[med-svn] [Git][med-team/gnumed-server][master] 6 commits: routine-update: New upstream version

Andreas Tille gitlab at salsa.debian.org
Fri Jul 24 08:17:12 BST 2020



Andreas Tille pushed to branch master at Debian Med / gnumed-server


Commits:
440d986e by Andreas Tille at 2020-07-24T09:03:38+02:00
routine-update: New upstream version

- - - - -
edf8d011 by Andreas Tille at 2020-07-24T09:03:39+02:00
New upstream version 22.13
- - - - -
61b525d1 by Andreas Tille at 2020-07-24T09:04:39+02:00
Update upstream source from tag 'upstream/22.13'

Update to upstream version '22.13'
with Debian dir 41f7eb013092fe5083c236e9ca7ae5a1c5122610
- - - - -
d327a388 by Andreas Tille at 2020-07-24T09:04:39+02:00
routine-update: debhelper-compat 13

- - - - -
4424bf75 by Andreas Tille at 2020-07-24T09:04:44+02:00
routine-update: Rules-Requires-Root: no

- - - - -
3700d973 by Andreas Tille at 2020-07-24T09:06:20+02:00
routine-update: Ready to upload to unstable

- - - - -


20 changed files:

- debian/changelog
- debian/control
- server/bootstrap/bootstrap_gm_db_system.py
- server/doc/schema/gnumed-entire_schema.html
- server/gm-fingerprint_db.py
- server/pycommon/gmBackendListener.py
- server/pycommon/gmBusinessDBObject.py
- server/pycommon/gmCfg2.py
- server/pycommon/gmConnectionPool.py
- server/pycommon/gmDateTime.py
- server/pycommon/gmDispatcher.py
- server/pycommon/gmGuiBroker.py
- server/pycommon/gmI18N.py
- server/pycommon/gmLog2.py
- server/pycommon/gmLoginInfo.py
- server/pycommon/gmMimeLib.py
- server/pycommon/gmNetworkTools.py
- server/pycommon/gmPG2.py
- server/pycommon/gmTools.py
- server/sql/v21-v22/fixups/v22-release_notes-fixup.sql


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+gnumed-server (22.13-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper-compat 13 (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+
+ -- Andreas Tille <tille at debian.org>  Fri, 24 Jul 2020 09:04:48 +0200
+
 gnumed-server (22.12-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille at debian.org>,
            Sebastian Hilbert <sebastian.hilbert at gmx.net>
 Section: misc
 Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
                dh-python,
                python3
 Build-Depends-Indep: po-debconf
@@ -12,6 +12,7 @@ Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/gnumed-server
 Vcs-Git: https://salsa.debian.org/med-team/gnumed-server.git
 Homepage: https://www.gnumed.de
+Rules-Requires-Root: no
 
 Package: gnumed-server
 Architecture: all


=====================================
server/bootstrap/bootstrap_gm_db_system.py
=====================================
@@ -290,7 +290,7 @@ def connect(host, port, db, user, passwd, conn_name=None):
 
 #==================================================================
 class user:
-	def __init__(self, anAlias = None, aPassword = None):
+	def __init__(self, anAlias = None, aPassword = None, force_interactive=False):
 		if anAlias is None:
 			raise ConstructorError("need user alias")
 		self.alias = anAlias
@@ -314,10 +314,21 @@ class user:
 			# defined but empty:
 			# this means to ask the user if interactive
 			elif self.password == '':
-				if _interactive:
+				if _interactive or force_interactive:
+					_log.info('password for [%s] defined as "", asking user', self.name)
 					print("I need the password for the database user [%s]." % self.name)
 					self.password = getpass.getpass("Please type the password: ")
+					_log.info('got password')
+					pwd4check = None
+					while pwd4check != self.password:
+						_log.info('asking for confirmation')
+						pwd2 = getpass.getpass("Please retype the password: ")
+						if pwd2 == self.password:
+							break
+						_log.error('password mismatch, asking again')
+						print('Password mismatch. Try again or CTRL-C to abort.')
 				else:
+					_log.warning('password for [%s] defined as "" (meaning <ask-user>), but running non-interactively, aborting', self.name)
 					_log.warning('cannot get password for database user [%s]', self.name)
 					raise ValueError('no password for user %s' % self.name)
 
@@ -495,7 +506,7 @@ unless it is pre-defined in the configuration file.
 
 Make sure to remember the password for later use !
 """) % name)
-		_dbowner = user(anAlias = dbowner_alias)
+		_dbowner = user(anAlias = dbowner_alias, force_interactive = True)
 
 		cmd = 'create user "%s" with password \'%s\' createdb createrole in group "%s", "gm-logins"' % (_dbowner.name, _dbowner.password, self.auth_group)
 		try:
@@ -615,6 +626,18 @@ class database:
 			_log.error(u"Cannot connect to template database.")
 			return False
 
+		# fingerprint template db
+		try:
+			gmLog2.log_multiline (
+				logging.INFO,
+				message = 'template database fingerprint',
+				text = gmPG2.get_db_fingerprint(conn = self.conn, eol = '\n')
+			)
+		except Exception:
+			_log.exception('cannot fingerprint template database')
+
+		self.conn.rollback()
+
 		# make sure db exists
 		if not self.__create_db():
 			_log.error(u"Cannot create database.")
@@ -1754,6 +1777,24 @@ def handle_cfg():
 	if not import_data():
 		exit_with_msg("Bootstrapping failed: unable to import data")
 
+	# fingerprint target db
+	# (the ugliest of hacks)
+	db = None
+	for db_key in _bootstrapped_dbs.keys():
+		db = _bootstrapped_dbs[db_key]
+	if db is not None:
+		try:
+			gmLog2.log_multiline (
+				logging.INFO,
+				message = 'target database fingerprint',
+				text = gmPG2.get_db_fingerprint(conn = db.conn, eol = '\n')
+			)
+		except Exception:
+			_log.error('cannot fingerprint database')
+		finally:
+			db.conn.rollback()
+	return True
+
 #==================================================================
 def main():
 


=====================================
server/doc/schema/gnumed-entire_schema.html
=====================================
@@ -112,7 +112,7 @@
   <body>
 
     <!-- Primary Index -->
-	<p><br><br>Dumped on 2020-03-25</p>
+	<p><br><br>Dumped on 2020-07-23</p>
 <h1><a name="index">Index of database - gnumed_v22</a></h1>
 <ul>
     


=====================================
server/gm-fingerprint_db.py
=====================================
@@ -12,7 +12,9 @@
 
 import sys
 import psycopg2
-import io
+#import io
+
+from Gnumed.pycommon import gmPG2
 
 database = sys.argv[1]
 passwd = sys.argv[2]
@@ -40,28 +42,33 @@ queries = [
 
 fname = u'gm_db-%s-fingerprint.log' % database
 #==============================================================
-outfile = io.open(fname, mode = 'wt', encoding = 'utf8')
+#outfile = io.open(fname, mode = 'wt', encoding = 'utf8')
 
-outfile.write(u"Fingerprinting GNUmed database ...\n")
-outfile.write(u"\n")
-outfile.write(u"%20s: %s\n" % (u"Name (DB)", database))
+#outfile.write(u"Fingerprinting GNUmed database ...\n")
+#outfile.write(u"\n")
+#outfile.write(u"%20s: %s\n" % (u"Name (DB)", database))
 
 conn = psycopg2.connect(dsn=dsn)
-curs = conn.cursor()
-
-for cmd, label in queries:
-	curs.execute(cmd)
-	rows = curs.fetchall()
-	outfile.write(u"%20s: %s\n" % (label, rows[0][0]))
-
+#curs = conn.cursor()
+#
+#for cmd, label in queries:
+#	curs.execute(cmd)
+#	rows = curs.fetchall()
+#	outfile.write(u"%20s: %s\n" % (label, rows[0][0]))
+#
 if len(sys.argv) > 3:
 	if sys.argv[3] == '--with-dump':
-		curs.execute('SELECT gm.concat_table_structure()')
-		rows = curs.fetchall()
-		outfile.write(u"\n%s\n" % rows[0][0])
+		with_dump = True
+	else:
+		with_dump = False
+#		curs.execute('SELECT gm.concat_table_structure()')
+#		rows = curs.fetchall()
+#		outfile.write(u"\n%s\n" % rows[0][0])
+
+gmPG2.fingerprint_db(conn = conn, with_dump = with_dump, fname = fname)
 
-curs.close()
+#curs.close()
 conn.rollback()
 
-outfile.close()
+#outfile.close()
 #==============================================================


=====================================
server/pycommon/gmBackendListener.py
=====================================
@@ -393,7 +393,7 @@ if __name__ == "__main__":
 			except KeyError:
 				print('==> received signal from client: "%s"' % kwargs['signal'])
 			del kwargs['signal']
-			for key in kwargs.keys():
+			for key in kwargs:
 				print('    [%s]: %s' % (key, kwargs[key]))
 
 		gmDispatcher.connect(receiver = monitoring_callback)


=====================================
server/pycommon/gmBusinessDBObject.py
=====================================
@@ -355,7 +355,7 @@ def manage_xxx()
 		result = self.refetch_payload(link_obj = link_obj)
 		if result is True:
 			self.payload_most_recently_fetched = {}
-			for field in self._idx.keys():
+			for field in self._idx:
 				self.payload_most_recently_fetched[field] = self._payload[self._idx[field]]
 			return True
 
@@ -398,7 +398,7 @@ def manage_xxx()
 			self.pk_obj = row['pk_obj']
 
 		self.payload_most_recently_fetched = {}
-		for field in self._idx.keys():
+		for field in self._idx:
 			self.payload_most_recently_fetched[field] = self._payload[self._idx[field]]
 
 	#--------------------------------------------------------
@@ -413,7 +413,7 @@ def manage_xxx()
 	def __str__(self):
 		lines = []
 		try:
-			for attr in self._idx.keys():
+			for attr in self._idx:
 				if self._payload[self._idx[attr]] is None:
 					lines.append('%s: NULL' % attr)
 				else:
@@ -440,7 +440,7 @@ def manage_xxx()
 		getter = getattr(self, 'get_%s' % attribute, None)
 		if not callable(getter):
 			_log.warning('[%s]: no attribute [%s]' % (self.__class__.__name__, attribute))
-			_log.warning('[%s]: valid attributes: %s' % (self.__class__.__name__, str(self._idx.keys())))
+			_log.warning('[%s]: valid attributes: %s', self.__class__.__name__, list(self._idx))
 			_log.warning('[%s]: no getter method [get_%s]' % (self.__class__.__name__, attribute))
 			methods = [ m for m in inspect.getmembers(self, inspect.ismethod) if m[0].startswith('get_') ]
 			_log.warning('[%s]: valid getter methods: %s' % (self.__class__.__name__, str(methods)))
@@ -502,7 +502,7 @@ def manage_xxx()
 	#--------------------------------------------------------
 	def get_fields(self):
 		try:
-			return self._idx.keys()
+			return list(self._idx)
 		except AttributeError:
 			return 'nascent [%s @ %s], cannot return keys' %(self.__class__.__name__, id(self))
 
