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From: Naama M. <naa...@gm...> - 2017-04-13 02:01:18
|
Config.pm is in the GMOD git repo (and not in Bio::GMOD that you get from CPAN) https://github.com/GMOD/Chado/tree/master/chado/lib/Bio/GMOD you should have the chado scripts in a chado/bin directory, and the Bio::GMOD modules in chado/lib/GMOD... then add the path for chado/lib to your $PERL5LIB -Naama On Wed, Apr 12, 2017 at 2:23 PM Mara Kim <mar...@gm...> wrote: > Ok, so I checked the location of my Bio::GMOD and I noticed that there is > no subfolder `Config` which the script seems to be looking for: > > $ ls /home/kimmm/perl5/lib/perl5/Bio/GMOD > > *Adaptor* Adaptor.pm *Admin* *Query* Query.pm StandardURLs.pm *Util* > > > Am I missing something? I have version 0.028 installed using cpanm. > > On Wed, Apr 12, 2017 at 12:46 PM Naama Menda <naa...@gm...> > wrote: > > hi Mara, > > where did you install Bio::GMOD ? > If that directory is not in @INC then you need to add it to your $PERL5LIB > > -Naama > > > > On Wed, Apr 12, 2017 at 1:30 PM Mara Kim <mar...@gm...> wrote: > > Hi Naama, > > I am trying to use the gmod_load_cvterms.pl script, but I get the > following error: > > $ perl gmod_load_cvterms.pl -H localhost -D genestation > /raid/chado/ontology/ff-phase2-140729.obo > > Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: > /home/kimmm/perl5/lib/perl5/5.10.1/x86_64-linux-thread-multi > /home/kimmm/perl5/lib/perl5/5.10.1 > /home/kimmm/perl5/lib/perl5/x86_64-linux-thread-multi > /home/kimmm/perl5/lib/perl5/5.10.0 /home/kimmm/perl5/lib/perl5 > /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl > /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at > gmod_load_cvterms.pl line 155. > > BEGIN failed--compilation aborted at gmod_load_cvterms.pl line 155. > > > I have Bio::GMOD installed. Are there other dependencies that I am > missing? > > On Mon, Mar 27, 2017 at 12:21 PM Naama Menda <naa...@gm...> > wrote: > > hi Mara, > > you could try to use the gmod_load_cvterms.pl > <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> > script > It should handle updating an existing ontology > > > -Naama > > > -- > > On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: > > I temporarily renamed my `chado` schema to `public`. Now I am getting a > different error: > > $ stag-storenode.pl -d > 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado > ff.xml > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > > I am guessing this is because I am loading the Fantom5 ontology, which > references terms from the UBERON ontology. I have already loaded the > UBERON ontology and am using it extensively. Is stag-storenode unable to > resolve this by not recreating duplicated terms? > > On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: > > Hi, > > When we installed chado we found a number of places > where "public" was hardcoded. > > The places I identify now from a quick review of our notes are: > > initialize.sql > /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm > ---------------------<snip>-------------------- > --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 > +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 > @@ -34,7 +34,8 @@ > > =cut > > -sub default_db_schema { 'public'; } > +#sub default_db_schema { 'public'; } > +sub default_db_schema { 'chado'; } > > sub columns { > my($proto, $dbh, $table) = @_; > ---------------------<snip>-------------------- > > I recall getting chado to install somewhere other than the public > schema to be tedious. > > Regards, > > Karl <ko...@me...> > Free Software: "You don't pay back, you pay forward." > -- Robert A. Heinlein > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > |
From: Mara K. <mar...@gm...> - 2017-04-12 18:23:27
|
Ok, so I checked the location of my Bio::GMOD and I noticed that there is no subfolder `Config` which the script seems to be looking for: $ ls /home/kimmm/perl5/lib/perl5/Bio/GMOD *Adaptor* Adaptor.pm *Admin* *Query* Query.pm StandardURLs.pm *Util* Am I missing something? I have version 0.028 installed using cpanm. On Wed, Apr 12, 2017 at 12:46 PM Naama Menda <naa...@gm...> wrote: > hi Mara, > > where did you install Bio::GMOD ? > If that directory is not in @INC then you need to add it to your $PERL5LIB > > -Naama > > > > On Wed, Apr 12, 2017 at 1:30 PM Mara Kim <mar...@gm...> wrote: > > Hi Naama, > > I am trying to use the gmod_load_cvterms.pl script, but I get the > following error: > > $ perl gmod_load_cvterms.pl -H localhost -D genestation > /raid/chado/ontology/ff-phase2-140729.obo > > Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: > /home/kimmm/perl5/lib/perl5/5.10.1/x86_64-linux-thread-multi > /home/kimmm/perl5/lib/perl5/5.10.1 > /home/kimmm/perl5/lib/perl5/x86_64-linux-thread-multi > /home/kimmm/perl5/lib/perl5/5.10.0 /home/kimmm/perl5/lib/perl5 > /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl > /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at > gmod_load_cvterms.pl line 155. > > BEGIN failed--compilation aborted at gmod_load_cvterms.pl line 155. > > > I have Bio::GMOD installed. Are there other dependencies that I am > missing? > > On Mon, Mar 27, 2017 at 12:21 PM Naama Menda <naa...@gm...> > wrote: > > hi Mara, > > you could try to use the gmod_load_cvterms.pl > <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> > script > It should handle updating an existing ontology > > > -Naama > > > -- > > On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: > > I temporarily renamed my `chado` schema to `public`. Now I am getting a > different error: > > $ stag-storenode.pl -d > 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado > ff.xml > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > > I am guessing this is because I am loading the Fantom5 ontology, which > references terms from the UBERON ontology. I have already loaded the > UBERON ontology and am using it extensively. Is stag-storenode unable to > resolve this by not recreating duplicated terms? > > On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: > > Hi, > > When we installed chado we found a number of places > where "public" was hardcoded. > > The places I identify now from a quick review of our notes are: > > initialize.sql > /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm > ---------------------<snip>-------------------- > --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 > +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 > @@ -34,7 +34,8 @@ > > =cut > > -sub default_db_schema { 'public'; } > +#sub default_db_schema { 'public'; } > +sub default_db_schema { 'chado'; } > > sub columns { > my($proto, $dbh, $table) = @_; > ---------------------<snip>-------------------- > > I recall getting chado to install somewhere other than the public > schema to be tedious. > > Regards, > > Karl <ko...@me...> > Free Software: "You don't pay back, you pay forward." > -- Robert A. Heinlein > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > |
From: Naama M. <naa...@gm...> - 2017-04-12 17:46:20
|
hi Mara, where did you install Bio::GMOD ? If that directory is not in @INC then you need to add it to your $PERL5LIB -Naama On Wed, Apr 12, 2017 at 1:30 PM Mara Kim <mar...@gm...> wrote: > Hi Naama, > > I am trying to use the gmod_load_cvterms.pl script, but I get the > following error: > > $ perl gmod_load_cvterms.pl -H localhost -D genestation > /raid/chado/ontology/ff-phase2-140729.obo > > Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: > /home/kimmm/perl5/lib/perl5/5.10.1/x86_64-linux-thread-multi > /home/kimmm/perl5/lib/perl5/5.10.1 > /home/kimmm/perl5/lib/perl5/x86_64-linux-thread-multi > /home/kimmm/perl5/lib/perl5/5.10.0 /home/kimmm/perl5/lib/perl5 > /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl > /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at > gmod_load_cvterms.pl line 155. > > BEGIN failed--compilation aborted at gmod_load_cvterms.pl line 155. > > > I have Bio::GMOD installed. Are there other dependencies that I am > missing? > > On Mon, Mar 27, 2017 at 12:21 PM Naama Menda <naa...@gm...