Organism access dropdown menu redesign

[obsidian83]

For VEuPathDB we have over 400 organisms that will be loaded eventually into our Apollo instance.

Switching between organisms via both the jbrowse menu and annotator tab menus with an exhaustive list of organisms makes it difficult to find the desired one.

I propose a more faceted menu, with a tree like structure, for either or both menus.

[nathandunn]

Adding the genus and species makes a lot of sense.

• add genus and species to drop-down / lookup

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• add "category" option to organism and add it to drop-down
• update organism panel to show with genus, species, and category?
• implement trackPanel like interface through there with search?

[nathandunn]

I'll have to play with the rest a bit to see if it makes sense.

[obsidian83]

Is there a way to add a manual tag, that can be assigned, in the examples here "PiroplasmaDB" "AmoebaDB", or higher order taxonomy terms, as I think will stay be too busy?

[nathandunn]

@obsidian83 That was what I was thinking, but I need to explore if even adding the genus and species makes sense to the drop-down, first or if these are all features that would be better in JB2. I should have an answer for you by the end of the week.

[nathandunn]

On the flip side, we could show the organism panel without the other controls if a non-admin for organisms the user has access to. However, it doesn't help with genus, species, and other drop-downs, unless we did something similar to what we do with the track list.

[nathandunn]

Potentially add category similar to tracks?

[nathandunn]

I think that the tree structure would be amazing, but a lot of work for something we are going to replace with react.

I will try to make use of the genus and species instead and use the organism panel and add the category

[nathandunn]

@obsidian83 I did a small implementation GMOD/Apollo#2537 adding genus, species, etc. to the names and sorting appropriately.

However, we are going to be implementing a react component that does a lot of the same stuff. Ultimately I want something that looks like the current track list (or faceted browser), but we'll have a lot more control in the newer stack (in this repo).

[garrettjstevens]

Species selection in Apollo 3 is handled completely by JBrowse 2. Some sort of hierarchical selector could be possible, but would probably need to be implemented as a JBrowse plugin.