@@ -517,7 +517,7 @@ def manage_xxx()
 		else:
 			bools = {True: bool_strings[0], False: bool_strings[1]}
 		data = {}
-		for field in self._idx.keys():
+		for field in self._idx:
 			# FIXME: harden against BYTEA fields
 			#if type(self._payload[self._idx[field]]) == ...
 			#	data[field] = _('<%s bytes of binary data>') % len(self._payload[self._idx[field]])
@@ -707,7 +707,7 @@ def manage_xxx()
 			return (True, None)
 
 		args = {}
-		for field in self._idx.keys():
+		for field in self._idx:
 			args[field] = self._payload[self._idx[field]]
 		self.payload_most_recently_attempted_to_store = args
 
@@ -763,7 +763,7 @@ def manage_xxx()
 
 		# update to new "original" payload
 		self.payload_most_recently_fetched = {}
-		for field in self._idx.keys():
+		for field in self._idx:
 			self.payload_most_recently_fetched[field] = self._payload[self._idx[field]]
 
 		return (True, None)


=====================================
server/pycommon/gmCfg2.py
=====================================
@@ -388,7 +388,7 @@ class gmCfgData(gmBorg.cBorg):
 			try: source_data = self.__cfg_data[source]
 			except KeyError:
 				_log.error('invalid config source [%s]', source)
-				_log.debug('currently known sources: %s', self.__cfg_data.keys())
+				_log.debug('currently known sources: %s', list(self.__cfg_data))
 				continue
 
 			try: value = source_data[option_path]


=====================================
server/pycommon/gmConnectionPool.py
=====================================
@@ -12,6 +12,9 @@ __author__ = "karsten.hilbert at gmx.net"
 __license__ = "GPL v2 or later (details at http://www.gnu.org)"
 
 
+_DISABLE_CONNECTION_POOL = False		# set to True to disable the connection pool for debugging (= always return new connection)
+
+
 # standard library imports
 import os
 import sys
@@ -29,7 +32,7 @@ import psycopg2 as dbapi
 if not (float(dbapi.apilevel) >= 2.0):
 	raise ImportError('gmPG2: supported DB-API level too low')
 
-if not (dbapi.threadsafety > 0):
+if not (dbapi.threadsafety == 2):
 	raise ImportError('gmPG2: lacking minimum thread safety in psycopg2')
 
 if not (dbapi.paramstyle == 'pyformat'):
@@ -50,6 +53,7 @@ try:
 except ValueError:
 	raise ImportError('gmPG2: lacking v3 backend protocol support in psycopg2')
 
+
 import psycopg2.extensions
 import psycopg2.extras
 import psycopg2.errorcodes as SQL_error_codes
@@ -84,6 +88,10 @@ _log.info('psycopg2 module version: %s' % dbapi.__version__)
 _log.info('PostgreSQL via DB-API module "%s": API level %s, thread safety %s, parameter style "%s"' % (dbapi, dbapi.apilevel, dbapi.threadsafety, dbapi.paramstyle))
 _log.info('libpq version (compiled in): %s', psycopg2.__libpq_version__)
 _log.info('libpq version (loaded now) : %s', psycopg2.extensions.libpq_version())
+#if '2.8' in dbapi.__version__:
+#	_log.info('psycopg2 v2.8 detected, disabling connection pooling for the time being')
+#	_DISABLE_CONNECTION_POOL = True
+
 
 postgresql_version = None
 
@@ -117,54 +125,52 @@ _map_psyco_iso_level2str = {
 class cPGCredentials:
 
 	def __init__(self) -> None:
-		self.__host = None			# None: left out of DSN -> defaults to $PGHOST or implicit <localhost>
-		self.__port = None			# None: left out of DSN -> defaults to $PGPORT or libpq compiled-in default (typically 5432)
+		self.__host = None			# None: left out -> defaults to $PGHOST or implicit <localhost>
+		self.__port = None			# None: left out -> defaults to $PGPORT or libpq compiled-in default (typically 5432)
 		self.__database = None		# must be set before connecting
 		self.__user = None			# must be set before connecting
-		self.__password = None		# None: left out of DSN
+		self.__password = None		# None: left out
 									# -> try password-less connect (TRUST/IDENT/PEER)
-									# -> try connect with password from DSN:<passfile> or $PGPASSFILE or ~/.pgpass
+									# -> try connect with password from <passfile> parameter or $PGPASSFILE or ~/.pgpass
 
 	#--------------------------------------------------
 	# properties
 	#--------------------------------------------------
 	def __format_credentials(self):
-		dsn_parts = [
+		cred_parts = [
 			'dbname=%s' % self.__database,
 			'host=%s' % self.__host,
 			'port=%s' % self.__port,
 			'user=%s' % self.__user
 		]
-		return ' '.join(dsn_parts)
+		return ' '.join(cred_parts)
 
-	formatted_dsn = property(__format_credentials)
+	formatted_credentials = property(__format_credentials)
 
