Thanks very much Alain for helping Roberto out! Great to see the ctakes user community working together. Tim
On Thu, 2020-12-17 at 14:53 +0100, Roberto Zanoli wrote: > * External Email - Caution * > > > Great! > I've followed your instructions step by step and I succeeded in > installing cTAKES. Everything was exactly as you said it would be! > > Thank you very much for your help > Best > Roberto > > On Thu, Dec 17, 2020 at 1:04 PM Alain Leblanc <aal...@gmail.com> > wrote: > > OK then. > > > > > > > > You mentioned Microsoft in your original post so I thought you were > > doing everything with windows. Anyway first step is to check out > > the code: I would create a new directory, go into it then type: > > > > > > > > svn co https://svn.apache.org/repos/asf/ctakes/trunk/ > > > > > > > > This will create a ‘trunk’ directory. Go into it, type > > > > > > > > mvn compile > > > > > > > > This will compile and test the code. You may want to grab a coffee > > or a beer while it’s running. At the end it will tell you if > > there’s any error. If there’s no error type > > > > > > > > mvn install > > > > > > > > When this is done you will have a file ./org/apache/ctakes/ctakes- > > distribution/4.0.1-SNAPSHOT/ctakes-distribution-4.0.1-SNAPSHOT- > > bin.zip. > > > > > > > > From there you follow the instructions on > > https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide > > , including the addition of ctakes-resources, modifying the > > file/path names based on your new package name. > > > > > > > > The only step not included in the instructions is how to add your > > key. If you’re the only one using your computer you can just add > > the lines > > > > > > > > set ctakes.umls_apikey=<your key> > > > > set ctakes.umlsaddr=https://utslogin.nlm.nih.gov/cas/v1/api-key > > > > > > > > (or export ctakes.umls_apikey … if on Linux) > > > > > > > > on top of the runctakesCVD.bat file (or .sh, on Linux), or add the > > options to the command line as explained in the instructions (- > > Dctakes.umls_...). I suspect that setting ctakes.umlsaddr won’t be > > necessary in the final version, but when I tested last week the old > > URL was being used if this option was not set. > > > > > > > > Let us know how it works for you. > > > > > > > > A > > > > > > > > > > > > > > > > > > > > > > > > > > > > From: Roberto Zanoli > > Sent: Thursday, December 17, 2020 5:36 AM > > To: user@ctakes.apache.org > > Subject: Re: How to add the UMLS credential [EXTERNAL] > > > > > > > > > > > > Thanks Alain. I'm used to linux but I've created the installation > > for windows to be aligned with you. > > > > I think I'm ready to follow the next steps. > > > > > > > > On Wed, Dec 16, 2020 at 5:22 PM Alain Leblanc <aal...@gmail.com> > > wrote: > > > > > Sure Roberto. > > > > > > > > > > > > I don't know how much of a programmer you are and how comfortable > > > you are with using the command line (on windows using the > > > powershell or the old Command Prompt program) and installing > > > software. You may need a bit of time to learn the basic commands, > > > but it may come handy later. I assume you're on Windows. Let me > > > know if you're using something else. > > > > > > > > > > > > The first step would be to install java 8, subversion and maven. > > > > > > > > > > > > You have many options for subversion. I would suggest SilkSVN > > > since it doesn't try to take over your machine. Download link is > > > https://sliksvn.com/download/ > > > > > > > > > > > > You need to install java 8 before Maven. Link is > > > https://www.oracle.com/java/technologies/javase/javase-jdk8-downloads.html > > > . You may have to register with Oracle. You need the file jdk- > > > 8u271-windows-x64.exe (as of today). The 8u271 part may change > > > if a new version is released. > > > > > > > > > > > > Then for maven there are good instructions here: > > > https://www.baeldung.com/install-maven-on-windows-linux-mac > > > > > > > > > > > > > > > > > > Let me know when they are installed. > > > > > > > > > > > > a > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Le mer. 16 déc. 2020 à 10:18, Roberto Zanoli <zan...@fbk.eu> a > > > écrit : > > > > > > > > > > > > > > > > > > > > > > > On Wed, Dec 16, 2020 at 3:30 PM Miller, Timothy < > > > > timothy.mil...@childrens.harvard.edu> wrote: > > > > > > > > > That's unfortunate but great to know, and good to know about > > > > > the > > > > > changes you needed as well. > > > > > Thanks > > > > > Tim > > > > > > > > > > On Wed, 2020-12-16 at 08:31 -0500, Alain Leblanc wrote: > > > > > > * External Email - Caution * > > > > > > > > > > > > The old user/password method stopped working for me a week > > > > > or so ago. > > > > > > However I was able to use the api key method after checking > > > > > out the > > > > > > latest (as of last week) source code from subversion and > > > > > building > > > > > > locally. The only changes I had to make was to set the > > > > > environment > > > > > > variables ctakes.umlsaddr to > > > > > > https://utslogin.nlm.nih.gov/cas/v1/api-key (otherwise the > > > > > old url > > > > > > was used) and ctakes.umls_apikey to my api key. > > > > > > > > > > > > Roberto if you need more detailed instructions I can post > > > > > them. > > > > > > > > > > > > > > > > > > > > > It would be very useful if you could provide some more > > > > information > > > > > > > > Thanks a lot > > > > > > > > Roberto > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > a > > > > > > > > > > > > > > > > > > Le mer. 16 déc. 2020 à 06:37, Miller, Timothy < > > > > > > timothy.mil...@childrens.harvard.edu> a écrit : > > > > > > > Hi Roberto, > > > > > > > The existing mechanism should be functional until January > > > > > 15. After > > > > > > > that point changes to the cTAKES code are required to use > > > > > the new > > > > > > > UMLS authentication mechanism. We are working on this and > > > > > will > > > > > > > release patches and/or new releases. > > > > > > > > > > > > > > Tim > > > > > > > > > > > > > > > > > > > > > On Wed, 2020-12-16 at 10:12 +0100, Roberto Zanoli wrote: > > > > > > > > * External Email - Caution * > > > > > > > > > > > > > > > > > > > > > > > > Dear All, > > > > > > > > > > > > > > > > I'm new to cTAKES and I'd like to analyze some texts by > > > > > using > > > > > > > > AggregatePlaintextUMLSProcessor that requires the UMLS > > > > > resource. > > > > > > > > > > > > > > > > According to the runctakesCVD file, to enable the use > > > > > of the UMLS > > > > > > > > resources you have to set your UMLS credential, i.e., > > > > > > > > Dctakes.umlsuser, Dctakes.umlspw > > > > > > > > > > > > > > > > Since, UMLS Terminology Services accounts have been > > > > > migrated to a > > > > > > > > service that allows you to sign in to UTS using > > > > > Google, > > > > > > > Microsoft, > > > > > > > > ... I don't have any username and password with which > > > > > to set the > > > > > > > > variables above. Do you have any suggestions? > > > > > > > > > > > > > > > > Thanks in advance > > > > > > > > Roberto > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > Le informazioni contenute nella presente comunicazione > > > > > sono di > > > > > > > > natura privata e come tali sono da considerarsi > > > > > riservate ed > > > > > > > > indirizzate esclusivamente ai destinatari indicati e > > > > > per le > > > > > > > finalità > > > > > > > > strettamente legate al relativo contenuto. 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