi Sean >> >> >> >> I am testing the stuff on the fast and AggregratePlainTextUMLSProcessor(slow) >> . I found that one of the drug everolimus 2.5 mg is not found by the >> fast version. it is actually in RXNORM of my MRCONSO.RRF file. >> >> C2920405|ENG|P|L9442487|PF|S11732013|Y|A18083986|3277628|998 >> 191||RXNORM|SBD|998191|*everolimus 2.5 MG* Oral Tablet >> [Afinitor]|0|N|4352|. Let me know if you have any inputs on this. >> >> Also other case is : >> >> SENTENCE: higher testosterone levels >> >> JJR NN NNS >> >> |==========| >> >> Procedure >> >> C0202227 >> >> C0523912 >> >> |==========| >> >> Drug >> >> C0039601 >> >> AggregratePlainTextUMLSProcessor is able to find from higher testosterone >> levels: >> >> *testosterone levels* >> >> <refsem:UmlsConcept xmi:id="167" codingScheme="SNOMED" code="104957004" >> oid="104957004#SNOMED" score="0.0" disambiguated="false" cui="C0523912" >> tui="T059"/> >> >> C0523912|ENG|S|L0865889|PF|S1044605|Y|A3209597|1219087010|104957004||SNOMEDCT_US|SY|104957004|Testosterone >> level|9|N|256| >> >> I am not able to understand why fast version is not able to do so. >> >> >> >> MoreOver in comparison to Metamap, we are not able to do this. >> >> Phrase: higher testosterone levels >> >> Meta Mapping (966): >> >> 966 C1295653:High testosterone level (Increased testosterone level) >> [Finding] >> >> >> >> On Tue, Jan 24, 2017 at 8:19 PM, Finan, Sean < >> sean.fi...@childrens.harvard.edu> wrote: >> >> Hi Shahid, >> >> >> >> I’m glad that the fix worked! >> >> Unfortunately, the fast dictionary format will not work with the old >> Dictionary Lookup Module that is used by AggregratePlainTextUMLSProcessor >> >> You can manually create an updated dictionary for the older module, but >> it is more involved. >> >> In our tests and those done by others the new “fast” lookup has as good >> or better accuracy depending upon the test corpus. Plus it is runs in 1/500 >> th the time. I recommend that you stick to it. >> >> >> >> Sean >> >> >> >> *From:* shahid ashraf [mailto:sha...@trialx.com] >> *Sent:* Tuesday, January 24, 2017 5:50 AM >> *To:* Finan, Sean >> *Cc:* dev@ctakes.apache.org; kant2...@googlemail.com; pratik agarwal >> >> >> *Subject:* Re: Ctakes Dictionary Gui >> >> >> >> Thanks Sean >> >> >> >> That was the case for not finding the class. there were space in the xml >> generated by dictionary-gui. >> >> Also i am curious how we can use new umls with normal >> AggregratePlainTextUMLSProcessor. >> >> >> >> >> >> On Mon, Jan 23, 2017 at 9:36 PM, Finan, Sean < >> sean.fi...@childrens.harvard.edu> wrote: >> >> Ah – there might be an erroneous space in the classname. >> >> >> >> Go to your dictionary settings xml. In the line: >> >> <implementationName>org.apache.ctakes.dictionary.lookup2. >> concept.JdbcConceptFactory</implementationName> >> >> >> >> Look for a space between “JdbcConceptFactory” and “</implementationName>” >> >> If you see a space, remove it. >> >> >> >> It looks like I introduced this bug a few weeks ago. >> >> >> >> Thanks, >> >> Sean >> >> >> >> >> >> *From:* shahid ashraf [mailto:sha...@trialx.com] >> *Sent:* Saturday, January 21, 2017 1:42 PM >> *To:* dev@ctakes.apache.org; Finan, Sean; kant2...@googlemail.com; >> pratik agarwal >> *Subject:* Re: Ctakes Dictionary Gui >> >> >> >> Have put username and password (umls) in custom.xml as well. Still >> getting this error: >> >> 1/22/17 12:09:18 AM - 14: >> org.apache.uima.tools.cvd.MainFrame.handleException(526): >> SEVERE: Initialization of annotator class "org.apache.ctakes.dictionary. >> lookup2.ae >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=> >> .DefaultJCasTermAnnotator" failed. (Descriptor: >> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-l >> ookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml) >> >> org.apache.uima.resource.ResourceInitializationException: Initialization >> of annotator class "org.apache.ctakes.dictionary.lookup2.ae >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=> >> .DefaultJCasTermAnnotator" failed. (Descriptor: >> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-l >> ookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml) >> >> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine >> _impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) >> >> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine >> _impl.initialize(PrimitiveAnalysisEngine_impl.java:156) >> >> at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResou >> rce(AnalysisEngineFactory_impl.java:94) >> >> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe >> source(CompositeResourceFactory_impl.java:62) >> >> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) >> >> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram >> ework.java:387) >> >> 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.produceResou >> rce(AnalysisEngineFactory_impl.java:94) >> >> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe >> source(CompositeResourceFactory_impl.java:62) >> >> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) >> >> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram >> ework.java:354) >> >> at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484) >> >> at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFra >> me.java:476) >> >> at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler. >> actionPerformed(AnnotatorOpenEventHandler.java:52) >> >> at javax.swing.AbstractButton.fireActionPerformed(AbstractButto >> n.java:2022) >> >> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractB >> utton.java:2346) >> >> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultBu >> ttonModel.java:402) >> >> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) >> >> at javax.swing.AbstractButton.doClick(AbstractButton.java:376) >> >> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItem >> UI.java:833) >> >> at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) >> >> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased >> (BasicMenuItemUI.java:877) >> >> at java.awt.Component.processMouseEvent(Component.java:6525) >> >> at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) >> >> at java.awt.Component.processEvent(Component.java:6290) >> >> at java.awt.Container.processEvent(Container.java:2234) >> >> at java.awt.Component.dispatchEventImpl(Component.java:4881) >> >> at java.awt.Container.dispatchEventImpl(Container.java:2292) >> >> at java.awt.Component.dispatchEvent(Component.java:4703) >> >> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898) >> >> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533) >> >> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462) >> >> at java.awt.Container.dispatchEventImpl(Container.java:2278) >> >> at java.awt.Window.dispatchEventImpl(Window.java:2750) >> >> at java.awt.Component.dispatchEvent(Component.java:4703) >> >> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) >> >> at java.awt.EventQueue.access$500(EventQueue.java:97) >> >> at java.awt.EventQueue$3.run(EventQueue.java:709) >> >> at java.awt.EventQueue$3.run(EventQueue.java:703) >> >> at java.security.AccessController.doPrivileged(Native Method) >> >> at java.security.ProtectionDomain$1.doIntersectionPrivilege(Pro >> tectionDomain.java:75) >> >> at java.security.ProtectionDomain$1.doIntersectionPrivilege(Pro >> tectionDomain.java:86) >> >> at java.awt.EventQueue$4.run(EventQueue.java:731) >> >> at java.awt.EventQueue$4.run(EventQueue.java:729) >> >> at java.security.AccessController.doPrivileged(Native Method) >> >> at java.security.ProtectionDomain$1.doIntersectionPrivilege(Pro >> tectionDomain.java:75) >> >> at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) >> >> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDis >> patchThread.java:201) >> >> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispat >> chThread.java:116) >> >> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDis >> patchThread.java:105) >> >> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) >> >> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) >> >> at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) >> >> Caused by: org.apache.uima.resource.ResourceInitializationException: >> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: >> Can't find resource for bundle java.util.PropertyResourceBundle, key >> Unknown class org.apache.ctakes.dictionary.l >> ookup2.concept.JdbcConceptFactory >> >> at org.apache.ctakes.dictionary.lookup2.ae >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=> >> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132) >> >> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine >> _impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) >> >> ... 55 more >> >> Caused by: >> org.apache.uima.analysis_engine.annotator.AnnotatorContextException: >> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: >> Can't find resource for bundle java.util.PropertyResourceBundle, key >> Unknown class org.apache.ctakes.dictionary.l >> ookup2.concept.JdbcConceptFactory >> >> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >> scriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:255) >> >> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >> scriptorParser.parseConceptFactories(DictionaryDescriptorParser.java:226) >> >> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >> scriptorParser.parseDescriptor(DictionaryDescriptorParser.java:133) >> >> at org.apache.ctakes.dictionary.lookup2.ae >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=> >> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130) >> >> ... 56 more >> >> Caused by: java.lang.ClassNotFoundException: >> org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory >> >> at java.net.URLClassLoader.findClass(URLClassLoader.java:381) >> >> at java.lang.ClassLoader.loadClass(ClassLoader.java:424) >> >> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331) >> >> at java.lang.ClassLoader.loadClass(ClassLoader.java:357) >> >> at java.lang.Class.forName0(Native Method) >> >> at java.lang.Class.forName(Class.java:264) >> >> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >> scriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:253) >> >> ... 59 more >> >> >> >> >> >> On Sat, Jan 21, 2017 at 5:36 PM, shahid ashraf <sha...@trialx.com> wrote: >> >> Hi I was able to run and produce the new custom umls files. and where put >> under ctakes binary (not dev). >> >> >> >> I changed the name under apache-ctakes-3.2.2/desc >> /ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLook >> upAnnotator.xml >> >> >> >> <name>DictionaryDescriptorFile</name> >> >> <description/> >> >> <fileResourceSpecifier> >> >> <fileUrl>file:org/apache/ctak >> es/dictionary/lookup/fast/custom.xml</fileUrl> >> >> >> >> when running AggregatePlantextFastUmlsProcessor.xml I am getting >> following error (not when using old org/apache/ctakes/dictiona >> ry/lookup/fast/cTakesHsql.xml) >> >> >> >> 5: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: >> Initialization of annotator class "org.apache.ctakes.dictionary. >> lookup2.ae >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=> >> .DefaultJCasTermAnnotator" failed. (Descriptor: >> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-l >> ookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml) >> >> org.apache.uima.resource.ResourceInitializationException: Initialization >> of annotator class "org.apache.ctakes.dictionary.lookup2.ae >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=> >> .DefaultJCasTermAnnotator" failed. (Descriptor: >> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-l >> ookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml) >> >> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine >> _impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) >> >> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine >> _impl.initialize(PrimitiveAnalysisEngine_impl.java:156) >> >> at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResou >> rce(AnalysisEngineFactory_impl.java:94) >> >> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe >> source(CompositeResourceFactory_impl.java:62) >> >> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) >> >> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram >> ework.java:387) >> >> 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.produceResou >> rce(AnalysisEngineFactory_impl.java:94) >> >> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe >> source(CompositeResourceFactory_impl.java:62) >> >> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) >> >> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram >> ework.java:354) >> >> at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484) >> >> at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFra >> me.java:476) >> >> at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler. >> actionPerformed(AnnotatorOpenEventHandler.java:52) >> >> at javax.swing.AbstractButton.fireActionPerformed(AbstractButto >> n.java:2022) >> >> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractB >> utton.java:2346) >> >> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultBu >> ttonModel.java:402) >> >> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) >> >> at javax.swing.AbstractButton.doClick(AbstractButton.java:376) >> >> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItem >> UI.java:833) >> >> at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) >> >> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased >> (BasicMenuItemUI.java:877) >> >> at java.awt.Component.processMouseEvent(Component.java:6525) >> >> at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) >> >> at