 	#--------------------------------------------------
-	def generate_dsn(self, connection_name=None):
+	def generate_credentials_kwargs(self, connection_name=None):
 		assert (self.__database is not None), 'self.__database must be defined'
 		assert (self.__user is not None), 'self.__user must be defined'
-
-		dsn_parts = [
-			'dbname=%s' % self.__database,
-			#'port=%s' % gmTools.coalesce(self.__port, '5432'),
-			'user=%s' % self.__user,
-			'application_name=%s' % gmTools.coalesce(connection_name, 'GNUmed'),
-			'fallback_application_name=GNUmed',
-			'sslmode=prefer',
+		kwargs = {
+			'dbname': self.__database,
+			'user': self.__user,
+			'application_name': gmTools.coalesce(connection_name, 'GNUmed'),
+			'fallback_application_name': 'GNUmed',
+			'sslmode': 'prefer',
 			# try to enforce a useful encoding early on so that we
 			# have a good chance of decoding authentication errors
 			# containing foreign language characters
-			'client_encoding=UTF8'
-		]
+			'client_encoding': 'UTF8'
+		}
 		if self.__host is not None:
-			dsn_parts.append('host=%s' % self.__host)
+			kwargs['host'] = self.__host
 		if self.__port is not None:
-			dsn_parts.append('port=%s' % self.__port)
+			kwargs['port'] = self.__port
 		if self.__password is not None:
-			dsn_parts.append('password=%s' % self.__password)
-		return ' '.join(dsn_parts)
+			kwargs['password'] = self.__password
+		return kwargs
 
-	validated_dsn = property(generate_dsn)
+	credentials_kwargs = property(generate_credentials_kwargs)
 
 	#--------------------------------------------------
 	def _get_database(self):
@@ -240,7 +246,7 @@ class gmConnectionPool(gmBorg.cBorg):
 			self.__initialized = True
 
 		_log.info('[%s]: first instantiation', self.__class__.__name__)
-		self.__ro_conn_pool = {}	# keyed by "DSN::thread ID"
+		self.__ro_conn_pool = {}	# keyed by "credentials::thread ID"
 		self.__SQL_set_client_timezone = None
 		self.__client_timezone = None
 		self.__creds = None
@@ -250,6 +256,10 @@ class gmConnectionPool(gmBorg.cBorg):
 	# connection API
 	#--------------------------------------------------
 	def get_connection(self, readonly=True, verbose=False, pooled=True, connection_name=None, autocommit=False, credentials=None):
+
+		if _DISABLE_CONNECTION_POOL:
+			pooled = False
+
 		if credentials is not None:
 			pooled = False
 		conn = None
@@ -328,12 +338,12 @@ class gmConnectionPool(gmBorg.cBorg):
 			creds2use = self.__creds
 		else:
 			creds2use = credentials
-		dsn = creds2use.generate_dsn(connection_name = connection_name)
+		creds_kwargs = creds2use.generate_credentials_kwargs(connection_name = connection_name)
 		try:
 			# DictConnection now _is_ a real dictionary
-			conn = dbapi.connect(dsn = dsn, connection_factory = psycopg2.extras.DictConnection)
+			conn = dbapi.connect(connection_factory = psycopg2.extras.DictConnection, **creds_kwargs)
 		except dbapi.OperationalError as e:
-			_log.error('failed to establish connection [%s]', creds2use.formatted_dsn)
+			_log.error('failed to establish connection [%s]', creds2use.formatted_credentials)
 			t, v, tb = sys.exc_info()
 			try:
 				msg = e.args[0]
@@ -343,7 +353,7 @@ class gmConnectionPool(gmBorg.cBorg):
 			if not self.__is_auth_fail_msg(msg):
 				raise
 
-			raise cAuthenticationError(creds2use.formatted_dsn, msg).with_traceback(tb)
+			raise cAuthenticationError(creds2use.formatted_credentials, msg).with_traceback(tb)
 
 		_log.debug('established connection "%s", backend PID: %s', gmTools.coalesce(connection_name, 'anonymous'), conn.get_backend_pid())
 		# - inspect server
@@ -580,9 +590,9 @@ class gmConnectionPool(gmBorg.cBorg):
 	def _set_credentials(self, creds=None):
 		if self.__creds is not None:
 			_log.debug('invalidating pooled connections on credentials change')
-			curr_dsn = self.__creds.formatted_dsn + '::'
+			curr_creds = self.__creds.formatted_credentials + '::'
 			for conn_key in self.__ro_conn_pool:
-				if not conn_key.startswith(curr_dsn):
+				if not conn_key.startswith(curr_creds):
 					continue
 				conn = self.__ro_conn_pool[conn_key]
 				self.__ro_conn_pool[conn_key] = None
@@ -601,7 +611,7 @@ class gmConnectionPool(gmBorg.cBorg):
 	#--------------------------------------------------
 	def _get_pool_key(self):
 		return '%s::%s' % (
-			self.__creds.formatted_dsn,
+			self.__creds.formatted_credentials,
 			threading.current_thread().ident
 		)
 
@@ -868,12 +878,12 @@ def _raise_exception_on_pooled_ro_conn_close():
 #========================================================================
 class cAuthenticationError(dbapi.OperationalError):
 
-	def __init__(self, dsn=None, prev_val=None):
-		self.dsn = dsn
+	def __init__(self, creds=None, prev_val=None):
+		self.creds = creds
 		self.prev_val = prev_val
 
 	def __str__(self):
-		return 'PostgreSQL: %sDSN: %s' % (self.prev_val, self.dsn)
+		return 'PostgreSQL: %sDSN: %s' % (self.prev_val, self.creds)
 
 #============================================================
 # Python -> PostgreSQL
@@ -920,7 +930,7 @@ if __name__ == "__main__":
 		print("testing exceptions")
 
 		try:
-			raise cAuthenticationError('no dsn', 'no previous exception')
+			raise cAuthenticationError('no credentials', 'no previous exception')
 		except cAuthenticationError:
 			t, v, tb = sys.exc_info()
 			print(t)
@@ -1047,6 +1057,22 @@ if __name__ == "__main__":
 		conn = pool.get_connection()
 
 	#--------------------------------------------------------------------
-	test_exceptions()
-	test_get_connection()
-	test_change_creds()
+	def test_credentials():
+		print("testing credentials with spaces")
+		pool = gmConnectionPool()
+		creds = cPGCredentials()
+		creds.database = 'gnumed_v22'
+		creds.user = 'any-doc'
+		creds.password = 'any-doc'
+		pool.credentials = creds
+		conn = pool.get_connection()
+		print(conn)
+		creds.password = 'a - b'
+		pool.credentials = creds
+		conn = pool.get_connection()
+
+	#--------------------------------------------------------------------
+	test_credentials()
+	#test_exceptions()
+	#test_get_connection()
+	#test_change_creds()


=====================================
server/pycommon/gmDateTime.py
=====================================
@@ -2162,7 +2162,7 @@ if __name__ == '__main__':
 	#-----------------------------------------------------------------------
 	def test_format_interval():
 		intv = pyDT.timedelta(minutes=1, seconds=2)
-		for acc in _accuracy_strings.keys():
+		for acc in _accuracy_strings:
 			print ('[%s]: "%s" -> "%s"' % (acc, intv, format_interval(intv, acc)))
 		return
 
@@ -2171,7 +2171,7 @@ if __name__ == '__main__':
 			if intv is None:
 				print(tmp, '->', intv)
 				continue
-			for acc in _accuracy_strings.keys():
+			for acc in _accuracy_strings:
 				print ('[%s]: "%s" -> "%s"' % (acc, tmp, format_interval(intv, acc)))
 
 	#-----------------------------------------------------------------------


=====================================
server/pycommon/gmDispatcher.py
=====================================
@@ -322,7 +322,7 @@ def _call(receiver, **kwds):
 	if not (func_code_def.co_flags & 0x08):
 		# func_code_def does not have a **kwds type parameter,
 		# therefore remove unacceptable arguments.
-		keys = list(kwds.keys())
+		keys = list(kwds)
 		for arg in keys:
 			if arg not in acceptable_args:
 				del kwds[arg]
@@ -337,8 +337,8 @@ def _call(receiver, **kwds):
 #---------------------------------------------------------------------
 def _removeReceiver(receiver):
 	"""Remove receiver from connections."""
-	for sender_identity in connections.keys():
-		for signal in connections[sender_identity].keys():
+	for sender_identity in connections:
+		for signal in connections[sender_identity]:
 			receivers = connections[sender_identity][signal]
 			try:
 				receivers.remove(receiver)


=====================================
server/pycommon/gmGuiBroker.py
=====================================
@@ -70,7 +70,7 @@ class GuiBroker:
 
 	def keylist(self):
 		" returns a list of all keys; see documentation for the dictionary data type"
-		return GuiBroker.__objects.keys()
+		return list(GuiBroker.__objects)
 
 
 


=====================================
server/pycommon/gmI18N.py
=====================================
@@ -107,37 +107,33 @@ def __split_locale_into_levels():
 #---------------------------------------------------------------------------
 def __log_locale_settings(message=None):
 	_setlocale_categories = {}
-	for category in 'LC_ALL LC_CTYPE LC_COLLATE LC_TIME LC_MONETARY LC_MESSAGES LC_NUMERIC'.split():
+	for category in 'LC_ALL LC_CTYPE LC_NUMERIC LC_TIME LC_COLLATE LC_MONETARY LC_MESSAGES LC_PAPER LC_NAME LC_ADDRESS LC_TELEPHONE LC_MEASUREMENT LC_IDENTIFICATION'.split():
 		try:
 			_setlocale_categories[category] = getattr(locale, category)
 		except Exception:
 			_log.warning('this OS does not have locale.%s', category)
-
 	_getlocale_categories = {}
-	for category in 'LC_CTYPE LC_COLLATE LC_TIME LC_MONETARY LC_MESSAGES LC_NUMERIC'.split():
+	for category in 'LC_CTYPE LC_NUMERIC LC_TIME LC_COLLATE LC_MONETARY LC_MESSAGES LC_PAPER LC_NAME LC_ADDRESS LC_TELEPHONE LC_MEASUREMENT LC_IDENTIFICATION'.split():
 		try:
 			_getlocale_categories[category] = getattr(locale, category)
 		except Exception:
 			pass
-
 	if message is not None:
 		_log.debug(message)
 
 	_log.debug('current locale settings:')
 	_log.debug('locale.getlocale(): %s' % str(locale.getlocale()))
-	for category in _getlocale_categories.keys():
+	for category in _getlocale_categories:
 		_log.debug('locale.getlocale(%s): %s' % (category, locale.getlocale(_getlocale_categories[category])))
-
-	for category in _setlocale_categories.keys():
+	for category in _setlocale_categories:
 		_log.debug('(locale.setlocale(%s): %s)' % (category, locale.setlocale(_setlocale_categories[category])))
-
 	try:
 		_log.debug('locale.getdefaultlocale() - default (user) locale: %s' % str(locale.getdefaultlocale()))
 	except ValueError:
 		_log.exception('the OS locale setup seems faulty')
 
 	_log.debug('encoding sanity check (also check "locale.nl_langinfo(CODESET)" below):')
-	pref_loc_enc = locale.getpreferredencoding(do_setlocale=False)
+	pref_loc_enc = locale.getpreferredencoding(do_setlocale = False)
 	loc_enc = locale.getlocale()[1]
 	py_str_enc = sys.getdefaultencoding()
 	sys_fs_enc = sys.getfilesystemencoding()
@@ -171,7 +167,7 @@ def __log_locale_settings(message=None):
 
