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

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

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 [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
    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