Extract Workflow Error
Can anyone shed any light on the following erro I get when trying to extract
a workflow from my history?
⇝ TypeError: <galaxy.tools.parameters.basic.UnvalidatedValue object at
0xa5ca790> is not JSON serializable
URL: http://localhost:8082/workflow/build_from_current_history
Module weberror.evalexception.middleware:*364* in respond
<http://localhost:8082/workflow/build_from_current_history#>
view <http://localhost:8082/workflow/build_from_current_history#>
>> <http://localhost:8082/workflow/build_from_current_history#>app_iter *=
* self*.*application*(*environ*,* detect_start_response*)*
Module paste.debug.prints:*98* in __call__
<http://localhost:8082/workflow/build_from_current_history#>
view <http://localhost:8082/workflow/build_from_current_history#>
>> <http://localhost:8082/workflow/build_from_current_history#>environ*,*
self*.*app*)*
Module paste.wsgilib:*539* in intercept_output
<http://localhost:8082/workflow/build_from_current_history#>
view <http://localhost:8082/workflow/build_from_current_history#>
>> <http://localhost:8082/workflow/build_from_current_history#>app_iter *=
* application*(*environ*,* replacement_start_response*)*
Module paste.recursive:*80* in __call__
<http://localhost:8082/workflow/build_from_current_history#>
view <http://localhost:8082/workflow/build_from_current_history#>
>> <http://localhost:8082/workflow/build_from_current_history#>*return*
self*.*application*(*environ*,* start_response*)*
Module paste.httpexceptions:*632* in __call__
<http://localhost:8082/workflow/build_from_current_history#>
view <http://localhost:8082/workflow/build_from_current_history#>
>> <http://localhost:8082/workflow/build_from_current_history#>*return*
self*.*application*(*environ*,* start_response*)*
Module galaxy.web.framework.base:*126* in __call__
<http://localhost:8082/workflow/build_from_current_history#>
view <http://localhost:8082/workflow/build_from_current_history#>
>> <http://localhost:8082/workflow/build_from_current_history#>body *=*
method*(* trans*,* ****kwargs *)*
Module galaxy.web.controllers.workflow:*921* in build_from_current_history
<http://localhost:8082/workflow/build_from_current_history#>
view<http://localhost:8082/workflow/build_from_current_history#>
>> <http://localhost:8082/workflow/build_from_current_history#>step*.*
tool_inputs *=* tool*.*params_to_strings*(* param_values*,* trans*.*app *)*
Module galaxy.tools:*1110* in params_to_strings
<http://localhost:8082/workflow/build_from_current_history#>
view <http://localhost:8082/workflow/build_from_current_history#>
>> <http://localhost:8082/workflow/build_from_current_history#>*return*
params_to_strings*(* self*.*inputs*,* params*,* app *)*
Module galaxy.tools.parameters:*80* in params_to_strings
<http://localhost:8082/workflow/build_from_current_history#>
view <http://localhost:8082/workflow/build_from_current_history#>
>> <http://localhost:8082/workflow/build_from_current_history#>rval*[* key
*]* *=* str*(* to_json_string*(* value *)* *)*
Module simplejson:*182* in dumps
<http://localhost:8082/workflow/build_from_current_history#>
view <http://localhost:8082/workflow/build_from_current_history#>
Module simplejson.encoder:*312* in encode
<http://localhost:8082/workflow/build_from_current_history#>
view <http://localhost:8082/workflow/build_from_current_history#>
Module simplejson.encoder:*265* in _iterencode
<http://localhost:8082/workflow/build_from_current_history#>
view <http://localhost:8082/workflow/build_from_current_history#>
Module simplejson.encoder:*235* in _iterencode_dict
<http://localhost:8082/workflow/build_from_current_history#>
view <http://localhost:8082/workflow/build_from_current_history#>
Module simplejson.encoder:*265* in _iterencode
<http://localhost:8082/workflow/build_from_current_history#>
view <http://localhost:8082/workflow/build_from_current_history#>
Module simplejson.encoder:*235* in _iterencode_dict
<http://localhost:8082/workflow/build_from_current_history#>
view <http://localhost:8082/workflow/build_from_current_history#>
Module simplejson.encoder:*273* in _iterencode
<http://localhost:8082/workflow/build_from_current_history#>
view <http://localhost:8082/workflow/build_from_current_history#>
Module simplejson.encoder:*279* in _iterencode_default
<http://localhost:8082/workflow/build_from_current_history#>
view <http://localhost:8082/workflow/build_from_current_history#>
Module simplejson.encoder:*300* in default
<http://localhost:8082/workflow/build_from_current_history#>
view <http://localhost:8082/workflow/build_from_current_history#>
*TypeError: <galaxy.tools.parameters.basic.UnvalidatedValue object at
0xa5ca790> is not JSON serializable*
--
Dennis Gascoigne
0407 639 995
dennis.gascoigne@gmail.com
Hi Dennis, It seems that a tool in your history is producing parameters that aren't amenable to building a workflow. To help you, we need more information/help: What tools are you using in this history? Can you try creating histories with a subset of tools in order to identify the problematic tool? Alternatively, you could recreate the history on our main server ( http://main.g2.bx.psu.edu/ ) and then, assuming you run into the same problem, share it with me. Thanks, J. On May 20, 2010, at 1:59 AM, Dennis Gascoigne wrote:
Can anyone shed any light on the following erro I get when trying to extract a workflow from my history?
