I ran the command and had the index files be re-created but sadly got the same result. Not sure what my next step should be ...
On Wed, Sep 4, 2013 at 12:11 PM, Bridget McInnes <[email protected]>wrote: > ** > > [Attachment(s) <#140e9e5e246ff089_TopText> from Bridget McInnes included > below] > > 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 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > >
