Sean, On Fri, Mar 6, 2015 at 2:30 PM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote:
> 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. > > Yes, I am getting validation output as follows: INFO UmlsUserApprover - UMLS Account at https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user xxxxxxx has been validated > > [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. > > It <seems> to work without showing any exceptions so far. Thanks, Tom Sean > > -----Original Message----- > From: Tom Devel [mailto:deve...@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 >