> > wrote: > > hi Mara, > > you could try to use the gmod_load_cvterms.pl > <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> > script > It should handle updating an existing ontology > > > -Naama > > > -- > > On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: > > I temporarily renamed my `chado` schema to `public`. Now I am getting a > different error: > > $ stag-storenode.pl -d > 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado > ff.xml > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > > I am guessing this is because I am loading the Fantom5 ontology, which > references terms from the UBERON ontology. I have already loaded the > UBERON ontology and am using it extensively. Is stag-storenode unable to > resolve this by not recreating duplicated terms? > > On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: > > Hi, > > When we installed chado we found a number of places > where "public" was hardcoded. > > The places I identify now from a quick review of our notes are: > > initialize.sql > /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm > ---------------------<snip>-------------------- > --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 > +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 > @@ -34,7 +34,8 @@ > > =cut > > -sub default_db_schema { 'public'; } > +#sub default_db_schema { 'public'; } > +sub default_db_schema { 'chado'; } > > sub columns { > my($proto, $dbh, $table) = @_; > ---------------------<snip>-------------------- > > I recall getting chado to install somewhere other than the public > schema to be tedious. > > Regards, > > Karl <ko...@me...> > Free Software: "You don't pay back, you pay forward." > -- Robert A. Heinlein > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > |
From: Mara K. <mar...@gm...> - 2017-04-12 17:30:56
|
Hi Naama, I am trying to use the gmod_load_cvterms.pl script, but I get the following error: $ perl gmod_load_cvterms.pl -H localhost -D genestation /raid/chado/ontology/ff-phase2-140729.obo Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: /home/kimmm/perl5/lib/perl5/5.10.1/x86_64-linux-thread-multi /home/kimmm/perl5/lib/perl5/5.10.1 /home/kimmm/perl5/lib/perl5/x86_64-linux-thread-multi /home/kimmm/perl5/lib/perl5/5.10.0 /home/kimmm/perl5/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at gmod_load_cvterms.pl line 155. BEGIN failed--compilation aborted at gmod_load_cvterms.pl line 155. I have Bio::GMOD installed. Are there other dependencies that I am missing? On Mon, Mar 27, 2017 at 12:21 PM Naama Menda <naa...@gm...> wrote: > hi Mara, > > you could try to use the gmod_load_cvterms.pl > <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> > script > It should handle updating an existing ontology > > > -Naama > > > -- > > On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: > > I temporarily renamed my `chado` schema to `public`. Now I am getting a > different error: > > $ stag-storenode.pl -d > 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado > ff.xml > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > > I am guessing this is because I am loading the Fantom5 ontology, which > references terms from the UBERON ontology. I have already loaded the > UBERON ontology and am using it extensively. Is stag-storenode unable to > resolve this by not recreating duplicated terms? > > On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: > > Hi, > > When we installed chado we found a number of places > where "public" was hardcoded. > > The places I identify now from a quick review of our notes are: > > initialize.sql > /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm > ---------------------<snip>-------------------- > --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 > +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 > @@ -34,7 +34,8 @@ > > =cut > > -sub default_db_schema { 'public'; } > +#sub default_db_schema { 'public'; } > +sub default_db_schema { 'chado'; } > > sub columns { > my($proto, $dbh, $table) = @_; > ---------------------<snip>-------------------- > > I recall getting chado to install somewhere other than the public > schema to be tedious. > > Regards, > > Karl <ko...@me...> > Free Software: "You don't pay back, you pay forward." > -- Robert A. Heinlein > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > |
From: Naama M. <naa...@gm...> - 2017-03-27 17:21:40
|
hi Mara, you could try to use the gmod_load_cvterms.pl <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> script It should handle updating an existing ontology -Naama -- On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: > I temporarily renamed my `chado` schema to `public`. Now I am getting a > different error: > > $ stag-storenode.pl -d > 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado > ff.xml > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > > I am guessing this is because I am loading the Fantom5 ontology, which > references terms from the UBERON ontology. I have already loaded the > UBERON ontology and am using it extensively. Is stag-storenode unable to > resolve this by not recreating duplicated terms? > > On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: > > Hi, > > When we installed chado we found a number of places > where "public" was hardcoded. > > The places I identify now from a quick review of our notes are: > > initialize.sql > /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm > ---------------------<snip>-------------------- > --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 > +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 > @@ -34,7 +34,8 @@ > > =cut > > -sub default_db_schema { 'public'; } > +#sub default_db_schema { 'public'; } > +sub default_db_schema { 'chado'; } > > sub columns { > my($proto, $dbh, $table) = @_; > ---------------------<snip>-------------------- > > I recall getting chado to install somewhere other than the public > schema to be tedious. > > Regards, > > Karl <ko...@me...> > Free Software: "You don't pay back, you pay forward." > -- Robert A. Heinlein > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > |
From: Mara K. <mar...@gm...> - 2017-03-27 17:16:41
|
I temporarily renamed my `chado` schema to `public`. Now I am getting a different error: $ stag-storenode.pl -d 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado ff.xml DBD::Pg::st execute failed: ERROR: duplicate key value violates unique constraint "cvterm_c1" DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. DBD::Pg::st execute failed: ERROR: duplicate key value violates unique constraint "cvterm_c1" DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. I am guessing this is because I am loading the Fantom5 ontology, which references terms from the UBERON ontology. I have already loaded the UBERON ontology and am using it extensively. Is stag-storenode unable to resolve this by not recreating duplicated terms? On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: > Hi, > > When we installed chado we found a number of places > where "public" was hardcoded. > > The places I identify now from a quick review of our notes are: > > initialize.sql > /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm > ---------------------<snip>-------------------- > --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 > +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 > @@ -34,7 +34,8 @@ > > =cut > > -sub default_db_schema { 'public'; } > +#sub default_db_schema { 'public'; } > +sub default_db_schema { 'chado'; } > > sub columns { > my($proto, $dbh, $table) = @_; > ---------------------<snip>-------------------- > > I recall getting chado to install somewhere other than the public > schema to be tedious. > > Regards, > > Karl <ko...@me...> > Free Software: "You don't pay back, you pay forward." > -- Robert A. Heinlein > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > |
From: Karl O. P. <ko...@me...> - 2017-03-24 15:53:01
|
Hi, When we installed chado we found a number of places where "public" was hardcoded. The places I identify now from a quick review of our notes are: initialize.sql /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm ---------------------<snip>-------------------- --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 @@ -34,7 +34,8 @@ =cut -sub default_db_schema { 'public'; } +#sub default_db_schema { 'public'; } +sub default_db_schema { 'chado'; } sub columns { my($proto, $dbh, $table) = @_; ---------------------<snip>-------------------- I recall getting chado to install somewhere other than the public schema to be tedious. Regards, Karl <ko...@me...> Free Software: "You don't pay back, you pay forward." -- Robert A. Heinlein |
From: Mara K. <mar...@va...> - 2017-03-24 00:11:06
|
