Hi all,

I was trying to update this workflow repository on the Test Tool Shed,
http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow

Attempting to upload the tar-ball appeared to fail as follows:

URL: 
http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=eb13e537583cdf2a
Module galaxy.web.framework.middleware.error:149 in __call__
>>  app_iter = self.application(environ, sr_checker)
Module paste.debug.prints:106 in __call__
>>  environ, self.app)
Module paste.wsgilib:543 in intercept_output
>>  app_iter = application(environ, replacement_start_response)
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.web.framework:98 in decorator
>>  return func( self, trans, *args, **kwargs )
Module galaxy.webapps.tool_shed.controllers.upload:203 in upload
>>  metadata_util.set_repository_metadata_due_to_new_tip( trans, repository, 
>> content_alert_str=content_alert_str, **kwd )
Module tool_shed.util.metadata_util:1850 in
set_repository_metadata_due_to_new_tip
>>  error_message, status = set_repository_metadata( trans, repository, 
>> content_alert_str=content_alert_str, **kwd )
Module tool_shed.util.metadata_util:1779 in set_repository_metadata
>>  persist=False )
Module tool_shed.util.metadata_util:698 in
generate_metadata_for_changeset_revision
>>  exported_workflow_dict = json.from_json_string( workflow_text )
Module simplejson:384 in loads
Module simplejson.decoder:402 in decode
Module simplejson.decoder:420 in raw_decode
JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0)

Confusingly the changes seem to get uploaded anyway but
seems to have generated a dummy file _secreted_protein_workflow.ga
(note the leading underscore)
http://testtoolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=36b2c2b5051e&id=eb13e537583cdf2a

Not realising this, I recreated and reupload the tarball (which worked
and removed the phantom file):
http://testtoolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=f32581ab2c35&id=eb13e537583cdf2a

The tar-ball (re)created for the upload was created using:
$ tar -cf secreted_protein_workflow_v0.0.2.tar.gz README.rst
repository_dependencies.xml secreted_protein_workflow.ga

I don't have the first tar-ball anymore, but I also don't have any
file named _secreted_protein_workflow.ga with a leading
underscore in my working directory so I am pretty sure this
was created by the Tool Shed somehow.

Peter
___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to