4.0.0 UMLS Authentication Patch - for Developers - Not a release

[Peter Abramowitsch]

Hi Sean

Given that you're still deciding about the tagging or branching for the
4.0.0 back-patch, I won't check the changes in, but they are attached
here.    They need to be unloaded at the top of the source tree.

Gandhi:  I've attached a slightly modified version of the instructions for
your Wiki updates.
If anyone wants the two unofficial 4.0.0 jars for testing, I would be happy
to put them in dropbox

Regards & Happy Thanksgiving
Peter

Readme for UMLS auth in ctakes 4.0.0

However you initialize your umls user, set the value to "umls_api_key"
However you initialize your umls pwd = put your API_KEY

Or you can dispense with user/password and simply set a JVM system property to  
ctakes.umls_apikey=<YOUR API KEY>

or an environment variable ctakes.umls_apikey=<YOUR API KEY>
or an environment variable ctakes_umls_apikey=<YOUR API KEY>

from 
desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
        
desc/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffectUMLS.xml
        
desc/ctakes-clinical-pipeline/desc/analysis_engine/auto/defaultPipeline.xml

set vendor, umlsuser, umlspw and umlsaddr values to an empty string:

    <nameValuePair>
      <name>ctakes.umlsaddr</name>
      <value>
        <string></string>
      </value>
    </nameValuePair>
    <nameValuePair>
      <name>ctakes.umlsvendor</name>
      <value>
        <string></string>
      </value>
    </nameValuePair>
    <nameValuePair>
      <name>ctakes.umlsuser</name>
      <value>
        <string></string>
      </value>
    </nameValuePair>
    <nameValuePair>
      <name>ctakes.umlspw</name>
      <value>
        <string></string>
      </value>
    </nameValuePair>

      
from any 
  resources/org/apache/ctakes/dictionary/lookup/fast/*.xml
  set these property values to an empty string 
     <property key="umlsUrl" value=""/>
     <property key="umlsVendor" value=""/>
     <property key="umlsUser" value=""/>
     <property key="umlsPass" value=""/>


I haven't tried it with auth values in the piper files, but it does work with 
the environment variable and system properties. For example, here's a snippet 
of my modifid runctakesCVD.sh

....
export ctakes_umls_apikey="<MY API KEY>"
PRG="$0"
while [ -h "$PRG" ]; do
  ls=`ls -ld "$PRG"`
.....