def reindex(self, args, config):
self.check_access(config=config)
import omero.java
server_dir = self.ctx.dir / "lib" / "server"
log4j = "-Dlog4j.configuration=log4j-cli.properties"
classpath = [file.abspath() for file in server_dir.files("*.jar")]
xargs = [log4j, "-Xmx1024M", "-cp", os.pathsep.join(classpath)]
cfg = config.as_map()
config.close() # Early close. See #9800
for x in ("name", "user", "host", "port"):
# NOT passing password on command-line
k = "omero.db.%s" % x
if k in cfg:
v = cfg[k]
xargs.append("-D%s=%s" % (k, v))
if "omero.data.dir" in cfg:
xargs.append("-Domero.data.dir=%s" % cfg["omero.data.dir"])
for k, v in cfg.items():
if k.startswith("omero.search"):
xargs.append("-D%s=%s" % (k, cfg[k]))
cmd = ["ome.services.fulltext.Main"]
if args.full:
cmd.append("full")
elif args.events:
cmd.append("events")
elif getattr(args, "class"):
cmd.append("reindex")
cmd.extend(getattr(args, "class"))
else:
self.ctx.die(502, "No valid action: %s" % args)
debug = False
if getattr(args, "jdwp"):
debug = True
self.ctx.dbg("Launching Java: %s, debug=%s, xargs=%s" %
(cmd, debug, xargs))
p = omero.java.popen(
cmd,
debug=debug,
xargs=xargs,
stdout=sys.stdout,
stderr=sys.stderr) # FIXME. Shouldn't use std{out,err}
self.ctx.rv = p.wait()
def reindex(self, args, config):
self.check_access(config=config)
import omero.java
server_dir = self.ctx.dir / "lib" / "server"
log_config_file = self.ctx.dir / "etc" / "logback-indexing-cli.xml"
logback = "-Dlogback.configurationFile=%s" % log_config_file
classpath = [file.abspath() for file in server_dir.files("*.jar")]
xargs = [logback, "-Xmx1024M", "-cp", os.pathsep.join(classpath)]
cfg = config.as_map()
config.close() # Early close. See #9800
for x in ("name", "user", "host", "port"):
# NOT passing password on command-line
k = "omero.db.%s" % x
if k in cfg:
v = cfg[k]
xargs.append("-D%s=%s" % (k, v))
if "omero.data.dir" in cfg:
xargs.append("-Domero.data.dir=%s" % cfg["omero.data.dir"])
for k, v in cfg.items():
if k.startswith("omero.search"):
xargs.append("-D%s=%s" % (k, cfg[k]))
cmd = ["ome.services.fulltext.Main"]
if args.full:
cmd.append("full")
elif args.events:
cmd.append("events")
elif getattr(args, "class"):
cmd.append("reindex")
cmd.extend(getattr(args, "class"))
else:
self.ctx.die(502, "No valid action: %s" % args)
debug = False
if getattr(args, "jdwp"):
debug = True
self.ctx.dbg(
"Launching Java: %s, debug=%s, xargs=%s" % (cmd, debug, xargs))
p = omero.java.popen(
cmd, debug=debug, xargs=xargs, stdout=sys.stdout,
stderr=sys.stderr) # FIXME. Shouldn't use std{out,err}
self.ctx.rv = p.wait()
def check_access(self, mask=os.R_OK | os.W_OK, config=None):
"""Check that 'var' is accessible by the current user."""
var = self.ctx.dir / 'var'
if not os.path.exists(var):
print "Creating directory %s" % var
os.makedirs(var, 0700)
else:
self.can_access(var, mask)
if config is not None:
omero_data_dir = '/OMERO'
config = config.as_map()
try:
omero_data_dir = config['omero.data.dir']
except KeyError:
pass
self.can_access(omero_data_dir)
for p in os.listdir(var):
subpath = os.path.join(var, p)
if os.path.isdir(subpath):
self.can_access(subpath, mask)
def check_access(self, mask=os.R_OK|os.W_OK, config=None):
"""Check that 'var' is accessible by the current user."""
