I tried to reply to similar posts, but couldn't figure out how to do it. So posting again:
Galaxy giving this error when editing workflow, just after creating workflow from existing history:
URL:http://localhost/galaxy/workflow/load_workflow?id=df7a1f0c02a5b08e&_=135... Moduleweberror.evalexception.middleware:*364*in|respond| |>> http://localhost/galaxy/workflow/editor?id=df7a1f0c02a5b08e#app_iter*=*self*.*application*(*environ*,*detect_start_response*)*| Modulepaste.debug.prints:*98*in|__call__| |>> http://localhost/galaxy/workflow/editor?id=df7a1f0c02a5b08e#environ*,*self*.*app*)*| Modulepaste.wsgilib:*539*in|intercept_output| |>> http://localhost/galaxy/workflow/editor?id=df7a1f0c02a5b08e#app_iter*=*application*(*environ*,*replacement_start_response*)*| Modulepaste.recursive:*80*in|__call__| |>> http://localhost/galaxy/workflow/editor?id=df7a1f0c02a5b08e#*return*self*.*application*(*environ*,*start_response*)*| Modulepaste.httpexceptions:*632*in|__call__| |>> http://localhost/galaxy/workflow/editor?id=df7a1f0c02a5b08e#*return*self*.*application*(*environ*,*start_response*)*| Modulegalaxy.web.framework.base:*160*in|__call__| |>> http://localhost/galaxy/workflow/editor?id=df7a1f0c02a5b08e#body*=*method*(*trans*,*****kwargs*)*| Modulegalaxy.web.framework:*73*in|decorator| |>> http://localhost/galaxy/workflow/editor?id=df7a1f0c02a5b08e#*return*simplejson*.*dumps*(*func*(*self*,*trans*,****args*,*****kwargs*)**)*| Modulegalaxy.webapps.galaxy.controllers.workflow:*733*in|load_workflow| |>> http://localhost/galaxy/workflow/editor?id=df7a1f0c02a5b08e#'tooltip'*:*module*.*get_tooltip*(*static_path*=*url_for*(*'/static'*)**)**,*| Modulegalaxy.workflow.modules:*258*in|get_tooltip| |>> http://localhost/galaxy/workflow/editor?id=df7a1f0c02a5b08e#*return*self*.*tool*.*help*.*render*(*static_path*=*static_path*)*| *AttributeError: 'NoneType' object has no attribute 'render'*
Could anyone help me to solve this problem?
Thanks, Sanjar.
Sanjar,
This is fixed as of 5013377e0bf7. This may not be in the next distribution, but will be in the one after that. Of course, you can manually pull the change from galaxy-central at any time.
-Dannon
On Nov 13, 2012, at 9:45 AM, Sanjarbek Hudaiberdiev hudaiber@icgeb.org wrote:
I tried to reply to similar posts, but couldn't figure out how to do it. So posting again:
Galaxy giving this error when editing workflow, just after creating workflow from existing history:
URL: http://localhost/galaxy/workflow/load_workflow?id=df7a1f0c02a5b08e&_=135... Module weberror.evalexception.middleware:364 in respond
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__
environ, self.app)
Module paste.wsgilib:539 in intercept_output
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__
return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__
body = method( trans, **kwargs )
Module galaxy.web.framework:73 in decorator
return simplejson.dumps( func( self, trans, *args, **kwargs ) )
Module galaxy.webapps.galaxy.controllers.workflow:733 in load_workflow
'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ),
Module galaxy.workflow.modules:258 in get_tooltip
return self.tool.help.render( static_path=static_path )
AttributeError: 'NoneType' object has no attribute 'render'
Could anyone help me to solve this problem?
Thanks, Sanjar. ___________________________________________________________ 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:
Thanks a lot Dannon, for your reply.
But hg keeps saying following when I try to pull: "abort: unknown revision '5013377e0bf7'!"
Is there any other way of manually getting it?
(Sorry, I'm not an expert on those new SCMs) Sanjar.
On 11/13/2012 06:33 PM, Dannon Baker wrote:
Sanjar,
This is fixed as of 5013377e0bf7. This may not be in the next distribution, but will be in the one after that. Of course, you can manually pull the change from galaxy-central at any time.
-Dannon
On Nov 13, 2012, at 9:45 AM, Sanjarbek Hudaiberdiev hudaiber@icgeb.org wrote:
I tried to reply to similar posts, but couldn't figure out how to do it. So posting again:
Galaxy giving this error when editing workflow, just after creating workflow from existing history:
URL: http://localhost/galaxy/workflow/load_workflow?id=df7a1f0c02a5b08e&_=135... Module weberror.evalexception.middleware:364 in respond
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__
environ, self.app)
Module paste.wsgilib:539 in intercept_output
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__
return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__
body = method( trans, **kwargs )
Module galaxy.web.framework:73 in decorator
return simplejson.dumps( func( self, trans, *args, **kwargs ) )
Module galaxy.webapps.galaxy.controllers.workflow:733 in load_workflow
'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ),
Module galaxy.workflow.modules:258 in get_tooltip
return self.tool.help.render( static_path=static_path )
AttributeError: 'NoneType' object has no attribute 'render'
Could anyone help me to solve this problem?
Thanks, Sanjar. ___________________________________________________________ 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:
This changeset is only in galaxy-central, at the moment, and not galaxy-dist. You have a few options here:
Pull directly from -central to the revision indicated (though this means you will be updating your instance to less thoroughly tested galaxy-central code):
hg pull -u -r 5013377e0bf7 http://bitbucket.org/galaxy/galaxy-central/
Or, probably preferable to that, you could apply just the individual changeset as a patch (which will merge in silently when you do update -dist). Simply execute the following within your galaxy-dist directory:
curl https://bitbucket.org/galaxy/galaxy-central/changeset/5013377e0bf7/raw > modulefix.patch hg patch --no-commit modulefix.patch
-Dannon
On Nov 14, 2012, at 8:04 AM, Sanjarbek Hudaiberdiev hudaiber@icgeb.org wrote:
Thanks a lot Dannon, for your reply.
But hg keeps saying following when I try to pull: "abort: unknown revision '5013377e0bf7'!"
Is there any other way of manually getting it?
(Sorry, I'm not an expert on those new SCMs) Sanjar.
On 11/13/2012 06:33 PM, Dannon Baker wrote:
Sanjar,
This is fixed as of 5013377e0bf7. This may not be in the next distribution, but will be in the one after that. Of course, you can manually pull the change from galaxy-central at any time.
-Dannon
On Nov 13, 2012, at 9:45 AM, Sanjarbek Hudaiberdiev hudaiber@icgeb.org wrote:
I tried to reply to similar posts, but couldn't figure out how to do it. So posting again:
Galaxy giving this error when editing workflow, just after creating workflow from existing history:
URL: http://localhost/galaxy/workflow/load_workflow?id=df7a1f0c02a5b08e&_=135... Module weberror.evalexception.middleware:364 in respond
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__
environ, self.app)
Module paste.wsgilib:539 in intercept_output
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__
return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__
body = method( trans, **kwargs )
Module galaxy.web.framework:73 in decorator
return simplejson.dumps( func( self, trans, *args, **kwargs ) )
Module galaxy.webapps.galaxy.controllers.workflow:733 in load_workflow
'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ),
Module galaxy.workflow.modules:258 in get_tooltip
return self.tool.help.render( static_path=static_path )
AttributeError: 'NoneType' object has no attribute 'render'
Could anyone help me to solve this problem?
Thanks, Sanjar. ___________________________________________________________ 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:
Dannon,
I wanted to apply the patch as well on our fresh instance. But it fails with the error of uncomitted changes.. But we only pull/merge/update using hg nothing else we do with it....any clues? We only locally modified files of course (like the wsgi.ini files and loc files).
