7:41 a.m.
Hi all,
I have developed a tool in our local Galaxy, and imported it in a local
toolshed. I next removed the 'dev' version of the tool in Galaxy, and
installed it now via het Tool Shed Manager.
I got an error that the dependencies could not be installed. If figured it
out that it (needed to add an extra shell_command in the tool_dependencies)
(and the mount point on my system needs to have exec permissions of
course).
So I updated the tool in the toolshed. BUT, then I uninstalled the tool
from Galaxy, and reinstalled it from the Tool Shed ... instead of just
updating. Anyway, it has happened.
Now I have the tool listed in my 'Install Tool Shed Repositories', and when
I click on it, it says 'this tool is not installed'. The only action I can
apply on this installed tool shed repository is 'Install' (...). But
clicking on that 'install' button, leads me to an error page (http error
500).
******************************
URL:
http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://...
Module weberror.evalexception.middleware:364 in respond view
> app_iter = self.application(environ, detect_start_response)
Module paste.recursive:84 in __call__ view
> return self.application(environ, start_response)
Module
paste.httpexceptions:633 in __call__ view
> return self.application(environ, start_response)
Module
galaxy.web.framework.base:132 in __call__ view
> return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request view
> body = method( trans, **kwargs )
Module
galaxy.web.framework:221 in decorator view
> return func( self, trans, *args, **kwargs )
Module
galaxy.webapps.galaxy.controllers.admin_toolshed:825 in
prepare_for_install view
> raw_text = common_util.tool_shed_get( trans.app, tool_shed_url,
url )
Module tool_shed.util.common_util:110 in tool_shed_get view
> response = urlopener.open( uri )
Module urllib2:397 in
open view
> response = meth(req, response)
Module urllib2:510 in
http_response view
> 'http', request, response, code, msg, hdrs)
Module
urllib2:435 in error view
> return self._call_chain(*args)
Module urllib2:369 in
_call_chain view
> result = func(*args)
Module urllib2:518 in
http_error_default view
> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 500: Internal Server Error
************************************
The same happens when I go to the Tool Shed, and try to install the tool
from there: Galaxy detects that the tool has been installed before, and
points me to that 500 error page.
Any help is heartily appreciated,
Thanks,
Joachim
--
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
--
@joachimjacob
2:15 p.m.
Hello Joachim,
What version of Galaxy are your running?
What does the tool shed paster go show for the 500 Internal Server Error?
Also, run the following sql manually in your Galaxy database and send the results.
select id, tool_shed, name, owner, installed_changeset_revision, status, error_message
from tool_shed_repository;
Thanks,
Greg Von Kuster
On Jun 14, 2013, at 3:41 AM, Joachim Jacob <joachim.jacob(a)gmail.com> wrote:
Hi all,
I have developed a tool in our local Galaxy, and imported it in a local toolshed. I next
removed the 'dev' version of the tool in Galaxy, and installed it now via het Tool
Shed Manager.
I got an error that the dependencies could not be installed. If figured it out that it
(needed to add an extra shell_command in the tool_dependencies) (and the mount point on my
system needs to have exec permissions of course).
So I updated the tool in the toolshed. BUT, then I uninstalled the tool from Galaxy, and
reinstalled it from the Tool Shed ... instead of just updating. Anyway, it has happened.
Now I have the tool listed in my 'Install Tool Shed Repositories', and when I
click on it, it says 'this tool is not installed'. The only action I can apply on
this installed tool shed repository is 'Install' (...). But clicking on that
'install' button, leads me to an error page (http error 500).
******************************
URL:
http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://...
Module weberror.evalexception.middleware:364 in respond view
>> app_iter = self.application(environ, detect_start_response)
Module paste.recursive:84 in __call__ view
>> return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__ view
>> return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__ view
>> return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request view
>> body = method( trans, **kwargs )
Module galaxy.web.framework:221 in decorator view
>> return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in prepare_for_install
view
>> raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
Module tool_shed.util.common_util:110 in tool_shed_get view
>> response = urlopener.open( uri )
Module urllib2:397 in open view
>> response = meth(req, response)
Module urllib2:510 in http_response view
>> 'http', request, response, code, msg, hdrs)
Module urllib2:435 in error view
>> return self._call_chain(*args)
Module urllib2:369 in _call_chain view
>> result = func(*args)
Module urllib2:518 in http_error_default view
>> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 500: Internal Server Error
************************************
The same happens when I go to the Tool Shed, and try to install the tool from there:
Galaxy detects that the tool has been installed before, and points me to that 500 error
page.
Any help is heartily appreciated,
Thanks,
Joachim
--
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
--
@joachimjacob
___________________________________________________________
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
12:05 p.m.
Hi Greg,
Sorry to dig up this unsolved thread from a few months back.
Recap of the bug: I have developed a small tool. I have put it in my
local Toolshed, and installed it. After applying some changes to the
tool, I 'hg push'ed the changes to my repository on my toolshed. I
uninstalled the tool, and reinstalled it. Since I work with job
handlers, I have to restart Galaxy. Since I had about ~4 committed
changes, I have repeated these steps about 4 times.
The bug: the tool appears multiple times in the tool management window.
2 times as new, and 1 time as uninstalled (since I uninstalled it). The
tool is still available in the toolbox, although it should not. The 2
installed tools have an option 'install', but when I click this I get an
internal server error 500.
Galaxy version:
*************
[galaxy@galaxy galaxy-dist]$ hg tip
changeset: 10411:c42567f43aa7
tag: tip
user: greg
date: Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of
repository_dependencies objects that are associated with a tool shed
repository installed into Galaxy.
*************
As per your request: the web log of this internal server error.
****************
193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] "GET
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3
HTTP/1.1" 500 -
"http://galaxy.bits.vib.be/admin_toolshed/browse_repositories"
"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
Ubuntu Chromium/28.0.1500.71 Chrome/28.0.1500.71 Safari/537.36"
Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486
****************
The postgres database shows:
************************
galaxydb=> select id, tool_shed, name, owner,
installed_changeset_revision, status, error_message from
tool_shed_repository where name = 'transpose';
id | tool_shed | name | owner |
installed_changeset_revision | status | error_message
----+----------------------+-----------+---------+------------------------------+-------------+---------------
45 | toolshed.bits.vib.be | transpose | joachim |
cee0157acee1 | Uninstalled |
44 | toolshed.bits.vib.be | transpose | joachim |
2fa0462b9303 | New |
43 | toolshed.bits.vib.be | transpose | joachim |
e08a6d9e97a3 | New |
(3 rows)
************************
How should I proceed ?
This is the second time I experience this. On a last note: I have noted
also that I managed to get a repository with different branches in this
tool shed repository, by mixing 'hg push' and uploading a tarball. There
seems no easy way to fixing this.
Kind regards,
Joachim
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 06/14/2013 04:15 PM, Greg Von Kuster wrote:
Hello Joachim,
What version of Galaxy are your running?
What does the tool shed paster go show for the 500 Internal Server Error?
Also, run the following sql manually in your Galaxy database and send
the results.
select id, tool_shed, name, owner, installed_changeset_revision,
status, error_message from tool_shed_repository;
Thanks,
Greg Von Kuster
On Jun 14, 2013, at 3:41 AM, Joachim Jacob <joachim.jacob(a)gmail.com
<mailto:joachim.jacob@gmail.com>> wrote:
> Hi all,
>
> I have developed a tool in our local Galaxy, and imported it in a
> local toolshed. I next removed the 'dev' version of the tool in
> Galaxy, and installed it now via het Tool Shed Manager.
>
> I got an error that the dependencies could not be installed. If
> figured it out that it (needed to add an extra shell_command in the
> tool_dependencies) (and the mount point on my system needs to have
> exec permissions of course).
>
> So I updated the tool in the toolshed. BUT, then I uninstalled the
> tool from Galaxy, and reinstalled it from the Tool Shed ... instead
> of just updating. Anyway, it has happened.
>
> Now I have the tool listed in my 'Install Tool Shed Repositories',
> and when I click on it, it says 'this tool is not installed'. The
> only action I can apply on this installed tool shed repository is
> 'Install' (...). But clicking on that 'install' button, leads me to
> an error page (http error 500).
>
> ******************************
> URL:
>
http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://...
>
> Module weberror.evalexception.middleware:364 in respond view
> >> app_iter = self.application(environ, detect_start_response)
> Module paste.recursive:84 in __call__ view
> >> return self.application(environ, start_response)
> Module paste.httpexceptions:633 in __call__ view
> >> return self.application(environ, start_response)
> Module galaxy.web.framework.base:132 in __call__ view
> >> return self.handle_request( environ, start_response )
> Module galaxy.web.framework.base:190 in handle_request view
> >> body = method( trans, **kwargs )
> Module galaxy.web.framework:221 in decorator view
> >> return func( self, trans, *args, **kwargs )
> Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in
> prepare_for_install view
> >> raw_text = common_util.tool_shed_get( trans.app, tool_shed_url,
> url )
> Module tool_shed.util.common_util:110 in tool_shed_get view
> >> response = urlopener.open( uri )
> Module urllib2:397 in open view
> >> response = meth(req, response)
> Module urllib2:510 in http_response view
> >> 'http', request, response, code, msg, hdrs)
> Module urllib2:435 in error view
> >> return self._call_chain(*args)
> Module urllib2:369 in _call_chain view
> >> result = func(*args)
> Module urllib2:518 in http_error_default view
> >> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
> HTTPError: HTTP Error 500: Internal Server Error
> ************************************
>
> The same happens when I go to the Tool Shed, and try to install the
> tool from there: Galaxy detects that the tool has been installed
> before, and points me to that 500 error page.
>
> Any help is heartily appreciated,
>
> Thanks,
> Joachim
>
> --
> Joachim Jacob
> Contact details: http://www.bits.vib.be/index.php/about/80-team
> --
> @joachimjacob
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
12:15 p.m.
On Mon, Sep 30, 2013 at 1:05 PM, Joachim Jacob | VIB |
<joachim.jacob(a)vib.be> wrote:
Hi Greg,
Sorry to dig up this unsolved thread from a few months back.
Recap of the bug: I have developed a small tool. I have put it in my local
Toolshed, and installed it. After applying some changes to the tool, I 'hg
push'ed the changes to my repository on my toolshed. I uninstalled the tool,
and reinstalled it. Since I work with job handlers, I have to restart
Galaxy. Since I had about ~4 committed changes, I have repeated these steps
about 4 times.
The bug: the tool appears multiple times in the tool management window. 2
times as new, and 1 time as uninstalled (since I uninstalled it). The tool
is still available in the toolbox, although it should not. The 2 installed
tools have an option 'install', but when I click this I get an internal
server error 500.
Galaxy version:
*************
[galaxy@galaxy galaxy-dist]$ hg tip
changeset: 10411:c42567f43aa7
tag: tip
user: greg
date: Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of
repository_dependencies objects that are associated with a tool shed
repository installed into Galaxy.
*************
As per your request: the web log of this internal server error.
****************
193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] "GET
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3
HTTP/1.1" 500 -
"http://galaxy.bits.vib.be/admin_toolshed/browse_repositories"
"Mozilla/5.0
(X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu
Chromium/28.0.1500.71 Chrome/28.0.1500.71 Safari/537.36"
Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486
****************
The postgres database shows:
************************
galaxydb=> select id, tool_shed, name, owner,
installed_changeset_revision, status, error_message from
tool_shed_repository where name = 'transpose';
id | tool_shed | name | owner |
installed_changeset_revision | status | error_message
----+----------------------+-----------+---------+------------------------------+-------------+---------------
45 | toolshed.bits.vib.be | transpose | joachim | cee0157acee1
| Uninstalled |
44 | toolshed.bits.vib.be | transpose | joachim | 2fa0462b9303
| New |
43 | toolshed.bits.vib.be | transpose | joachim | e08a6d9e97a3
| New |
(3 rows)
************************
How should I proceed ?
This is the second time I experience this. On a last note: I have noted also
that I managed to get a repository with different branches in this tool shed
repository, by mixing 'hg push' and uploading a tarball. There seems no easy
way to fixing this.
Kind regards,
Joachim
Hmm - do these "New" entries show up in white on the
"Manage installed tool shed repositories" admin page?
It sounds like a case of what was nicknamed "white ghosts",
some causes of which have been fixed - but I don't think there
was any automated removal of old "white ghosts" (I still have
two on my test system).
Peter
12:46 p.m.
See attachment.
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/30/2013 02:15 PM, Peter Cock wrote:
On Mon, Sep 30, 2013 at 1:05 PM, Joachim Jacob | VIB |
<joachim.jacob(a)vib.be> wrote:
> Hi Greg,
>
>
> Sorry to dig up this unsolved thread from a few months back.
>
> Recap of the bug: I have developed a small tool. I have put it in my local
> Toolshed, and installed it. After applying some changes to the tool, I 'hg
> push'ed the changes to my repository on my toolshed. I uninstalled the tool,
> and reinstalled it. Since I work with job handlers, I have to restart
> Galaxy. Since I had about ~4 committed changes, I have repeated these steps
> about 4 times.
>
> The bug: the tool appears multiple times in the tool management window. 2
> times as new, and 1 time as uninstalled (since I uninstalled it). The tool
> is still available in the toolbox, although it should not. The 2 installed
> tools have an option 'install', but when I click this I get an internal
> server error 500.
>
> Galaxy version:
> *************
> [galaxy@galaxy galaxy-dist]$ hg tip
> changeset: 10411:c42567f43aa7
> tag: tip
> user: greg
> date: Mon Aug 19 13:19:56 2013 -0400
> summary: Filter invalid objects when generating the list of
> repository_dependencies objects that are associated with a tool shed
> repository installed into Galaxy.
> *************
>
> As per your request: the web log of this internal server error.
>
> ****************
> 193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] "GET
>
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3
> HTTP/1.1" 500 -
> "http://galaxy.bits.vib.be/admin_toolshed/browse_repositories"
"Mozilla/5.0
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu
> Chromium/28.0.1500.71 Chrome/28.0.1500.71 Safari/537.36"
> Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486
> ****************
>
> The postgres database shows:
>
> ************************
> galaxydb=> select id, tool_shed, name, owner,
> installed_changeset_revision, status, error_message from
> tool_shed_repository where name = 'transpose';
> id | tool_shed | name | owner |
> installed_changeset_revision | status | error_message
>
----+----------------------+-----------+---------+------------------------------+-------------+---------------
> 45 | toolshed.bits.vib.be | transpose | joachim | cee0157acee1
> | Uninstalled |
> 44 | toolshed.bits.vib.be | transpose | joachim | 2fa0462b9303
> | New |
> 43 | toolshed.bits.vib.be | transpose | joachim | e08a6d9e97a3
> | New |
> (3 rows)
> ************************
> How should I proceed ?
>
>
> This is the second time I experience this. On a last note: I have noted also
> that I managed to get a repository with different branches in this tool shed
> repository, by mixing 'hg push' and uploading a tarball. There seems no easy
> way to fixing this.
>
>
> Kind regards,
> Joachim
Hmm - do these "New" entries show up in white on the
"Manage installed tool shed repositories" admin page?
It sounds like a case of what was nicknamed "white ghosts",
some causes of which have been fixed - but I don't think there
was any automated removal of old "white ghosts" (I still have
two on my test system).
Peter
12:15 p.m.
Hello Joachim,
What version of Galaxy / Tool Shed code are you using?
On Sep 30, 2013, at 8:05 AM, Joachim Jacob | VIB | <joachim.jacob(a)vib.be> wrote:
Hi Greg,
Sorry to dig up this unsolved thread from a few months back.
Recap of the bug: I have developed a small tool. I have put it in my local Toolshed, and
installed it. After applying some changes to the tool, I 'hg push'ed the changes
to my repository on my toolshed. I uninstalled the tool, and reinstalled it. Since I work
with job handlers, I have to restart Galaxy. Since I had about ~4 committed changes, I
have repeated these steps about 4 times.
What process do you use for "applying some changes to the tool"? Do you
make these changes in a separate development repository and push them to your repository
in your tool shed? Or are you making changes to the installed repository in your Galaxy
instance and attempting to push them back to the repository in your Tool Shed?
The bug: the tool appears multiple times in the tool management
window. 2 times as new, and 1 time as uninstalled (since I uninstalled it). The tool is
still available in the toolbox, although it should not. The 2 installed tools have an
option 'install', but when I click this I get an internal server error 500.
Galaxy version:
*************
[galaxy@galaxy galaxy-dist]$ hg tip
changeset: 10411:c42567f43aa7
tag: tip
user: greg
date: Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of repository_dependencies
objects that are associated with a tool shed repository installed into Galaxy.
*************
As per your request: the web log of this internal server error.
****************
193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] "GET
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3
HTTP/1.1" 500 -
"http://galaxy.bits.vib.be/admin_toolshed/browse_repositories" "Mozilla/5.0
(X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu Chromium/28.0.1500.71
Chrome/28.0.1500.71 Safari/537.36"
Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486
When you point your browser to the above "Debug URL", what is the stack trace
that is displayed?
****************
The postgres database shows:
************************
galaxydb=> select id, tool_shed, name, owner,
installed_changeset_revision, status, error_message from tool_shed_repository where name =
'transpose';
id | tool_shed | name | owner | installed_changeset_revision | status
| error_message
----+----------------------+-----------+---------+------------------------------+-------------+---------------
45 | toolshed.bits.vib.be | transpose | joachim | cee0157acee1 |
Uninstalled |
44 | toolshed.bits.vib.be | transpose | joachim | 2fa0462b9303 | New
|
43 | toolshed.bits.vib.be | transpose | joachim | e08a6d9e97a3 | New
|
(3 rows)
************************
These repositories in the "New" state look like the so-called "white
ghosts" that cropped up for a time. The issues that resulted in their creation have
been resolved, but some of the fixes will not be available in the distribution until the
next Galaxy release, which is not yet scheduled.
How should I proceed ?
You'll undoubtedly need to manually fix your database with sql - delete these records
in the "New" state and all associated recoirds defined by foreign keys.
This is the second time I experience this. On a last note: I have noted also that I
managed to get a repository with different branches in this tool shed repository, by
mixing 'hg push' and uploading a tarball. There seems no easy way to fixing this.
Kind regards,
Joachim
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 06/14/2013 04:15 PM, Greg Von Kuster wrote:
> Hello Joachim,
>
> What version of Galaxy are your running?
>
> What does the tool shed paster go show for the 500 Internal Server Error?
>
> Also, run the following sql manually in your Galaxy database and send the results.
>
> select id, tool_shed, name, owner, installed_changeset_revision, status,
error_message from tool_shed_repository;
>
> Thanks,
>
> Greg Von Kuster
>
>
> On Jun 14, 2013, at 3:41 AM, Joachim Jacob <joachim.jacob(a)gmail.com
<mailto:joachim.jacob@gmail.com>> wrote:
>
>> Hi all,
>>
>> I have developed a tool in our local Galaxy, and imported it in a local toolshed.
