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
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