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GMOD / jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser
https://jbrowse.org/jb2
Apache License 2.0
205 stars 61 forks source link

More generic add track GUI #1319

Closed cmdcolin closed 3 years ago

cmdcolin commented 3 years ago

Adding a synteny track is a customized process where you need to select two assembly names corresponding to the "column" 1 and 2 of the PAF

In some sense, I am almost beginning to think adding a track should be a decentralized process? The guessAdapter logic being centralized makes it hard to be extensible

cmdcolin commented 3 years ago

This issue was renamed to "More generic add track workflow" following some discussion with @rbuels with the idea that we should make the add track workflow pop up a more generic configEditor type thing upon adding a track

The idea would be

select a data adapter type a track type is automatically guessed from this as now then a "blank track config" for all of this is created where you can insert the file locations

The config slots might have a flag called "import": true or "important": true, which would then show only those selected config slots available during the add track workflow

cmdcolin commented 3 years ago

This current issue is a little bit ungroomed, and if we really want this, we might need grooming

First of all, workarounds have been added for at least two pain points that made this issue needed

That includes

a) Ability to custom add a path to a index file b) Ability to add PAF track with assembly names (which can be done in dotplot/synteny view import form)

So what remains here, with how to proceed, should be done carefully IMO, in order to not make add track workflow more clunky. It might be this can be de-prioritized too

cmdcolin commented 3 years ago

My comment above proposed custom config editor slots such as "important": true but this may overlap with types.optional/types.maybe in config

rbuels commented 3 years ago

re: the dotplot/synteny import form, does a PAF track added there get actually added to config? Will it be persisted by the admin-server?

On Mon, Nov 23, 2020 at 10:41 AM Colin Diesh notifications@github.com wrote:

This current issue is a little bit ungroomed, and if we really want this, we might need grooming

First of all, workarounds have been added for at least two pain points that made this issue needed

That includes

a) Ability to custom add a path to a index file b) Ability to add PAF track with assembly names (which can be done in dotplot/synteny view import form)

So what remains here, with how to proceed, should be done carefully IMO, in order to not make add track workflow more clunky. It might be this can be de-prioritized too

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cmdcolin commented 3 years ago

That should get added and persisted by admin-server

The special PAF adder uses session.addTrackConf which should "do the right thing" in this case