$ hg patch --no-commit modulefix.patch abort: outstanding uncommitted changes
Alex
-----Oorspronkelijk bericht----- Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Dannon Baker Verzonden: woensdag 14 november 2012 14:18 Aan: Sanjarbek Hudaiberdiev CC: galaxy-dev@bx.psu.edu Onderwerp: Re: [galaxy-dev] Can't edit galaxy workflow
This changeset is only in galaxy-central, at the moment, and not galaxy-dist. You have a few options here:
Pull directly from -central to the revision indicated (though this means you will be updating your instance to less thoroughly tested galaxy-central code):
hg pull -u -r 5013377e0bf7 http://bitbucket.org/galaxy/galaxy-central/
Or, probably preferable to that, you could apply just the individual changeset as a patch (which will merge in silently when you do update -dist). Simply execute the following within your galaxy-dist directory:
curl https://bitbucket.org/galaxy/galaxy-central/changeset/5013377e0bf7/raw > modulefix.patch hg patch --no-commit modulefix.patch
-Dannon
On Nov 14, 2012, at 8:04 AM, Sanjarbek Hudaiberdiev hudaiber@icgeb.org wrote:
Thanks a lot Dannon, for your reply.
But hg keeps saying following when I try to pull: "abort: unknown revision '5013377e0bf7'!"
Is there any other way of manually getting it?
(Sorry, I'm not an expert on those new SCMs) Sanjar.
On 11/13/2012 06:33 PM, Dannon Baker wrote:
Sanjar,
This is fixed as of 5013377e0bf7. This may not be in the next distribution, but will be in the one after that. Of course, you can manually pull the change from galaxy-central at any time.
-Dannon
On Nov 13, 2012, at 9:45 AM, Sanjarbek Hudaiberdiev hudaiber@icgeb.org wrote:
I tried to reply to similar posts, but couldn't figure out how to do it. So posting again:
Galaxy giving this error when editing workflow, just after creating workflow from existing history:
URL: http://localhost/galaxy/workflow/load_workflow?id=df7a1f0c02a5b08e&_ =1352817462148 Module weberror.evalexception.middleware:364 in respond
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__
environ, self.app)
Module paste.wsgilib:539 in intercept_output
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__
return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__
body = method( trans, **kwargs )
Module galaxy.web.framework:73 in decorator
return simplejson.dumps( func( self, trans, *args, **kwargs ) )
Module galaxy.webapps.galaxy.controllers.workflow:733 in load_workflow
'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ),
Module galaxy.workflow.modules:258 in get_tooltip
return self.tool.help.render( static_path=static_path )
AttributeError: 'NoneType' object has no attribute 'render'
Could anyone help me to solve this problem?
Thanks, Sanjar. ___________________________________________________________ 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:
___________________________________________________________ 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:
Make sure that you are pulling from galaxy-central and not galaxy-dist. I believe something like: hg pull -r rev# -u http://bitbucket.org/galaxy/galaxy-central
should work. The problem may be that you are pointing to galaxy-dist by default, which will not know about that revision (yet).
-Scott
----- Original Message -----
Thanks a lot Dannon, for your reply.
But hg keeps saying following when I try to pull: "abort: unknown revision '5013377e0bf7'!"
Is there any other way of manually getting it?
(Sorry, I'm not an expert on those new SCMs) Sanjar.
On 11/13/2012 06:33 PM, Dannon Baker wrote:
Sanjar,
This is fixed as of 5013377e0bf7. This may not be in the next distribution, but will be in the one after that. Of course, you can manually pull the change from galaxy-central at any time.
-Dannon
On Nov 13, 2012, at 9:45 AM, Sanjarbek Hudaiberdiev hudaiber@icgeb.org wrote:
I tried to reply to similar posts, but couldn't figure out how to do it. So posting again:
Galaxy giving this error when editing workflow, just after creating workflow from existing history:
URL: http://localhost/galaxy/workflow/load_workflow?id=df7a1f0c02a5b08e&_=135... Module weberror.evalexception.middleware:364 in respond
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__
environ, self.app)
Module paste.wsgilib:539 in intercept_output
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__
return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__
body = method( trans, **kwargs )
Module galaxy.web.framework:73 in decorator
return simplejson.dumps( func( self, trans, *args, **kwargs ) )
Module galaxy.webapps.galaxy.controllers.workflow:733 in load_workflow
'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ),
Module galaxy.workflow.modules:258 in get_tooltip
return self.tool.help.render( static_path=static_path )
AttributeError: 'NoneType' object has no attribute 'render'
Could anyone help me to solve this problem?
