Re: [galaxy-dev] Fwd: 'UsesFormDefinitions' is not defined

2012-10-19 Thread Alexander Graf 
Hi Scott and Hans-Rudolf,

thank you both for your efforts.
The fix works perfectly.

Alex

2012/10/18 Hans-Rudolf Hotz 

> Hi Scott
>
> Thank you very much for your quick reply!
>
> after fixing (ie replacing "galaxy.web.controllers.**library_common" with
> "galaxy.webapps.galaxy.**controllers.library_common") in the following
> four files:
>
> ~/templates/library/common/**library_dataset_search_**results.mako
>ldda_info.mako
>browse_library_opt.mako
>browse_library.mako
>
>
> it works!  -  both on the fresh install and the upgraded server
>
>
> @Alex:  I hope this solves your problem as well.
>
>
>
> Regards Hans-Rudolf
>
>
> Than
>
>
> On 10/18/2012 06:12 PM, Scott McManus wrote:
>
>>
>> This was fixed in galaxy-central last week and should be part of
>> galaxy-dist. What happened is that controllers were migrated and a
>> couple of modules were left out. See changeset 210c39f4bf7f or later,
>> which I believe was fixed on October 4th.
>>
>> In particular, the problem you're seeing had to do with the
>> templates/library/common/**library_common.mako pointing to
>> galaxy.web.controllers.**library_common instead of
>> galaxy.webapps.galaxy.**controllers.library_common.
>> A few other files had also been affected.
>>
>> -Scott
>>
>> - Original Message -
>>
>>> Hi Alex
>>>
>>> I am in the same situation, updating our galaxy servers to the "Oct
>>> 5th"
>>> release (changeset: 7824:b5bda7a5c345), and I have encountered the
>>> same
>>> problem. I guess, there are actually two problems:
>>>
>>>
>>> First problem - this happens with a fresh install:
>>> ==**
>>>
>>> I can't create a library at all, I get the following error message:
>>>
>>> Error attempting to display contents of library (foo): No
>>> module named  controllers.library_common.
>>>
>>>
>>>
>>> There have been a few commits on "library_common.py" over the last
>>> few
>>> days, which might solve this problem.?
>>>
>>>
>>>
>>> Second problem - this happens after upgrading an existing
>>> installation
>>> ==**==**
>>> ==
>>>
>>> Like the situation you reported earlier this morning, I get:
>>>
>>>
>>> Error attempting to display contents of library (haruhotz):
>>> name 'UsesFormDefinitions' is not defined.
>>>
>>>
>>> I manage to track down the problem to the fact that
>>>
>>> in the old version, we've had
>>>
>>> ~/lib/galaxy/web/controllers/
>>>
>>>
>>> which apparently has been replaced by
>>>
>>> ~/lib/galaxy/webapps/galaxy/**controllers/
>>>
>>>
>>> if I remove ~/lib/galaxy/web/controllers/
>>>
>>>
>>> I get a new error:
>>>
>>> Error attempting to display contents of library (haruhotz): No
>>> module named library_common.
>>>
>>>
>>> which is very similar to the error you get with a fresh install
>>>
>>>
>>> Obviously, old stuff (ie ~/lib/galaxy/web/controllers/) is still used
>>> after the upgrade.
>>>
>>>
>>> Sorry, no solution yet, but maybe it helps the developers to track
>>> down
>>> the problem and help us getting the servers running again.
>>>
>>>
>>>
>>> Regards Hans-Rudolf
>>>
>>>
>>> On 10/18/2012 10:48 AM, Alexander Graf wrote:
>>>
 Hi,
 yesterday I updated Galaxy to the latest revision and now it is not
 possible to access any Data Libraries or to create a new one.
 Galaxy shows me a read box with following error message:

 *Error attempting to display contents of library
 (100326_HWUSI-EAS632R_0002): name 'UsesFormDefinitions' is not
 defined.*

 The log file message is:

 /"GET
 /galaxy/library_common/browse_**library?sort=name&webapp=**
 galaxy&f-description=All&f-**name=All&page=1&cntrller=**
 library&show_item_checkboxes=**false&async=false&operation=**
 browse&id=9d04ee723dc2cac7
 HTTP/1.1" 302 -
 "http://x.x.x.x/galaxy/**library/browse_libraries?**
 status=error&use_panels=False&**message=Error+attempting+to+**
 display+contents+of+library+%**100326_HWUSI-EAS632R_0002%29%**
 3A+name+__sq__**UsesFormDefinitions__sq__+is+**not+defined
 ."
 "Mozilla/5.0 (X11; Linux x86_64) /

 Any ideas how to solve this problem or were to start
 troubleshooting?

 Thank you in advance

 Alex




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Re: [galaxy-dev] Fwd: 'UsesFormDefinitions' is not defined

2012-10-18 Thread Hans-Rudolf Hotz 

Hi Scott

Thank you very much for your quick reply!

after fixing (ie replacing "galaxy.web.controllers.library_common" with 
"galaxy.webapps.galaxy.controllers.library_common") in the following 
four files:


~/templates/library/common/library_dataset_search_results.mako
   ldda_info.mako
   browse_library_opt.mako
   browse_library.mako


it works!  -  both on the fresh install and the upgraded server


@Alex:  I hope this solves your problem as well.



Regards Hans-Rudolf


Than

On 10/18/2012 06:12 PM, Scott McManus wrote:


This was fixed in galaxy-central last week and should be part of
galaxy-dist. What happened is that controllers were migrated and a
couple of modules were left out. See changeset 210c39f4bf7f or later,
which I believe was fixed on October 4th.

In particular, the problem you're seeing had to do with the
templates/library/common/library_common.mako pointing to
galaxy.web.controllers.library_common instead of
galaxy.webapps.galaxy.controllers.library_common.
A few other files had also been affected.

-Scott

- Original Message -

Hi Alex

I am in the same situation, updating our galaxy servers to the "Oct
5th"
release (changeset: 7824:b5bda7a5c345), and I have encountered the
same
problem. I guess, there are actually two problems:


First problem - this happens with a fresh install:
==

I can't create a library at all, I get the following error message:

Error attempting to display contents of library (foo): No
module named  controllers.library_common.



There have been a few commits on "library_common.py" over the last
few
days, which might solve this problem.?



Second problem - this happens after upgrading an existing
installation
==

Like the situation you reported earlier this morning, I get:


Error attempting to display contents of library (haruhotz):
name 'UsesFormDefinitions' is not defined.


I manage to track down the problem to the fact that

in the old version, we've had

~/lib/galaxy/web/controllers/


which apparently has been replaced by

~/lib/galaxy/webapps/galaxy/controllers/


if I remove ~/lib/galaxy/web/controllers/


I get a new error:

Error attempting to display contents of library (haruhotz): No
module named library_common.


which is very similar to the error you get with a fresh install


Obviously, old stuff (ie ~/lib/galaxy/web/controllers/) is still used
after the upgrade.


Sorry, no solution yet, but maybe it helps the developers to track
down
the problem and help us getting the servers running again.



Regards Hans-Rudolf


On 10/18/2012 10:48 AM, Alexander Graf wrote:

Hi,
yesterday I updated Galaxy to the latest revision and now it is not
possible to access any Data Libraries or to create a new one.
Galaxy shows me a read box with following error message:

*Error attempting to display contents of library
(100326_HWUSI-EAS632R_0002): name 'UsesFormDefinitions' is not
defined.*

The log file message is:

/"GET
/galaxy/library_common/browse_library?sort=name&webapp=galaxy&f-description=All&f-name=All&page=1&cntrller=library&show_item_checkboxes=false&async=false&operation=browse&id=9d04ee723dc2cac7
HTTP/1.1" 302 -
"http://x.x.x.x/galaxy/library/browse_libraries?status=error&use_panels=False&message=Error+attempting+to+display+contents+of+library+%100326_HWUSI-EAS632R_0002%29%3A+name+__sq__UsesFormDefinitions__sq__+is+not+defined.";
"Mozilla/5.0 (X11; Linux x86_64) /

Any ideas how to solve this problem or were to start
troubleshooting?

Thank you in advance

Alex




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Re: [galaxy-dev] Fwd: 'UsesFormDefinitions' is not defined

2012-10-18 Thread Scott McManus 

Excuse me - I meant to say that this will part of the upcoming 
galaxy-dist.

-Scott

- Original Message -
> 
> This was fixed in galaxy-central last week and should be part of
> galaxy-dist. What happened is that controllers were migrated and a
> couple of modules were left out. See changeset 210c39f4bf7f or later,
> which I believe was fixed on October 4th.
> 
> In particular, the problem you're seeing had to do with the
> templates/library/common/library_common.mako pointing to
> galaxy.web.controllers.library_common instead of
> galaxy.webapps.galaxy.controllers.library_common.
> A few other files had also been affected.
> 
> -Scott
> 
> - Original Message -
> > Hi Alex
> > 
> > I am in the same situation, updating our galaxy servers to the "Oct
> > 5th"
> > release (changeset: 7824:b5bda7a5c345), and I have encountered the
> > same
> > problem. I guess, there are actually two problems:
> > 
> > 
> > First problem - this happens with a fresh install:
> > ==
> > 
> > I can't create a library at all, I get the following error message:
> > 
> > Error attempting to display contents of library (foo): No
> > module named  controllers.library_common.
> > 
> > 
> > 
> > There have been a few commits on "library_common.py" over the last
> > few
> > days, which might solve this problem.?
> > 
> > 
> > 
> > Second problem - this happens after upgrading an existing
> > installation
> > ==
> > 
> > Like the situation you reported earlier this morning, I get:
> > 
> > 
> > Error attempting to display contents of library (haruhotz):
> > name 'UsesFormDefinitions' is not defined.
> > 
> > 
> > I manage to track down the problem to the fact that
> > 
> > in the old version, we've had
> > 
> > ~/lib/galaxy/web/controllers/
> > 
> > 
> > which apparently has been replaced by
> > 
> > ~/lib/galaxy/webapps/galaxy/controllers/
> > 
> > 
> > if I remove ~/lib/galaxy/web/controllers/
> > 
> > 
> > I get a new error:
> > 
> > Error attempting to display contents of library (haruhotz): No
> > module named library_common.
> > 
> > 
> > which is very similar to the error you get with a fresh install
> > 
> > 
> > Obviously, old stuff (ie ~/lib/galaxy/web/controllers/) is still
> > used
> > after the upgrade.
> > 
> > 
> > Sorry, no solution yet, but maybe it helps the developers to track
> > down
> > the problem and help us getting the servers running again.
> > 
> > 
> > 
> > Regards Hans-Rudolf
> > 
> > 
> > On 10/18/2012 10:48 AM, Alexander Graf wrote:
> > > Hi,
> > > yesterday I updated Galaxy to the latest revision and now it is
> > > not
> > > possible to access any Data Libraries or to create a new one.
> > > Galaxy shows me a read box with following error message:
> > >
> > > *Error attempting to display contents of library
> > > (100326_HWUSI-EAS632R_0002): name 'UsesFormDefinitions' is not
> > > defined.*
> > >
> > > The log file message is:
> > >
> > > /"GET
> > > /galaxy/library_common/browse_library?sort=name&webapp=galaxy&f-description=All&f-name=All&page=1&cntrller=library&show_item_checkboxes=false&async=false&operation=browse&id=9d04ee723dc2cac7
> > > HTTP/1.1" 302 -
> > > "http://x.x.x.x/galaxy/library/browse_libraries?status=error&use_panels=False&message=Error+attempting+to+display+contents+of+library+%100326_HWUSI-EAS632R_0002%29%3A+name+__sq__UsesFormDefinitions__sq__+is+not+defined.";
> > > "Mozilla/5.0 (X11; Linux x86_64) /
> > >
> > > Any ideas how to solve this problem or were to start
> > > troubleshooting?
> > >
> > > Thank you in advance
> > >
> > > Alex
> > >
> > >
> > >
> > >
> > > ___
> > > 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/
> > >
> > ___
> > 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] Fwd: 'UsesFormDefinitions' is not defined

2012-10-18 Thread Scott McManus 

This was fixed in galaxy-central last week and should be part of 
galaxy-dist. What happened is that controllers were migrated and a
couple of modules were left out. See changeset 210c39f4bf7f or later,
which I believe was fixed on October 4th.

In particular, the problem you're seeing had to do with the 
templates/library/common/library_common.mako pointing to 
galaxy.web.controllers.library_common instead of 
galaxy.webapps.galaxy.controllers.library_common.
A few other files had also been affected.

-Scott

- Original Message -
> Hi Alex
> 
> I am in the same situation, updating our galaxy servers to the "Oct
> 5th"
> release (changeset: 7824:b5bda7a5c345), and I have encountered the
> same
> problem. I guess, there are actually two problems:
> 
> 
> First problem - this happens with a fresh install:
> ==
> 
> I can't create a library at all, I get the following error message:
> 
>   Error attempting to display contents of library (foo): No
>   module named  controllers.library_common.
> 
> 
> 
> There have been a few commits on "library_common.py" over the last
> few
> days, which might solve this problem.?
> 
> 
> 
> Second problem - this happens after upgrading an existing
> installation
> ==
> 
> Like the situation you reported earlier this morning, I get:
> 
> 
>   Error attempting to display contents of library (haruhotz):
>   name 'UsesFormDefinitions' is not defined.
> 
> 
> I manage to track down the problem to the fact that
> 
> in the old version, we've had
> 
> ~/lib/galaxy/web/controllers/
> 
> 
> which apparently has been replaced by
> 
> ~/lib/galaxy/webapps/galaxy/controllers/
> 
> 
> if I remove ~/lib/galaxy/web/controllers/
> 
> 
> I get a new error:
> 
>   Error attempting to display contents of library (haruhotz): No
>   module named library_common.
> 
> 
> which is very similar to the error you get with a fresh install
> 
> 
> Obviously, old stuff (ie ~/lib/galaxy/web/controllers/) is still used
> after the upgrade.
> 
> 
> Sorry, no solution yet, but maybe it helps the developers to track
> down
> the problem and help us getting the servers running again.
> 
> 
> 
> Regards Hans-Rudolf
> 
> 
> On 10/18/2012 10:48 AM, Alexander Graf wrote:
> > Hi,
> > yesterday I updated Galaxy to the latest revision and now it is not
> > possible to access any Data Libraries or to create a new one.
> > Galaxy shows me a read box with following error message:
> >
> > *Error attempting to display contents of library
> > (100326_HWUSI-EAS632R_0002): name 'UsesFormDefinitions' is not
> > defined.*
> >
> > The log file message is:
> >
> > /"GET
> > /galaxy/library_common/browse_library?sort=name&webapp=galaxy&f-description=All&f-name=All&page=1&cntrller=library&show_item_checkboxes=false&async=false&operation=browse&id=9d04ee723dc2cac7
> > HTTP/1.1" 302 -
> > "http://x.x.x.x/galaxy/library/browse_libraries?status=error&use_panels=False&message=Error+attempting+to+display+contents+of+library+%100326_HWUSI-EAS632R_0002%29%3A+name+__sq__UsesFormDefinitions__sq__+is+not+defined.";
> > "Mozilla/5.0 (X11; Linux x86_64) /
> >
> > Any ideas how to solve this problem or were to start
> > troubleshooting?
> >
> > Thank you in advance
> >
> > Alex
> >
> >
> >
> >
> > ___
> > 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/
> >
> ___
> 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] Fwd: 'UsesFormDefinitions' is not defined

