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