def __init__( self, user, token=None):
if token:
self.token = token
else:
self.token = unique_id()
self.user = user
self.expiration_time = now() + timedelta(hours=24)
def __init__(self, user, token=None):
if token:
self.token = token
else:
self.token = unique_id()
self.user = user
self.expiration_time = now() + timedelta(hours=24)
def queue_job(self, job_wrapper):
resource_parameters = job_wrapper.get_resource_parameters()
try:
test_name = resource_parameters["test_name"]
except KeyError:
job_wrapper.fail(
"Job resource parameter test_name not set as required for this job runner."
)
return
job_dest_params = job_wrapper.job_destination.params
if test_name == "test_walltime_resubmission":
assert job_dest_params["dest_name"] == "retry_test_more_walltime"
elif test_name == "test_memory_resubmission":
assert job_dest_params["dest_name"] == "retry_test_more_mem"
elif test_name == "test_unknown_error":
assert job_dest_params["dest_name"] == "retry_unknown_error"
elif test_name == "test_resubmission_after_delay":
assert job_dest_params["dest_name"] == "retry_after_delay"
job = job_wrapper.get_job()
if (now() - job.create_time).total_seconds() < 5:
self._fail_job_local(job_wrapper, "Job completed too quickly")
return
super(AssertionJobRunner, self).queue_job(job_wrapper)
def get_active_processes(self, last_seen_seconds=None):
"""Return all processes seen in ``last_seen_seconds`` seconds."""
if last_seen_seconds is None:
last_seen_seconds = self.heartbeat_interval
seconds_ago = now() - datetime.timedelta(seconds=last_seen_seconds)
return self.sa_session.query(WorkerProcess).filter(
WorkerProcess.table.c.update_time > seconds_ago).all()
def _workflow_invocation_update(self):
session = object_session(self)
table = self.table
now_val = now()
stmt = table.update().values(update_time=now_val).where(
and_(table.c.id == self.id, table.c.update_time < now_val))
session.execute(stmt)
def update_watcher_designation(self):
worker_process = self.worker_process
if not worker_process:
worker_process = WorkerProcess(server_name=self.server_name, hostname=self.hostname)
worker_process.update_time = now()
worker_process.pid = self.pid
self.sa_session.add(worker_process)
self.sa_session.flush()
# We only want a single process watching the various config files on the file system.
# We just pick the max server name for simplicity
is_config_watcher = self.server_name == max(
(p.server_name for p in self.get_active_processes(self.heartbeat_interval + 1)))
if is_config_watcher != self.is_config_watcher:
self.is_config_watcher = is_config_watcher
def send_database_heartbeat(self):
if self.active:
while not self.exit.isSet():
worker_process = self.sa_session.query(
WorkerProcess).filter_by(
server_name=self.server_name,
hostname=self.hostname,
).first()
if not worker_process:
worker_process = WorkerProcess(
server_name=self.server_name, hostname=self.hostname)
worker_process.update_time = now()
self.sa_session.add(worker_process)
self.sa_session.flush()
self.exit.wait(self.heartbeat_interval)
def ready_galaxy_markdown_for_export(trans, internal_galaxy_markdown):
"""Fill in details needed to render Galaxy flavored markdown.
Take it from a minimal internal version to an externally render-able version
with more details populated and actual IDs replaced with encoded IDs to render
external links. Return expanded markdown and extra data useful for rendering
custom container tags.
"""
extra_rendering_data = {
"generate_time": now().isoformat(),
"generate_version": trans.app.config.version_major,
}
# Walk Galaxy directives inside the Galaxy Markdown and collect dict-ified data
# needed to render this efficiently.
directive_handler = ReadyForExportMarkdownDirectiveHandler(trans, extra_rendering_data)
export_markdown = directive_handler.walk(trans, internal_galaxy_markdown)
return export_markdown, extra_rendering_data
def queue_job(self, job_wrapper):
resource_parameters = job_wrapper.get_resource_parameters()
try:
test_name = resource_parameters["test_name"]
except KeyError:
job_wrapper.fail("Job resource parameter test_name not set as required for this job runner.")
