So, tableName="@[email protected]_snomed_fword_lookup" to tableName="ytex.v_snomed_fword_lookup" in LookupDesc_Db.xml?
If so, I tried this and same error, with just the names swapped. Thanks Vijay, JG On Wed, Jul 16, 2014 at 11:20 AM, vijay garla <[email protected]> wrote: > 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. >>>> >>>> >>>> >>> >>> >> >