var = self.ctx.dir / 'var'
if not os.path.exists(var):
print "Creating directory %s" % var
os.makedirs(var, 0700)
else:
self.can_access(var, mask)
if config is not None:
omero_data_dir = '/OMERO'
config = config.as_map()
try:
omero_data_dir = config['omero.data.dir']
except KeyError:
pass
self.can_access(omero_data_dir)
for p in os.listdir(var):
subpath = os.path.join(var, p)
if os.path.isdir(subpath):
self.can_access(subpath, mask)
def diagnostics(self, args, config):
self.check_access()
config = config.as_map()
omero_data_dir = '/OMERO'
try:
omero_data_dir = config['omero.data.dir']
except KeyError:
pass
self.ctx.out("""
%s
OMERO Diagnostics %s
%s
""" % ("=" * 80, VERSION, "=" * 80))
def sz_str(sz):
for x in ["KB", "MB", "GB"]:
sz /= 1000
if sz < 1000:
break
sz = "%.1f %s" % (sz, x)
return sz
def item(cat, msg):
cat = cat + ":"
cat = "%-12s" % cat
self.ctx.out(cat, False)
msg = "%-30s " % msg
self.ctx.out(msg, False)
def exists(p):
if p.isdir():
if not p.exists():
self.ctx.out("doesn't exist")
else:
self.ctx.out("exists")
else:
if not p.exists():
self.ctx.out("n/a")
else:
warn = 0
err = 0
for l in p.lines():
if l.find("ERROR") >= 0:
err += 1
elif l.find("WARN") >= 0:
warn += 1
msg = ""
if warn or err:
msg = " errors=%-4s warnings=%-4s" % (err, warn)
self.ctx.out("%-12s %s" % (sz_str(p.size), msg))
def version(cmd):
"""
Returns a true response only
if a valid version was found.
"""
item("Commands", "%s" % " ".join(cmd))
try:
p = self.ctx.popen(cmd)
except OSError:
self.ctx.err("not found")
return False
rv = p.wait()
io = p.communicate()
try:
v = io[0].split()
v.extend(io[1].split())
v = "".join(v)
m = re.match("^\D*(\d[.\d]+\d)\D?.*$", v)
v = "%-10s" % m.group(1)
self.ctx.out(v, False)
try:
where = whichall(cmd[0])
sz = len(where)
if sz == 0:
where = "unknown"
else:
where = where[0]
if sz > 1:
where += " -- %s others" % sz
except:
where = "unknown"
self.ctx.out("(%s)" % where)
return True
except exceptions.Exception, e:
self.ctx.err("error:%s" % e)
return False
def diagnostics(self, args, config):
self.check_access()
config = config.as_map()
omero_data_dir = '/OMERO'
try:
omero_data_dir = config['omero.data.dir']
except KeyError:
pass
self.ctx.out("""
%s
OMERO Diagnostics %s
%s
""" % ("="*80, VERSION, "="*80))
def sz_str(sz):
for x in ["KB", "MB", "GB"]:
sz /= 1000
if sz < 1000:
break
sz = "%.1f %s" % (sz, x)
return sz
def item(cat, msg):
cat = cat + ":"
cat = "%-12s" % cat
self.ctx.out(cat, False)
msg = "%-30s " % msg
self.ctx.out(msg, False)
def exists(p):
if p.isdir():
if not p.exists():
self.ctx.out("doesn't exist")
else:
self.ctx.out("exists")
else:
if not p.exists():
self.ctx.out("n/a")
else:
warn = 0
err = 0
for l in p.lines():
if l.find("ERROR") >= 0:
err += 1
elif l.find("WARN") >= 0:
warn += 1
msg = ""
if warn or err:
msg = " errors=%-4s warnings=%-4s" % (err, warn)
self.ctx.out("%-12s %s" % (sz_str(p.size), msg))
def version(cmd):
"""
Returns a true response only
if a valid version was found.
