Hi Juliana,
My mistake, sorry. Our sysadmin found a problem with the socket
location. He had to do a symlink in the expected location and it worked.
Regards,
Emilio
On 07/30/2016 03:18 AM, juliana md [email protected] [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 [email protected]
<mailto:[email protected]> [umls-similarity]"
<[email protected]
<mailto:[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] <mailto:[email protected]>
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: [email protected] <mailto:[email protected]>
http://ibi.imim.es
