replace db.schema with your database schema name. For sql server, this is dbo, for mysql this is the database/schema name, for oracle this is the schema name. This should have been done automatically by the ant setup script, not sure why it isn't happening in some configs.
-vj On Wed, Jul 16, 2014 at 4:53 PM, John Green <[email protected]> wrote: > Hi Vijay - I am at the same impasse as Mr Lee and Mr Abhishek, and I didnt > come across any other solutions in the archives. > > Through intuition I figured out what you mention in this post on my own, > and tried it. It didnt work. It seems to revolve around this line: > Unexpected token: @ in statement [SELECT tui,cui,tok_str FROM > @[email protected]_snomed_fword_lookup > WHERE fword = ?] > > It seems the query is coming from LookupDesc_SNOMED.xml, but I cant find > the @db.schema@... is this a windows/linux issue? > > Before Vijay spends his precious time on answering this, did anyone else > get resolution on this? > > Best, > JG > > > On Wed, Jun 18, 2014 at 10:11 AM, vijay garla <[email protected]> wrote: > >> The YTEX AggregatePlaintextUMLSProcessor differs from the default >> AggregatePlaintextUMLSProcessor in the following a ways: >> * Use SegmentRegexAnnotator instead of SimpleSegmentAnnotator >> * Use SentenceDetectorAnnotator without splitting on newlines >> * Added SenseDisambiguatorAnnotator >> ** Use YTEX DictionaryLookupAnnotatorDB instead of cTAKES >> DictionaryLookupAnnotatorDB* >> >> The YTEX dictionary lookup is different from cTAKES': >> * uses the old dictionary lookup >> * uses a single dictionary >> * uses a single lookup consumer that creates plain-vanilla EntityMention >> annotations (none of the subtypes) >> >> I think that if you change the YTEX AggregatePlaintextUMLSProcessor to >> point at the cTAKES dictionary lookup, you will get approximately same >> annotations (probably more if sentences do not end on newlines, as >> dictionary lookup is not performed across sentences) >> >> could you try the following please: >> In >> desc\ctakes-ytex-uima\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml >> change >> <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB"> >> <import location="./DictionaryLookupAnnotator.xml" /> >> </delegateAnalysisEngine> >> To >> <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB"> >> <import >> location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml"/> >> </delegateAnalysisEngine> >> >> And re-run. You should get the same results (keep in mind the newline >> thing). >> >> >> >> >> >> On Wed, Jun 18, 2014 at 9:46 AM, Lee, Richard A. [USA] < >> [email protected]> wrote: >> >>> Yes, that exactly the problem I’ve been reporting. I think you’ll see >>> that it you still get the non-Medical annotations, like Date, RomanNumeral, >>> et al, but not DiseaseDisorderMention and the other Medical ones, right? >>> >>> >>> >>> I’m still hoping someone can assist with this. >>> >>> >>> >>> *From:* Abhishek Raj [mailto:[email protected]] >>> *Sent:* Wed, 18 Jun, 2014 04:43 >>> *To:* [email protected] >>> *Subject:* Re: [External] Re: Cannot load >>> AggregatePlainTextUmlsProcessor.xml >>> >>> >>> >>> Found a fix. Will post it here in case it helps someone. When using >>> ctakes-3.1.2, load the AggregatePlainTextUmlsProcessor.xml from " >>> CTAKES_HOME/desc/ytex-uima/desc/analysis_engine/ >>> AggregatePlaintextUMLSProcessor.xml" and not from the usual " >>> CTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/ >>> AggregatePlaintextUMLSProcessor.xml" as given here >>> <https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide>. >>> >>> However strangely, >>> "ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml" >>> produced even less annotations than " >>> ctakes-clinical-pipeline/desc/analysis_engine/ >>> AggregatePlaintextUMLSProcessor.xml". >>> >>> I expected ytex-specific AE to produce better results. But clearly >>> that's not the case. >>> >>> >>> >>> On Thu, Jun 12, 2014 at 2:51 AM, Abhishek Raj <[email protected]> >>> wrote: >>> >>> Hi. Thanks for the reply. >>> I have a file named LookupDesc_Db.xml which has the line <jdbcImpl >>> tableName="@[email protected]_snomed_fword_lookup"/> >>> >>> instead of LookupDesc_SNOMED.*template*.xml. Also, my ytex.properties >>> file seems fine. I have attached the file for your reference. >>> And yes, when running the ant setup by following #7 on this >>> <https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation> link, >>> it sends the output to "setup.out". The build was successful though. I >>> didn't see any errors. I am attaching the file for your reference as well. >>> Please have a look and let me know. >>> >>> >>> >> >> >
