Hi Bridget (and others) I am still having issues. I am not passing the "make test" when compiling the UMLS Interface. This is my error message:
Test Summary Report ------------------- t/mysql.t (Wstat: 0 Tests: 8 Failed: 3) Failed tests: 4-6 Files=25, Tests=268, 232 wallclock secs ( 0.12 usr 0.07 sys + 29.29 cusr 4.08 csys = 33.56 CPU) Result: FAIL Failed 1/25 test programs. 3/268 subtests failed. make: *** [test_dynamic] Error 255 I tried just "pushing forward" but when I use the UMLS similarity script every comparison I make between UMLS IDs gives me the similarity score of -1. Any idea what I am missing / is not working? Thank you, ~ Mark On Wed, Aug 28, 2013 at 7:02 PM, Bridget McInnes <[email protected]>wrote: > ** > > > Hi Mark, > > That is a good question, I have always just granted all permissions. For > umlsinterfaceindex, the user needs to be able to create and delete tables, > and insert and delete items from them. For umls, it just needs permission > to access information from it. Does that help? > > Thanks, > > Bridget > > > > > > > On Wed, Aug 28, 2013 at 3:09 PM, Mark Lawson <[email protected]>wrote: > >> ** >> >> >> Thanks Bridget, that did the trick. I will see if I can get through the >> remaining setup and running it. >> >> Follow up question: Does this umls user I created require these >> permissions going forward as well? Or will it work alright with simple >> select permissions? >> >> >> On Wed, Aug 28, 2013 at 1:36 PM, Bridget McInnes <[email protected]>wrote: >> >>> ** >>> >>> >>> Hi Mark, >>> >>> Yes, the db name should be 'umls'. From your access denied message it >>> looks as if your user name is also umls, is this correct? And if so, then >>> it looks like the permissions to create a database on mysql are not >>> available to user umls. During the set up did you grant permissions to the >>> user? For example: >>> >>> mysql> GRANT ALL ON *.* TO umls; >>> >>> Please let us know if you have any additional questions. Or if that >>> didn't solve the problem. We can continue to help trouble shoot. >>> >>> Thanks, >>> >>> Bridget >>> >>> >>> On Wed, Aug 28, 2013 at 12:45 PM, Mark Lawson <[email protected]>wrote: >>> >>>> ** >>>> >>>> >>>> Hello UMLS Similarity users, >>>> >>>> I am trying to install the UMLS Interface package with the ultimate >>>> goal of using the UMLS similarity tool on my Mac but am having issues. I >>>> have followed the steps outlined in the installation guidelines and have >>>> created a UMLS MySQL Db named "umls". However, when I try and install the >>>> UMLS Interface package, I cannot make it passed the 'make test' step. I >>>> repeatedly get the error: >>>> Access denied for user 'umls'@'localhost' to database >>>> 'umlsinterfaceindex' >>>> >>>> Should my database be named this? Or can I set a different default >>>> database name? I am confused because the instructions repeatedly call for >>>> this DB to be called 'umls' and i want to make sure that this isn't a step >>>> creating a new DB based on the 'umls' one. >>>> >>>> Any light you can shed on this would be greatly appreciated. >>>> >>>> ~ Mark >>>> >>>> >>> >> > >
