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From "John Green" <hephaestus.stu...@gmail.com>
Subject Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Date Wed, 30 Jul 2014 19:29:11 GMT
Hi Vijay - I tried this again with a fresh install including ant and Im getting the same error.
Any hints as to what direction I should turn my investigation? Im a bit at a loss... 


Thanks as always for your time,

John
—
Sent from Mailbox for iPhone

On Wed, Jul 16, 2014 at 11:20 AM, vijay garla <vngarla@gmail.com> 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 <hephaestus.studio@gmail.com>
> 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 @db.schema@.v_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 <vngarla@gmail.com> 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] <
>>> lee_richard@bah.com> 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:abhishekrm@iitrpr.ac.in]
>>>> *Sent:* Wed, 18 Jun, 2014 04:43
>>>> *To:* user@ctakes.apache.org
>>>> *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 <abhishekrm@iitrpr.ac.in>
>>>> wrote:
>>>>
>>>> Hi. Thanks for the reply.
>>>> I have a file named LookupDesc_Db.xml which has the line <jdbcImpl
>>>> tableName="@db.schema@.v_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.
>>>>
>>>>
>>>>
>>>
>>>
>>
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