gmod-tripal — Announcements and questions about Tripal.

[Gmod-tripal] tripal feature accession

[P. Z. <pzi...@up...>]

Hi!
	I am new to tripal(awesome project). I have found that the accession
used in tripal is a sum of a site specific prefix and chado feature_id.
Is it possible to use the chado's feature's uniquename as accession of
tripal?

	This is useful when you try to access a tripal feature page from an
external application without access to chado database. 
	I thing is not a good idea to use feature_id as accession because
feature_id is an internal id of chado and it could change in a database
regeneration. Showing this data to users could confuse them if 

Maybe I haven't understand tripal, so I someone could clarify me...

Thanks in advance
p.

Re: [Gmod-tripal] [Gmod-schema] Natural Diversity -Drupal Stock & Natural Diversity Modules

[Meg S. <me...@ya...>]

Tripal is being actively developed under the tfGDR project (http://www.rosaceae.org/), and there is continued support and small updates still going on at Clemson.  We will be incorporating the natural diversity modules in tfGDR over the next two years, but our plans are very preliminary.   I hope to get a more robust plan together soon, and I'll share it with the Tripal list. 

We don't currently have a plan to create an API to interact with the database.  Stephen and I have an extensive list of improvements we'd like to implement for Tripal, but alas, no funding to work on them right now.  The tfGDR grant has very specific target products and only two-part time developers right now, so that project will probably not take on larger improvements that do not directly affect the goals of the project.

Thanks,
Meg Staton

 -- 
Margaret E. Staton
Clemson University Genomics Institute
me...@ya...
864-656-4643




________________________________
From: Bob MacCallum <r.m...@im...>
To: Stephen Ficklin <FI...@cl...>
Cc: Lacey-Anne Sanderson <Lac...@sh...>; GMOD Tripal <gmo...@li...>; GMOD Schema <gmo...@li...>; Meg Staton <me...@ya...>
Sent: Wed, May 26, 2010 7:40:04 AM
Subject: Re: [Gmod-schema] [Gmod-tripal] Natural Diversity -Drupal Stock &  Natural Diversity Modules

Tripal looks like a really viable option for the UI for the natural
diversity db and I've just signed up for the gmod-tripal mailing list.

We have some concerns though, for example, there seems to be a lot of
bare SQL in the Tripal modules (although we like the modular design).
Using a schema as flexible as Chado across many physical sites (as
VectorBase will be doing), we would prefer to have all data go in/out
of the database via an API; this means loader scripts, web UI
read/write, BioMart dumper scripts, everything, to ensure that the
data is consistently represented in the db.  I'm not a PHP expert, but
have read about doctrine 1.2 and 2.0, and it seems as if some
higher-level code could be developed with a doctrine ORM layer.
(www.doctrine-project.org)

So I have a couple of questions:

1. What API development plans do people have for the NatDiv schema (in
whatever language)?
2. Could an API be made to work across sites (e.g. apples, rice,
mosquitoes, ...) or are we using the schema in too different ways?
3. Is there any Tripal/ORM development going on at the moment?

cheers,
Bob.

On Wed, May 12, 2010 at 3:16 PM, Stephen Ficklin <FI...@cl...> wrote:
> Hi Lacey,
>
>
>
> Chado currently does have some recommendations for table auditing (history
> keeping) at http://gmod.org/wiki/Chado_Audit_Module.  These recommendations
> are not implemented in Chado, just recommendations.  I do, however, like
> your idea of only storing the edited column as this will reduce database
> bloat over time.
>
>
>
> Also, this past January at the GMOD annual meeting the folks from GNPannot
> at CIRAD showed a very nice trigger based wrapper for Chado called Chado
> controller:  http://www.gnpannot.org/content/chado-controller .  It helps
> control user access and auditing of a chado database.  It’s all based on
> Postgres and requires no other software.  I can contact them and see if they
> would mind sharing with us.
>
>
>
> Stephen
>
>
>
>
>
> From: Lacey-Anne Sanderson [mailto:Lac...@sh...]
> Sent: Monday, May 10, 2010 6:27 PM
> To: GMOD Tripal; GMOD Schema; Meg Staton; Stephen Ficklin
> Subject: Re: [Gmod-tripal] Natural Diversity -Drupal Stock & Natural
> Diversity Modules
>
>
>
> PS. Stephen -See my comments below #2 in regards to the delete issue. This
> way I can implement marking as obsolete separately from deleting which is
> likely a more general use case. What do you think?
>
>
>
> ------------------------------------------------------
>
> Lacey-Anne Sanderson
>
> Bioinformaticist
>
> Pulse Crop Breeding and Genetics
>
> Phone: (306) 966-2430
>
> Room 3D10 Argriculture
>
> Department of Plant Sciences
>
> University of Saskatchewan
>
>
>
> On 2010-05-10, at 10:36 AM, Meg Staton wrote:
>
>
> 2.  Drupal does have a versioning system, but we don't use it.  Chado just
> isn't built to handle versioning of records, so we haven't tackled it.  We
> want to enable community annotation, but backing out to old versions is
> tough.
>
> The first idea that comes to mind is to create a new chado stock record each
> time a node is changed, and have each drupal node revision point to a
> different stock record in chado.  You'd have to copy over any related data
> (props, cvterms, pubs) as well.  You'd have to think through every possible
> relationship in the database.  And this solution seems like a "hack" of
> chado - if you handed your database to someone else, it wouldn't make sense
> to them, because the stock table would have many revisions of what should be
> a single stock record.
>
> My second idea would be to somehow store the stock record details in a
> drupal field that is parseable later.  If you needed to roll back, you would
> just pick up the old fields in drupal, and restore them to chado.  This has
> the problem of being redundant and bloating your drupal nodes.  Basically,
> if we implemented this for all the modules, we might as well get rid of
> chado entirely and just store everything in drupal.
>
> I'm not a fan of either of these solutions, but I think the first one is
> better.  Are there any other ideas out there?
>
>
>
> I think this needs to be handled by a versioning chado schema module. What
> comes to mind is adding a stock_revision table which has a stock_id, date,
> wwwuser, column_name old_value, new_value & just updating the stock
> everytime. You could even implement triggers which automatically add to the
> stock_revision table on update. Then when you need to rollback you can just
> select all old_values from the date period you want to roll back to and
> update the stock table to have these values.
>
>
>
> This would at least keep the stock table uncluttered & unchanged... Also it
> should be pretty generic.
>
>
> Thanks!
> Meg
>
>
> --
> Margaret E. Staton
> Clemson University Genomics Institute
> me...@ya...
> 864-656-4643
>
>
>
>
>
> ________________________________
>
> From: Stephen Ficklin <FI...@cl...>
> To: Lacey-Anne Sanderson <Lac...@sh...>; GMOD Schema
> <gmo...@li...>; GMOD Tripal
> <gmo...@li...>
> Sent: Fri, May 7, 2010 7:00:33 PM
> Subject: Re: [Gmod-tripal] Natural Diversity -Drupal Stock & Natural
> Diversity Modules
>
> Hi Lacey,
>
> Sounds like you've done a great job with a new Drupal stock module for
> Chado!
>
> In response to your first question below, perhaps you could maintain the
> 'is_obsolete' column of chado as an option in your Drupal module as well.
> Therefore when a user really wants to delete the stock it is really
> deleted.  But, if the user wants to make a stock obsolete then it gets
> flagged as obsolete in Chado and reflected as such in Drupal.  The GMOD
> folks can correct me if I'm wrong but I believe the is_obsolete field is
> intended to keep data around for historical purposes so it doesn't have to
> be deleted.  In which case you would still want to maintain and show the
> Drupal node for stocks that have the is_obsolete set to true.
>
> In response to your third question.  I know the folks at WSU are planning to
> do some Drupal work that would plug into Tripal for the natural diversity
> tables that are being developed.  I have not followed that discussion very
> closely on the mailing list, but I don't think it was decided how that would
> be distributed.  My opinion is that I would like to see Drupal modules that
> are more generic in nature that correspond to data management of chado
> modules be incorporated as "core" modules in Tripal.  Other modules that are
> highly tailored, for example for different analysis methods should be
> offered separate from Tripal. We will probably take the analysis modules
> that we developed and pull them out of the "core" as well.  But for now it's
> just easier to distribute them all together.  We are willing to house a
> repository of user-contributed Tripal/Drupal compatible modules, and give
> appropriate credit to the authors.  This will create a single place to find
> them all.  But, ultimately where a module goes should be up to the
> developers.  I'd be happy to discuss with you the possibility of
> incorporating your stock module into Tripal if you would like it to go that
> route.
>
> Cheers,
> Stephen
> ________________________________________
> From: Lacey-Anne Sanderson [Lac...@sh...]
> Sent: Friday, May 07, 2010 5:51 PM
> To: GMOD Schema; GMOD Tripal
> Subject: [Gmod-tripal] Natural Diversity -Drupal Stock & Natural Diversity
>     Modules
>
> I'm creating a chado_stock drupal module that is almost ready to be released
> as an alpha version (sometime next week).
>
> Details:
> - only stores stock_id mapped to a drupal node in drupal
> - all other data is queried from chado when the node is loaded
> - data from chado that is supported includes all fields from the stock
> table, those from stockprop (including a separate listing of those with
> cvterm 'synonym'), from stock_dbxref and from stock_relationship
> -the fields from stock are listed in a table format at the top of the node
> and data from the other three tables are shown below each inside its own
> signature tripal expandable box.
> -syncing of data between drupal & chado (essentially creating drupal nodes
> for all chado stock records & storing the stock_id) is supported
> -as is entering stocks through the web interface (currently need to finish
> this for the other 3 tables) which writes directly to chado.
>
> Features not yet supported (Still in the works):
> A number of admin features including cleanup, reindexing and taxonomy
> tracking of who entered the data in chado -some type of versioning?
> More user friendly selecting of stocks for relationships and cvterms
> (currently is a Very long drop-down select)
>
> What needs to be done next:
> 2. Create a generic nd_assay module
> 3. Create genotype, phenotype, crossexperiment and fieldcollection modules
> each will all the features from nd_assay but with added required fields and
> customized display
> 4. Create a project module which groups together data into projects. This
> one is not specific to the natural diversity project but one of the types of
> data that can be added to a project with be a nd_assay.
>
> A couple of Questions:
> 1. Deleting a stock node in drupal -> how should this be reflected in drupal
> - although stock.is_obsolete can be set to True there doesn't seem to be a
> similar way to indicate that stock relationships or properties have been
> deleted...
> - stocks which are marked as obsolete won't be added back into drupal during
> syncing therefore does it matter if the relationships and properties aren't
> marked since they are only available by accessing chado directly?
>
> 2. This is a more chado-oriented question: How is versioning handled?
> -In drupal you can easily edit a stock which currently just writes over the
> original content in chado...
> - Is there a way to keep the original in case you want to rollback?
>
> 3. Should this stock module be part of tripal rather than the drupal natural
> diversity module?
> Should the Drupal Natural Diversity module be separate from Tripal
> (distributed separately as an add-on?
>
> Thanks for any input!
> Lacey
>
>
> ------------------------------------------------------
> Lacey-Anne Sanderson
> Bioinformaticist
> Pulse Crop Breeding and Genetics
> Phone: (306) 966-2430
> Room 3D10 Argriculture
> Department of Plant Sciences
> University of Saskatchewan
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-tripal mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>
>
>
>
>
>



      

Re: [Gmod-tripal] [Gmod-schema] Natural Diversity -Drupal Stock & Natural Diversity Modules

[Bob M. <r.m...@im...>]

Tripal looks like a really viable option for the UI for the natural
diversity db and I've just signed up for the gmod-tripal mailing list.

