Loading ontologies to a non-public schema

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Loading ontologies to a non-public schema

Scott Cain
Hi Karl,

Ugh, that's an old bug in software we don't control.  I believe I emailed the author about it years ago and he basically indicated he had no desire to fix it.

The available options are to use Tripal to load ontologies, as it's loader knows how to load a non-public schema, but I think it probably only loads into a schema called "chado" which is only slightly better and doesn't really help.

Another option that I haven't tried by I suspect will work is to edit DBIx::DBSchema::DBD::Pg directly. Towards the top of the file, there is this line:

sub default_db_schema { 'public'; }

Changing that to the name of the schema you want to load into might do the trick. Definitely ugly.

Scott



On Wed, Apr 30, 2014 at 2:35 PM, Karl O. Pinc <[hidden email]> wrote:
On 04/30/2014 12:32:19 PM, Seth Munholland wrote:
> Hi Everyone,
>
> I'm trying to setup a Chado DB for some local testing before
> implementing
> changes to the webserver, however, I'm running into an odd error.  I
> make
> the chado database and prepare it for gmod_bulk_load_gff3.pl but I
> get
> a
> warning as soon as I start:
>
> WARNING:
> Unable to find a 'part_of' term in the relationship ontology;
> It's absense indicates that there is something really wrong with the
> database.
> Consider stopping and checking the state of your cvterm table.
>
> Then it appears to continue loading the DB.  I tried Manually loading
> the
> ontologies and still got the warning.  I tried deleting the
> downloaded
> ontologies and reloading (automated and manual) and still got the
> warning.
> Next, I hit google and read one issue is that the plant onotology now
> has a
> 'part_of' term as well, and the advice there was to delete the PO
> entry,
> which I did, but still got the warning.  I then manually reloaded the
> RO,
> but I still got the warning.

Loading the ontologies into some schema other than public
you need to change line 37 of
/usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm
(!?)

It's broken.



Karl <[hidden email]>
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Re: Loading ontologies to a non-public schema

Karl O. Pinc
On 04/30/2014 01:48:01 PM, Scott Cain wrote:

> The available options are to use Tripal to load ontologies, as it's
> loader
> knows how to load a non-public schema, but I think it probably only
> loads
> into a schema called "chado" which is only slightly better and
> doesn't
> really help.
>
> Another option that I haven't tried by I suspect will work is to edit
> DBIx::DBSchema::DBD::Pg
> directly. Towards the top of the file, there is this line:
>
> sub default_db_schema { 'public'; }
>
> Changing that to the name of the schema you want to load into might
> do
> the
> trick. Definitely ugly.

Hi Scott,

Editing that line works and was how I loaded the ontologies
here.  (I thought I sent a note to the list at the time.)



Karl <[hidden email]>
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Re: Loading ontologies to a non-public schema

Stephen Ficklin-3
HI Karl,

I'm not sure of the exact problem as I seemed to have deleted the
earlier emails in the thread, but if you set the PostgreSQL search_path
variable for the user account to be the schema where Chado is housed
perhaps that might help.  The following SQL can do that:

ALTER USER [username] SET search_path TO [schema];

where [username] is the name of the user that you will use for
gmod_bulk_load_gff3.pl script and [schema] is the name of your schema
where the Chado database is housed.   Then run the script.

Stephen

On 4/30/2014 3:12 PM, Karl O. Pinc wrote:

> On 04/30/2014 01:48:01 PM, Scott Cain wrote:
>
>> The available options are to use Tripal to load ontologies, as it's
>> loader
>> knows how to load a non-public schema, but I think it probably only
>> loads
>> into a schema called "chado" which is only slightly better and
>> doesn't
>> really help.
>>
>> Another option that I haven't tried by I suspect will work is to edit
>> DBIx::DBSchema::DBD::Pg
>> directly. Towards the top of the file, there is this line:
>>
>> sub default_db_schema { 'public'; }
>>
>> Changing that to the name of the schema you want to load into might
>> do
>> the
>> trick. Definitely ugly.
> Hi Scott,
>
> Editing that line works and was how I loaded the ontologies
> here.  (I thought I sent a note to the list at the time.)
>
>
>
> Karl <[hidden email]>
> Free Software:  "You don't pay back, you pay forward."
>                   -- Robert A. Heinlein
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


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Re: Loading ontologies to a non-public schema

Stephen Ficklin-3
Oh, from your other email I now understand.  'public' is hard-coded.  So
my suggestion won't work....

On 4/30/2014 3:22 PM, Stephen Ficklin wrote:

> HI Karl,
>
> I'm not sure of the exact problem as I seemed to have deleted the
> earlier emails in the thread, but if you set the PostgreSQL
> search_path variable for the user account to be the schema where Chado
> is housed perhaps that might help.  The following SQL can do that:
>
> ALTER USER [username] SET search_path TO [schema];
>
> where [username] is the name of the user that you will use for
> gmod_bulk_load_gff3.pl script and [schema] is the name of your schema
> where the Chado database is housed.   Then run the script.
>
> Stephen
>
> On 4/30/2014 3:12 PM, Karl O. Pinc wrote:
>> On 04/30/2014 01:48:01 PM, Scott Cain wrote:
>>
>>> The available options are to use Tripal to load ontologies, as it's
>>> loader
>>> knows how to load a non-public schema, but I think it probably only
>>> loads
>>> into a schema called "chado" which is only slightly better and
>>> doesn't
>>> really help.
>>>
>>> Another option that I haven't tried by I suspect will work is to edit
>>> DBIx::DBSchema::DBD::Pg
>>> directly. Towards the top of the file, there is this line:
>>>
>>> sub default_db_schema { 'public'; }
>>>
>>> Changing that to the name of the schema you want to load into might
>>> do
>>> the
>>> trick. Definitely ugly.
>> Hi Scott,
>>
>> Editing that line works and was how I loaded the ontologies
>> here.  (I thought I sent a note to the list at the time.)
>>
>>
>>
>> Karl <[hidden email]>
>> Free Software:  "You don't pay back, you pay forward."
>>                   -- Robert A. Heinlein
>>
>> ------------------------------------------------------------------------------
>>
>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
>> unparalleled scalability from the best Selenium testing platform
>> available.
>> Simple to use. Nothing to install. Get started now for free."
>> http://p.sf.net/sfu/SauceLabs
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>


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