java.awt.Component.processEvent(Component.java:6290) >> >> at java.awt.Container.processEvent(Container.java:2234) >> >> at java.awt.Component.dispatchEventImpl(Component.java:4881) >> >> at java.awt.Container.dispatchEventImpl(Container.java:2292) >> >> at java.awt.Component.dispatchEvent(Component.java:4703) >> >> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898) >> >> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533) >> >> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462) >> >> at java.awt.Container.dispatchEventImpl(Container.java:2278) >> >> at java.awt.Window.dispatchEventImpl(Window.java:2750) >> >> at java.awt.Component.dispatchEvent(Component.java:4703) >> >> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) >> >> at java.awt.EventQueue.access$500(EventQueue.java:97) >> >> at java.awt.EventQueue$3.run(EventQueue.java:709) >> >> at java.awt.EventQueue$3.run(EventQueue.java:703) >> >> at java.security.AccessController.doPrivileged(Native Method) >> >> at java.security.ProtectionDomain$1.doIntersectionPrivilege(Pro >> tectionDomain.java:75) >> >> at java.security.ProtectionDomain$1.doIntersectionPrivilege(Pro >> tectionDomain.java:86) >> >> at java.awt.EventQueue$4.run(EventQueue.java:731) >> >> at java.awt.EventQueue$4.run(EventQueue.java:729) >> >> at java.security.AccessController.doPrivileged(Native Method) >> >> at java.security.ProtectionDomain$1.doIntersectionPrivilege(Pro >> tectionDomain.java:75) >> >> at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) >> >> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDis >> patchThread.java:201) >> >> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispat >> chThread.java:116) >> >> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDis >> patchThread.java:105) >> >> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) >> >> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) >> >> at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) >> >> Caused by: org.apache.uima.resource.ResourceInitializationException: >> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: >> Can't find resource for bundle java.util.PropertyResourceBundle, key >> Unknown class org.apache.ctakes.dictionary.l >> ookup2.concept.JdbcConceptFactory >> >> at org.apache.ctakes.dictionary.lookup2.ae >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=> >> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132) >> >> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine >> _impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) >> >> ... 55 more >> >> Caused by: >> org.apache.uima.analysis_engine.annotator.AnnotatorContextException: >> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: >> Can't find resource for bundle java.util.PropertyResourceBundle, key >> Unknown class org.apache.ctakes.dictionary.l >> ookup2.concept.JdbcConceptFactory >> >> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >> scriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:255) >> >> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >> scriptorParser.parseConceptFactories(DictionaryDescriptorParser.java:226) >> >> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >> scriptorParser.parseDescriptor(DictionaryDescriptorParser.java:133) >> >> at org.apache.ctakes.dictionary.lookup2.ae >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=> >> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130) >> >> ... 56 more >> >> Caused by: java.lang.ClassNotFoundException: >> org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory >> >> at java.net.URLClassLoader.findClass(URLClassLoader.java:381) >> >> at java.lang.ClassLoader.loadClass(ClassLoader.java:424) >> >> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331) >> >> at java.lang.ClassLoader.loadClass(ClassLoader.java:357) >> >> at java.lang.Class.forName0(Native Method) >> >> at java.lang.Class.forName(Class.java:264) >> >> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >> scriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:253) >> >> ... 59 more >> >> >> >> -- >> >> with Regards >> >> Shahid Ashraf >> >> >> >> >> >> -- >> >> with Regards >> >> Shahid Ashraf >> >> >> >> >> >> -- >> >> with Regards >> >> Shahid Ashraf >> >> >> >> >> >> -- >> >> with Regards >> >> Shahid Ashraf >> >> >> >> >> >> -- >> >> with Regards >> >> Shahid Ashraf >> >> >> >> >> >> -- >> >> with Regards >> >> Shahid Ashraf >> > > > > -- > with Regards > Shahid Ashraf > -- with Regards Shahid Ashraf
