def add(self):
"""
Add this file system by creating a dedicated path (i.e., self.fs.mount_point)
and exporting it over NFS. Set the owner of the repo as ``ubuntu`` user.
"""
try:
log.debug("Adding transient file system at {0}".format(
self.fs.mount_point))
if not os.path.exists(self.fs.mount_point):
os.mkdir(self.fs.mount_point)
os.chown(self.fs.mount_point, pwd.getpwnam(
"ubuntu")[2], grp.getgrnam("ubuntu")[2])
self.device = commands.getoutput("df -h %s | grep -v Filesystem | awk '{print $1}'"
% self.fs.mount_point)
# If based on bucket, extract bucket contents onto new volume
try:
if self.from_archive:
log.info("Extracting archive url: {0} to mount point: {1}. This could take a while...".format(self.from_archive['url'], self.fs.mount_point))
misc.extract_archive_content_to_path(self.from_archive['url'], self.fs.mount_point, self.from_archive['md5_sum'])
self.fs.persistent = True
except Exception, e:
log.error("Error while extracting archive: {0}".format(e))
return False
if self.fs.add_nfs_share(self.fs.mount_point):
self.status()
return True
else:
log.warning('Trouble sharing {0} over NFS?'.format(
self.fs.mount_point))
def mount(self, mount_point):
"""
Mount this volume as a locally accessible file system and make it
available over NFS
"""
for counter in range(30):
if self.status == volume_status.ATTACHED:
if os.path.exists(mount_point):
# Check if the mount location is empty
if len(os.listdir(mount_point)) != 0:
log.warning("A file system at {0} already exists and is not empty; cannot "
"mount volume {1}".format(mount_point, self.volume_id))
return False
else:
os.mkdir(mount_point)
# Potentially wait for the device to actually become available in the system
# TODO: Do something if the device is not available in the
# given time period
for i in range(10):
if os.path.exists(self.device):
log.debug("Device path {0} checked and it exists.".format(
self.device))
break
else:
log.debug("Device path {0} does not yet exist; waiting...".format(
self.device))
time.sleep(4)
# Until the underlying issue is fixed (see FIXME below), mask this
# even more by custom-handling the run command and thus not
# printing the err
cmd = '/bin/mount %s %s' % (self.device, mount_point)
process = subprocess.Popen(
cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
_, _ = process.communicate()
if process.returncode != 0:
# FIXME: Assume if a file system cannot be mounted that it's because
# there is not a file system on the device so try creating
# one
if run('/sbin/mkfs.xfs %s' % self.device,
"Failed to create a files ystem on device %s" % self.device,
"Created a file system on device %s" % self.device):
if not run(
'/bin/mount %s %s' % (self.device, mount_point),
"Error mounting file system %s from %s" % (
mount_point, self.device),
"Successfully mounted file system %s from %s" %
(mount_point, self.device)):
log.error("Failed to mount device '%s' to mount point '%s'"
% (self.device, mount_point))
return False
# Resize the volume if it was created from a snapshot
else:
if self.snapshot and self.volume.size > self.snapshot.volume_size:
run('/usr/sbin/xfs_growfs %s' % mount_point)
log.info("Successfully grew file system {0}".format(self.fs.get_full_name()))
log.info("Successfully mounted file system {0} from {1}".format(mount_point,
self.device))
try:
# Default owner of all mounted file systems to `galaxy`
# user
os.chown(mount_point, pwd.getpwnam(
"galaxy")[2], grp.getgrnam("galaxy")[2])
# Add Galaxy- and CloudBioLinux-required files under the
# 'data' dir
if ServiceRole.GALAXY_DATA in self.fs.svc_roles:
for sd in ['files', 'tmp', 'upload_store', 'export']:
path = os.path.join(
self.app.path_resolver.galaxy_data, sd)
if not os.path.exists(path):
os.mkdir(path)
# Make 'export' dir that's shared over NFS be
# owned by `ubuntu` user so it's accesible
# for use to the rest of the cluster
if sd == 'export':
os.chown(path, pwd.getpwnam(
"ubuntu")[2], grp.getgrnam("ubuntu")[2])
else:
os.chown(path, pwd.getpwnam(
"galaxy")[2], grp.getgrnam("galaxy")[2])
except OSError, e:
log.debug(
"Tried making 'galaxyData' sub-dirs but failed: %s" % e)
# If based on bucket, extract bucket contents onto new volume
try:
if self.from_archive:
log.info("Extracting archive url: {0} to mount point: {1}. This could take a while...".format(self.from_archive['url'], mount_point))
misc.extract_archive_content_to_path(self.from_archive['url'], mount_point, self.from_archive['md5_sum'])
except Exception, e:
log.error("Error while extracting archive: {0}".format(e))
return False
# Lastly, share the newly mounted file system over NFS
if self.fs.add_nfs_share(mount_point):
return True