`search_path` seems to be set correctly: $ psql -U rokaschado genestation psql (9.6.2) Type "help" for help. genestation=# SHOW search_path; search_path --------------- chado, public (1 row) genestation=# SELECT * FROM cv LIMIT 1; cv_id | name | definition -------+--------------+------------ 1 | relationship | (1 row) On Thu, Mar 23, 2017 at 4:26 PM Scott Cain <sc...@sc...> wrote: > Hi Mara, > > Is your chado database in a schema other than public? If so, you'll have > to modify your search path for the user that is running stag-storenode. > See http://tripal.info/documentation/search_path for more info. > > Scott > > > On Thu, Mar 23, 2017 at 2:43 PM, Mara Kim <mar...@va...> wrote: > > Hello, > > I am trying to use stag-storenode.pl to load the Fantom5 FF ontology. > > I took the following steps: > > wget > http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Ontology/ff-phase2-140729.obo.txt #Download > ontology > > ex ff-phase2-140729.obo.txt -c '%s/{.*} ' -c 'wq' #Remove comments > > go2chadoxml ff-phase2-140729.obo.txt > ff.xml #Convert to XML > > stag-storenode.pl -d 'dbi:Pg:dbname=genestation;host=localhost;port=5432' > --user rokaschado ff.xml #Load into DB > > > > When invoking stag-storenode.pl I get the following error: > > $ stag-storenode.pl -d > 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado > ff.xml > > Can't get table cv from db. > > Maybe DBIx::DBSchema does not work with your database? at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 427 > > DBIx::DBStag::get_pk_col('DBIx::DBStag=HASH(0x1950fb8)', 'cv') > called at /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 1265 > > DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x1950fb8)', > 'Data::Stag::StagImpl=ARRAY(0x2749fe8)') called at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 1180 > > DBIx::DBStag::storenode('DBIx::DBStag=HASH(0x1950fb8)', > 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at /home/kimmm/perl5/bin/ > stag-storenode.pl line 85 > > eval {...} called at /home/kimmm/perl5/bin/stag-storenode.pl line > 84 > > main::store('Data::Stag::BaseHandler=HASH(0x2542658)', > 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at /home/kimmm/perl5/bin/ > stag-storenode.pl line 134 > > main::__ANON__('Data::Stag::BaseHandler=HASH(0x2542658)', > 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at > /home/kimmm/perl5/lib/perl5/Data/Stag/BaseHandler.pm line 594 > > Data::Stag::BaseHandler::end_event('Data::Stag::BaseHandler=HASH(0x2542658)', > 'cv') called at /home/kimmm/perl5/lib/perl5/Data/Stag/BaseHandler.pm line > 742 > > Data::Stag::BaseHandler::end_element('Data::Stag::BaseHandler=HASH(0x2542658)', > 'HASH(0x1a02da0)') called at > /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm line 239 > > XML::Parser::PerlSAX::_handle_end('XML::Parser::PerlSAX=HASH(0x26543e8)', > 'XML::Parser::Expat=HASH(0x25898a8)', 'cv') called at > /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm line 79 > > XML::Parser::PerlSAX::__ANON__('XML::Parser::Expat=HASH(0x25898a8)', > 'cv') called at /usr/lib64/perl5/XML/Parser/Expat.pm line 469 > > XML::Parser::Expat::parse('XML::Parser::Expat=HASH(0x25898a8)', > 'FileHandle=GLOB(0x2688330)') called at /usr/lib64/perl5/XML/Parser.pm line > 187 > > eval {...} called at /usr/lib64/perl5/XML/Parser.pm line 186 > > XML::Parser::parse('XML::Parser=HASH(0x24a4200)', > 'FileHandle=GLOB(0x2688330)') called at > /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm line 146 > > XML::Parser::PerlSAX::parse('XML::Parser::PerlSAX=HASH(0x26543e8)', > 'Handler', 'Data::Stag::BaseHandler=HASH(0x2542658)', 'Source', > 'HASH(0x26547f0)') called at > /home/kimmm/perl5/lib/perl5/Data/Stag/XMLParser.pm line 69 > > Data::Stag::XMLParser::parse_fh('Data::Stag::XMLParser=HASH(0x2542400)', > 'FileHandle=GLOB(0x2688330)') called at > /home/kimmm/perl5/lib/perl5/Data/Stag/BaseGenerator.pm line 476 > > Data::Stag::BaseGenerator::parse('Data::Stag::XMLParser=HASH(0x2542400)', > '-file', 'ff.xml', '-str', undef, '-fh', undef) called at > /home/kimmm/perl5/lib/perl5/Data/Stag/XMLParser.pm line 58 > > Data::Stag::XMLParser::parse('Data::Stag::XMLParser=HASH(0x2542400)', > '-file', 'ff.xml', '-str', undef, '-fh', undef) called at > /home/kimmm/perl5/lib/perl5/Data/Stag/StagImpl.pm line 275 > > Data::Stag::StagImpl::parse('Data::Stag', '-format', undef, > '-file', 'ff.xml', '-handler', 'Data::Stag::BaseHandler=HASH(0x2542658)') > called at /home/kimmm/perl5/lib/perl5/Data/Stag.pm line 181 > > Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, '-file', > 'ff.xml', '-handler', 'Data::Stag::BaseHandler=HASH(0x2542658)') called at > /home/kimmm/perl5/bin/stag-storenode.pl line 140 > > > Any ideas what might be the problem? > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > 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 > <(216)%20392-3087> > Ontario Institute for Cancer Research > |
From: Chris M. <cjm...@lb...> - 2017-03-23 23:53:16
|
I don't know what OM/ORM is favored for Chado these days. Where would the ticket go? With the OBO JSON format it should be easy to write a translation to the OM https://douroucouli.wordpress.com/2016/10/04/a-developer-friendly-json-exchange-format-for-ontologies/ https://github.com/geneontology/obographs On 23 Mar 2017, at 16:41, Scott Cain wrote: > Probably. I'd love to if I had a drop in replacement :-) > > On Thu, Mar 23, 2017 at 7:23 PM, Chris Mungall <cjm...@lb...> > wrote: > >> Is there a ticket already open somewhere about replacing >> stag-storenode? >> >> On 23 Mar 2017, at 16:17, Scott Cain wrote: >> >> It seems like DBIx::DBSchema is failing from the first error message, >> and >> if that's failing, nothing else is going to work. It's trying to >> call the >> DBSchema table method. I just looked at the test suite for DBSchema >> and it >> is surprisingly useless. It might be worthwhile to create a simple >> test >> script that talks to your Chado database via DBSchema and calls the >> table >> method for the cv table to see if it works. >> >> One thing I wonder about is the version of Postgres: 9.6.2 is newer >> than >> any I've seen used, but I would hope that it would still work. >> >> >> On Thu, Mar 23, 2017 at 5:36 PM, Mara Kim <mar...@va...> >> wrote: >> >>> `search_path` seems to be set correctly: >>> >>> $ psql -U rokaschado genestation >>> >>> psql (9.6.2) >>> >>> Type "help" for help. >>> >>> >>> genestation=# SHOW search_path; >>> >>> search_path >>> >>> --------------- >>> >>> chado, public >>> >>> (1 row) >>> >>> >>> genestation=# SELECT * FROM cv LIMIT 1; >>> >>> cv_id | name | definition >>> >>> -------+--------------+------------ >>> >>> 1 | relationship | >>> >>> (1 row) >>> >>> On Thu, Mar 23, 2017 at 4:26 PM Scott Cain <sc...@sc...> >>> wrote: >>> >>>> Hi Mara, >>>> >>>> Is your chado database in a schema other than public? If so, >>>> you'll >>>> have to modify your search path for the user that is running >>>> stag-storenode. See http://tripal.info/documentation/search_path >>>> for >>>> more info. >>>> >>>> Scott >>>> >>>> >>>> On Thu, Mar 23, 2017 at 2:43 PM, Mara Kim <mar...@va...> >>>> wrote: >>>> >>>> Hello, >>>> >>>> I am trying to use stag-storenode.pl to load the Fantom5 FF >>>> ontology. >>>> >>>> I took the following steps: >>>> >>>> wget http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Ontology >>>> /ff-phase2-140729.obo.txt #Download ontology >>>> >>>> ex ff-phase2-140729.obo.txt -c '%s/{.*} ' -c 'wq' #Remove comments >>>> >>>> go2chadoxml ff-phase2-140729.obo.txt > ff.xml #Convert to XML >>>> >>>> stag-storenode.pl -d >>>> 'dbi:Pg:dbname=genestation;host=localhost;port=5432' >>>> --user rokaschado ff.xml #Load into DB >>>> >>>> >>>> >>>> When invoking stag-storenode.pl I get the following error: >>>> >>>> $ stag-storenode.pl -d >>>> 'dbi:Pg:dbname=genestation;host=localhost;port=5432' >>>> --user rokaschado ff.xml >>>> >>>> Can't get table cv from db. >>>> >>>> Maybe DBIx::DBSchema does not work with your database? at >>>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 427 >>>> >>>> DBIx::DBStag::get_pk_col('DBIx::DBStag=HASH(0x1950fb8)', >>>> 'cv') >>>> called at /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 1265 >>>> >>>> DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x1950fb8)', >>>> 'Data::Stag::StagImpl=ARRAY(0x2749fe8)') called at >>>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 1180 >>>> >>>> DBIx::DBStag::storenode('DBIx::DBStag=HASH(0x1950fb8)', >>>> 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at >>>> /home/kimmm/perl5/bin/stag-storenode.pl line 85 >>>> >>>> eval {...