We have some concerns though, for example, there seems to be a lot of
bare SQL in the Tripal modules (although we like the modular design).
Using a schema as flexible as Chado across many physical sites (as
VectorBase will be doing), we would prefer to have all data go in/out
of the database via an API; this means loader scripts, web UI
read/write, BioMart dumper scripts, everything, to ensure that the
data is consistently represented in the db.  I'm not a PHP expert, but
have read about doctrine 1.2 and 2.0, and it seems as if some
higher-level code could be developed with a doctrine ORM layer.
(www.doctrine-project.org)

So I have a couple of questions:

1. What API development plans do people have for the NatDiv schema (in
whatever language)?
2. Could an API be made to work across sites (e.g. apples, rice,
mosquitoes, ...) or are we using the schema in too different ways?
3. Is there any Tripal/ORM development going on at the moment?

cheers,
Bob.

On Wed, May 12, 2010 at 3:16 PM, Stephen Ficklin <FI...@cl...> wrote:
> Hi Lacey,
>
>
>
> Chado currently does have some recommendations for table auditing (history
> keeping) at http://gmod.org/wiki/Chado_Audit_Module.  These recommendations
> are not implemented in Chado, just recommendations.  I do, however, like
> your idea of only storing the edited column as this will reduce database
> bloat over time.
>
>
>
> Also, this past January at the GMOD annual meeting the folks from GNPannot
> at CIRAD showed a very nice trigger based wrapper for Chado called Chado
> controller:  http://www.gnpannot.org/content/chado-controller .  It helps
> control user access and auditing of a chado database.  It’s all based on
> Postgres and requires no other software.  I can contact them and see if they
> would mind sharing with us.
>
>
>
> Stephen
>
>
>
>
>
> From: Lacey-Anne Sanderson [mailto:Lac...@sh...]
> Sent: Monday, May 10, 2010 6:27 PM
> To: GMOD Tripal; GMOD Schema; Meg Staton; Stephen Ficklin
> Subject: Re: [Gmod-tripal] Natural Diversity -Drupal Stock & Natural
> Diversity Modules
>
>
>
> PS. Stephen -See my comments below #2 in regards to the delete issue. This
> way I can implement marking as obsolete separately from deleting which is
> likely a more general use case. What do you think?
>
>
>
> ------------------------------------------------------
>
> Lacey-Anne Sanderson
>
> Bioinformaticist
>
> Pulse Crop Breeding and Genetics
>
> Phone: (306) 966-2430
>
> Room 3D10 Argriculture
>
> Department of Plant Sciences
>
> University of Saskatchewan
>
>
>
> On 2010-05-10, at 10:36 AM, Meg Staton wrote:
>
>
> 2.  Drupal does have a versioning system, but we don't use it.  Chado just
> isn't built to handle versioning of records, so we haven't tackled it.  We
> want to enable community annotation, but backing out to old versions is
> tough.
>
> The first idea that comes to mind is to create a new chado stock record each
> time a node is changed, and have each drupal node revision point to a
> different stock record in chado.  You'd have to copy over any related data
> (props, cvterms, pubs) as well.  You'd have to think through every possible
> relationship in the database.  And this solution seems like a "hack" of
> chado - if you handed your database to someone else, it wouldn't make sense
> to them, because the stock table would have many revisions of what should be
> a single stock record.
>
> My second idea would be to somehow store the stock record details in a
> drupal field that is parseable later.  If you needed to roll back, you would
> just pick up the old fields in drupal, and restore them to chado.  This has
> the problem of being redundant and bloating your drupal nodes.  Basically,
> if we implemented this for all the modules, we might as well get rid of
> chado entirely and just store everything in drupal.
>
> I'm not a fan of either of these solutions, but I think the first one is
> better.  Are there any other ideas out there?
>
>
>
> I think this needs to be handled by a versioning chado schema module. What
> comes to mind is adding a stock_revision table which has a stock_id, date,
> wwwuser, column_name old_value, new_value & just updating the stock
> everytime. You could even implement triggers which automatically add to the
> stock_revision table on update. Then when you need to rollback you can just
> select all old_values from the date period you want to roll back to and
> update the stock table to have these values.
>
>
>
> This would at least keep the stock table uncluttered & unchanged... Also it
> should be pretty generic.
>
>
> Thanks!
> Meg
>
>
> --
> Margaret E. Staton
> Clemson University Genomics Institute
> me...@ya...
> 864-656-4643
>
>
>
>
>
> ________________________________
>
> From: Stephen Ficklin <FI...@cl...>
> To: Lacey-Anne Sanderson <Lac...@sh...>; GMOD Schema
> <gmo...@li...>; GMOD Tripal
> <gmo...@li...>
> Sent: Fri, May 7, 2010 7:00:33 PM
> Subject: Re: [Gmod-tripal] Natural Diversity -Drupal Stock & Natural
> Diversity Modules
>
> Hi Lacey,
>
> Sounds like you've done a great job with a new Drupal stock module for
> Chado!
>
> In response to your first question below, perhaps you could maintain the
> 'is_obsolete' column of chado as an option in your Drupal module as well.
> Therefore when a user really wants to delete the stock it is really
> deleted.  But, if the user wants to make a stock obsolete then it gets
> flagged as obsolete in Chado and reflected as such in Drupal.  The GMOD
> folks can correct me if I'm wrong but I believe the is_obsolete field is
> intended to keep data around for historical purposes so it doesn't have to
> be deleted.  In which case you would still want to maintain and show the
> Drupal node for stocks that have the is_obsolete set to true.
>
> In response to your third question.  I know the folks at WSU are planning to
> do some Drupal work that would plug into Tripal for the natural diversity
> tables that are being developed.  I have not followed that discussion very
> closely on the mailing list, but I don't think it was decided how that would
> be distributed.  My opinion is that I would like to see Drupal modules that
> are more generic in nature that correspond to data management of chado
> modules be incorporated as "core" modules in Tripal.  Other modules that are
> highly tailored, for example for different analysis methods should be
> offered separate from Tripal. We will probably take the analysis modules
> that we developed and pull them out of the "core" as well.  But for now it's
> just easier to distribute them all together.  We are willing to house a
> repository of user-contributed Tripal/Drupal compatible modules, and give
> appropriate credit to the authors.  This will create a single place to find
> them all.  But, ultimately where a module goes should be up to the
> developers.  I'd be happy to discuss with you the possibility of
> incorporating your stock module into Tripal if you would like it to go that
> route.
>
> Cheers,
> Stephen
> ________________________________________
> From: Lacey-Anne Sanderson [Lac...@sh...]
> Sent: Friday, May 07, 2010 5:51 PM
> To: GMOD Schema; GMOD Tripal
> Subject: [Gmod-tripal] Natural Diversity -Drupal Stock & Natural Diversity
>     Modules
>
> I'm creating a chado_stock drupal module that is almost ready to be released
> as an alpha version (sometime next week).
>
> Details:
> - only stores stock_id mapped to a drupal node in drupal
> - all other data is queried from chado when the node is loaded
> - data from chado that is supported includes all fields from the stock
> table, those from stockprop (including a separate listing of those with
> cvterm 'synonym'), from stock_dbxref and from stock_relationship
> -the fields from stock are listed in a table format at the top of the node
> and data from the other three tables are shown below each inside its own
> signature tripal expandable box.
> -syncing of data between drupal & chado (essentially creating drupal nodes
> for all chado stock records & storing the stock_id) is supported
> -as is entering stocks through the web interface (currently need to finish
> this for the other 3 tables) which writes directly to chado.
>
> Features not yet supported (Still in the works):
> A number of admin features including cleanup, reindexing and taxonomy
> tracking of who entered the data in chado -some type of versioning?
> More user friendly selecting of stocks for relationships and cvterms
> (currently is a Very long drop-down select)
>
> What needs to be done next:
> 2. Create a generic nd_assay module
> 3. Create genotype, phenotype, crossexperiment and fieldcollection modules
> each will all the features from nd_assay but with added required fields and
> customized display
> 4. Create a project module which groups together data into projects. This
> one is not specific to the natural diversity project but one of the types of
> data that can be added to a project with be a nd_assay.
>
> A couple of Questions:
> 1. Deleting a stock node in drupal -> how should this be reflected in drupal
> - although stock.is_obsolete can be set to True there doesn't seem to be a
> similar way to indicate that stock relationships or properties have been
> deleted...
> - stocks which are marked as obsolete won't be added back into drupal during
> syncing therefore does it matter if the relationships and properties aren't
> marked since they are only available by accessing chado directly?
>
> 2. This is a more chado-oriented question: How is versioning handled?
> -In drupal you can easily edit a stock which currently just writes over the
> original content in chado...
> - Is there a way to keep the original in case you want to rollback?
>
> 3. Should this stock module be part of tripal rather than the drupal natural
> diversity module?
> Should the Drupal Natural Diversity module be separate from Tripal
> (distributed separately as an add-on?
>
> Thanks for any input!
> Lacey
>
>
> ------------------------------------------------------
> Lacey-Anne Sanderson
> Bioinformaticist
> Pulse Crop Breeding and Genetics
> Phone: (306) 966-2430
> Room 3D10 Argriculture
> Department of Plant Sciences
> University of Saskatchewan
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-tripal mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>
>
>
>
>
>

Re: [Gmod-tripal] Chado Stock Module

[Stephen F. <FI...@cl...>]

Hi Lacey,

Great job on the stock module. I'm impressed with how much you got done considering we don't quite have the API documentation finished in the User's Guide.    Thanks for being patient on the response.

Here are some of my thoughts to your questions below.

1.   To keep with "spirit" of the Drupal design, I think it would be best to put your forms for updating the properties, relationships and dbxrefs on the 'Edit' page for the node rather than on the 'View' page.  I realize that makes the form design a bit more complex but I think that's the right place to put that, especially since Drupal permissions allow/disallow 'editing' of the node but cannot extend those permissions to your form elements on the 'View' page.   On the 'view' page a user is only required to have 'access content' permissions.

