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#!/usr/bin/env python
"""GNUmed schema installation.
This script bootstraps a GNUmed database system.
This will set up databases, tables, groups, permissions and
possibly users. Most of this will be handled via SQL
scripts, not directly in the bootstrapper itself.
There's a special user called "gm-dbo" who owns all the
database objects.
For all this to work you must be able to access the database
server as the standard "postgres" superuser.
This script does NOT set up user specific configuration options.
All definitions are loaded from a config file.
Please consult the User Manual in the GNUmed CVS for
further details.
--quiet
--log-file=
--conf-file=
"""
#==================================================================
# TODO
# - perhaps create PGPASSFILE
# - warn if empty password
# - verify that pre-created database is owned by "gm-dbo"
# - rework under assumption that there is only one DB
#==================================================================
__author__ = "Karsten.Hilbert@gmx.net"
__license__ = "GPL"
# standard library
import sys, string, os.path, fileinput, os, time, getpass, glob, re as regex, tempfile, logging
# adjust Python path
local_python_base_dir = os.path.dirname (
os.path.abspath(os.path.join(sys.argv[0], '..', '..'))
)
# does the GNUmed import path exist at all, physically ?
# (*broken* links are reported as False)
if not os.path.exists(os.path.join(local_python_base_dir, 'Gnumed')):
real_dir = os.path.join(local_python_base_dir, 'server')
is_useful_import_dir = (
os.path.exists(os.path.join(real_dir, 'pycommon'))
and
os.path.exists(os.path.join(real_dir, '__init__.py'))
)
if not is_useful_import_dir:
real_dir = os.path.join(local_python_base_dir, 'client') # CVS tree
link_name = os.path.join(local_python_base_dir, 'Gnumed')
print "Creating module import symlink ..."
print ' real dir:', real_dir
print ' link:', link_name
os.symlink(real_dir, link_name)
print "Adjusting PYTHONPATH ..."
sys.path.insert(0, local_python_base_dir)
# GNUmed imports
try:
from Gnumed.pycommon import gmLog2
except ImportError:
print """Please make sure the GNUmed Python modules are in the Python path !"""
raise
from Gnumed.pycommon import gmCfg2, gmPsql, gmPG2, gmTools, gmI18N
from Gnumed.pycommon.gmExceptions import ConstructorError
# local imports
import gmAuditSchemaGenerator
aud_gen = gmAuditSchemaGenerator
import gmNotificationSchemaGenerator
notify_gen = gmNotificationSchemaGenerator
_log = logging.getLogger('gm.bootstrapper')
_cfg = gmCfg2.gmCfgData()
_interactive = False
_bootstrapped_servers = {}
_bootstrapped_dbs = {}
_dbowner = None
cached_host = None
cached_passwd = {}
_keep_temp_files = False
conn_ref_count = []
#==================================================================
pg_hba_sermon = """
I have found a connection to the database, but I am forbidden
to connect due to the settings in pg_hba.conf. This is a
PostgreSQL configuration file that controls who can connect
to the database.
Depending on your setup, it can be found in
/etc/postgresql/pg_hba.conf (Debian)
/usr/local/pgsql/pgdata/pg_hba.conf (FreeBSD, ?? Mac OS X)
FIXME: where do RedHat & friends put it
or whichever directory your database files are located.
For gnumed, pg_hba.conf must allow password authentication.
For deveopment systems, I suggest the following
local template1 postgres ident sameuser
local gnumed all md5
host gnumed all 127.0.0.1 255.255.255.255 md5
For production systems, a different configuration will be
required, but gnumed is not production ready.
There is also a pg_hba.conf.example in this directory.
You must then restart (or SIGHUP) your PostgreSQL server.
"""
no_server_sermon = """
I cannot find a PostgreSQL server running on this machine.
Try (as root):
/etc/init.d/postgresql start
if that fails, you can build a database from scratch:
PGDATA=some directory you can use
initdb
cp pg_hba.conf.example $PGDATA/pg_hba.conf
pg_ctl start
if none of these commands work, or you don't know what PostgreSQL
is, go to the website to download for your OS at:
http://www.postgresql.org/
On the other hand, if you have a PostgreSQL server
running somewhere strange, type hostname[:port]
below, or press RETURN to quit.
"""
superuser_sermon = """
I can't log on as the PostgreSQL database owner.
Try running this script as the system administrator (user "root")
to get the neccessary permissions.
NOTE: I expect the PostgreSQL database owner to be called "%s"
If for some reason it is not, you need to adjust my configuration
script, and run again as that user.
"""
no_clues = """
Logging on to the PostgreSQL database returned this error
%s
on %s
Please contact the GNUmed development team on gnumed-devel@gnu.org.
Make sure you include this error message in your mail.
"""
welcome_sermon = """
Welcome to the GNUmed server instllation script.
You must have a PostgreSQL server running and
administrator access.
Please select a database configuation from the list below.
"""
SQL_add_foreign_key = u"""
ALTER TABLE %(src_schema)s.%(src_tbl)s
ADD FOREIGN KEY (%(src_col)s)
REFERENCES %(target_schema)s.%(target_tbl)s(%(target_col)s)
ON UPDATE CASCADE
ON DELETE RESTRICT
;"""
SQL_sanity_check_trigger_func = u"""
DROP FUNCTION IF EXISTS clin.trf_sanity_check_enc_epi_insert() CASCADE;
create function clin.trf_sanity_check_enc_epi_insert()
returns trigger
language 'plpgsql'
as '
declare
_identity_from_encounter integer;
_identity_from_episode integer;
begin
-- sometimes .fk_episode can actually be NULL (eg. clin.substance_intake)
-- in which case we do not need to run the sanity check
if NEW.fk_episode is NULL then
return NEW;
end if;
select fk_patient into _identity_from_encounter from clin.encounter where pk = NEW.fk_encounter;
select fk_patient into _identity_from_episode from clin.encounter where pk = (
select fk_encounter from clin.episode where pk = NEW.fk_episode
);
if _identity_from_encounter <> _identity_from_episode then
raise exception ''INSERT into %.%: Sanity check failed. Encounter % patient = %. Episode % patient = %.'',
TG_TABLE_SCHEMA,
TG_TABLE_NAME,
NEW.fk_encounter,
_identity_from_encounter,
NEW.fk_episode,
_identity_from_episode
;
return NULL;
end if;
return NEW;
end;
';"""
#==================================================================
def user_exists(cursor=None, user=None):
cmd = "SELECT usename FROM pg_user WHERE usename = %(usr)s"
args = {'usr': user}
try:
cursor.execute(cmd, args)
except:
_log.exception(">>>[%s]<<< failed for user [%s]", cmd, user)
return None
res = cursor.fetchone()
if cursor.rowcount == 1:
_log.info("user [%s] exists", user)
return True
_log.info("user [%s] does not exist", user)
return None
#------------------------------------------------------------------
def db_group_exists(cursor=None, group=None):
cmd = 'SELECT groname FROM pg_group WHERE groname = %(grp)s'
args = {'grp': group}
try:
cursor.execute(cmd, args)
except:
_log.exception(">>>[%s]<<< failed for group [%s]", cmd, group)
return False
rows = cursor.fetchall()
if len(rows) > 0:
_log.info("group [%s] exists" % group)
return True
_log.info("group [%s] does not exist" % group)
return False
#------------------------------------------------------------------
def create_db_group(cursor=None, group=None):
# does this group already exist ?
if db_group_exists(cursor, group):
return True
cmd = 'create group "%s"' % group
try:
cursor.execute(cmd)
except:
_log.exception(">>>[%s]<<< failed for group [%s]", cmd, group)
return False
# paranoia is good
if not db_group_exists(cursor, group):
return False
return True
#==================================================================
def connect(host, port, db, user, passwd):
"""
This is a wrapper to the database connect function.
Will try to recover gracefully from connection errors where possible
"""
global cached_host
if len(host) == 0 or host == 'localhost':
if cached_host:
host, port = cached_host
else:
host = ''
if passwd == 'blank' or passwd is None or len(passwd) == 0:
if cached_passwd.has_key (user):
passwd = cached_passwd[user]
else:
passwd = ''
dsn = gmPG2.make_psycopg2_dsn(database=db, host=host, port=port, user=user, password=passwd)
_log.info("trying DB connection to %s on %s as %s", db, host or 'localhost', user)
try:
conn = gmPG2.get_connection(dsn=dsn, readonly=False, pooled=False, verbose=True)
except:
_log.exception(u'connection failed')
raise
cached_host = (host, port) # learn from past successes
cached_passwd[user] = passwd
conn_ref_count.append(conn)
_log.info('successfully connected')
return conn
#==================================================================
class user:
def __init__(self, anAlias = None, aPassword = None):
if anAlias is None:
raise ConstructorError, "need user alias"
self.alias = anAlias
self.group = "user %s" % self.alias
self.name = cfg_get(self.group, "name")
if self.name is None:
raise ConstructorError, "cannot get user name"
self.password = aPassword
# password not passed in, try to get it from elsewhere
if self.password is None:
# look into config file
self.password = cfg_get(self.group, "password")
# undefined or commented out:
# this means the user does not need a password
# but connects via IDENT or TRUST
if self.password is None:
_log.info('password not defined, assuming connect via IDENT/TRUST')
# defined but empty:
# this means to ask the user if interactive
elif self.password == '':
if _interactive:
print "I need the password for the database user [%s]." % self.name
self.password = getpass.getpass("Please type the password: ")
else:
_log.warning('cannot get password for database user [%s]', self.name)
raise ValueError('no password for user %s' % self.name)
return None
#==================================================================
class db_server:
def __init__(self, aSrv_alias, auth_group):
_log.info("bootstrapping server [%s]" % aSrv_alias)
global _bootstrapped_servers
if _bootstrapped_servers.has_key(aSrv_alias):
_log.info("server [%s] already bootstrapped" % aSrv_alias)
return None
self.alias = aSrv_alias
self.section = "server %s" % self.alias
self.auth_group = auth_group
self.conn = None
if not self.__bootstrap():
raise ConstructorError, "db_server.__init__(): Cannot bootstrap db server."
_bootstrapped_servers[self.alias] = self
_log.info('done bootstrapping server [%s]', aSrv_alias)
#--------------------------------------------------------------
def __bootstrap(self):
self.superuser = user(anAlias = cfg_get(self.section, "super user alias"))
# connect to server level template database
if not self.__connect_superuser_to_srv_template():
_log.error("Cannot connect to server template database.")
return None
# add users/groups
if not self.__bootstrap_db_users():
_log.error("Cannot bootstrap database users.")
return None
self.conn.close()
return True
#--------------------------------------------------------------
def __connect_superuser_to_srv_template(self):
_log.info("connecting to server template database")
# sanity checks
self.template_db = cfg_get(self.section, "template database")
if self.template_db is None:
_log.error("Need to know the template database name.")
return None
self.name = cfg_get(self.section, "name")
if self.name is None:
_log.error("Need to know the server name.")
return None
env_var = 'GM_DB_PORT'
self.port = os.getenv(env_var)
if self.port is None:
_log.info('environment variable [%s] is not set, using database port from config file' % env_var)
self.port = cfg_get(self.section, "port")
else:
_log.info('using database port [%s] from environment variable [%s]' % (self.port, env_var))
if self.port is None:
_log.error("Need to know the database server port address.")
return None
if self.conn is not None:
if self.conn.closed == 0:
self.conn.close()
self.conn = connect(self.name, self.port, self.template_db, self.superuser.name, self.superuser.password)
if self.conn is None:
_log.error('Cannot connect.')
return None
self.conn.cookie = 'db_server.__connect_superuser_to_srv_template'
# verify encoding
curs = self.conn.cursor()
curs.execute(u"select setting from pg_settings where name = 'lc_ctype'")
data = curs.fetchall()
lc_ctype = data[0][0]
_log.info('template database LC_CTYPE is [%s]', lc_ctype)
lc_ctype = lc_ctype.lower()
if lc_ctype in ['c', 'posix']:
_log.warning('while this cluster setting allows to store databases')
_log.warning('in any encoding as is it does not allow for locale')
_log.warning('sorting etc, hence it is not recommended for use')
_log.warning('(although it will, technically, work)')
elif not (lc_ctype.endswith('.utf-8') or lc_ctype.endswith('.utf8')):
_log.error('LC_CTYPE does not end in .UTF-8 or .UTF8')
curs.execute(u"show server_encoding")
data = curs.fetchall()
srv_enc = data[0][0]
_log.info('server_encoding is [%s]', srv_enc)
srv_enc = srv_enc.lower()
if not srv_enc in ['utf8', 'utf-8']:
_log.error('cluster encoding incompatible with utf8 encoded databases but')
_log.error('for GNUmed installation the cluster must accept this encoding')
_log.error('you may need to re-initdb or create a new cluster')
return None
_log.info('server encoding seems compatible despite not being reported in LC_CTYPE')
# make sure we get english messages
curs.execute(u"set lc_messages to 'C'")
curs.close()
_log.info("successfully connected to template database [%s]" % self.template_db)
return True
#--------------------------------------------------------------
# user and group related
#--------------------------------------------------------------
def __bootstrap_db_users(self):
_log.info("bootstrapping database users and groups")
# insert standard groups
if not self.__create_groups():
_log.error("Cannot create GNUmed standard groups.")
return None
# create GNUmed owner
if self.__create_dbowner() is None:
_log.error("Cannot install GNUmed database owner.")
return None
# if not _import_schema(group=self.section, schema_opt='schema', conn=self.conn):
# _log.error("Cannot import schema definition for server [%s] into database [%s]." % (self.name, self.template_db))
# return None
return True
#--------------------------------------------------------------
def __create_dbowner(self):
global _dbowner
dbowner_alias = cfg_get("GnuMed defaults", "database owner alias")
if dbowner_alias is None:
_log.error("Cannot load GNUmed database owner name from config file.")
return None
cursor = self.conn.cursor()
# does this user already exist ?
name = cfg_get('user %s' % dbowner_alias, 'name')
if user_exists(cursor, name):
cmd = (
'alter group "gm-logins" add user "%s";' # postgres
'alter group "gm-logins" add user "%s";' # gm-dbo
'alter group "%s" add user "%s";'
'alter role "%s" createdb createrole;'
) % (
self.superuser.name,
name,
self.auth_group, name,
name,
)
try:
cursor.execute(cmd)
except:
_log.error(">>>[%s]<<< failed." % cmd)
_log.exception("Cannot add GNUmed database owner [%s] to groups [gm-logins] and [%s]." % (name, self.auth_group))
cursor.close()
return False
self.conn.commit()
cursor.close()
_dbowner = user(anAlias = dbowner_alias, aPassword = 'should not matter')
return True
print_msg ((
"""The database owner [%s] will be created.
You will have to provide a new password for it
unless it is pre-defined in the configuration file.
Make sure to remember the password for later use !
""") % name)
_dbowner = user(anAlias = dbowner_alias)
cmd = 'create user "%s" with password \'%s\' createdb createrole in group "%s", "gm-logins"' % (_dbowner.name, _dbowner.password, self.auth_group)
try:
cursor.execute(cmd)
except:
_log.error(">>>[%s]<<< failed." % cmd)
_log.exception("Cannot create GNUmed database owner [%s]." % _dbowner.name)
cursor.close()
return None
# paranoia is good
if not user_exists(cursor, _dbowner.name):
cursor.close()
return None
self.conn.commit()
cursor.close()
return True
#--------------------------------------------------------------
def __create_groups(self, aSection = None):
if aSection is None:
section = "GnuMed defaults"
else:
section = aSection
groups = cfg_get(section, "groups")
if groups is None:
_log.error("Cannot load GNUmed group names from config file (section [%s])." % section)
groups = [self.auth_group]
else:
groups.append(self.auth_group)
cursor = self.conn.cursor()
for group in groups:
if not create_db_group(cursor, group):
cursor.close()
return False
self.conn.commit()
cursor.close()
return True
#==================================================================
class database:
def __init__(self, aDB_alias):
_log.info("bootstrapping database [%s]" % aDB_alias)
self.section = "database %s" % aDB_alias
# find database name
overrider = cfg_get(self.section, 'override name by')
if overrider is not None:
self.name = os.getenv(overrider)
if self.name is None:
_log.info('environment variable [%s] is not set, using database name from config file' % overrider)
self.name = cfg_get(self.section, 'name')
else:
self.name = cfg_get(self.section, 'name')
if self.name is None or str(self.name).strip() == '':
_log.error("Need to know database name.")
raise ConstructorError, "database.__init__(): Cannot bootstrap database."
# already bootstrapped ?
global _bootstrapped_dbs
if _bootstrapped_dbs.has_key(aDB_alias):
if _bootstrapped_dbs[aDB_alias].name == self.name:
_log.info("database [%s] already bootstrapped", self.name)
return None
# no, so bootstrap from scratch
_log.info('bootstrapping database [%s] alias "%s"', self.name, aDB_alias)
for db in _bootstrapped_dbs.values():
if db.conn.closed == 0:
db.conn.close()
_bootstrapped_dbs = {}
self.conn = None
self.server_alias = cfg_get(self.section, "server alias")
if self.server_alias is None:
_log.error("Server alias missing.")
raise ConstructorError, "database.__init__(): Cannot bootstrap database."
self.template_db = cfg_get(self.section, "template database")
if self.template_db is None:
_log.error("Template database name missing.")
raise ConstructorError, "database.__init__(): Cannot bootstrap database."
# make sure server is bootstrapped
db_server(self.server_alias, auth_group = self.name)
self.server = _bootstrapped_servers[self.server_alias]
if not self.__bootstrap():
raise ConstructorError, "database.__init__(): Cannot bootstrap database."
_bootstrapped_dbs[aDB_alias] = self
return None
#--------------------------------------------------------------
def __bootstrap(self):
global _dbowner
# get owner
if _dbowner is None:
_dbowner = user(anAlias = cfg_get("GnuMed defaults", "database owner alias"))
if _dbowner is None:
_log.error("Cannot load GNUmed database owner name from config file.")
return None
# get owner
self.owner = _dbowner
# connect as owner to template
if not self.__connect_superuser_to_template():
_log.error("Cannot connect to template database.")
return False
# make sure db exists
if not self.__create_db():
_log.error("Cannot create database.")
return False
# reconnect as superuser to db
if not self.__connect_superuser_to_db():
_log.error("Cannot connect to database.")
return None
# create authentication group
_log.info('creating database-specific authentication group role')
curs = self.conn.cursor()
if not create_db_group(cursor = curs, group = self.name):
curs.close()
_log.error('cannot create authentication group role')
return False
self.conn.commit()
curs.close()
# paranoia check
curs = self.conn.cursor()
if not db_group_exists(cursor = curs, group = self.name):
curs.close()
_log.error('cannot find authentication group role')
return False
curs.close()
tmp = cfg_get(self.section, 'superuser schema')
if tmp is not None:
if not _import_schema(group=self.section, schema_opt='superuser schema', conn=self.conn):
_log.error("cannot import schema definition for database [%s]" % (self.name))
return False
del tmp
# transfer users
if not self.transfer_users():
_log.error("Cannot transfer users from old to new database.")
return False
# reconnect as owner to db
if not self.__connect_owner_to_db():
_log.error("Cannot connect to database.")
