Thanks Sarah. I was having trouble reproducing because I hadn't set a runtime 
parameter. I've fixed the bug in galaxy-central changeset 5387:835656900dd0 ; 
after making this change, I was able to successfully export and import 
workflows with runtime parameters.

Best,
J.

On Apr 14, 2011, at 10:01 AM, Sarah Diehl wrote:

> I could narrow it down even further. As soon as I set anything to "To be set 
> at runtime" the download fails.
> 
> 
> On 04/14/2011 03:46 PM, Sarah Diehl wrote:
>> Hi Jeremy,
>> 
>> I could narrow the problem down to the histogram tool. I attached a
>> screenshot of a really simple workflow whose download fails. I recreated
>> the workflow at the public instance at http://main.g2.bx.psu.edu and
>> shared it with you. There the download also fails for me.
>> 
>> Best regards,
>> Sarah
>> 
>> On 04/14/2011 02:55 PM, Jeremy Goecks wrote:
>>> Sarah,
>>> 
>>> Can you make your server available to me and I'll take a look? If not,
>>> you'll have to do some debugging yourself. Here are some things you
>>> might try:
>>> 
>>> *on your local instance, try exporting simpler workflows and seeing if
>>> there's a tool or configuration that does or does work.
>>> *on our public instance, try creating a workflow identical to the one
>>> that's failing for you and seeing if you can export it.
>>> 
>>> If we can figure out how to reproduce the problem on a Galaxy instance
>>> that I have access to, I can probably fix it.
>>> 
>>> Thanks,
>>> J.
>>> 
>>> On Apr 14, 2011, at 3:11 AM, Sarah Diehl wrote:
>>> 
>>>> Hi Jeremy,
>>>> 
>>>> I just updated to the newest galaxy-dist and the export of the
>>>> workflow still does not work. The error is the same.
>>>> 
>>>> Best regards,
>>>> Sarah
>>>> 
>>>> 
>>>> On 04/07/2011 03:37 PM, Jeremy Goecks wrote:
>>>>> Hi Sarah,
>>>>> 
>>>>> I created your workflow on my Galaxy instance and was able to export
>>>>> it successfully, so updating your Galaxy instance may solve your
>>>>> problem. If not, let us know and we'll take a closer look.
>>>>> 
>>>>> Finally, please direct your questions to one of our mailing lists
>>>>> rather than individual galaxy developers for community and archival
>>>>> purposes; I've cc'd this one to galaxy-dev.
>>>>> 
>>>>> Thanks,
>>>>> J.
>>>>> 
>>>>> 
>>>>> On Apr 7, 2011, at 8:00 AM, Sarah Diehl wrote:
>>>>> 
>>>>>> Hi Jeremy,
>>>>>> 
>>>>>> I encounter a similar error like the one already posted on the
>>>>>> galaxy-dev list
>>>>>> (http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003699.html)
>>>>>> when trying to download a workflow.
>>>>>> 
>>>>>> Were you able to find a solution or are you still working on it? I
>>>>>> attached a screenshot of the workflow (like you also requested on
>>>>>> the list). Let me know if I can provide you with any additional
>>>>>> details to help with the debugging.
>>>>>> 
>>>>>> Best regards,
>>>>>> Sarah
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 10.1.5.190 - - [07/Apr/2011:13:33:42 +0200] "GET
>>>>>> /workflow/export_to_file?id=0ac5da8467dc9e07 HTTP/1.1" 500 -
>>>>>> "http://solweb2.immunbio.mpg.de/workflow/export?id=0ac5da8467dc9e07"; 
>>>>>> "Mozilla/5.0
>>>>>> (X11; U; Linux x86_64; en-US; rv:1.9.2.16) Gecko/20110322
>> fil
>>>>> e:///home/diehl/Pictures/Screenshot.png
>>>>>> Fedora/3.6.16-1.fc14 Firefox/3.6.16"
>>>>>> Error -<type 'exceptions.TypeError'>: 'WorkflowStep' object is
>>>>>> unsubscriptable
>>>>>> URL:
>>>>>> http://solweb2.immunbio.mpg.de/workflow/export_to_file?id=0ac5da8467dc9e07
>>>>>> 
>>>>>> File
>>>>>> '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
>>>>>> line 143 in __call__
>>>>>> app_iter = self.application(environ, start_response)
>>>>>> File
>>>>>> '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line
>>>>>> 80 in __call__
>>>>>> return self.application(environ, start_response)
>>>>>> File
>>>>>> '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
>>>>>> line 632 in __call__
>>>>>> return self.application(environ, start_response)
>>>>>> File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line
>>>>>> 145 in __call__
>>>>>> body = method( trans, **kwargs )
>>>>>> File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py',
>>>>>> line 74 in decorator
>>>>>> return simplejson.dumps( func( self, trans, *args, **kwargs ),
>>>>>> indent=4, sort_keys=True )
>>>>>> File
>>>>>> '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py',
>>>>>> line 1078 in export_to_file
>>>>>> stored_dict = self._workflow_to_dict( trans, stored )
>>>>>> File
>>>>>> '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py',
>>>>>> line 1571 in _workflow_to_dict
>>>>>> step['inputs'].append( { "name" : name, "description" : "runtime
>>>>>> parameter for tool %s" % module.get_name() } )
>>>>>> TypeError: 'WorkflowStep' object is unsubscriptable
>>>>>> <Screenshot.png>
>>>>> 
>>>>> 
>>>>> ___________________________________________________________
>>>>> Please keep all replies on the list by using "reply all"
>>>>> in your mail client. To manage your subscriptions to this
>>>>> and other Galaxy lists, please use the interface at:
>>>>> 
>>>>> http://lists.bx.psu.edu/
>>>>> 
>>>> 
>>> 
>>> 
>> 
>> 
>> 
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> 
>>   http://lists.bx.psu.edu/
> 


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to