2.  Again, deletion of properties should be handled on the 'Edit' page form as well.   Perhaps for each property, relationship or dbxref you could add a simple checkbox that if checked will delete the item when the form is submitted.    We haven't included elements in the existing Tripal edit forms for properties or other relationships.  We really need to do this as well for feature properties, etc.  So, I'm willing to work with you on getting a good implementation for this that we can use as a model for our other modules.

3.  I think it would be  good to support stock collections and require that a stock be part of a collection.  This way you can use Drupal Taxonomy terms to allow users to search for stocks within  a single collection.   Even if there is only a single stock in the collection it is housed someplace.   Also, you could easily place a box on each organism page listing the available stock collections with links to a page that describe the collection.

4.  What if you list the current stock as just text with a drop down beside it with the options 'object' or 'target'.  Then have your relationship drop down and another dropdown that lists other stocks.  If the users selects 'object' you know then that the other stock is the 'target'.   This would be easier to code, but may confuse the users who may have a hard time remembering the difference between 'object' and 'target'.   To help with that, maybe you could add a simple Javascript that on change of any of the fields would write out the sentence for the relationship.  So, if you have a stock named 'Bug1' and another 'Bug2' with relationship  type 'is_the_paternal_parent_of' and the user selects the current stock as 'target' then  it would write out 'Bug2 is the paternal parent of Bug1'.     If the user then switches the dropdown to 'object', the sentence would change:  'Bug1 is the paternal parent of Bug2'.

I think you did a good job matching up with Tripal and your module directly correlates with a Chado module so if you would like to have us include your module as part of the "core" set of modules we'd be happy to do so.   I have a few suggestions to make it fit the development paradigm of Tripal and can share  those if you are interested.

Stephen

From: Lacey-Anne Sanderson [mailto:lac...@sh...]
Sent: Friday, May 14, 2010 4:27 PM
To: GMOD Tripal
Cc: Stephen Ficklin; Sook Jung
Subject: [Gmod-tripal] Chado Stock Module

Okay, so it took a little longer than expected due to the ever present unforeseen errors but the first draft is finally done!

Download available at: http://knowpulse.usask.ca/d/node/1342163

My Blurb Describing it:
This module provides an interface between the drupal web interface and the following chado tables: stock, stockprop, stock_relationship, stock_dbxref_dbxref. It provides administrative tools for choosing controlled vocabularies and sync'ing chado with drupal (creating drupal nodes for all stocks in chado). It also provides the ability to add/edit/delete the basic information about a stock(that stocked in the chado stock table) and add properties (with special display for synonyms), relationships between stocks and links from the current resource to external databases such as NCBI. For more information see the user manual included in the download.

It you have time I would really appreciate it if you could download this module and test it out!

Some more Development/Preferences Questions:
1. Currently I have included collapsed forms on the chado_stock node page for adding properties, relationships and external database references. Does anyone have an objection to this? I had toyed around with popup windows but then dismissed it due to adding dependancies to the module and general dislike of popups.

2. I haven't yet added in the ability to edit/delete properties, external db references, and relationships because I'm not sure where to put them/ how to implement them. I think it makes the most sense to put an edit & delete link beside the property/dbxref/relationship in the node page. This could then either:
            - open a new window/popup with the edit form or delete confirmation
            - redirect to a new page where you edit/confirm delete and then redirect you back.
I'm completely divided on this one. Do you guys have any preference?

3. This module doesn't support stock collections. Do you think it should? Is anyone actively using them?

4. Choosing of stocks for the stock relationship. There is validation that one of them needs to be the current stock however making the current stock the default value for each of them turned out to be harder than expected. Does anyone know how to do this? Also (and this is the bigger concern), eventually you are going to have a lot of stocks in your database making these selects very unwieldy... I have filtered to only display stocks with the same organism source but f eel more needs to be done. One though I had was to make each an autocomplete textfield/select and then display a table of all stocks either within the form in a scrollable iframe/textarea or in a popup window. Any thoughts?

Thanks,
Lacey
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Argriculture
Department of Plant Sciences
University of Saskatchewan

[Gmod-tripal] Chado Stock Module

[Lacey-Anne S. <lac...@sh...>]

Okay, so it took a little longer than expected due to the ever present unforeseen errors but the first draft is finally done! 

Download available at: http://knowpulse.usask.ca/d/node/1342163

My Blurb Describing it: 
This module provides an interface between the drupal web interface and the following chado tables: stock, stockprop, stock_relationship, stock_dbxref_dbxref. It provides administrative tools for choosing controlled vocabularies and sync'ing chado with drupal (creating drupal nodes for all stocks in chado). It also provides the ability to add/edit/delete the basic information about a stock(that stocked in the chado stock table) and add properties (with special display for synonyms), relationships between stocks and links from the current resource to external databases such as NCBI. For more information see the user manual included in the download.

It you have time I would really appreciate it if you could download this module and test it out!

Some more Development/Preferences Questions:
1. Currently I have included collapsed forms on the chado_stock node page for adding properties, relationships and external database references. Does anyone have an objection to this? I had toyed around with popup windows but then dismissed it due to adding dependancies to the module and general dislike of popups.

2. I haven't yet added in the ability to edit/delete properties, external db references, and relationships because I'm not sure where to put them/ how to implement them. I think it makes the most sense to put an edit & delete link beside the property/dbxref/relationship in the node page. This could then either:
	- open a new window/popup with the edit form or delete confirmation
	- redirect to a new page where you edit/confirm delete and then redirect you back. 
I'm completely divided on this one. Do you guys have any preference?

3. This module doesn't support stock collections. Do you think it should? Is anyone actively using them?

4. Choosing of stocks for the stock relationship. There is validation that one of them needs to be the current stock however making the current stock the default value for each of them turned out to be harder than expected. Does anyone know how to do this? Also (and this is the bigger concern), eventually you are going to have a lot of stocks in your database making these selects very unwieldy... I have filtered to only display stocks with the same organism source but f eel more needs to be done. One though I had was to make each an autocomplete textfield/select and then display a table of all stocks either within the form in a scrollable iframe/textarea or in a popup window. Any thoughts?

Thanks,
Lacey
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Argriculture
Department of Plant Sciences
University of Saskatchewan

Re: [Gmod-tripal] Natural Diversity -Drupal Stock & Natural Diversity Modules

[Stephen F. <FI...@cl...>]

Hi Lacey,

Chado currently does have some recommendations for table auditing (history keeping) at http://gmod.org/wiki/Chado_Audit_Module.  These recommendations are not implemented in Chado, just recommendations.  I do, however, like your idea of only storing the edited column as this will reduce database bloat over time.

Also, this past January at the GMOD annual meeting the folks from GNPannot at CIRAD showed a very nice trigger based wrapper for Chado called Chado controller:  http://www.gnpannot.org/content/chado-controller .  It helps control user access and auditing of a chado database.  It's all based on Postgres and requires no other software.  I can contact them and see if they would mind sharing with us.

Stephen


From: Lacey-Anne Sanderson [mailto:Lac...@sh...]
Sent: Monday, May 10, 2010 6:27 PM
To: GMOD Tripal; GMOD Schema; Meg Staton; Stephen Ficklin
Subject: Re: [Gmod-tripal] Natural Diversity -Drupal Stock & Natural Diversity Modules

PS. Stephen -See my comments below #2 in regards to the delete issue. This way I can implement marking as obsolete separately from deleting which is likely a more general use case. What do you think?

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Argriculture
Department of Plant Sciences
University of Saskatchewan

On 2010-05-10, at 10:36 AM, Meg Staton wrote:



2.  Drupal does have a versioning system, but we don't use it.  Chado just isn't built to handle versioning of records, so we haven't tackled it.  We want to enable community annotation, but backing out to old versions is tough.

The first idea that comes to mind is to create a new chado stock record each time a node is changed, and have each drupal node revision point to a different stock record in chado.  You'd have to copy over any related data (props, cvterms, pubs) as well.  You'd have to think through every possible relationship in the database.  And this solution seems like a "hack" of chado - if you handed your database to someone else, it wouldn't make sense to them, because the stock table would have many revisions of what should be a single stock record.

My second idea would be to somehow store the stock record details in a drupal field that is parseable later.  If you needed to roll back, you would just pick up the old fields in drupal, and restore them to chado.  This has the problem of being redundant and bloating your drupal nodes.  Basically, if we implemented this for all the modules, we might as well get rid of chado entirely and just store everything in drupal.

I'm not a fan of either of these solutions, but I think the first one is better.  Are there any other ideas out there?

I think this needs to be handled by a versioning chado schema module. What comes to mind is adding a stock_revision table which has a stock_id, date, wwwuser, column_name old_value, new_value & just updating the stock everytime. You could even implement triggers which automatically add to the stock_revision table on update. Then when you need to rollback you can just select all old_values from the date period you want to roll back to and update the stock table to have these values.

This would at least keep the stock table uncluttered & unchanged... Also it should be pretty generic.



Thanks!
Meg


--
Margaret E. Staton
Clemson University Genomics Institute
me...@ya...<mailto:me...@ya...>
864-656-4643


________________________________
From: Stephen Ficklin <FI...@cl...<mailto:FI...@cl...>>
To: Lacey-Anne Sanderson <Lac...@sh...<mailto:Lac...@sh...>>; GMOD Schema <gmo...@li...<mailto:gmo...@li...>>; GMOD Tripal <gmo...@li...<mailto:gmo...@li...>>
Sent: Fri, May 7, 2010 7:00:33 PM
Subject: Re: [Gmod-tripal] Natural Diversity -Drupal Stock & Natural Diversity Modules

Hi Lacey,

Sounds like you've done a great job with a new Drupal stock module for Chado!

In response to your first question below, perhaps you could maintain the 'is_obsolete' column of chado as an option in your Drupal module as well.  Therefore when a user really wants to delete the stock it is really deleted.  But, if the user wants to make a stock obsolete then it gets flagged as obsolete in Chado and reflected as such in Drupal.  The GMOD folks can correct me if I'm wrong but I believe the is_obsolete field is intended to keep data around for historical purposes so it doesn't have to be deleted.  In which case you would still want to maintain and show the Drupal node for stocks that have the is_obsolete set to true.

In response to your third question.  I know the folks at WSU are planning to do some Drupal work that would plug into Tripal for the natural diversity tables that are being developed.  I have not followed that discussion very closely on the mailing list, but I don't think it was decided how that would be distributed.  My opinion is that I would like to see Drupal modules that are more generic in nature that correspond to data management of chado modules be incorporated as "core" modules in Tripal.  Other modules that are highly tailored, for example for different analysis methods should be offered separate from Tripal. We will probably take the analysis modules that we developed and pull them out of the "core" as well.  But for now it's just easier to distribute them all together.  We are willing to house a repository of user-contributed Tripal/Drupal compatible modules, and give appropriate credit to the authors.  This will create a single place to find them all.  But, ultimately where a module goes should be up to the developers.  I'd be happy to discuss with you the possibility of incorporating your stock module into Tripal if you would like it to go that route.