return
job_dest_params = job_wrapper.job_destination.params
if test_name == "test_walltime_resubmission":
assert job_dest_params["dest_name"] == "retry_test_more_walltime"
elif test_name == "test_memory_resubmission":
assert job_dest_params["dest_name"] == "retry_test_more_mem"
elif test_name == "test_unknown_error":
assert job_dest_params["dest_name"] == "retry_unknown_error"
elif test_name == "test_resubmission_after_delay":
assert job_dest_params["dest_name"] == "retry_after_delay"
job = job_wrapper.get_job()
if (now() - job.create_time).total_seconds() < 5:
self._fail_job_local(job_wrapper, "Job completed too quickly")
return
super(AssertionJobRunner, self).queue_job(job_wrapper)
def _remap(container, line):
id_match = re.search(UNENCODED_ID_PATTERN, line)
object_id = None
encoded_id = None
if id_match:
object_id = int(id_match.group(2))
encoded_id = trans.security.encode_id(object_id)
line = line.replace(id_match.group(), f"{id_match.group(1)}={encoded_id}")
if container == "history_link":
_check_object(object_id, line)
history = history_manager.get_accessible(object_id, trans.user)
rval = self.handle_history_link(line, history)
elif container == "history_dataset_display":
_check_object(object_id, line)
hda = hda_manager.get_accessible(object_id, trans.user)
rval = self.handle_dataset_display(line, hda)
elif container == "history_dataset_link":
_check_object(object_id, line)
hda = hda_manager.get_accessible(object_id, trans.user)
rval = self.handle_dataset_display(line, hda)
elif container == "history_dataset_index":
_check_object(object_id, line)
hda = hda_manager.get_accessible(object_id, trans.user)
rval = self.handle_dataset_display(line, hda)
elif container == "history_dataset_embedded":
_check_object(object_id, line)
hda = hda_manager.get_accessible(object_id, trans.user)
rval = self.handle_dataset_embedded(line, hda)
elif container == "history_dataset_as_image":
_check_object(object_id, line)
hda = hda_manager.get_accessible(object_id, trans.user)
rval = self.handle_dataset_as_image(line, hda)
elif container == "history_dataset_peek":
_check_object(object_id, line)
hda = hda_manager.get_accessible(object_id, trans.user)
rval = self.handle_dataset_peek(line, hda)
elif container == "history_dataset_info":
_check_object(object_id, line)
hda = hda_manager.get_accessible(object_id, trans.user)
rval = self.handle_dataset_info(line, hda)
elif container == "history_dataset_type":
_check_object(object_id, line)
hda = hda_manager.get_accessible(object_id, trans.user)
rval = self.handle_dataset_type(line, hda)
elif container == "history_dataset_name":
_check_object(object_id, line)
hda = hda_manager.get_accessible(object_id, trans.user)
rval = self.handle_dataset_name(line, hda)
elif container == "workflow_display":
stored_workflow = workflow_manager.get_stored_accessible_workflow(trans, encoded_id)
rval = self.handle_workflow_display(line, stored_workflow)
elif container == "history_dataset_collection_display":
hdca = collection_manager.get_dataset_collection_instance(trans, "history", encoded_id)
rval = self.handle_dataset_collection_display(line, hdca)
elif container == "tool_stdout":
job = job_manager.get_accessible_job(trans, object_id)
rval = self.handle_tool_stdout(line, job)
elif container == "tool_stderr":
job = job_manager.get_accessible_job(trans, object_id)
rval = self.handle_tool_stderr(line, job)
elif container == "job_parameters":
job = job_manager.get_accessible_job(trans, object_id)
rval = self.handle_job_parameters(line, job)
elif container == "job_metrics":
job = job_manager.get_accessible_job(trans, object_id)
rval = self.handle_job_metrics(line, job)
elif container == "generate_galaxy_version":
version = trans.app.config.version_major
rval = self.handle_generate_galaxy_version(line, version)
elif container == "generate_time":
rval = self.handle_generate_time(line, now())
elif container == "invocation_time":
invocation = workflow_manager.get_invocation(trans, object_id)
rval = self.handle_invocation_time(line, invocation)
elif container == "visualization":
rval = None
else:
raise MalformedContents(f"Unknown Galaxy Markdown directive encountered [{container}].")
if rval is not None:
return rval
else:
return (line, False)
def _new_invocation(self):
invocation = model.WorkflowInvocation()
invocation.id = 1
invocation.create_time = now()
return invocation
