Thanks for getting back to me Bridget. I checked the UMLS database and all three of these tables are present and are populated. The only difference is that the tables I have are lower case. This obviously makes no difference in MySQL but I am not sure if the script requires them to be uppercase. Probably not the reason things aren't passing the test, but I thought I would give as much info as possible.
So after installing the UMLS Similarity package I ran the umls-similarity.plthusly: perl umls-similarity.u.pl C0035078 C0403448 Two renal failure type effects, so I could see how closely related they are. The result I got was this: -1.0000<>C0035078(Failures, Kidney)<>C0403448() Any change in method gave the same result of -1. I also tried two types of thrombosis like so: perl umls-similarity.u.pl --measure wup C0151942 C0010072 Which gave me the result: -1.0000<>C0151942(THROMBOSIS ARTERIAL)<>C0010072(THROMBOSIS CORONARY) Thoughts? Anything else I should check out? ~ Mark On Wed, Sep 4, 2013 at 11:11 AM, Bridget McInnes <[email protected]>wrote: > ** > > > 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 >>>>>> >>>>>> >>>>> >>>> >>> >> > >