 	_log.debug('database of locale conventions:')
 	data = locale.localeconv()
-	for key in data.keys():
+	for key in data:
 		if loc_enc is None:
 			_log.debug('locale.localeconv(%s): %s', key, data[key])
 		else:
@@ -186,7 +182,7 @@ def __log_locale_settings(message=None):
 		except Exception:
 			_log.warning('this OS does not support nl_langinfo category locale.%s' % category)
 	try:
-		for category in _nl_langinfo_categories.keys():
+		for category in _nl_langinfo_categories:
 			if loc_enc is None:
 				_log.debug('locale.nl_langinfo(%s): %s' % (category, locale.nl_langinfo(_nl_langinfo_categories[category])))
 			else:
@@ -231,37 +227,25 @@ def _translate_safely(term):
 def activate_locale():
 	"""Get system locale from environment."""
 	global system_locale
-
-	__log_locale_settings('unmodified startup locale settings (should be [C])')
-
-	# activate user-preferred locale
+	__log_locale_settings('unmodified startup locale settings (could be [C])')
 	loc, enc = None, None
+	# activate user-preferred locale
 	try:
-		# check whether already set
-		loc, loc_enc = locale.getlocale()
-		if loc is None:
-			loc = locale.setlocale(locale.LC_ALL, '')
-			_log.debug("activating user-default locale with <locale.setlocale(locale.LC_ALL, '')> returns: [%s]" % loc)
-		else:
-			_log.info('user-default locale already activated')
-		loc, loc_enc = locale.getlocale()
+		loc = locale.setlocale(locale.LC_ALL, '')
+		_log.debug("activating user-default locale with <locale.setlocale(locale.LC_ALL, '')> returns: [%s]" % loc)
 	except AttributeError:
 		_log.exception('Windows does not support locale.LC_ALL')
 	except Exception:
 		_log.exception('error activating user-default locale')
-
 	__log_locale_settings('locale settings after activating user-default locale')
-
-	# did we find any locale setting ? assume en_EN if not
+	# assume en_EN if we did not find any locale settings
 	if loc in [None, 'C']:
 		_log.error('the current system locale is still [None] or [C], assuming [en_EN]')
 		system_locale = "en_EN"
 	else:
 		system_locale = loc
-
 	# generate system locale levels
 	__split_locale_into_levels()
-
 	return True
 
 #---------------------------------------------------------------------------


=====================================
server/pycommon/gmLog2.py
=====================================
@@ -339,6 +339,9 @@ if __name__ == '__main__':
 	#-----------------------------------------------------------
 	def test():
 		logger = logging.getLogger('gmLog2.test')
+
+		logger.error('test %s', [1,2,3])
+
 		logger.error("I expected to see %s::test()" % __file__)
 		add_word2hide('super secret passphrase')
 		logger.debug('credentials: super secret passphrase')


=====================================
server/pycommon/gmLoginInfo.py
=====================================
@@ -11,12 +11,6 @@ _log = logging.getLogger('gm.db')
 class LoginInfo:
 	"""a class to encapsulate Postgres login information to default database"""
 
-	# private variables
-#	user = ''
-#	password = ''
-#	host = ''
-#	port = 5432
-#	database = ''
 	#------------------------------------------
 	def __init__(self, user=None, password=None, host=None, port=5432, database=None):
 		self.user = user
@@ -33,80 +27,6 @@ class LoginInfo:
 
 	port = property(_get_port, _set_port)
 	#------------------------------------------
-	def GetInfo(self):
-		return (
-			self.GetUser(),
-			self.GetPassword(),
-			self.GetHost(),
-			self.GetPort(),
-			self.GetDatabase(),
-			self.GetProfile()
-		)
-	#------------------------------------------
-	def GetInfoStr(self):
-		# don't hand out passwords just like that
-		info = "host:port=%s:%s, db=%s, user=%s, pw=??" % (
-					self.GetHost(),
-					str(self.GetPort()),
-					self.GetDatabase(),
-					self.GetUser()
-				)
-		return info
-	#------------------------------------------
-	def GetPGDB_DSN(self):
-		host = self.GetHost()
-		port = str(self.GetPort())
-		# for local UNIX domain sockets connections: leave host/port empty
-		# IH: *PLEASE* option of local TCP/IP connection must be available
-#		if host in ['', 'localhost']:
-#			host = ""
-		if host == '':
-			port = ''
-		dsn = "%s:%s:%s:%s" % (
-			host,
-			self.GetDatabase(),
-			self.GetUser(),
-			self.GetPassword()
-		)
-		host_port = "%s:%s" % (host, port)
-		return dsn, host_port
-	#------------------------------------------
-	def get_psycopg2_dsn(self):
-		dsn_parts = []
-
-		if self.database.strip() != '':
-			dsn_parts.append('dbname=%s' % self.database)
-
-		if self.host.strip() != '':
-			dsn_parts.append('host=%s' % self.host)
-
-		dsn_parts.append('port=%s' % self.port)
-
-		if self.user.strip() != '':
-			dsn_parts.append('user=%s' % self.user)
-
-		if self.password.strip() != '':
-			dsn_parts.append('password=%s' % self.password)
-
-		return ' '.join(dsn_parts)
-	#------------------------------------------
-	def GetDBAPI_DSN(self):
-		host = self.GetHost()
-		port = str(self.GetPort())
-		# for local UNIX domain sockets connections: leave host/port empty
-#		if host in ['', 'localhost']:
-#			host = ''
-		if host == '':
-			port = ''
-		dsn = "%s:%s:%s:%s:%s" % (
-			host,
-			port,
-			self.GetDatabase(),
-			self.GetUser(),
-			self.GetPassword()
-		)
-		return dsn
-	#------------------------------------------
 	def SetUser(self, user):
 		self.user = user
 	#------------------------------------------


=====================================
server/pycommon/gmMimeLib.py
=====================================
@@ -228,7 +228,7 @@ def _get_system_startfile_cmd(filename):
 	if _system_startfile_cmd is not None:
 		return True, _system_startfile_cmd % filename
 
-	open_cmd_candidates = open_cmds.keys()
+	open_cmd_candidates = list(open_cmds)
 
 	for candidate in open_cmd_candidates:
 		found, binary = gmShellAPI.detect_external_binary(binary = candidate)


=====================================
server/pycommon/gmNetworkTools.py
=====================================
@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
 
-
-
 __doc__ = """GNUmed internetworking tools."""
 
