Tripal 4 Fields -upgrading core fields

[laceysanderson]

Core Tripal 4 Development Task

Branch Name: tv4g1-issue1414-[name of field you are working on]

This issue is providing an organization spot to upgrade all the core Tripal fields. Please comment here with the field you are going to upgrade and create a branch using the naming schema above to contain your work. When done, create a PR for your field.

Here is the documentation for Tripal Fields

Fields in order of complexity

• [x] data__sequence_checksum Pull #1419 closed #1607 merged
• [x] data__sequence_length Pull #1419 closed #1607 merged
• [x] operation__analysis Pull #1578 merged
• [x] local__contact Pull #1599 merged
• [x] sep__protocol Pull #1743 merged
• [x] uo__unit Pull #1680 merged
• [x] local__source_data Pull #1504 merged
• [x] data__sequence_coordinates Pull #1700 merged
• [x] operation__analysis Pull #1578 merged
• [x] local__contact Pull #1431 merged
• [x] sbo__database_cross_reference Pull #1710 merged
• [x] schema__alternate_name Pull #1447 closed #1650 merged
• [ ] sbo__relationship

• sio__references - with a complete set of linker fields now available, this specialized field is likely no longer needed 😐

Some other fields needed are listed here https://github.com/tripal/tripal/issues/1550#issuecomment-1623912019

[dsenalik]

I am working on the local__contact field :grin:

[srobb1]

I would like to work on data__sequence_length

[spficklin]

Just FYI.... we have a new way to add fields via YAML files which is currently in PR #1413 so the documentation for fields needs to be updated. Also, we have a new naming convention that was discussed in the Hackathon in January. @Ferrisx4 I don't remember where that was documented, can you link to it here?

[laceysanderson]

Yes, people can just use the old way for now and we'll update the way fields are added when that PR get's merged. The naming conventions were a PR in the TripalDoc repo that I just merged.

You can find them here: https://tripaldoc.readthedocs.io/en/latest/dev_guide/module_dev/fields.html#naming-convention

[srobb1]

I also worked on the checksum

[srobb1]

Sukha is working on local__source_data

[srobb1]

My pull request #1419 which contains both length and md5 are ready for review.

[srobb1]

I would like to attempt schema__alternate_name next. I have started on it and am having an error that I also get when I try to add a new chado organism reference to my gene. see issue #1432 . I used the organism field as a starting point since there are primary and foreign keys.

[dsenalik]

ChadoAnalysisDefault field

I am creating branch tv4g1-issue1414-ChadoAnalysisDefault to implement the ChadoAnalysisDefault field. This field is needed for issue #1550.

I am testing it on the phylogenetic tree content type, but we don't have a dbxref field yet, so right now you can't manually enter a tree. To be able to test, I have to temporarily do two things to allow me to create a phylotree record:

1. ALTER TABLE chado.phylotree ALTER COLUMN dbxref_id DROP NOT NULL;
2. In tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php line 1048 I temporarily add a return(); to disable validation.

Then I can create a tree, and test adding and changing an analysis record.

Pull request: #1578

[imnuvi]

Hi Team, I would like to work on data__sequence_coordinates.

[dsenalik]

I'm sorry I didn't take the time to update the field list here, that field is already being worked on in branch tv4g1-issue1414-data__sequence_length by Sukha I think the other two are still available, as @srobb1 has not posted on schema__alternate_name since February.

[imnuvi]

Thanks @dsenalik for the info, I am starting work on schema__alternate_name

[dsenalik]

PR #1599 implements the ChadoContactDefault field

[laceysanderson]

Thanks for all the hard work here everyone! I'm removing the "Good first issue" tag from this issue as the only remaining field listed here is the relationship field, which is a harder one. That said, if you are looking for another issue to work on, I have tagged a few more issues and expanded their descriptions with information for how to fix them :-)

[pdtouch]

Thanks for the reviews and merges. Appreciate your help.