Problem with the bulk uploader

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Problem with the bulk uploader

Andrew Oberlin
Hello all,

When I go to use the gmod_bulk_uploader.pl script it get the following error.

Can't locate Bio/GMOD/DB/Adapter.pm in @INC (@INC contains: /home/scott/cvs_stuff/schema/chado/lib /home/cain/cvs_stuff/schema/chado/lib /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at /usr/local/bin/gmod_gff3_preprocessor.pl line 12. BEGIN failed--compilation aborted at /usr/local/bin/gmod_gff3_preprocessor.pl line 12.

However, I believe I am using the correct version of Perl that was used to install it although I really do not know how to check as I don't use Perl very often. I also did a locate on Adapter.pm, but I didn't find it on the machine.

Thanks,

Andrew Oberlin

--
Andrew Oberlin
Miami University 2013
Computer Science & Mathematics
[hidden email]  (330) 998-1603


------------------------------------------------------------------------------
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
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Re: Problem with the bulk uploader

Scott Cain
Hi Andrew,

So you did "locate Adapter.pm" and it came up empty?  I assume your
locate database is up to date (via "(sudo) updatedb")?  If that's the
case, then I'm guessing you don't have it installed, which is weird
since you seem to have gmod_gff3_preprocessor.pl.  I suppose you could
reinstall from a tarball.

Scott


On Fri, Feb 17, 2012 at 3:31 PM, Andrew Oberlin <[hidden email]> wrote:

> Hello all,
>
> When I go to use the gmod_bulk_uploader.pl script it get the following
> error.
>
> Can't locate Bio/GMOD/DB/Adapter.pm in @INC (@INC contains:
> /home/scott/cvs_stuff/schema/chado/lib /home/cain/cvs_stuff/schema/chado/lib
> /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1
> /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
> /usr/local/lib/site_perl .) at /usr/local/bin/gmod_gff3_preprocessor.pl line
> 12. BEGIN failed--compilation aborted at
> /usr/local/bin/gmod_gff3_preprocessor.pl line 12.
>
> However, I believe I am using the correct version of Perl that was used to
> install it although I really do not know how to check as I don't use Perl
> very often. I also did a locate on Adapter.pm, but I didn't find it on the
> machine.
>
> Thanks,
>
> Andrew Oberlin
>
> --
> Andrew Oberlin
> Miami University 2013
> Computer Science & Mathematics
> [hidden email]  (330) 998-1603
>
> ------------------------------------------------------------------------------
> Virtualization & Cloud Management Using Capacity Planning
> Cloud computing makes use of virtualization - but cloud computing
> also focuses on allowing computing to be delivered as a service.
> http://www.accelacomm.com/jaw/sfnl/114/51521223/
> _______________________________________________
> 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

------------------------------------------------------------------------------
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Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
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Re: Problem with the bulk uploader

Andrew Oberlin
I got that working thanks. However when I go to insert a genome into the database using the bulk_uploader I keep getting a message that looks like this:

Preparing data for inserting into the chado database (This may take a while ...) Unable to find srcfeature NC_014751 in the database. Perhaps you need to rerun your data load with the '--recreate_cache' option. at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 4555 Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x3775298)', 'Bio::SeqFeature::Annotated=HASH(0x3af2018)') called at /usr/local/bin/gmod_bulk_load_gff3.pl line 841 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...

Any ideas as to why this error would occur?


Thanks,

Andrew Oberlin

On Fri, Feb 17, 2012 at 4:12 PM, Scott Cain <[hidden email]> wrote:
Hi Andrew,

So you did "locate Adapter.pm" and it came up empty?  I assume your
locate database is up to date (via "(sudo) updatedb")?  If that's the
case, then I'm guessing you don't have it installed, which is weird
since you seem to have gmod_gff3_preprocessor.pl.  I suppose you could
reinstall from a tarball.

Scott


On Fri, Feb 17, 2012 at 3:31 PM, Andrew Oberlin <[hidden email]> wrote:
> Hello all,
>
> When I go to use the gmod_bulk_uploader.pl script it get the following
> error.
>
> Can't locate Bio/GMOD/DB/Adapter.pm in @INC (@INC contains:
> /home/scott/cvs_stuff/schema/chado/lib /home/cain/cvs_stuff/schema/chado/lib
> /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1
> /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
> /usr/local/lib/site_perl .) at /usr/local/bin/gmod_gff3_preprocessor.pl line
> 12. BEGIN failed--compilation aborted at
> /usr/local/bin/gmod_gff3_preprocessor.pl line 12.
>
> However, I believe I am using the correct version of Perl that was used to
> install it although I really do not know how to check as I don't use Perl
> very often. I also did a locate on Adapter.pm, but I didn't find it on the
> machine.
>
> Thanks,
>
> Andrew Oberlin
>
> --
> Andrew Oberlin
> Miami University 2013
> Computer Science & Mathematics
> [hidden email]  <a href="tel:%28330%29%20998-1603" value="+13309981603">(330) 998-1603
>
> ------------------------------------------------------------------------------
> Virtualization & Cloud Management Using Capacity Planning
> Cloud computing makes use of virtualization - but cloud computing
> also focuses on allowing computing to be delivered as a service.
> http://www.accelacomm.com/jaw/sfnl/114/51521223/
> _______________________________________________
> 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">216-392-3087
Ontario Institute for Cancer Research



