Re: [galaxy-dev] JAVASCRIPT error - ctd.

[Carl Eberhard]

Hello, Joachim

Can you grep your server logs for 'history_contents ERROR'. You can include
the date after that if you need to narrow it down (hopefully you don't :)
). *The javascript error you're seeing should have a matching log.error on
the server side*, but I'm not seeing it in the entry you posted. If
nothing's there, that's a worse issue.
C


On Wed, Feb 6, 2013 at 6:45 AM, Joachim Jacob |VIB| wrote:

> Hi all,
>
>
> Occasionally, a JAVASCRIPT error appears. I think now this has to do with
> the app running Galaxy embedded (Fogger).
>
> This time, when I run a workflow on multiple input files (fastqc on a
> bunch of fastq files).
>
> The Javascript error is:
> ERROR updating hdas from api history contents:efd5a801e04dff8d,**
> aa41b6bf76b5d046,**399f7558b6aa905b,**2817a997b5242e3d,**58a41d419e31105a,
> **2377f6835e89edaf,**1fb058b7916cd73f
>
> The relating entry in the web log is:
> web12.log:193.191.128.2 - - [06/Feb/2013:11:37:19 +0200] "GET
> /api/histories/**10fc65318d20c004/contents?ids=**efd5a801e04dff8d%**
> 2Caa41b6bf76b5d046%**2C399f7558b6aa905b%**2C2817a997b5242e3d%**
> 2C58a41d419e31105a%**2C2377f6835e89edaf%**2C1fb058b7916cd73f HTTP/1.1"
> 200 - "http://galaxy.bits.vib.be/**history"
> "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.22+ (KHTML, like Gecko)
> Chromium/17.0.963.56 Chrome/17.0.963.56 Safari/535.22+"
>
>
> Cheers,
> Joachim
>
>
> --
> Joachim Jacob
>
> Rijvisschestraat 120, 9052 Zwijnaarde
> Tel: +32 9 244.66.34
> Bioinformatics Training and Services (BITS)
> http://www.bits.vib.be
> @bitsatvib
>
> __**_
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>
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>
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[galaxy-dev] JAVASCRIPT error - ctd.

[Joachim Jacob |VIB|]

Hi all,


Occasionally, a JAVASCRIPT error appears. I think now this has to do 
with the app running Galaxy embedded (Fogger).


This time, when I run a workflow on multiple input files (fastqc on a 
bunch of fastq files).


The Javascript error is:
ERROR updating hdas from api history 
contents:efd5a801e04dff8d,aa41b6bf76b5d046,399f7558b6aa905b,2817a997b5242e3d,58a41d419e31105a,2377f6835e89edaf,1fb058b7916cd73f


The relating entry in the web log is:
web12.log:193.191.128.2 - - [06/Feb/2013:11:37:19 +0200] "GET 
/api/histories/10fc65318d20c004/contents?ids=efd5a801e04dff8d%2Caa41b6bf76b5d046%2C399f7558b6aa905b%2C2817a997b5242e3d%2C58a41d419e31105a%2C2377f6835e89edaf%2C1fb058b7916cd73f 
HTTP/1.1" 200 - "http://galaxy.bits.vib.be/history"; "Mozilla/5.0 (X11; 
Linux x86_64) AppleWebKit/535.22+ (KHTML, like Gecko) 
Chromium/17.0.963.56 Chrome/17.0.963.56 Safari/535.22+"



Cheers,
Joachim


--
Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

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Re: [galaxy-dev] JAVAscript error after initiating tool

[Joachim Jacob |VIB|]

Hi Carl,

Sorry for the long delay!

It did not happen in a published or shared history. But it did 
definitely happen in a history where some datasets where copied from 
another history, since I've been copying a lot lately.



Thanks,
J

Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 01/17/2013 05:32 PM, Carl Eberhard wrote:

Joachim,

That certainly helps. Thanks.

