def __call__(self, args):
super(DbCommand, self).__call__(args)
self.configure_logging(args)
# Since EnvDefault.__action__ is only called if a user actively passes
# a variable, there's no way to do the string replacing in the action
# itself. Instead, we're post-processing them here, but this could be
# improved.
names = sorted(x.dest for x in self.parser._actions)
for dest in names:
if dest in ("help", "verbose", "quiet"):
continue
value = getattr(args, dest)
if value and isinstance(value, basestring):
replacement = value % dict(args._get_kwargs())
log.debug("% 20s => %s" % (dest, replacement))
setattr(args, dest, replacement)
if args.serverdir:
d = args.serverdir
else:
raise Stop(1, 'OMERO server directory required')
ext = External(d)
ext.setup_omero_cli()
DbAdmin(d, args.dbcommand, args, ext)
class Install(object):
def __init__(self, cmd, args):
self.args = args
log.info("%s: %s", self.__class__.__name__, cmd)
log.debug("Current directory: %s", os.getcwd())
if cmd == "upgrade":
newinstall = False
if not os.path.exists(args.sym):
raise Stop(30, "Symlink is missing: %s" % args.sym)
elif cmd == "install":
newinstall = True
if os.path.exists(args.sym):
raise Stop(30, "Symlink already exists: %s" % args.sym)
else:
raise Exception("Unexpected command: %s" % cmd)
server_dir = self.get_server_dir()
if newinstall:
# Create a symlink to simplify the rest of the logic-
# just need to check if OLD == NEW
self.symlink(server_dir, args.sym)
log.info("Installing %s (%s)...", server_dir, args.sym)
else:
log.info("Upgrading %s (%s)...", server_dir, args.sym)
self.external = External(server_dir)
self.external.setup_omero_cli()
if not newinstall:
self.external.setup_previous_omero_env(args.sym, args.savevarsfile)
# Need lib/python set above
import path
self.dir = path.path(server_dir)
if not newinstall:
self.stop()
self.archive_logs()
copyold = not newinstall and not args.ignoreconfig
self.configure(copyold, args.prestartfile)
self.directories()
if newinstall:
self.init_db()
self.upgrade_db()
self.external.save_env_vars(args.savevarsfile, args.savevars.split())
self.start()
def get_server_dir(self):
"""
Either downloads and/or unzips the server if necessary
return: the directory of the unzipped server
"""
if not self.args.server:
if self.args.skipunzip:
raise Stop(0, "Unzip disabled, exiting")
log.info("Downloading server")
artifacts = Artifacts(self.args)
server = artifacts.download("server")
else:
progress = 0
if self.args.verbose:
progress = 20
ptype, server = fileutils.get_as_local_path(
self.args.server,
self.args.overwrite,
progress=progress,
httpuser=self.args.httpuser,
httppassword=self.args.httppassword,
)
if ptype == "file":
if self.args.skipunzip:
raise Stop(0, "Unzip disabled, exiting")
log.info("Unzipping %s", server)
server = fileutils.unzip(server, match_dir=True, destdir=self.args.unzipdir)
log.debug("Server directory: %s", server)
return server
def stop(self):
try:
log.info("Stopping server")
self.bin("admin status --nodeonly")
self.bin("admin stop")
except Exception as e:
log.error("Error whilst stopping server: %s", e)
if not self.args.no_web:
try:
log.info("Stopping web")
self.stopweb()
except Exception as e:
log.error("Error whilst stopping web: %s", e)
def configure(self, copyold, prestartfile):
def samecontents(a, b):
# os.path.samefile is not available on Windows
try:
return os.path.samefile(a, b)
except AttributeError:
with open(a) as fa:
with open(b) as fb:
return fa.read() == fb.read()
target = self.dir / "etc" / "grid" / "config.xml"
if copyold:
from path import path
old_grid = path(self.args.sym) / "etc" / "grid"
old_cfg = old_grid / "config.xml"
log.info("Copying old configuration from %s", old_cfg)
if not old_cfg.exists():
raise Stop(40, "config.xml not found")
if target.exists() and samecontents(old_cfg, target):
# This likely is caused by the symlink being
# created early on an initial install.
pass
else:
old_cfg.copy(target)
else:
if target.exists():
log.info("Deleting configuration file %s", target)
target.remove()
if prestartfile:
for f in prestartfile:
log.info("Loading prestart file %s", f)
ftype, fpath = fileutils.get_as_local_path(f, "backup")
if ftype != "file":
raise Stop(50, "Expected file, found: %s %s" % (ftype, f))
self.run(["load", fpath])
def archive_logs(self):
if self.args.archivelogs:
logdir = os.path.join(self.args.sym, "var", "log")
archive = self.args.archivelogs
log.info("Archiving logs to %s", archive)
fileutils.zip(archive, logdir, os.path.join(self.args.sym, "var"))
return archive
def directories(self):
if self.samedir(self.dir, self.args.sym):
log.warn("Upgraded server was the same, not deleting")
return
try:
target = self.readlink(self.args.sym)
targetzip = target + ".zip"
except IOError:
log.error("Unable to get symlink target: %s", self.args.sym)
target = None
targetzip = None
if self.args.delete_old and target:
try:
log.info("Deleting %s", target)
shutil.rmtree(target)
except OSError as e:
log.error("Failed to delete %s: %s", target, e)
if not self.args.keep_old_zip and targetzip:
try:
log.info("Deleting %s", targetzip)
os.unlink(targetzip)
except OSError as e:
log.error("Failed to delete %s: %s", targetzip, e)
self.rmlink(self.args.sym)
self.symlink(self.dir, self.args.sym)
def init_db(self):
if self.args.initdb:
log.debug("Initialising database")
DbAdmin(self.dir, "init", self.args, self.external)
def upgrade_db(self):
if self.args.upgradedb:
log.debug("Upgrading database")
DbAdmin(self.dir, "upgrade", self.args, self.external)
def start(self):
if self.args.no_start:
log.debug("Not starting OMERO")
return
self.run("admin start")
if not self.args.no_web:
log.info("Starting web")
self.startweb()
def run(self, command):
"""
Runs a command as if from the command-line
without the need for using popen or subprocess
"""
if isinstance(command, basestring):
command = command.split()
else:
command = list(command)
self.external.omero_cli(command)
def bin(self, command):
"""
Runs the omero command-line client with an array of arguments using the
old environment
"""
if isinstance(command, basestring):
command = command.split()
self.external.omero_bin(command)
class Install(object):
def __init__(self, cmd, args):
self.args = args
log.info("%s: %s", self.__class__.__name__, cmd)
log.debug("Current directory: %s", os.getcwd())
if cmd == 'upgrade':
newinstall = False
if not os.path.exists(args.sym):
raise Stop(30, 'Symlink is missing: %s' % args.sym)
elif cmd == 'install':
newinstall = True
if os.path.exists(args.sym):
raise Stop(30, 'Symlink already exists: %s' % args.sym)
else:
raise Exception('Unexpected command: %s' % cmd)
server_dir = self.get_server_dir()
if newinstall:
# Create a symlink to simplify the rest of the logic-
# just need to check if OLD == NEW
self.symlink(server_dir, args.sym)
log.info("Installing %s (%s)...", server_dir, args.sym)
else:
log.info("Upgrading %s (%s)...", server_dir, args.sym)
self.external = External(server_dir)
self.external.setup_omero_cli()
if not newinstall:
self.external.setup_previous_omero_env(args.sym, args.savevarsfile)
# Need lib/python set above
import path
self.dir = path.path(server_dir)
if not newinstall:
self.stop()
self.archive_logs()
copyold = not newinstall and not args.ignoreconfig
self.configure(copyold, args.prestartfile)
self.directories()
if newinstall:
self.init_db()
self.upgrade_db()
self.external.save_env_vars(args.savevarsfile, args.savevars.split())
self.start()
def get_server_dir(self):
"""
Either downloads and/or unzips the server if necessary
return: the directory of the unzipped server
"""
if not self.args.server:
if self.args.skipunzip:
raise Stop(0, 'Unzip disabled, exiting')
log.info('Downloading server')
artifacts = Artifacts(self.args)
server = artifacts.download('server')
else:
progress = 0
if self.args.verbose:
progress = 20
ptype, server = fileutils.get_as_local_path(
self.args.server,
self.args.overwrite,
progress=progress,
httpuser=self.args.httpuser,
httppassword=self.args.httppassword)
if ptype == 'file':
if self.args.skipunzip:
raise Stop(0, 'Unzip disabled, exiting')
log.info('Unzipping %s', server)
server = fileutils.unzip(server,
match_dir=True,
destdir=self.args.unzipdir)
log.debug('Server directory: %s', server)
return server
def stop(self):
try:
log.info("Stopping server")
self.bin("admin status --nodeonly")
self.bin("admin stop")
except Exception as e:
log.error('Error whilst stopping server: %s', e)
if not self.args.no_web:
try:
log.info("Stopping web")
self.stopweb()
except Exception as e:
log.error('Error whilst stopping web: %s', e)
def configure(self, copyold, prestartfile):
def samecontents(a, b):
# os.path.samefile is not available on Windows
try:
return os.path.samefile(a, b)
except AttributeError:
with open(a) as fa:
with open(b) as fb:
return fa.read() == fb.read()
target = self.dir / "etc" / "grid" / "config.xml"
if copyold:
from path import path
old_grid = path(self.args.sym) / "etc" / "grid"
old_cfg = old_grid / "config.xml"
log.info("Copying old configuration from %s", old_cfg)
if not old_cfg.exists():
raise Stop(40, 'config.xml not found')
if target.exists() and samecontents(old_cfg, target):