I next removed the 'dev' version of the tool in Galaxy, and installed it now via
het Tool Shed Manager.
>>
>> I got an error that the dependencies could not be installed. If figured it out
that it (needed to add an extra shell_command in the tool_dependencies) (and the mount
point on my system needs to have exec permissions of course).
>>
>> So I updated the tool in the toolshed. BUT, then I uninstalled the tool from
Galaxy, and reinstalled it from the Tool Shed ... instead of just updating. Anyway, it has
happened.
>>
>> Now I have the tool listed in my 'Install Tool Shed Repositories', and
when I click on it, it says 'this tool is not installed'. The only action I can
apply on this installed tool shed repository is 'Install' (...). But clicking on
that 'install' button, leads me to an error page (http error 500).
>>
>> ******************************
>> URL:
http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://...
>> Module weberror.evalexception.middleware:364 in respond view
>> >> app_iter = self.application(environ, detect_start_response)
>> Module paste.recursive:84 in __call__ view
>> >> return self.application(environ, start_response)
>> Module paste.httpexceptions:633 in __call__ view
>> >> return self.application(environ, start_response)
>> Module galaxy.web.framework.base:132 in __call__ view
>> >> return self.handle_request( environ, start_response )
>> Module galaxy.web.framework.base:190 in handle_request view
>> >> body = method( trans, **kwargs )
>> Module galaxy.web.framework:221 in decorator view
>> >> return func( self, trans, *args, **kwargs )
>> Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in
prepare_for_install view
>> >> raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
>> Module tool_shed.util.common_util:110 in tool_shed_get view
>> >> response = urlopener.open( uri )
>> Module urllib2:397 in open view
>> >> response = meth(req, response)
>> Module urllib2:510 in http_response view
>> >> 'http', request, response, code, msg, hdrs)
>> Module urllib2:435 in error view
>> >> return self._call_chain(*args)
>> Module urllib2:369 in _call_chain view
>> >> result = func(*args)
>> Module urllib2:518 in http_error_default view
>> >> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
>> HTTPError: HTTP Error 500: Internal Server Error
>> ************************************
>>
>> The same happens when I go to the Tool Shed, and try to install the tool from
there: Galaxy detects that the tool has been installed before, and points me to that 500
error page.
>>
>> Any help is heartily appreciated,
>>
>> Thanks,
>> Joachim
>>
>> --
>> Joachim Jacob
>> Contact details: http://www.bits.vib.be/index.php/about/80-team
>> --
>> @joachimjacob
>> ___________________________________________________________
>> 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/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
>
>
>
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
12:56 p.m.
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/30/2013 02:15 PM, Greg Von Kuster wrote:
Hello Joachim,
What version of Galaxy / Tool Shed code are you using?
[galaxy@galaxy galaxy-dist]$
hg tip
changeset: 10411:c42567f43aa7
On Sep 30, 2013, at 8:05 AM, Joachim Jacob | VIB | <joachim.jacob(a)vib.be> wrote:
> Hi Greg,
>
>
> Sorry to dig up this unsolved thread from a few months back.
>
> Recap of the bug: I have developed a small tool. I have put it in my local Toolshed,
and installed it. After applying some changes to the tool, I 'hg push'ed the
changes to my repository on my toolshed. I uninstalled the tool, and reinstalled it. Since
I work with job handlers, I have to restart Galaxy. Since I had about ~4 committed
changes, I have repeated these steps about 4 times.
>
What process do you use for "applying some changes to the tool"? Do you make
these changes in a separate development repository and push them to your repository in
your tool shed? Or are you making changes to the installed repository in your Galaxy
instance and attempting to push them back to the repository in your Tool Shed?
