def __init__(self, app):
super(PostgresService, self).__init__(app)
self.name = ServiceRole.to_string(ServiceRole.GALAXY_POSTGRES)
self.svc_roles = [ServiceRole.GALAXY_POSTGRES]
self.psql_port = app.path_resolver.psql_db_port
self.dependencies = [ServiceDependency(self, ServiceRole.GALAXY_DATA),
ServiceDependency(self, ServiceRole.MIGRATION)]
def __init__(self, app):
super(NodejsProxyService, self).__init__(app)
self.svc_roles = [ServiceRole.NODEJSPROXY]
self.name = ServiceRole.to_string(ServiceRole.NODEJSPROXY)
self.dependencies = [
ServiceDependency(self, ServiceRole.GALAXY_TOOLS),
ServiceDependency(self, ServiceRole.SUPERVISOR)
]
self.np_port = 8800
self.supervisor_conf_dir = '/etc/supervisor/conf.d'
self.supervisor_prog_name = 'galaxy_nodejs_proxy'
def __init__(self, app):
super(PulsarService, self).__init__(app)
self.name = ServiceRole.to_string(ServiceRole.PULSAR)
self.svc_roles = [ServiceRole.PULSAR]
self.dependencies = [
ServiceDependency(self, ServiceRole.JOB_MANAGER),
ServiceDependency(self, ServiceRole.SUPERVISOR)
]
self.pulsar_home = '/mnt/pulsar'
self.pulsar_port = 8913
self.supervisor_conf_dir = '/etc/supervisor/conf.d'
self.supervisor_prog_name = 'pulsar'
def __init__(self, app):
"""
Initialize the service class by setting role and indicating dependencies
"""
super(ProFTPdService, self).__init__(app)
log.debug("Initializing ProFTPdService")
self.svc_roles = [ServiceRole.PROFTPD]
self.name = ServiceRole.to_string(ServiceRole.PROFTPD)
self.dependencies = [
ServiceDependency(self, ServiceRole.GALAXY_POSTGRES),
ServiceDependency(self, ServiceRole.GALAXY_DATA)
]
def __init__(self, app):
super(GalaxyReportsService, self).__init__(app)
self.galaxy_home = self.app.path_resolver.galaxy_home
self.reports_port = DEFAULT_REPORTS_PORT
self.name = ServiceRole.to_string(ServiceRole.GALAXY_REPORTS)
self.svc_roles = [ServiceRole.GALAXY_REPORTS]
# Hopefully Galaxy dependency alone enough to ensure database migrated, etc...
self.dependencies = [
ServiceDependency(self, ServiceRole.GALAXY),
ServiceDependency(self, ServiceRole.GALAXY_POSTGRES)
]
self.conf_dir = os.path.join(self.app.path_resolver.galaxy_home,
'reports.conf.d')
def __init__(self, app):
super(HadoopService, self).__init__(app)
self.svc_roles = [ServiceRole.HADOOP]
self.name = ServiceRole.to_string(ServiceRole.HADOOP)
self.dependencies = [ServiceDependency(self, ServiceRole.SGE)]
self.id_rsa_path = os.path.join(paths.P_HADOOP_HOME, "id_rsa")
self.id_rsa_pub_key_path = os.path.join(paths.P_HADOOP_HOME,
"id_rsa.pub")
def __init__(self, app):
super(MigrationService, self).__init__(app)
self.svc_roles = [ServiceRole.MIGRATION]
self.name = ServiceRole.to_string(ServiceRole.MIGRATION)
self.svc_type = ServiceType.CM_SERVICE
self.dependencies = []
if 'filesystems' in self.app.config.user_data:
for fs in self.app.config.user_data.get('filesystems') or []:
# Wait for galaxy data, indices and tools to come up before attempting migration
if ServiceRole.GALAXY_DATA in ServiceRole.from_string_array(fs['roles']):
self.dependencies.append(ServiceDependency(self, ServiceRole.GALAXY_DATA))
if ServiceRole.GALAXY_TOOLS in ServiceRole.from_string_array(fs['roles']):
self.dependencies.append(ServiceDependency(self, ServiceRole.GALAXY_TOOLS))
if ServiceRole.GALAXY_INDICES in ServiceRole.from_string_array(fs['roles']):
self.dependencies.append(ServiceDependency(self, ServiceRole.GALAXY_INDICES))
def __init__(self, app):
super(CloudgeneService, self).__init__(app)
self.svc_roles = [ServiceRole.CLOUDGENE]
self.name = ServiceRole.to_string(ServiceRole.CLOUDGENE)
self.dependencies = [ServiceDependency(self, ServiceRole.CLOUDERA_MANAGER)]
self.port = 8085
self.cg_url = "https://cloudman.s3.amazonaws.com/files/cloudgene-cloudman-daemon.tar.gz"
self.cg_base_dir = '/mnt/galaxy/cloudgene/'
