Chado installed External/Internal to Drupal?

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Chado installed External/Internal to Drupal?

Lacey-Anne Sanderson-3
Hi Everyone,
I’m just wondering how many of you have chado installed internally, within the same database as Drupal (this is how it’s installed via Tripal) or externally, in it’s own database?

I’ve been working on improving the views for Tripal 2.x (Drupal 7 compatible) and am wondering how important it is to make them compatible with an external chado. Currently it’s looking like they may not be for the alpha release of Tripal 2.x but if enough of you have this type of setup, I will devote extra time into making the administrative views just as useful for your setup…

So reply to this email with your tripal site name (or project if your still experimenting with Tripal) and either
        internal (chado installed within the chado schema of your drupal db; default for chado installed via Tripal) or
        external (chado installed in it’s own db; need to specify your chado in the settings.php file).

Thanks in advance for your feedback!
~Lacey


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Re: Chado installed External/Internal to Drupal?

Alex Rice
- Legume Information System (experimental)
- internal chado schema

re: the views, are there any plans to support PostgreSQL 9.3
materialized views?

On 2/10/14, 9:56 AM, Lacey-Anne Sanderson wrote:

> Hi Everyone,
> I’m just wondering how many of you have chado installed internally, within the same database as Drupal (this is how it’s installed via Tripal) or externally, in it’s own database?
>
> I’ve been working on improving the views for Tripal 2.x (Drupal 7 compatible) and am wondering how important it is to make them compatible with an external chado. Currently it’s looking like they may not be for the alpha release of Tripal 2.x but if enough of you have this type of setup, I will devote extra time into making the administrative views just as useful for your setup…
>
> So reply to this email with your tripal site name (or project if your still experimenting with Tripal) and either
> internal (chado installed within the chado schema of your drupal db; default for chado installed via Tripal) or
> external (chado installed in it’s own db; need to specify your chado in the settings.php file).
>
> Thanks in advance for your feedback!
> ~Lacey
>
>
> ------------------------------------------------------------------------------
> Android™ apps run on BlackBerry®10
> Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
> Now with support for Jelly Bean, Bluetooth, Mapview and more.
> Get your Android app in front of a whole new audience.  Start now.
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> [hidden email]
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>


--
Alex Rice <[hidden email]>
Software Engineer
National Center for Genome Resources (NCGR)
http://ncgr.org
(505)995-4457

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Re: Chado installed External/Internal to Drupal?

Lacey-Anne Sanderson-3
In reply to this post by Lacey-Anne Sanderson-3
Hi Gerard,

If you want to set up your chado externally then you need to add an extra database to your settings configuration. That’s really the only extra Tripal/Chado setup.

The recommendation towards an internal chado is made more for views functionality than performance. Since you cannot make joins between and external chado and Drupal much of the administration functionality in Tripal is reduced. Furthermore, many of the search views will have reduced functionality. Lost functionality of note includes the inability to link search results to their node/page, cannot add edit/delete/view links to administration views.

Much of this can be overcome with custom views handlers that select the data separately and join it in the application layer (in the handler) but this requires a lot of specialized programming on my part and would obviously have performance implications on your part.

This informal survey is to try to get an idea of how needed these specialized handlers are…

Furthermore, since both me & Stephen’s Tripal sites have internal chado installations, there is very limited testing of chado externally so you might find a small loss in stability. That said, if you do, just point out any errors/bugs on this mailing list and we will do our best to fix them!

Hope that helps explain the disadvantages a little better,
~Lacey

On Feb 10, 2014, at 11:55 AM, Gerard Lazo <[hidden email]> wrote:

GrainGenes Project
installed internally

However, an external version is now preferred since we will be also
running another database off of chado. Perhaps you might address the
speed hits and other possible extra Drupal/Tripal steps to accommodate
this sort of set-up. If it is too much trouble we may just maintain
two separate chado databases.

On Mon, Feb 10, 2014 at 8:56 AM, Lacey-Anne Sanderson
<[hidden email]> wrote:
Hi Everyone,
I'm just wondering how many of you have chado installed internally, within the same database as Drupal (this is how it's installed via Tripal) or externally, in it's own database?

I've been working on improving the views for Tripal 2.x (Drupal 7 compatible) and am wondering how important it is to make them compatible with an external chado. Currently it's looking like they may not be for the alpha release of Tripal 2.x but if enough of you have this type of setup, I will devote extra time into making the administrative views just as useful for your setup...

So reply to this email with your tripal site name (or project if your still experimenting with Tripal) and either
       internal (chado installed within the chado schema of your drupal db; default for chado installed via Tripal) or
       external (chado installed in it's own db; need to specify your chado in the settings.php file).

Thanks in advance for your feedback!
~Lacey


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-- 
Gerard R. Lazo
PO Box 6335, Albany, CA 94706 USA

Cell:510-734-5190


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Re: Chado installed External/Internal to Drupal?

Lacey-Anne Sanderson-3
In reply to this post by Lacey-Anne Sanderson-3
Hi Gerard,

I also want to point out that having chado installed internally should not interfere with it’s ability to work with other GMOD tools. 

In order to get an internal chado to work with other tools you need to create a postgres user and set the search path to ‘chado’. This ensures that whenever that user connects to your drupal database and submits a generic “SELECT * FROM feature” request (or any other sql statement that doesn’t hardcode the schema) they will get the same result as if chado were alone  in the public schema. This is because you have made the chado schema the default for that user where normally the public schema is the default when searching for tables to act on. The following are commands for how you would accomplish this for a postgres user with the name gmoduser.

psql [yourdrupaldb]
CREATE USER gmoduser WITH PASSWORD 'myPassword’;
GRANT ALL PRIVILEGES ON ALL TABLES IN SCHEMA chado TO gmoduser;
ALTER USER gmoduser SET search_path TO chado;

Then when configuring the other tools, provide that user to access your chado database. As long as the other tool has not hard-coded any ‘public’ schema requests (which shouldn’t have been necessary) then it should work error free with your internal chado.

I suggest trying this method first before giving up and creating an external chado. If you run into any errors with this approach, please email us with any details including the name of the gmod tool you were trying to use. We are trying to work with the other tool developers to remove any of these public schema assumptions and would love to hear your feedback!

~Lacey

On Feb 10, 2014, at 11:55 AM, Gerard Lazo <[hidden email]> wrote:

GrainGenes Project
installed internally

However, an external version is now preferred since we will be also
running another database off of chado. Perhaps you might address the
speed hits and other possible extra Drupal/Tripal steps to accommodate
this sort of set-up. If it is too much trouble we may just maintain
two separate chado databases.

On Mon, Feb 10, 2014 at 8:56 AM, Lacey-Anne Sanderson
<[hidden email]> wrote:
Hi Everyone,
I'm just wondering how many of you have chado installed internally, within the same database as Drupal (this is how it's installed via Tripal) or externally, in it's own database?

I've been working on improving the views for Tripal 2.x (Drupal 7 compatible) and am wondering how important it is to make them compatible with an external chado. Currently it's looking like they may not be for the alpha release of Tripal 2.x but if enough of you have this type of setup, I will devote extra time into making the administrative views just as useful for your setup...

So reply to this email with your tripal site name (or project if your still experimenting with Tripal) and either
       internal (chado installed within the chado schema of your drupal db; default for chado installed via Tripal) or
       external (chado installed in it's own db; need to specify your chado in the settings.php file).

Thanks in advance for your feedback!
~Lacey


------------------------------------------------------------------------------
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Get your Android app in front of a whole new audience.  Start now.
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-- 
Gerard R. Lazo
PO Box 6335, Albany, CA 94706 USA

Cell:510-734-5190


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Re: Chado installed External/Internal to Drupal?

Cannon, Ethalinda K [COM S]
In reply to this post by Lacey-Anne Sanderson-3
Hi Lacey,

For both PeanutBase and LegumeInfo, chado is installed internally.

Ethy

________________________________________
From: Lacey-Anne Sanderson [[hidden email]]
Sent: Monday, February 10, 2014 10:56 AM
To: GMOD Tripal; gmod tripal devel
Subject: [Gmod-tripal] Chado installed External/Internal to Drupal?

Hi Everyone,
I’m just wondering how many of you have chado installed internally, within the same database as Drupal (this is how it’s installed via Tripal) or externally, in it’s own database?

