Thanks!
On Wed, Mar 8, 2017 at 11:04 AM, Martin Čech <marten(a)bx.psu.edu> wrote:
Can you please share your
'/client/galaxy/scripts/layout/menu.js' file
with me? (e.g. using
https://gist.github.com or similar).
thanks
M.
On Wed, Mar 8, 2017 at 1:34 PM D K <danielfortin86(a)gmail.com> wrote:
> Hi Martin,
>
> I've tried this on both v16.07 and v16.10
>
> D
>
>
>
> On Wed, Mar 8, 2017 at 10:29 AM, Martin Čech <marten(a)bx.psu.edu> wrote:
>
> Daniel:
>
> what version is your Galaxy?
>
> Martin
>
> On Wed, Mar 8, 2017 at 12:40 PM D K <danielfortin86(a)gmail.com> wrote:
>
> I've copied and pasted the javascript error below. Any help would be
> greatly appreciated. Thanks!
>
> Uncaught TypeError: Cannot read property 'masthead' of undefined
> at n.<anonymous> (menu.js:120)
> at Function.each (jquery.js:370)
> at HTMLDocument.<anonymous> (menu.js:117)
> at l (jquery.js:3232)
> at Object.add [as done] (jquery.js:3291)
> at t.fn.init.vt.fn.ready (jquery.js:3542)
> at callback (menu.js:116)
> at Object.t.success (backbone.js:1051)
> at l (jquery.js:3232)
> at Object.fireWith [as resolveWith] (jquery.js:3362)
>
>
> On Thu, Mar 2, 2017 at 10:43 AM, D K <danielfortin86(a)gmail.com> wrote:
>
> Hi Martin,
>
> I do get a javascript error, I've attached a screenshot of the relevant
> window. I also tried logging in as a non-admin user and had the same issue.
> In this Galaxy instance are 5 data libraries, each with about 150
> individual folders, and each folder has a variable number of fastq.gz files.
>
> Thanks!
>
> On Thu, Mar 2, 2017 at 10:13 AM, Martin Čech <marten(a)bx.psu.edu> wrote:
>
> Daniel:
>
> Could you please open browser console and look for javascript errors on
> the page that fails to load for you? Additionally I assume you are an admin
> when trying this (admins load all of the instance's libraries) could you
> try loading the library list as a normal user? How many libraries do you
> have on the instance?
>
> Thanks
>
> Martin
>
> On Thu, Mar 2, 2017 at 12:38 PM D K <danielfortin86(a)gmail.com> wrote:
>
> Hi Martin / Hans / Devon,
>
> I can confirm that I am using the new UI from the top menu. Right now
> when I click on the link I often do not even get the list of libraries
> whereas when I click on the admin Data Library link I at least see the list
> of libraries (although I can't open any of them since they are so large).
> I've tried refreshing the page, deleting the cookies for the session and
> using Incognito mode, using chrome and firefox both from a linux and
> windows machine and can confirm this behavior on all systems. However,
> occasionally when clicking the Shared Data Library link from the top I do
> get a list of libraries and can navigate them, but this has only happened
> once during my tests and I cannot replicate this behavior.
>
> Thanks for the assistance!
>
> On Thu, Mar 2, 2017 at 5:47 AM, Martin Čech <marten(a)bx.psu.edu> wrote:
>
> Hi all,
>
> *Devon* is correct -the old data library UI under Admin menu is still in
> place (because it has some features perceived as important to some admins).
> However majority of users and most of the admins are using the interface
> under 'Shared Data' I hope and the old UI is deprecated since 15.10 (
>
https://docs.galaxyproject.org/en/master/releases/15.10_announce.html).
> I created a PR to adjust the label in the admin interface to make this
> clear:
https://github.com/galaxyproject/galaxy/pull/3694
>
> The old UI is very slow for large libraries but the new UI under Shared
> Data/Data Libraries in the top menu shouldn't have this kind of issues for
> hundreds of folders/datasets that are mentioned here.
>
> *Daniel* are you using the new UI form the top menu? If so are you
> experiencing this only with a specific folder full of linked datasets or
> does it occur for any folder with many datasets in it?
