Hi Peter, You are probably using a mac if you are seeing this, so can you check to see if your .ga file permissions include an @ sign? This an Apple osx issue, and you'll need to do the following: xattr -d com.apple.quarantine <name of your exported.ga file> When you do this, it will fix the permissions, and uploading to the tool shed should work. Greg Von Kuster On Aug 21, 2013, at 11:23 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
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 ___________________________________________________________ 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/
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