def _fix_util_arch(self):
"""
Edit ``$SGE_ROOT/util/`` to prevent ``Unexpected operator`` error to
show up at shell login (SGE bug on Ubuntu).
"""
misc.replace_string(
self.app.path_resolver.sge_root +
'/util/arch', " libc_version=`echo $libc_string | tr ' ,' '\\n' | grep \"2\.\" | cut -f 2 -d \".\"`",
" libc_version=`echo $libc_string | tr ' ,' '\\n' | grep \"2\.\" | cut -f 2 -d \".\" | sort -u`")
# Support 3.0, 3.2, 3.5 kernels in Ubuntu 11.10 & 12.04 & 12.10
# Future proof it a bit to work with new 3.x kernels as they
# come online
misc.replace_string(
self.app.path_resolver.sge_root + '/util/arch', " 2.[46].*)",
" [23].[24567890].*)")
misc.replace_string(
self.app.path_resolver.sge_root + '/util/arch', " 2.6.*)",
" [23].[24567890].*)")
misc.run("sed -i.bak 's/sort -u/sort -u | head -1/g' %s/util/arch" % self.app.path_resolver.sge_root, "Error modifying %s/util/arch" %
self.app.path_resolver.sge_root, "Modified %s/util/arch" % self.app.path_resolver.sge_root)
misc.run("chmod +rx %s/util/arch" % self.app.path_resolver.sge_root, "Error chmod %s/util/arch" %
self.app.path_resolver.sge_root, "Successfully chmod %s/util/arch" % self.app.path_resolver.sge_root)
# Ensure lines starting with 127.0.1. are not included in /etc/hosts
# because SGE fails to install if that's the case. This line is added
# to /etc/hosts by cloud-init
# (http://www.cs.nott.ac.uk/~aas/Software%2520Installation%2520and%2520Development%2520Problems.html)
misc.run(
"sed -i.bak '/^127.0.1./s/^/# (Commented by CloudMan) /' /etc/hosts")
def _fix_util_arch(self):
"""
Edit ``$SGE_ROOT/util/`` to prevent ``Unexpected operator`` error to
show up at shell login (SGE bug on Ubuntu).
"""
misc.replace_string(
self.app.path_resolver.sge_root + '/util/arch',
" libc_version=`echo $libc_string | tr ' ,' '\\n' | grep \"2\.\" | cut -f 2 -d \".\"`",
" libc_version=`echo $libc_string | tr ' ,' '\\n' | grep \"2\.\" | cut -f 2 -d \".\" | sort -u`"
)
# Support 3.0, 3.2, 3.5 kernels in Ubuntu 11.10 & 12.04 & 12.10
# Future proof it a bit to work with new 3.x kernels as they
# come online
misc.replace_string(self.app.path_resolver.sge_root + '/util/arch',
" 2.[46].*)", " [23].[24567890].*)")
misc.replace_string(self.app.path_resolver.sge_root + '/util/arch',
" 2.6.*)", " [23].[24567890].*)")
misc.run(
"sed -i.bak 's/sort -u/sort -u | head -1/g' %s/util/arch" %
self.app.path_resolver.sge_root,
"Error modifying %s/util/arch" % self.app.path_resolver.sge_root,
"Modified %s/util/arch" % self.app.path_resolver.sge_root)
misc.run(
"chmod +rx %s/util/arch" % self.app.path_resolver.sge_root,
"Error chmod %s/util/arch" % self.app.path_resolver.sge_root,
"Successfully chmod %s/util/arch" %
self.app.path_resolver.sge_root)
# Ensure lines starting with 127.0.1. are not included in /etc/hosts
# because SGE fails to install if that's the case. This line is added
# to /etc/hosts by cloud-init
# (http://www.cs.nott.ac.uk/~aas/Software%2520Installation%2520and%2520Development%2520Problems.html)
misc.run(
"sed -i.bak '/^127.0.1./s/^/# (Commented by CloudMan) /' /etc/hosts"
)
def configure_proftpd(self):
"""
Configure environment for running ProFTPd service.
