Hi Mark, Would you try:
umls-similarity.pl hand skull and see what is returned? Thanks! Bridget On Wed, Sep 4, 2013 at 1:32 PM, Mark Lawson <[email protected]> wrote: > ** > > > 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) <#140ea11dfab45b07_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 >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > >
