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From "Tsung-Ting Kuo" <ts...@ucsd.edu>
Subject RE: Question about YTEX
Date Wed, 10 Jun 2015 16:49:20 GMT
Hi Vijay,


You are absolutely right – after changing the permission of the “resource” directory,
YTEX start installing without problem! In the meanwhile, I have a quick question: since I
have installed the UMLS database and set the “umls.schema” to UMLS database name (I am
using MySQL), how do I know whether YTEX successfully creates a dictionary lookup table with
all concepts from the UMLS or not?


Thanks again!


Best regards,



From: Vijay Garla [mailto:vijay.garla@yale.edu] 
Sent: Tuesday, June 9, 2015 11:31 PM
To: tskuo@ucsd.edu; dev@ctakes.apache.org
Cc: vijay.garla@yale.edu
Subject: Re: Question about YTEX


Hi Tsung-Ting,


I see the following error:



     [echo] unpacking ytex templates from /usr/local/apache-ctakes-3.2.2/lib/ctakes-ytex-res-3.2.2.jar
to /usr/local/apache-ctakes-3.2.2/resources

    [unzip] Expanding: /usr/local/apache-ctakes-3.2.2/lib/ctakes-ytex-res-3.2.2.jar into /usr/local/apache-ctakes-3.2.2/resources

    [unzip] Unable to expand to file /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.template.xml

    [unzip] Unable to expand to file /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/conceptGraph/sct-msh-csp-aod.template.xml

    [unzip] Unable to expand to file /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/conceptGraph/sct-umls.template.xml

    [unzip] Unable to expand to file /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/umls/model/UMLS.hbm.template.xml

    [unzip] Unable to expand to file /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_stem_SNOMED.template.xml

    [unzip] Unable to expand to file /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_SNOMED.template.xml


I don't know why there was an issue extracting ctakes-ytex-res-3.2.2.jar.  Can you make sure
that  /usr/local/apache-ctakes-3.2.2/resources exists and is writable?




On Wed, Jun 10, 2015 at 12:17 AM, Tsung-Ting Kuo <tskuo@ucsd.edu <mailto:tskuo@ucsd.edu>
> wrote:

Hi Vijay Garla,


I am Tsung-Ting Kuo from UCSD, and I am interested in your YTEX project. I tried to download
it and setup based on the following page:


https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation <https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_YTEX-2BInstallation&d=AwMFAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=rw3vAb56jh8xMYlMHfE0hS2hfbV3RFxqvusA5jfoLnc&m=b0QIg7D5IImLEUt69gE-sqJU5GHeSBEMS_oz2Uddul4&s=Jyu357olHH-y9kNgTHIj2B01-i6DhsiGYH2HOwu9yok&e=>


However, in the final step (step 7), I was not able to setup. The attached “setup.out”
seems to show that the “UMLS.hbm.xml” is missing. Could you kindly help to tell me how
to set it up?


Thanks very much!


Best regards,




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