"""
# In the config, set the port on which postgres is running
log.debug("Configuring ProFTPd")
# This is a bit dodgy but ports are hardcoded in CBL so shoudl be a pretty
# safe bet for the time being
misc.replace_string('/usr/proftpd/etc/proftpd.conf',
'galaxy@localhost:5840',
'galaxy@localhost:{0}'.format(paths.C_PSQL_PORT))
misc.replace_string('/usr/proftpd/etc/proftpd.conf',
'/mnt/galaxyData',
self.app.path_resolver.galaxy_data)
# Verify that the expected config path exists. This is expected to be
# /mnt/galaxy/tools/proftpd
# TODO just use /usr/proftpd. Should be a simple update to the init.d
expected_config_path = os.path.join(self.app.path_resolver.galaxy_data, 'tools', 'proftpd')
if not os.path.exists(expected_config_path):
misc.run('ln -s /usr/profpd %s' % expected_config_path)
# Setup the data dir for FTP
ftp_data_dir = '%s/tmp/ftp' % self.app.path_resolver.galaxy_data
if not os.path.exists(ftp_data_dir):
os.makedirs(ftp_data_dir)
attempt_chown_galaxy(ftp_data_dir)
# Some images have vsFTPd server included so stop it first
vsFTPd_exists = misc.run('status vsftpd', quiet=True)
if vsFTPd_exists and 'start/running' in vsFTPd_exists:
log.debug("Stopping vsFTPd")
misc.run('stop vsftpd')
# Start the server now
if misc.run('/etc/init.d/proftpd start'):
self.state = service_states.RUNNING
return True
else:
log.debug("Trouble starting ProFTPd")
return False
def _fix_util_arch(self):
# Prevent 'Unexpected operator' to show up at shell login (SGE bug on Ubuntu)
misc.replace_string(paths.P_SGE_ROOT + '/util/arch', " libc_version=`echo $libc_string | tr ' ,' '\\n' | grep \"2\.\" | cut -f 2 -d \".\"`", " libc_version=`echo $libc_string | tr ' ,' '\\n' | grep \"2\.\" | cut -f 2 -d \".\" | sort -u`")
# Support 3.0 & 3.2 kernels in Ubuntu 11.10 & 12.04
misc.replace_string(paths.P_SGE_ROOT + '/util/arch', " 2.[46].*)",
" [23].[2460].*)")
misc.replace_string(paths.P_SGE_ROOT + '/util/arch', " 2.6.*)",
" [23].[260].*)")
misc.run("sed -i.bak 's/sort -u/sort -u | head -1/g' %s/util/arch" % paths.P_SGE_ROOT, "Error modifying %s/util/arch" % paths.P_SGE_ROOT, "Modified %s/util/arch" % paths.P_SGE_ROOT)
misc.run("chmod +rx %s/util/arch" % paths.P_SGE_ROOT, "Error chmod %s/util/arch" % paths.P_SGE_ROOT, "Successfully chmod %s/util/arch" % paths.P_SGE_ROOT)
# Ensure lines starting with 127.0.1. are not included in /etc/hosts
# because SGE fails to install if that's the case. This line is added
# to /etc/hosts by cloud-init
# (http://www.cs.nott.ac.uk/~aas/Software%2520Installation%2520and%2520Development%2520Problems.html)
misc.run("sed -i.bak '/^127.0.1./s/^/# (Commented by CloudMan) /' /etc/hosts")
def manage_postgres( self, to_be_started=True ):
if self.app.TESTFLAG is True:
log.debug( "Attempted to manage Postgres, but TESTFLAG is set." )
return
psql_data_dir = paths.P_PSQL_DIR
# Make sure postgres is owner of its directory before any operations
if os.path.exists(os.path.split(paths.P_PSQL_DIR)[0]):
misc.run("%s --recursive postgres:postgres %s" % (paths.P_CHOWN, os.path.split(paths.P_PSQL_DIR)[0]), "Error changing ownership of just created directory", "Successfully set ownership of Postgres data directory")
# Check on the status of PostgreSQL server
self.status()
if to_be_started and not self.state==service_states.RUNNING:
to_be_configured = False
# Check if 'psql_data_dir' exists first; it not, configure PostgreSQL
if not os.path.exists( psql_data_dir ):
log.debug("{0} dir does not exist; will be configuring Postgres".format(psql_data_dir))
to_be_configured = True
if to_be_configured:
log.info( "Configuring PostgreSQL with a database for Galaxy..." )
cont = True # Flag to indicate if previous operation completed successfully
# Make Galaxy database directory
if os.path.exists(paths.P_GALAXY_DATA) and not os.path.exists(psql_data_dir):
cont = misc.run('mkdir -p %s' % psql_data_dir, "Error creating Galaxy database cluster dir", "Successfully created Galaxy database cluster dir")
else:
log.error( "'%s' directory doesn't exist yet; will configure PostgreSQL later." % paths.P_GALAXY_DATA )
return False
# Change ownership of just created directory
if cont:
cont = misc.run( '%s -R postgres:postgres %s/pgsql' % ( paths.P_CHOWN, paths.P_GALAXY_DATA ), "Error changing ownership of just created directory", "Successfully changed ownership of just created directory" )
# Initialize/configure database cluster
if cont:
log.debug( "Initializing PostgreSQL database for Galaxy..." )
cont = misc.run( '%s - postgres -c "%s/initdb -D %s"' % (paths.P_SU, paths.P_PG_HOME, psql_data_dir), "Error initializing Galaxy database", "Successfully initialized Galaxy database")
if cont:
misc.replace_string('%s/postgresql.conf' % psql_data_dir, '#port = 5432', 'port = %s' % self.psql_port)
os.chown('%s/postgresql.conf' % psql_data_dir, pwd.getpwnam( "postgres" )[2], grp.getgrnam( "postgres" )[2] )
# Start PostgreSQL server so a role for Galaxy user can be created
if cont:
log.debug( "Starting PostgreSQL as part of the initial setup..." )
cont = misc.run( '%s - postgres -c "%s/pg_ctl -w -D %s -l /tmp/pgSQL.log -o \\\"-p %s\\\" start"' % (paths.P_SU, paths.P_PG_HOME, psql_data_dir, self.psql_port), "Error starting postgres server as part of the initial configuration", "Successfully started postgres server as part of the initial configuration." )
# Create role for galaxy user
if cont:
log.debug( "PostgreSQL started OK (log available at /tmp/pgSQL.log).")
