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
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 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=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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