Hi Mark, The error 4-6 on mysql.t are the system not being able to find the MRREL, MRCONSO and MRSAB tables. So I think first, would you check to make certain that umls is loaded in mysql and that the tables exist. I am not certain of your familiarity with mysql so I put the commands below:
login: mysql -u <username> -p check the umls database: use umls; show tables; This should show you a list of tables in the UMLS -- hopefully you will see the MRREL, MRCONSO and MRSAB tables. Would you also send the umls-similarity.pl command that you are using? That might help trouble shoot a bit more. Thanks! Bridget On Wed, Sep 4, 2013 at 10:00 AM, Mark Lawson <[email protected]> wrote: > ** > > > 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 >>>>> >>>>> >>>> >>> >> > >
