It didn't fix the @db.schema@ - I just went in and manually changed it whenever the CPE complained. I assume that's supposed to be reading from ytex.properties, but mine was set and it didn't resolve that @db.schema@ issue.
On Thu, Aug 21, 2014 at 5:00 PM, John Green <john.travis.gr...@gmail.com> wrote: > Clayton - this indeed did fix the @db.schema@ for you? Im gonna try and > reproduce (havent had time yet) then ill close the Jira ticket out. > > > JG > — > Sent from Mailbox for iPhone > > On Thu, Aug 21, 2014 at 1:24 PM, Clayton Turner <caturn...@g.cofc.edu> > wrote: > > > Ah, I just switched to the ytex branch and all is good now. The SNOMED_US > > issue has been plaguing me for weeks now so thanks a million for that. > > On Thu, Aug 21, 2014 at 2:13 PM, Clayton Turner <caturn...@g.cofc.edu> > > wrote: > >> Awesome. This is just what I needed for the longest time. > >> > >> I'm having a slight issue. When running either the ytex pipeline or ytex > >> version of the AggregatePlaintextUMLSProcessor I get an error during > >> initialization. > >> > >> My DictionaryLookupAnnotator.xml is raising a > >> org.apache.uima.resource.ResourceInitializationException causedby: > >> java.lang.ClassNotFoundException: > >> edu.mayo.bmi.uima.lookup.ae.FirstTokenPermLookupInitializerImpl > >> > >> I feel like I may have drifted away from what I need, though, because > >> before this the CPE was complaining about a lack of > LookupDesc_SNOMED.xml > >> file. I found a ytex version of this on a google code site somewhere and > >> pasted it where the CPE was looking for it. Now this error is coming up. > >> > >> Could my problem be solved with just a re-run of the ant script (was > just > >> trying to avoid since it takes ages) or is it a different issue? > >> > >> > >> On Tue, Aug 19, 2014 at 12:58 PM, Tim O'Connell <tim.oconn...@gmail.com > > > >> wrote: > >> > >>> Hi John, > >>> > >>> I'm not sure what was going on with the @db.schema@ error, although I > was > >>> getting it as well before with my prior build of 3.1.2 - I assume that > >>> you've fixed something (thank you!) to make this go away. I rebuilt > >>> everything from scratch and it's working now. > >>> > >>> I think one other thing I had to change was that after I had finished > the > >>> install/build, the cTakes version of LookupDesc_Db.xml doesn't work (in > >>> resources\org\apache\ctakes\dictionary\lookup) - I'm pretty sure I had > to > >>> copy in an older version of the file from 3.1.1 to get the default > cTakes > >>> AggregatePlaintextUMLSProcessor pipeline working, although please > >>> double-check that as my memory is a little foggy. > >>> > >>> But yes, here's what I have working since re-building: > >>> 1. ytex-pipeline.xml > >>> 2. ytex version of AggregatePlaintextUMLSProcessor.xml > >>> 3. cTakes version of AggregatePlaintextUMLSProcessor.xml (with swapping > >>> the > >>> LookupDesc_Db.xml file as above) > >>> > >>> I've even made modifications to the ytex version of > LookupDesc_SNOMED.xml > >>> to get it tagging Disease Disorders, along with database modifications > to > >>> have it store these entries as well, which is working great. > Literally, > >>> everything is working perfectly now. > >>> > >>> Still so much for me to learn! Let me know if you need any more > details. > >>> > >>> All the best, > >>> Tim > >>> > >>> > >>> > >>> On Tue, Aug 19, 2014 at 4:31 AM, John Green < > john.travis.gr...@gmail.com> > >>> wrote: > >>> > >>> > I have not had time to implement this - to clarify out of curiosity, > >>> does > >>> > this clear up the @db.schema@ error Tim? And did you successfully > run > >>> > ytex with the ctakes dictionary-lookup? > >>> > > >>> > > >>> > JG > >>> > — > >>> > Sent from Mailbox for iPhone > >>> > > >>> > On Sat, Aug 16, 2014 at 2:53 AM, Tim O'Connell < > tim.oconn...