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=eb13e537583cdf... 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