Cheers,
Stephen
________________________________________
From: Lacey-Anne Sanderson [Lac...@sh...<mailto:Lac...@sh...>]
Sent: Friday, May 07, 2010 5:51 PM
To: GMOD Schema; GMOD Tripal
Subject: [Gmod-tripal] Natural Diversity -Drupal Stock & Natural Diversity      Modules

I'm creating a chado_stock drupal module that is almost ready to be released as an alpha version (sometime next week).

Details:
- only stores stock_id mapped to a drupal node in drupal
- all other data is queried from chado when the node is loaded
- data from chado that is supported includes all fields from the stock table, those from stockprop (including a separate listing of those with cvterm 'synonym'), from stock_dbxref and from stock_relationship
-the fields from stock are listed in a table format at the top of the node and data from the other three tables are shown below each inside its own signature tripal expandable box.
-syncing of data between drupal & chado (essentially creating drupal nodes for all chado stock records & storing the stock_id) is supported
-as is entering stocks through the web interface (currently need to finish this for the other 3 tables) which writes directly to chado.

Features not yet supported (Still in the works):
A number of admin features including cleanup, reindexing and taxonomy
tracking of who entered the data in chado -some type of versioning?
More user friendly selecting of stocks for relationships and cvterms (currently is a Very long drop-down select)

What needs to be done next:
2. Create a generic nd_assay module
3. Create genotype, phenotype, crossexperiment and fieldcollection modules each will all the features from nd_assay but with added required fields and customized display
4. Create a project module which groups together data into projects. This one is not specific to the natural diversity project but one of the types of data that can be added to a project with be a nd_assay.

A couple of Questions:
1. Deleting a stock node in drupal -> how should this be reflected in drupal
- although stock.is_obsolete can be set to True there doesn't seem to be a similar way to indicate that stock relationships or properties have been deleted...
- stocks which are marked as obsolete won't be added back into drupal during syncing therefore does it matter if the relationships and properties aren't marked since they are only available by accessing chado directly?

2. This is a more chado-oriented question: How is versioning handled?
-In drupal you can easily edit a stock which currently just writes over the original content in chado...
- Is there a way to keep the original in case you want to rollback?

3. Should this stock module be part of tripal rather than the drupal natural diversity module?
Should the Drupal Natural Diversity module be separate from Tripal (distributed separately as an add-on?

Thanks for any input!
Lacey


------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Argriculture
Department of Plant Sciences
University of Saskatchewan


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

_______________________________________________
Gmod-tripal mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

Re: [Gmod-tripal] Natural Diversity -Drupal Stock & Natural Diversity Modules

[Lacey-Anne S. <Lac...@sh...>]

Hi Meg,

I'm definitely interested in collaborating! I assume we'd start a wiki page (maybe on GMOD?) and start recording our progress and plans on there? I'm willing to take charge of this project (ie: keep the wiki page up to date and organize any meetings needed) unless one of you want to do it?

As to the Stock module: (see below)

Lacey

PS. Stephen -See my comments below #2 in regards to the delete issue. This way I can implement marking as obsolete separately from deleting which is likely a more general use case. What do you think?

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Argriculture
Department of Plant Sciences
University of Saskatchewan

On 2010-05-10, at 10:36 AM, Meg Staton wrote:

> Hi, Lacy!  I'm working with the GDR, but Stephen's right, we haven't started designing Tripal modules for the natural diversity schema yet.  But we would love to work with you when we do get started!  It would be much better to have a single set of natural diversity modules that to produce two overlapping code bases.  I'm CCing the person heading up natural diversity for GDR, Sook Jung, as well as the PI, Dorrie Main.  They can chime in on how to start up a collaboration if you are interested.
> 
> My thoughts on your questions:
> 1.  Your solution to the stock obselete_id seems perfectly reasonable to me.  If its marked obsolete, then chado won't try to go looking for the associated property data, so I think its fine to leave the associated properties.  I would only see this being a problem if it has associated data such as features that would be indexed and available to users.  If you wanted those to be come obsolete along with the stock, that would need some more thought.  

Another option I just thought of which might be better & handle still viewing obsolete stocks but not deleted ones:
On Delete from the node add/edit/delete page by user simply mark the node as unpublished & set a marked_as_deleted field in chado_stock
Then create an administration page (or even just a page with different access permissions) that lists all chado_stock nodes marked_as_deleted & allows you to confirm delete.
Once a node marked as deleted is confirmed by someone then it is deleted from both drupal and chado.

Then we can keep the is_obsolete completely separate & ensure that most users don't completely delete data from chado.

While we are waiting for the node delete to be confirmed by someone with the correct permissions we can display a Warning notice on the node page which indicates this uncertain status.

> 
> This is currently a problem with the Tripal analysis modules - you can add features associated with an analysis, but when you delete the analysis, those features don't go away.  I think deleting the features should be optional.

So in the case of stocks -> you might want to delete all associated genotypes & phenotypes... but only genotypes & phenotypes that don't have any other associated stocks. You could also potentially want to delete the features associated with the genotype that you just deleted. I think we are going to run into a Very long Query in order to provide people the option of deleting everything associated with a given stock.

Maybe the best balance would be to list the ids and links to the nodes for all associated genotypes & phenotypes on the Confirm delete page with a note that these genotypes & phenotype will no longer be associated with this stock but will not be deleted. That way the user has a list if they want to manually delete all the genotypes & phenotype... but we don't have to handle any of the actual deleting. 

> 
> 2.  Drupal does have a versioning system, but we don't use it.  Chado just isn't built to handle versioning of records, so we haven't tackled it.  We want to enable community annotation, but backing out to old versions is tough.
> 
> The first idea that comes to mind is to create a new chado stock record each time a node is changed, and have each drupal node revision point to a different stock record in chado.  You'd have to copy over any related data (props, cvterms, pubs) as well.  You'd have to think through every possible relationship in the database.  And this solution seems like a "hack" of chado - if you handed your database to someone else, it wouldn't make sense to them, because the stock table would have many revisions of what should be a single stock record.  
> 
> My second idea would be to somehow store the stock record details in a drupal field that is parseable later.  If you needed to roll back, you would just pick up the old fields in drupal, and restore them to chado.  This has the problem of being redundant and bloating your drupal nodes.  Basically, if we implemented this for all the modules, we might as well get rid of chado entirely and just store everything in drupal. 
> 
> I'm not a fan of either of these solutions, but I think the first one is better.  Are there any other ideas out there?  

I think this needs to be handled by a versioning chado schema module. What comes to mind is adding a stock_revision table which has a stock_id, date, wwwuser, column_name old_value, new_value & just updating the stock everytime. You could even implement triggers which automatically add to the stock_revision table on update. Then when you need to rollback you can just select all old_values from the date period you want to roll back to and update the stock table to have these values.

This would at least keep the stock table uncluttered & unchanged... Also it should be pretty generic. 

> 
> Thanks!
> Meg
> 
> 
> -- 
> Margaret E. Staton
> Clemson University Genomics Institute
> me...@ya...
> 864-656-4643
> 
> 
> From: Stephen Ficklin <FI...@cl...>
> To: Lacey-Anne Sanderson <Lac...@sh...>; GMOD Schema <gmo...@li...>; GMOD Tripal <gmo...@li...>
> Sent: Fri, May 7, 2010 7:00:33 PM
> Subject: Re: [Gmod-tripal] Natural Diversity -Drupal Stock & Natural Diversity Modules
> 
> Hi Lacey,
> 
> Sounds like you've done a great job with a new Drupal stock module for Chado!
> 
> In response to your first question below, perhaps you could maintain the 'is_obsolete' column of chado as an option in your Drupal module as well.  Therefore when a user really wants to delete the stock it is really deleted.  But, if the user wants to make a stock obsolete then it gets flagged as obsolete in Chado and reflected as such in Drupal.  The GMOD folks can correct me if I'm wrong but I believe the is_obsolete field is intended to keep data around for historical purposes so it doesn't have to be deleted.  In which case you would still want to maintain and show the Drupal node for stocks that have the is_obsolete set to true.
> 
> In response to your third question.  I know the folks at WSU are planning to do some Drupal work that would plug into Tripal for the natural diversity tables that are being developed.  I have not followed that discussion very closely on the mailing list, but I don't think it was decided how that would be distributed.  My opinion is that I would like to see Drupal modules that are more generic in nature that correspond to data management of chado modules be incorporated as "core" modules in Tripal.  Other modules that are highly tailored, for example for different analysis methods should be offered separate from Tripal. We will probably take the analysis modules that we developed and pull them out of the "core" as well.  But for now it's just easier to distribute them all together.  We are willing to house a repository of user-contributed Tripal/Drupal compatible modules, and give appropriate credit to the authors.  This will create a single place to find them all.  But, ultimately where a module goes should be up to the developers.  I'd be happy to discuss with you the possibility of incorporating your stock module into Tripal if you would like it to go that route.
> 
> Cheers,
> Stephen
> ________________________________________
> From: Lacey-Anne Sanderson [Lac...@sh...]
> Sent: Friday, May 07, 2010 5:51 PM
> To: GMOD Schema; GMOD Tripal
> Subject: [Gmod-tripal] Natural Diversity -Drupal Stock & Natural Diversity      Modules
> 
> I'm creating a chado_stock drupal module that is almost ready to be released as an alpha version (sometime next week).
> 
> Details:
> - only stores stock_id mapped to a drupal node in drupal
> - all other data is queried from chado when the node is loaded
> - data from chado that is supported includes all fields from the stock table, those from stockprop (including a separate listing of those with cvterm 'synonym'), from stock_dbxref and from stock_relationship
> -the fields from stock are listed in a table format at the top of the node and data from the other three tables are shown below each inside its own signature tripal expandable box.
> -syncing of data between drupal & chado (essentially creating drupal nodes for all chado stock records & storing the stock_id) is supported
> -as is entering stocks through the web interface (currently need to finish this for the other 3 tables) which writes directly to chado.
> 
> Features not yet supported (Still in the works):
> A number of admin features including cleanup, reindexing and taxonomy
> tracking of who entered the data in chado -some type of versioning?
> More user friendly selecting of stocks for relationships and cvterms (currently is a Very long drop-down select)
> 
> What needs to be done next:
> 2. Create a generic nd_assay module
> 3. Create genotype, phenotype, crossexperiment and fieldcollection modules each will all the features from nd_assay but with added required fields and customized display
> 4. Create a project module which groups together data into projects. This one is not specific to the natural diversity project but one of the types of data that can be added to a project with be a nd_assay.
> 
> A couple of Questions:
> 1. Deleting a stock node in drupal -> how should this be reflected in drupal
> - although stock.is_obsolete can be set to True there doesn't seem to be a similar way to indicate that stock relationships or properties have been deleted...
> - stocks which are marked as obsolete won't be added back into drupal during syncing therefore does it matter if the relationships and properties aren't marked since they are only available by accessing chado directly?
> 
> 2. This is a more chado-oriented question: How is versioning handled?
> -In drupal you can easily edit a stock which currently just writes over the original content in chado...
> - Is there a way to keep the original in case you want to rollback?
> 
> 3. Should this stock module be part of tripal rather than the drupal natural diversity module?
> Should the Drupal Natural Diversity module be separate from Tripal (distributed separately as an add-on?
> 
> Thanks for any input!
> Lacey
> 
> 
> ------------------------------------------------------
> Lacey-Anne Sanderson
> Bioinformaticist
> Pulse Crop Breeding and Genetics
> Phone: (306) 966-2430
> Room 3D10 Argriculture
> Department of Plant Sciences
> University of Saskatchewan
> 
> 
> ------------------------------------------------------------------------------
> 
> _______________________________________________
> Gmod-tripal mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
> 
> 

