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GFF bulk loader - fail

Shane McCoy

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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Re: GFF bulk loader - fail

Scott Cain
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 <[hidden email]> 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
> _______________________________________________
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> [hidden email]
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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

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Re: GFF bulk loader - fail

Eric Rasche-3
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 out for one that works.

Scott: no time like the present to try out the chado docker images ;)

Cheers,

Eric






ons. 26. okt. 2016 kl. 15.35 skrev Scott Cain <[hidden email]>:
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 <[hidden email]> 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
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" class="gmail_msg" target="_blank">216-392-3087
Ontario Institute for Cancer Research
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Reconnect with the command line and become more productive.
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Re: GFF bulk loader - fail

Shane McCoy
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 <[hidden email]> 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 out for one that works.

Scott: no time like the present to try out the chado docker images ;)

Cheers,

Eric






ons. 26. okt. 2016 kl. 15.35 skrev Scott Cain <[hidden email]>:
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 <[hidden email]> 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
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" class="m_-5881175455994423461gmail_msg" target="_blank">216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
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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!
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema


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Re: GFF bulk loader - fail

Scott Cain
In reply to this post by Scott Cain
(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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: GFF bulk loader - fail

Shane McCoy
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, 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> Ontario Institute for Cancer Research
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: GFF bulk loader - fail

Shane McCoy
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 <[hidden email]> 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, 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> Ontario Institute for Cancer Research
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
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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!
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Re: GFF bulk loader - fail

nathandunn

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 <[hidden email]> 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 <[hidden email]> 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, 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank" class="">216-392-3087
>> Ontario Institute for Cancer Research
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank" class="">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
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
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!
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_______________________________________________
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