 #===========================================================================
@@ -155,10 +153,19 @@ def compare_versions(left_version, right_version):
 	-1: left < right
 	 1: left > right
 	"""
+	_log.debug('comparing [%s] with [%s]', left_version, right_version)
 	if left_version == right_version:
-		_log.debug('same version: [%s] = [%s]', left_version, right_version)
+		_log.debug('same version')
 		return 0
 
+	if right_version in ['head', 'dev', 'devel']:
+		_log.debug('development code')
+		return -1
+
+	if left_version in ['head', 'dev', 'devel']:
+		_log.debug('development code')
+		return 1
+
 	left_parts = left_version.split('.')
 	right_parts = right_version.split('.')
 
@@ -194,8 +201,12 @@ def check_for_update(url=None, current_branch=None, current_version=None, consid
 	False: up to date
 	None: don't know
 	"""
-	if current_version == 'GIT HEAD':
-		_log.debug('GIT HEAD always up to date')
+	if current_version is None:
+		_log.debug('<current_version> is None, currency unknown')
+		return (None, None)
+
+	if current_version.lower() in ['git head', 'head', 'tip', 'dev', 'devel']:
+		_log.debug('[%s] always considered up to date', current_version)
 		return (False, None)
 
 	try:


=====================================
server/pycommon/gmPG2.py
=====================================
@@ -300,6 +300,7 @@ def __request_login_params_tui():
 		gmLog2.add_word2hide(login.password)
 		login.port = prompted_input(prompt = "port", default = 5432)
 	except KeyboardInterrupt:
+		del login
 		_log.warning("user cancelled text mode login dialog")
 		print("user cancelled text mode login dialog")
 		raise gmExceptions.ConnectionError(_("Cannot connect to database without login information!"))
@@ -346,21 +347,28 @@ def __request_login_params_gui_wx():
 	return login, creds
 
 #---------------------------------------------------
-def request_login_params():
+def request_login_params(setup_pool=False):
 	"""Request login parameters for database connection."""
-
 	# are we inside X ?
 	# if we aren't wxGTK will crash hard at the C-level with "can't open Display"
 	if 'DISPLAY' in os.environ:
 		# try wxPython GUI
 		try:
-			return __request_login_params_gui_wx()
+			login, creds = __request_login_params_gui_wx()
 		except Exception:
 			pass
+		if setup_pool:
+			pool = gmConnectionPool.gmConnectionPool()
+			pool.credentials = creds
+		return login, creds
 
 	# well, either we are on the console or
 	# wxPython does not work, use text mode
-	return __request_login_params_tui()
+	login, creds = __request_login_params_tui()
+	if setup_pool:
+		pool = gmConnectionPool.gmConnectionPool()
+		pool.credentials = creds
+	return login, creds
 
 # =======================================================================
 # netadata API
@@ -435,6 +443,70 @@ def get_schema_revision_history(link_obj=None):
 
 	rows, idx = run_ro_queries(link_obj = link_obj, queries = [{'cmd': cmd}])
 	return rows
+
+#------------------------------------------------------------------------
+def get_db_fingerprint(conn=None, fname=None, with_dump=False, eol=None):
+	queries = [
+		("SELECT setting FROM pg_settings WHERE name = 'server_version'", "Version (PG)"),
+		("SELECT setting FROM pg_settings WHERE name = 'server_encoding'", "Encoding (PG)"),
+		("SELECT setting FROM pg_settings WHERE name = 'lc_collate'", "LC_COLLATE (PG)"),
+		("SELECT setting FROM pg_settings WHERE name = 'lc_ctype'", "LC_CTYPE (PG)"),
+		("SELECT count(1) FROM dem.identity", "Patients"),
+		("SELECT count(1) FROM clin.encounter", "Contacts"),
+		("SELECT count(1) FROM clin.episode", "Episodes"),
+		("SELECT count(1) FROM clin.health_issue", "Issues"),
+		("SELECT count(1) FROM clin.test_result", "Results"),
+		("SELECT count(1) FROM clin.vaccination", "Vaccinations"),
+		("SELECT count(1) FROM blobs.doc_med", "Documents"),
+		("SELECT count(1) FROM blobs.doc_obj", "Objects"),
+		("SELECT count(1) FROM dem.org", "Organizations"),
+		("SELECT count(1) FROM dem.org_unit", "Organizational units"),
+		("SELECT max(modified_when) FROM audit.audit_fields", "Most recent .modified_when"),
+		("SELECT max(audit_when) FROM audit.audit_trail", "Most recent .audit_when")
+	]
+	if conn is None:
+		conn = get_connection(readonly = True)
+	database = conn.get_dsn_parameters()['dbname']
+	lines = [
+		'Fingerprinting GNUmed database ...',
+		'',
+		'%20s: %s' % ('Name (DB)', database)
+	]
+	curs = conn.cursor()
+	# get size
+	cmd = "SELECT pg_size_pretty(pg_database_size('%s'))" % database
+	curs.execute(cmd)
+	rows = curs.fetchall()
+	lines.append('%20s: %s' % ('Size (DB)', rows[0][0]))
+	# get hash
+	cmd = "SELECT md5(gm.concat_table_structure())"
+	curs.execute(cmd)
+	rows = curs.fetchall()
+	md5_sum = rows[0][0]
+	try:
+		lines.append('%20s: %s (v%s)' % ('Schema hash', md5_sum, map_schema_hash2version[md5_sum]))
+	except KeyError:
+		lines.append('%20s: %s' % ('Schema hash', md5_sum))
+	for cmd, label in queries:
+		curs.execute(cmd)
+		rows = curs.fetchall()
+		lines.append('%20s: %s' % (label, rows[0][0]))
+	if with_dump:
+		curs.execute('SELECT gm.concat_table_structure()')
+		rows = curs.fetchall()
+		lines.append('')
+		lines.append(rows[0][0])
+	curs.close()
+	if fname is None:
+		if eol is None:
+			return lines
+		return eol.join(lines)
+
+	outfile = open(fname, mode = 'wt', encoding = 'utf8')
+	outfile.write('\n'.join(lines))
+	outfile.close()
+	return fname
+
 #------------------------------------------------------------------------
 def get_current_user():
 	rows, idx = run_ro_queries(queries = [{'cmd': 'select CURRENT_USER'}])
@@ -1803,7 +1875,7 @@ def run_insert(link_obj=None, schema=None, table=None, values=None, returning=No
 	if schema is None:
 		schema = 'public'
 