--
Andrew Oberlin
Miami University 2013
Computer Science & Mathematics
[hidden email]  (330) 998-1603


------------------------------------------------------------------------------
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
_______________________________________________
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[hidden email]
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Re: Problem with the bulk uploader

Scott Cain
Hi Andrew,

This is usually a result of a few things:

1. You didn't load NC_014751 into the database first.  This is not usually the problem, as it is fairly obvious given the error message.

2. The load cache in the database got corrupted, but this isn't very common any more either, since the loader is a little smarter about cleaning up the cache when bad things happen.  You can try running the loader with --recreate_cache just to double check.  If you have a very large database, this will add a fairly significant startup time to the loading script.

3. This is probably the most likely: the loader didn't like the gff line that defined the NC_014751 feature. The easiest thing to check is that that line has both Name and ID set to NC_014751.  (the loader doesn't absolutely require that, but things can get wonky if that's not the case.)

Scott


Sent from my iPad

On Feb 22, 2012, at 3:38 PM, Andrew Oberlin <[hidden email]> wrote:

I got that working thanks. However when I go to insert a genome into the database using the bulk_uploader I keep getting a message that looks like this:

Preparing data for inserting into the chado database (This may take a while ...) Unable to find srcfeature NC_014751 in the database. Perhaps you need to rerun your data load with the '--recreate_cache' option. at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 4555 Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x3775298)', 'Bio::SeqFeature::Annotated=HASH(0x3af2018)') called at /usr/local/bin/gmod_bulk_load_gff3.pl line 841 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...

Any ideas as to why this error would occur?


Thanks,

Andrew Oberlin

On Fri, Feb 17, 2012 at 4:12 PM, Scott Cain <[hidden email]> wrote:
Hi Andrew,

So you did "locate Adapter.pm" and it came up empty?  I assume your
locate database is up to date (via "(sudo) updatedb")?  If that's the
case, then I'm guessing you don't have it installed, which is weird
since you seem to have gmod_gff3_preprocessor.pl.  I suppose you could
reinstall from a tarball.

Scott


On Fri, Feb 17, 2012 at 3:31 PM, Andrew Oberlin <[hidden email]> wrote:
> Hello all,
>
> When I go to use the gmod_bulk_uploader.pl script it get the following
> error.
>
> Can't locate Bio/GMOD/DB/Adapter.pm in @INC (@INC contains:
> /home/scott/cvs_stuff/schema/chado/lib /home/cain/cvs_stuff/schema/chado/lib
> /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1
> /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
> /usr/local/lib/site_perl .) at /usr/local/bin/gmod_gff3_preprocessor.pl line
> 12. BEGIN failed--compilation aborted at
> /usr/local/bin/gmod_gff3_preprocessor.pl line 12.
>
> However, I believe I am using the correct version of Perl that was used to
> install it although I really do not know how to check as I don't use Perl
> very often. I also did a locate on Adapter.pm, but I didn't find it on the
> machine.
>
> Thanks,
>
> Andrew Oberlin
>
> --
> Andrew Oberlin
> Miami University 2013
> Computer Science & Mathematics
> [hidden email]  <a href="tel:%28330%29%20998-1603" value="+13309981603">(330) 998-1603
>
> ------------------------------------------------------------------------------
> Virtualization & Cloud Management Using Capacity Planning
> Cloud computing makes use of virtualization - but cloud computing
> also focuses on allowing computing to be delivered as a service.
> http://www.accelacomm.com/jaw/sfnl/114/51521223/
> _______________________________________________
> 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">216-392-3087
Ontario Institute for Cancer Research



--
Andrew Oberlin
Miami University 2013
Computer Science & Mathematics
[hidden email]  (330) 998-1603


------------------------------------------------------------------------------
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
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Re: Problem with the bulk uploader

Andrew Oberlin
I actually feel like it is the first one. But I'm not seeing how I am not adding this to the database. I typically load a new organism every time I use the bulk uploader. is there a specific way to load the accession as well that I am missing?

Andrew Oberlin

On Fri, Feb 24, 2012 at 1:18 PM, Scott Cain <[hidden email]> wrote:
Hi Andrew,

This is usually a result of a few things:

1. You didn't load NC_014751 into the database first.  This is not usually the problem, as it is fairly obvious given the error message.

2. The load cache in the database got corrupted, but this isn't very common any more either, since the loader is a little smarter about cleaning up the cache when bad things happen.  You can try running the loader with --recreate_cache just to double check.  If you have a very large database, this will add a fairly significant startup time to the loading script.

3. This is probably the most likely: the loader didn't like the gff line that defined the NC_014751 feature. The easiest thing to check is that that line has both Name and ID set to NC_014751.  (the loader doesn't absolutely require that, but things can get wonky if that's not the case.)

Scott


Sent from my iPad

On Feb 22, 2012, at 3:38 PM, Andrew Oberlin <[hidden email]> wrote:

I got that working thanks. However when I go to insert a genome into the database using the bulk_uploader I keep getting a message that looks like this:

Preparing data for inserting into the chado database (This may take a while ...) Unable to find srcfeature NC_014751 in the database. Perhaps you need to rerun your data load with the '--recreate_cache' option. at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 4555 Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x3775298)', 'Bio::SeqFeature::Annotated=HASH(0x3af2018)') called at /usr/local/bin/gmod_bulk_load_gff3.pl line 841 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...

Any ideas as to why this error would occur?


Thanks,

Andrew Oberlin

On Fri, Feb 17, 2012 at 4:12 PM, Scott Cain <[hidden email]> wrote:
Hi Andrew,

So you did "locate Adapter.pm" and it came up empty?  I assume your
locate database is up to date (via "(sudo) updatedb")?  If that's the
case, then I'm guessing you don't have it installed, which is weird
since you seem to have gmod_gff3_preprocessor.pl.  I suppose you could
reinstall from a tarball.

Scott


On Fri, Feb 17, 2012 at 3:31 PM, Andrew Oberlin <[hidden email]> wrote:
> Hello all,
>
> When I go to use the gmod_bulk_uploader.pl script it get the following
> error.
>
> Can't locate Bio/GMOD/DB/Adapter.pm in @INC (@INC contains:
> /home/scott/cvs_stuff/schema/chado/lib /home/cain/cvs_stuff/schema/chado/lib
> /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1
> /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
> /usr/local/lib/site_perl .) at /usr/local/bin/gmod_gff3_preprocessor.pl line
> 12. BEGIN failed--compilation aborted at
> /usr/local/bin/gmod_gff3_preprocessor.pl line 12.
>
> However, I believe I am using the correct version of Perl that was used to
> install it although I really do not know how to check as I don't use Perl
> very often. I also did a locate on Adapter.pm, but I didn't find it on the
> machine.
>
> Thanks,
>
> Andrew Oberlin
>
> --
> Andrew Oberlin
> Miami University 2013
> Computer Science & Mathematics
> [hidden email]  <a href="tel:%28330%29%20998-1603" value="+13309981603" target="_blank">(330) 998-1603
>
> ------------------------------------------------------------------------------
> Virtualization & Cloud Management Using Capacity Planning
> Cloud computing makes use of virtualization - but cloud computing
> also focuses on allowing computing to be delivered as a service.
> http://www.accelacomm.com/jaw/sfnl/114/51521223/
> _______________________________________________
> 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



--
Andrew Oberlin
Miami University 2013
Computer Science & Mathematics
[hidden email]  (330) 998-1603




--
Andrew Oberlin
Miami University 2013
Computer Science & Mathematics
[hidden email]  (330) 998-1603


------------------------------------------------------------------------------
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Re: Problem with the bulk uploader

Scott Cain
Hi Andrew,

At the top of your GFF file should be a line that looks something like this:

NC_014751  .   chromosome   1   123456   .   .   .
ID=NC_014751;Name=NC_014751...

Given that you've already successfully loaded data into Chado, I was
assuming you'd have this already.  That's what I was referring to.

Scott


On Mon, Feb 27, 2012 at 3:22 PM, Andrew Oberlin <[hidden email]> wrote:

> I actually feel like it is the first one. But I'm not seeing how I am not
> adding this to the database. I typically load a new organism every time I
> use the bulk uploader. is there a specific way to load the accession as well
> that I am missing?
>
> Andrew Oberlin
>
>
> On Fri, Feb 24, 2012 at 1:18 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Andrew,
>>
>> This is usually a result of a few things:
>>
>> 1. You didn't load NC_014751 into the database first.  This is not usually
>> the problem, as it is fairly obvious given the error message.
>>
>> 2. The load cache in the database got corrupted, but this isn't very
>> common any more either, since the loader is a little smarter about cleaning
>> up the cache when bad things happen.  You can try running the loader with
>> --recreate_cache just to double check.  If you have a very large database,
>> this will add a fairly significant startup time to the loading script.
>>
>> 3. This is probably the most likely: the loader didn't like the gff line
>> that defined the NC_014751 feature. The easiest thing to check is that that
>> line has both Name and ID set to NC_014751.  (the loader doesn't absolutely
>> require that, but things can get wonky if that's not the case.)
>>
>> Scott
>>
>>
>> Sent from my iPad
>>
>> On Feb 22, 2012, at 3:38 PM, Andrew Oberlin <[hidden email]> wrote:
>>
>> I got that working thanks. However when I go to insert a genome into the
>> database using the bulk_uploader I keep getting a message that looks like
>> this:
>>
>> Preparing data for inserting into the chado database (This may take a
>> while ...) Unable to find srcfeature NC_014751 in the database. Perhaps you
>> need to rerun your data load with the '--recreate_cache' option. at
>> /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 4555
>> Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x3775298)',
>> 'Bio::SeqFeature::Annotated=HASH(0x3af2018)') called at
>> /usr/local/bin/gmod_bulk_load_gff3.pl line 841 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...
>>
>> Any ideas as to why this error would occur?
>>
>>
>> Thanks,
>>
>> Andrew Oberlin
>>
>> On Fri, Feb 17, 2012 at 4:12 PM, Scott Cain <[hidden email]> wrote:
>>>
>>> Hi Andrew,
>>>
>>> So you did "locate Adapter.pm" and it came up empty?  I assume your
>>> locate database is up to date (via "(sudo) updatedb")?  If that's the
>>> case, then I'm guessing you don't have it installed, which is weird
>>> since you seem to have gmod_gff3_preprocessor.pl.  I suppose you could
>>> reinstall from a tarball.
>>>
>>> Scott
>>>
>>>
>>> On Fri, Feb 17, 2012 at 3:31 PM, Andrew Oberlin <[hidden email]>
>>> wrote:
>>> > Hello all,
>>> >
>>> > When I go to use the gmod_bulk_uploader.pl script it get the following
>>> > error.
>>> >
>>> > Can't locate Bio/GMOD/DB/Adapter.pm in @INC (@INC contains:
>>> > /home/scott/cvs_stuff/schema/chado/lib
>>> > /home/cain/cvs_stuff/schema/chado/lib
>>> > /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1
>>> > /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
>>> > /usr/local/lib/site_perl .) at /usr/local/bin/gmod_gff3_preprocessor.pl
>>> > line
>>> > 12. BEGIN failed--compilation aborted at
>>> > /usr/local/bin/gmod_gff3_preprocessor.pl line 12.
>>> >
>>> > However, I believe I am using the correct version of Perl that was used
>>> > to
>>> > install it although I really do not know how to check as I don't use
>>> > Perl
>>> > very often. I also did a locate on Adapter.pm, but I didn't find it on
>>> > the
>>> > machine.
>>> >
>>> > Thanks,
>>> >
>>> > Andrew Oberlin
>>> >
>>> > --
>>> > Andrew Oberlin
>>> > Miami University 2013
>>> > Computer Science & Mathematics
>>> > [hidden email]  (330) 998-1603
>>> >
>>> >
>>> > ------------------------------------------------------------------------------
>>> > Virtualization & Cloud Management Using Capacity Planning
>>> > Cloud computing makes use of virtualization - but cloud computing
>>> > also focuses on allowing computing to be delivered as a service.
>>> > http://www.accelacomm.com/jaw/sfnl/114/51521223/
>>> > _______________________________________________
>>> > 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
>>
>>
>>
>>
>> --
>> Andrew Oberlin
>> Miami University 2013
>> Computer Science & Mathematics
>> [hidden email]  (330) 998-1603
>
>
>
>
> --
> Andrew Oberlin
> Miami University 2013
> Computer Science & Mathematics
> [hidden email]  (330) 998-1603



--
------------------------------------------------------------------------
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: Problem with the bulk uploader

Andrew Oberlin
Any ideas about why this is happening?

Thanks,

Andrew Oberlin

On Mon, Feb 27, 2012 at 4:02 PM, Andrew Oberlin <[hidden email]> wrote:
Ok thanks. The file that is not .sorted is the unprocessed gff. The other one is what I am getting after using the preprocessor.

Andrew Oberlin


On Mon, Feb 27, 2012 at 3:57 PM, Scott Cain <[hidden email]> wrote:
Sure looks like a bug.  Can you send me the unprocessed gff file so I can try?

