adding chado tables to my tripal

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adding chado tables to my tripal

Alex Rice
If a table of interest is not shown anywhere in the tripal UI, for
example: phylotree, then should I go ahead and create an entirely new
Tripal Module and new node type? Or is there some other manner of
extending tripal I have overlooked? It would get unwieldy to administer
tripal if the number of drupal modules starts to get into the dozens or
hundreds, right?

I have been reading the Tripal Developer handbook. Is there any
difference between "tripal module" and "tripal extension module", or are
you using those terms synonymously?

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

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Re: adding chado tables to my tripal

Stephen Ficklin-2
Hi Alex,

The Tripal modules that correspond to Chado modules
(http://gmod.org/wiki/Chado_Modules) and which come with Tripal are what
we would call Tripal Modules. For example, the Tripal Stock module
provides support for all of the tables in the Chado Stock module.  
Tripal modules are usually generic to be useful to the greatest number
of people.  A Tripal Extension module would be one that does not come
packaged with Tripal.  They must be downloaded and installed separately
(although we list them on the Tripal website to make them easier to
find). These are typically more specific. The Tripal Analysis Blast
module is an example of an extension module.  It does not provide the
basic support for any Chado module, but rather provides a data loader
and viewer for blast results.  Folks who don't like that blast module
could write their own using the Tripal API to display blast data however
they wanted.

The phylotree table belongs to the Phylogeny Chado module and so, the
Tripal Phylogeny module would provide support for all of the tables in
the Chado Phylogeny table.  But as you have noticed we do not yet have a
Phylogeny module for Tripal.   So, you can either wait for us to get
around to making one, or if you are inclined you can create one.  If you
would like to create a Phylogeny module you can do it in two ways:  1)  
You can coordinate with other Tripal developers on the gmod-tripal-devel
mailing list or 2) You can work on it on your own.   If you coordinate
with other developers you'll get some help developing it in such a way
that it could potentially get incorporated as a full Tripal module...
the Phylogeny module is needed.  It would have to be programmed
according to certain specifications and would need to be generic and
follow the coding standards and pass muster with other developers.  If
you go about it on your own you can still get a working module and it
might come out a bit faster for you, and in this case would be
classified as an extension module which can be made available for others
to plug into their Tripal installations if they like the way you've done it.

Hope that wasn't too long an answer,
Stephen


On 1/10/2014 4:17 PM, Alex Rice wrote:

> If a table of interest is not shown anywhere in the tripal UI, for
> example: phylotree, then should I go ahead and create an entirely new
> Tripal Module and new node type? Or is there some other manner of
> extending tripal I have overlooked? It would get unwieldy to administer
> tripal if the number of drupal modules starts to get into the dozens or
> hundreds, right?
>
> I have been reading the Tripal Developer handbook. Is there any
> difference between "tripal module" and "tripal extension module", or are
> you using those terms synonymously?
>


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Re: adding chado tables to my tripal

Stephen Ficklin-2
Hi Alex,

One other item.  If you are just working with a single table and you
have data in it, it is possible to display that data or search that data
without writing a module.  If you just need the phylotree table you can
use Drupal Views to create pages or search forms for that content
depending on how you want to display it. All of the Chado tables are
available in Drupal Views.   How are you hoping to interact with data in
the phylotree table?  Or was that just an example and you are interested
in working with all of the tables in the Phylogeny module?

Stephen

On 1/10/2014 4:51 PM, Stephen Ficklin wrote:

> Hi Alex,
>
> The Tripal modules that correspond to Chado modules
> (http://gmod.org/wiki/Chado_Modules) and which come with Tripal are
> what we would call Tripal Modules. For example, the Tripal Stock
> module provides support for all of the tables in the Chado Stock
> module.  Tripal modules are usually generic to be useful to the
> greatest number of people.  A Tripal Extension module would be one
> that does not come packaged with Tripal.  They must be downloaded and
> installed separately (although we list them on the Tripal website to
> make them easier to find). These are typically more specific. The
> Tripal Analysis Blast module is an example of an extension module.  It
> does not provide the basic support for any Chado module, but rather
> provides a data loader and viewer for blast results.  Folks who don't
> like that blast module could write their own using the Tripal API to
> display blast data however they wanted.
>
> The phylotree table belongs to the Phylogeny Chado module and so, the
> Tripal Phylogeny module would provide support for all of the tables in
> the Chado Phylogeny table.  But as you have noticed we do not yet have
> a Phylogeny module for Tripal.   So, you can either wait for us to get
> around to making one, or if you are inclined you can create one.  If
> you would like to create a Phylogeny module you can do it in two
> ways:  1)  You can coordinate with other Tripal developers on the
> gmod-tripal-devel mailing list or 2) You can work on it on your own.  
> If you coordinate with other developers you'll get some help
> developing it in such a way that it could potentially get incorporated
> as a full Tripal module... the Phylogeny module is needed.  It would
> have to be programmed according to certain specifications and would
> need to be generic and follow the coding standards and pass muster
> with other developers.  If you go about it on your own you can still
> get a working module and it might come out a bit faster for you, and
> in this case would be classified as an extension module which can be
> made available for others to plug into their Tripal installations if
> they like the way you've done it.
>
> Hope that wasn't too long an answer,
> Stephen
>
>
> On 1/10/2014 4:17 PM, Alex Rice wrote:
>> If a table of interest is not shown anywhere in the tripal UI, for
>> example: phylotree, then should I go ahead and create an entirely new
>> Tripal Module and new node type? Or is there some other manner of
>> extending tripal I have overlooked? It would get unwieldy to administer
>> tripal if the number of drupal modules starts to get into the dozens or
>> hundreds, right?
>>
>> I have been reading the Tripal Developer handbook. Is there any
>> difference between "tripal module" and "tripal extension module", or are
>> you using those terms synonymously?
>>
>