# This likely is caused by the symlink being
# created early on an initial install.
pass
else:
old_cfg.copy(target)
else:
if target.exists():
log.info('Deleting configuration file %s', target)
target.remove()
if prestartfile:
for f in prestartfile:
log.info('Loading prestart file %s', f)
ftype, fpath = fileutils.get_as_local_path(f, 'backup')
if ftype != 'file':
raise Stop(50, 'Expected file, found: %s %s' % (ftype, f))
self.run(['load', fpath])
def archive_logs(self):
if self.args.archivelogs:
logdir = os.path.join(self.args.sym, 'var', 'log')
archive = self.args.archivelogs
log.info('Archiving logs to %s', archive)
fileutils.zip(archive, logdir, os.path.join(self.args.sym, 'var'))
return archive
def directories(self):
if self.samedir(self.dir, self.args.sym):
log.warn("Upgraded server was the same, not deleting")
return
try:
target = self.readlink(self.args.sym)
targetzip = target + '.zip'
except IOError:
log.error('Unable to get symlink target: %s', self.args.sym)
target = None
targetzip = None
if self.args.delete_old and target:
try:
log.info("Deleting %s", target)
shutil.rmtree(target)
except OSError as e:
log.error("Failed to delete %s: %s", target, e)
if not self.args.keep_old_zip and targetzip:
try:
log.info("Deleting %s", targetzip)
os.unlink(targetzip)
except OSError as e:
log.error("Failed to delete %s: %s", targetzip, e)
self.rmlink(self.args.sym)
self.symlink(self.dir, self.args.sym)
def init_db(self):
if self.args.initdb:
log.debug('Initialising database')
DbAdmin(self.dir, 'init', self.args, self.external)
def upgrade_db(self):
if self.args.upgradedb:
log.debug('Upgrading database')
DbAdmin(self.dir, 'upgrade', self.args, self.external)
def start(self):
if self.args.no_start:
log.debug('Not starting OMERO')
return
self.run("admin start")
if not self.args.no_web:
log.info("Starting web")
self.startweb()
def run(self, command):
"""
Runs a command as if from the command-line
without the need for using popen or subprocess
"""
if isinstance(command, basestring):
command = command.split()
else:
command = list(command)
self.external.omero_cli(command)
def bin(self, command):
"""
Runs the omero command-line client with an array of arguments using the
old environment
"""
if isinstance(command, basestring):
command = command.split()
self.external.omero_bin(command)
class Install(object):
def __init__(self, cmd, args):
self.args, newinstall = self._handle_args(cmd, args)
log.info("%s: %s", self.__class__.__name__, cmd)
log.debug("Current directory: %s", os.getcwd())
self.symlink_check_and_set()
if newinstall is None:
# Automatically install or upgrade
newinstall = not os.path.exists(args.sym)
elif newinstall is False:
if not os.path.exists(args.sym):
raise Stop(30, 'Symlink is missing: %s' % args.sym)
elif newinstall is True:
if os.path.exists(args.sym):
raise Stop(30, 'Symlink already exists: %s' % args.sym)
else:
assert False
server_dir = self.get_server_dir()
if newinstall:
# Create a symlink to simplify the rest of the logic-
# just need to check if OLD == NEW
self.symlink(server_dir, args.sym)
log.info("Installing %s (%s)...", server_dir, args.sym)
else:
log.info("Upgrading %s (%s)...", server_dir, args.sym)
self.external = External(server_dir)
self.external.setup_omero_cli()
if not newinstall:
self.external.setup_previous_omero_env(args.sym, args.savevarsfile)
# Need lib/python set above
import path
self.dir = path.path(server_dir)
if not newinstall:
self.stop()
self.archive_logs()
copyold = not newinstall and not args.ignoreconfig
self.configure(copyold, args.prestartfile)
self.directories()
self.handle_database()