I’ve been working on improving the views for Tripal 2.x (Drupal 7 compatible) and am wondering how important it is to make them compatible with an external chado. Currently it’s looking like they may not be for the alpha release of Tripal 2.x but if enough of you have this type of setup, I will devote extra time into making the administrative views just as useful for your setup…

So reply to this email with your tripal site name (or project if your still experimenting with Tripal) and either
        internal (chado installed within the chado schema of your drupal db; default for chado installed via Tripal) or
        external (chado installed in it’s own db; need to specify your chado in the settings.php file).

Thanks in advance for your feedback!
~Lacey


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Get your Android app in front of a whole new audience.  Start now.
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Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
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Re: Chado installed External/Internal to Drupal?

Stephen Ficklin-2
In reply to this post by Alex Rice
Hi Alex,

We haven't yet discussed supporting PostgreSQL native materialized views
but I don't think it would be difficult at all to do.  I'm not quite
sure of the benefits over the current implementation so we'd have to
explore a bit.  We'd welcome any additional comments you may have.

Stephen

On 2/10/2014 12:32 PM, Alex Rice wrote:

> - Legume Information System (experimental)
> - internal chado schema
>
> re: the views, are there any plans to support PostgreSQL 9.3
> materialized views?
>
> On 2/10/14, 9:56 AM, Lacey-Anne Sanderson wrote:
>> Hi Everyone,
>> I’m just wondering how many of you have chado installed internally, within the same database as Drupal (this is how it’s installed via Tripal) or externally, in it’s own database?
>>
>> I’ve been working on improving the views for Tripal 2.x (Drupal 7 compatible) and am wondering how important it is to make them compatible with an external chado. Currently it’s looking like they may not be for the alpha release of Tripal 2.x but if enough of you have this type of setup, I will devote extra time into making the administrative views just as useful for your setup…
>>
>> So reply to this email with your tripal site name (or project if your still experimenting with Tripal) and either
>> internal (chado installed within the chado schema of your drupal db; default for chado installed via Tripal) or
>> external (chado installed in it’s own db; need to specify your chado in the settings.php file).
>>
>> Thanks in advance for your feedback!
>> ~Lacey
>>
>>
>> ------------------------------------------------------------------------------
>> Android&trade; apps run on BlackBerry&reg;10
>> Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
>> Now with support for Jelly Bean, Bluetooth, Mapview and more.
>> Get your Android app in front of a whole new audience.  Start now.
>> http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Gmod-tripal mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>


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Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
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Re: Chado installed External/Internal to Drupal?

Hugo-pH
In reply to this post by Lacey-Anne Sanderson-3
Hi Lacey,

For the transgenic strawberry project (still under construction), chado
is installed internally.

Thanks,

Hugo

On 02/11/2014 09:54 AM, Antonio J Matas Arroyo wrote:

>
>
>
> -------- Original Message --------
> Subject: [Gmod-tripal] Chado installed External/Internal to Drupal?
> Date: Mon, 10 Feb 2014 10:56:44 -0600
> From: Lacey-Anne Sanderson <[hidden email]>
> To: GMOD Tripal <[hidden email]>, gmod tripal devel
> <[hidden email]>
>
> Hi Everyone,
> I’m just wondering how many of you have chado installed internally,
> within the same database as Drupal (this is how it’s installed via
> Tripal) or externally, in it’s own database?
>
> I’ve been working on improving the views for Tripal 2.x (Drupal 7
> compatible) and am wondering how important it is to make them
> compatible with an external chado. Currently it’s looking like they
> may not be for the alpha release of Tripal 2.x but if enough of you
> have this type of setup, I will devote extra time into making the
> administrative views just as useful for your setup…
>
> So reply to this email with your tripal site name (or project if your
> still experimenting with Tripal) and either
>     internal (chado installed within the chado schema of your drupal
> db; default for chado installed via Tripal) or
>     external (chado installed in it’s own db; need to specify your
> chado in the settings.php file).
>
> Thanks in advance for your feedback!
> ~Lacey
>
>
> ------------------------------------------------------------------------------
>
> Android&trade; apps run on BlackBerry&reg;10
> Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
> Now with support for Jelly Bean, Bluetooth, Mapview and more.
> Get your Android app in front of a whole new audience.  Start now.
> http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk
>
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>
>


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Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
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