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tripal / tripal_doc

Official Documentation for the Tripal Platform
https://tripaldoc.readthedocs.io/en/latest/
GNU General Public License v3.0
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Docs: Adopting non-Chado schema in Tripal 3 #19

Open sdash-github opened 6 years ago

sdash-github commented 6 years ago

Tripal3 supports non-Chado schema per announcement. It will be very useful to have documentation to implement this feature.

At NCGR we have developed a new generic schema (outside our Chado instance) for RNASeq/gene expression data and have been serving this expression data via a Drupal module. My specific need is to explain the schema to Tripal so that I can develop a Tripal extension that integrates well with other data in Chado. --Sudhansu Dash

spficklin commented 6 years ago

Okay! We'll prioritize getting that together for you!

spficklin commented 6 years ago

Oh, and perhaps we should have a meeting to discuss your needs in this regard so we get the documentation containing what you need.

sdash-github commented 6 years ago

Thanks. The following may give you some idea on what I am expecting. Level: Not expert developers. Need:

  1. Where to start.
  2. Examples to specify tables, relations and table columns.
  3. Any tricks to relate to Chado tables (particularly to feature table).
  4. Just enough code examples to extract the data in template files.

Meeting: Good idea! Please suggest a time (below are times I don't have flexibility; Mountain Daylight saving Times). Tue: 2-3, Wed: 10:30-11:30, 12:30-1:00, 2-3 Thu: 2-3

laceysanderson commented 6 years ago

Hi @spficklin, I talked to @sdash-github at the recent LegFed workshop regarding this module. You can find the module code here and an example here. I already advised them to move the functionality into a custom Tripal3 Field (Documentation) to make it easier to integrate.

@sdash-github, is your new generic schema in the same database as chado/drupal? Also, does it stand alone or are the tables within the public schema?

sdash-github commented 6 years ago

@laceysanderson: -- Same database as Chado and I access the tables with ongenome.* #schea name: 'ongenome' -- All the tables are in ongenome schema.

spficklin commented 6 years ago

I don't see this getting done before the Tv3 stable release. So I'm taking off the release blocker. It's not essential that we have this for the release. But it is very important.

spficklin commented 5 years ago

Getting back to this. It will require a bit of work to come up with an example use case and document it and make sure there are no bugs in the code to support another back-end. So, I'm marking this for a 3.3 release.