Re: [Gmod-tripal] Natural Diversity -Drupal Stock & Natural Diversity Modules

[Meg S. <me...@ya...>]

Hi, Lacy!  I'm working with the GDR, but Stephen's right, we haven't started designing Tripal modules for the natural diversity schema yet.  But we would love to work with you when we do get started!  It would be much better to have a single set of natural diversity modules that to produce two overlapping code bases.  I'm CCing the person heading up natural diversity for GDR, Sook Jung, as well as the PI, Dorrie Main.  They can chime in on how to start up a collaboration if you are interested.

My thoughts on your questions:
1.  Your solution to the stock obselete_id seems perfectly reasonable to me.  If its marked obsolete, then chado won't try to go looking for the associated property data, so I think its fine to leave the associated properties.  I would only see this being a problem if it has associated data such as features that would be indexed and available to users.  If you wanted those to be come obsolete along with the stock, that would need some more thought.  

This is currently a problem with the Tripal analysis modules - you can add features associated with an analysis, but when you delete the analysis, those features don't go away.  I think deleting the features should be optional.

2.  Drupal does have a versioning system, but we don't use it.  Chado just isn't built to handle versioning of records, so we haven't tackled it.  We want to enable community annotation, but backing out to old versions is tough.

The first idea that comes to mind is to create a new chado stock record each time a node is changed, and have each drupal node revision point to a different stock record in chado.  You'd have to copy over any related data (props, cvterms, pubs) as well.  You'd have to think through every possible relationship in the database.  And this solution seems like a "hack" of chado - if you handed your database to someone else, it wouldn't make sense to them, because the stock table would have many revisions of what should be a single stock record.  

My second idea would be to somehow store the stock record details in a drupal field that is parseable later.  If you needed to roll back, you would just pick up the old fields in drupal, and restore them to chado.  This has the problem of being redundant and bloating your drupal nodes.  Basically, if we implemented this for all the modules, we might as well get rid of chado entirely and just store everything in drupal. 

I'm not a fan of either of these solutions, but I think the first one is better.  Are there any other ideas out there?  

Thanks!
Meg


-- 
Margaret E. Staton
Clemson University Genomics Institute
me...@ya...
864-656-4643




________________________________
From: Stephen Ficklin <FI...@cl...>
To: Lacey-Anne Sanderson <Lac...@sh...>; GMOD Schema <gmo...@li...>; GMOD Tripal <gmo...@li...>
Sent: Fri, May 7, 2010 7:00:33 PM
Subject: Re: [Gmod-tripal] Natural Diversity -Drupal Stock & Natural Diversity Modules

Hi Lacey,

Sounds like you've done a great job with a new Drupal stock module for Chado!

In response to your first question below, perhaps you could maintain the 'is_obsolete' column of chado as an option in your Drupal module as well.  Therefore when a user really wants to delete the stock it is really deleted.  But, if the user wants to make a stock obsolete then it gets flagged as obsolete in Chado and reflected as such in Drupal.  The GMOD folks can correct me if I'm wrong but I believe the is_obsolete field is intended to keep data around for historical purposes so it doesn't have to be deleted.  In which case you would still want to maintain and show the Drupal node for stocks that have the is_obsolete set to true.

In response to your third question.  I know the folks at WSU are planning to do some Drupal work that would plug into Tripal for the natural diversity tables that are being developed.  I have not followed that discussion very closely on the mailing list, but I don't think it was decided how that would be distributed.   My opinion is that I would like to see Drupal modules that are more generic in nature that correspond to data management of chado modules be incorporated as "core" modules in Tripal.   Other modules that are highly tailored, for example for different analysis methods should be offered separate from Tripal. We will probably take the analysis modules that we developed and pull them out of the "core" as well.  But for now it's just easier to distribute them all together.  We are willing to house a repository of user-contributed Tripal/Drupal compatible modules, and give appropriate credit to the authors.  This will create a single place to
 find them all.  But, ultimately where a module goes should be up to the developers.  I'd be happy to discuss with you the possibility of incorporating your stock module into Tripal if you would like it to go that route.

Cheers,
Stephen
________________________________________
From: Lacey-Anne Sanderson [Lac...@sh...]
Sent: Friday, May 07, 2010 5:51 PM
To: GMOD Schema; GMOD Tripal
Subject: [Gmod-tripal] Natural Diversity -Drupal Stock & Natural Diversity      Modules

I'm creating a chado_stock drupal module that is almost ready to be released as an alpha version (sometime next week).

Details:
- only stores stock_id mapped to a drupal node in drupal
- all other data is queried from chado when the node is loaded
- data from chado that is supported includes all fields from the stock table, those from stockprop (including a separate listing of those with cvterm 'synonym'), from stock_dbxref and from stock_relationship
-the fields from stock are listed in a table format at the top of the node and data from the other three tables are shown below each inside its own signature tripal expandable box.
-syncing of data between drupal & chado (essentially creating drupal nodes for all chado stock records & storing the stock_id) is supported
-as is entering stocks through the web interface (currently need to finish this for the other 3 tables) which writes directly to chado.

Features not yet supported (Still in the works):
A number of admin features including cleanup, reindexing and taxonomy
tracking of who entered the data in chado -some type of versioning?
More user friendly selecting of stocks for relationships and cvterms (currently is a Very long drop-down select)

What needs to be done next:
2. Create a generic nd_assay module
3. Create genotype, phenotype, crossexperiment and fieldcollection modules each will all the features from nd_assay but with added required fields and customized display
4. Create a project module which groups together data into projects. This one is not specific to the natural diversity project but one of the types of data that can be added to a project with be a nd_assay.

A couple of Questions:
1. Deleting a stock node in drupal -> how should this be reflected in drupal
- although stock.is_obsolete can be set to True there doesn't seem to be a similar way to indicate that stock relationships or properties have been deleted...
- stocks which are marked as obsolete won't be added back into drupal during syncing therefore does it matter if the relationships and properties aren't marked since they are only available by accessing chado directly?

2. This is a more chado-oriented question: How is versioning handled?
-In drupal you can easily edit a stock which currently just writes over the original content in chado...
- Is there a way to keep the original in case you want to rollback?

3. Should this stock module be part of tripal rather than the drupal natural diversity module?
Should the Drupal Natural Diversity module be separate from Tripal (distributed separately as an add-on?

Thanks for any input!
Lacey


------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Argriculture
Department of Plant Sciences
University of Saskatchewan


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

_______________________________________________
Gmod-tripal mailing list
Gmo...@li...
https://lists.sourceforge.net/lists/listinfo/gmod-tripal



      

Re: [Gmod-tripal] Natural Diversity -Drupal Stock & Natural Diversity Modules

[Stephen F. <FI...@cl...>]

Hi Lacey,

Sounds like you've done a great job with a new Drupal stock module for Chado!

In response to your first question below, perhaps you could maintain the 'is_obsolete' column of chado as an option in your Drupal module as well.  Therefore when a user really wants to delete the stock it is really deleted.  But, if the user wants to make a stock obsolete then it gets flagged as obsolete in Chado and reflected as such in Drupal.  The GMOD folks can correct me if I'm wrong but I believe the is_obsolete field is intended to keep data around for historical purposes so it doesn't have to be deleted.  In which case you would still want to maintain and show the Drupal node for stocks that have the is_obsolete set to true.

In response to your third question.  I know the folks at WSU are planning to do some Drupal work that would plug into Tripal for the natural diversity tables that are being developed.  I have not followed that discussion very closely on the mailing list, but I don't think it was decided how that would be distributed.   My opinion is that I would like to see Drupal modules that are more generic in nature that correspond to data management of chado modules be incorporated as "core" modules in Tripal.   Other modules that are highly tailored, for example for different analysis methods should be offered separate from Tripal. We will probably take the analysis modules that we developed and pull them out of the "core" as well.  But for now it's just easier to distribute them all together.  We are willing to house a repository of user-contributed Tripal/Drupal compatible modules, and give appropriate credit to the authors.  This will create a single place to find them all.  But, ultimately where a module goes should be up to the developers.  I'd be happy to discuss with you the possibility of incorporating your stock module into Tripal if you would like it to go that route.

Cheers,
Stephen
________________________________________
From: Lacey-Anne Sanderson [Lac...@sh...]
Sent: Friday, May 07, 2010 5:51 PM
To: GMOD Schema; GMOD Tripal
Subject: [Gmod-tripal] Natural Diversity -Drupal Stock & Natural Diversity      Modules

I'm creating a chado_stock drupal module that is almost ready to be released as an alpha version (sometime next week).

Details:
- only stores stock_id mapped to a drupal node in drupal
- all other data is queried from chado when the node is loaded
- data from chado that is supported includes all fields from the stock table, those from stockprop (including a separate listing of those with cvterm 'synonym'), from stock_dbxref and from stock_relationship
-the fields from stock are listed in a table format at the top of the node and data from the other three tables are shown below each inside its own signature tripal expandable box.
-syncing of data between drupal & chado (essentially creating drupal nodes for all chado stock records & storing the stock_id) is supported
-as is entering stocks through the web interface (currently need to finish this for the other 3 tables) which writes directly to chado.

Features not yet supported (Still in the works):
A number of admin features including cleanup, reindexing and taxonomy
tracking of who entered the data in chado -some type of versioning?
More user friendly selecting of stocks for relationships and cvterms (currently is a Very long drop-down select)

What needs to be done next:
2. Create a generic nd_assay module
3. Create genotype, phenotype, crossexperiment and fieldcollection modules each will all the features from nd_assay but with added required fields and customized display
4. Create a project module which groups together data into projects. This one is not specific to the natural diversity project but one of the types of data that can be added to a project with be a nd_assay.