Thanks,
Scott


On Mon, Feb 27, 2012 at 3:55 PM, Andrew Oberlin <[hidden email]> wrote:
> Here's the first line of my gff file after I pass it through the
> preprocessor.
>
> NC_014751       GenBank binding_site    841442  841534  .       -
> 1      ID=GenBank:binding_site:NC_014751:841442:841534
>
> However, it looks more like what you are describing before the preprocessor.
> Here that is:
>
> NC_014751       GenBank region  1       1008951 .       +       1
> ID=NC_014751;Dbxref=Project:60849,taxon:880447;Name=NC_014751;Note=Mycoplasma
> leachii PG50 chromosome%2C complete genome.
>
> So, could this be a problem with the preprocessor?
>
> Andrew Oberlin
>
>
> On Mon, Feb 27, 2012 at 3:34 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Andrew,
>>
>> At the top of your GFF file should be a line that looks something like
>> this:
>>
>> NC_014751  .   chromosome   1   123456   .   .   .
>> ID=NC_014751;Name=NC_014751...
>>
>> Given that you've already successfully loaded data into Chado, I was
>> assuming you'd have this already.  That's what I was referring to.
>>
>> Scott
>>
>>
>> On Mon, Feb 27, 2012 at 3:22 PM, Andrew Oberlin <[hidden email]>
>> wrote:
>> > I actually feel like it is the first one. But I'm not seeing how I am
>> > not
>> > adding this to the database. I typically load a new organism every time
>> > I
>> > use the bulk uploader. is there a specific way to load the accession as
>> > well
>> > that I am missing?
>> >
>> > Andrew Oberlin
>> >
>> >
>> > On Fri, Feb 24, 2012 at 1:18 PM, Scott Cain <[hidden email]> wrote:
>> >>
>> >> Hi Andrew,
>> >>
>> >> This is usually a result of a few things:
>> >>
>> >> 1. You didn't load NC_014751 into the database first.  This is not
>> >> usually
>> >> the problem, as it is fairly obvious given the error message.
>> >>
>> >> 2. The load cache in the database got corrupted, but this isn't very
>> >> common any more either, since the loader is a little smarter about
>> >> cleaning
>> >> up the cache when bad things happen.  You can try running the loader
>> >> with
>> >> --recreate_cache just to double check.  If you have a very large
>> >> database,
>> >> this will add a fairly significant startup time to the loading script.
>> >>
>> >> 3. This is probably the most likely: the loader didn't like the gff
>> >> line
>> >> that defined the NC_014751 feature. The easiest thing to check is that
>> >> that
>> >> line has both Name and ID set to NC_014751.  (the loader doesn't
>> >> absolutely
>> >> require that, but things can get wonky if that's not the case.)
>> >>
>> >> Scott
>> >>
>> >>
>> >> Sent from my iPad
>> >>
>> >> On Feb 22, 2012, at 3:38 PM, Andrew Oberlin <[hidden email]>
>> >> wrote:
>> >>
>> >> I got that working thanks. However when I go to insert a genome into
>> >> the
>> >> database using the bulk_uploader I keep getting a message that looks
>> >> like
>> >> this:
>> >>
>> >> Preparing data for inserting into the chado database (This may take a
>> >> while ...) Unable to find srcfeature NC_014751 in the database. Perhaps
>> >> you
>> >> need to rerun your data load with the '--recreate_cache' option. at
>> >> /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 4555
>> >>
>> >> Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x3775298)',
>> >> 'Bio::SeqFeature::Annotated=HASH(0x3af2018)') called at
>> >> /usr/local/bin/gmod_bulk_load_gff3.pl line 841 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...
>> >>
>> >> Any ideas as to why this error would occur?
>> >>
>> >>
>> >> Thanks,
>> >>
>> >> Andrew Oberlin
>> >>
>> >> On Fri, Feb 17, 2012 at 4:12 PM, Scott Cain <[hidden email]>
>> >> wrote:
>> >>>
>> >>> Hi Andrew,
>> >>>
>> >>> So you did "locate Adapter.pm" and it came up empty?  I assume your
>> >>> locate database is up to date (via "(sudo) updatedb")?  If that's the
>> >>> case, then I'm guessing you don't have it installed, which is weird
>> >>> since you seem to have gmod_gff3_preprocessor.pl.  I suppose you could
>> >>> reinstall from a tarball.
>> >>>
>> >>> Scott
>> >>>
>> >>>
>> >>> On Fri, Feb 17, 2012 at 3:31 PM, Andrew Oberlin
>> >>> <[hidden email]>
>> >>> wrote:
>> >>> > Hello all,
>> >>> >
>> >>> > When I go to use the gmod_bulk_uploader.pl script it get the
>> >>> > following
>> >>> > error.
>> >>> >
>> >>> > Can't locate Bio/GMOD/DB/Adapter.pm in @INC (@INC contains:
>> >>> > /home/scott/cvs_stuff/schema/chado/lib
>> >>> > /home/cain/cvs_stuff/schema/chado/lib
>> >>> > /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1
>> >>> > /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10
>> >>> > /usr/share/perl/5.10
>> >>> > /usr/local/lib/site_perl .) at
>> >>> > /usr/local/bin/gmod_gff3_preprocessor.pl
>> >>> > line
>> >>> > 12. BEGIN failed--compilation aborted at
>> >>> > /usr/local/bin/gmod_gff3_preprocessor.pl line 12.
>> >>> >
>> >>> > However, I believe I am using the correct version of Perl that was
>> >>> > used
>> >>> > to
>> >>> > install it although I really do not know how to check as I don't use
>> >>> > Perl
>> >>> > very often. I also did a locate on Adapter.pm, but I didn't find it
>> >>> > on
>> >>> > the
>> >>> > machine.
>> >>> >
>> >>> > Thanks,
>> >>> >
>> >>> > Andrew Oberlin
>> >>> >
>> >>> > --
>> >>> > Andrew Oberlin
>> >>> > Miami University 2013
>> >>> > Computer Science & Mathematics
>> >>> > [hidden email]  <a href="tel:%28330%29%20998-1603" value="+13309981603" target="_blank">(330) 998-1603
>> >>> >
>> >>> >
>> >>> >
>> >>> > ------------------------------------------------------------------------------
>> >>> > Virtualization & Cloud Management Using Capacity Planning
>> >>> > Cloud computing makes use of virtualization - but cloud computing
>> >>> > also focuses on allowing computing to be delivered as a service.
>> >>> > http://www.accelacomm.com/jaw/sfnl/114/51521223/
>> >>> > _______________________________________________
>> >>> > 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
>> >>
>> >>
>> >>
>> >>
>> >> --
>> >> Andrew Oberlin
>> >> Miami University 2013
>> >> Computer Science & Mathematics
>> >> [hidden email]  <a href="tel:%28330%29%20998-1603" value="+13309981603" target="_blank">(330) 998-1603
>> >
>> >
>> >
>> >
>> > --
>> > Andrew Oberlin
>> > Miami University 2013
>> > Computer Science & Mathematics
>> > [hidden email]  <a href="tel:%28330%29%20998-1603" value="+13309981603" target="_blank">(330) 998-1603
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> 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
>
>
>
>
> --
> Andrew Oberlin
> Miami University 2013
> Computer Science & Mathematics
> [hidden email]  <a href="tel:%28330%29%20998-1603" value="+13309981603" target="_blank">(330) 998-1603