Do you recall if this error happened (or happens more often) with a 
published or shared history? Or if it was imported or copied from a 
published or shared history?


Thanks for the info,
C



On Thu, Jan 17, 2013 at 9:58 AM, Joachim Jacob > wrote:


Hi,

In the server logs I've found:

web0.log: galaxy.webapps.galaxy.api.histories ERROR 2013-01-11
19:56:21,071 Error in history API at showing history detail:
History is not accessible to the current user
web1.log: galaxy.webapps.galaxy.api.histories ERROR 2013-01-11
19:55:14,341 Error in history API at showing history detail:
History is not accessible to the current user
web5.log: galaxy.webapps.galaxy.api.histories ERROR 2013-01-11
20:29:11,138 Error in history API at showing history detail:
History is not accessible to the current user

The specific situation here is that I am almost at my 100% quotum
of storage space... Don't know if this gives some hint. The
problem appear sporadically, not reproducibabilibity :-)


Cheers,
Joachim




Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34 
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 01/16/2013 05:33 PM, Carl Eberhard wrote:

Hi, Joachim

If you have access to your server logs, do you see any log
messages containing 'Error in history API' around the time
those happen?

Is there a situation where this happens more often (or a way
to reliably reproduce)?

I'm unable to reproduce this locally so far.

The error definitely can be handled better on the javascript
side, but I'd like to track down the API error as well before
I change the javascript.

Thanks for the help,
C




On Wed, Jan 16, 2013 at 7:57 AM, Joachim Jacob
mailto:joachim.ja...@vib.be>
>>
wrote:

Hi all,

For who is interested. Occasionally I get this strange
Javascript
error, just after clicking 'run' on a tool.

ERROR updating hdas from api history contents:e47699a32b93ce7f

The tool gets running, but the history panel is not updated. I
click 'analyse data' to see the updated history.


Cheers,
Joachim

-- Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34 


Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

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Re: [galaxy-dev] JAVAscript error after initiating tool

[Carl Eberhard]

Joachim,

That certainly helps. Thanks.

Do you recall if this error happened (or happens more often) with a
published or shared history? Or if it was imported or copied from a
published or shared history?

Thanks for the info,
C



On Thu, Jan 17, 2013 at 9:58 AM, Joachim Jacob  wrote:

> Hi,
>
> In the server logs I've found:
>
> web0.log: galaxy.webapps.galaxy.api.**histories ERROR 2013-01-11
> 19:56:21,071 Error in history API at showing history detail: History is not
> accessible to the current user
> web1.log: galaxy.webapps.galaxy.api.**histories ERROR 2013-01-11
> 19:55:14,341 Error in history API at showing history detail: History is not
> accessible to the current user
> web5.log: galaxy.webapps.galaxy.api.**histories ERROR 2013-01-11
> 20:29:11,138 Error in history API at showing history detail: History is not
> accessible to the current user
>
> The specific situation here is that I am almost at my 100% quotum of
> storage space... Don't know if this gives some hint. The problem appear
> sporadically, not reproducibabilibity :-)
>
>
> Cheers,
> Joachim
>
>
>
>
> Joachim Jacob
>
> Rijvisschestraat 120, 9052 Zwijnaarde
> Tel: +32 9 244.66.34
> Bioinformatics Training and Services (BITS)
> http://www.bits.vib.be
> @bitsatvib
>
> On 01/16/2013 05:33 PM, Carl Eberhard wrote:
>
>> Hi, Joachim
>>
>> If you have access to your server logs, do you see any log messages
>> containing 'Error in history API' around the time those happen?
>>
>> Is there a situation where this happens more often (or a way to reliably
>> reproduce)?
>>
>> I'm unable to reproduce this locally so far.
>>
>> The error definitely can be handled better on the javascript side, but
>> I'd like to track down the API error as well before I change the javascript.
>>
>> Thanks for the help,
>> C
>>
>>
>>
>>
>> On Wed, Jan 16, 2013 at 7:57 AM, Joachim Jacob > joachim.ja...@vib.be>> wrote:
>>
>> Hi all,
>>
>> For who is interested. Occasionally I get this strange Javascript
>> error, just after clicking 'run' on a tool.
>>
>> ERROR updating hdas from api history contents:e47699a32b93ce7f
>>
>> The tool gets running, but the history panel is not updated. I
>> click 'analyse data' to see the updated history.
>>
>>
>> Cheers,
>> Joachim
>>
>> -- Joachim Jacob
>>
>> Rijvisschestraat 120, 9052 Zwijnaarde
>> Tel: +32 9 244.66.34 
>>
>> Bioinformatics Training and Services (BITS)
>> http://www.bits.vib.be
>> @bitsatvib
>>
>> __**_
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>> http://lists.bx.psu.edu/
>>
>>
>>
>
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Re: [galaxy-dev] JAVAscript error after initiating tool