self.external.save_env_vars(args.savevarsfile, args.savevars.split())
self.start()
def _handle_args(self, cmd, args):
"""
We need to support deprecated behaviour for now which makes this
quite complicated
Current behaviour:
- install: Installs a new server, existing server causes an error
- install --upgrade: Installs or upgrades a server
- install --managedb: Automatically initialise or upgrade the db
Deprecated:
- install --upgradedb --initdb: Replaced by install --managedb
- install --upgradedb: upgrade the db, must exist
- install --initdb: initialise the db
- upgrade: Upgrades a server, must already exist
- upgrade --upgradedb: Automatically upgrade the db
returns:
- Modified args object, flag to indicate new/existing/auto install
"""
if cmd == 'install':
if args.upgrade:
# Current behaviour: install or upgrade
if args.initdb or args.upgradedb:
raise Stop(10, (
'Deprecated --initdb --upgradedb flags '
'are incompatible with --upgrade'))
newinstall = None
else:
# Current behaviour: Server must not exist
newinstall = True
if args.managedb:
# Current behaviour
if args.initdb or args.upgradedb:
raise Stop(10, (
'Deprecated --initdb --upgradedb flags '
'are incompatible with --managedb'))
args.initdb = True
args.upgradedb = True
else:
if args.initdb or args.upgradedb:
log.warn('--initdb and --upgradedb are deprecated, '
'use --managedb')
elif cmd == 'upgrade':
# Deprecated behaviour
log.warn(
'"omero upgrade" is deprecated, use "omego install --upgrade"')
cmd = 'install'
args.upgrade = True
# Deprecated behaviour: Server must exist
newinstall = False
else:
raise Exception('Unexpected command: %s' % cmd)
return args, newinstall
def get_server_dir(self):
"""
Either downloads and/or unzips the server if necessary
return: the directory of the unzipped server
"""
if not self.args.server:
if self.args.skipunzip:
raise Stop(0, 'Unzip disabled, exiting')
log.info('Downloading server')
# The downloader automatically symlinks the server, however if
# we are upgrading we want to delay the symlink swap, so this
# overrides args.sym
# TODO: Find a nicer way to do this?
artifact_args = copy.copy(self.args)
artifact_args.sym = ''
artifacts = Artifacts(artifact_args)
server = artifacts.download('server')
else:
progress = 0
if self.args.verbose:
progress = 20
ptype, server = fileutils.get_as_local_path(
self.args.server, self.args.overwrite, progress=progress,
httpuser=self.args.httpuser,
httppassword=self.args.httppassword)
if ptype == 'file':
if self.args.skipunzip:
raise Stop(0, 'Unzip disabled, exiting')
log.info('Unzipping %s', server)
server = fileutils.unzip(
server, match_dir=True, destdir=self.args.unzipdir)
log.debug('Server directory: %s', server)
return server
def stop(self):
try:
log.info("Stopping server")
self.bin("admin status --nodeonly")
self.bin("admin stop")
except Exception as e:
log.error('Error whilst stopping server: %s', e)
if not self.args.no_web:
try:
log.info("Stopping web")
self.stopweb()
except Exception as e:
log.error('Error whilst stopping web: %s', e)
def configure(self, copyold, prestartfile):
def samecontents(a, b):
# os.path.samefile is not available on Windows
try:
return os.path.samefile(a, b)
except AttributeError:
with open(a) as fa:
with open(b) as fb:
return fa.read() == fb.read()
target = self.dir / "etc" / "grid" / "config.xml"
if copyold:
from path import path
old_grid = path(self.args.sym) / "etc" / "grid"
old_cfg = old_grid / "config.xml"
log.info("Copying old configuration from %s", old_cfg)
if not old_cfg.exists():
raise Stop(40, 'config.xml not found')
if target.exists() and samecontents(old_cfg, target):
