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Re: [Gmod-gbrowse] Gmod-gbrowse2 MYSQL Access troubleshoot
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From: Wes B. <wes...@cs...> - 2010-03-25 01:13:52
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Jayararaman, Pushkala wrote: > hello, > I seem to have been doing okay with the in-memory databases. I even > tried to create my own volvox database on localhost and I was able to > access it and visualize it on gbrowse2. > But when I try accessing the mysql database on a remote server through > the conf file, I fail and get an > > > Internal Server error > "The server encountered an internal error or misconfiguration and was > unable to complete your request. > > Please contact the server administrator, root@localhost and inform them > of the time the error occurred, and anything you might have done that > may have caused the error. > > More information about this error may be available in the server error log. > Apache/2.2.3 (CentOS) Server at localhost Port 80". > > > > I know it is because of a permissions issue but I do not know where to > grant permissions and what to modify. First, when you create the mysql database on the database server you would grant select permissions so that the web server can access the data: mysql -e "grant select on volvox.* to no...@my..." You will have to make sure you use the correct database name, apache user, and web host name. Then in your .conf file you will have to include the database server hostname: -dsn dbi:mysql:database=volvox;host=mydataserver.somewhere.com You will have to make sure you use the correct database name, and database server host name. > I configured Gbrowse2 as root on a centOS 5. > I am running as apache and I have changed all the folders under > /var/www/html/gbrowse2 under group apache. The web server only needs read access to these files. > Also, > if I am accessing a mysql database that is on a remote server and is > maintained by a separate DB Admin, would I still have to make a folder > under the /var/www/html/databases ? No, you would not. > All the gff3 files were already loaded onto the database and I guessed > there was no need for a folder under the databases/ directory. That is correct. There is no need for a folder under the databases dir. > I went ahead and made it nevertheless and copied the gff3 files in them. > > Is that logically correct? > > Pushkala > > P.S: herewith is attached the error_logs from apache > > ============================================================================================================= > > [Wed Mar 24 17:25:18 2010] [error] [client 127.0.0.1] [17048] RUN(): > POST: http://localhost/gb2/gbrowse/volvox_db/ force_subm > it=0;plugin_find=0;name=ctgA%3A5000..10000;Search=Search at > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio > /Graphics/Browser2/Render.pm line 160., referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:18 2010] [error] [client 127.0.0.1] [17048] > add_user_tracks() at /usr/local/lib/perl5/site_perl/5.10.1/i686 > -linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 167., referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox > _db > [Wed Mar 24 17:25:18 2010] [error] [client 127.0.0.1] [17048] testing > for asynchronous event() at /usr/local/lib/perl5/site_p > erl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line > 178., referer: http://localhost/gb2/gbrowse/volvox_db > /?source=volvox_db > [Wed Mar 24 17:25:18 2010] [error] [client 127.0.0.1] [17048] init() at > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thre > ad-multi/Bio/Graphics/Browser2/Render.pm line 185., referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:18 2010] [error] [client 127.0.0.1] open database > -adaptor DBI::mysql -dsn volvox -user nobody at /usr/loca > l/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm > line 42., referer: http://localhost/gb > 2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:18 2010] [error] [client 127.0.0.1] [17048] > update_state() at /usr/local/lib/perl5/site_perl/5.10.1/i686-li > nux-thread-multi/Bio/Graphics/Browser2/Render.pm line 188., referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:18 2010] [error] [client 127.0.0.1] [17048] render() > at /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-th > read-multi/Bio/Graphics/Browser2/Render.pm line 195., referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:18 2010] [error] [client 127.0.0.1] GBROWSE NOTICE: To > enable PDF generation, please enter the directory "/ > var/www" and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo > chown apache .inkscape .gnome2". To turn off this me > ssage add "generate pdf = 0" to the [GENERAL] section of your > GBrowse.conf configuration file., referer: http://localhost/gb2 > /gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:19 2010] [error] [client 127.0.0.1] [17048] cleanup at > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thr > ead-multi/Bio/Graphics/Browser2/Render.pm line 199., referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:19 2010] [error] [client 127.0.0.1] [17048] session > flush at /usr/local/lib/perl5/site_perl/5.10.1/i686-lin > ux-thread-multi/Bio/Graphics/Browser2/Render.pm line 203., referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:19 