Re: [galaxy-dev] Problems uploading files to a data library

2014-08-12 Thread Nate Coraor 
On Tue, Aug 12, 2014 at 3:03 AM, Juan Vladimir de la Rosa Medina <
jvdelar...@hotmail.com> wrote:

> Hi everyone,
>
> I recently have installed a local instance of galaxy in my computer,
> everything worked fine until I changed the path for *library_import_dir* in
> the *universe_wsgi.ini* file, to upload files to data libraries.
> I followed the Galaxy documentation to setup this feature:
>
> This is the path in the *universe_wsgi.ini* file
> *library_import_dir = /media/New/Vladimir/My_RNA-seq/*
>
> The steps I followed are:
> *Admin > Data Library > Create new data library > Add datasets >
> Upload directory of files*
> file format was set to *auto-detect*
> server Directory was */media/New/Vladimir/My_RNA-seq/*
> and we chose the option to *link to files* instead of copying them
>
> When I try to upload files, galaxy displays the following error:
>
>
> *Error Traceback:*
>
> *⇝ AttributeError: 'NoneType' object has no attribute 'new_state'*
>

Juan,


A bit of a guess here - have you removed the upload tool from your
tool_conf.xml?


--nate


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> * version="2.7.3">Python
> weberror.evalexception.middleware
>  
> /home/labinmunologiaulpgc/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py
> 364respond
>  app_iter = self.application(environ,
> detect_start_response)
> try: __traceback_supplement__ = errormiddleware.Supplement,
> self, environapp_iter = self.application(environ,
> detect_start_response)try:return_iter =
> list(app_iter) 
>  paste.recursive
>  
> /home/labinmunologiaulpgc/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py
> 84__call__
>  return self.application(environ,
> start_response)
> environ['paste.recursive.script_name'] = my_script_name
> try:return self.application(environ, start_response)
> except ForwardRequestException, e:middleware =
> CheckForRecursionMiddleware(
>  paste.httpexceptions
>  
> /home/labinmunologiaulpgc/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py
>  633
>  __call__return
> self.application(environ, start_response)
> []).append(HTTPException)
> try:return self.application(environ,
> start_response)except HTTPException, exc:return
> exc(environ, start_response)
>  galaxy.web.framework.base
>  
> /home/labinmunologiaulpgc/galaxy-dist/lib/galaxy/web/framework/base.py
>  132 __call__
>  return self.handle_request( environ, start_response
> )self.trace(
> message="Starting request" ) try:return
> self.handle_request( environ, start_response )finally:
> self.trace( message="Handle request finished"
> ) 
>  galaxy.web.framework.base
>  
> /home/labinmunologiaulpgc/galaxy-dist/lib/galaxy/web/framework/base.py
>  190 handle_request
>  body = method( trans, **kwargs )
>  kwargs.pop( '_', None ) try:
> body = method( trans, **kwargs )except Exception, e:
> body = self.handle_controller_exception( e, trans, **kwargs
> ) 
>  galaxy.webapps.galaxy.controllers.library_common
>
>  
> /home/labinmunologiaulpgc/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/library_common.py
> 927
>  upload_library_dataset**kwd
> )
>  
> widgets=widgets,
>
> replace_dataset=replace_dataset,
> **kwd ) if created_outputs_dict:if
> cntrller == 'api':
>  galaxy.webapps.galaxy.controllers.library_common
>
>  
> /home/labinmunologiaulpgc/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/library_common.py
>  1049upload_dataset
> state = tool.new_state( trans )
>  tool_id = 'upload1'tool =
> trans.app.toolbox.get_tool( tool_id )state = tool.new_state( trans
> ) errors = tool.update_state( trans, tool.inputs_by_page[0],
> state.inputs, kwd )tool_params = state.inputs
>  
>  AttributeError'NoneType' object has no
> attribute 'new_state'*
>
>
>
> I have been looking for a solution to fix this problem on the web without
> success.
>
>
> thank you very much
>
> ___
> 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 G

[galaxy-dev] Problems uploading files to a data library

2014-08-12 Thread Juan Vladimir de la Rosa Medina 
Hi everyone,I recently have installed a local instance of galaxy in my 
computer, everything worked fine until I changed the path for 
library_import_dir in the universe_wsgi.ini file, to upload files to data 
libraries.I followed the Galaxy documentation to setup this feature:This is the 
path in the universe_wsgi.ini filelibrary_import_dir = 
/media/New/Vladimir/My_RNA-seq/The steps I followed are:Admin > Data 
Library > Create new data library > Add datasets > Upload directory of files
file format was set to auto-detectserver Directory was 
/media/New/Vladimir/My_RNA-seq/and we chose the option to link to files 
instead of copying themWhen I try to upload files, galaxy displays the 
following error:Error Traceback:⇝ AttributeError: 'NoneType' object has no 
attribute 'new_state'
Python
weberror.evalexception.middleware   
 
/home/labinmunologiaulpgc/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py
364respond
app_iter = self.application(environ, 
detect_start_response)try:   
 __traceback_supplement__ = errormiddleware.Supplement, self, environ   
 app_iter = self.application(environ, detect_start_response)
try:return_iter = list(app_iter)
paste.recursive
/home/labinmunologiaulpgc/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py
84__call__
return self.application(environ, start_response) 
   environ['paste.recursive.script_name'] = 
my_script_nametry:return self.application(environ, 
start_response)except ForwardRequestException, e:middleware 
= CheckForRecursionMiddleware(
paste.httpexceptions
/home/labinmunologiaulpgc/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py
633__call__   
 return self.application(environ, start_response)
   []).append(HTTPException) 
   try:return self.application(environ, start_response)
except HTTPException, exc:return exc(environ, 
start_response)
galaxy.web.framework.base
/home/labinmunologiaulpgc/galaxy-dist/lib/galaxy/web/framework/base.py
132__call__   
 return self.handle_request( environ, start_response )   
 self.trace( message="Starting 
request" )try:return self.handle_request( environ, 
start_response )finally:self.trace( message="Handle 
request finished" ) 
   galaxy.web.framework.base
/home/labinmunologiaulpgc/galaxy-dist/lib/galaxy/web/framework/base.py
190handle_request 
   body = method( trans, **kwargs )
kwargs.pop( '_', None )try:body 
= method( trans, **kwargs )except Exception, e:body = 
self.handle_controller_exception( e, trans, **kwargs )  
  
galaxy.webapps.galaxy.controllers.library_common
/home/labinmunologiaulpgc/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/library_common.py
927
upload_library_dataset**kwd 
)

widgets=widgets,
replace_dataset=replace_dataset,

**kwd )if created_outputs_dict:if 
cntrller == 'api':   
 galaxy.webapps.galaxy.controllers.library_common
/home/labinmunologiaulpgc/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/library_common.py
1049upload_dataset
state = tool.new_state( trans )
tool_id = 'upload1'tool = 
trans.app.toolbox.get_tool( tool_id )state = tool.new_state( trans )
errors = tool.update_state( trans, tool.inputs_by_page[0], state.inputs, 
kwd )tool_params = state.inputs
AttributeError
'NoneType' object has no attribute 'new_state'
 I have been looking for a solution to fix this problem 
on the web without success.

thank you very much   ___
Please keep all replies on the list by using "reply all"
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