Esempio n. 1
0
    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()
Esempio n. 2
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    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()
Esempio n. 3
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    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)
Esempio n. 4
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    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)
Esempio n. 5
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    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
Esempio n. 6
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    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
Esempio n. 7
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    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
Esempio n. 8
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    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)
Esempio n. 9
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    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
Esempio n. 10
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    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)