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From: Shane M. <sha...@gm...> - 2016-10-26 12:57:59
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Hello, Using Chado VERSION=1.31 I am getting this error when using the gmod bulk load for Chado: $ *gmod_bulk_load_gff3.pl <http://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 > <http://gmod_bulk_load_gff3.pl> line 13.BEGIN failed--compilation aborted > at /usr/local/bin/gmod_bulk_load_gff3.pl <http://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/ <https://cpt.tamu.edu/computer-resources/chado-prebuilt-schema/> recommended sql for this build. Any thoughts why this is failing? Thanks! Shane M. |
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From: Scott C. <sc...@sc...> - 2016-10-26 15:34:12
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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_defined/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 |
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From: Eric R. <es...@ta...> - 2016-10-26 16:34:40
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Shane, Some notes about the prebuilt-schemas that my organisation hosts: - Our latest releases are available here: https://github.com/erasche/chado-schema-builder/releases. Hosting on github should be much more reliable than the copies hosted on my organisation's server. - We've recently produced images for 1.31, for a long while they had been out of date. Now they're being (semi-regularly) built again with fresh data! - As mentioned by Scott, we've switched the RO <https://github.com/erasche/chado-schema-builder/blob/master/load.conf.tt2#L45> out for one that works. Scott: no time like the present to try out the chado docker images <https://hub.docker.com/r/erasche/chado/> ;) Cheers, Eric ons. 26. okt. 2016 kl. 15.35 skrev Scott Cain <sc...@sc...>: > 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_defined/chado/lib/Bio/GMOD/DB/Adapter.pm > <https://urldefense.proofpoint.com/v2/url?u=https-3A__raw.githubusercontent.com_GMOD_Chado_fix-5Fshift-5Fif-5Fdefined_chado_lib_Bio_GMOD_DB_Adapter.pm&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=oxMjvL9zq_3ASiqEL_47oV1-hAH3Ss_sO9cZ4OQmCfo&e=> > > 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 > <https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.obolibrary.org_obo_ro_subsets_ro-2Dchado.obo&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=TzkzSeAw9RlbSkMGGODRqZc8HXazHWoEDWoZQ1ngUQk&e=> > > and use the commands described in INSTALL.Chado. In brief: > > $ go2fmt.pl > <https://urldefense.proofpoint.com/v2/url?u=http-3A__go2fmt.pl&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=sdfjunH0ATTldVhxMBtSE8a1UBO55HrvQRNrWyZA1xg&e=> > -p obo_text -w xml /path/to/obofile | \ > go-apply-xslt oboxml_to_chadoxml - > obo_text.xml > > and > > $ stag-storenode.pl > <https://urldefense.proofpoint.com/v2/url?u=http-3A__stag-2Dstorenode.pl&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=-FVBNPnYiIQ29Ag3WAn-PAX26CkRsx07zEOPARZpWp8&e=> > \ > -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 > <https://urldefense.proofpoint.com/v2/url?u=http-3A__stag-2Dstorenode.pl&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=-FVBNPnYiIQ29Ag3WAn-PAX26CkRsx07zEOPARZpWp8&e=> > 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 > <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod-5Fbulk-5Fload-5Fgff3.pl&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=99cqirF-J4zQD0Lz3ByPjnpyvymIyfBMo4SrKTg3THk&e=> > --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 > <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod-5Fbulk-5Fload-5Fgff3.pl&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=99cqirF-J4zQD0Lz3ByPjnpyvymIyfBMo4SrKTg3THk&e=> > line 13. > >> BEGIN failed--compilation aborted at /usr/local/bin/ > gmod_bulk_load_gff3.pl > <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod-5Fbulk-5Fload-5Fgff3.pl&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=99cqirF-J4zQD0Lz3ByPjnpyvymIyfBMo4SrKTg3THk&e=> > 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 > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.obofoundry.org_ro_ro.obo&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=Eb2r0GJoa2JSwxPHl073N7jB8cutmXoEWS6STpqV3jw&e=> > >> 404 Not Found (http://www.obofoundry.org/ro/ro.obo > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.obofoundry.org_ro_ro.obo&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=Eb2r0GJoa2JSwxPHl073N7jB8cutmXoEWS6STpqV3jw&e=> > ) > >> 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 > <https://urldefense.proofpoint.com/v2/url?u=http-3A__ASP.NET&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=nKwFb83LeNaF3wApKFbnlxwN-UFyGstL2UtCUFnL-EI&e=> > CLI. Get your free copy! > > http://sdm.link/telerik > <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_telerik&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=NlGNlOR4YjtjjADCZ_Qh6rCVLfJrnHm6auWtH0w62PQ&e=> > > _______________________________________________ > > Gmod-schema mailing list > > Gmo...@li... > > https://lists.sourceforge.net/lists/listinfo/gmod-schema > <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_gmod-2Dschema&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=4oI_IKQKzs2lqp-Nv6o91SMm3HqytU4EpSio4QaSO18&e=> > > > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain > dot net > GMOD Coordinator (http://gmod.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=lNLOua1_XytvtZSfKsyGEBQrIZ3QpaUqUoAumzpbasw&e=>) > 216-392-3087 <(216)%20392-3087> > Ontario Institute for Cancer Research > > ------------------------------------------------------------------------------ > 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 > |
