> Date: Tue, 12 Aug 2014 13:15:50 -0400
> Subject: Re: [galaxy-dev] FW: Problems uploading files to a data library
> From: jmchilton@gmail.com
> To: jvdelarosa@hotmail.com
> CC: nate@bx.psu.edu; galaxy-dev@bx.psu.edu
>
> You don't need a tool to upload - you need 'upload1' (i.e.
> tools/data_source/upload.xml) and it cannot come from the tool shed -
> this will make its id something other than upload1. You can make some
> modifications to it, relocate it, etc... but that needs to be there in
> some form.
>
> In universe_wsgi.ini, your tool_config_file option can include
> tool_conf.xml in addition to shed_tool_conf.xml and upload1 can be the
> only thing in it (tool_conf.xml). For instance:
>
> tool_config_file = tool_conf.xml,shed_tool_conf.xml
>
> You may even be able to place <tool file="data_source/upload.xml" />
> in shed_tool_conf.xml directly - I don't know.
>
> But the upload tool definitely can not be installed via the tool shed.
>
> Hopefully this helps.
>
> -John
>
>
> On Tue, Aug 12, 2014 at 12:47 PM, Juan Vladimir de la Rosa Medina
> <jvdelarosa@hotmail.com> wrote:
> > Thanks Nate, I must say that I did not have the upload tool in the
> > tool_conf.xml because I am using the shed_tool_conf.xml to have a customized
> > tools panel, and this xml file is empty by default. I've installed the
> > upload tool throught the Galaxy main tool shed, I rebooted the system, and
> > checked that the tool is in the shed_tool_conf.xml.
> >
> > here is the code in the shed_tool_conf.xml
> >
> > <section id="getext" name="Get Data" version="">
> > <tool
> > file="toolshed.g2.bx.psu.edu/repos/alermine/upload_local_file/6b590f108b48/upload_local_file/upload_local_file/upload_local_file.xml"
> > guid="toolshed.g2.bx.psu.edu/repos/alermine/upload_local_file/upload_local_file/1.0.0">
> > <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
> > <repository_name>upload_local_file</repository_name>
> > <repository_owner>alermine</repository_owner>
> >
> > <installed_changeset_revision>6b590f108b48</installed_changeset_revision>
> >
> > <id>toolshed.g2.bx.psu.edu/repos/alermine/upload_local_file/upload_local_file/1.0.0</id>
> > <version>1.0.0</version>
> > </tool>
> > </section>
> >
> > But when I try to upload the files to a data library, I got the same error.
> >
> > What can I do?
> >
> > ________________________________
> > From: nate@bx.psu.edu
> > Date: Tue, 12 Aug 2014 09:55:07 -0400
> > Subject: Re: [galaxy-dev] Problems uploading files to a data library
> > To: jvdelarosa@hotmail.com
> > CC: galaxy-dev@bx.psu.edu
> >
> >
> > On Tue, Aug 12, 2014 at 3:03 AM, Juan Vladimir de la Rosa Medina
> > <jvdelarosa@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
> >
> >
> > <?xml version="1.0" ?>
> > <traceback>
> > <sysinfo>
> > <language version="2.7.3">Python</language>
> > </sysinfo>
> > <stack>
> > <frame>
> > <module>weberror.evalexception.middleware</module>
> >
> > <filename>/home/labinmunologiaulpgc/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py</filename>
> > <line>364</line>
> > <function>respond</function>
> > <operation>app_iter = self.application(environ,
> > detect_start_response)</operation>
> > <operation_context> try:
> > __traceback_supplement__ = errormiddleware.Supplement, self,
> > environ
> > app_iter = self.application(environ, detect_start_response)
> > try:
> > return_iter = list(app_iter)
> > </operation_context>
> > </frame>
> > <frame>
> > <module>paste.recursive</module>
> >
> > <filename>/home/labinmunologiaulpgc/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py</filename>
> > <line>84</line>
> > <function>__call__</function>
> > <operation>return self.application(environ,
> > start_response)</operation>
> > <operation_context>
> > environ['paste.recursive.script_name'] = my_script_name
> > try:
> > return self.application(environ, start_response)
> > except ForwardRequestException, e:
> > middleware = CheckForRecursionMiddleware(
> > </operation_context>
> > </frame>
> > <frame>
> > <module>paste.httpexceptions</module>
> >
> > <filename>/home/labinmunologiaulpgc/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py</filename>
> > <line>633</line>
> > <function>__call__</function>
> > <operation>return self.application(environ,
> > start_response)</operation>
> > <operation_context>
> > []).append(HTTPException)
> > try:
> > return self.application(environ, start_response)
> > except HTTPException, exc:
> > return exc(environ, start_response)
> > </operation_context>
> > </frame>
> > <frame>
> > <module>galaxy.web.framework.base</module>
> >
> > <filename>/home/labinmunologiaulpgc/galaxy-dist/lib/galaxy/web/framework/base.py</filename>
> > <line>132</line>
> > <function>__call__</function>
> > <operation>return self.handle_request( environ, start_response
> > )</operation>
> > <operation_context> self.trace( message=&quot;Starting
> > request&quot; )
> > try:
> > return self.handle_request( environ, start_response )
> > finally:
> > self.trace( message=&quot;Handle request finished&quot; )
> > </operation_context>
> > </frame>
> > <frame>
> > <module>galaxy.web.framework.base</module>
> >
> > <filename>/home/labinmunologiaulpgc/galaxy-dist/lib/galaxy/web/framework/base.py</filename>
> > <line>190</line>
> > <function>handle_request</function>
> > <operation>body = method( trans, **kwargs )</operation>
> > <operation_context> kwargs.pop( '_', None )
> > try:
> > body = method( trans, **kwargs )
> > except Exception, e:
> > body = self.handle_controller_exception( e, trans, **kwargs )
> > </operation_context>
> > </frame>
> > <frame>
> >
> > <module>galaxy.webapps.galaxy.controllers.library_common</module>
> >
> > <filename>/home/labinmunologiaulpgc/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/library_common.py</filename>
> > <line>927</line>
> > <function>upload_library_dataset</function>
> > <operation>**kwd )</operation>
> > <operation_context>
> > widgets=widgets,
> >
> > replace_dataset=replace_dataset,
> >
> > **kwd )
> > if created_outputs_dict:
> > if cntrller == 'api':
> > </operation_context>
> > </frame>
> > <frame>
> >
> > <module>galaxy.webapps.galaxy.controllers.library_common</module>
> >
> > <filename>/home/labinmunologiaulpgc/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/library_common.py</filename>
> > <line>1049</line>
> > <function>upload_dataset</function>
> > <operation>state = tool.new_state( trans )</operation>
> > <operation_context> 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
> > </operation_context>
> > </frame>
> > </stack>
> > <exception>
> > <type>AttributeError</type>
> > <value>'NoneType' object has no attribute 'new_state'</value>
> > </exception>
> > </traceback>
> >
> >
> >
> > I have been looking for a solution to fix this problem on the web without
> > success.
> >
> >
> > thank you very much
> >
> >
> > ___________________________________________________________
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> >
> >
> >
> > ___________________________________________________________
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