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GMOD / Apollo3

JBrowse 2 plugin for editing annotations on an Apollo server
Apache License 2.0
7 stars 4 forks source link

Organism access dropdown menu redesign #2

Closed obsidian83 closed 1 month ago

obsidian83 commented 3 years ago

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.

Screenshot 2020-11-30 at 14 29 37

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

Screenshot 2020-11-30 at 15 08 04
nathandunn commented 3 years ago

Adding the genus and species makes a lot of sense.

nathandunn commented 3 years ago

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

obsidian83 commented 3 years ago

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 commented 3 years ago

@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 commented 3 years ago

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 commented 3 years ago

Potentially add category similar to tracks?

nathandunn commented 3 years ago

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 commented 3 years ago

@obsidian83 I did a small implementation https://github.com/GMOD/Apollo/pull/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 commented 1 month ago

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.