2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6f07000db257/ Changeset: 6f07000db257 User: jmchilton Date: 2014-05-05 18:35:31 Summary: Remove duplicated code block - error in stable->central merge at some point I guess? Affected #: 1 file diff -r e7c77cb338c64f72310d844ee9e605e7b5438f94 -r 6f07000db257139dee35696da6dd840b240caef3 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -237,12 +237,6 @@ dependency_shell_commands = "&&".join( dependency_shell_commands ) external_metadata_script = "%s&&%s" % ( dependency_shell_commands, external_metadata_script ) log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) - if resolve_requirements: - dependency_shell_commands = self.app.datatypes_registry.set_external_metadata_tool.build_dependency_shell_commands() - if dependency_shell_commands: - if isinstance( dependency_shell_commands, list ): - dependency_shell_commands = "&&".join( dependency_shell_commands ) - external_metadata_script = "%s&&%s" % ( dependency_shell_commands, external_metadata_script ) external_metadata_proc = subprocess.Popen( args=external_metadata_script, shell=True, env=os.environ, https://bitbucket.org/galaxy/galaxy-central/commits/fe6c48de949d/ Changeset: fe6c48de949d User: jmchilton Date: 2014-05-05 18:35:31 Summary: Rework some error handling in local runner. This way if something goes wrong in failing job - the original exception is reported. Affected #: 1 file diff -r 6f07000db257139dee35696da6dd840b240caef3 -r fe6c48de949dd4e640d3632ab23cfe6ab5fa0494 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -109,8 +109,8 @@ stderr_file.close() log.debug('execution finished: %s' % command_line) except Exception: + log.exception("failure running job %d" % job_wrapper.job_id) job_wrapper.fail( "failure running job", exception=True ) - log.exception("failure running job %d" % job_wrapper.job_id) return self._handle_metadata_externally( job_wrapper, resolve_requirements=True ) # Finish the job! Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.