Importing workflow from file fails in Galaxy instance on Amazon Cloud
Hi, I can't import workflows from file on a freshly installed instance of Galaxy on Amazon Cloud. The error message is copied below. Do you have some idea on how to fix this? Thanks, Sébastien Internal Server Error
Galaxy was unable to sucessfully complete your request URL: http://ec2-50-19-79-199.compute-1.amazonaws.com/workflow/import_workflow Module galaxy.web.framework.middleware.error:149 in __call__
app_iter = self.application(environ, sr_checker) Module paste.recursive:84 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.workflow:1127 in import_workflow workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source=src,add_to_menu=add_to_menu ) Module galaxy.webapps.galaxy.controllers.workflow:1823 in _workflow_from_dict module = module_factory.from_dict( trans, step_dict, secure=False ) Module galaxy.workflow.modules:428 in from_dict return self.module_types[type].from_dict( trans, d, **kwargs ) Module galaxy.workflow.modules:222 in from_dict module.state.decode( d[ "tool_state" ], module.tool, module.trans.app, secure=secure ) Module galaxy.tools:849 in decode self.inputs = params_from_strings( tool.inputs, values, app, ignore_errors=True ) Module galaxy.tools.parameters:92 in params_from_strings value = json_fix( from_json_string( value ) ) Module simplejson:384 in loads Module simplejson.decoder:402 in decode TypeError: expected string or buffer
Sébastien, This seems to be a galaxy bug from a little while back. To fix your cloud instance, go to the cloud admin console and click "Update Galaxy", and the problem should be resolved once galaxy updates and restarts. -Dannon On Fri, Jan 3, 2014 at 6:42 PM, Sébastien Vigneau < sebastien.vigneau@gmail.com> wrote:
Hi,
I can't import workflows from file on a freshly installed instance of Galaxy on Amazon Cloud. The error message is copied below. Do you have some idea on how to fix this?
Thanks,
Sébastien
Internal Server Error
Galaxy was unable to sucessfully complete your request URL: http://ec2-50-19-79-199.compute-1.amazonaws.com/workflow/import_workflow Module galaxy.web.framework.middleware.error:149 in __call__
app_iter = self.application(environ, sr_checker) Module paste.recursive:84 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.workflow:1127 in import_workflow workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source=src,add_to_menu=add_to_menu ) Module galaxy.webapps.galaxy.controllers.workflow:1823 in _workflow_from_dict module = module_factory.from_dict( trans, step_dict, secure=False ) Module galaxy.workflow.modules:428 in from_dict return self.module_types[type].from_dict( trans, d, **kwargs ) Module galaxy.workflow.modules:222 in from_dict module.state.decode( d[ "tool_state" ], module.tool, module.trans.app, secure=secure ) Module galaxy.tools:849 in decode self.inputs = params_from_strings( tool.inputs, values, app, ignore_errors=True ) Module galaxy.tools.parameters:92 in params_from_strings value = json_fix( from_json_string( value ) ) Module simplejson:384 in loads Module simplejson.decoder:402 in decode TypeError: expected string or buffer
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participants (2)
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Dannon Baker -
Sébastien Vigneau