} called at >>>> /home/kimmm/perl5/bin/stag-storenode.pl >>>> line 84 >>>> >>>> main::store('Data::Stag::BaseHandler=HASH(0x2542658)', >>>> 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at >>>> /home/kimmm/perl5/bin/stag-storenode.pl line 134 >>>> >>>> main::__ANON__('Data::Stag::BaseHandler=HASH(0x2542658)', >>>> 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at >>>> /home/kimmm/perl5/lib/perl5/Data/Stag/BaseHandler.pm line 594 >>>> >>>> Data::Stag::BaseHandler::end_event('Data::Stag::BaseHandler=HASH(0x2542658)', >>>> 'cv') called at >>>> /home/kimmm/perl5/lib/perl5/Data/Stag/BaseHandler.pm >>>> line 742 >>>> >>>> Data::Stag::BaseHandler::end_element('Data::Stag::BaseHandler=HASH(0x2542658)', >>>> 'HASH(0x1a02da0)') called at >>>> /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm >>>> line 239 >>>> >>>> XML::Parser::PerlSAX::_handle_end('XML::Parser::PerlSAX=HASH(0x26543e8)', >>>> 'XML::Parser::Expat=HASH(0x25898a8)', 'cv') called at >>>> /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm line 79 >>>> >>>> XML::Parser::PerlSAX::__ANON__('XML::Parser::Expat=HASH(0x25898a8)', >>>> 'cv') called at /usr/lib64/perl5/XML/Parser/Expat.pm line 469 >>>> >>>> XML::Parser::Expat::parse('XML::Parser::Expat=HASH(0x25898a8)', >>>> 'FileHandle=GLOB(0x2688330)') called at >>>> /usr/lib64/perl5/XML/Parser.pm line >>>> 187 >>>> >>>> eval {...} called at /usr/lib64/perl5/XML/Parser.pm line >>>> 186 >>>> >>>> XML::Parser::parse('XML::Parser=HASH(0x24a4200)', >>>> 'FileHandle=GLOB(0x2688330)') called at >>>> /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm >>>> line 146 >>>> >>>> XML::Parser::PerlSAX::parse('XML::Parser::PerlSAX=HASH(0x26543e8)', >>>> 'Handler', 'Data::Stag::BaseHandler=HASH(0x2542658)', 'Source', >>>> 'HASH(0x26547f0)') called at >>>> /home/kimmm/perl5/lib/perl5/Data/Stag/XMLParser.pm >>>> line 69 >>>> >>>> Data::Stag::XMLParser::parse_fh('Data::Stag::XMLParser=HASH(0x2542400)', >>>> 'FileHandle=GLOB(0x2688330)') called at >>>> /home/kimmm/perl5/lib/perl5/Data/Stag/BaseGenerator.pm >>>> line 476 >>>> >>>> Data::Stag::BaseGenerator::parse('Data::Stag::XMLParser=HASH(0x2542400)', >>>> '-file', 'ff.xml', '-str', undef, '-fh', undef) called at >>>> /home/kimmm/perl5/lib/perl5/Data/Stag/XMLParser.pm line 58 >>>> >>>> Data::Stag::XMLParser::parse('Data::Stag::XMLParser=HASH(0x2542400)', >>>> '-file', 'ff.xml', '-str', undef, '-fh', undef) called at >>>> /home/kimmm/perl5/lib/perl5/Data/Stag/StagImpl.pm line 275 >>>> >>>> Data::Stag::StagImpl::parse('Data::Stag', '-format', undef, >>>> '-file', 'ff.xml', '-handler', >>>> 'Data::Stag::BaseHandler=HASH(0x2542658)') >>>> called at /home/kimmm/perl5/lib/perl5/Data/Stag.pm line 181 >>>> >>>> Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, >>>> '-file', >>>> 'ff.xml', '-handler', 'Data::Stag::BaseHandler=HASH(0x2542658)') >>>> called >>>> at /home/kimmm/perl5/bin/stag-storenode.pl line 140 >>>> >>>> >>>> Any ideas what might be the problem? >>>> >>>> ------------------------------------------------------------ >>>> ------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>> _______________________________________________ >>>> 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 >>>> <(216)%20392-3087> >>>> Ontario Institute for Cancer Research >>>> >>> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at >> scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> <(216)%20392-3087> >> Ontario Institute for Cancer Research >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______ >> _________________________________________ >> 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 |
From: Mara K. <mar...@gm...> - 2017-03-23 23:45:30
|
I am unfamiliar with DBSchema. How would I go about testing that? On Thu, Mar 23, 2017 at 7:41 PM Scott Cain <sc...@sc...> wrote: > Probably. I'd love to if I had a drop in replacement :-) > > On Thu, Mar 23, 2017 at 7:23 PM, Chris Mungall <cjm...@lb...> wrote: > > Is there a ticket already open somewhere about replacing stag-storenode? > > On 23 Mar 2017, at 16:17, Scott Cain wrote: > > It seems like DBIx::DBSchema is failing from the first error message, and > if that's failing, nothing else is going to work. It's trying to call the > DBSchema table method. I just looked at the test suite for DBSchema and it > is surprisingly useless. It might be worthwhile to create a simple test > script that talks to your Chado database via DBSchema and calls the table > method for the cv table to see if it works. > > One thing I wonder about is the version of Postgres: 9.6.2 is newer than > any I've seen used, but I would hope that it would still work. > > > On Thu, Mar 23, 2017 at 5:36 PM, Mara Kim <mar...@va...> wrote: > > `search_path` seems to be set correctly: > > $ psql -U rokaschado genestation > > psql (9.6.2) > > Type "help" for help. > > > genestation=# SHOW search_path; > > search_path > > --------------- > > chado, public > > (1 row) > > > genestation=# SELECT * FROM cv LIMIT 1; > > cv_id | name | definition > > -------+--------------+------------ > > 1 | relationship | > > (1 row) > > On Thu, Mar 23, 2017 at 4:26 PM Scott Cain <sc...@sc...> wrote: > > Hi Mara, > > Is your chado database in a schema other than public? If so, you'll have > to modify your search path for the user that is running stag-storenode. > See http://tripal.info/documentation/search_path for more info. > > Scott > > > On Thu, Mar 23, 2017 at 2:43 PM, Mara Kim <mar...@va...> wrote: > > Hello, > > I am trying to use stag-storenode.pl to load the Fantom5 FF ontology. > > I took the following steps: > > wget > http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Ontology/ff-phase2-140729.obo.txt #Download > ontology > > ex ff-phase2-140729.obo.txt -c '%s/{.*} ' -c 'wq' #Remove comments > > go2chadoxml ff-phase2-140729.obo.txt > ff.xml #Convert to XML > > stag-storenode.pl -d 'dbi:Pg:dbname=genestation;host=localhost;port=5432' > --user rokaschado ff.xml #Load into DB > > > > When invoking stag-storenode.pl I get the following error: > > $ stag-storenode.pl -d > 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado > ff.xml > > Can't get table cv from db. > > Maybe DBIx::DBSchema does not work with your database? at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 427 > > DBIx::DBStag::get_pk_col('DBIx::DBStag=HASH(0x1950fb8)', 'cv') > called at /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 1265 > > DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x1950fb8)', > 'Data::Stag::StagImpl=ARRAY(0x2749fe8)') called at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 1180 > > DBIx::DBStag::storenode('DBIx::DBStag=HASH(0x1950fb8)', > 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at /home/kimmm/perl5/bin/ > stag-storenode.pl line 85 > > eval {...} called at /home/kimmm/perl5/bin/stag-storenode.pl line > 84 > > main::store('Data::Stag::BaseHandler=HASH(0x2542658)', > 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at /home/kimmm/perl5/bin/ > stag-storenode.pl line 134 > > main::__ANON__('Data::Stag::BaseHandler=HASH(0x2542658)', > 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at > /home/kimmm/perl5/lib/perl5/Data/Stag/BaseHandler.pm line 594 > > Data::Stag::BaseHandler::end_event('Data::Stag::BaseHandler=HASH(0x2542658)', > 'cv') called at /home/kimmm/perl5/lib/perl5/Data/Stag/BaseHandler.pm line > 742 > > Data::Stag::BaseHandler::end_element('Data::Stag::BaseHandler=HASH(0x2542658)', > 'HASH(0x1a02da0)') called at > /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm line 239 > > XML::Parser::PerlSAX::_handle_end('XML::Parser::PerlSAX=HASH(0x26543e8)', > 'XML::Parser::Expat=HASH(0x25898a8)', 'cv') called at > /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm line 79 > > XML::Parser::PerlSAX::__ANON__('XML::Parser::Expat=HASH(0x25898a8)', > 'cv') called at /usr/lib64/perl5/XML/Parser/Expat.pm line 469 > > XML::Parser::Expat::parse('XML::Parser::Expat=HASH(0x25898a8)', > 'FileHandle=GLOB(0x2688330)') called at /usr/lib64/perl5/XML/Parser.pm line > 187 > > eval {...