# This likely is caused by the symlink being
# created early on an initial install.
pass
else:
old_cfg.copy(target)
else:
if target.exists():
log.info('Deleting configuration file %s', target)
target.remove()
if prestartfile:
for f in prestartfile:
log.info('Loading prestart file %s', f)
ftype, fpath = fileutils.get_as_local_path(f, 'backup')
if ftype != 'file':
raise Stop(50, 'Expected file, found: %s %s' % (
ftype, f))
self.run(['load', fpath])
def archive_logs(self):
if self.args.archivelogs:
logdir = os.path.join(self.args.sym, 'var', 'log')
archive = self.args.archivelogs
log.info('Archiving logs to %s', archive)
fileutils.zip(archive, logdir, os.path.join(self.args.sym, 'var'))
return archive
def directories(self):
if self.samedir(self.dir, self.args.sym):
log.warn("Upgraded server was the same, not deleting")
return
try:
target = self.readlink(self.args.sym)
targetzip = target + '.zip'
except IOError:
log.error('Unable to get symlink target: %s', self.args.sym)
target = None
targetzip = None
if self.args.delete_old and target:
try:
log.info("Deleting %s", target)
shutil.rmtree(target)
except OSError as e:
log.error("Failed to delete %s: %s", target, e)
if not self.args.keep_old_zip and targetzip:
try:
log.info("Deleting %s", targetzip)
os.unlink(targetzip)
except OSError as e:
log.error("Failed to delete %s: %s", targetzip, e)
self.rmlink(self.args.sym)
self.symlink(self.dir, self.args.sym)
def handle_database(self):
"""
Handle database initialisation and upgrade, taking into account
command line arguments
"""
# TODO: When initdb and upgradedb are dropped we can just test
# managedb, but for backwards compatibility we need to support
# initdb without upgradedb and vice-versa
if self.args.initdb or self.args.upgradedb:
db = DbAdmin(self.dir, None, self.args, self.external)
status = db.check()
log.debug('OMERO database upgrade status: %s', status)
else:
log.warn('OMERO database check disabled')
return DB_INIT_NEEDED
if status == DB_INIT_NEEDED:
if self.args.initdb:
log.debug('Initialising OMERO database')
db.init()
else:
log.error('OMERO database not found')
raise Stop(DB_INIT_NEEDED,
'Install/Upgrade failed: OMERO database not found')
elif status == DB_UPGRADE_NEEDED:
log.warn('OMERO database exists but is out of date')
if self.args.upgradedb:
log.debug('Upgrading OMERO database')
db.upgrade()
else:
raise Stop(
DB_UPGRADE_NEEDED,
'Pass --managedb or upgrade your OMERO database manually')
else:
assert status == DB_UPTODATE
return status
def start(self):
if self.args.no_start:
log.debug('Not starting OMERO')
return
self.run("admin start")
if not self.args.no_web:
log.info("Starting web")
self.startweb()
def run(self, command):
"""
Runs a command as if from the command-line
without the need for using popen or subprocess
"""
if isinstance(command, basestring):
command = command.split()
else:
command = list(command)
self.external.omero_cli(command)
def bin(self, command):
"""
Runs the omero command-line client with an array of arguments using the
old environment
"""
if isinstance(command, basestring):
command = command.split()
self.external.omero_bin(command)
def symlink_check_and_set(self):
"""
The default symlink was changed from OMERO-CURRENT to OMERO.server.
If `--sym` was not specified and OMERO-CURRENT exists in the current
directory stop and warn.
"""
if self.args.sym == '':
if os.path.exists('OMERO-CURRENT'):
log.error('Deprecated OMERO-CURRENT found but --sym not set')
raise Stop(
30, 'The default for --sym has changed to OMERO.server '
'but the current directory contains OMERO-CURRENT. '
'Either remove OMERO-CURRENT or explicity pass --sym.')