First I develop an XML, README, and tool_dependencies.xml in a
development directory. When finished, I put them in a tool shed repo, by
uploading a tar ball of these files. I clone the tool shed repo, and
delete my development directory. I adjust files in that cloned tool
shed repo (e.g. fixing typos, adding help,...) and push them back to the
tool shed repo.
Now, I did some changes to the tool_dependencies.xml and pushed them
back to the tool shed. Next I update or remove/reinstall the tool via
the Admin menu. I try to install the dependencies.
That's how I work. I have a feeling that I know what's coming next. :-)
> The bug: the tool appears multiple times in the tool management
window. 2 times as new, and 1 time as uninstalled (since I uninstalled it). The tool is
still available in the toolbox, although it should not. The 2 installed tools have an
option 'install', but when I click this I get an internal server error 500.
>
> Galaxy version:
> *************
> [galaxy@galaxy galaxy-dist]$ hg tip
> changeset: 10411:c42567f43aa7
> tag: tip
> user: greg
> date: Mon Aug 19 13:19:56 2013 -0400
> summary: Filter invalid objects when generating the list of
repository_dependencies objects that are associated with a tool shed repository installed
into Galaxy.
> *************
>
> As per your request: the web log of this internal server error.
>
> ****************
> 193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] "GET
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3
HTTP/1.1" 500 -
"http://galaxy.bits.vib.be/admin_toolshed/browse_repositories" "Mozilla/5.0
(X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu Chromium/28.0.1500.71
Chrome/28.0.1500.71 Safari/537.36"
> Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486
When you point your browser to the above "Debug URL", what is the stack trace
that is displayed?
URL:
http://galaxy.bits.vib.be/admin_toolshed/prepare_for_install?tool_shed_ur...
File
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py',
line 84 in __call__
return self.application(environ, start_response)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py',
line 633 in __call__
return self.application(environ, start_response)
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
132 in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
190 in handle_request
body = method( trans, **kwargs )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 221 in decorator
return func( self, trans, *args, **kwargs )
File
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
line 840 in prepare_for_install
raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
File '/home/galaxy/galaxy-dist/lib/tool_shed/util/common_util.py', line
110 in tool_shed_get
response = urlopener.open( uri )
File '/usr/lib64/python2.6/urllib2.py', line 397 in open
response = meth(req, response)
File '/usr/lib64/python2.6/urllib2.py', line 510 in http_response
'http', request, response, code, msg, hdrs)
File '/usr/lib64/python2.6/urllib2.py', line 435 in error
return self._call_chain(*args)
File '/usr/lib64/python2.6/urllib2.py', line 369 in _call_chain
result = func(*args)
File '/usr/lib64/python2.6/urllib2.py', line 518 in http_error_default
raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 500: Internal Server Error
> ****************
>
> The postgres database shows:
>
> ************************
> galaxydb=> select id, tool_shed, name, owner,
installed_changeset_revision, status, error_message from tool_shed_repository where name =
'transpose';
> id | tool_shed | name | owner | installed_changeset_revision |
status | error_message
>
----+----------------------+-----------+---------+------------------------------+-------------+---------------
> 45 | toolshed.bits.vib.be | transpose | joachim | cee0157acee1 |
Uninstalled |
> 44 | toolshed.bits.vib.be | transpose | joachim | 2fa0462b9303 | New
|
> 43 | toolshed.bits.vib.be | transpose | joachim | e08a6d9e97a3 | New
|
> (3 rows)
> ************************
These repositories in the "New" state look like the so-called "white
ghosts" that cropped up for a time. The issues that resulted in their creation have
been resolved, but some of the fixes will not be available in the distribution until the
next Galaxy release, which is not yet scheduled.
> How should I proceed ?
You'll undoubtedly need to manually fix your database with sql - delete these records
in the "New" state and all associated recoirds defined by foreign keys.
OK, thanks.
>
> This is the second time I experience this. On a last note: I have noted also that I
managed to get a repository with different branches in this tool shed repository, by
mixing 'hg push' and uploading a tarball. There seems no easy way to fixing this.
