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 [email protected] [umls-similarity]" <[email protected]> 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: [email protected] > http://ibi.imim.es > >