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Re: adding chado tables to my tripal

Alex Rice
Stephen, thanks for your replies- much appreciated. We are working on
some visualizations of phylogenetic trees, and also visualizations of
gene ontology relations across collections of features. These d3js
visualizations want to consume JSON. It appears the Drupal Views module
wont enable enough querying flexibility  to produce the json. So I think
I will go ahead with creating a custom tripal extension module- but it
wont be a general purpose phylogeny module.

On 1/10/14, 2:59 PM, Stephen Ficklin wrote:

> Hi Alex,
>
> One other item.  If you are just working with a single table and you
> have data in it, it is possible to display that data or search that data
> without writing a module.  If you just need the phylotree table you can
> use Drupal Views to create pages or search forms for that content
> depending on how you want to display it. All of the Chado tables are
> available in Drupal Views.   How are you hoping to interact with data in
> the phylotree table?  Or was that just an example and you are interested
> in working with all of the tables in the Phylogeny module?
>
> Stephen
>

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

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Re: adding chado tables to my tripal

Stephen Ficklin-2
Sounds like a plan :-)  If you need help, suggestions or would like to
bounce ideas off other developers as you develop your module feel free
to use the gmod-tripal-devel mailing list.

Stephen

On 1/10/2014 6:00 PM, Alex Rice wrote:

> Stephen, thanks for your replies- much appreciated. We are working on
> some visualizations of phylogenetic trees, and also visualizations of
> gene ontology relations across collections of features. These d3js
> visualizations want to consume JSON. It appears the Drupal Views
> module wont enable enough querying flexibility  to produce the json.
> So I think I will go ahead with creating a custom tripal extension
> module- but it wont be a general purpose phylogeny module.
>
> On 1/10/14, 2:59 PM, Stephen Ficklin wrote:
>> Hi Alex,
>>
>> One other item.  If you are just working with a single table and you
>> have data in it, it is possible to display that data or search that data
>> without writing a module.  If you just need the phylotree table you can
>> use Drupal Views to create pages or search forms for that content
>> depending on how you want to display it. All of the Chado tables are
>> available in Drupal Views.   How are you hoping to interact with data in
>> the phylotree table?  Or was that just an example and you are interested
>> in working with all of the tables in the Phylogeny module?
>>
>> Stephen
>>
>


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Re: adding chado tables to my tripal

Lacey-Anne Sanderson-3
In reply to this post by Alex Rice
Hi Alex,
It’s a little known, not well-documented feature but you can actually intercept a views query and re-write it using the exact SQL you need. That said, in this case, I think it would be more work than it’s worth to use Views since you would need to not only re-write the SQL but also create your own display handler to accomplish the visualizations. I would suggest taking a look at the Tripal API while writing your module. The chado_query function allows you to write pure SQL while abstracting away the actual connecting to the correct database and making sure your in the right namespace.

Good luck with your first Tripal Extension module! Remember, we are always here if you run into problems or even just need a sounding board for your ideas :)
~Lacey

On Jan 10, 2014, at 5:00 PM, Alex Rice <[hidden email]> wrote:

> Stephen, thanks for your replies- much appreciated. We are working on
> some visualizations of phylogenetic trees, and also visualizations of
> gene ontology relations across collections of features. These d3js
> visualizations want to consume JSON. It appears the Drupal Views module
> wont enable enough querying flexibility  to produce the json. So I think
> I will go ahead with creating a custom tripal extension module- but it
> wont be a general purpose phylogeny module.
>
> On 1/10/14, 2:59 PM, Stephen Ficklin wrote:
>> Hi Alex,
>>
>> One other item.  If you are just working with a single table and you
>> have data in it, it is possible to display that data or search that data
>> without writing a module.  If you just need the phylotree table you can
>> use Drupal Views to create pages or search forms for that content
>> depending on how you want to display it. All of the Chado tables are
>> available in Drupal Views.   How are you hoping to interact with data in
>> the phylotree table?  Or was that just an example and you are interested
>> in working with all of the tables in the Phylogeny module?
>>
>> Stephen
>>
>
> --
> Alex Rice <[hidden email]>
> Software Engineer
> National Center for Genome Resources (NCGR)
> http://ncgr.org
> (505)995-4457
>
> ------------------------------------------------------------------------------
> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> Learn Why More Businesses Are Choosing CenturyLink Cloud For
> Critical Workloads, Development Environments & Everything In Between.
> Get a Quote or Start a Free Trial Today.
> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
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