def _configure(self):
"""
Configure the Pulsar application.
"""
self.state = service_states.CONFIGURING
misc.make_dir(self.pulsar_home)
# Write out app.yml
token = ''.join(random.SystemRandom().choice(string.ascii_uppercase +
string.lowercase + string.digits) for _ in range(25))
app_template = Template(app_yml)
app_yml_file = os.path.join(self.pulsar_home, 'app.yml')
misc.write_template_file(app_template, {'token': token}, app_yml_file)
# Write out server.ini
srvr_template = Template(server_ini)
server_ini_file = os.path.join(self.pulsar_home, 'server.ini')
misc.write_template_file(srvr_template, {'pulsar_port': self.pulsar_port},
server_ini_file)
# Write out local_env.sh
lcl_template = Template(local_env_sh)
lcl_file = os.path.join(self.pulsar_home, 'local_env.sh')
misc.write_template_file(lcl_template, {'galaxy_home': '/mnt/galaxy/galaxy-app'},
lcl_file)
# Set the owner to 'galaxy' system user
attempt_chown_galaxy(self.pulsar_home, recursive=True)
if self.supervisor:
# Create a supervisor conf file
supervisor_conf_file = os.path.join(self.supervisor.conf_dir,
'{0}.conf'.format(self.supervisor_prog_name))
template = Template(supervisor_conf)
misc.write_template_file(template, None, supervisor_conf_file)
else:
log.warning("No supervisor service?")
def _configure(self):
"""
Setup Supervisor for running via CloudMan by creating
``supervisord.conf`` file.
"""
log.debug("Configuring supervisord")
# Create supervisord config file
sv_vars = {
'supervisord_pid': self.pid_file,
'sv_port': self.sv_port,
'conf_dir': self.conf_dir,
'supervisord_log': self.log_file
}
template = conf_manager.load_conf_template(conf_manager.SUPERVISOR_TEMPLATE)
misc.write_template_file(template, sv_vars, self.main_conf_file)
# Make sure the config dir exists for programs managed by supervisor
misc.make_dir(self.conf_dir)
def _configure(self):
"""
Setup Supervisor for running via CloudMan by creating
``supervisord.conf`` file.
"""
log.debug("Configuring supervisord")
# Create supervisord config file
sv_vars = {
'supervisord_pid': self.pid_file,
'sv_port': self.sv_port,
'conf_dir': self.conf_dir,
'supervisord_log': self.log_file
}
template = conf_manager.load_conf_template(
conf_manager.SUPERVISOR_TEMPLATE)
misc.write_template_file(template, sv_vars, self.main_conf_file)
# Make sure the config dir exists for programs managed by supervisor
misc.make_dir(self.conf_dir)
def _update_job_conf(app, num_handlers, plugin_id='slurm'):
"""
Update Galaxy job_conf.xml.
At the moment, only job handlers are set. Number of handlers are added that
correspond to ``num_handlers``.
"""
galaxy_config_dir = app.path_resolver.galaxy_config_dir
job_conf_file_path = join(galaxy_config_dir, 'job_conf.xml')
log.debug("Updating Galaxy's job conf file {0}".format(job_conf_file_path))
template = conf_manager.load_conf_template(
conf_manager.GALAXY_JOB_CONF_TEMPLATE)
handler_xml = ""
for i in range(num_handlers):
handler_xml += (
'\t\t<handler id="handler{0}" tags="handlers" />\n'.format(i))
params = {'cloudman_handlers': handler_xml}
misc.write_template_file(template, params, job_conf_file_path)
def _configure(self):
"""
Setup NodeJS Proxy within CloudMan and Galaxy contexts.
This will create a config file for Supervisor while other,
Galaxy-specific, requirements are assumed present
(https://wiki.galaxyproject.org/Admin/IEs).
"""
log.debug("Configuring NodeJS Proxy.")
template_vars = {
'supervisor_prog_name': self.supervisor_prog_name,
'galaxy_home': self.app.path_resolver.galaxy_home,
'np_port': self.np_port,
'galaxy_user': paths.GALAXY_USER_NAME
}
if self.supervisor:
supervisor_conf_file = os.path.join(self.supervisor.conf_dir,
'{0}.conf'.format(self.supervisor_prog_name))
template = Template(supervisor_conf)
misc.write_template_file(template, template_vars, supervisor_conf_file)
return True
return False
def _setup(self):
log.debug("Running GalaxyReportsService _setup")
# WORKAROUND: The run_reports.sh command refers to a parameter
# named --safe-pidfile which is not supported by the uwsgi binary.
# Replace it with --pidfile instead.
patch_start_command = ("sudo sed -i \"s/--safe-pidfile/--pidfile/g"
"\" %s/scripts/common_startup_functions.sh"
% self.galaxy_home)
misc.run(patch_start_command)
# Create default output dir for files
file_path = os.path.join(self.app.path_resolver.galaxy_home, "database/files")
misc.make_dir(file_path, owner='galaxy')
tmp_file_path = os.path.join(self.app.path_resolver.galaxy_home, "database/tmp")
misc.make_dir(tmp_file_path, owner='galaxy')
# Create the new reports config
params = {
'galaxy_db_port': self.app.path_resolver.psql_db_port
}
template = conf_manager.load_conf_template(conf_manager.GALAXY_REPORTS_TEMPLATE)
misc.write_template_file(template, params, self.conf_file)
attempt_chown_galaxy(self.conf_file)
def _configure(self):
"""
Setup NodeJS Proxy within CloudMan and Galaxy contexts.
This will create a config file for Supervisor while other,
Galaxy-specific, requirements are assumed present
(https://wiki.galaxyproject.org/Admin/IEs).
"""
log.debug("Configuring NodeJS Proxy.")
template_vars = {
'supervisor_prog_name': self.supervisor_prog_name,
'galaxy_home': self.app.path_resolver.galaxy_home,
'np_port': self.np_port,
'galaxy_user': paths.GALAXY_USER_NAME
}
if self.supervisor:
supervisor_conf_file = os.path.join(
self.supervisor.conf_dir,
'{0}.conf'.format(self.supervisor_prog_name))
template = Template(supervisor_conf)
misc.write_template_file(template, template_vars,
supervisor_conf_file)
return True
return False
def _configure(self):
"""
Configure the Pulsar application.
"""
self.state = service_states.CONFIGURING
misc.make_dir(self.pulsar_home)
# Write out app.yml
token = ''.join(
random.SystemRandom().choice(string.ascii_uppercase +
string.lowercase + string.digits)
for _ in range(25))
app_template = Template(app_yml)
app_yml_file = os.path.join(self.pulsar_home, 'app.yml')
misc.write_template_file(app_template, {'token': token}, app_yml_file)
# Write out server.ini
srvr_template = Template(server_ini)
server_ini_file = os.path.join(self.pulsar_home, 'server.ini')
misc.write_template_file(srvr_template,
{'pulsar_port': self.pulsar_port},
server_ini_file)
# Write out local_env.sh
lcl_template = Template(local_env_sh)
lcl_file = os.path.join(self.pulsar_home, 'local_env.sh')
misc.write_template_file(lcl_template,
{'galaxy_home': '/mnt/galaxy/galaxy-app'},
lcl_file)
# Set the owner to 'galaxy' system user
attempt_chown_galaxy(self.pulsar_home, recursive=True)
if self.supervisor:
# Create a supervisor conf file
supervisor_conf_file = os.path.join(
self.supervisor.conf_dir,
'{0}.conf'.format(self.supervisor_prog_name))
template = Template(supervisor_conf)
misc.write_template_file(template, None, supervisor_conf_file)
else:
log.warning("No supervisor service?")