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
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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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Modi, Amit