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