"""
item("Commands","%s" % " ".join(cmd))
try:
p = self.ctx.popen(cmd)
except OSError:
self.ctx.err("not found")
return False
rv = p.wait()
io = p.communicate()
try:
v = io[0].split()
v.extend(io[1].split())
v = "".join(v)
m = re.match("^\D*(\d[.\d]+\d)\D?.*$", v)
v = "%-10s" % m.group(1)
self.ctx.out(v, False)
try:
where = whichall(cmd[0])
sz = len(where)
if sz == 0:
where = "unknown"
else:
where = where[0]
if sz > 1:
where += " -- %s others" % sz
except:
where = "unknown"
self.ctx.out("(%s)" % where)
return True
except exceptions.Exception, e:
self.ctx.err("error:%s" % e)
return False
def diagnostics(self, args, config):
self.check_access()
config = config.as_map()
omero_data_dir = '/OMERO'
try:
omero_data_dir = config['omero.data.dir']
except KeyError:
pass
from omero.util.temp_files import gettempdir
# gettempdir returns ~/omero/tmp/omero_%NAME/%PROCESS
# To find something more generally useful for calculating
# size, we go up two directories
omero_temp_dir = gettempdir()
omero_temp_dir = os.path.abspath(
os.path.join(omero_temp_dir, os.path.pardir, os.path.pardir))
self.ctx.out("""
%s
OMERO Diagnostics %s
%s
""" % ("="*80, VERSION, "="*80))
def sz_str(sz):
for x in ["KB", "MB", "GB"]:
sz /= 1000
if sz < 1000:
break
sz = "%.1f %s" % (sz, x)
return sz
def item(cat, msg):
cat = cat + ":"
cat = "%-12s" % cat
self.ctx.out(cat, False)
msg = "%-30s " % msg
self.ctx.out(msg, False)
def exists(p):
if p.isdir():
if not p.exists():
self.ctx.out("doesn't exist")
else:
self.ctx.out("exists")
else:
if not p.exists():
self.ctx.out("n/a")
else:
warn = 0
err = 0
for l in p.lines():
# ensure errors/warnings search is case-insensitive
lcl = l.lower()
found_err = lcl.find("error") >= 0
found_warn = lcl.find("warn") >= 0
if found_err:
err += 1
elif found_warn:
warn += 1
msg = ""
if warn or err:
msg = " errors=%-4s warnings=%-4s" % (err, warn)
self.ctx.out("%-12s %s" % (sz_str(p.size), msg))
def version(cmd):
"""
Returns a true response only
if a valid version was found.
"""
item("Commands", "%s" % " ".join(cmd))
try:
p = self.ctx.popen(cmd)
except OSError:
self.ctx.err("not found")
return False
p.wait()
io = p.communicate()
try:
v = io[0].split()
v.extend(io[1].split())
v = "".join(v)
m = re.match("^\D*(\d[.\d]+\d)\D?.*$", v)
v = "%-10s" % m.group(1)
self.ctx.out(v, False)
try:
where = whichall(cmd[0])
sz = len(where)
if sz == 0:
where = "unknown"
else:
where = where[0]
if sz > 1:
where += " -- %s others" % sz
except:
where = "unknown"
self.ctx.out("(%s)" % where)
return True
except Exception, e:
self.ctx.err("error:%s" % e)
return False
def startasync(self, args, config):
"""
First checks for a valid installation, then checks the grid,
then registers the action: "node HOST start"
"""
self.check_access(config=config)
self.checkice()
self.check_node(args)
if self._isWindows():
self.checkwindows(args)
if 0 == self.status(args, node_only=True):
self.ctx.die(876, "Server already running")
self._initDir()
