JSON error trying to update Tool Shed workflow
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
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.
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On Wed, Aug 21, 2013 at 4:30 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
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?
Yes, I am, and yes, they have 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>
$ xattr -d com.apple.quarantine secreted_protein_workflow.ga xattr: secreted_protein_workflow.ga: No such xattr: com.apple.quarantine Odd. Anyway, '@' sign gone.
When you do this, it will fix the permissions, and uploading to the tool shed should work.
It looks like my second upload attempt already solved this. I don't quite understand what went wrong on the Tool Shed, but is this something you need to handle gracefully? Thanks, Peter
participants (2)
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Greg Von Kuster -
Peter Cock