} called at /usr/lib64/perl5/XML/Parser.pm line 186 > > XML::Parser::parse('XML::Parser=HASH(0x24a4200)', > 'FileHandle=GLOB(0x2688330)') called at > /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm line 146 > > XML::Parser::PerlSAX::parse('XML::Parser::PerlSAX=HASH(0x26543e8)', > 'Handler', 'Data::Stag::BaseHandler=HASH(0x2542658)', 'Source', > 'HASH(0x26547f0)') called at > /home/kimmm/perl5/lib/perl5/Data/Stag/XMLParser.pm line 69 > > Data::Stag::XMLParser::parse_fh('Data::Stag::XMLParser=HASH(0x2542400)', > 'FileHandle=GLOB(0x2688330)') called at > /home/kimmm/perl5/lib/perl5/Data/Stag/BaseGenerator.pm line 476 > > Data::Stag::BaseGenerator::parse('Data::Stag::XMLParser=HASH(0x2542400)', > '-file', 'ff.xml', '-str', undef, '-fh', undef) called at > /home/kimmm/perl5/lib/perl5/Data/Stag/XMLParser.pm line 58 > > Data::Stag::XMLParser::parse('Data::Stag::XMLParser=HASH(0x2542400)', > '-file', 'ff.xml', '-str', undef, '-fh', undef) called at > /home/kimmm/perl5/lib/perl5/Data/Stag/StagImpl.pm line 275 > > Data::Stag::StagImpl::parse('Data::Stag', '-format', undef, > '-file', 'ff.xml', '-handler', 'Data::Stag::BaseHandler=HASH(0x2542658)') > called at /home/kimmm/perl5/lib/perl5/Data/Stag.pm line 181 > > Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, '-file', > 'ff.xml', '-handler', 'Data::Stag::BaseHandler=HASH(0x2542658)') called at > /home/kimmm/perl5/bin/stag-storenode.pl line 140 > > > Any ideas what might be the problem? > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > 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 > <(216)%20392-3087> > Ontario Institute for Cancer Research > > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain > dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > <(216)%20392-3087> > Ontario Institute for Cancer Research > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! > http://sdm.link/slashdot_______________________________________________ > 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 > <(216)%20392-3087> > Ontario Institute for Cancer Research > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > |
From: Scott C. <sc...@sc...> - 2017-03-23 23:41:50
|
Probably. I'd love to if I had a drop in replacement :-) On Thu, Mar 23, 2017 at 7:23 PM, Chris Mungall <cjm...@lb...> wrote: > Is there a ticket already open somewhere about replacing stag-storenode? > > On 23 Mar 2017, at 16:17, Scott Cain wrote: > > It seems like DBIx::DBSchema is failing from the first error message, and > if that's failing, nothing else is going to work. It's trying to call the > DBSchema table method. I just looked at the test suite for DBSchema and it > is surprisingly useless. It might be worthwhile to create a simple test > script that talks to your Chado database via DBSchema and calls the table > method for the cv table to see if it works. > > One thing I wonder about is the version of Postgres: 9.6.2 is newer than > any I've seen used, but I would hope that it would still work. > > > On Thu, Mar 23, 2017 at 5:36 PM, Mara Kim <mar...@va...> wrote: > >> `search_path` seems to be set correctly: >> >> $ psql -U rokaschado genestation >> >> psql (9.6.2) >> >> Type "help" for help. >> >> >> genestation=# SHOW search_path; >> >> search_path >> >> --------------- >> >> chado, public >> >> (1 row) >> >> >> genestation=# SELECT * FROM cv LIMIT 1; >> >> cv_id | name | definition >> >> -------+--------------+------------ >> >> 1 | relationship | >> >> (1 row) >> >> On Thu, Mar 23, 2017 at 4:26 PM Scott Cain <sc...@sc...> wrote: >> >>> Hi Mara, >>> >>> Is your chado database in a schema other than public? If so, you'll >>> have to modify your search path for the user that is running >>> stag-storenode. See http://tripal.info/documentation/search_path for >>> more info. >>> >>> Scott >>> >>> >>> On Thu, Mar 23, 2017 at 2:43 PM, Mara Kim <mar...@va...> >>> wrote: >>> >>> Hello, >>> >>> I am trying to use stag-storenode.pl to load the Fantom5 FF ontology. >>> >>> I took the following steps: >>> >>> wget http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Ontology >>> /ff-phase2-140729.obo.txt #Download ontology >>> >>> ex ff-phase2-140729.obo.txt -c '%s/{.*} ' -c 'wq' #Remove comments >>> >>> go2chadoxml ff-phase2-140729.obo.txt > ff.xml #Convert to XML >>> >>> stag-storenode.pl -d 'dbi:Pg:dbname=genestation;host=localhost;port=5432' >>> --user rokaschado ff.xml #Load into DB >>> >>> >>> >>> When invoking stag-storenode.pl I get the following error: >>> >>> $ stag-storenode.pl -d 'dbi:Pg:dbname=genestation;host=localhost;port=5432' >>> --user rokaschado ff.xml >>> >>> Can't get table cv from db. >>> >>> Maybe DBIx::DBSchema does not work with your database? at >>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 427 >>> >>> DBIx::DBStag::get_pk_col('DBIx::DBStag=HASH(0x1950fb8)', 'cv') >>> called at /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 1265 >>> >>> DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x1950fb8)', >>> 'Data::Stag::StagImpl=ARRAY(0x2749fe8)') called at >>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 1180 >>> >>> DBIx::DBStag::storenode('DBIx::DBStag=HASH(0x1950fb8)', >>> 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at >>> /home/kimmm/perl5/bin/stag-storenode.pl line 85 >>> >>> eval {...} called at /home/kimmm/perl5/bin/stag-storenode.pl >>> line 84 >>> >>> main::store('Data::Stag::BaseHandler=HASH(0x2542658)', >>> 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at >>> /home/kimmm/perl5/bin/stag-storenode.pl line 134 >>> >>> main::__ANON__('Data::Stag::BaseHandler=HASH(0x2542658)', >>> 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at >>> /home/kimmm/perl5/lib/perl5/Data/Stag/BaseHandler.pm line 594 >>> >>> Data::Stag::BaseHandler::end_event('Data::Stag::BaseHandler=HASH(0x2542658)', >>> 'cv') called at /home/kimmm/perl5/lib/perl5/Data/Stag/BaseHandler.pm >>> line 742 >>> >>> Data::Stag::BaseHandler::end_element('Data::Stag::BaseHandler=HASH(0x2542658)', >>> 'HASH(0x1a02da0)') called at /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm >>> line 239 >>> >>> XML::Parser::PerlSAX::_handle_end('XML::Parser::PerlSAX=HASH(0x26543e8)', >>> 'XML::Parser::Expat=HASH(0x25898a8)', 'cv') called at >>> /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm line 79 >>> >>> XML::Parser::PerlSAX::__ANON__('XML::Parser::Expat=HASH(0x25898a8)', >>> 'cv') called at /usr/lib64/perl5/XML/Parser/Expat.pm line 469 >>> >>> XML::Parser::Expat::parse('XML::Parser::Expat=HASH(0x25898a8)', >>> 'FileHandle=GLOB(0x2688330)') called at /usr/lib64/perl5/XML/Parser.pm line >>> 187 >>> >>> eval {...} called at /usr/lib64/perl5/XML/Parser.pm line 186 >>> >>> XML::Parser::parse('XML::Parser=HASH(0x24a4200)', >>> 'FileHandle=GLOB(0x2688330)') called at /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm >>> line 146 >>> >>> XML::Parser::PerlSAX::parse('XML::Parser::PerlSAX=HASH(0x26543e8)', >>> 'Handler', 'Data::Stag::BaseHandler=HASH(0x2542658)', 'Source', >>> 'HASH(0x26547f0)') called at /home/kimmm/perl5/lib/perl5/Data/Stag/XMLParser.pm >>> line 69 >>> >>> Data::Stag::XMLParser::parse_fh('Data::Stag::XMLParser=HASH(0x2542400)', >>> 'FileHandle=GLOB(0x2688330)') called at /home/kimmm/perl5/lib/perl5/Data/Stag/BaseGenerator.pm >>> line 476 >>> >>> Data::Stag::BaseGenerator::parse('Data::Stag::XMLParser=HASH(0x2542400)', >>> '-file', 'ff.xml', '-str', undef, '-fh', undef) called at >>> /home/kimmm/perl5/lib/perl5/Data/Stag/XMLParser.pm line 58 >>> >>> Data::Stag::XMLParser::parse('Data::Stag::XMLParser=HASH(0x2542400)', >>> '-file', 'ff.xml', '-str', undef, '-fh', undef) called at >>> /home/kimmm/perl5/lib/perl5/Data/Stag/StagImpl.pm line 275 >>> >>> Data::Stag::StagImpl::parse('Data::Stag', '-format', undef, >>> '-file', 'ff.xml', '-handler', 'Data::Stag::BaseHandler=HASH(0x2542658)') >>> called at /home/kimmm/perl5/lib/perl5/Data/Stag.pm line 181 >>> >>> Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, '-file', >>> 'ff.xml', '-handler', 'Data::Stag::BaseHandler=HASH(0x2542658)') called >>> at /home/kimmm/perl5/bin/stag-storenode.pl line 140 >>> >>> >>> Any ideas what might be the problem? >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> 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 >>> <(216)%20392-3087> >>> Ontario Institute for Cancer Research >>> >> > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain > dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > <(216)%20392-3087> > Ontario Institute for Cancer Research > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot______ > _________________________________________ > 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 |
From: Chris M. <cjm...@lb...> - 2017-03-23 23:24:23
|