# Do a check to see if we've started before.
self._regdata()
self.check([])
user = args.user
pasw = args.password
descript = self._descript(args)
if self._isWindows():
svc_name = "OMERO.%s" % args.node
output = self._query_service(svc_name)
# Now check if the server exists
if 0 <= output.find("DOESNOTEXIST"):
binpath = """icegridnode.exe "%s" --deploy "%s" --service\
%s""" % (self._icecfg(), descript, svc_name)
# By default: "NT Authority\Local System"
if not user:
try:
user = config.as_map()["omero.windows.user"]
except KeyError:
user = None
if user is not None and len(user) > 0:
if "\\" not in user:
computername = win32api.GetComputerName()
user = "******".join([computername, user])
try:
# See #9967, code based on http://mail.python.org/\
# pipermail/python-win32/2010-October/010791.html
self.ctx.out("Granting SeServiceLogonRight to service"
" user \"%s\"" % user)
policy_handle = win32security.LsaOpenPolicy(
None, win32security.POLICY_ALL_ACCESS)
sid_obj, domain, tmp = \
win32security.LookupAccountName(None, user)
win32security.LsaAddAccountRights(
policy_handle, sid_obj, ('SeServiceLogonRight',))
win32security.LsaClose(policy_handle)
except pywintypes.error, details:
self.ctx.die(200, "Error during service user set up:"
" (%s) %s" % (details[0], details[2]))
if not pasw:
try:
pasw = config.as_map()["omero.windows.pass"]
except KeyError:
pasw = self._ask_for_password(
" for service user \"%s\"" % user)
else:
pasw = None
hscm = win32service.OpenSCManager(
None, None, win32service.SC_MANAGER_ALL_ACCESS)
try:
self.ctx.out("Installing %s Windows service." % svc_name)
hs = win32service.CreateService(
hscm, svc_name, svc_name,
win32service.SERVICE_ALL_ACCESS,
win32service.SERVICE_WIN32_OWN_PROCESS,
win32service.SERVICE_AUTO_START,
win32service.SERVICE_ERROR_NORMAL, binpath, None, 0,
None, user, pasw)
self.ctx.out("Successfully installed %s Windows service."
% svc_name)
win32service.CloseServiceHandle(hs)
finally:
win32service.CloseServiceHandle(hscm)
# Then check if the server is already running
if 0 <= output.find("RUNNING"):
self.ctx.die(201, "%s is already running. Use stop first"
% svc_name)
# Finally, try to start the service - delete if startup fails
hscm = win32service.OpenSCManager(
None, None, win32service.SC_MANAGER_ALL_ACCESS)
try:
try:
hs = win32service.OpenService(
hscm, svc_name, win32service.SC_MANAGER_ALL_ACCESS)
win32service.StartService(hs, None)
self.ctx.out("Starting %s Windows service." % svc_name)
except pywintypes.error, details:
self.ctx.out("%s service startup failed: (%s) %s"
% (svc_name, details[0], details[2]))
win32service.DeleteService(hs)
self.ctx.die(202, "%s service deleted." % svc_name)
finally:
win32service.CloseServiceHandle(hs)
win32service.CloseServiceHandle(hscm)
def diagnostics(self, args, config):
self.check_access()
config = config.as_map()
omero_data_dir = '/OMERO'
try:
omero_data_dir = config['omero.data.dir']
except KeyError:
pass
from omero.util.temp_files import gettempdir
# gettempdir returns ~/omero/tmp/omero_%NAME/%PROCESS
# To find something more generally useful for calculating
# size, we go up two directories
omero_temp_dir = gettempdir()
omero_temp_dir = os.path.abspath(
os.path.join(omero_temp_dir, os.path.pardir, os.path.pardir))
self.ctx.out("""
%s
OMERO Diagnostics %s
%s
""" % ("=" * 80, VERSION, "=" * 80))
def sz_str(sz):
for x in ["KB", "MB", "GB"]:
sz /= 1000
if sz < 1000:
break
sz = "%.1f %s" % (sz, x)
return sz
def item(cat, msg):
cat = cat + ":"
cat = "%-12s" % cat
self.ctx.out(cat, False)
msg = "%-30s " % msg
self.ctx.out(msg, False)
def exists(p):
if p.isdir():
if not p.exists():
self.ctx.out("doesn't exist")
else:
self.ctx.out("exists")
else:
if not p.exists():
self.ctx.out("n/a")
else:
warn = 0
err = 0
for l in p.lines():
# ensure errors/warnings search is case-insensitive
lcl = l.lower()
found_err = lcl.find("error") >= 0
found_warn = lcl.find("warn") >= 0
if found_err:
err += 1
elif found_warn:
warn += 1
msg = ""
if warn or err:
msg = " errors=%-4s warnings=%-4s" % (err, warn)
self.ctx.out("%-12s %s" % (sz_str(p.size), msg))
def version(cmd):
"""
Returns a true response only
if a valid version was found.