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From: Shane M. <sha...@gm...> - 2016-10-26 21:26:32
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Thanks Eric! I wasn't aware of this resource. I downloaded chado-1.31.sql.gz and used the Apollo script to upload to db. Easiest setup yet! thanks! > /Apollo$ *scripts/load_chado_schema.sh -u bjreadin -d apollo-db -h > localhost -p 5432 -r -s scripts/chado-1.31.sql.gz* > ERROR: database "apollo-db" already exists > Database 'apollo-db' already exists. Backing up data via pg_dump. > pg_dump -U bjreadin -d apollo-db -h localhost -p 5432 -f > apollo-db_database_dump_2016-10-26_16:11:20.sql -b > pg_dump was successful. > Dropping and creating database 'apollo-db'. > DROP DATABASE > CREATE DATABASE > Loading chado schema scripts/chado-1.31.sql.gz to database 'apollo-db'. > Chado schema loaded successfully to apollo-db. Check > load_chado_schema_2016-10-26_16:11:20.log for more information. On Wed, Oct 26, 2016 at 12:08 PM, Eric Rasche <es...@ta...> wrote: > Shane, > > Some notes about the prebuilt-schemas that my organisation hosts: > > - Our latest releases are available here: https://github.com/erasche/ > chado-schema-builder/releases. Hosting on github should be much more > reliable than the copies hosted on my organisation's server. > - We've recently produced images for 1.31, for a long while they had > been out of date. Now they're being (semi-regularly) built again with fresh > data! > - As mentioned by Scott, we've switched the RO > <https://github.com/erasche/chado-schema-builder/blob/master/load.conf.tt2#L45> > out for one that works. > > Scott: no time like the present to try out the chado docker images > <https://hub.docker.com/r/erasche/chado/> ;) > > Cheers, > > Eric > > > > > > ons. 26. okt. 2016 kl. 15.35 skrev Scott Cain <sc...@sc...>: > >> 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_ >> defined/chado/lib/Bio/GMOD/DB/Adapter.pm >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__raw.githubusercontent.com_GMOD_Chado_fix-5Fshift-5Fif-5Fdefined_chado_lib_Bio_GMOD_DB_Adapter.pm&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=oxMjvL9zq_3ASiqEL_47oV1-hAH3Ss_sO9cZ4OQmCfo&e=> >> >> 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 >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.obolibrary.org_obo_ro_subsets_ro-2Dchado.obo&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=TzkzSeAw9RlbSkMGGODRqZc8HXazHWoEDWoZQ1ngUQk&e=> >> >> and use the commands described in INSTALL.Chado. In brief: >> >> $ go2fmt.pl >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__go2fmt.pl&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=sdfjunH0ATTldVhxMBtSE8a1UBO55HrvQRNrWyZA1xg&e=> >> -p obo_text -w xml /path/to/obofile | \ >> go-apply-xslt oboxml_to_chadoxml - > obo_text.xml >> >> and >> >> $ stag-storenode.pl >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__stag-2Dstorenode.pl&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=-FVBNPnYiIQ29Ag3WAn-PAX26CkRsx07zEOPARZpWp8&e=> >> \ >> -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 >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__stag-2Dstorenode.pl&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=-FVBNPnYiIQ29Ag3WAn-PAX26CkRsx07zEOPARZpWp8&e=> >> 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 >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod-5Fbulk-5Fload-5Fgff3.pl&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=99cqirF-J4zQD0Lz3ByPjnpyvymIyfBMo4SrKTg3THk&e=> >> --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 >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod-5Fbulk-5Fload-5Fgff3.pl&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=99cqirF-J4zQD0Lz3ByPjnpyvymIyfBMo4SrKTg3THk&e=> >> line 13. >> >> BEGIN failed--compilation aborted at /usr/local/bin/gmod_bulk_load_ >> gff3.pl >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod-5Fbulk-5Fload-5Fgff3.pl&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=99cqirF-J4zQD0Lz3ByPjnpyvymIyfBMo4SrKTg3THk&e=> >> 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 >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.obofoundry.org_ro_ro.obo&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=Eb2r0GJoa2JSwxPHl073N7jB8cutmXoEWS6STpqV3jw&e=> >> >> 404 Not Found (http://www.obofoundry.org/ro/ro.obo >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.obofoundry.org_ro_ro.obo&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=Eb2r0GJoa2JSwxPHl073N7jB8cutmXoEWS6STpqV3jw&e=> >> ) >> >> 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 >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__ASP.NET&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=nKwFb83LeNaF3wApKFbnlxwN-UFyGstL2UtCUFnL-EI&e=> >> CLI. Get your free copy! >> > http://sdm.link/telerik >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_telerik&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=NlGNlOR4YjtjjADCZ_Qh6rCVLfJrnHm6auWtH0w62PQ&e=> >> > _______________________________________________ >> > Gmod-schema mailing list >> > Gmo...@li... >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_gmod-2Dschema&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=4oI_IKQKzs2lqp-Nv6o91SMm3HqytU4EpSio4QaSO18&e=> >> > >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/ >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=lNLOua1_XytvtZSfKsyGEBQrIZ3QpaUqUoAumzpbasw&e=>) >> 216-392-3087 <(216)%20392-3087> >> Ontario Institute for Cancer Research >> ------------------------------------------------------------ >> ------------------ >> 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 >> > |
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From: Scott C. <sc...@sc...> - 2016-10-26 21:39:44
|
(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_defined/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 |
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From: Shane M. <sha...@gm...> - 2016-10-26 22:01:35
|
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_ > defined/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 > |
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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 >> > > |
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From: Nathan D. <nat...@lb...> - 2016-10-28 18:44:40
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FYI, I think that script / schema comes from the original schema data that Eric provided as well and was integrated by Deepak. Nathan > On Oct 28, 2016, at 2:15 PM, Shane McCoy <sha...@gm...> wrote: > > 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... <mailto: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 <http://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... <mailto: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... <mailto: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 <http://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 <http://gmod_bulk_load_gff3.pl/> line 13. > >> BEGIN failed--compilation aborted at /usr/local/bin/gmod_bulk_load_gff3.pl <http://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... <mailto: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_defined/chado/lib/Bio/GMOD/DB/Adapter.pm <https://raw.githubusercontent.com/GMOD/Chado/fix_shift_if_defined/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 <http://purl.obolibrary.org/obo/ro/subsets/ro-chado.obo> > >> > >> and use the commands described in INSTALL.Chado. In brief: > >> > >> $ go2fmt.pl <http://go2fmt.pl/> -p obo_text -w xml /path/to/obofile | \ > >> go-apply-xslt oboxml_to_chadoxml - > obo_text.xml > >> > >> and > >> > >> $ stag-storenode.pl <http://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 <http://stag-storenode.pl/> might have to be removed. > >> > >> Good luck! > >> Scott > >> > >> > >> On Wed, Oct 26, 2016 at 8:57 AM, Shane McCoy <sha...@gm... <mailto: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 <http://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 <http://gmod_bulk_load_gff3.pl/> line 13. > >> >> BEGIN failed--compilation aborted at /usr/local/bin/gmod_bulk_load_gff3.pl <http://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 <http://www.obofoundry.org/ro/ro.obo> > >> >> 404 Not Found (http://www.obofoundry.org/ro/ro.obo <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/ <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 <http://asp.net/> CLI. Get your free copy! > >> > http://sdm.link/telerik <http://sdm.link/telerik> > >> > _______________________________________________ > >> > Gmod-schema mailing list > >> > Gmo...@li... <mailto:Gmo...@li...> > >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema <https://lists.sourceforge.net/lists/listinfo/gmod-schema> > >> > > >> > >> > >> > >> -- > >> ------------------------------------------------------------------------ > >> Scott Cain, Ph. D. scott at scottcain dot net > >> GMOD Coordinator (http://gmod.org/ <http://gmod.org/>) 216-392-3087 <tel:216-392-3087> > >> Ontario Institute for Cancer Research > > > > > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/ <http://gmod.org/>) 216-392-3087 <tel:216-392-3087> > Ontario Institute for Cancer Research > > > ------------------------------------------------------------------------------ > 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 |
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