--
------------------------------------------------------------------------
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



--
Andrew Oberlin
Miami University 2013
Computer Science & Mathematics
[hidden email]  (330) 998-1603




--
Andrew Oberlin
Miami University 2013
Computer Science & Mathematics
[hidden email]  (330) 998-1603


------------------------------------------------------------------------------
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Re: Problem with the bulk uploader

Scott Cain
Hi Andrew,

I am reasonably sure that the genbank2gff3.pl script always produces
sorted GFF, so no, the step is probably not necessary.  I generally
advise people to not preprocess unless they know they need it, because
it can be a fairly time consuming thing to do (though probably not
with mycobacteria genomes, it's probably not an issue).  It's a bit of
a catch-22, though, because usually the way you figure out that you
need it is by trying to load the database and having it fail, which
can also be a time consuming process.

About the failure, I figured out the problem.  Here's the nut of it:

DBD::Pg::st execute failed: ERROR:  value too long for type character
varying(4000) at /Library/Perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 4722,
<IN> line 7.

That's the error I got when I tried to sort the GFF file you sent me.
When I wrote the sorter, I figured "who's ever going to have a GFF
line that is longer than 4000 characters?"  Well, now I know.  So what
happened was the insert into the database for that line of GFF failed,
at which point the sorter should have died (it will with the next
release, as I am going to make that fix now, as well as lengthening
that varchar field), but it didn't, and you were short one very
important GFF line in the resulting sorted GFF file.

Sorry it took me so long to help you with this.

Scott


On Mon, Mar 12, 2012 at 3:00 PM, Andrew Oberlin <[hidden email]> wrote:

> Something else I discovered about my install is that if I use the gmod
> uploader without preprocessing, it seems to wrok perfectly. Should I skip
> this step?
>
> Is it really necessary?
>
> Andrew Oberlin
>
>
> On Mon, Mar 12, 2012 at 2:26 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Andrew,
>>
>> I was on vacation last week and am getting out from under a pile of email,
>> but you are first in the queue to get "real" attention.  I should get back
>> to you tomorrow.
>>
>> Scott
>>
>> Sent from my iPad
>>
>> On Mar 12, 2012, at 2:22 PM, Andrew Oberlin <[hidden email]> wrote:
>>
>> Any ideas about why this is happening?
>>
>> Thanks,
>>
>> Andrew Oberlin
>>
>> On Mon, Feb 27, 2012 at 4:02 PM, Andrew Oberlin <[hidden email]>
>> wrote:
>>>
>>> Ok thanks. The file that is not .sorted is the unprocessed gff. The other
>>> one is what I am getting after using the preprocessor.
>>>
>>> Andrew Oberlin
>>>
>>>
>>> On Mon, Feb 27, 2012 at 3:57 PM, Scott Cain <[hidden email]> wrote:
>>>>
>>>> Sure looks like a bug.  Can you send me the unprocessed gff file so I
>>>> can try?
>>>>
>>>> Thanks,
>>>> Scott
>>>>
>>>>
>>>> On Mon, Feb 27, 2012 at 3:55 PM, Andrew Oberlin <[hidden email]>
>>>> wrote:
>>>> > Here's the first line of my gff file after I pass it through the
>>>> > preprocessor.
>>>> >
>>>> > NC_014751       GenBank binding_site    841442  841534  .       -
>>>> > 1      ID=GenBank:binding_site:NC_014751:841442:841534
>>>> >
>>>> > However, it looks more like what you are describing before the
>>>> > preprocessor.
>>>> > Here that is:
>>>> >
>>>> > NC_014751       GenBank region  1       1008951 .       +       1
>>>> >
>>>> > ID=NC_014751;Dbxref=Project:60849,taxon:880447;Name=NC_014751;Note=Mycoplasma
>>>> > leachii PG50 chromosome%2C complete genome.
>>>> >
>>>> > So, could this be a problem with the preprocessor?
>>>> >
>>>> > Andrew Oberlin
>>>> >
>>>> >
>>>> > On Mon, Feb 27, 2012 at 3:34 PM, Scott Cain <[hidden email]>
>>>> > wrote:
>>>> >>
>>>> >> Hi Andrew,
>>>> >>
>>>> >> At the top of your GFF file should be a line that looks something
>>>> >> like
>>>> >> this:
>>>> >>
>>>> >> NC_014751  .   chromosome   1   123456   .   .   .
>>>> >> ID=NC_014751;Name=NC_014751...
>>>> >>
>>>> >> Given that you've already successfully loaded data into Chado, I was
>>>> >> assuming you'd have this already.  That's what I was referring to.
>>>> >>
>>>> >> Scott
>>>> >>
>>>> >>
>>>> >> On Mon, Feb 27, 2012 at 3:22 PM, Andrew Oberlin
>>>> >> <[hidden email]>
>>>> >> wrote:
>>>> >> > I actually feel like it is the first one. But I'm not seeing how I
>>>> >> > am
>>>> >> > not
>>>> >> > adding this to the database. I typically load a new organism every
>>>> >> > time
>>>> >> > I
>>>> >> > use the bulk uploader. is there a specific way to load the
>>>> >> > accession as
>>>> >> > well
>>>> >> > that I am missing?
>>>> >> >
>>>> >> > Andrew Oberlin
>>>> >> >
>>>> >> >
>>>> >> > On Fri, Feb 24, 2012 at 1:18 PM, Scott Cain <[hidden email]>
>>>> >> > wrote:
>>>> >> >>
>>>> >> >> Hi Andrew,
>>>> >> >>
>>>> >> >> This is usually a result of a few things:
>>>> >> >>
>>>> >> >> 1. You didn't load NC_014751 into the database first.  This is not
>>>> >> >> usually
>>>> >> >> the problem, as it is fairly obvious given the error message.
>>>> >> >>
>>>> >> >> 2. The load cache in the database got corrupted, but this isn't
>>>> >> >> very
>>>> >> >> common any more either, since the loader is a little smarter about
>>>> >> >> cleaning
>>>> >> >> up the cache when bad things happen.  You can try running the
>>>> >> >> loader
>>>> >> >> with
>>>> >> >> --recreate_cache just to double check.  If you have a very large
>>>> >> >> database,
>>>> >> >> this will add a fairly significant startup time to the loading
>>>> >> >> script.
>>>> >> >>
>>>> >> >> 3. This is probably the most likely: the loader didn't like the
>>>> >> >> gff
>>>> >> >> line
>>>> >> >> that defined the NC_014751 feature. The easiest thing to check is
>>>> >> >> that
>>>> >> >> that
>>>> >> >> line has both Name and ID set to NC_014751.  (the loader doesn't
>>>> >> >> absolutely
>>>> >> >> require that, but things can get wonky if that's not the case.)
>>>> >> >>
>>>> >> >> Scott
>>>> >> >>
>>>> >> >>
>>>> >> >> Sent from my iPad
>>>> >> >>
>>>> >> >> On Feb 22, 2012, at 3:38 PM, Andrew Oberlin
>>>> >> >> <[hidden email]>
>>>> >> >> wrote:
>>>> >> >>
>>>> >> >> I got that working thanks. However when I go to insert a genome
>>>> >> >> into
>>>> >> >> the
>>>> >> >> database using the bulk_uploader I keep getting a message that
>>>> >> >> looks
>>>> >> >> like
>>>> >> >> this:
>>>> >> >>
>>>> >> >> Preparing data for inserting into the chado database (This may
>>>> >> >> take a
>>>> >> >> while ...) Unable to find srcfeature NC_014751 in the database.
>>>> >> >> Perhaps
>>>> >> >> you
>>>> >> >> need to rerun your data load with the '--recreate_cache' option.