A couple of Questions:
1. Deleting a stock node in drupal -> how should this be reflected in drupal
- although stock.is_obsolete can be set to True there doesn't seem to be a similar way to indicate that stock relationships or properties have been deleted...
- stocks which are marked as obsolete won't be added back into drupal during syncing therefore does it matter if the relationships and properties aren't marked since they are only available by accessing chado directly?

2. This is a more chado-oriented question: How is versioning handled?
-In drupal you can easily edit a stock which currently just writes over the original content in chado...
- Is there a way to keep the original in case you want to rollback?

3. Should this stock module be part of tripal rather than the drupal natural diversity module?
Should the Drupal Natural Diversity module be separate from Tripal (distributed separately as an add-on?

Thanks for any input!
Lacey


------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Argriculture
Department of Plant Sciences
University of Saskatchewan

[Gmod-tripal] Natural Diversity -Drupal Stock & Natural Diversity Modules

[Lacey-Anne S. <Lac...@sh...>]

I'm creating a chado_stock drupal module that is almost ready to be released as an alpha version (sometime next week).

Details:
- only stores stock_id mapped to a drupal node in drupal
- all other data is queried from chado when the node is loaded
- data from chado that is supported includes all fields from the stock table, those from stockprop (including a separate listing of those with cvterm 'synonym'), from stock_dbxref and from stock_relationship
-the fields from stock are listed in a table format at the top of the node and data from the other three tables are shown below each inside its own signature tripal expandable box.
-syncing of data between drupal & chado (essentially creating drupal nodes for all chado stock records & storing the stock_id) is supported
-as is entering stocks through the web interface (currently need to finish this for the other 3 tables) which writes directly to chado.

Features not yet supported (Still in the works):
A number of admin features including cleanup, reindexing and taxonomy
tracking of who entered the data in chado -some type of versioning?
More user friendly selecting of stocks for relationships and cvterms (currently is a Very long drop-down select) 

What needs to be done next:
2. Create a generic nd_assay module
3. Create genotype, phenotype, crossexperiment and fieldcollection modules each will all the features from nd_assay but with added required fields and customized display
4. Create a project module which groups together data into projects. This one is not specific to the natural diversity project but one of the types of data that can be added to a project with be a nd_assay.

A couple of Questions:
1. Deleting a stock node in drupal -> how should this be reflected in drupal
	- although stock.is_obsolete can be set to True there doesn't seem to be a similar way to indicate that stock relationships or properties have been deleted...
	- stocks which are marked as obsolete won't be added back into drupal during syncing therefore does it matter if the relationships and properties aren't marked since they are only available by accessing chado directly?

2. This is a more chado-oriented question: How is versioning handled?
	-In drupal you can easily edit a stock which currently just writes over the original content in chado...
	- Is there a way to keep the original in case you want to rollback?

3. Should this stock module be part of tripal rather than the drupal natural diversity module? 
	Should the Drupal Natural Diversity module be separate from Tripal (distributed separately as an add-on?

Thanks for any input!
Lacey


------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Argriculture
Department of Plant Sciences
University of Saskatchewan

Re: [Gmod-tripal] Natural Diversity Module

[Stephen F. <FI...@cl...>]

Hi Lacey,

I believe Dr. Main's group at WSU is planning to do some work with this in the future. I've CC'ed her and Sook on this email so they can chime in.

When you get to the point that you want to do module development feel free  to let me know and I can provide some assistance with working with the Tripal API, which is not well documented at the moment.

Stephen

From: Lacey-Anne Sanderson [mailto:Lac...@sh...]
Sent: Friday, March 26, 2010 12:45 PM
To: GMOD Tripal
Subject: [Gmod-tripal] Natural Diversity Module

Hi,

I am very interested in the Natural Diversity Module (Stocks, Genotypes and Phenotypes) currently being developed and wondered if anyone was actively working on developing a triple add-on for this module. If there is a group already working on it, I would be open to helping them and if not I will probably take on this project myself. However, I am very new to module development and as such it might take time/guidance...

Just thought I'd put my intentions out there,
Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Argriculture
Department of Plant Sciences
University of Saskatchewan

[Gmod-tripal] Natural Diversity Module

[Lacey-Anne S. <Lac...@sh...>]

Hi,

I am very interested in the Natural Diversity Module (Stocks, Genotypes and Phenotypes) currently being developed and wondered if anyone was actively working on developing a triple add-on for this module. If there is a group already working on it, I would be open to helping them and if not I will probably take on this project myself. However, I am very new to module development and as such it might take time/guidance...

Just thought I'd put my intentions out there,
Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Argriculture
Department of Plant Sciences
University of Saskatchewan

Re: [Gmod-tripal] Filtering Views based on chado DB a feature references

[Stephen F. <FI...@cl...>]

Hi Lacey,

Attached is a php script that Chun-Huai wrote that you can use to set the external database taxonomy for your features.  It's a band-aid fix but should get you what you need and will only set taxonomy for the external database.   It's something we should expand and roll into a full blown module so that folks can create views using the taxonomy.  

Here are the instructions:

1. Copy the script to the web server's file system. (e.g. <drupal_base>/sites/all/modules/tripal_feature)
2. Change to <drupal_base>
3. Replace <admin_user> in the following command and run the script.
php ./site/all/modules/tripal_feature/feature_assign_dbxref.php <admin_user>

Let us know if this helps,
Stephen


-----Original Message-----
From: Stephen Ficklin [mailto:FI...@cl...] 
Sent: Friday, February 26, 2010 9:48 PM
To: Lacey Sanderson; gmo...@li...
Subject: Re: [Gmod-tripal] Filtering Views based on chado DB a feature references

Dear Lacey,

We've spent some time looking at this and are reminded of why we did not set this up initially.  Unfortunately, the Views in Drupal require an inner join with the tables for which they allow for filtering data for viewing.  This can't be done because Drupal and Chado are in two separate chado databases. If we duplicate chado data in Drupal it can work but we'd prefer not to do that.  There may be a way we can get around this but for now it looks like Taxonomy is your only way.   We're trying to put together a small little PHP script that will allow you to set taxonomy the way you want.  It's a temporary work around but should help you get your site the way you want it.

Stephen

________________________________________
From: Lacey Sanderson [lac...@sh...]
Sent: Tuesday, February 23, 2010 11:31 AM
To: gmo...@li...
Subject: [Gmod-tripal] Filtering Views based on chado DB a feature references

Hi,

I would like to make a large table of features filterable by database the feature is associated with. For example, I have some features with NCBI accessions and some with DFCI accessions but I only want those from NCBI in the view...

I know I can do this with views using taxonomy terms but am unsure how to add the db to the feature taxonomy. I have looked up a number of bulk taxonomy assigning modules but they all seem to require me to select each node I want to add the term to which would take forever with the number of features in chado...

How would I add the functionality available for organism and type feature taxonomy to also add db referenced? Or is there another way for me to make my views filterable by content of a feature node?

Thanks!
Lacey

---------------------------------
Lacey Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Department of Plant Sciences
University of Saskatchewan.


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Re: [Gmod-tripal] Filtering Views based on chado DB a feature references

[Stephen F. <FI...@cl...>]

Dear Lacey,

We've spent some time looking at this and are reminded of why we did not set this up initially.  Unfortunately, the Views in Drupal require an inner join with the tables for which they allow for filtering data for viewing.  This can't be done because Drupal and Chado are in two separate chado databases. If we duplicate chado data in Drupal it can work but we'd prefer not to do that.  There may be a way we can get around this but for now it looks like Taxonomy is your only way.   We're trying to put together a small little PHP script that will allow you to set taxonomy the way you want.  It's a temporary work around but should help you get your site the way you want it.

Stephen

________________________________________
From: Lacey Sanderson [lac...@sh...]
Sent: Tuesday, February 23, 2010 11:31 AM
To: gmo...@li...
Subject: [Gmod-tripal] Filtering Views based on chado DB a feature references

Hi,

I would like to make a large table of features filterable by database the feature is associated with. For example, I have some features with NCBI accessions and some with DFCI accessions but I only want those from NCBI in the view...

I know I can do this with views using taxonomy terms but am unsure how to add the db to the feature taxonomy. I have looked up a number of bulk taxonomy assigning modules but they all seem to require me to select each node I want to add the term to which would take forever with the number of features in chado...

How would I add the functionality available for organism and type feature taxonomy to also add db referenced? Or is there another way for me to make my views filterable by content of a feature node?

Thanks!
Lacey

---------------------------------
Lacey Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Department of Plant Sciences
University of Saskatchewan.

Re: [Gmod-tripal] Filtering Views based on chado DB a feature references

[Stephen F. <FI...@cl...>]

Hi Lacey,

You've hit on one of the areas we have on our TODO list, which is to make available to the Drupal Views module some of the other column data in chado so that you can do exactly what you're asking even without having to use taxonomy.   I'll talk with some folks here and see if we can put something together for you so you can do this...

Stephen

From: Lacey Sanderson [mailto:lac...@sh...]
Sent: Tuesday, February 23, 2010 11:32 AM
To: gmo...@li...
Subject: [Gmod-tripal] Filtering Views based on chado DB a feature references

Hi,

I would like to make a large table of features filterable by database the feature is associated with. For example, I have some features with NCBI accessions and some with DFCI accessions but I only want those from NCBI in the view...

I know I can do this with views using taxonomy terms but am unsure how to add the db to the feature taxonomy. I have looked up a number of bulk taxonomy assigning modules but they all seem to require me to select each node I want to add the term to which would take forever with the number of features in chado...

How would I add the functionality available for organism and type feature taxonomy to also add db referenced? Or is there another way for me to make my views filterable by content of a feature node?

Thanks!
Lacey

---------------------------------
Lacey Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Department of Plant Sciences
University of Saskatchewan.

[Gmod-tripal] Filtering Views based on chado DB a feature references

[Lacey S. <lac...@sh...>]

Hi,

I would like to make a large table of features filterable by database  
the feature is associated with. For example, I have some features with  
NCBI accessions and some with DFCI accessions but I only want those  
from NCBI in the view...

I know I can do this with views using taxonomy terms but am unsure how  
to add the db to the feature taxonomy. I have looked up a number of  
bulk taxonomy assigning modules but they all seem to require me to  
select each node I want to add the term to which would take forever  
with the number of features in chado...

How would I add the functionality available for organism and type  
feature taxonomy to also add db referenced? Or is there another way  
for me to make my views filterable by content of a feature node?

Thanks!
Lacey

---------------------------------
Lacey Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Department of Plant Sciences
University of Saskatchewan.