[Joachim Jacob]

Hi,

In the server logs I've found:

web0.log: galaxy.webapps.galaxy.api.histories ERROR 2013-01-11 
19:56:21,071 Error in history API at showing history detail: History is 
not accessible to the current user
web1.log: galaxy.webapps.galaxy.api.histories ERROR 2013-01-11 
19:55:14,341 Error in history API at showing history detail: History is 
not accessible to the current user
web5.log: galaxy.webapps.galaxy.api.histories ERROR 2013-01-11 
20:29:11,138 Error in history API at showing history detail: History is 
not accessible to the current user


The specific situation here is that I am almost at my 100% quotum of 
storage space... Don't know if this gives some hint. The problem appear 
sporadically, not reproducibabilibity :-)



Cheers,
Joachim



Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 01/16/2013 05:33 PM, Carl Eberhard wrote:

Hi, Joachim

If you have access to your server logs, do you see any log messages 
containing 'Error in history API' around the time those happen?


Is there a situation where this happens more often (or a way to 
reliably reproduce)?


I'm unable to reproduce this locally so far.

The error definitely can be handled better on the javascript side, but 
I'd like to track down the API error as well before I change the 
javascript.


Thanks for the help,
C




On Wed, Jan 16, 2013 at 7:57 AM, Joachim Jacob > wrote:


Hi all,

For who is interested. Occasionally I get this strange Javascript
error, just after clicking 'run' on a tool.

ERROR updating hdas from api history contents:e47699a32b93ce7f

The tool gets running, but the history panel is not updated. I
click 'analyse data' to see the updated history.


Cheers,
Joachim

-- 
Joachim Jacob


Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34 
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

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Re: [galaxy-dev] JAVAscript error after initiating tool

[Carl Eberhard]

Hi, Joachim

If you have access to your server logs, do you see any log messages
containing 'Error in history API' around the time those happen?

Is there a situation where this happens more often (or a way to reliably
reproduce)?

I'm unable to reproduce this locally so far.

The error definitely can be handled better on the javascript side, but I'd
like to track down the API error as well before I change the javascript.

Thanks for the help,
C




On Wed, Jan 16, 2013 at 7:57 AM, Joachim Jacob  wrote:

> Hi all,
>
> For who is interested. Occasionally I get this strange Javascript error,
> just after clicking 'run' on a tool.
>
> ERROR updating hdas from api history contents:e47699a32b93ce7f
>
> The tool gets running, but the history panel is not updated. I click
> 'analyse data' to see the updated history.
>
>
> Cheers,
> Joachim
>
> --
> Joachim Jacob
>
> Rijvisschestraat 120, 9052 Zwijnaarde
> Tel: +32 9 244.66.34
> Bioinformatics Training and Services (BITS)
> http://www.bits.vib.be
> @bitsatvib
>
> __**_
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
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[galaxy-dev] JAVAscript error after initiating tool

[Joachim Jacob]

Hi all,

For who is interested. Occasionally I get this strange Javascript error, 
just after clicking 'run' on a tool.