if self.args.sym in ('', 'auto'):
self.args.sym = 'OMERO.server'
class Install(object):
def __init__(self, cmd, args):
self.args, newinstall = self._handle_args(cmd, args)
log.info("%s: %s", self.__class__.__name__, cmd)
log.debug("Current directory: %s", os.getcwd())
self.symlink_check_and_set()
if newinstall is None:
# Automatically install or upgrade
newinstall = not os.path.exists(args.sym)
elif newinstall is False:
if not os.path.exists(args.sym):
raise Stop(30, 'Symlink is missing: %s' % args.sym)
elif newinstall is True:
if os.path.exists(args.sym):
raise Stop(30, 'Symlink already exists: %s' % args.sym)
else:
assert False
server_dir = self.get_server_dir()
if newinstall:
# Create a symlink to simplify the rest of the logic-
# just need to check if OLD == NEW
self.symlink(server_dir, args.sym)
log.info("Installing %s (%s)...", server_dir, args.sym)
else:
log.info("Upgrading %s (%s)...", server_dir, args.sym)
self.external = External(server_dir)
self.external.setup_omero_cli()
if not newinstall:
self.external.setup_previous_omero_env(args.sym, args.savevarsfile)
# Need lib/python set above
import path
self.dir = path.path(server_dir)
if not newinstall:
self.stop()
self.archive_logs()
copyold = not newinstall and not args.ignoreconfig
self.configure(copyold, args.prestartfile)
self.directories()
self.handle_database()
self.external.save_env_vars(args.savevarsfile, args.savevars.split())
self.start()
def _handle_args(self, cmd, args):
"""
We need to support deprecated behaviour for now which makes this
quite complicated
Current behaviour:
- install: Installs a new server, existing server causes an error
- install --upgrade: Installs or upgrades a server
- install --managedb: Automatically initialise or upgrade the db
Deprecated:
- install --upgradedb --initdb: Replaced by install --managedb
- install --upgradedb: upgrade the db, must exist
- install --initdb: initialise the db
- upgrade: Upgrades a server, must already exist
- upgrade --upgradedb: Automatically upgrade the db
returns:
- Modified args object, flag to indicate new/existing/auto install
"""
if cmd == 'install':
if args.upgrade:
# Current behaviour: install or upgrade
if args.initdb or args.upgradedb:
raise Stop(10, ('Deprecated --initdb --upgradedb flags '
'are incompatible with --upgrade'))
newinstall = None
else:
# Current behaviour: Server must not exist
newinstall = True
if args.managedb:
# Current behaviour
if args.initdb or args.upgradedb:
raise Stop(10, ('Deprecated --initdb --upgradedb flags '
'are incompatible with --managedb'))
args.initdb = True
args.upgradedb = True
else:
if args.initdb or args.upgradedb:
log.warn('--initdb and --upgradedb are deprecated, '
'use --managedb')
elif cmd == 'upgrade':
# Deprecated behaviour
log.warn(
'"omero upgrade" is deprecated, use "omego install --upgrade"')
cmd = 'install'
args.upgrade = True
# Deprecated behaviour: Server must exist
newinstall = False
else:
raise Exception('Unexpected command: %s' % cmd)
return args, newinstall
def get_server_dir(self):
"""
Either downloads and/or unzips the server if necessary
return: the directory of the unzipped server
"""
if not self.args.server:
if self.args.skipunzip:
raise Stop(0, 'Unzip disabled, exiting')
log.info('Downloading server')
# The downloader automatically symlinks the server, however if
# we are upgrading we want to delay the symlink swap, so this
# overrides args.sym
# TODO: Find a nicer way to do this?
artifact_args = copy.copy(self.args)
artifact_args.sym = ''
artifacts = Artifacts(artifact_args)
server = artifacts.download('server')
else:
progress = 0
if self.args.verbose:
progress = 20
ptype, server = fileutils.get_as_local_path(
self.args.server,
self.args.overwrite,
progress=progress,
httpuser=self.args.httpuser,
httppassword=self.args.httppassword)
if ptype == 'file':
if self.args.skipunzip:
raise Stop(0, 'Unzip disabled, exiting')
log.info('Unzipping %s', server)
server = fileutils.unzip(server,
match_dir=True,
destdir=self.args.unzipdir)
log.debug('Server directory: %s', server)
return server
def stop(self):
try:
log.info("Stopping server")
self.bin("admin status --nodeonly")
self.bin("admin stop")
except Exception as e:
log.error('Error whilst stopping server: %s', e)
if not self.args.no_web:
try:
log.info("Stopping web")
self.stopweb()
except Exception as e:
log.error('Error whilst stopping web: %s', e)
def configure(self, copyold, prestartfile):
def samecontents(a, b):
# os.path.samefile is not available on Windows
try:
return os.path.samefile(a, b)
except AttributeError:
with open(a) as fa:
with open(b) as fb:
return fa.read() == fb.read()
target = self.dir / "etc" / "grid" / "config.xml"
if copyold:
from path import path
old_grid = path(self.args.sym) / "etc" / "grid"
old_cfg = old_grid / "config.xml"
log.info("Copying old configuration from %s", old_cfg)
if not old_cfg.exists():
raise Stop(40, 'config.xml not found')
if target.exists() and samecontents(old_cfg, target):