return None
if not _import_schema(group=self.section, schema_opt='schema', conn=self.conn):
_log.error("cannot import schema definition for database [%s]" % (self.name))
return None
# don't close this here, the connection will
# be reused later by check_data*/import_data etc.
#self.conn.close()
return True
#--------------------------------------------------------------
def __connect_superuser_to_template(self):
if self.conn is not None:
if self.conn.closed == 0:
self.conn.close()
self.conn = connect (
self.server.name,
self.server.port,
self.template_db,
self.server.superuser.name,
self.server.superuser.password
)
self.conn.cookie = 'database.__connect_superuser_to_template'
curs = self.conn.cursor()
curs.execute(u"set lc_messages to 'C'")
curs.close()
return self.conn and 1
#--------------------------------------------------------------
def __connect_superuser_to_db(self):
if self.conn is not None:
if self.conn.closed == 0:
self.conn.close()
self.conn = connect (
self.server.name,
self.server.port,
self.name,
self.server.superuser.name,
self.server.superuser.password
)
self.conn.cookie = 'database.__connect_superuser_to_db'
curs = self.conn.cursor()
curs.execute(u'set default_transaction_read_only to off')
# we need English messages to detect errors
curs.execute(u"set lc_messages to 'C'")
curs.execute(u"alter database %s set lc_messages to 'C'" % self.name)
# we need inheritance or else things will fail miserably
curs.execute("alter database %s set sql_inheritance to on" % self.name)
# we want READ ONLY default transactions for maximum patient data safety
curs.execute("alter database %s set default_transaction_read_only to on" % self.name)
# we want checking of function bodies
curs.execute("alter database %s set check_function_bodies to on" % self.name)
curs.close()
self.conn.commit()
# we want checking of data checksums if available
# remove exception handler when 9.3 is default
curs = self.conn.cursor()
try:
curs.execute("alter database %s set ignore_checksum_failure to off" % self.name)
except:
_log.exception('PostgreSQL version < 9.3 does not support <ignore_checksum_failure>')
curs.close()
self.conn.commit()
curs = self.conn.cursor()
gmPG2._log_PG_settings(curs = curs)
curs.close()
self.conn.commit()
return self.conn and 1
#--------------------------------------------------------------
def __connect_owner_to_db(self):
# reconnect as superuser to db
if not self.__connect_superuser_to_db():
_log.error("Cannot connect to database.")
return False
self.conn.cookie = 'database.__connect_owner_to_db via database.__connect_superuser_to_db'
curs = self.conn.cursor()
cmd = "set session authorization %(usr)s"
curs.execute(cmd, {'usr': self.owner.name})
curs.close()
return self.conn and 1
#--------------------------------------------------------------
def __db_exists(self):
cmd = "BEGIN; SELECT datname FROM pg_database WHERE datname='%s'" % self.name
aCursor = self.conn.cursor()
try:
aCursor.execute(cmd)
except:
_log.exception(">>>[%s]<<< failed." % cmd)
return None
res = aCursor.fetchall()
tmp = aCursor.rowcount
aCursor.close()
if tmp == 1:
_log.info("Database [%s] exists." % self.name)
return True
_log.info("Database [%s] does not exist." % self.name)
return None
#--------------------------------------------------------------
def __create_db(self):
# verify template database hash
template_version = cfg_get(self.section, 'template version')
if template_version is None:
_log.warning('cannot check template database identity hash, no version specified')
else:
converted, version = gmTools.input2int(template_version.lstrip('v'), 0)
if not converted:
_log.error('invalid template database definition: %s', template_version)
return False
if not gmPG2.database_schema_compatible(link_obj = self.conn, version = version):
_log.error('invalid [%s] schema structure in GNUmed template database [%s]', template_version, self.template_db)
return False
# check for target database
if self.__db_exists():
drop_existing = bool(int(cfg_get(self.section, 'drop target database')))
if drop_existing:
print_msg("==> dropping pre-existing target database [%s] ..." % self.name)
_log.info('trying to drop target database')
cmd = 'drop database "%s"' % self.name
self.conn.set_isolation_level(0)
cursor = self.conn.cursor()
try:
cursor.execute(cmd)
except:
_log.exception(">>>[%s]<<< failed" % cmd)
cursor.close()
return False
cursor.close()
self.conn.commit()
else:
use_existing = bool(int(cfg_get(self.section, 'use existing target database')))
if use_existing:
# FIXME: verify that database is owned by "gm-dbo"
print_msg("==> using pre-existing *target* database [%s] ..." % self.name)
_log.info('using existing database [%s]', self.name)
return True
else:
_log.info('not using existing database [%s]', self.name)
return False
tablespace = cfg_get(self.section, 'tablespace')
if tablespace is None:
cmd = """
create database \"%s\" with
owner = \"%s\"
template = \"%s\"
encoding = 'unicode'
;""" % (self.name, self.owner.name, self.template_db)
else:
cmd = """
create database \"%s\" with
owner = \"%s\"
template = \"%s\"
encoding = 'unicode'
tablespace = '%s'
;""" % (self.name, self.owner.name, self.template_db, tablespace)
# create database
self.conn.set_isolation_level(0)
cursor = self.conn.cursor()
cursor.execute("select pg_size_pretty(pg_database_size('%s'))" % self.template_db)
size = cursor.fetchone()[0]
print_msg("==> cloning [%s] (%s) as target database [%s] ..." % (self.template_db, size, self.name))
try:
cursor.execute(cmd)
except:
_log.exception(">>>[%s]<<< failed" % cmd)
cursor.close()
return False
cursor.close()
self.conn.commit()
if not self.__db_exists():
return None
_log.info("Successfully created GNUmed database [%s]." % self.name)
return True
#--------------------------------------------------------------
def check_data_plausibility(self):
print_msg("==> checking migrated data for plausibility ...")
