Hi Mark, I will check on the table name upper or lower case for mysql.t -- this might be causing it. I do have it so it doesn't matter within the package itself but I am not certain about the test case.
For the -1 problem, the next thing would be to run removeConfigData.pl, I think. It looks then like the umlsinterfaceindex table for this configuration didn't get created properly. I attached the config file (called config) for the default configuration. To run: removeConfigData.pl config This should remove the index files. Then run again: umls-similarity.pl C0035078 C0403448 You should be prompted to see if you want to create the index files. Type 'y' and then wait. The program is running a BFS over MSH creating the index table in the umlsinterfaceindex database. This will take a bit depending on your machine but it only happens on the first run. Subsequent runs use this information and run quicker. Hopefully, this will fix it. If it doesn't please let us know. And of course, if have any other questions, please email. Thanks! Bridget On Wed, Sep 4, 2013 at 11:53 AM, Mark Lawson <[email protected]> wrote: > ** > > > 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.pl thusly: > > 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 >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > >
