The time to build an index really varies quite a bit, and depends both on the hardware you have available and the particular sources and relations you are using. If possible be patient and let the index build finish, since that really does speed up queries. And I hope your index has already been built by the time you read this!
Good luck, Ted On Thu, Aug 4, 2016 at 8:57 AM, Emilio Centeno Ortiz [email protected] [umls-similarity] <[email protected]> wrote: > > > Hi Ted, > > Thanks for the reply. I finally could make it work. > > I didn't know that the UMLS Semantic Network was necessary in the > initialization of the UMLS::Interface object. Since we don't have the > Semantic Network for umls_2016AA I just switched to umls_2015AB. Now it is > working. > > Now that I'm running a test, the package is creating an index database > that, in the end, it will save time in future queries. How long this will > take? > > I hope I will ask about more interesting issues shortly :) > > Thanks again, > > Emilio > > > > On 08/04/2016 03:30 PM, Ted Pedersen [email protected] > [umls-similarity] wrote: > > > 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 [email protected] > [umls-similarity] <[email protected]> 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 [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] >> [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 <%2B34%2093%20316%200536> >>> E-mail: [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 <%2B34%2093%20316%200536> >> E-mail: [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] > http://ibi.imim.es > > >