plausibility_queries = cfg_get(self.section, 'upgrade plausibility checks')
if plausibility_queries is None:
_log.warning('no plausibility checks defined')
print_msg(" ... skipped (no checks defined)")
return True
no_of_queries, remainder = divmod(len(plausibility_queries), 2)
if remainder != 0:
_log.error('odd number of plausibility queries defined, aborting')
print_msg(" ... failed (configuration error)")
return False
template_conn = connect (
self.server.name,
self.server.port,
self.template_db,
self.server.superuser.name,
self.server.superuser.password
)
template_conn.cookie = 'check_data_plausibility: template'
target_conn = connect (
self.server.name,
self.server.port,
self.name,
self.server.superuser.name,
self.server.superuser.password
)
target_conn.cookie = 'check_data_plausibility: target'
for idx in range(no_of_queries):
tag, old_query = plausibility_queries[idx*2].split('::::')
new_query = plausibility_queries[(idx*2) + 1]
try:
rows, idx = gmPG2.run_ro_queries (
link_obj = template_conn,
queries = [{'cmd': unicode(old_query)}]
)
old_val = rows[0][0]
except:
_log.exception('error in plausibility check [%s] (old), aborting' % tag)
print_msg(" ... failed (SQL error)")
return False
try:
rows, idx = gmPG2.run_ro_queries (
link_obj = target_conn,
queries = [{'cmd': unicode(new_query)}]
)
new_val = rows[0][0]
except:
_log.exception('error in plausibility check [%s] (new), aborting' % tag)
print_msg(" ... failed (SQL error)")
return False
if new_val != old_val:
_log.error('plausibility check [%s] failed, expected [%s], found [%s]' % (tag, old_val, new_val))
print_msg(" ... failed (check [%s])" % tag)
return False
_log.info('plausibility check [%s] succeeded' % tag)
template_conn.close()
target_conn.close()
return True
#--------------------------------------------------------------
def check_holy_auth_line(self):
holy_pattern = 'local.*samerole.*\+gm-logins'
holy_pattern_inactive = '#\s*local.*samerole.*\+gm-logins'
conn = connect (
self.server.name,
self.server.port,
self.name,
self.server.superuser.name,
self.server.superuser.password
)
conn.cookie = 'holy auth check connection'
cmd = u"select setting from pg_settings where name = 'hba_file'"
rows, idx = gmPG2.run_ro_queries(link_obj = conn, queries = [{'cmd': cmd}])
conn.close()
if len(rows) == 0:
_log.info('cannot check pg_hba.conf for authentication information - not detectable in pg_settings')
return
hba_file = rows[0][0]
_log.info('hba file: %s', hba_file)
try:
f = open(hba_file, 'r')
f.close()
except StandardError:
_log.exception('cannot check pg_hba.conf for authentication information - not readable')
return
found_holy_line = False
for line in fileinput.input(hba_file):
if regex.match(holy_pattern, line) is not None:
found_holy_line = True
_log.info('found standard GNUmed authentication directive in pg_hba.conf')
_log.info('[%s]', line)
_log.info('it may still be in the wrong place, though, so double-check if clients cannot connect')
break
if not found_holy_line:
_log.info('did not find active standard GNUmed authentication directive in pg_hba.conf')
_log.info('regex: %s' % holy_pattern)
found_holy_line_inactive = False
for line in fileinput.input(hba_file):
if regex.match(holy_pattern_inactive, line) is not None:
found_holy_line_inactive = True
_log.info('found inactive standard GNUmed authentication directive in pg_hba.conf')
_log.info('[%s]', line)
_log.info('it may still be in the wrong place, though, so double-check if clients cannot connect')
break
if not found_holy_line_inactive:
_log.info('did not find inactive standard GNUmed authentication directive in pg_hba.conf either')
_log.info('regex: %s' % holy_pattern_inactive)
_log.info('bootstrapping is likely to have succeeded but clients probably cannot connect yet')
print_msg('==> sanity checking PostgreSQL authentication settings ...')
print_msg('')
print_msg('Note that even after successfully bootstrapping the GNUmed ')
print_msg('database PostgreSQL may still need to be configured to')
print_msg('allow GNUmed clients to connect to it.')
print_msg('')
print_msg('In many standard PostgreSQL installations this amounts to')
print_msg('adding (or uncommenting) the authentication directive:')
print_msg('')
print_msg(' "local samerole +gm-logins md5"')
print_msg('')
print_msg('in the proper place of the file:')
print_msg('')
print_msg(' %s' % hba_file)
print_msg('')
print_msg('For details refer to the GNUmed documentation at:')
print_msg('')
print_msg(' http://wiki.gnumed.de/bin/view/Gnumed/ConfigurePostgreSQL')
print_msg('')
#--------------------------------------------------------------
def import_data(self):
print_msg("==> upgrading reference data sets ...")
import_scripts = cfg_get(self.section, "data import scripts")
if (import_scripts is None) or (len(import_scripts) == 0):
_log.info('skipped data import: no scripts to run')
print_msg(" ... skipped (no scripts to run)")
return True
script_base_dir = cfg_get(self.section, "script base directory")
script_base_dir = os.path.expanduser(script_base_dir)
# doesn't work on MacOSX:
#script_base_dir = os.path.abspath(os.path.expanduser(script_base_dir))
script_base_dir = os.path.normcase(os.path.normpath(os.path.join('.', script_base_dir)))
for import_script in import_scripts:
try:
script = gmTools.import_module_from_directory(module_path = script_base_dir, module_name = import_script, always_remove_path = True)
except ImportError:
print_msg(" ... failed (cannot load script [%s])" % import_script)
_log.error('cannot load data set import script [%s/%s]' % (script_base_dir, import_script))
return False
try:
script.run(conn = self.conn)
except:
print_msg(" ... failed (cannot run script [%s])" % import_script)
_log.exception('cannot run import script [%s]' % import_script)
return False
if import_script.endswith('.py'):
import_script = import_script[:-3]
import gc
try:
del sys.modules[import_script]
del script
gc.collect()
except:
_log.exception('cannot remove data import script module [%s], hoping for the best', import_script)
return True
#--------------------------------------------------------------
def verify_result_hash(self):
# verify template database hash
print_msg("==> verifying target database schema ...")
target_version = cfg_get(self.section, 'target version')
if target_version == 'devel':
print_msg(" ... skipped (devel version)")
_log.info('result schema hash: %s', gmPG2.get_schema_hash(link_obj = self.conn))
_log.warning('testing/development only, not failing due to invalid target database identity hash')
return True
converted, version = gmTools.input2int(target_version.lstrip('v'), 2)
if not converted:
_log.error('cannot convert target database version: %s', target_version)
print_msg(" ... failed (invalid target version specification)")
return False
if gmPG2.database_schema_compatible(link_obj = self.conn, version = version):
_log.info('database identity hash properly verified')
return True
_log.error('target database identity hash invalid')
print_msg(" ... failed (hash mismatch)")
return False
#--------------------------------------------------------------
def transfer_users(self):
print_msg("==> transferring users ...")
do_user_transfer = cfg_get(self.section, 'transfer users')
if do_user_transfer is None:
_log.info('user transfer not defined')
print_msg(" ... skipped (unconfigured)")
return True
do_user_transfer = int(do_user_transfer)
if not do_user_transfer:
_log.info('configured to not transfer users')
print_msg(" ... skipped (disabled)")
return True
cmd = u"select gm.transfer_users('%s'::text)" % self.template_db
try:
rows, idx = gmPG2.run_rw_queries(link_obj = self.conn, queries = [{'cmd': cmd}], end_tx = True, return_data = True)
except gmPG2.dbapi.ProgrammingError:
# maybe an old database
_log.info('problem running gm.transfer_users(), trying gm_transfer_users()')
cmd = u"select gm_transfer_users('%s'::text)" % self.template_db
rows, idx = gmPG2.run_rw_queries(link_obj = self.conn, queries = [{'cmd': cmd}], end_tx = True, return_data = True)
if rows[0][0]:
_log.info('users properly transferred from [%s] to [%s]' % (self.template_db, self.name))
return True
_log.error('error transferring user from [%s] to [%s]' % (self.template_db, self.name))
print_msg(" ... failed")
return False
#--------------------------------------------------------------
def bootstrap_auditing(self):
print_msg("==> setting up auditing ...")