2012-10-18 Thread Hans-Rudolf Hotz 

Hi Alex

I am in the same situation, updating our galaxy servers to the "Oct 5th" 
release (changeset: 7824:b5bda7a5c345), and I have encountered the same 
problem. I guess, there are actually two problems:



First problem - this happens with a fresh install:
==

I can't create a library at all, I get the following error message:

Error attempting to display contents of library (foo): No
module named  controllers.library_common.



There have been a few commits on "library_common.py" over the last few 
days, which might solve this problem.?




Second problem - this happens after upgrading an existing installation
==

Like the situation you reported earlier this morning, I get:


Error attempting to display contents of library (haruhotz):
name 'UsesFormDefinitions' is not defined.


I manage to track down the problem to the fact that

in the old version, we've had

~/lib/galaxy/web/controllers/


which apparently has been replaced by

~/lib/galaxy/webapps/galaxy/controllers/


if I remove ~/lib/galaxy/web/controllers/


I get a new error:

Error attempting to display contents of library (haruhotz): No
module named library_common.


which is very similar to the error you get with a fresh install


Obviously, old stuff (ie ~/lib/galaxy/web/controllers/) is still used 
after the upgrade.



Sorry, no solution yet, but maybe it helps the developers to track down 
the problem and help us getting the servers running again.




Regards Hans-Rudolf


On 10/18/2012 10:48 AM, Alexander Graf wrote:

Hi,
yesterday I updated Galaxy to the latest revision and now it is not
possible to access any Data Libraries or to create a new one.
Galaxy shows me a read box with following error message:

*Error attempting to display contents of library
(100326_HWUSI-EAS632R_0002): name 'UsesFormDefinitions' is not defined.*

The log file message is:

/"GET
/galaxy/library_common/browse_library?sort=name&webapp=galaxy&f-description=All&f-name=All&page=1&cntrller=library&show_item_checkboxes=false&async=false&operation=browse&id=9d04ee723dc2cac7
HTTP/1.1" 302 -
"http://x.x.x.x/galaxy/library/browse_libraries?status=error&use_panels=False&message=Error+attempting+to+display+contents+of+library+%100326_HWUSI-EAS632R_0002%29%3A+name+__sq__UsesFormDefinitions__sq__+is+not+defined.";
"Mozilla/5.0 (X11; Linux x86_64) /

Any ideas how to solve this problem or were to start troubleshooting?

Thank you in advance

Alex




___
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[galaxy-dev] Fwd: 'UsesFormDefinitions' is not defined

2012-10-18 Thread Alexander Graf 
Hi,
yesterday I updated Galaxy to the latest revision and now it is not
possible to access any Data Libraries or to create a new one.
Galaxy shows me a read box with following error message:

*Error attempting to display contents of library
(100326_HWUSI-EAS632R_0002): name 'UsesFormDefinitions' is not defined.*

The log file message is:

*"GET
/galaxy/library_common/browse_library?sort=name&webapp=galaxy&f-description=All&f-name=All&page=1&cntrller=library&show_item_checkboxes=false&async=false&operation=browse&id=9d04ee723dc2cac7
HTTP/1.1" 302 - "
http://x.x.x.x/galaxy/library/browse_libraries?status=error&use_panels=False&message=Error+attempting+to+display+contents+of+library+%100326_HWUSI-EAS632R_0002%29%3A+name+__sq__UsesFormDefinitions__sq__+is+not+defined.";
"Mozilla/5.0 (X11; Linux x86_64) *

Any ideas how to solve this problem or were to start troubleshooting?

Thank you in advance

Alex
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