Question: Problem to upload files to a data library in Galaxy local
0
gravatar for jvdlrm
3.3 years ago by
jvdlrm0
jvdlrm0 wrote:

Hi,

I've recently installed galaxy locally on my computer, I got it run but I can't upload files to a data library. I tried to set up 'upload directory of files'. I created a folder outside of galaxy-dist and inserting the right path in the universe_wsgi.ini: library_import_dir = /home/jvdelarosa/galaxy/import

Every time the loading fails with this error message:

 

<?xml version="1.0" ?>
<traceback>
    <sysinfo>
        <language version="2.7.6">Python</language>
    </sysinfo>
    <stack>
        <frame>
            <module>weberror.evalexception.middleware</module>
            <filename>/home/jvdelarosa/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/jvdelarosa/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/jvdelarosa/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/jvdelarosa/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/jvdelarosa/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/jvdelarosa/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/jvdelarosa/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 on the web, without success.

has someone any solution to fix this problem?

A lot of thanks

galaxy • 1.6k views
ADD COMMENTlink modified 3.3 years ago by Jennifer Hillman Jackson23k • written 3.3 years ago by jvdlrm0
2
gravatar for jmchilton
3.3 years ago by
jmchilton1.0k
United States
jmchilton1.0k wrote:

Have you modified your tool_conf.xml file to remove this line - <tool file="data_source/upload.xml" />? An upload tool is needed to import data library items.

It looks like this was the problem - more information on galaxy-dev http://dev.list.galaxyproject.org/Problems-uploading-files-to-a-data-library-td4665327.html.

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by jmchilton1.0k
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