Is there a ticket already open somewhere about replacing stag-storenode? On 23 Mar 2017, at 16:17, Scott Cain wrote: > It seems like DBIx::DBSchema is failing from the first error message, > and > if that's failing, nothing else is going to work. It's trying to call > the > DBSchema table method. I just looked at the test suite for DBSchema > and it > is surprisingly useless. It might be worthwhile to create a simple > test > script that talks to your Chado database via DBSchema and calls the > table > method for the cv table to see if it works. > > One thing I wonder about is the version of Postgres: 9.6.2 is newer > than > any I've seen used, but I would hope that it would still work. > > > On Thu, Mar 23, 2017 at 5:36 PM, Mara Kim <mar...@va...> > wrote: > >> `search_path` seems to be set correctly: >> >> $ psql -U rokaschado genestation >> >> psql (9.6.2) >> >> Type "help" for help. >> >> >> genestation=# SHOW search_path; >> >> search_path >> >> --------------- >> >> chado, public >> >> (1 row) >> >> >> genestation=# SELECT * FROM cv LIMIT 1; >> >> cv_id | name | definition >> >> -------+--------------+------------ >> >> 1 | relationship | >> >> (1 row) >> >> On Thu, Mar 23, 2017 at 4:26 PM Scott Cain <sc...@sc...> >> wrote: >> >>> Hi Mara, >>> >>> Is your chado database in a schema other than public? If so, you'll >>> have >>> to modify your search path for the user that is running >>> stag-storenode. >>> See http://tripal.info/documentation/search_path for more info. >>> >>> Scott >>> >>> >>> On Thu, Mar 23, 2017 at 2:43 PM, Mara Kim <mar...@va...> >>> wrote: >>> >>> Hello, >>> >>> I am trying to use stag-storenode.pl to load the Fantom5 FF >>> ontology. >>> >>> I took the following steps: >>> >>> wget http://fantom.gsc.riken.jp/5/datafiles/latest/extra/ >>> Ontology/ff-phase2-140729.obo.txt #Download ontology >>> >>> ex ff-phase2-140729.obo.txt -c '%s/{.*} ' -c 'wq' #Remove comments >>> >>> go2chadoxml ff-phase2-140729.obo.txt > ff.xml #Convert to XML >>> >>> stag-storenode.pl -d >>> 'dbi:Pg:dbname=genestation;host=localhost;port=5432' >>> --user rokaschado ff.xml #Load into DB >>> >>> >>> >>> When invoking stag-storenode.pl I get the following error: >>> >>> $ stag-storenode.pl -d >>> 'dbi:Pg:dbname=genestation;host=localhost;port=5432' >>> --user rokaschado ff.xml >>> >>> Can't get table cv from db. >>> >>> Maybe DBIx::DBSchema does not work with your database? at >>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 427 >>> >>> DBIx::DBStag::get_pk_col('DBIx::DBStag=HASH(0x1950fb8)', >>> 'cv') >>> called at /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 1265 >>> >>> DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x1950fb8)', >>> 'Data::Stag::StagImpl=ARRAY(0x2749fe8)') called at >>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 1180 >>> >>> DBIx::DBStag::storenode('DBIx::DBStag=HASH(0x1950fb8)', >>> 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at >>> /home/kimmm/perl5/bin/ >>> stag-storenode.pl line 85 >>> >>> eval {...} called at /home/kimmm/perl5/bin/stag-storenode.pl >>> line 84 >>> >>> main::store('Data::Stag::BaseHandler=HASH(0x2542658)', >>> 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at >>> /home/kimmm/perl5/bin/ >>> stag-storenode.pl line 134 >>> >>> main::__ANON__('Data::Stag::BaseHandler=HASH(0x2542658)', >>> 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at >>> /home/kimmm/perl5/lib/perl5/Data/Stag/BaseHandler.pm line 594 >>> >>> Data::Stag::BaseHandler::end_event('Data::Stag::BaseHandler=HASH(0x2542658)', >>> 'cv') called at /home/kimmm/perl5/lib/perl5/Data/Stag/BaseHandler.pm >>> line 742 >>> >>> Data::Stag::BaseHandler::end_element('Data::Stag::BaseHandler=HASH(0x2542658)', >>> 'HASH(0x1a02da0)') called at >>> /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm >>> line 239 >>> >>> XML::Parser::PerlSAX::_handle_end('XML::Parser::PerlSAX=HASH(0x26543e8)', >>> 'XML::Parser::Expat=HASH(0x25898a8)', 'cv') called at >>> /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm line 79 >>> >>> XML::Parser::PerlSAX::__ANON__('XML::Parser::Expat=HASH(0x25898a8)', >>> 'cv') called at /usr/lib64/perl5/XML/Parser/Expat.pm line 469 >>> >>> XML::Parser::Expat::parse('XML::Parser::Expat=HASH(0x25898a8)', >>> 'FileHandle=GLOB(0x2688330)') called at >>> /usr/lib64/perl5/XML/Parser.pm line >>> 187 >>> >>> eval {...} called at /usr/lib64/perl5/XML/Parser.pm line 186 >>> >>> XML::Parser::parse('XML::Parser=HASH(0x24a4200)', >>> 'FileHandle=GLOB(0x2688330)') called at >>> /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm >>> line 146 >>> >>> XML::Parser::PerlSAX::parse('XML::Parser::PerlSAX=HASH(0x26543e8)', >>> 'Handler', 'Data::Stag::BaseHandler=HASH(0x2542658)', 'Source', >>> 'HASH(0x26547f0)') called at >>> /home/kimmm/perl5/lib/perl5/Data/Stag/XMLParser.pm >>> line 69 >>> >>> Data::Stag::XMLParser::parse_fh('Data::Stag::XMLParser=HASH(0x2542400)', >>> 'FileHandle=GLOB(0x2688330)') called at >>> /home/kimmm/perl5/lib/perl5/Data/Stag/BaseGenerator.pm >>> line 476 >>> >>> Data::Stag::BaseGenerator::parse('Data::Stag::XMLParser=HASH(0x2542400)', >>> '-file', 'ff.xml', '-str', undef, '-fh', undef) called at >>> /home/kimmm/perl5/lib/perl5/Data/Stag/XMLParser.pm line 58 >>> >>> Data::Stag::XMLParser::parse('Data::Stag::XMLParser=HASH(0x2542400)', >>> '-file', 'ff.xml', '-str', undef, '-fh', undef) called at >>> /home/kimmm/perl5/lib/perl5/Data/Stag/StagImpl.pm line 275 >>> >>> Data::Stag::StagImpl::parse('Data::Stag', '-format', undef, >>> '-file', 'ff.xml', '-handler', >>> 'Data::Stag::BaseHandler=HASH(0x2542658)') >>> called at /home/kimmm/perl5/lib/perl5/Data/Stag.pm line 181 >>> >>> Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, >>> '-file', >>> 'ff.xml', '-handler', 'Data::Stag::BaseHandler=HASH(0x2542658)') >>> called >>> at /home/kimmm/perl5/bin/stag-storenode.pl line 140 >>> >>> >>> Any ideas what might be the problem? >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> 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 >>> <(216)%20392-3087> >>> 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 > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! > http://sdm.link/slashdot_______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema |
From: Scott C. <sc...@sc...> - 2017-03-23 23:17:54
|
It seems like DBIx::DBSchema is failing from the first error message, and if that's failing, nothing else is going to work. It's trying to call the DBSchema table method. I just looked at the test suite for DBSchema and it is surprisingly useless. It might be worthwhile to create a simple test script that talks to your Chado database via DBSchema and calls the table method for the cv table to see if it works. One thing I wonder about is the version of Postgres: 9.6.2 is newer than any I've seen used, but I would hope that it would still work. On Thu, Mar 23, 2017 at 5:36 PM, Mara Kim <mar...@va...> wrote: > `search_path` seems to be set correctly: > > $ psql -U rokaschado genestation > > psql (9.6.2) > > Type "help" for help. > > > genestation=# SHOW search_path; > > search_path > > --------------- > > chado, public > > (1 row) > > > genestation=# SELECT * FROM cv LIMIT 1; > > cv_id | name | definition > > -------+--------------+------------ > > 1 | relationship | > > (1 row) > > On Thu, Mar 23, 2017 at 4:26 PM Scott Cain <sc...@sc...> wrote: > >> Hi Mara, >> >> Is your chado database in a schema other than public? If so, you'll have >> to modify your search path for the user that is running stag-storenode. >> See http://tripal.info/documentation/search_path for more info. >> >> Scott >> >> >> On Thu, Mar 23, 2017 at 2:43 PM, Mara Kim <mar...@va...> >> wrote: >> >> Hello, >> >> I am trying to use stag-storenode.pl to load the Fantom5 FF ontology. >> >> I took the following steps: >> >> wget http://fantom.gsc.riken.jp/5/datafiles/latest/extra/ >> Ontology/ff-phase2-140729.obo.txt #Download ontology >> >> ex ff-phase2-140729.obo.txt -c '%s/{.*} ' -c 'wq' #Remove comments >> >> go2chadoxml ff-phase2-140729.obo.txt > ff.xml #Convert to XML >> >> stag-storenode.pl -d 'dbi:Pg:dbname=genestation;host=localhost;port=5432' >> --user rokaschado ff.xml #Load into DB >> >> >> >> When invoking stag-storenode.pl I get the following error: >> >> $ stag-storenode.pl -d 'dbi:Pg:dbname=genestation;host=localhost;port=5432' >> --user rokaschado ff.xml >> >> Can't get table cv from db. >> >> Maybe DBIx::DBSchema does not work with your database? at >> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 427 >> >> DBIx::DBStag::get_pk_col('DBIx::DBStag=HASH(0x1950fb8)', 'cv') >> called at /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 1265 >> >> DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x1950fb8)', >> 'Data::Stag::StagImpl=ARRAY(0x2749fe8)') called at >> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 1180 >> >> DBIx::DBStag::storenode('DBIx::DBStag=HASH(0x1950fb8)', >> 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at /home/kimmm/perl5/bin/ >> stag-storenode.pl line 85 >> >> eval {...