>
> Martin
>
>
>
> On Thu, Mar 2, 2017 at 3:49 AM Devon Ryan <dpryan(a)dpryan.com> wrote:
>
> I observe the same thing on 16.07. As an example, I'm just opened a
> data library under Admin->Data->Data Libraries and this took about a
> minute and a half. It looks like this is related to the quantity of
> data in this folder. The associated entry in the uwsgi log is as
> follows:
>
> [pid: 357|app: 0|req: 2059/5647] 10.1.6.77 () {44 vars in 1220 bytes}
> [Thu Mar 2 08:40:19 2017] GET
> /library_common/browse_library?sort=name&f-description=All&f-name=All&f-
>
deleted=False&cntrller=library_admin&operation=browse&id=355326571f7132ff
> => generated 21761790 bytes in 108644 msecs (HTTP/1.1 200) 2 headers
> in 73 bytes (14 switches on core 2)
>
> So this library is causing ~21 megs of data to be returned to the
> browser, which I presume is the source of the issue.
>
> As an aside, the old data library API is still in use in the admin
> section until at least 16.07. Perhaps this has been changed since
> then, I hadn't planed to update our system until the end of the month.
> For what it's worth, opening the same library via "shared data" takes
> ~100 msec.
>
> Devon
> --
> Devon Ryan, Ph.D.
> Email: dpryan(a)dpryan.com
> Data Manager/Bioinformatician
> Max Planck Institute of Immunobiology and Epigenetics
> Stübeweg 51
> 79108 Freiburg
> Germany
>
>
> On Thu, Mar 2, 2017 at 8:30 AM, Hans-Rudolf Hotz <hrh(a)fmi.ch> wrote:
> >
> > this sounds more like a browser issue to me
> > which browser do you use? what happens when you use a different
> browser? and
> > what happens when you just reload the page
> >
> >
> > Hans-Rudolf
> >
> > On 03/01/2017 06:17 PM, D K wrote:
> >>
> >> Actually, when I click on the Shared Data-> Data Libraries link I get
> >> only the Galaxy banner and a blank page, so I'm not even seeing the
> data
> >> libraries themselves.
> >>
> >> If I use the Admin link and then click Data libraries, I can see the
> >> actual libraries. But when I try to enter one of the libraries with
> lots
> >> of files it hangs.
> >>
> >>
> >> On Wed, Mar 1, 2017 at 9:03 AM, D K <danielfortin86(a)gmail.com
> >> <mailto:danielfortin86@gmail.com>> wrote:
> >>
> >> Hi Hans,
> >>
> >> I'm running 16.10. If I'm not mistaken, the old Data Library
> >> interface is still accessible in the Admin menu isn't it? I have
> the
> >> same issue when navigating to a Data Library either from the Admin
> >> or Shared Data links. I also tried this in 16.07 with the same
> >> result. If it makes a difference, I'm using PostgreSQL and Apache.
> >>
> >> Dwight
> >>
> >>
> >>
> >> On Tue, Feb 28, 2017 at 11:47 PM, Hans-Rudolf Hotz <hrh(a)fmi.ch
> >> <mailto:hrh@fmi.ch>> wrote:
> >>
> >> Hi Daniel
> >>
> >> Just double checking which version of galaxy are you running?
> In
> >> other words: are you still using the old Data Library
> interface?
> >> (if I remember correctly, the old UI was deprecated in 15.10)
> >> We had similar issues with the old UI.
> >>
> >> The new one works fine and is very fast. E.g. we have a
'MISEQ'
> >> folder with more than 100 sub folders and a HISEQ folder with
> >> more than 600 sub folders. Each containing up to 100plus fastq
> >> and text files.
> >>
> >> Regards, Hans-Rudolf
> >>
> >>
> >>
> >> On 03/01/2017 12:13 AM, D K wrote:
> >>
> >> Hi,
> >>
> >> I've noticed that the more files / folders (think hundreds
> >> of folders
> >> each with 20+ fastq files) I add to a Shared Data Library,
> >> the longer
> >> and longer it takes to initially navigate the folder
> >> structure (after
> >> clicking on the specific Shared Data Library). Just opening
> >> up the
> >> Shared Data Library can take several minutes and often the
> >> browser times
> >> out. Is there a way to speed this up?
> >>
> >> If it's relevant, when I add shared data, it's linked
> rather
> >> than copied
> >> into Galaxy. Any suggestions would be greatly appreciated
> >>
> >> Thanks!
> >>
> >>
> >> _____________________________
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> >>
> >>
> >>
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