loadLink with loc=some_name

[abretaud]

Hi,
In one of my webapp, I'd like to add links with urls like the following to let users open apollo on a specific organism (Some organism), and at a specific position using the name of a feature indexed in the jbrowse data dir by generate-names.pl (FOOBAR026052-RA)

https://bipaa.genouest.org/apollo/annotator/loadLink?organism=Some%20organism&loc=FOOBAR026052-RA

Selecting the organism works great, but the loc parameter has no effect (unless I set it to a chr1:1..1000 value, but that's not possible in my case).

With an url like this, I get redirected to another url like that: https://bipaa.genouest.org/apollo/annotator/index?clientToken=<random_id> (so, no loc parameter)

Of course, when writing manually the FOOBAR026052-RA id in the jbrowse search box, it is found, so I don't think the problem is on the jbrowse side.

Do you have any clue why it's not working?

[nathandunn]

Hmmm . . . . having it use the search explicitly might be hard. The track service could iterate and do a linear scan and search and scan. I do this for track services already, but usually I specify the track.

I think this would work unless you have a ton of tracks with no way to specify them.

We could also do this by flagging specific annotations. Just let me know.

[abretaud]

Wouldn't it be possible to just pass it to jbrowse and let it find the correct position?

[nathandunn]

If it can be passed into the JBrowse url, then probably.

[abretaud]

yep, it's the loc url param I use for standalone jbrowse

[nathandunn]

Okay, I will see what I can do. I can make it part of RC2 2.6.0

[abretaud]

that would be great, thanks :)
(by the way, I just release python-apollo 4.2)

[nathandunn]

Perfect I just updated it for the specific version.

[nathandunn]

Note to self:

loadLink is a method on the AnnotatorController. The current method sets a preference and then calls "setCurrentSequenceLocation".

What we'll have to do instead is to do a index?search=XXX instead and pass that directly to the client with selectedSequence = "searchString" minRegion = null, maxRegion = null and forceUrl = true

[nathandunn]

public URL:

https://localhost:8080/apollo/6791/jbrowse/index.html?loc=Group3.9:1174809..1194693&tracks=Official%20Gene%20Set%20v3.2

this also works:

https://localhost:8080/apollo/6791/jbrowse/index.html?loc=GB53650-RA&tracks=Official%20Gene%20Set%20v3.2

logged in URL:

https://localhost:8080/apollo/annotator/loadLink?loc=Group3.9:1174809..1194693&organism=6791&tracks=Official%20Gene%20Set%20v3.2

we should be able to pass in:

https://localhost:8080/apollo/annotator/loadLink?loc=GB53650-RA&organism=6791&tracks=Official%20Gene%20Set%20v3.2

[nathandunn]

https://localhost:8080/apollo/annotator/loadLink?loc=GB55650-RA&organism=6791&tracks=Official%20Gene%20Set%20v3.2

also works

[abretaud]

Thanks for the fix @nathandunn! It works great