Re: [Gmod-schema] GFF bulk loader - fail

[Scott C. <sc...@sc...>]

(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.
>> >
>> >
>> >
>> >
>> >
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>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> 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