log.debug( "Creating role for 'galaxy' user in PostgreSQL..." )
cont = misc.run('%s - postgres -c "%s/psql -p %s -c \\\"CREATE ROLE galaxy LOGIN CREATEDB\\\" "' % (paths.P_SU, paths.P_PG_HOME, self.psql_port), "Error creating role for 'galaxy' user", "Successfully created role for 'galaxy' user" )
# Create database for Galaxy, as galaxy user
if cont:
log.debug( "Creating PostgreSQL database as 'galaxy' user..." )
cont = misc.run('%s - galaxy -c "%s/createdb -p %s galaxy"' % (paths.P_SU, paths.P_PG_HOME, self.psql_port), "Error creating 'galaxy' database", "Successfully created 'galaxy' database")
# Now create role and permissons for galaxyftp user on the created 'galaxy' database
if cont:
log.debug( "Creating role for 'galaxyftp' user in PostgreSQL..." )
cont = misc.run('%s - postgres -c "%s/psql -p %s -c \\\"CREATE ROLE galaxyftp LOGIN PASSWORD \'fu5yOj2sn\'\\\" "' % (paths.P_SU, paths.P_PG_HOME, self.psql_port), "Error creating role for 'galaxyftp' user", "Successfully created role for 'galaxyftp' user" )
else:
log.error("Setting up Postgres did not go smoothly.")
self.state = service_states.ERROR
return False
# Check on the status of PostgreSQL server
self.status()
if to_be_started and not self.state==service_states.RUNNING:
# Start PostgreSQL database
log.info( "Starting PostgreSQL..." )
misc.run( '%s -R postgres:postgres %s' % (paths.P_CHOWN, paths.P_GALAXY_DATA+'/pgsql'), "Error changing owner of postgres data dir", "Successfully changed owner of postgres data dir" )
if misc.run( '%s - postgres -c "%s/pg_ctl -w -D %s -l /tmp/pgSQL.log -o\\\"-p %s\\\" start"' % (paths.P_SU, paths.P_PG_HOME, psql_data_dir, self.psql_port), "Error starting PostgreSQL server", "Successfully started PostgreSQL server"):
self.status()
if self.state==service_states.RUNNING:
log.info( "Successfully started PostgreSQL." )
else:
log.warning("Successfully started PosgreSQL but did it start and is it accessible?")
else:
log.debug("PostgreSQL already running (%s, %s)" % (to_be_started, self.state))
elif not to_be_started:
# Stop PostgreSQL database
log.info( "Stopping PostgreSQL..." )
self.state = service_states.SHUTTING_DOWN
if misc.run('%s - postgres -c "%s/pg_ctl -w -D %s -o\\\"-p %s\\\" stop"' % (paths.P_SU, paths.P_PG_HOME, psql_data_dir, self.psql_port), "Encountered problem while stopping PostgreSQL", "Successfully stopped PostgreSQL"):
self.state = service_states.SHUT_DOWN
else:
self.state = service_states.ERROR
return False
return True
def manage_postgres(self, to_be_started=True):
psql_data_dir = self.app.path_resolver.psql_dir
# Make sure postgres is owner of its directory before any operations
if os.path.exists(self.app.path_resolver.psql_dir):
misc.run(
"%s --recursive postgres:postgres %s" % (
paths.P_CHOWN, psql_data_dir),
"Error setting ownership of Postgres data directory %s" % psql_data_dir,
"Successfully set ownership of Postgres data directory %s" % psql_data_dir)
# Check on the status of PostgreSQL server
self.status()
if to_be_started and self.state is not service_states.RUNNING:
to_be_configured = False
# Check if 'psql_data_dir' exists first; it not, configure
# PostgreSQL
if not os.path.exists(psql_data_dir):
log.debug("{0} dir does not exist; will be configuring Postgres".format(
psql_data_dir))
to_be_configured = True
if to_be_configured:
log.debug(
"Configuring PostgreSQL with a database for Galaxy...")