} called at /home/kimmm/perl5/bin/stag-storenode.pl >> line 84 >> >> main::store('Data::Stag::BaseHandler=HASH(0x2542658)', >> 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at /home/kimmm/perl5/bin/ >> stag-storenode.pl line 134 >> >> main::__ANON__('Data::Stag::BaseHandler=HASH(0x2542658)', >> 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at >> /home/kimmm/perl5/lib/perl5/Data/Stag/BaseHandler.pm line 594 >> >> Data::Stag::BaseHandler::end_event('Data::Stag::BaseHandler=HASH(0x2542658)', >> 'cv') called at /home/kimmm/perl5/lib/perl5/Data/Stag/BaseHandler.pm >> line 742 >> >> Data::Stag::BaseHandler::end_element('Data::Stag::BaseHandler=HASH(0x2542658)', >> 'HASH(0x1a02da0)') called at /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm >> line 239 >> >> XML::Parser::PerlSAX::_handle_end('XML::Parser::PerlSAX=HASH(0x26543e8)', >> 'XML::Parser::Expat=HASH(0x25898a8)', 'cv') called at >> /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm line 79 >> >> XML::Parser::PerlSAX::__ANON__('XML::Parser::Expat=HASH(0x25898a8)', >> 'cv') called at /usr/lib64/perl5/XML/Parser/Expat.pm line 469 >> >> XML::Parser::Expat::parse('XML::Parser::Expat=HASH(0x25898a8)', >> 'FileHandle=GLOB(0x2688330)') called at /usr/lib64/perl5/XML/Parser.pm line >> 187 >> >> eval {...} called at /usr/lib64/perl5/XML/Parser.pm line 186 >> >> XML::Parser::parse('XML::Parser=HASH(0x24a4200)', >> 'FileHandle=GLOB(0x2688330)') called at /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm >> line 146 >> >> XML::Parser::PerlSAX::parse('XML::Parser::PerlSAX=HASH(0x26543e8)', >> 'Handler', 'Data::Stag::BaseHandler=HASH(0x2542658)', 'Source', >> 'HASH(0x26547f0)') called at /home/kimmm/perl5/lib/perl5/Data/Stag/XMLParser.pm >> line 69 >> >> Data::Stag::XMLParser::parse_fh('Data::Stag::XMLParser=HASH(0x2542400)', >> 'FileHandle=GLOB(0x2688330)') called at /home/kimmm/perl5/lib/perl5/Data/Stag/BaseGenerator.pm >> line 476 >> >> Data::Stag::BaseGenerator::parse('Data::Stag::XMLParser=HASH(0x2542400)', >> '-file', 'ff.xml', '-str', undef, '-fh', undef) called at >> /home/kimmm/perl5/lib/perl5/Data/Stag/XMLParser.pm line 58 >> >> Data::Stag::XMLParser::parse('Data::Stag::XMLParser=HASH(0x2542400)', >> '-file', 'ff.xml', '-str', undef, '-fh', undef) called at >> /home/kimmm/perl5/lib/perl5/Data/Stag/StagImpl.pm line 275 >> >> Data::Stag::StagImpl::parse('Data::Stag', '-format', undef, >> '-file', 'ff.xml', '-handler', 'Data::Stag::BaseHandler=HASH(0x2542658)') >> called at /home/kimmm/perl5/lib/perl5/Data/Stag.pm line 181 >> >> Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, '-file', >> 'ff.xml', '-handler', 'Data::Stag::BaseHandler=HASH(0x2542658)') called >> at /home/kimmm/perl5/bin/stag-storenode.pl line 140 >> >> >> Any ideas what might be the problem? >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> 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 >> <(216)%20392-3087> >> 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 |
From: Scott C. <sc...@sc...> - 2017-03-23 20:49:22
|
Hi Mara, Is your chado database in a schema other than public? If so, you'll have to modify your search path for the user that is running stag-storenode. See http://tripal.info/documentation/search_path for more info. Scott On Thu, Mar 23, 2017 at 2:43 PM, Mara Kim <mar...@va...> wrote: > Hello, > > I am trying to use stag-storenode.pl to load the Fantom5 FF ontology. > > I took the following steps: > > wget http://fantom.gsc.riken.jp/5/datafiles/latest/extra/ > Ontology/ff-phase2-140729.obo.txt #Download ontology > > ex ff-phase2-140729.obo.txt -c '%s/{.*} ' -c 'wq' #Remove comments > > go2chadoxml ff-phase2-140729.obo.txt > ff.xml #Convert to XML > > stag-storenode.pl -d 'dbi:Pg:dbname=genestation;host=localhost;port=5432' > --user rokaschado ff.xml #Load into DB > > > > When invoking stag-storenode.pl I get the following error: > > $ stag-storenode.pl -d 'dbi:Pg:dbname=genestation;host=localhost;port=5432' > --user rokaschado ff.xml > > Can't get table cv from db. > > Maybe DBIx::DBSchema does not work with your database? at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 427 > > DBIx::DBStag::get_pk_col('DBIx::DBStag=HASH(0x1950fb8)', 'cv') > called at /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 1265 > > DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x1950fb8)', > 'Data::Stag::StagImpl=ARRAY(0x2749fe8)') called at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 1180 > > DBIx::DBStag::storenode('DBIx::DBStag=HASH(0x1950fb8)', > 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at /home/kimmm/perl5/bin/ > stag-storenode.pl line 85 > > eval {...} called at /home/kimmm/perl5/bin/stag-storenode.pl line > 84 > > main::store('Data::Stag::BaseHandler=HASH(0x2542658)', > 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at /home/kimmm/perl5/bin/ > stag-storenode.pl line 134 > > main::__ANON__('Data::Stag::BaseHandler=HASH(0x2542658)', > 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at > /home/kimmm/perl5/lib/perl5/Data/Stag/BaseHandler.pm line 594 > > Data::Stag::BaseHandler::end_event('Data::Stag::BaseHandler=HASH(0x2542658)', > 'cv') called at /home/kimmm/perl5/lib/perl5/Data/Stag/BaseHandler.pm line > 742 > > Data::Stag::BaseHandler::end_element('Data::Stag::BaseHandler=HASH(0x2542658)', > 'HASH(0x1a02da0)') called at /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm > line 239 > > XML::Parser::PerlSAX::_handle_end('XML::Parser::PerlSAX=HASH(0x26543e8)', > 'XML::Parser::Expat=HASH(0x25898a8)', 'cv') called at > /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm line 79 > > XML::Parser::PerlSAX::__ANON__('XML::Parser::Expat=HASH(0x25898a8)', > 'cv') called at /usr/lib64/perl5/XML/Parser/Expat.pm line 469 > > XML::Parser::Expat::parse('XML::Parser::Expat=HASH(0x25898a8)', > 'FileHandle=GLOB(0x2688330)') called at /usr/lib64/perl5/XML/Parser.pm line > 187 > > eval {...} called at /usr/lib64/perl5/XML/Parser.pm line 186 > > XML::Parser::parse('XML::Parser=HASH(0x24a4200)', > 'FileHandle=GLOB(0x2688330)') called at /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm > line 146 > > XML::Parser::PerlSAX::parse('XML::Parser::PerlSAX=HASH(0x26543e8)', > 'Handler', 'Data::Stag::BaseHandler=HASH(0x2542658)', 'Source', > 'HASH(0x26547f0)') called at /home/kimmm/perl5/lib/perl5/Data/Stag/XMLParser.pm > line 69 > > Data::Stag::XMLParser::parse_fh('Data::Stag::XMLParser=HASH(0x2542400)', > 'FileHandle=GLOB(0x2688330)') called at /home/kimmm/perl5/lib/perl5/Data/Stag/BaseGenerator.pm > line 476 > > Data::Stag::BaseGenerator::parse('Data::Stag::XMLParser=HASH(0x2542400)', > '-file', 'ff.xml', '-str', undef, '-fh', undef) called at > /home/kimmm/perl5/lib/perl5/Data/Stag/XMLParser.pm line 58 > > Data::Stag::XMLParser::parse('Data::Stag::XMLParser=HASH(0x2542400)', > '-file', 'ff.xml', '-str', undef, '-fh', undef) called at > /home/kimmm/perl5/lib/perl5/Data/Stag/StagImpl.pm line 275 > > Data::Stag::StagImpl::parse('Data::Stag', '-format', undef, > '-file', 'ff.xml', '-handler', 'Data::Stag::BaseHandler=HASH(0x2542658)') > called at /home/kimmm/perl5/lib/perl5/Data/Stag.pm line 181 > > Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, '-file', > 'ff.xml', '-handler', 'Data::Stag::BaseHandler=HASH(0x2542658)') called > at /home/kimmm/perl5/bin/stag-storenode.pl line 140 > > > Any ideas what might be the problem? > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > 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 |
From: Mara K. <mar...@va...> - 2017-03-23 18:43:52
|