Re: [Gmod-tripal] GMOD Logo Program

[Dave C. G. H. D. <he...@gm...>]

Hello all,

This is a reminder that the deadline for applications to the GMOD Logo
Program (http://gmod.org/wiki/GMOD_Logo_Program) is March 1, one week from
today.

See the program wiki page (http://gmod.org/wiki/GMOD_Logo_Program) and below
for details.  Please let me know if you have any questions.

Thanks,

Dave C.

PS: And the deadline for applying to 2010 GMOD Summer School Americas is
TODAY!  See http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas for
details.

On Thu, Feb 4, 2010 at 9:29 AM, Dave Clements, GMOD Help Desk <he...@gm...
> wrote:

> Hello all,
>
> Need a logo that tells people what your web site, database or GMOD
> component is about?  If your resource needs a logo then the GMOD Logo
> Program (http://gmod.org/wiki/GMOD_Logo_Program) can help.
>
>
> I am pleased to announce the first call for participation in the GMOD
> Logo Program. This program is for GMOD users and developers that would
> like have a custom designed logo for their web site, database or GMOD
> component. The program pairs GMOD community members with students in
> advanced design classes at colleges and universities.  This spring we
> will be working with a class at Linn-Benton Community College.
> Participants will meet several times (remotely) over a 3 week period,
> with the end result being a new logo for your resource.
>
> Participation is limited to non-profits, and costs US$75. If you are
> interested, please see http://gmod.org/wiki/GMOD_Logo_Program for
> additional details and requirements, and an application form. The
> program is accepting applications until March 1.
>
> Thanks,
>
> Dave Clements
> GMOD Help Desk
>
> PS: This program was inspired by ZFIN's success with its logo (see
> http://zfin.org).  ZFIN's excellent logo was created by working with a
> design class at the University of Oregon.
>
> --
> Please keep responses on the list!
> http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
> http://gmod.org/wiki/GMOD_Logo_Program
> http://gmod.org/wiki/GMOD_News
> Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback
>



-- 
===> PLEASE KEEP RESPONSES ON THE LIST <===
http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
http://gmod.org/wiki/GMOD_Logo_Program
http://gmod.org/wiki/GMOD_News
Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback

Re: [Gmod-tripal] 2010 GMOD Summer School - Americas

[Dave C. G. H. D. <he...@gm...>]

Hello all,

This is a reminder that the deadline for applying to the 2010 GMOD
Summer School - Americas is the end of the day on Monday, February 22,
which is now less than a week away.  Any applications received after
that will automatically be placed on the waiting list.

Admission is competitive and is based on the strength of the
application, especially the statement of interest.  See
http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas for additional
information.

Thanks,

Dave Clements

On Fri, Jan 29, 2010 at 2:02 PM, Dave Clements, GMOD Help Desk
<he...@gm...> wrote:
> Hello all,
>
> I am pleased to announce that we are now accepting applications for:
>
>   2010 GMOD Summer School - Americas
>     6-9 May 2010
>     NESCent, Durham, NC, USA
>     http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
>
> This will be a hands-on multi-day course aimed at teaching new GMOD
> users/administrators how to get GMOD Components up and running. The
> course will introduce participants to the GMOD project and then focus
> on installation, configuration and integration of popular GMOD
> Components. The course will be held May 6-9, at NESCent in Durham, NC.
>
> These components will be covered:
>    * Apollo - genome annotation editor
>    * Chado - a modular and extensible database schema
>    * Galaxy - workflow system
>    * GBrowse - the Generic Genome Browser
>    * GBrowse_syn - A generic synteny browser
>    * JBrowse - genome browser
>    * MAKER - genome annotation pipeline
>    * Tripal - web front end for Chado
>
> The deadline for applying is the end of Friday, February 22. Admission
> is competitive and is based on the strength of the application
> (especially the statement of interest). In 2009 there were over 50
> applications for the 25 slots. Any applications received after the
> deadline will be placed on the waiting list.
>
> See the course page for details and an application link:
>  http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
>
> Thanks,
>
> Dave Clements
> GMOD Help Desk
>
> PS: We are also investigating holding a GMOD course in the
> Asia/Pacific region, sometime this fall. Watch the GMOD mailing lists
> and the GMOD News page/RSS feed for updates.
> --
> Please keep responses on the list!
> http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
> http://gmod.org/wiki/GMOD_News
> Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback
>



-- 
===> PLEASE KEEP RESPONSES ON THE LIST <===
http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
http://gmod.org/wiki/GMOD_Logo_Program
http://gmod.org/wiki/GMOD_News
Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback

Re: [Gmod-tripal] Adding Content to Tripal Templates

[Stephen F. <FI...@cl...>]

I should clarify... you want to make the fields hidden otherwise they will show up twice on the page.  Once in the table because of the editing to the node-chado_organism.tpl.php file and once again when Drupal tries to insert the fields on the page.  Since you're manually adding them using the template you don't need them to show up again. 

-----Original Message-----
From: Stephen Ficklin [mailto:FI...@cl...] 
Sent: Tuesday, February 16, 2010 1:54 PM
To: Lacey Sanderson
Cc: gmo...@li...
Subject: Re: [Gmod-tripal] Adding Content to Tripal Templates

Hi Lacey,

You can add this HTML to the table in the node-chado_organism.tpl.php file in Tripal theme for each one of your new content types:

              <tr>
                 <th>Field Title</th>
                 <td><?php foreach($node->field_name as $item) print $item['value'] . "<br>"  ?></td>
              </tr>

And then go back to the organism content type and make the new fields hidden.  You can do this by clicking the 'Display fields' tab and then setting the 'Full Node' dropdown to 'Hidden".

Stephen

________________________________________
From: Lacey Sanderson [Lac...@sh...]
Sent: Tuesday, February 16, 2010 1:32 PM
To: Stephen Ficklin
Cc: gmo...@li...
Subject: Re: [Gmod-tripal] Adding Content to Tripal Templates

Perfect! Thanks!

Now if I want to display those values in the table with the Genus and Species instead of as paragraphs at the bottom (displayed using <?php print $content ?> in the template), how would I access the values?

I already tried <?php print $field_name ?>, <?php print $content->field_name ?>, and <?php $nutrition = content_fields('field_nutrition'); print $nutrition[0]; ?>

This is probably a factor of my lack of php knowledge but I appretiate any help you can give me... I'm on a tight timeline right now and don't have time to learn php...

Thanks!
Lacey

On 16-Feb-10, at 11:25 AM, Stephen Ficklin wrote:

Hi Lacey,

This can be done easily using the CCK module (Content Construction Kit).  You can download it from here: http://drupal.org/project/cck

After you enable the module you can add new fields to the Organism page by clicking 'Administer' -> 'Content Management' -> 'Content Types'.

You'll then see the list of all content types, one of which is 'Organism' of type 'chado_organism'.  Click 'Manage Fields'.  You can then add a brand new field, for example 'Morphology'.  You'll tell it what kind of field it is and set some parameters for it.  You can even drag it higher or lower in the field list to place where you want it to show up.  If you place it directly under 'Menu Settings' then your new content should appear just under the organism description.  Finally, go to your organism and edit it. You'll see your new field.  Add content and save it and you should see it on the page.  All of these new fields will be stored in Drupal as opposed to Chado.

Good question. This is information we should add to the User's Guide.

Stephen

-----Original Message-----
From: Lacey Sanderson [mailto:Lac...@sh...]
Sent: Tuesday, February 16, 2010 12:04 PM
To: gmo...@li...<mailto:gmo...@li...>
Subject: [Gmod-tripal] Adding Content to Tripal Templates

Hi,

I am trying to add content/fields such as s cultivation, taxonomy,
morphology, etc. to the organism pages. I would like to store the data
for these fields in drupal rather than chado in order to not customize
the chado schema. However, I am Really new to drupal and have no idea
how to add/edit fields which can then be accessed using $variable in
the tripal templates. If someone could point me in the right direction
as to how to do this, that would be Great!

Thanks,
Lacey

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_______________________________________________
Gmod-tripal mailing list
Gmo...@li...
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

---------------------------------
Lacey Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Department of Plant Sciences
University of Saskatchewan.


------------------------------------------------------------------------------
SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
http://p.sf.net/sfu/solaris-dev2dev
_______________________________________________
Gmod-tripal mailing list
Gmo...@li...
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

Re: [Gmod-tripal] Adding Content to Tripal Templates

[Stephen F. <FI...@cl...>]

Hi Lacey,

You can add this HTML to the table in the node-chado_organism.tpl.php file in Tripal theme for each one of your new content types:

              <tr>
                 <th>Field Title</th>
                 <td><?php foreach($node->field_name as $item) print $item['value'] . "<br>"  ?></td>
              </tr>

And then go back to the organism content type and make the new fields hidden.  You can do this by clicking the 'Display fields' tab and then setting the 'Full Node' dropdown to 'Hidden".

Stephen

________________________________________
From: Lacey Sanderson [Lac...@sh...]
Sent: Tuesday, February 16, 2010 1:32 PM
To: Stephen Ficklin
Cc: gmo...@li...
Subject: Re: [Gmod-tripal] Adding Content to Tripal Templates

Perfect! Thanks!

Now if I want to display those values in the table with the Genus and Species instead of as paragraphs at the bottom (displayed using <?php print $content ?> in the template), how would I access the values?

I already tried <?php print $field_name ?>, <?php print $content->field_name ?>, and <?php $nutrition = content_fields('field_nutrition'); print $nutrition[0]; ?>

This is probably a factor of my lack of php knowledge but I appretiate any help you can give me... I'm on a tight timeline right now and don't have time to learn php...

Thanks!
Lacey

On 16-Feb-10, at 11:25 AM, Stephen Ficklin wrote:

Hi Lacey,

This can be done easily using the CCK module (Content Construction Kit).  You can download it from here: http://drupal.org/project/cck

After you enable the module you can add new fields to the Organism page by clicking 'Administer' -> 'Content Management' -> 'Content Types'.

You'll then see the list of all content types, one of which is 'Organism' of type 'chado_organism'.  Click 'Manage Fields'.  You can then add a brand new field, for example 'Morphology'.  You'll tell it what kind of field it is and set some parameters for it.  You can even drag it higher or lower in the field list to place where you want it to show up.  If you place it directly under 'Menu Settings' then your new content should appear just under the organism description.  Finally, go to your organism and edit it. You'll see your new field.  Add content and save it and you should see it on the page.  All of these new fields will be stored in Drupal as opposed to Chado.

Good question. This is information we should add to the User's Guide.