Thanks, Sanjar. ___________________________________________________________ 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:
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:
Hi, Can you please send the entire link to access this changeset? I keep searching for 5013377e0bf7 but can not find it.
Thanks in advance, Liisa
From: Dannon Baker dannonbaker@me.com To: Sanjarbek Hudaiberdiev hudaiber@icgeb.org Cc: galaxy-dev@bx.psu.edu Date: 13/11/2012 12:34 PM Subject: Re: [galaxy-dev] Can't edit galaxy workflow Sent by: galaxy-dev-bounces@lists.bx.psu.edu
Sanjar,
This is fixed as of 5013377e0bf7. This may not be in the next distribution, but will be in the one after that. Of course, you can manually pull the change from galaxy-central at any time.
-Dannon
On Nov 13, 2012, at 9:45 AM, Sanjarbek Hudaiberdiev hudaiber@icgeb.org wrote:
I tried to reply to similar posts, but couldn't figure out how to do it.
So posting again:
Galaxy giving this error when editing workflow, just after creating
workflow from existing history:
URL:
http://localhost/galaxy/workflow/load_workflow?id=df7a1f0c02a5b08e&_=135...
Module weberror.evalexception.middleware:364 in respond
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__
environ, self.app)
Module paste.wsgilib:539 in intercept_output
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__
return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__
body = method( trans, **kwargs )
Module galaxy.web.framework:73 in decorator
return simplejson.dumps( func( self, trans, *args, **kwargs ) )
Module galaxy.webapps.galaxy.controllers.workflow:733 in load_workflow
'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ),
Module galaxy.workflow.modules:258 in get_tooltip
return self.tool.help.render( static_path=static_path )
AttributeError: 'NoneType' object has no attribute 'render'
Could anyone help me to solve this problem?
Thanks, Sanjar. ___________________________________________________________ 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:
___________________________________________________________ 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:
Bitbucket will only show the first 7 characters when browsing through commits. Try this: https://bitbucket.org/galaxy/galaxy-central/changeset/5013377e0bf7a656ea5930...
-Scott
----- Original Message -----
Hi, Can you please send the entire link to access this changeset? I keep searching for 5013377e0bf7 but can not find it.
Thanks in advance, Liisa
From: Dannon Baker dannonbaker@me.com To: Sanjarbek Hudaiberdiev hudaiber@icgeb.org Cc: galaxy-dev@bx.psu.edu Date: 13/11/2012 12:34 PM Subject: Re: [galaxy-dev] Can't edit galaxy workflow Sent by: galaxy-dev-bounces@lists.bx.psu.edu
Sanjar,
This is fixed as of 5013377e0bf7. This may not be in the next distribution, but will be in the one after that. Of course, you can manually pull the change from galaxy-central at any time.
-Dannon
On Nov 13, 2012, at 9:45 AM, Sanjarbek Hudaiberdiev hudaiber@icgeb.org wrote:
I tried to reply to similar posts, but couldn't figure out how to do it. So posting again:
Galaxy giving this error when editing workflow, just after creating workflow from existing history:
URL: http://localhost/galaxy/workflow/load_workflow?id=df7a1f0c02a5b08e&_=135... Module weberror.evalexception.middleware:364 in respond
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__
environ, self.app)
Module paste.wsgilib:539 in intercept_output
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__
return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__
body = method( trans, **kwargs )
Module galaxy.web.framework:73 in decorator
return simplejson.dumps( func( self, trans, *args, **kwargs ) )
Module galaxy.webapps.galaxy.controllers.workflow:733 in load_workflow
'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ),
Module galaxy.workflow.modules:258 in get_tooltip
return self.tool.help.render( static_path=static_path )
AttributeError: 'NoneType' object has no attribute 'render'
Could anyone help me to solve this problem?
Thanks, Sanjar. ___________________________________________________________ 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:
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:
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:
galaxy-dev@lists.galaxyproject.org
-
Bossers, Alex -
Dannon Baker -
Liisa Koski -
Sanjarbek Hudaiberdiev -
Scott McManus