clicking "show annotator panel" fails in logged-in apollo mode

[nathandunn]

Clicking on "show annotator panel" in full-screen mode leads to this screen, where the clientToken is obviously not being transformed into a string properly.:

http://icebox.lbl.gov/Apollo-staging/annotator/index?clientToken=[Ljava.lang.String;@6acd68b8&tracklist=1&highlight=0..-1&tracks=DNA,Annotations,Nurse,Forager,Official%20Gene%20Set%20v3.2&nav=1&overview=1

[nathandunn]

So, this is pretty inconsistent and flaky. I think, related to #1126, we should change the behavior to open and close the side-bar only. It would be a lot cleaner and give the eventual correct behavior:

[monicacecilia]

I did not see the 404 error; instead if I am currently in the Full-screen view and choose to Show Annotator Panel, then the annotator panel shows up again, and the JBrowse list of available tracks remains in the window as such:

[nathandunn]

Would it be okay if the show annotate / full screen options just opened and closed the annotator panel (i.e., the same as the button at the top)?

Nathan

On Jul 29, 2016, at 1:38 PM, Monica Munoz-Torres notifications@github.com wrote:

I did not see the 404 error; instead if I am currently in the Full-screen view and choose to Show Annotator Panel, then the annotator panel shows up again, and the JBrowse list of available tracks remains in the window as such:

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[monicacecilia]

No, I think that dismisses the original intent of having the Full-screen view: to offer the ability to include the JBrowse menu, or remove it.

[nathandunn]

You can do that already be choosing the native track list from the track menu.

Nathan

On Jul 29, 2016, at 2:01 PM, Monica Munoz-Torres notifications@github.com wrote:

No, I think that dismisses the original intent of having the Full-screen view: to offer the ability to include the JBrowse menu, or remove it.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[nathandunn]

We can fix that either way.

Nathan

On Jul 29, 2016, at 2:01 PM, Monica Munoz-Torres notifications@github.com wrote:

No, I think that dismisses the original intent of having the Full-screen view: to offer the ability to include the JBrowse menu, or remove it.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[monicacecilia]

Yes. That's already addressed with the toggle menu to Show JBrowse Track Selector. Unfortunately, at the moment, the Full-screen view is the only way in which we can display the data in the browser without being logged into Apollo.

[nathandunn]

Talked with NAL/USDA people today and I proposed a solution where full-screen mode would just slide out the annotator panel. They said they would be fine with that, but that users would be confused as to where the track panel went to and how do you get it back. This brings up why doesn't the track panel not have a show-hide button in the first-place, which we could add?

WRT to logged out, jbrowse only view, that shouldn't be affected, but that is an important use-case as well when switching.

To test:

• [x] handle logged-in, full-screen view - to annotator view, multiple times
• [x] handle logged-out, full-screen view to annotator view, multiple times
• [x] handle logged-out, full-screen view to logged-in view, multiple times
• [x] test load public link across same browser tabs
• [x] test load public link across separate browsers
• [x] test load annotator link across same browser tabs
• [x] test load annotator link across separate browsers
• [x] view public genome (without permissions), login (currently fails to set the proper organism if no permissions)

[nathandunn]

To fix:

• [x] initially (prior to this), we have 3 preferences set to current for the same organism, but we only want the one with the sequence populated (others should be deleted, or never created). If it is a different sequence it could just be ignored
• OR -
• when coming back (clicking AnnotatorPanel) we should delete any preference that shares the organism and doesn't have a sequence (if a sequence already exists)
• [x] when coming back (clicking AnnotatorPanel), tracklist is not set to 0, which seems to confuse the native track selector in the Annotator Panel
• add a "view track panel" button somewhere in JBrowse-land? (not necessary)

[monicacecilia]

@nathandunn This may be a little 'meta' but if you look up this thread, you can see that I had already shared the same objection to your idea that "full screen mode just slide[s] out the Annotator Panel". Your solution was to toggle the JBrowse track list, as it is already possible from the Annotator Panel using the Show JBrowse Track Selector button. Again I add: Unfortunately, at the moment, the Full-screen view is the only way in which we can display the data in the browser without being logged into Apollo. Please keep that in mind as well. As (I think) you mention, this function cannot be lost.

[nathandunn]

Please keep that in mind as well. As (I think) you mention, this function cannot be lost.

Yeah. That is what I was responding to. We definitely need that functionality as well.

[nathandunn]

This proposal was just a proposal . . I'm going try and address the stuff in this comment first.

[nathandunn]

ClientToken was being handled in twice, so it was a string array instead of a string . . which confused java

[monicacecilia]

Tested all functionality. Nearly all steps worked as expected, except:

• if users is not given permissions, then they are unable to browse public genomes using the link in the 'You do not have permissions' dialog box. Instead, they see this window:
• if later on, users re-enter this URL http://icebox.lbl.gov/Apollo-staging/jbrowse/ then the list of organisms available for public browsing appears.

@nathandunn are you experiencing the same? (is this what you were referring to above in your list 'To test'?

[nathandunn]

To reproduce, login, go to /apollo/jbrowse/ . . was because it was returning the index.html if you had a valid user, but not a valid organism or client_token.

Fixed.

[monicacecilia]

It is fixed. All other steps in the above testing work. Gets a 💃 !