Re: [umls-similarity] UMLS database in a remote machine

[Emilio Centeno Ortiz ecent...@imim.es [umls-similarity]]

Hi Ted,

Thanks for the reply. I finally could make it work.
I didn't know that the UMLS Semantic Network was necessary in the 
initialization of the UMLS::Interface object. Since we don't have the 
Semantic Network for umls_2016AA I just switched to umls_2015AB. Now it 
is working.

Now that I'm running a test, the package is creating an index database 
that, in the end, it will save time in future queries. How long this 
will take?

I hope I will ask about more interesting issues shortly :)

Thanks again,

Emilio


On 08/04/2016 03:30 PM, Ted Pedersen duluth...@gmail.com 
[umls-similarity] wrote:
Hi Emilio,

I'm afraid I haven't seen this error before. It looks like a fairly 
generic Perl DBI error, so I wonder if everything is working ok with 
that module? If possible it might be good to run the DBI tests again 
just to make sure that is installed and working ok. Please let us know 
what you find if you are able to do that...

Sorry I can't be more specific, but keep us posted and we might be 
able to do more...

Good luck,
Ted

On Tue, Aug 2, 2016 at 2:21 AM, Emilio Centeno Ortiz ecent...@imim.es 
<mailto:ecent...@imim.es> [umls-similarity] 
<umls-similarity@yahoogroups.com 
<mailto:umls-similarity@yahoogroups.com>> wrote:

    Hi again,

    Now that our sysadmin granted a full working access to the UMLS
    database, I'm trying to create the UMLS::Interface object:

    my $umls = UMLS::Interface->new({"driver" => "mysql",

             "database" => "umls_2016AA",

             "username" => "myusername",

             "password" => "mypassword",

             "hostname" => "localhost",

             "port" => "3306"

         });


    But I get this output:

    UMLS-Interface Configuration Information:

    (Default Information - no config file)

       Sources (SAB):

          MSH

       Relations (REL):

          PAR

          CHD

       Sources (SABDEF):

          UMLS_ALL

       Relations (RELDEF):

          UMLS_ALL

    ERROR: UMLS::Interface::STFinder->_loadSemanticNetwork

    Database error (Error Code 1).

    Error executing database query: DBI::st=HASH(0x3b643e8)->errstr()).


    Any hint about this?

    Thanks in advance,

    Emilio

    On 07/30/2016 03:18 AM, juliana md julian...@gmail.com
    <mailto:julian...@gmail.com> [umls-similarity] wrote:

    Hi Emilio,

    Did you grant access to myusername@mylocalmachine to your
    umls_2016AA database?
    Are you able to connect to your database from mylocalmachine (by
    using workbench for example) using those credentials?

    Regards,
    Juliana

    Em 29 de jul de 2016 21:05, "Emilio Centeno Ortiz
    ecent...@imim.es <mailto:ecent...@imim.es> [umls-similarity]"
    <umls-similarity@yahoogroups.com
    <mailto:umls-similarity@yahoogroups.com>> escreveu:

        Hello,

        I have just installed the UMLS::Similarity package and
        copy-pasted the example code Since the MySQL is hosted in
        another machine (172.20.16.15) I tried to initialize the
        interface with our connection parameters:

        use UMLS::Interface;
        use UMLS::Similarity::lch;
        use UMLS::Similarity::path;
          
        $umls = UMLS::Interface->new({"driver" => "mysql",
                                          "database" => "umls_2016AA",
                                          "username" => "myusername",
                                          "password" => "mypassword",
                                          "hostname" => "myMySQLHostIP",
                                          "port" => "3306"});

        die "Unable to create UMLS::Interface object.\n" if(!$umls);
          
        my $lch = UMLS::Similarity::lch->new($umls);
        die "Unable to create measure object.\n" if(!$lch);
          
        my $path = UMLS::Similarity::path->new($umls);
        die "Unable to create measure object.\n" if(!$path);
          
        my $cui1 = "C0005767";
        my $cui2 = "C0007634";
          
        $ts1 = $umls->getTermList($cui1);
        my $term1 = pop @{$ts1};
          
        $ts2 = $umls->getTermList($cui2);
        my $term2 = pop @{$ts2};
          
        my $lvalue = $lch->getRelatedness($cui1, $cui2);
          
        my $pvalue = $path->getRelatedness($cui1, $cui2);
          
        print "The lch similarity between $cui1 ($term1) and $cui2 ($term2) is $lvalue\n";
          
        print "The path similarity between $cui1 ($term1) and $cui2 ($term2) is $pvalue\n";


        but it complains like that:

        DBI 
connect('database=umls_2016AA;mysql_socket=/var/run/mysqld/mysqld.sock;host=myMySQLHostIP','myusername',...)
 failed: Access denied for user 'myusername'@'mylocalmachinename' (using 
password: YES) at 
/soft/devel/perl-5.16.3/lib/site_perl/5.16.3/UMLS/Interface/CuiFinder.pm line 
2458.

        Can't call method "err" on an undefined value at 
/soft/devel/perl-5.16.3/lib/site_perl/5.16.3/UMLS/Interface/ErrorHandler.pm line 113.


        I have just replaced hostnames, user, etc. with "my..." names.
        It looks like it tries to connect to MySQL using sockets? Any
        advice about how I could overcome this issue?

        Thanks in advance,
        Emilio

        -- 
        Emilio Centeno Ortiz

        Research Programme on Biomedical Informatics (GRIB)
        Department of Experimental and Health Sciences
        Universitat Pompeu Fabra
        IMIM (Hospital del Mar Medical Research Institute)
        C/ Dr. Aiguader, 88
        Barcelona, Spain
        Tel.: +34 93 316 0536 <tel:%2B34%2093%20316%200536>
        E-mail: ecent...@imim.es <mailto:ecent...@imim.es>
        http://ibi.imim.es


    -- 
    Emilio Centeno Ortiz

    Research Programme on Biomedical Informatics (GRIB)
    Department of Experimental and Health Sciences
    Universitat Pompeu Fabra
    IMIM (Hospital del Mar Medical Research Institute)
    C/ Dr. Aiguader, 88
    Barcelona, Spain
    Tel.: +34 93 316 0536 <tel:%2B34%2093%20316%200536>
    E-mail: ecent...@imim.es <mailto:ecent...@imim.es>
    http://ibi.imim.es




--
Emilio Centeno Ortiz

Research Programme on Biomedical Informatics (GRIB)
Department of Experimental and Health Sciences
Universitat Pompeu Fabra
IMIM (Hospital del Mar Medical Research Institute)
C/ Dr. Aiguader, 88
Barcelona, Spain
Tel.: +34 93 316 0536
E-mail: ecent...@imim.es <mailto:ecent...@imim.es>
http://ibi.imim.es