From: Shane M. <sha...@gm...> - 2016-10-28 18:15:11
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Hello! I resolved the gff bulk loader issue. I patched the Adapter.pm file like Scott explained and used this script (packaged in Apollo 2.0.4) to upload the schema/ontologies: scripts/load_chado_schema.sh -u username -d apollo-db -h localhost -p 5432 -r -s scripts/chado-schema-with-ontologies.sql.gz Thanks Scott & Eric! On Wed, Oct 26, 2016 at 6:01 PM, Shane McCoy <sha...@gm...> wrote: > You were right - I accidentally removed the new Adapter.pm. Thanks! > Running the script is throwing another error though. It did show the > 'unable to find synonym type' error for all 200,000+ lines of this sample > gff. I uploaded the ontologies/schema from Eric here > <https://github.com/erasche/chado-schema-builder/releases>, 1.31-jenkins93 > / chado-1.31.sql.gz. > > unable to find synonym type in cvterm table at >> /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm line 3088, <GEN0> >> line 202429. >> unable to find synonym type in cvterm table at >> /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm line 3088, <GEN0> >> line 202430. >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: I couldn't find the 'Note' cvterm in the database; >> Did you load the feature property controlled vocabulary? >> STACK: Error::throw >> STACK: Bio::Root::Root::throw /home/bjreadin/src/bioperl- >> live/Bio/Root/Root.pm:444 >> STACK: Bio::GMOD::DB::Adapter::handle_note /usr/local/share/perl/5.22.1/ >> Bio/GMOD/DB/Adapter.pm:3901 >> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:974 >> ----------------------------------------------------------- >> Abnormal termination, trying to clean up... >> Attempting to clean up the loader temp table (so that --recreate_cache >> won't be needed)... >> Trying to remove the run lock (so that --remove_lock won't be needed)... >> Exiting... > > > I just ran this and wanted to share - I'll look into the other errors too. > Thanks! > > > On Wed, Oct 26, 2016 at 5:39 PM, Scott Cain <sc...@sc...> wrote: > >> (re cc-ing the schema mailing list) >> >> Hi Shane, >> >> I think you must not have put the new version of Adapter.pm in >> /usr/local/share/perl/5.22.1/Bio/GMOD/DB/ because line 498 of that >> module doesn't mention shift, it's: >> >> my $arg = shift; >> >> Can you double check that file? >> >> Scott >> >> >> >> On Wed, Oct 26, 2016 at 5:22 PM, Shane McCoy <sha...@gm...> >> wrote: >> > >> > Hi Scott! >> > Thanks for the information. >> > I did replace the Adapter.pm file and did a clean restart of chado and >> still got the error: >> >> >> >> $ gmod_bulk_load_gff3.pl --noexon --analysis --organism Stripedbass >> --gfffile SBDraft_Pt5.nodna.gff --dbname apollo-db >> >> Can't use 'defined(@array)' (Maybe you should just omit the >> defined()?) at /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm line >> 498. >> >> Compilation failed in require at /usr/local/bin/gmod_bulk_load_gff3.pl >> line 13. >> >> BEGIN failed--compilation aborted at /usr/local/bin/gmod_bulk_load_ >> gff3.pl line 13. >> > >> > >> > Should I setup an earlier version Perl maybe? I used v5.18.2 previously >> on another server and did not have this issue. >> > Thanks! >> > Shane M. >> > >> > On Wed, Oct 26, 2016 at 11:34 AM, Scott Cain <sc...@sc...> >> wrote: >> >> >> >> Hi Shane, >> >> >> >> The loader module, lib/Bio/GMOD/DB/Adaptor.pm, is quite old and uses >> an ugly idiom that I'd rather not talk about but it's use has be deprecated >> in modern Perl. I don't have a working instance of Chado I can test with >> handy (later in the week I could spin something up on AWS, but I don't have >> time now), but I did commit this to github if you want to try it out: >> >> >> >> https://raw.githubusercontent.com/GMOD/Chado/fix_shift_if_de >> fined/chado/lib/Bio/GMOD/DB/Adapter.pm >> >> >> >> Just download this and replace the one it's complaining about in >> /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm. >> >> >> >> Also, you won't be able to load the Relations Ontology via the make >> command. You'll need to download >> >> >> >> http://purl.obolibrary.org/obo/ro/subsets/ro-chado.obo >> >> >> >> and use the commands described in INSTALL.Chado. In brief: >> >> >> >> $ go2fmt.pl -p obo_text -w xml /path/to/obofile | \ >> >> go-apply-xslt oboxml_to_chadoxml - > obo_text.xml >> >> >> >> and >> >> >> >> $ stag-storenode.pl \ >> >> -d 'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT' >> \ >> >> --user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD obo_text.xml >> >> >> >> Depending on how you installed DBIx::DBStag, the ".pl" on >> stag-storenode.pl might have to be removed. >> >> >> >> Good luck! >> >> Scott >> >> >> >> >> >> On Wed, Oct 26, 2016 at 8:57 AM, Shane McCoy <sha...@gm...> >> wrote: >> >> > >> >> > >> >> > Hello, >> >> > Using Chado VERSION=1.31 >> >> > I am getting this error when using the gmod bulk load for Chado: >> >> > >> >> >> $ gmod_bulk_load_gff3.pl --noexon --analysis --organism >> "stripedbass" --gfffile SBDraft_Full.nodna.gff --dbname apollo-db >> >> >> Can't use 'defined(@array)' (Maybe you should just omit the >> defined()?) at /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm line >> 498. >> >> >> Compilation failed in require at /usr/local/bin/gmod_bulk_load_ >> gff3.pl line 13. >> >> >> BEGIN failed--compilation aborted at /usr/local/bin/gmod_bulk_load_ >> gff3.pl line 13. >> >> > >> >> > >> >> > I have bioperl 1.006925 installed. I did see that the make >> ontologies fails now, >> >> >> >> >> >> Which ontologies would you like to load (Comma delimited)? [0] >> 1,2,3,4 >> >> >> fetching files for Relationship Ontology >> >> >> +http://www.obofoundry.org/ro/ro.obo >> >> >> 404 Not Found (http://www.obofoundry.org/ro/ro.obo) >> >> >> fetching files for Sequence Ontology >> >> > >> >> > >> >> > I am using the https://cpt.tamu.edu/computer- >> resources/chado-prebuilt-schema/ recommended sql for this build. >> >> > >> >> > Any thoughts why this is failing? Thanks! >> >> > Shane M. >> >> > >> >> > >> >> > >> >> > >> >> > ------------------------------------------------------------ >> ------------------ >> >> > The Command Line: Reinvented for Modern Developers >> >> > Did the resurgence of CLI tooling catch you by surprise? >> >> > Reconnect with the command line and become more productive. >> >> > Learn the new .NET and ASP.NET CLI. Get your free copy! >> >> > http://sdm.link/telerik >> >> > _______________________________________________ >> >> > Gmod-schema mailing list >> >> > Gmo...@li... >> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema >> >> > >> >> >> >> >> >> >> >> -- >> >> ------------------------------------------------------------ >> ------------ >> >> Scott Cain, Ph. D. scott at >> scottcain dot net >> >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> >> Ontario Institute for Cancer Research >> > >> > >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> > > |