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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: Is it necessary to put UMLS login into files when passing them with -D to the JVM?
Date Fri, 06 Mar 2015 20:30:56 GMT
Hi Tom,

> I am passing my UMLS login and password on startup as arguments ... "-Dctakes.umlsuser=myusername
-Dctakes.umlspw=mypassword"
That is fine.  If I understand correctly you are already running this way without problem.
 The comments in the .xml files should probably be extended to include mention of the cmd
parameters.


> [I] downloaded [AggregatePlaintextFastUmlsProcessor.xml] from the svn and replaced the
old cTAKES 3.2.1 ...
I think that this should be fine.  Java code for each annotator may have changed, but I don't
think that any class names (by which annotators are called) have changed.  The best way to
know for certain is to run it, and if you haven't seen any problems then I think that you
are in good shape.

Sean

-----Original Message-----
From: Tom Devel [mailto:develxy@gmail.com] 
Sent: Friday, March 06, 2015 3:20 PM
To: dev@ctakes.apache.org
Subject: Is it necessary to put UMLS login into files when passing them with -D to the JVM?

Hi,

in AggregatePlaintextFastUMLSProcessor.xml of cTAKES it states that:

[...] Please update DictionaryLookupAnnotatorUMLS.xml file with your UMLS username and password.

Similarly, in AggregatePlaintextFastUMLSProcessor.xml from https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D344&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZOef73O4fpDF9CZPAZHmVyDZDQDa6jKWyTTU1kikj9o&s=7C1osQzBp5-aSIXPeqWPXcafrLDGCeEkR3sfbiJMRDQ&e=


[...] Please update
resources/org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml file with your UMLS username
and password

I am passing my UMLS login and password on startup as arguments, when starting the either
CVD/CPE or org.apache.uima.examples.cpe.SimpleRunCPE
argumets such as:

"-Dctakes.umlsuser=myusername -Dctakes.umlspw=mypassword"

In such a case, it is still necessary to modify the file(s) above?

Additional question: It seems that the
AggregatePlaintextFastUMLSProcessor.xml from https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D344&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZOef73O4fpDF9CZPAZHmVyDZDQDa6jKWyTTU1kikj9o&s=7C1osQzBp5-aSIXPeqWPXcafrLDGCeEkR3sfbiJMRDQ&e=
 has some nice improvements (using DrugNER and default fast pipeline). I just downloaded it
from the svn and replaced the old cTAKES 3.2.1 file with this one, and it seems to run just
fine and cTAKES does annotations. Can somebody from the devs or users tell me if this manual
replacement step is OK and does not break anything that I am not aware of?

Many thanks for answers on any of my questions, Tom
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