Hi Ali, I'm not entirely sure of the answer to your question, but I suspect it has something to do with how your mysql user is created and initialized. That is described in UMLS::Interace in the following :
http://cpansearch.perl.org/src/BTMCINNES/UMLS-Interface-1.43/INSTALL mysql> CREATE USER bthomson IDENTIFIED BY 'psswrd'; Query OK, 0 rows affected (0.00 sec) mysql> GRANT ALL ON *.* TO bthomson; Query OK, 0 rows affected (0.00 sec) You may want to check out the mysql documentation to see if that gives you a way to set up a user without write-access. Please let us know if you find anything useful there, this seems like something that might be of broader interest. http://dev.mysql.com/doc/refman/5.1/en/adding-users.html Cordially, Ted On Thu, Jul 2, 2015 at 3:54 PM, Ali Siavosh-Haghighi <[email protected]> wrote: > Hi Ted, > Another question, > Is it possible to take away write permission from the umlsuser after > installation? The fact that a user have full access to umls database is a > bit uncomfortable. > Thanks > > ======================================= > Ali Siavosh-Haghighi, Ph.D. > HPC System Administrator > High Performance Computing Facility > Center for Health Informatics and Bioinformatics > NYU Langone Medical Center > Phone: (646) 501-2907 > http://nyuinformatics.org/services/hpcf > ======================================= > > > On Jul 1, 2015, at 8:58 PM, Ted Pedersen <[email protected]> wrote: > > Hi Ali, > > The use of the client section in my.cnf is optional, and it sounds > like in your environment it might be better not to use it. In that > case you can pass that same info from my.cnf via the database command > line options, which you can see here : > > https://metacpan.org/pod/umls-similarity.pl > > Most/all of the command line utilities support these database options. > So, I think that might be a reasonable thing to try. If you are not > using the command line tools but instead are running the actual code, > you can set these parameters in the code. An example of how that > happens can be found here : > > https://metacpan.org/pod/UMLS::Interface#INITIALIZING-THE-MODULE > > I hope this helps. Please let us know if other questions arise. > > Good luck! > Ted > > On Wed, Jul 1, 2015 at 4:24 PM, Ali Siavosh-Haghighi <[email protected]> > wrote: > > Hi, > Turns out that adding the section “client” to my.cnf makes “umlsuser”, umls > password and umls data base as defaults if a user runs mysql without > specifying these variables. This has caused us a problem because some of our > cluster management services login to mysql database without specifying the > name of their database. Thus these services try to access umls database and > since the access is not granted, they error out. Is there any solution to > this problem? > The problem is more dramatic since whoever issues “mysql” becomes “umlsuser” > with full access to the database and No password needed. > Thanks > ======================================= > Ali Siavosh-Haghighi, Ph.D. > HPC System Administrator > High Performance Computing Facility > Center for Health Informatics and Bioinformatics > NYU Langone Medical Center > http://nyuinformatics.org/services/hpcf > ======================================= > > > >
