Thank you Ted, it works fine on windows. But why does Lin similarity between two concepts in MeSH, C0633633 and C1311834, is -1?
Best regards Le Mardi 4 février 2014 15h20, Ted Pedersen <duluth...@gmail.com> a écrit : It looks like you got somewhat closer to running successfully. The error message you got is actually fairly descriptive - apparently at some point earlier a command may have been run that started to create an index, but that didn't finish for some reason. That has left behind an incomplete index that you could remove via the removeConfigData.pl program. Then, when you run this command again it should build an index and return a result. The intial building of the index can take a few minutes, but once you have done that one time you don't have to do it again. And of course running on Ubuntu is another option, although if you are submitting this command to the same server you may still have this index problem. So, you may need to resolve this even if running on Ubuntu. Good luck! Ted On Tue, Feb 4, 2014 at 7:07 AM, Drame Khadim <khadimdrame...@yahoo.fr> wrote: > >Hi Ted, > >In the first case, I set the parameters in the my.ini file in Windows, but it >doesn't work . The program doesn't take account the configuration. >When I use --socket option with empty value, It throws another error: > >C:\>umls-similarity.pl --socket='' --hostname=172.16.5.107:22774 >--username=Khad >im --password=************ --database=UMLS2012AA --measure lch hand skull >Default Settings: > --precision 4 > > >User Settings: > --username Khadim > --password XXXXXXX > --database UMLS2012AA > --hostname 172.16.5.107:22774 > --socket '' > --measure lch > > > >UMLS-Interface Configuration Information: >(Default Information - no config file) > > Sources (SAB): > MSH > Relations (REL): > PAR > CHD > > Sources (SABDEF): > UMLS_ALL > Relations (RELDEF): > UMLS_ALL > > >ERROR: UMLS::Interface::PathFinder->_checkIndex >Index Error (Error Code 9). >Index did not complete. Remove using the removeConfigData.pl program and >re-run. > >I will try to use it on ubuntu. > >Thank you, > > > > >Le Lundi 3 février 2014 18h32, Drame Khadim <khadimdrame...@yahoo.fr> a écrit : > > > >Thanks Ted. > >I will follow your instructions and let you know later. > >Regards, > > >Khadm > > > > >Le Lundi 3 février 2014 18h03, Ted Pedersen <duluth...@gmail.com> a écrit : > > >There was a recent post to this group that gave a few steps in installing on >Windows. Perhaps that would be helpful. > > >https://www.mail-archive.com/umls-similarity@yahoogroups.com/msg00303.html > > > >Also, the following thread is from a Windows user who had exactly the same >error. > > >https://www.mail-archive.com/umls-similarity@yahoogroups.com/msg00122.html > > > >In the first case the user set these parameters in the my.ini file in Windows, >and in the second case it involved the installation of the DBI module. > > >But, you might need to provide a different value for --socket - the default is >based on Linux and won't work on Windows. I'm not sure if that is the cause of >your problem, but it would be something to look at. I would also check and >make sure the DBI module was installed correctly, it seems like problems with >that not installing can cause this particular error. > > >Let us know how things go. > > >Good luck, >Ted > > > >On Mon, Feb 3, 2014 at 10:34 AM, <khadimdrame...@yahoo.fr> wrote: > > >> >>This is my error : >> >>C:\UMLS-Similarity>umls-similarity.pl --hostname=172.16.5.107:22774 >>--username=K >>hadim --password=******** --database=UMLS2012AA hand skull >>Default Settings: >> --precision 4 >> --socket /tmp/mysql.sock >> >> --measure path >> >>User Settings: >> --username Khadim >> --password XXXXXXX >> --database UMLS2012AA >> --hostname 172.16.5.107:22774 >> >>DBI connect('database=UMLS2012AA;mysql_socket=/tmp/mysql.sock >>;host=172.16.5.107:22774','Khadim',...) failed: AccÞs refusÚ pour >>l'utilisateur: >> 'Khadim'@'@localhost' (mot de passe: NON) at >>C:/perl/site/lib/UMLS/Interface/Cu >>iFinder.pm line 2425 >>Can't call method "err" on an undefined value at >>C:/perl/site/lib/UMLS/Interface >>/ErrorHandler.pm line 113. > > > >-- >Ted Pedersen >http://www.d.umn.edu/~tpederse > > > > -- Ted Pedersen http://www.d.umn.edu/~tpederse