self.cg_home = os.path.join(self.cg_base_dir, 'cloudgene-daemon')
def __init__(self, app):
super(SlurmdService, self).__init__(app)
self.svc_roles = [ServiceRole.SLURMD]
self.name = ServiceRole.to_string(ServiceRole.SLURMD)
self.dependencies = [
ServiceDependency(self, ServiceRole.SLURMCTLD),
]
self.num_restarts = 0
self.max_restarts = 3
def __init__(self, app):
super(SlurmctldService, self).__init__(app)
self.svc_roles = [ServiceRole.SLURMCTLD, ServiceRole.JOB_MANAGER]
self.name = ServiceRole.to_string(ServiceRole.SLURMCTLD)
self.dependencies = [
ServiceDependency(self, ServiceRole.MIGRATION),
ServiceDependency(self, ServiceRole.TRANSIENT_NFS),
]
self.slurm_info = SlurmInfo()
self.num_restarts = 0
self.max_restarts = 3
# This must be the same on the workers
self.slurm_lock_file = os.path.join(
self.app.path_resolver.slurm_root_nfs, 'slurm.lockfile')
# Following a cluster reboot, this file may have been left over so
# clean it up before starting the service
if os.path.exists(self.slurm_lock_file):
os.remove(self.slurm_lock_file)
def __init__(self, app):
super(GalaxyService, self).__init__(app)
self.name = ServiceRole.to_string(ServiceRole.GALAXY)
self.svc_roles = [ServiceRole.GALAXY]
self.remaining_start_attempts = NUM_START_ATTEMPTS
# Indicates if the environment for running Galaxy has been configured
self.configured = False
self.ssl_is_on = False
# Environment variables to set before executing galaxy's run.sh
self.env_vars = {}
self.dependencies = [
ServiceDependency(self, ServiceRole.JOB_MANAGER),
ServiceDependency(self, ServiceRole.GALAXY_POSTGRES),
ServiceDependency(self, ServiceRole.GALAXY_DATA),
ServiceDependency(self, ServiceRole.GALAXY_INDICES),
# ServiceDependency(self, ServiceRole.PROFTPD),
ServiceDependency(self, ServiceRole.GALAXY_TOOLS)
]
self.option_manager = galaxy_option_manager(app)
def __init__(self, app, as_min=-1, as_max=-1, instance_type=None):
super(AutoscaleService, self).__init__(app)
self.state = service_states.UNSTARTED
self.svc_roles = [ServiceRole.AUTOSCALE]
self.svc_type = ServiceType.CM_SERVICE
self.name = ServiceRole.to_string(ServiceRole.AUTOSCALE)
self.dependencies = [ServiceDependency(self, ServiceRole.MIGRATION)]
self.as_max = as_max # Max number of nodes autoscale should maintain
self.as_min = as_min # Min number of nodes autoscale should maintain
self.instance_type = instance_type # Type of instances to start
def __init__(self,
app,
as_min=-1,
as_max=-1,
instance_type=None,
num_queued_jobs=2,
mean_runtime_threshold=60,
num_instances_to_add=1):
"""
:type as_min: int
:param as_min: The minimum number of worker nodes of maintain.
:type as_max: int
:param as_max: The maximum number of worker nodes to maintain.
:type instance_type: str
:param instance_type: The type of instance to use.
:type num_queued_jobs: int
:param num_queued_jobs: Minimum number of jobs that need to be queued
before autoscaling will trigger.
:type mean_runtime_threshold: int
:param mean_runtime_threshold: Mean running job runtime before
autoscaling will trigger.
:type num_instances_to_add: int
:param num_instances_to_add: Number of instances to add when scaling up.
"""
super(AutoscaleService, self).__init__(app)
self.state = service_states.UNSTARTED
self.svc_roles = [ServiceRole.AUTOSCALE]
self.svc_type = ServiceType.CM_SERVICE
self.name = ServiceRole.to_string(ServiceRole.AUTOSCALE)
self.dependencies = [ServiceDependency(self, ServiceRole.MIGRATION)]
self.as_max = as_max
self.as_min = as_min
self.instance_type = instance_type
def __init__(self, app):
super(SGEService, self).__init__(app)
self.svc_roles = [ServiceRole.SGE, ServiceRole.JOB_MANAGER]
self.name = ServiceRole.to_string(ServiceRole.SGE)
self.dependencies = [ServiceDependency(self, ServiceRole.MIGRATION)]
self.sge_info = SGEInfo()