# get audit trail configuration
tmp = cfg_get(self.section, 'audit disable')
# if this option is not given, assume we want auditing
if tmp is not None:
# if we don't want auditing on these tables, return without error
if int(tmp) == 1:
print_msg(' ... skipped (disabled)')
return True
tmp = cfg_get(self.section, 'audit trail parent table')
if tmp is None:
return None
aud_gen.audit_trail_parent_table = tmp
tmp = cfg_get(self.section, 'audit trail table prefix')
if tmp is None:
return None
aud_gen.audit_trail_table_prefix = tmp
tmp = cfg_get(self.section, 'audit fields table')
if tmp is None:
return None
aud_gen.audit_fields_table = tmp
# create auditing schema
curs = self.conn.cursor()
audit_schema = gmAuditSchemaGenerator.create_audit_ddl(curs)
curs.close()
if audit_schema is None:
_log.error('cannot generate audit trail schema for GNUmed database [%s]' % self.name)
return None
# write schema to file
tmpfile = os.path.join(tempfile.gettempdir(), 'audit-trail-schema.sql')
file = open(tmpfile, 'wb')
for line in audit_schema:
file.write("%s;\n" % line)
file.close()
# import auditing schema
psql = gmPsql.Psql(self.conn)
if psql.run(tmpfile) != 0:
_log.error("cannot import audit schema definition for database [%s]" % (self.name))
return None
if _keep_temp_files:
return True
try:
os.remove(tmpfile)
except StandardError:
_log.exception('cannot remove audit trail schema file [%s]' % tmpfile)
return True
#--------------------------------------------------------------
def bootstrap_notifications(self):
# setup clin.clin_root_item child tables FK's
print_msg("==> verifying FKs on clin.clin_root_item child tables ...")
child_tables = gmPG2.get_child_tables(link_obj = self.conn, schema = 'clin', table = 'clin_root_item')
_log.info('clin.clin_root_item child tables:')
for child in child_tables:
_log.info('%s.%s', child['namespace'], child['table'])
for child in child_tables:
# .fk_episode
FKs = gmPG2.get_foreign_key_names (
link_obj = self.conn,
src_schema = child['namespace'],
src_table = child['table'],
src_column = 'fk_episode',
target_schema = 'clin',
target_table = 'episode',
target_column = 'pk',
)
if len(FKs) > 0:
#_log.info('%s FK(s) exist: [#1 = %s.%s] %s.%s.fk_episode -> clin.episode.pk', len(FKs), FKs[0]['constraint_schema'], FKs[0]['constraint_name'], child['namespace'], child['table'])
_log.info('%s FK(s) exist:', len(FKs))
for idx in range(len(FKs)):
FK = FKs[idx]
_log.info(u' #%s = %s.%s: %s.%s.%s -> %s.%s.%s', idx + 1, FK['constraint_schema'], FK['constraint_name'], FK['source_schema'], FK['source_table'], FK['source_column'], FK['target_schema'], FK['target_table'], FK['target_column'])
else:
_log.info('adding FK: %s.%s.fk_episode -> clin.episode.pk', child['namespace'], child['table'])
cmd = SQL_add_foreign_key % {
'src_schema': child['namespace'],
'src_tbl': child['table'],
'src_col': 'fk_episode',
'target_schema': 'clin',
'target_tbl': 'episode',
'target_col': 'pk'
}
gmPG2.run_rw_queries(link_obj = self.conn, queries = [{'cmd': cmd}])
# .fk_encounter
FKs = gmPG2.get_foreign_key_names (
link_obj = self.conn,
src_schema = child['namespace'],
src_table = child['table'],
src_column = 'fk_encounter',
target_schema = 'clin',
target_table = 'encounter',
target_column = 'pk'
)
if len(FKs) > 0:
#_log.info('%s FK(s) exist: [#1 = %s.%s] %s.%s.fk_encounter -> clin.encounter.pk', len(FKs), FKs[0]['constraint_schema'], FKs[0]['constraint_name'], child['namespace'], child['table'])
_log.info('%s FK(s) exist:', len(FKs))
for idx in range(len(FKs)):
FK = FKs[idx]
_log.info(u' #%s = %s.%s: %s.%s.%s -> %s.%s.%s', idx + 1, FK['constraint_schema'], FK['constraint_name'], FK['source_schema'], FK['source_table'], FK['source_column'], FK['target_schema'], FK['target_table'], FK['target_column'])
else:
_log.info('adding FK: %s.%s.fk_encounter -> clin.encounter.pk', child['namespace'], child['table'])
cmd = SQL_add_foreign_key % {
'src_schema': child['namespace'],
'src_tbl': child['table'],
'src_col': 'fk_encounter',
'target_schema': 'clin',
'target_tbl': 'encounter',
'target_col': 'pk'
}
gmPG2.run_rw_queries(link_obj = self.conn, queries = [{'cmd': cmd}])
# always re-create generic super signal (if exists)
print_msg("==> setting up generic notifications ...")
_log.debug('creating generic modification announcement triggers on all registered tables')
curs = self.conn.cursor()
cmd = u"""
SELECT EXISTS (
SELECT 1 FROM information_schema.routines WHERE
routine_name = 'create_all_table_mod_triggers'
AND
routine_schema = 'gm'
)"""
curs.execute(cmd)
result = curs.fetchone()
if result[0] is True:
_log.debug('creating generic modification announcement triggers on registered tables')
curs.execute(SQL_sanity_check_trigger_func)
cmd = u"SELECT gm.create_all_table_mod_triggers(True::boolean)"
curs.execute(cmd)
result = curs.fetchone()
curs.close()
if result[0] is False:
_log.error('cannot create generic modification announcement triggers on all tables')
return None
else:
curs.close()
_log.debug('NOT creating generic modification announcement triggers, functionality not available')
print_msg("==> setting up (old style) notifications ...")
