Hey Daniel,
Please neglect the previous mail.
I realized that after refreshing the history panel I get both the files.
Thanks and Regards,
Amit Modi
On 5/14/10 12:27 PM, "Modi, Amit" <Amit.Modi@nationwidechildrens.org> wrote:
Hi Daniel,
Thanks for the fix.
There’s one more issue that I am facing it would be really great if you could help me on that.
I created two file formats “mapf” and “pedf”
I upload a file as “mapf” and then I go to edit attributes and save it was “pedf”
But even after updating, the file extension visible in the green panel on the right that displayed my file contents displays the extension as “mapf”
Though when I click again on edit attributes and cross check the file extension it shows it as “pedf”
Can you please cross check this.
Thanks a lot
Regards,
Amit Modi
On 5/12/10 4:01 PM, "Daniel Blankenberg" <dan@bx.psu.edu> wrote:
Hi Amit,
Thanks for reporting this error. It has been resolved in changeset 3777:b762ea8e5508. Let us know if you have additional issues.
Thanks for using Galaxy,
Dan
On May 7, 2010, at 10:47 AM, Modi, Amit wrote:
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 <http://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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