A manual query such as SELECT * FROM ytex.v_snomed_fword_lookup WHERE fword="mesna"; works OK btw.
On Wed, Jul 16, 2014 at 11:24 AM, John Green <[email protected]> wrote: > 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. >>>>> >>>>> >>>>> >>>> >>>> >>> >> >
