Problems uploading files to a data library

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Problems uploading files to a data library

jvdelarosa

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'

<?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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Re: Problems uploading files to a data library

Nate Coraor (nate@bx.psu.edu)
On Tue, Aug 12, 2014 at 3:03 AM, Juan Vladimir de la Rosa Medina <[hidden email]> 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/


___________________________________________________________
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/

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FW: Problems uploading files to a data library

jvdelarosa
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: [hidden email]
Date: Tue, 12 Aug 2014 09:55:07 -0400
Subject: Re: [galaxy-dev] Problems uploading files to a data library
To: [hidden email]
CC: [hidden email]

On Tue, Aug 12, 2014 at 3:03 AM, Juan Vladimir de la Rosa Medina <[hidden email]> 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/


___________________________________________________________
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/
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Re: FW: Problems uploading files to a data library

John Chilton-4
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
<[hidden email]> 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: [hidden email]
> Date: Tue, 12 Aug 2014 09:55:07 -0400
> Subject: Re: [galaxy-dev] Problems uploading files to a data library
> To: [hidden email]
> CC: [hidden email]
>
>
> On Tue, Aug 12, 2014 at 3:03 AM, Juan Vladimir de la Rosa Medina
> <[hidden email]> 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/
>
>
>
> ___________________________________________________________
> 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/

___________________________________________________________
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:
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FW: FW: Problems uploading files to a data library

jvdelarosa
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: [hidden email]
> To: [hidden email]
> CC: [hidden email]; [hidden email]
>
> 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
> <[hidden email]> 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: [hidden email]
> > Date: Tue, 12 Aug 2014 09:55:07 -0400
> > Subject: Re: [galaxy-dev] Problems uploading files to a data library
> > To: [hidden email]
> > CC: [hidden email]
> >
> >
> > On Tue, Aug 12, 2014 at 3:03 AM, Juan Vladimir de la Rosa Medina
> > <[hidden email]> 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/
> >
> >
> >
> > ___________________________________________________________
> > 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/

___________________________________________________________
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/