# This likely is caused by the symlink being
# created early on an initial install.
pass
else:
old_cfg.copy(target)
else:
if target.exists():
log.info('Deleting configuration file %s', target)
target.remove()
if prestartfile:
for f in prestartfile:
log.info('Loading prestart file %s', f)
ftype, fpath = fileutils.get_as_local_path(f, 'backup')
if ftype != 'file':
raise Stop(50, 'Expected file, found: %s %s' % (ftype, f))
self.run(['load', fpath])
def archive_logs(self):
if self.args.archivelogs:
logdir = os.path.join(self.args.sym, 'var', 'log')
archive = self.args.archivelogs
log.info('Archiving logs to %s', archive)
fileutils.zip(archive, logdir, os.path.join(self.args.sym, 'var'))
return archive
def directories(self):
if self.samedir(self.dir, self.args.sym):
log.warn("Upgraded server was the same, not deleting")
return
try:
target = self.readlink(self.args.sym)
targetzip = target + '.zip'
except IOError:
log.error('Unable to get symlink target: %s', self.args.sym)
target = None
targetzip = None
if self.args.delete_old and target:
try:
log.info("Deleting %s", target)
shutil.rmtree(target)
except OSError as e:
log.error("Failed to delete %s: %s", target, e)
if not self.args.keep_old_zip and targetzip:
try:
log.info("Deleting %s", targetzip)
os.unlink(targetzip)
except OSError as e:
log.error("Failed to delete %s: %s", targetzip, e)
self.rmlink(self.args.sym)
self.symlink(self.dir, self.args.sym)
def handle_database(self):
"""
Handle database initialisation and upgrade, taking into account
command line arguments
"""
# TODO: When initdb and upgradedb are dropped we can just test
# managedb, but for backwards compatibility we need to support
# initdb without upgradedb and vice-versa
if self.args.initdb or self.args.upgradedb:
db = DbAdmin(self.dir, None, self.args, self.external)
status = db.check()
log.debug('OMERO database upgrade status: %s', status)
else:
log.warn('OMERO database check disabled')
return DB_INIT_NEEDED
if status == DB_INIT_NEEDED:
if self.args.initdb:
log.debug('Initialising OMERO database')
db.init()
else:
log.error('OMERO database not found')
raise Stop(DB_INIT_NEEDED,
'Install/Upgrade failed: OMERO database not found')
elif status == DB_UPGRADE_NEEDED:
log.warn('OMERO database exists but is out of date')
if self.args.upgradedb:
log.debug('Upgrading OMERO database')
db.upgrade()
else:
raise Stop(
DB_UPGRADE_NEEDED,
'Pass --managedb or upgrade your OMERO database manually')
else:
assert status == DB_UPTODATE
return status
def start(self):
if self.args.no_start:
log.debug('Not starting OMERO')
return
self.run("admin start")
if not self.args.no_web:
log.info("Starting web")
self.startweb()
def run(self, command):
"""
Runs a command as if from the command-line
without the need for using popen or subprocess
"""
if isinstance(command, basestring):
command = command.split()
else:
command = list(command)
self.external.omero_cli(command)
def bin(self, command):
"""
Runs the omero command-line client with an array of arguments using the
old environment
"""
if isinstance(command, basestring):
command = command.split()
self.external.omero_bin(command)
def symlink_check_and_set(self):
"""
The default symlink was changed from OMERO-CURRENT to OMERO.server.
If `--sym` was not specified and OMERO-CURRENT exists in the current
directory stop and warn.
"""
if self.args.sym == '':
if os.path.exists('OMERO-CURRENT'):
log.error('Deprecated OMERO-CURRENT found but --sym not set')
raise Stop(
30, 'The default for --sym has changed to OMERO.server '
'but the current directory contains OMERO-CURRENT. '
'Either remove OMERO-CURRENT or explicity pass --sym.')
if self.args.sym in ('', 'auto'):
self.args.sym = 'OMERO.server'