1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/2f592b5f1883/ Changeset: 2f592b5f1883 User: jmchilton Date: 2014-05-16 17:14:52 Summary: Update LWR client and behavior through LWR changeset 8ea7265. LWR now informed of job submission failures in MQ mode so jobs shouldn't sit in queued state forever if job fails to queue remotely. Also small fixes and more logging. Affected #: 4 files
diff -r 26b9fe985ee718ddf25ee2e9e9d5096e8b315fad -r 2f592b5f1883520d62fc6ceab6a1657edd188294 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -28,6 +28,7 @@
NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE = "LWR misconfiguration - LWR client configured to set metadata remotely, but remote LWR isn't properly configured with a galaxy_home directory." NO_REMOTE_DATATYPES_CONFIG = "LWR client is configured to use remote datatypes configuration when setting metadata externally, but LWR is not configured with this information. Defaulting to datatypes_conf.xml." +GENERIC_REMOTE_ERROR = "Failed to communicate with remote job server."
# Is there a good way to infer some default for this? Can only use # url_for from web threads. https://gist.github.com/jmchilton/9098762 @@ -266,7 +267,7 @@ if failed: job_wrapper.fail("Failed to find or download one or more job outputs from remote server.", exception=True) except Exception: - message = "Failed to communicate with remote job server." + message = GENERIC_REMOTE_ERROR job_wrapper.fail( message, exception=True ) log.exception("failure finishing job %d" % job_wrapper.job_id) return @@ -284,7 +285,7 @@ Seperated out so we can use the worker threads for it. """ self.stop_job( self.sa_session.query( self.app.model.Job ).get( job_state.job_wrapper.job_id ) ) - job_state.job_wrapper.fail( job_state.fail_message ) + job_state.job_wrapper.fail( getattr( job_state, "fail_message", GENERIC_REMOTE_ERROR ) )
def check_pid( self, pid ): try:
diff -r 26b9fe985ee718ddf25ee2e9e9d5096e8b315fad -r 2f592b5f1883520d62fc6ceab6a1657edd188294 lib/galaxy/jobs/runners/lwr_client/client.py --- a/lib/galaxy/jobs/runners/lwr_client/client.py +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -300,7 +300,7 @@ launch_params = dict(command_line=command_line, job_id=self.job_id) submit_params_dict = submit_params(self.destination_params) if submit_params_dict: - launch_params['params'] = submit_params_dict + launch_params['submit_params'] = submit_params_dict if dependencies_description: launch_params['dependencies_description'] = dependencies_description.to_dict() if env:
diff -r 26b9fe985ee718ddf25ee2e9e9d5096e8b315fad -r 2f592b5f1883520d62fc6ceab6a1657edd188294 lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -97,6 +97,7 @@ try: if "job_id" in body: self.status_cache[body["job_id"]] = body + log.debug("Handling asynchronous status update from remote LWR.") callback(body) except Exception: log.exception("Failure processing job status update message.") @@ -104,6 +105,7 @@
def run(): self.exchange.consume("status_update", callback_wrapper, check=self) + log.debug("Leaving LWR client status update thread, no additional LWR updates will be processed.")
thread = threading.Thread( name="lwr_client_%s_status_update_callback" % self.manager_name,
diff -r 26b9fe985ee718ddf25ee2e9e9d5096e8b315fad -r 2f592b5f1883520d62fc6ceab6a1657edd188294 lib/galaxy/jobs/runners/lwr_client/util.py --- a/lib/galaxy/jobs/runners/lwr_client/util.py +++ b/lib/galaxy/jobs/runners/lwr_client/util.py @@ -62,6 +62,7 @@ contents.append(name) return contents
+ def parse_amqp_connect_ssl_params(params): ssl = None rval = None
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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