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
Mod
ule weberror.evalexception.middleware:364 in resp
ond         view
>>
app_iter = self.application(environ, detect_start_response)
Mo
d
ule paste.debug.prints:97 in __call__         view
>>
status, headers, body = wsgilib.intercept_output(
Mo
d
ule paste.wsgilib:539 in intercept_output         view
>>
app_iter = application(environ, replacement_start_response)
Mo
d
ule paste.recursive:80 in __call__         view
>>
return self.application(environ, start_response)
Mo
d
ule paste.httpexceptions:632 in __call__         view
>>
return self.application(environ, start_response)
Mo
d
ule galaxy.web.framework.base:125 in __call__         view
>>
body = method( trans, **kwargs )
M
od
ule galaxy.web.controllers.tool_runner:53 in index         view
>>
template, vars = tool.handle_input( trans, params.__dict__ )
M
od
ule galaxy.tools:795 in handle_input         view
>>
_, out_data = self.execute( trans, incoming=params )
M
od
ule galaxy.tools:1067 in execute         view
>>
return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid )
M
od
ule galaxy.tools.actions.upload:18 in execute         view
>>
uploaded_datasets = upload_common.get_uploaded_datasets( trans, incoming, precreated_datasets, dataset_upload_inputs )
M
od
ule galaxy.tools.actions.upload_common:214 in get_uploaded_datasets         view
>>
uploaded_datasets.extend( dataset_upload_input.get_uploaded_datasets( trans, params ) )
Mod
ule galaxy.tools.parameters.grouping:301 in get_uploaded_datasets         view
>>
dataset.space_to_tab = file_bunch.space_to_tab
Att
ributeError: 'Bunch' object has no attribute 'space_to_tab'



Extra Features
>>    
D
isplay 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) &gt; 0:
            trans.log_event( &quot;Tool params: %s&quot; % (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`.
        &quot;&quot;&quot;
        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

------ End of Forwarded Message




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