@gmail.com> > >>> > wrote: > >>> > > >>> > > Hi folks, > >>> > > I was having an issue with the current build (from svn) of > ctakes/ytex > >>> > not > >>> > > identifying any annotations as some folks on this board. I traced > it > >>> to > >>> > > the fact that the UMLS database has at sometime in the relatively > >>> recent > >>> > > past changed the SAB tag in the MRCONSO table for SNOMED terms from > >>> > > SNOMEDCT to SNOMEDCT_US. I just had a newer version of UMLS that > uses > >>> > > SNOMEDCT_US. Thus when the install script tried to create the > >>> > > v_snomed_fword_lookup table, it wasn't finding any of the SNOMEDCT > >>> terms, > >>> > > thus nothing was getting annotated. > >>> > > The ytex install script was just looking for things in MRCONSO with > >>> the > >>> > > SNOMEDCT SAB tag when it created the ytex lookup table - so, by > >>> changing > >>> > > this to SNOMEDCT_US in the file > >>> > > > >>> > > >>> > CTAKES_HOME/bin/ctakes-ytex/scripts/data/mysql/umls/insert_view_template.sql > >>> > > it now works (for mysql users) to find the annotations. You can > just > >>> > re-run > >>> > > the ytex setup script, but that takes hours - instead, I just > deleted > >>> all > >>> > > the data from the v_snomed_fword_lookup table and basically ran the > >>> sql > >>> > > command to repopulate the table and it worked fine. Here's the > code, > >>> n.b. > >>> > > my schema name for my umls database is 'umls' - change the code > below > >>> if > >>> > > yours is different. > >>> > > delete from v_snomed_fword_lookup; > >>> > > insert into v_snomed_fword_lookup (cui, tui, fword, fstem, tok_str, > >>> > > stem_str) > >>> > > select mrc.cui, t.tui, c.fword, c.fstem, c.tok_str, c.stem_str > >>> > > from umls_aui_fword c > >>> > > inner join umls.MRCONSO mrc on c.aui = mrc.aui and mrc.SAB in ( > >>> > > 'SNOMEDCT_US', 'RXNORM') > >>> > > inner join > >>> > > ( > >>> > > select cui, min(tui) tui > >>> > > from umls.MRSTY sty > >>> > > where sty.tui in > >>> > > ( > >>> > > 'T019', 'T020', 'T037', 'T046', 'T047', 'T048', 'T049', 'T050', > >>> > > 'T190', 'T191', 'T033', > >>> > > 'T184', > >>> > > 'T017', 'T029', 'T023', 'T030', 'T031', 'T022', 'T025', 'T026', > >>> > > 'T018', 'T021', 'T024', > >>> > > 'T116', 'T195', 'T123', 'T122', 'T118', 'T103', 'T120', 'T104', > >>> > > 'T200', 'T111', 'T196', 'T126', 'T131', 'T125', 'T129', > 'T130', > >>> > > 'T197', 'T119', 'T124', 'T114', 'T109', 'T115', 'T121', > 'T192', > >>> > > 'T110', 'T127', > >>> > > 'T060', 'T065', 'T058', 'T059', 'T063', 'T062', 'T061', > >>> > > 'T074', 'T075', > >>> > > 'T059' > >>> > > ) > >>> > > group by cui > >>> > > ) t on t.cui = mrc.cui > >>> > > ; > >>> > > Hope it helps - cheers, > >>> > > Tim > >>> > > >>> > >> > >> > >> > >> -- > >> -- > >> Clayton Turner > >> email: caturn...@g.cofc.edu > >> phone: (843)-424-3784 > >> web: claytonturner.blogspot.com > >> > >> > ------------------------------------------------------------------------------------------------- > >> “When scientifically investigating the natural world, the only thing > worse > >> than a blind believer is a seeing denier.” > >> - Neil deGrasse Tyson > >> > > -- > > -- > > Clayton Turner > > email: caturn...@g.cofc.edu > > phone: (843)-424-3784 > > web: claytonturner.blogspot.com > > > ------------------------------------------------------------------------------------------------- > > “When scientifically investigating the natural world, the only thing > worse > > than a blind believer is a seeing denier.” > > - Neil deGrasse Tyson > -- -- Clayton Turner email: caturn...@g.cofc.edu phone: (843)-424-3784 web: claytonturner.blogspot.com ------------------------------------------------------------------------------------------------- “When scientifically investigating the natural world, the only thing worse than a blind believer is a seeing denier.” - Neil deGrasse Tyson