"""
item("Commands", "%s" % " ".join(cmd))
try:
p = self.ctx.popen(cmd)
except OSError:
self.ctx.err("not found")
return False
p.wait()
io = p.communicate()
try:
v = io[0].split()
v.extend(io[1].split())
v = "".join(v)
m = re.match("^\D*(\d[.\d]+\d)\D?.*$", v)
v = "%-10s" % m.group(1)
self.ctx.out(v, False)
try:
where = whichall(cmd[0])
sz = len(where)
if sz == 0:
where = "unknown"
else:
where = where[0]
if sz > 1:
where += " -- %s others" % sz
except:
where = "unknown"
self.ctx.out("(%s)" % where)
return True
except Exception, e:
self.ctx.err("error:%s" % e)
return False
def startasync(self, args, config):
"""
First checks for a valid installation, then checks the grid,
then registers the action: "node HOST start"
"""
self.check_access(config=config)
self.checkice()
self.check_node(args)
if self._isWindows():
self.checkwindows(args)
if 0 == self.status(args, node_only=True):
self.ctx.die(876, "Server already running")
self._initDir()
# Do a check to see if we've started before.
self._regdata()
self.check([])
user = args.user
pasw = args.password
descript = self._descript(args)
if self._isWindows():
svc_name = "OMERO.%s" % args.node
output = self._query_service(svc_name)
# Now check if the server exists
if 0 <= output.find("DOESNOTEXIST"):
binpath = """icegridnode.exe "%s" --deploy "%s" --service\
%s""" % (self._icecfg(), descript, svc_name)
# By default: "NT Authority\Local System"
if not user:
try:
user = config.as_map()["omero.windows.user"]
except KeyError:
user = None
if user is not None and len(user) > 0:
if not "\\" in user:
computername = win32api.GetComputerName()
user = "******".join([computername, user])
try:
# See #9967, code based on http://mail.python.org/\
# pipermail/python-win32/2010-October/010791.html
self.ctx.out("Granting SeServiceLogonRight to service"
" user \"%s\"" % user)
policy_handle = win32security.LsaOpenPolicy(
None, win32security.POLICY_ALL_ACCESS)
sid_obj, domain, tmp = \
win32security.LookupAccountName(None, user)
win32security.LsaAddAccountRights(
policy_handle, sid_obj, ('SeServiceLogonRight', ))
win32security.LsaClose(policy_handle)
except pywintypes.error, details:
self.ctx.die(
200, "Error during service user set up:"
" (%s) %s" % (details[0], details[2]))
if not pasw:
try:
pasw = config.as_map()["omero.windows.pass"]
except KeyError:
pasw = self._ask_for_password(
" for service user \"%s\"" % user)
else:
pasw = None
hscm = win32service.OpenSCManager(
None, None, win32service.SC_MANAGER_ALL_ACCESS)
try:
self.ctx.out("Installing %s Windows service." % svc_name)
hs = win32service.CreateService(
hscm, svc_name, svc_name,
win32service.SERVICE_ALL_ACCESS,
win32service.SERVICE_WIN32_OWN_PROCESS,
win32service.SERVICE_AUTO_START,
win32service.SERVICE_ERROR_NORMAL, binpath, None, 0,
None, user, pasw)
self.ctx.out("Successfully installed %s Windows service." %
svc_name)
win32service.CloseServiceHandle(hs)
finally:
win32service.CloseServiceHandle(hscm)
# Then check if the server is already running
if 0 <= output.find("RUNNING"):
self.ctx.die(
201, "%s is already running. Use stop first" % svc_name)
# Finally, try to start the service - delete if startup fails
hscm = win32service.OpenSCManager(
None, None, win32service.SC_MANAGER_ALL_ACCESS)
try:
try:
hs = win32service.OpenService(
hscm, svc_name, win32service.SC_MANAGER_ALL_ACCESS)
win32service.StartService(hs, None)
self.ctx.out("Starting %s Windows service." % svc_name)
except pywintypes.error, details:
self.ctx.out("%s service startup failed: (%s) %s" %
(svc_name, details[0], details[2]))
win32service.DeleteService(hs)
self.ctx.die(202, "%s service deleted." % svc_name)
finally:
win32service.CloseServiceHandle(hs)
win32service.CloseServiceHandle(hscm)