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

12 Aug 2014

      Thanks guys, with your help I have fixed the problem.
The upload tool was missing, because I put the same path for both tool_dependency_dir and tool_path in the universe_wsgi.ini file, they were pointing to the shed_tools directory,  outside the Galaxy dir. I resolved the problem leaving tool_path, with its value by default in the universe_wsgi.ini file. To customize my tool panel, I have instanced it as tool_config_file = tool_conf.xml,shed_tool_conf.xml, and I have changed the tool_conf.xml as John has recommended to me.
once again
A lot of thanks
...
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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[galaxy-dev] FW: FW: Problems uploading files to a data library