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: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
