[Gmod-tripal] Chado Stock Module

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[Gmod-tripal] Chado Stock Module

Lacey-Anne Sanderson
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


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Re: Chado Stock Module

Stephen Ficklin

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:[hidden email]]
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

 


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