⇝ TypeError: <galaxy.tools.parameters.basic.UnvalidatedValue object at 0xa5ca790> is not JSON serializable URL: http://localhost:8082/workflow/build_from_current_history Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view environ, self.app) 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:126 in __call__ view body = method( trans, **kwargs ) Module galaxy.web.controllers.workflow:921 in build_from_current_history view step.tool_inputs = tool.params_to_strings( param_values, trans.app ) Module galaxy.tools:1110 in params_to_strings view return params_to_strings( self.inputs, params, app ) Module galaxy.tools.parameters:80 in params_to_strings view rval[ key ] = str( to_json_string( value ) ) Module simplejson:182 in dumps view Module simplejson.encoder:312 in encode view Module simplejson.encoder:265 in _iterencode view Module simplejson.encoder:235 in _iterencode_dict view Module simplejson.encoder:265 in _iterencode view Module simplejson.encoder:235 in _iterencode_dict view Module simplejson.encoder:273 in _iterencode view Module simplejson.encoder:279 in _iterencode_default view Module simplejson.encoder:300 in default view TypeError: <galaxy.tools.parameters.basic.UnvalidatedValue object at 0xa5ca790> is not JSON serializable
-- Dennis Gascoigne 0407 639 995 dennis.gascoigne@gmail.com _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi Dennis, To debug this, we need a better idea of what is in your history. Is there one particular step/dataset that causes this problem? What revision of Galaxy are you running (I've fixed bugs that manifest this way in the past -- shouldn't currently be possible ;) Thanks, James On May 20, 2010, at 1:59 AM, Dennis Gascoigne wrote:
Can anyone shed any light on the following erro I get when trying to extract a workflow from my history?
app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view environ, self.app) 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:126 in __call__ view body = method( trans, **kwargs ) Module galaxy.web.controllers.workflow:921 in build_from_current_history view step.tool_inputs = tool.params_to_strings( param_values,
⇝ TypeError: <galaxy.tools.parameters.basic.UnvalidatedValue object at 0xa5ca790> is not JSON serializable URL: http://localhost:8082/workflow/build_from_current_history Module weberror.evalexception.middleware:364 in respond view trans.app ) Module galaxy.tools:1110 in params_to_strings view
return params_to_strings( self.inputs, params, app ) Module galaxy.tools.parameters:80 in params_to_strings view rval[ key ] = str( to_json_string( value ) ) Module simplejson:182 in dumps view Module simplejson.encoder:312 in encode view Module simplejson.encoder:265 in _iterencode view Module simplejson.encoder:235 in _iterencode_dict view Module simplejson.encoder:265 in _iterencode view Module simplejson.encoder:235 in _iterencode_dict view Module simplejson.encoder:273 in _iterencode view Module simplejson.encoder:279 in _iterencode_default view Module simplejson.encoder:300 in default view TypeError: <galaxy.tools.parameters.basic.UnvalidatedValue object at 0xa5ca790> is not JSON serializable
-- Dennis Gascoigne 0407 639 995 dennis.gascoigne@gmail.com _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
participants (3)
-
Dennis Gascoigne -
James Taylor -
Jeremy Goecks