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="Starting request" )
try: return self.handle_request( environ, start_response ) finally: self.trace( message="Handle request finished" ) </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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