Hi,
that PR has been merged so, if you are still on the release_16.10
branch, you can update your Galaxy instance with a `git pull` .
Cheers,
Nicola
On 15/03/17 16:53, D K wrote:
Hi Martin,
Finally got a chance to test out your PR. This does in fact fix the
issue. Thanks again for your help!
On Wed, Mar 8, 2017 at 12:19 PM, Martin Čech <marten(a)bx.psu.edu
<mailto:marten@bx.psu.edu>> wrote:
The code at L120 does not exist in 16.07. It was broken in 16.10
and fixed for 17.01. I made a PR to backport the fix to 16.10:
https://github.com/galaxyproject/galaxy/pull/3728
<
https://github.com/galaxyproject/galaxy/pull/3728>
You shouldn't be seeing the 'Cannot read property 'masthead' of
undefined' error in 16.07 and it should be fixed in 16.10 after
that PR is merged. 17.01 or dev shouldn't have this problem already.
Please let me know how this works for you.
Thanks,
Martin
On Wed, Mar 8, 2017 at 3:09 PM D K <danielfortin86(a)gmail.com
<mailto:danielfortin86@gmail.com>> wrote:
Hi Martin,
I've pasted the file you requested here:
http://collabedit.com/xcx5b
Thanks!
On Wed, Mar 8, 2017 at 11:04 AM, Martin Čech
<marten(a)bx.psu.edu <mailto:marten@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
<mailto:danielfortin86@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 <mailto:marten@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
<mailto:danielfortin86@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
<mailto:danielfortin86@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
<mailto:marten@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
<mailto:danielfortin86@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
<mailto:marten@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
<
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
<
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
<mailto:dpryan@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
<mailto:dpryan@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
<mailto:hrh@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>
>>
<mailto:danielfortin86@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>
>> <mailto:hrh@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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