>
>
> Kind regards,
> Joachim
>
> Joachim Jacob
> Contact details: http://www.bits.vib.be/index.php/about/80-team
>
>
> On 06/14/2013 04:15 PM, Greg Von Kuster wrote:
>> Hello Joachim,
>>
>> What version of Galaxy are your running?
>>
>> What does the tool shed paster go show for the 500 Internal Server Error?
>>
>> Also, run the following sql manually in your Galaxy database and send the
results.
>>
>> select id, tool_shed, name, owner, installed_changeset_revision, status,
error_message from tool_shed_repository;
>>
>> Thanks,
>>
>> Greg Von Kuster
>>
>>
>> On Jun 14, 2013, at 3:41 AM, Joachim Jacob <joachim.jacob(a)gmail.com
<mailto:joachim.jacob@gmail.com>> wrote:
>>
>>> Hi all,
>>>
>>> I have developed a tool in our local Galaxy, and imported it in a local
toolshed. I next removed the 'dev' version of the tool in Galaxy, and installed it
now via het Tool Shed Manager.
>>>
>>> I got an error that the dependencies could not be installed. If figured it
out that it (needed to add an extra shell_command in the tool_dependencies) (and the mount
point on my system needs to have exec permissions of course).
>>>
>>> So I updated the tool in the toolshed. BUT, then I uninstalled the tool from
Galaxy, and reinstalled it from the Tool Shed ... instead of just updating. Anyway, it has
happened.
>>>
>>> Now I have the tool listed in my 'Install Tool Shed Repositories',
and when I click on it, it says 'this tool is not installed'. The only action I
can apply on this installed tool shed repository is 'Install' (...). But clicking
on that 'install' button, leads me to an error page (http error 500).
>>>
>>> ******************************
>>> URL:
http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://...
>>> Module weberror.evalexception.middleware:364 in respond view
>>>>> app_iter = self.application(environ, detect_start_response)
>>> Module paste.recursive:84 in __call__ view
>>>>> return self.application(environ, start_response)
>>> Module paste.httpexceptions:633 in __call__ view
>>>>> return self.application(environ, start_response)
>>> Module galaxy.web.framework.base:132 in __call__ view
>>>>> return self.handle_request( environ, start_response )
>>> Module galaxy.web.framework.base:190 in handle_request view
>>>>> body = method( trans, **kwargs )
>>> Module galaxy.web.framework:221 in decorator view
>>>>> return func( self, trans, *args, **kwargs )
>>> Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in
prepare_for_install view
>>>>> raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url
)
>>> Module tool_shed.util.common_util:110 in tool_shed_get view
>>>>> response = urlopener.open( uri )
>>> Module urllib2:397 in open view
>>>>> response = meth(req, response)
>>> Module urllib2:510 in http_response view
>>>>> 'http', request, response, code, msg, hdrs)
>>> Module urllib2:435 in error view
>>>>> return self._call_chain(*args)
>>> Module urllib2:369 in _call_chain view
>>>>> result = func(*args)
>>> Module urllib2:518 in http_error_default view
>>>>> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
>>> HTTPError: HTTP Error 500: Internal Server Error
>>> ************************************
>>>
>>> The same happens when I go to the Tool Shed, and try to install the tool from
there: Galaxy detects that the tool has been installed before, and points me to that 500
error page.
>>>
>>> Any help is heartily appreciated,
>>>
>>> Thanks,
>>> Joachim
>>>
>>> --
>>> Joachim Jacob
>>> Contact details: http://www.bits.vib.be/index.php/about/80-team
>>> --
>>> @joachimjacob
>>> ___________________________________________________________
>>> 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/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>> http://galaxyproject.org/search/mailinglists/
>>
>>
>> ___________________________________________________________
>> 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/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
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participants (4)
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Joachim Jacob -
Joachim Jacob | VIB | -
Peter Cock