>>>> >> >> at
>>>> >> >> /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 4555
>>>> >> >>
>>>> >> >>
>>>> >> >> Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x3775298)',
>>>> >> >> 'Bio::SeqFeature::Annotated=HASH(0x3af2018)') called at
>>>> >> >> /usr/local/bin/gmod_bulk_load_gff3.pl line 841 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...
>>>> >> >>
>>>> >> >> Any ideas as to why this error would occur?
>>>> >> >>
>>>> >> >>
>>>> >> >> Thanks,
>>>> >> >>
>>>> >> >> Andrew Oberlin
>>>> >> >>
>>>> >> >> On Fri, Feb 17, 2012 at 4:12 PM, Scott Cain <[hidden email]>
>>>> >> >> wrote:
>>>> >> >>>
>>>> >> >>> Hi Andrew,
>>>> >> >>>
>>>> >> >>> So you did "locate Adapter.pm" and it came up empty?  I assume
>>>> >> >>> your
>>>> >> >>> locate database is up to date (via "(sudo) updatedb")?  If that's
>>>> >> >>> the
>>>> >> >>> case, then I'm guessing you don't have it installed, which is
>>>> >> >>> weird
>>>> >> >>> since you seem to have gmod_gff3_preprocessor.pl.  I suppose you
>>>> >> >>> could
>>>> >> >>> reinstall from a tarball.
>>>> >> >>>
>>>> >> >>> Scott
>>>> >> >>>
>>>> >> >>>
>>>> >> >>> On Fri, Feb 17, 2012 at 3:31 PM, Andrew Oberlin
>>>> >> >>> <[hidden email]>
>>>> >> >>> wrote:
>>>> >> >>> > Hello all,
>>>> >> >>> >
>>>> >> >>> > When I go to use the gmod_bulk_uploader.pl script it get the
>>>> >> >>> > following
>>>> >> >>> > error.
>>>> >> >>> >
>>>> >> >>> > Can't locate Bio/GMOD/DB/Adapter.pm in @INC (@INC contains:
>>>> >> >>> > /home/scott/cvs_stuff/schema/chado/lib
>>>> >> >>> > /home/cain/cvs_stuff/schema/chado/lib
>>>> >> >>> > /etc/perl /usr/local/lib/perl/5.10.1
>>>> >> >>> > /usr/local/share/perl/5.10.1
>>>> >> >>> > /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10
>>>> >> >>> > /usr/share/perl/5.10
>>>> >> >>> > /usr/local/lib/site_perl .) at
>>>> >> >>> > /usr/local/bin/gmod_gff3_preprocessor.pl
>>>> >> >>> > line
>>>> >> >>> > 12. BEGIN failed--compilation aborted at
>>>> >> >>> > /usr/local/bin/gmod_gff3_preprocessor.pl line 12.
>>>> >> >>> >
>>>> >> >>> > However, I believe I am using the correct version of Perl that
>>>> >> >>> > was
>>>> >> >>> > used
>>>> >> >>> > to
>>>> >> >>> > install it although I really do not know how to check as I
>>>> >> >>> > don't use
>>>> >> >>> > Perl
>>>> >> >>> > very often. I also did a locate on Adapter.pm, but I didn't
>>>> >> >>> > find it
>>>> >> >>> > on
>>>> >> >>> > the
>>>> >> >>> > machine.
>>>> >> >>> >
>>>> >> >>> > Thanks,
>>>> >> >>> >
>>>> >> >>> > Andrew Oberlin
>>>> >> >>> >
>>>> >> >>> > --
>>>> >> >>> > Andrew Oberlin
>>>> >> >>> > Miami University 2013
>>>> >> >>> > Computer Science & Mathematics
>>>> >> >>> > [hidden email]  (330) 998-1603
>>>> >> >>> >
>>>> >> >>> >
>>>> >> >>> >
>>>> >> >>> >
>>>> >> >>> > ------------------------------------------------------------------------------
>>>> >> >>> > Virtualization & Cloud Management Using Capacity Planning
>>>> >> >>> > Cloud computing makes use of virtualization - but cloud
>>>> >> >>> > computing
>>>> >> >>> > also focuses on allowing computing to be delivered as a
>>>> >> >>> > service.
>>>> >> >>> > http://www.accelacomm.com/jaw/sfnl/114/51521223/
>>>> >> >>> > _______________________________________________
>>>> >> >>> > 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
>>>> >> >>
>>>> >> >>
>>>> >> >>
>>>> >> >>
>>>> >> >> --
>>>> >> >> Andrew Oberlin
>>>> >> >> Miami University 2013
>>>> >> >> Computer Science & Mathematics
>>>> >> >> [hidden email]  (330) 998-1603
>>>> >> >
>>>> >> >
>>>> >> >
>>>> >> >
>>>> >> > --
>>>> >> > Andrew Oberlin
>>>> >> > Miami University 2013
>>>> >> > Computer Science & Mathematics
>>>> >> > [hidden email]  (330) 998-1603
>>>> >>
>>>> >>
>>>> >>
>>>> >> --
>>>> >>
>>>> >> ------------------------------------------------------------------------
>>>> >> Scott Cain, Ph. D.                                   scott at
>>>> >> scottcain
>>>> >> dot net
>>>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> >> Ontario Institute for Cancer Research
>>>> >
>>>> >
>>>> >
>>>> >
>>>> > --
>>>> > Andrew Oberlin
>>>> > Miami University 2013
>>>> > Computer Science & Mathematics
>>>> > [hidden email]  (330) 998-1603
>>>>
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain
>>>> dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>
>>>
>>>
>>>
>>> --
>>> Andrew Oberlin
>>> Miami University 2013
>>> Computer Science & Mathematics
>>> [hidden email]  (330) 998-1603
>>
>>
>>
>>
>> --
>> Andrew Oberlin
>> Miami University 2013
>> Computer Science & Mathematics
>> [hidden email]  (330) 998-1603
>
>
>
>
> --
> Andrew Oberlin
> Miami University 2013
> Computer Science & Mathematics
> [hidden email]  (330) 998-1603



--
------------------------------------------------------------------------
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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