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


___________________________________________________________
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/