ERROR updating hdas from api history contents:e47699a32b93ce7f

The tool gets running, but the history panel is not updated. I click 
'analyse data' to see the updated history.



Cheers,
Joachim

--
Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

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Re: [galaxy-dev] javascript

[Cathy Riemer]

Ok.  Thanks Jeremy!

-Cathy


On Wed, Jul 11, 2012 at 08:13:47AM -0400, Jeremy Goecks wrote:
> > I just now tried visiting Galaxy main with my browser's javascript
> > turned off.  Formerly the left Tools panel would appear with all
> > of the sections expanded, however now it is empty except for
> > "Workflows".  Also, some of the top menu bar items work without
> > scripting, but others (including Help and User) do not.
> 
> This is expected behavior. 
> 
> In order to create a more dynamic, flexible, and interactive UI, we're 
> increasingly using JavaScript in Galaxy. We believe that the JavaScript 
> requirement is a reasonable tradeoff for what can be done using client-side 
> scripting.
> 
> > Ideally Galaxy would be usable without scripting, but if that is
> > not feasible then I suggest checking whether javascript is available
> > (as many other sites do) and displaying a prominent explanatory
> > message if it is not.  This would be much more helpful than an
> > inexplicably near-empty tool panel and broken menus.
> 
> Good idea; we plan to implement this soon.
> 
> Best,
> J.
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Re: [galaxy-dev] javascript

[Jeremy Goecks]

> I just now tried visiting Galaxy main with my browser's javascript
> turned off.  Formerly the left Tools panel would appear with all
> of the sections expanded, however now it is empty except for
> "Workflows".  Also, some of the top menu bar items work without
> scripting, but others (including Help and User) do not.

This is expected behavior. 

In order to create a more dynamic, flexible, and interactive UI, we're 
increasingly using JavaScript in Galaxy. We believe that the JavaScript 
requirement is a reasonable tradeoff for what can be done using client-side 
scripting.

> Ideally Galaxy would be usable without scripting, but if that is
> not feasible then I suggest checking whether javascript is available
> (as many other sites do) and displaying a prominent explanatory
> message if it is not.  This would be much more helpful than an
> inexplicably near-empty tool panel and broken menus.

Good idea; we plan to implement this soon.

Best,
J.
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[galaxy-dev] javascript

[Cathy Riemer]

Hi all,

I just now tried visiting Galaxy main with my browser's javascript
turned off.  Formerly the left Tools panel would appear with all
of the sections expanded, however now it is empty except for
"Workflows".  Also, some of the top menu bar items work without
scripting, but others (including Help and User) do not.

Ideally Galaxy would be usable without scripting, but if that is
not feasible then I suggest checking whether javascript is available
(as many other sites do) and displaying a prominent explanatory
message if it is not.  This would be much more helpful than an
inexplicably near-empty tool panel and broken menus.

In case it is relevant, I'm running Firefox 3.6.23 with the NoScript
extension (2.4.7), on CentOS Linux with kernel 2.6.18-238.12.1.el5.

Thanks,
-Cathy
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[galaxy-dev] Javascript out of date - history widgets don't expand.

[James Bullard]

This is probably not a galaxy problem at all, however it is manifesting
itself in the history pane of galaxy. The history widgets don't expand
-- everything else works fine. 

The relevant javascript error looks to be:

Uncaught TypeError: Cannot call method 'init' of undefined
 init_history_items galaxy.base.js:468
 updater history:32
 jQuery.extend.ready jquery.js:392
 DOMContentLoaded jquery.js:745

I saw a previous post which is related to an update of galaxy, however,
I haven't updated galaxy, but rather my OS (in fact the problem occurs
in Firefox/Chrome; I'm ubuntu 11.04). 

Creating a new user doesn't help, restarting server doesn't help. 

Any thoughts on this, and once again I apologize for the fact that this
isn't galaxy per se. 

jim

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