Hello, I am trying to use stag-storenode.pl to load the Fantom5 FF ontology. I took the following steps: wget http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Ontology/ff-phase2-140729.obo.txt #Download ontology ex ff-phase2-140729.obo.txt -c '%s/{.*} ' -c 'wq' #Remove comments go2chadoxml ff-phase2-140729.obo.txt > ff.xml #Convert to XML stag-storenode.pl -d 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado ff.xml #Load into DB When invoking stag-storenode.pl I get the following error: $ stag-storenode.pl -d 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado ff.xml Can't get table cv from db. Maybe DBIx::DBSchema does not work with your database? at /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 427 DBIx::DBStag::get_pk_col('DBIx::DBStag=HASH(0x1950fb8)', 'cv') called at /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 1265 DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x1950fb8)', 'Data::Stag::StagImpl=ARRAY(0x2749fe8)') called at /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 1180 DBIx::DBStag::storenode('DBIx::DBStag=HASH(0x1950fb8)', 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at /home/kimmm/perl5/bin/ stag-storenode.pl line 85 eval {...} called at /home/kimmm/perl5/bin/stag-storenode.pl line 84 main::store('Data::Stag::BaseHandler=HASH(0x2542658)', 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at /home/kimmm/perl5/bin/ stag-storenode.pl line 134 main::__ANON__('Data::Stag::BaseHandler=HASH(0x2542658)', 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at /home/kimmm/perl5/lib/perl5/Data/Stag/BaseHandler.pm line 594 Data::Stag::BaseHandler::end_event('Data::Stag::BaseHandler=HASH(0x2542658)', 'cv') called at /home/kimmm/perl5/lib/perl5/Data/Stag/BaseHandler.pm line 742 Data::Stag::BaseHandler::end_element('Data::Stag::BaseHandler=HASH(0x2542658)', 'HASH(0x1a02da0)') called at /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm line 239 XML::Parser::PerlSAX::_handle_end('XML::Parser::PerlSAX=HASH(0x26543e8)', 'XML::Parser::Expat=HASH(0x25898a8)', 'cv') called at /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm line 79 XML::Parser::PerlSAX::__ANON__('XML::Parser::Expat=HASH(0x25898a8)', 'cv') called at /usr/lib64/perl5/XML/Parser/Expat.pm line 469 XML::Parser::Expat::parse('XML::Parser::Expat=HASH(0x25898a8)', 'FileHandle=GLOB(0x2688330)') called at /usr/lib64/perl5/XML/Parser.pm line 187 eval {...} called at /usr/lib64/perl5/XML/Parser.pm line 186 XML::Parser::parse('XML::Parser=HASH(0x24a4200)', 'FileHandle=GLOB(0x2688330)') called at /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm line 146 XML::Parser::PerlSAX::parse('XML::Parser::PerlSAX=HASH(0x26543e8)', 'Handler', 'Data::Stag::BaseHandler=HASH(0x2542658)', 'Source', 'HASH(0x26547f0)') called at /home/kimmm/perl5/lib/perl5/Data/Stag/XMLParser.pm line 69 Data::Stag::XMLParser::parse_fh('Data::Stag::XMLParser=HASH(0x2542400)', 'FileHandle=GLOB(0x2688330)') called at /home/kimmm/perl5/lib/perl5/Data/Stag/BaseGenerator.pm line 476 Data::Stag::BaseGenerator::parse('Data::Stag::XMLParser=HASH(0x2542400)', '-file', 'ff.xml', '-str', undef, '-fh', undef) called at /home/kimmm/perl5/lib/perl5/Data/Stag/XMLParser.pm line 58 Data::Stag::XMLParser::parse('Data::Stag::XMLParser=HASH(0x2542400)', '-file', 'ff.xml', '-str', undef, '-fh', undef) called at /home/kimmm/perl5/lib/perl5/Data/Stag/StagImpl.pm line 275 Data::Stag::StagImpl::parse('Data::Stag', '-format', undef, '-file', 'ff.xml', '-handler', 'Data::Stag::BaseHandler=HASH(0x2542658)') called at /home/kimmm/perl5/lib/perl5/Data/Stag.pm line 181 Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, '-file', 'ff.xml', '-handler', 'Data::Stag::BaseHandler=HASH(0x2542658)') called at /home/kimmm/perl5/bin/stag-storenode.pl line 140 Any ideas what might be the problem? |
From: Cannon, E. K [C. S] <ekc...@ia...> - 2017-02-07 14:17:04
|
I want to proceed with caution on this point, especially as there has been general discomfort with removing ontology relationships from Chado if they don't appear in a subsequent version of an ontology OBO file. In the Tripal cv loader, all existing terms and relationships are left in place even if they have disappeared from the ontology that is being updated. There appears to be little harm in keeping the terms - a term removed from a subsequent version of the ontology may have been attached to a data object and so should perhaps not be deleted in the chado schema. (My understanding is that terms should not disappear in any case, but be marked 'obsolete'.) My concern is with the relationships. While trying (and failing) to update the GO cv tables from the current OBO file using the Tripal cv loader, I traced the error to a circular reference in the cvterm_relationship table. As a result, recursive calls to the stored procedure _fill_cvtermpath4node quickly blew out the stack. The circular reference was not in the OBO file, but in the cvterm_relationship table, possibly resulting from leftover relationships from an earlier load of GO combined with relationships in the updated GO file. It was fixable by removing cvterm_relationship records for relationships that don't appear in a subsequent version of the ontology. Relationships do disappear from ontologies. An example from GO: Parent term - GO:0000042 protein targeting to Golgi old relationships (present in 12/21/2013 copy of the OBO file): GO:0000301 | retrograde transport, vesicle recycling within Golgi GO:0006605 | protein targeting GO:0016482 | cytoplasmic transport <--- this one disappeared GO:0072600 | establishment of protein localization to Golgi new relationships (in the current OBO file) is_a: GO:0000301 ! retrograde transport, vesicle recycling within Golgi is_a: GO:0006605 ! protein targeting is_a: GO:0072600 ! establishment of protein localization to Golgi Can anyone think of a reason it would be risky to remove relationships appear in older versions of an ontology but not a newer one? It seems to me that they should be removed. |
From: Scott C. <sc...@sc...> - 2016-11-04 19:25:09
|
Time is short! If you want to attend PAG <http://www.intlpag.org/> and would like to present on a topic that would be of interest to the GMOD community, please send an abstract or at least a descriptive title to he...@gm.... Types of talks typically include updates on GMOD software projects, usage stories for successful sites, proposals for new GMOD projects and descriptions of plugins for existing GMOD software projects like Tripal <http://gmod.org/wiki/Tripal>, JBrowse <http://gmod.org/wiki/JBrowse> and Galaxy <http://gmod.org/wiki/Galaxy>. Please consider giving a talk and sharing your experience and ideas! Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Chris M. <cjm...@lb...> - 2016-10-28 22:01:41
|
A number of GMOD related groups are exploring the idea of building GMOD components on top of graph databases, or layering Chado on top of a graph or RDF back end. I know SANBI talked briefly about this at the last GMOD meeting. I started on a google doc trying to weave these threads together, but it's still a very messy early draft: https://docs.google.com/document/d/1iZbtUurhUuqsM2oxnfklXa18yGlNZwEYI8npWRukGyY/edit#heading=h.ne5osa106xyc I got some great comments from some of you, but have not yet done a good job of integrating these. If there is interest, perhaps we could coordinate a few short talks at the GMOD workshop at PAG? |
From: Scott C. <sc...@sc...> - 2016-10-28 20:57:14
|
Hi, I am pleased to announce a call for talks to be given at the Plant and Animal Genomes conference this January in the GMOD workshop on Wednesday, January 18th. Any talks that involve the development or use of GMOD software are welcome. In particular this year, I'd really like to highlight plugins for the various GMOD software packages that support them, like JBrowse, Galaxy and Tripal (of course, Galaxy and Tripal have their own sessions, so you should consider submitting to them too). Please get an abstract, brief summary or a vague title to me as soon as possible so I can start getting it put together. Also, if you'd like to be a co-organizer, please let me drop me a line about that too. I might be able to get you some meeting-related niceties for not very much work. For more information about PAG, see: http://www.intlpag.org Thanks and I look forward to seeing in January, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Nathan D. <nat...@lb...> - 2016-10-28 18:44:40
|
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 |
From: Shane M. <sha...@gm...> - 2016-10-28 18:15:11
|
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 >> > > |
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 > |
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 |
From: Shane M. <sha...@gm...> - 2016-10-26 21:26:32
|
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 >> > |
From: Eric R. <es...@ta...> - 2016-10-26 16:34:40
|
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 > |