# get configuration
tmp = cfg_get(self.section, 'notification disable')
# if this option is not given, assume we want notification
if tmp is not None:
# if we don't want notification on these tables, return without error
if int(tmp) == 1:
print_msg(' ... skipped (disabled)')
return True
# create notification schema
curs = self.conn.cursor()
notification_schema = notify_gen.create_notification_schema(curs)
notification_schema.extend(notify_gen.create_narrative_notification_schema(curs))
curs.close()
if notification_schema is None:
_log.error('cannot generate notification schema for GNUmed database [%s]' % self.name)
return None
# write schema to file
tmpfile = os.path.join(tempfile.gettempdir(), 'notification-schema.sql')
file = open (tmpfile, 'wb')
for line in notification_schema:
file.write("%s;\n" % line)
file.close()
# import notification schema
psql = gmPsql.Psql(self.conn)
if psql.run(tmpfile) != 0:
_log.error("cannot import notification schema definition for database [%s]" % (self.name))
return None
if _keep_temp_files:
return True
try:
os.remove(tmpfile)
except StandardError:
_log.exception('cannot remove notification schema file [%s]' % tmpfile)
return True
#==================================================================
class gmBundle:
def __init__(self, aBundleAlias = None):
# sanity check
if aBundleAlias is None:
raise ConstructorError, "Need to know bundle name to install it."
self.alias = aBundleAlias
self.section = "bundle %s" % aBundleAlias
#--------------------------------------------------------------
def bootstrap(self):
_log.info("bootstrapping bundle [%s]" % self.alias)
# load bundle definition
database_alias = cfg_get(self.section, "database alias")
if database_alias is None:
_log.error("Need to know database name to install bundle [%s]." % self.alias)
return None
# bootstrap database
try:
database(aDB_alias = database_alias)
except:
_log.exception(u"Cannot bootstrap bundle [%s].", self.alias)
return None
self.db = _bootstrapped_dbs[database_alias]
# check PostgreSQL version
if not self.__verify_pg_version():
_log.error("Wrong PostgreSQL version.")
return None
# import schema
if not _import_schema(group=self.section, schema_opt='schema', conn=self.db.conn):
_log.error("Cannot import schema definition for bundle [%s] into database [%s]." % (self.alias, database_alias))
return None
return True
#--------------------------------------------------------------
def __verify_pg_version(self):
"""Verify database version information."""
required_version = cfg_get(self.section, "minimum postgresql version")
if required_version is None:
_log.error("Cannot load minimum required PostgreSQL version from config file.")
return None
_log.info("minimum required PostgreSQL version: %s" % required_version)
converted, pg_ver = gmTools.input2decimal(gmPG2.postgresql_version)
if not converted:
_log.error('error checking PostgreSQL version')
return None
converted, req_version = gmTools.input2decimal(required_version)
if not converted:
_log.error('error checking PostgreSQL version')
_log.error('required: %s', required_version)
return None
if pg_ver < req_version:
_log.error("Reported live PostgreSQL version [%s] is smaller than the required minimum version [%s]." % (gmPG2.postgresql_version, required_version))
return None
_log.info("installed PostgreSQL version: %s - this is fine with me" % gmPG2.postgresql_version)
return True
#==================================================================
def bootstrap_bundles():
# get bundle list
bundles = cfg_get("installation", "bundles")
if bundles is None:
exit_with_msg("Bundle list empty. Nothing to do here.")
# run through bundles
for bundle_alias in bundles:
print_msg('==> bootstrapping "%s" ...' % bundle_alias)
bundle = gmBundle(bundle_alias)
if not bundle.bootstrap():
return None
return True
#--------------------------------------------------------------
def import_data():
for db_key in _bootstrapped_dbs.keys():
db = _bootstrapped_dbs[db_key]
if not db.import_data():
return None
return True
#--------------------------------------------------------------
def bootstrap_auditing():
"""bootstrap auditing in all bootstrapped databases"""
for db_key in _bootstrapped_dbs.keys():
db = _bootstrapped_dbs[db_key]
if not db.bootstrap_auditing():
return None
return True
#--------------------------------------------------------------
def bootstrap_notifications():
"""bootstrap notification in all bootstrapped databases"""
for db_key in _bootstrapped_dbs.keys():
db = _bootstrapped_dbs[db_key]
if not db.bootstrap_notifications():
return None
return True
#------------------------------------------------------------------
def _run_query(aCurs, aQuery, args=None):
# FIXME: use gmPG2.run_rw_query()
if args is None:
try:
aCurs.execute(aQuery)
except:
_log.exception(">>>%s<<< failed" % aQuery)
return False
else:
try:
aCurs.execute(aQuery, args)
except:
_log.exception(">>>%s<<< failed" % aQuery)
_log.error(str(args))
return False
return True
#------------------------------------------------------------------
def ask_for_confirmation():
bundles = cfg_get("installation", "bundles")
if bundles is None:
return True
if len(bundles) == 0:
return True
if not _interactive:
print_msg("You are about to install the following parts of GNUmed:")
print_msg("-------------------------------------------------------")
for bundle in bundles:
db_alias = cfg_get("bundle %s" % bundle, "database alias")
db_name = cfg_get("database %s" % db_alias, "name")
srv_alias = cfg_get("database %s" % db_alias, "server alias")
srv_name = cfg_get("server %s" % srv_alias, "name")
print_msg('bundle "%s" in <%s> (or overridden) on <%s>' % (bundle, db_name, srv_name))
print_msg("-------------------------------------------------------")
desc = cfg_get("installation", "description")
if desc is not None:
for line in desc:
print_msg(line)
else:
print "You are about to install the following parts of GNUmed:"
print "-------------------------------------------------------"
for bundle in bundles:
db_alias = cfg_get("bundle %s" % bundle, "database alias")
db_name = cfg_get("database %s" % db_alias, "name")
srv_alias = cfg_get("database %s" % db_alias, "server alias")
srv_name = cfg_get("server %s" % srv_alias, "name")
print 'bundle "%s" in <%s> (or overridden) on <%s>' % (bundle, db_name, srv_name)
print "-------------------------------------------------------"
desc = cfg_get("installation", "description")
if desc is not None:
for line in desc:
print line
print "Do you really want to install this database setup ?"
answer = raw_input("Type yes or no: ")
if answer == "yes":
return True
else:
return None
return True
#--------------------------------------------------------------
def _import_schema (group=None, schema_opt="schema", conn=None):
# load schema
schema_files = cfg_get(group, schema_opt)
if schema_files is None:
_log.error("Need to know schema definition to install it.")
return None
schema_base_dir = cfg_get(group, "schema base directory")
if schema_base_dir is None:
_log.warning("no schema files base directory specified")
# look for base dirs for schema files
if os.path.exists (os.path.join ('.', 'sql')):
schema_base_dir = '.'
if os.path.exists ('../sql'):
schema_base_dir = '..'
if os.path.exists ('/usr/share/gnumed/server/sql'):
schema_base_dir = '/usr/share/gnumed/server'
if os.path.exists (os.path.expandvars('$GNUMED_DIR/server/sql')):
schema_base_dir = os.path.expandvars('$GNUMED_DIR/server')
# and import them
psql = gmPsql.Psql(conn)
for file in schema_files:
the_file = os.path.join(schema_base_dir, file)
if psql.run(the_file) == 0:
_log.info('successfully imported [%s]' % the_file)
else:
_log.error('failed to import [%s]' % the_file)
return None
return True
#------------------------------------------------------------------
def exit_with_msg(aMsg = None):
if aMsg is not None:
print aMsg
print ''
print "Please check the log file for details:"
print ''
print ' ', gmLog2._logfile_name
print ''
_log.error(aMsg)
_log.info("shutdown")
sys.exit(1)
#------------------------------------------------------------------
def print_msg(msg=None):
if quiet:
return
print msg
#-----------------------------------------------------------------
def become_pg_demon_user():
"""Become "postgres" user.
