New subject: FW: Error in file upload for new metadata

5 May 2010

      Hi,

I created a metadata to hold 5 files together (1 primary and 4 data files). The file extension corresponding to the following metadata appears correctly in the list.
But When I try to upload the files. I get the following error.

Could you please help me fix this.

Here is the small class that I created to hold metadata:
class CompositeTest( Data ):
        file_ext="comptest"
        MetadataElement( name="data_lines", default=0, desc="Number of data lines", readonly=True, optional=True, visible=False, no_value=0 )
        composite_type="basic"

        def __init__(self,**kwd):
                Data.__init__(self,**kwd)
                self.add_composite_file('pedfile.txt')
                self.add_composite_file('mapfile.txt')
                self.add_composite_file('frequencyfile.txt')
                self.add_composite_file('datafile.txt')

        def init_meta(self,dataset,copy_from=None ):
                Data.init_meta(self,dataset,copy_from=copy_from)

Source Template Extra Data Traceback
Error Traceback:
View as:   Interactive  | Text  | XML (full)
⇝ AttributeError: 'Bunch' object has no attribute 'space_to_tab'
URL: http://10.70.250.254:8080/tool_runner/index
Module weberror.evalexception.middleware:364 in respond         view
...
...
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:97 in __call__         view
status, headers, body = wsgilib.intercept_output(
Module paste.wsgilib:539 in intercept_output         view
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__         view
return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__         view
return self.application(environ, start_response)
Module galaxy.web.framework.base:125 in __call__         view
body = method( trans, **kwargs )
Module galaxy.web.controllers.tool_runner:53 in index         view
template, vars = tool.handle_input( trans, params.__dict__ )
Module galaxy.tools:795 in handle_input         view
_, out_data = self.execute( trans, incoming=params )
Module galaxy.tools:1067 in execute         view
return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid )
Module galaxy.tools.actions.upload:18 in execute         view
uploaded_datasets = upload_common.get_uploaded_datasets( trans, incoming, precreated_datasets, dataset_upload_inputs )
Module galaxy.tools.actions.upload_common:214 in get_uploaded_datasets         view
uploaded_datasets.extend( dataset_upload_input.get_uploaded_datasets( trans, params ) )
Module galaxy.tools.parameters.grouping:301 in get_uploaded_datasets         view
dataset.space_to_tab = file_bunch.space_to_tab
AttributeError: 'Bunch' object has no attribute 'space_to_tab'
Extra Features
...
...
Display the lines of code near each part of the traceback
    Show a debug prompt to allow you to directly debug the code at the traceback
In Text Tab :
URL: http://10.70.250.254:8080/tool_runner/index
File '/export/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.4.egg/weberror/evalexception/middleware.py', line 364 in respond
  app_iter = self.application(environ, detect_start_response)
File '/export/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/debug/prints.py', line 97 in __call__
  status, headers, body = wsgilib.intercept_output(
File '/export/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/wsgilib.py', line 539 in intercept_output
  app_iter = application(environ, replacement_start_response)
File '/export/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/recursive.py', line 80 in __call__
  return self.application(environ, start_response)
File '/export/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/httpexceptions.py', line 632 in __call__
  return self.application(environ, start_response)
File '/export/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 125 in __call__
  body = method( trans, **kwargs )
File '/export/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/tool_runner.py', line 53 in index
  template, vars = tool.handle_input( trans, params.__dict__ )
File '/export/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 795 in handle_input
  _, out_data = self.execute( trans, incoming=params )
File '/export/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 1067 in execute
  return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid )
File '/export/home/galaxy/galaxy-dist/lib/galaxy/tools/actions/upload.py', line 18 in execute
  uploaded_datasets = upload_common.get_uploaded_datasets( trans, incoming, precreated_datasets, dataset_upload_inputs )
File '/export/home/galaxy/galaxy-dist/lib/galaxy/tools/actions/upload_common.py', line 214 in get_uploaded_datasets
  uploaded_datasets.extend( dataset_upload_input.get_uploaded_datasets( trans, params ) )
File '/export/home/galaxy/galaxy-dist/lib/galaxy/tools/parameters/grouping.py', line 301 in get_uploaded_datasets
  dataset.space_to_tab = file_bunch.space_to_tab
AttributeError: 'Bunch' object has no attribute 'space_to_tab'

In XML(full) TAB:
<?xml version="1.0" ?>
<traceback>
    <sysinfo>
        <language version="2.4.3">
            Python
        </language>
    </sysinfo>
    <stack>
        <frame>
            <module>
                weberror.evalexception.middleware
            </module>
            <filename>
                /export/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.4.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.debug.prints
            </module>
            <filename>
                /export/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/debug/prints.py
            </filename>
            <line>
                97
            </line>
            <function>
                __call__
            </function>
            <operation>
                status, headers, body = wsgilib.intercept_output(
            </operation>
            <operation_context>
                        threadedprint.register(replacement_stdout)
        try:
            status, headers, body = wsgilib.intercept_output(
                environ, self.app)
            if status is None:

            </operation_context>
        </frame>
        <frame>
            <module>
                paste.wsgilib
            </module>
            <filename>
                /export/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/wsgilib.py
            </filename>
            <line>
                539
            </line>
            <function>
                intercept_output
            </function>
            <operation>
                app_iter = application(environ, replacement_start_response)
            </operation>
            <operation_context>
                        data.append(headers)
        return output.write
    app_iter = application(environ, replacement_start_response)
    if data[0] is None:
        return (None, None, app_iter)

            </operation_context>
        </frame>
        <frame>
            <module>
                paste.recursive
            </module>
            <filename>
                /export/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/recursive.py
            </filename>
            <line>
                80
            </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>
                /export/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/httpexceptions.py
            </filename>
            <line>
                632
            </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>
                /export/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py
            </filename>
            <line>
                125
            </line>
            <function>
                __call__
            </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.web.controllers.tool_runner
            </module>
            <filename>
                /export/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/tool_runner.py
            </filename>
            <line>
                53
            </line>
            <function>
                index
            </function>
            <operation>
                template, vars = tool.handle_input( trans, params.__dict__ )
            </operation>
            <operation_context>
                        # so make sure to create a new history if we've never had one before.
        history = trans.get_history( create=True )
        template, vars = tool.handle_input( trans, params.__dict__ )
        if len(params) > 0:
            trans.log_event( "Tool params: %s" % (str(params)), tool_id=tool_id )

            </operation_context>
        </frame>
        <frame>
            <module>
                galaxy.tools
            </module>
            <filename>
                /export/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py
            </filename>
            <line>
                795
            </line>
            <function>
                handle_input
            </function>
            <operation>
                _, out_data = self.execute( trans, incoming=params )
            </operation>
            <operation_context>
                            # If we've completed the last page we can execute the tool
            elif state.page == self.last_page:
                _, out_data = self.execute( trans, incoming=params )
                try:
                    assert isinstance( out_data, odict )

            </operation_context>
        </frame>
        <frame>
            <module>
                galaxy.tools
            </module>
            <filename>
                /export/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py
            </filename>
            <line>
                1067
            </line>
            <function>
                execute
            </function>
            <operation>
                return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid )
            </operation>
            <operation_context>
                        when run will build the tool's outputs, e.g. `DefaultToolAction`.
        """
        return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid )

    def params_to_strings( self, params, app ):

            </operation_context>
        </frame>
        <frame>
            <module>
                galaxy.tools.actions.upload
            </module>
            <filename>
                /export/home/galaxy/galaxy-dist/lib/galaxy/tools/actions/upload.py
            </filename>
            <line>
                18
            </line>
            <function>
                execute
            </function>
            <operation>
                uploaded_datasets = upload_common.get_uploaded_datasets( trans, incoming, precreated_datasets, dataset_upload_inputs )
            </operation>
            <operation_context>
                        precreated_datasets = upload_common.get_precreated_datasets( trans, incoming, trans.app.model.HistoryDatasetAssociation )
        incoming = upload_common.persist_uploads( incoming )
        uploaded_datasets = upload_common.get_uploaded_datasets( trans, incoming, precreated_datasets, dataset_upload_inputs )
        upload_common.cleanup_unused_precreated_datasets( precreated_datasets )

            </operation_context>
        </frame>
        <frame>
            <module>
                galaxy.tools.actions.upload_common
            </module>
            <filename>
                /export/home/galaxy/galaxy-dist/lib/galaxy/tools/actions/upload_common.py
            </filename>
            <line>
                214
            </line>
            <function>
                get_uploaded_datasets
            </function>
            <operation>
                uploaded_datasets.extend( dataset_upload_input.get_uploaded_datasets( trans, params ) )
            </operation>
            <operation_context>
                    uploaded_datasets = []
    for dataset_upload_input in dataset_upload_inputs:
        uploaded_datasets.extend( dataset_upload_input.get_uploaded_datasets( trans, params ) )
    for uploaded_dataset in uploaded_datasets:
        data = get_precreated_dataset( precreated_datasets, uploaded_dataset.name )

            </operation_context>
        </frame>
        <frame>
            <module>
                galaxy.tools.parameters.grouping
            </module>
            <filename>
                /export/home/galaxy/galaxy-dist/lib/galaxy/tools/parameters/grouping.py
            </filename>
            <line>
                301
            </line>
            <function>
                get_uploaded_datasets
            </function>
            <operation>
                dataset.space_to_tab = file_bunch.space_to_tab
            </operation>
            <operation_context>
                                writable_files_offset = 1
                dataset.primary_file = file_bunch.path
                dataset.space_to_tab = file_bunch.space_to_tab
                dataset.precreated_name = file_bunch.precreated_name
                dataset.name = file_bunch.precreated_name

            </operation_context>
        </frame>
    </stack>
    <exception>
        <type>
            AttributeError
        </type>
        <value>
            'Bunch' object has no attribute 'space_to_tab'
        </value>
    </exception>
</traceback>

Thanks and Regards,
Amit Modi

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Error in file upload for new metadata

Modi, Amit

Modi, Amit

Daniel Blankenberg

Modi, Amit

Modi, Amit

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participants (2)