2010] [error] [client 127.0.0.1] [17048] > synchronous exit at /usr/local/lib/perl5/site_perl/5.10.1/i686- > linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 205., referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_ > db > > [Wed Mar 24 17:25:19 2010] [error] [client 127.0.0.1] [17051] RUN(): > POST: http://localhost/gb2/gbrowse/volvox_db/ action=nav > igate;navigate=left%200 at > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/Render.pm > line > 160., referer: http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:19 2010] [error] [client 127.0.0.1] [17051] > add_user_tracks() at /usr/local/lib/perl5/site_perl/5.10.1/i686 > -linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 167., referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox > _db > [Wed Mar 24 17:25:19 2010] [error] [client 127.0.0.1] [17051] testing > for asynchronous event() at /usr/local/lib/perl5/site_p > erl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line > 178., referer: http://localhost/gb2/gbrowse/volvox_db > /?source=volvox_db > [Wed Mar 24 17:25:19 2010] [error] [client 127.0.0.1] open database > -adaptor DBI::mysql -dsn volvox -user nobody at /usr/loca > l/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm > line 42., referer: http://localhost/gb > 2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:20 2010] [error] [client 127.0.0.1] [17051] > asynchronous exit at /usr/local/lib/perl5/site_perl/5.10.1/i686 > -linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 180., referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox > _db > [Wed Mar 24 17:25:21 2010] [error] [client 127.0.0.1] [17059] RUN(): > POST: http://localhost/gb2/gbrowse/volvox_db/ action=upd > ate_sections;section_names=page_title;section_names=span;section_names=galaxy_form;section_names=search_form_objects > at /usr/ > local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/Render.pm > line 160., referer: http://localhost > /gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:21 2010] [error] [client 127.0.0.1] [17059] > add_user_tracks() at /usr/local/lib/perl5/site_perl/5.10.1/i686 > -linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 167., referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:21 2010] [error] [client 127.0.0.1] [17059] testing > for asynchronous event() at > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/Render.pm > line 178., referer: http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:21 2010] [error] [client 127.0.0.1] [17059] > asynchronous exit at > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/Render.pm > line 180., referer: http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > > [Wed Mar 24 17:25:21 2010] [error] [client 127.0.0.1] [17060] RUN(): > POST: http://localhost/gb2/gbrowse/volvox_db/ action=ret > rieve_multiple;track_ids=Motifs%3Aoverview;track_ids=ExampleFeatures;tk_Motifs%3Aoverview=e3905ee88892ae4eb1cf16947be9090b;tk > _ExampleFeatures=3cf2f12c40af3c009c9fae0e2fad84f2 at > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphi > cs/Browser2/Render.pm line 160., referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:21 2010] [error] [client 127.0.0.1] [17060] > add_user_tracks() at /usr/local/lib/perl5/site_perl/5.10.1/i68 > -linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 167., referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvo _dbse -adaptor > DBI::mysql -dsn volvox -user nobody at > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graph > [Wed Mar 24 17:25:21 2010] [error] [client 127.0.0.1] [17060] testing > for asynchronous event() at /usr/local/lib/perl5/site_ > erl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line > 178., referer: http://localhost/gb2/gbrowse/volvox_d > /?source=volvox_db/localhost/gb2/gbrowse/rgd_904_dev/ source=rgd_904_dev > at /usr/local/lib/perl5/site_perl/5.10.1/i686-linux- > [Wed Mar 24 17:25:21 2010] [error] [client 127.0.0.1] open database > -adaptor DBI::mysql -dsn volvox -user nobody at /usr/loc > l/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm > line 42., referer: http://localhost/g > 2/gbrowse/volvox_db/?source=volvox_dberl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/Render.pm > line 185., referer: h > [Wed Mar 24 17:25:21 2010] [error] [client 127.0.0.1] [17060] > asynchronous exit at /usr/local/lib/perl5/site_perl/5.10.1/i68 > -linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 180., referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvo _dbpen database: , > referer: http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] [17062] RUN(): > POST: http://localhost/gb2/gbrowse/volvox_db/ source=rg _904_dev at > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/Render.pm > line 160., referer > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_dblib/perl5/site_perl/5.10.1/Bio/DB/SeqFeature/Store/DBI/mysql.pm:1262 > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] [17063] RUN(): > GET: http://localhost/gb2/gbrowse/rgd_904_dev/ source=r d_904_dev at > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/Render.pm > line 160., refere : > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_dbr/local/lib/perl5/site_perl/5.10.1/Bio/DB/SeqFeature/Store/DBI/mysq > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] [17063] > add_user_tracks() at /usr/local/lib/perl5/site_perl/5.10.1/i68 > -linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 167., referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvo _db) > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm:44, > referer: http://loca > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] [17063] testing > for asynchronous event() at /usr/local/lib/perl5/site_ > erl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line > 178., referer: http://localhost/gb2/gbrowse/volvox_d > /?source=volvox_dber2::Render::init_database > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Brows > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] [17063] init() at > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thr > ad-multi/Bio/Graphics/Browser2/Render.pm line 185., referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db2/Render > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] open database > -adaptor DBI::mysql -dsn DBI:mysql:database=rgd_904_dev; > ost=forte.hmgc.mcw.edu -user gbrowser -pass [I used my password here]4 > at /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Gr > phics/Browser2/DataBase.pm line 42., referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] DBD::mysql::st > execute failed: Table 'rgd_904_dev.meta' doesn't exist a > t > /usr/local/lib/perl5/site_perl/5.10.1/Bio/DB/SeqFeature/Store/DBI/mysql.pm > line 1262., referer: http://localhost/gb2/gbrows > e/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] Could not open > database: , referer: http://localhost/gb2/gbrowse/volvox > _db/?source=volvox_db > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] > -------------------- EXCEPTION --------------------, referer: http://lo > calhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] MSG: Table > 'rgd_904_dev.meta' doesn't exist, referer: http://localhost/ > gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] STACK > Bio::DB::SeqFeature::Store::DBI::mysql::setting /usr/local/lib/p > rl5/site_perl/5.10.1/Bio/DB/SeqFeature/Store/DBI/mysql.pm:1262, referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volv > x_dbB::SeqFeature::Store::default_settings > /usr/local/lib/perl5/site_perl/5.10.1/Bio/DB/SeqFeature/Store.pm:2116, > referer: ht > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] STACK > Bio::DB::SeqFeature::Store::serializer /usr/local/lib/perl5/site > perl/5.10.1/Bio/DB/SeqFeature/Store.pm:1557, referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_dbysql.pm:220, re > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] STACK > Bio::DB::SeqFeature::Store::default_settings /usr/local/lib/perl > /site_perl/5.10.1/Bio/DB/SeqFeature/Store.pm:2116, referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_dbtp://loca > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] STACK > Bio::DB::SeqFeature::Store::DBI::mysql::default_settings /usr/lo > al/lib/perl5/site_perl/5.10.1/Bio/DB/SeqFeature/Store/DBI/mysql.pm:327, > referer: http://localhost/gb2/gbrowse/volvox_db/?sou > ce=volvox_db:Browser2::Render::init_database > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Brows > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] STACK > Bio::DB::SeqFeature::Store::DBI::mysql::init /usr/local/lib/perl > /site_perl/5.10.1/Bio/DB/SeqFeature/Store/DBI/mysql.pm:220, referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] STACK > Bio::DB::SeqFeature::Store::new /usr/local/lib/perl5/site_perl/5 > 10.1/Bio/DB/SeqFeature/Store.pm:370, referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] STACK (eval) > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-m > lti/Bio/Graphics/Browser2/DataBase.pm:44, referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] STACK > Bio::Graphics::Browser2::DataBase::open_database /usr/local/lib/ > erl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm:44, > referer: http://localhost/gb2/gbrowse/vo vox_db/?source=volvox_db > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] STACK > Bio::Graphics::Browser2::DataSource::open_database /usr/local/li > /perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm:768, > referer: http://localhost/gb2/gbrow e/volvox_db/?source=volvox_db > > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] STACK > Bio::Graphics::Browser2::Render::init_database /usr/local/lib/pe > l5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:995, > referer: http://localhost/gb2/gbrowse/volvo _db/?source=volvox_db > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] STACK > Bio::Graphics::Browser2::Render::init > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:231, > referer: http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] STACK > Bio::Graphics::Browser2::Render::run > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:186, > referer: http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] STACK toplevel > /var/www/cgi-bin/gb2/gbrowse:36, referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] > -------------------------------------------, referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > [Wed Mar 24 17:25:25 2010] [error] [client 127.0.0.1] Premature end of > script headers: gbrowse, referer: > http://localhost/gb2/gbrowse/volvox_db/?source=volvox_db > -- Wes Barris |