cont = True # Flag to indicate if previous operation completed successfully
# Make Galaxy database directory
if os.path.exists(self.app.path_resolver.galaxy_data) and not os.path.exists(psql_data_dir):
cont = misc.run('mkdir -p %s' % psql_data_dir,
"Error creating Galaxy database cluster dir",
"Successfully created Galaxy database cluster dir")
else:
log.error("'%s' directory doesn't exist yet; will configure PostgreSQL later." %
self.app.path_resolver.galaxy_data)
return False
# Change ownership of just created directory
if cont:
cont = misc.run(
'%s -R postgres:postgres %s' % (
paths.P_CHOWN, psql_data_dir),
"Error changing ownership of just created directory",
"Successfully changed ownership of just created directory")
# Initialize/configure database cluster
if cont:
log.debug(
"Initializing PostgreSQL database for Galaxy...")
cont = misc.run('%s - postgres -c "%s/initdb -D %s"' % (
paths.P_SU, self.app.path_resolver.pg_home, psql_data_dir),
"Error initializing Galaxy database.",
"Successfully initialized Galaxy database.")
if cont:
misc.replace_string(
'%s/postgresql.conf' % psql_data_dir,
'#port = 5432', 'port = %s' % self.psql_port)
os.chown('%s/postgresql.conf' % psql_data_dir, pwd.getpwnam(
"postgres")[2], grp.getgrnam("postgres")[2])
# Start PostgreSQL server so a role for Galaxy user can be
# created
if cont:
log.debug(
"Starting PostgreSQL on port {0} as part of the initial setup..."
.format(self.psql_port))
cmd = ('%s - postgres -c "%s/pg_ctl -w -D %s -l /tmp/pgSQL.log -o \\\"-p %s\\\" start"'
% (paths.P_SU, self.app.path_resolver.pg_home, psql_data_dir, self.psql_port))
cont = misc.run(
cmd,
"Error starting postgres server as part of the initial configuration",
"Successfully started Postgres on port {0} as part of the initial configuration."
.format(self.psql_port))
# Create role for galaxy user
if cont:
log.debug(
"PostgreSQL started OK (log available at /tmp/pgSQL.log).")
log.debug(
"Creating role for 'galaxy' user in PostgreSQL...")
cont = misc.run(
'%s - postgres -c "%s/psql -p %s -c \\\"CREATE ROLE galaxy LOGIN CREATEDB\\\" "' % (
paths.P_SU, self.app.path_resolver.pg_home, self.psql_port),
"Error creating role for 'galaxy' user",
"Successfully created role for 'galaxy' user")
# Create database for Galaxy, as galaxy user
if cont:
log.debug(
"Creating PostgreSQL database as 'galaxy' user...")
cont = misc.run('%s - galaxy -c "%s/createdb -p %s galaxy"' % (
paths.P_SU, self.app.path_resolver.pg_home, self.psql_port),
"Error creating 'galaxy' database", "Successfully created 'galaxy' database")
# Now create role and permissons for galaxyftp user on the
# created 'galaxy' database
if cont:
log.debug(
"Creating role for 'galaxyftp' user in PostgreSQL...")
cont = misc.run(
'%s - postgres -c "%s/psql -p %s -c \\\"CREATE ROLE galaxyftp LOGIN PASSWORD \'fu5yOj2sn\'\\\" "' % (
paths.P_SU, self.app.path_resolver.pg_home, self.psql_port),
"Error creating role for 'galaxyftp' user",
"Successfully created role for 'galaxyftp' user")
else:
log.error("Setting up Postgres did not go smoothly.")
self.state = service_states.ERROR
return False
# Check on the status of PostgreSQL server
self.status()
if to_be_started and self.state is not service_states.RUNNING:
# Start PostgreSQL database
log.debug("Starting PostgreSQL...")
if misc.run('%s - postgres -c "%s/pg_ctl -w -D %s -l /tmp/pgSQL.log -o\\\"-p %s\\\" start"' %
(paths.P_SU, self.app.path_resolver.pg_home, psql_data_dir, self.psql_port)):
self.status()
else:
log.debug("PostgreSQL already running (%s, %s)" % (
to_be_started, self.state))
elif not to_be_started:
# Stop PostgreSQL database
log.info("Stopping PostgreSQL from {0} on port {1}...".format(
psql_data_dir, self.psql_port))
self.state = service_states.SHUTTING_DOWN
if misc.run('%s - postgres -c "%s/pg_ctl -w -D %s -o\\\"-p %s\\\" stop"'
% (paths.P_SU, self.app.path_resolver.pg_home, psql_data_dir, self.psql_port)):
self.state = service_states.SHUT_DOWN
else:
self.state = service_states.ERROR
return False
return True
