This is the same error I reported a few weeks ago, but it probably got missed because I was also reporting that using the ytex-specific AE failed to produce any MedicalAnnotations…
From: Abhishek Raj [mailto:[email protected]] Sent: Wed, 11 Jun, 2014 12:11 To: [email protected] Subject: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml Thanks for the reply. I am using apace-cTakes-3.1.2 and yes, this is using YTEX. I followed these<https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation> instructions for installing ytex and #1 in the installation procedure was " installing ctakes+ytex distro 'as usual' " by following these<https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide> instructions. Not sure what is the reason for the error though. I have UMLS installed in my SQL database already. On Wed, Jun 11, 2014 at 9:24 PM, Chen, Pei <[email protected]<mailto:[email protected]>> wrote: Abhishek, There is an SQL exception because of the “@db.schema@.” in the sql: SELECT tui,cui,tok_str FROM @[email protected]_snomed_fword_lookup WHERE fword = ? Which version of cTAKES are you using and also is this using YTEX? As I am not sure where the special parameter markers are coming from. Normally, it would look something like: http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-dictionary-lookup-res/src/main/resources/org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml From: Abhishek Raj [mailto:[email protected]<mailto:[email protected]>] Sent: Wednesday, June 11, 2014 11:39 AM To: [email protected]<mailto:[email protected]> Subject: Re: Cannot load AggregatePlainTextUmlsProcessor.xml Hey! Thanks a lot for the reply. That totally worked. However, I have run into another problem now. After loading the "AggregatePlainTextUmlsProcessor.xml", when I try to run the it on some text sample I get an error saying org.apache.uima.analysis_engine.AnalysisEngineProcessException . More detailed information is in the log file I have attached the log in the attachments. Please do have a look. Any help will be appreciated. On Wed, Jun 11, 2014 at 7:06 PM, Chen, Pei <[email protected]<mailto:[email protected]>> wrote: Abhishek, Have you tried some of the suggestions from this thread: http://mail-archives.apache.org/mod_mbox/ctakes-dev/201304.mbox/%3CCD84AD35.169BD%25mcoarr%40mitre.org%3E From: Abhishek Raj [mailto:[email protected]<mailto:[email protected]>] Sent: Wednesday, June 11, 2014 4:17 AM To: [email protected]<mailto:[email protected]> Subject: Cannot load AggregatePlainTextUmlsProcessor.xml Hello I installed ctakes following https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation and https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide . After installation I ran the CVD for annotation purpose. When I try to load the AggregatePlainTextUmlsProcessor.xml I get error saying org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator" failed. (Descriptor: file:/home/gamerboy/apache-ctakes-3.1.2-SNAPSHOT/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml) I am behind a proxy network. Not sure this could be the reason though.