On UNIX type systems, attempt to use setuid() to
become the postgres user if possible.
This is so we can use the IDENT method to get to
the database (NB by default, at least on Debian and
postgres source installs, this is the only way,
as the postgres user has no password [-- and TRUST
is not allowed -KH])
"""
try:
import pwd
except ImportError:
_log.warning("running on broken OS -- can't import pwd module")
return None
try:
running_as = pwd.getpwuid(os.getuid())[0]
_log.info('running as user [%s]' % running_as)
except:
running_as = None
gmPG2.log_auth_environment()
pg_demon_user_passwd_line = None
try:
pg_demon_user_passwd_line = pwd.getpwnam('postgres')
# make sure we actually use this name to log in
_cfg.set_option(group = 'user postgres', option = 'name', value = 'postgres', source = 'file')
except KeyError:
try:
pg_demon_user_passwd_line = pwd.getpwnam ('pgsql')
_cfg.set_option(group = 'user postgres', option = 'name', value = 'pgsql', source = 'file')
except KeyError:
_log.warning('cannot find postgres user')
return None
if os.getuid() == 0: # we are the super-user
_log.info('switching to UNIX user [%s]' % pg_demon_user_passwd_line[0])
os.setuid(pg_demon_user_passwd_line[2])
gmPG2.log_auth_environment()
elif running_as == pg_demon_user_passwd_line[0]: # we are the postgres user already
_log.info('I already am the UNIX user [%s]' % pg_demon_user_passwd_line[0])
else:
_log.warning('not running as root or postgres, cannot become postmaster demon user')
_log.warning('may have trouble connecting as gm-dbo if IDENT auth is forced upon us')
if _interactive:
print_msg("WARNING: This script may not work if not running as the system administrator.")
#==============================================================================
def cfg_get(group=None, option=None):
return _cfg.get (
group = group,
option = option,
source_order = [('file', 'return')]
)
#==================================================================
def handle_cfg():
"""Bootstrap the source 'file' in _cfg."""
_log.info('config file: %s', _cfg.source_files['file'])
become_pg_demon_user()
tmp = cfg_get("installation", "interactive")
global _interactive
if tmp == "yes":
_interactive = True
elif tmp == "no":
_interactive = False
tmp = cfg_get('installation', 'keep temp files')
if tmp == "yes":
global _keep_temp_files
_keep_temp_files = True
if not ask_for_confirmation():
exit_with_msg("Bootstrapping aborted by user.")
if not bootstrap_bundles():
exit_with_msg("Cannot bootstrap bundles.")
if not bootstrap_auditing():
exit_with_msg("Cannot bootstrap audit trail.")
if not bootstrap_notifications():
exit_with_msg("Cannot bootstrap notification tables.")
if not import_data():
exit_with_msg("Bootstrapping failed: unable to import data")
#==================================================================
def main():
_cfg.add_cli(long_options = ['conf-file=', 'log-file=', 'quiet'])
global quiet
quiet = bool(_cfg.get(option = '--quiet', source_order = [('cli', 'return')]))
print_msg("=======================================")
print_msg("Bootstrapping GNUmed database system...")
print_msg("=======================================")
# get initial conf file from CLI
cfg_file = _cfg.get(option = '--conf-file', source_order = [('cli', 'return')])
if cfg_file is None:
_log.error("no config file specified on command line")
exit_with_msg('Cannot bootstrap without config file. Use --conf-file=<FILE>.')
_log.info('initial config file: %s', cfg_file)
# read that conf file
_cfg.add_file_source (
source = 'file',
file = cfg_file
)
# does it point to other conf files ?
cfg_files = _cfg.get (
group = 'installation',
option = 'config files',
source_order = [('file', 'return')]
)
if cfg_files is None:
_log.info('single-shot config file')
handle_cfg()
else:
_log.info('aggregation of config files')
for cfg_file in cfg_files:
# read that conf file
_cfg.add_file_source (
source = 'file',
file = cfg_file
)
handle_cfg()
global _bootstrapped_dbs
# verify result hash
db = _bootstrapped_dbs[_bootstrapped_dbs.keys()[0]]
if not db.verify_result_hash():
exit_with_msg("Bootstrapping failed: wrong result hash")
if not db.check_data_plausibility():
exit_with_msg("Bootstrapping failed: plausibility checks inconsistent")
# if not db.import_data():
# exit_with_msg("Bootstrapping failed: unable to import data")
db.check_holy_auth_line()
for conn in conn_ref_count:
if conn.closed == 0:
_log.warning('open connection detected: %s', conn.cookie)
_log.warning('%s', conn)
_log.warning('closing connection')
conn.close()
_log.info("shutdown")
print("Done bootstrapping GNUmed database: We very likely succeeded.")
print 'log:', gmLog2._logfile_name
#==================================================================
if __name__ == "__main__":
gmI18N.activate_locale()
gmLog2.set_string_encoding()
_log.info("startup")
try:
main()
except StandardError:
for c in conn_ref_count:
if c.closed == 0:
print 'closing open connection from:', c.cookie
print c
c.close()
_log.exception('unhandled exception caught')
exit_with_msg("Bootstrapping failed: unhandled exception occurred")
sys.exit(0)
else:
print "This currently is not intended to be used as a module."
sys.exit(1)
#==================================================================
# pipe = popen2.Popen3(cmd, 1==1)
# pipe.tochild.write("%s\n" % aPassword)
# pipe.tochild.flush()
# pipe.tochild.close()
# result = pipe.wait()
# print result
# read any leftovers
# pipe.fromchild.flush()
# pipe.childerr.flush()
# tmp = pipe.fromchild.read()
# lines = tmp.split("\n")
# for line in lines:
# _log.debug("child stdout: [%s]" % line, gmLog.lCooked)
# tmp = pipe.childerr.read()
# lines = tmp.split("\n")
# for line in lines:
# _log.error("child stderr: [%s]" % line, gmLog.lCooked)
# pipe.fromchild.close()
# pipe.childerr.close()
# del pipe
#==================================================================
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