Stephen

-----Original Message-----
From: Lacey Sanderson [mailto:Lac...@sh...]
Sent: Tuesday, February 16, 2010 12:04 PM
To: gmo...@li...<mailto:gmo...@li...>
Subject: [Gmod-tripal] Adding Content to Tripal Templates

Hi,

I am trying to add content/fields such as s cultivation, taxonomy,
morphology, etc. to the organism pages. I would like to store the data
for these fields in drupal rather than chado in order to not customize
the chado schema. However, I am Really new to drupal and have no idea
how to add/edit fields which can then be accessed using $variable in
the tripal templates. If someone could point me in the right direction
as to how to do this, that would be Great!

Thanks,
Lacey

------------------------------------------------------------------------------
SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
http://p.sf.net/sfu/solaris-dev2dev
_______________________________________________
Gmod-tripal mailing list
Gmo...@li...
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

---------------------------------
Lacey Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Department of Plant Sciences
University of Saskatchewan.

Re: [Gmod-tripal] Adding Content to Tripal Templates

[Lacey S. <Lac...@sh...>]

Perfect! Thanks!

Now if I want to display those values in the table with the Genus and  
Species instead of as paragraphs at the bottom (displayed using <?php  
print $content ?> in the template), how would I access the values?

I already tried <?php print $field_name ?>, <?php print $content- 
 >field_name ?>, and <?php $nutrition =  
content_fields('field_nutrition'); print $nutrition[0]; ?>

This is probably a factor of my lack of php knowledge but I appretiate  
any help you can give me... I'm on a tight timeline right now and  
don't have time to learn php...

Thanks!
Lacey

On 16-Feb-10, at 11:25 AM, Stephen Ficklin wrote:

> Hi Lacey,
>
> This can be done easily using the CCK module (Content Construction  
> Kit).  You can download it from here: http://drupal.org/project/cck
>
> After you enable the module you can add new fields to the Organism  
> page by clicking 'Administer' -> 'Content Management' -> 'Content  
> Types'.
>
> You'll then see the list of all content types, one of which is  
> 'Organism' of type 'chado_organism'.  Click 'Manage Fields'.  You  
> can then add a brand new field, for example 'Morphology'.  You'll  
> tell it what kind of field it is and set some parameters for it.   
> You can even drag it higher or lower in the field list to place  
> where you want it to show up.  If you place it directly under 'Menu  
> Settings' then your new content should appear just under the  
> organism description.  Finally, go to your organism and edit it.  
> You'll see your new field.  Add content and save it and you should  
> see it on the page.  All of these new fields will be stored in  
> Drupal as opposed to Chado.
>
> Good question. This is information we should add to the User's Guide.
>
> Stephen
>
> -----Original Message-----
> From: Lacey Sanderson [mailto:Lac...@sh...]
> Sent: Tuesday, February 16, 2010 12:04 PM
> To: gmo...@li...
> Subject: [Gmod-tripal] Adding Content to Tripal Templates
>
> Hi,
>
> I am trying to add content/fields such as s cultivation, taxonomy,
> morphology, etc. to the organism pages. I would like to store the data
> for these fields in drupal rather than chado in order to not customize
> the chado schema. However, I am Really new to drupal and have no idea
> how to add/edit fields which can then be accessed using $variable in
> the tripal templates. If someone could point me in the right direction
> as to how to do this, that would be Great!
>
> Thanks,
> Lacey
>
> ------------------------------------------------------------------------------
> SOLARIS 10 is the OS for Data Centers - provides features such as  
> DTrace,
> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
> http://p.sf.net/sfu/solaris-dev2dev
> _______________________________________________
> Gmod-tripal mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal

---------------------------------
Lacey Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Department of Plant Sciences
University of Saskatchewan.

Re: [Gmod-tripal] Adding Content to Tripal Templates

[Stephen F. <FI...@cl...>]

Hi Scott,

No it doesn't, but it should.  We can add this functionality easily and update the module in the repository.

To allow folks to add custom fields to the organism (or feature) page that could then go into the organismprop table would take a bit of looking at but should also available as well.  I'll put that on our list of items to add to the organism module.

Stephen

-----Original Message-----
From: Scott Cain [mailto:sc...@sc...] 
Sent: Tuesday, February 16, 2010 12:32 PM
To: Stephen Ficklin
Cc: Lacey Sanderson; gmo...@li...
Subject: Re: [Gmod-tripal] Adding Content to Tripal Templates

Hi Stephen and Lacey,

Presumably, at least some of the things you want to add could go in
the organismprop table.  Does tripal make use of the information in
organismprop?

Scott


On Tue, Feb 16, 2010 at 12:25 PM, Stephen Ficklin <FI...@cl...> wrote:
> Hi Lacey,
>
> This can be done easily using the CCK module (Content Construction Kit).  You can download it from here: http://drupal.org/project/cck
>
> After you enable the module you can add new fields to the Organism page by clicking 'Administer' -> 'Content Management' -> 'Content Types'.
>
> You'll then see the list of all content types, one of which is 'Organism' of type 'chado_organism'.  Click 'Manage Fields'.  You can then add a brand new field, for example 'Morphology'.  You'll tell it what kind of field it is and set some parameters for it.  You can even drag it higher or lower in the field list to place where you want it to show up.  If you place it directly under 'Menu Settings' then your new content should appear just under the organism description.  Finally, go to your organism and edit it. You'll see your new field.  Add content and save it and you should see it on the page.  All of these new fields will be stored in Drupal as opposed to Chado.
>
> Good question. This is information we should add to the User's Guide.
>
> Stephen
>
> -----Original Message-----
> From: Lacey Sanderson [mailto:Lac...@sh...]
> Sent: Tuesday, February 16, 2010 12:04 PM
> To: gmo...@li...
> Subject: [Gmod-tripal] Adding Content to Tripal Templates
>
> Hi,
>
> I am trying to add content/fields such as s cultivation, taxonomy,
> morphology, etc. to the organism pages. I would like to store the data
> for these fields in drupal rather than chado in order to not customize
> the chado schema. However, I am Really new to drupal and have no idea
> how to add/edit fields which can then be accessed using $variable in
> the tripal templates. If someone could point me in the right direction
> as to how to do this, that would be Great!
>
> Thanks,
> Lacey
>
> ------------------------------------------------------------------------------
> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
> http://p.sf.net/sfu/solaris-dev2dev
> _______________________________________________
> Gmod-tripal mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>
> ------------------------------------------------------------------------------
> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
> http://p.sf.net/sfu/solaris-dev2dev
> _______________________________________________
> Gmod-tripal mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>



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

Re: [Gmod-tripal] Adding Content to Tripal Templates

[Scott C. <sc...@sc...>]

Hi Stephen and Lacey,

Presumably, at least some of the things you want to add could go in
the organismprop table.  Does tripal make use of the information in
organismprop?

Scott


On Tue, Feb 16, 2010 at 12:25 PM, Stephen Ficklin <FI...@cl...> wrote:
> Hi Lacey,
>
> This can be done easily using the CCK module (Content Construction Kit).  You can download it from here: http://drupal.org/project/cck
>
> After you enable the module you can add new fields to the Organism page by clicking 'Administer' -> 'Content Management' -> 'Content Types'.
>
> You'll then see the list of all content types, one of which is 'Organism' of type 'chado_organism'.  Click 'Manage Fields'.  You can then add a brand new field, for example 'Morphology'.  You'll tell it what kind of field it is and set some parameters for it.  You can even drag it higher or lower in the field list to place where you want it to show up.  If you place it directly under 'Menu Settings' then your new content should appear just under the organism description.  Finally, go to your organism and edit it. You'll see your new field.  Add content and save it and you should see it on the page.  All of these new fields will be stored in Drupal as opposed to Chado.
>
> Good question. This is information we should add to the User's Guide.
>
> Stephen
>
> -----Original Message-----
> From: Lacey Sanderson [mailto:Lac...@sh...]
> Sent: Tuesday, February 16, 2010 12:04 PM
> To: gmo...@li...
> Subject: [Gmod-tripal] Adding Content to Tripal Templates
>
> Hi,
>
> I am trying to add content/fields such as s cultivation, taxonomy,
> morphology, etc. to the organism pages. I would like to store the data
> for these fields in drupal rather than chado in order to not customize
> the chado schema. However, I am Really new to drupal and have no idea
> how to add/edit fields which can then be accessed using $variable in
> the tripal templates. If someone could point me in the right direction
> as to how to do this, that would be Great!
>
> Thanks,
> Lacey
>
> ------------------------------------------------------------------------------
> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
> http://p.sf.net/sfu/solaris-dev2dev
> _______________________________________________
> Gmod-tripal mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>
> ------------------------------------------------------------------------------
> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
> http://p.sf.net/sfu/solaris-dev2dev
> _______________________________________________
> Gmod-tripal mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>



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

Re: [Gmod-tripal] Adding Content to Tripal Templates

[Stephen F. <FI...@cl...>]

Hi Lacey,

This can be done easily using the CCK module (Content Construction Kit).  You can download it from here: http://drupal.org/project/cck

After you enable the module you can add new fields to the Organism page by clicking 'Administer' -> 'Content Management' -> 'Content Types'.

You'll then see the list of all content types, one of which is 'Organism' of type 'chado_organism'.  Click 'Manage Fields'.  You can then add a brand new field, for example 'Morphology'.  You'll tell it what kind of field it is and set some parameters for it.  You can even drag it higher or lower in the field list to place where you want it to show up.  If you place it directly under 'Menu Settings' then your new content should appear just under the organism description.  Finally, go to your organism and edit it. You'll see your new field.  Add content and save it and you should see it on the page.  All of these new fields will be stored in Drupal as opposed to Chado. 

Good question. This is information we should add to the User's Guide.

Stephen

-----Original Message-----
From: Lacey Sanderson [mailto:Lac...@sh...] 
Sent: Tuesday, February 16, 2010 12:04 PM
To: gmo...@li...
Subject: [Gmod-tripal] Adding Content to Tripal Templates

Hi,

I am trying to add content/fields such as s cultivation, taxonomy,  
morphology, etc. to the organism pages. I would like to store the data  
for these fields in drupal rather than chado in order to not customize  
the chado schema. However, I am Really new to drupal and have no idea  
how to add/edit fields which can then be accessed using $variable in  
the tripal templates. If someone could point me in the right direction  
as to how to do this, that would be Great!

Thanks,
Lacey

------------------------------------------------------------------------------
SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
http://p.sf.net/sfu/solaris-dev2dev
_______________________________________________
Gmod-tripal mailing list
Gmo...@li...
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

[Gmod-tripal] Adding Content to Tripal Templates

[Lacey S. <Lac...@sh...>]

Hi,

I am trying to add content/fields such as s cultivation, taxonomy,  
morphology, etc. to the organism pages. I would like to store the data  
for these fields in drupal rather than chado in order to not customize  
the chado schema. However, I am Really new to drupal and have no idea  
how to add/edit fields which can then be accessed using $variable in  
the tripal templates. If someone could point me in the right direction  
as to how to do this, that would be Great!

Thanks,
Lacey