-	fields = values.keys()		# that way val_snippets and fields really should end up in the same order
+	fields = list(values)		# that way val_snippets and fields really should end up in the same order
 	val_snippets = []
 	for field in fields:
 		val_snippets.append('%%(%s)s' % field)
@@ -1841,11 +1913,11 @@ def run_insert(link_obj=None, schema=None, table=None, values=None, returning=No
 # =======================================================================
 # connection handling API
 # -----------------------------------------------------------------------
-def get_raw_connection(dsn=None, verbose=False, readonly=True, connection_name=None, autocommit=False):
+def get_raw_connection(verbose=False, readonly=True, connection_name=None, autocommit=False):
 	"""Get a raw, unadorned connection.
 
 	- this will not set any parameters such as encoding, timezone, datestyle
-	- the only requirement is a valid DSN
+	- the only requirement is valid connection parameters having been passed to the connection pool
 	- hence it can be used for "service" connections
 	  for verifying encodings etc
 	"""
@@ -1857,12 +1929,13 @@ def get_raw_connection(dsn=None, verbose=False, readonly=True, connection_name=N
 	)
 
 # =======================================================================
-def get_connection(dsn=None, readonly=True, verbose=False, pooled=True, connection_name=None, autocommit=False):
+def get_connection(readonly=True, verbose=False, pooled=True, connection_name=None, autocommit=False):
 	return gmConnectionPool.gmConnectionPool().get_connection (
 		readonly = readonly,
 		verbose = verbose,
 		connection_name = connection_name,
-		autocommit = autocommit
+		autocommit = autocommit,
+		pooled = pooled
 	)
 
 #-----------------------------------------------------------------------
@@ -1985,7 +2058,7 @@ def sanity_check_database_settings():
 	cmd = "SELECT name, setting from pg_settings where name in %(settings)s"
 	rows, idx = run_ro_queries (
 		link_obj = conn,
-		queries = [{'cmd': cmd, 'args': {'settings': tuple(options2check.keys())}}],
+		queries = [{'cmd': cmd, 'args': {'settings': tuple(options2check)}}],
 		get_col_idx = False
 	)
 
@@ -2513,6 +2586,15 @@ SELECT to_timestamp (foofoo,'YYMMDD.HH24MI') FROM (
 		conn = get_connection()
 		gmConnectionPool.log_pg_settings(curs = conn.cursor())
 
+	#--------------------------------------------------------------------
+	def test_get_db_fingerprint():
+		login, creds = request_login_params()
+		pool = gmConnectionPool.gmConnectionPool()
+		pool.credentials = creds
+		#conn = get_connection()
+		#print(get_db_fingerprint(conn, with_dump = True, eol = '\n'))
+		print(get_db_fingerprint(with_dump = True, eol = '\n'))
+
 	#--------------------------------------------------------------------
 	# run tests
 
@@ -2535,11 +2617,12 @@ SELECT to_timestamp (foofoo,'YYMMDD.HH24MI') FROM (
 	#test_get_index_name()
 	#test_set_user_language()
 	#test_get_schema_revision_history()
-	test_run_query()
+	#test_run_query()
 	#test_schema_exists()
 	#test_get_foreign_key_names()
 	#test_row_locks()
 	#test_faulty_SQL()
-	test_log_settings()
+	#test_log_settings()
+	test_get_db_fingerprint()
 
 # ======================================================================


=====================================
server/pycommon/gmTools.py
=====================================
@@ -698,7 +698,7 @@ def old_unicode_csv_reader(unicode_csv_data, dialect=csv.excel, encoding='utf-8'
 	for row in csv_reader:
 		# decode ENCODING back to Unicode, cell by cell:
 		if is_dict_reader:
-			for key in row.keys():
+			for key in row:
 				if key == default_csv_reader_rest_key:
 					old_data = row[key]
 					new_data = []
@@ -1436,8 +1436,8 @@ def compare_dict_likes(d1, d2, title1=None, title2=None):
 		d2 = dict(d2)
 	except TypeError:
 		pass
-	keys_d1 = frozenset(d1.keys())
-	keys_d2 = frozenset(d2.keys())
+	keys_d1 = list(d1)
+	keys_d2 = list(d2)
 	different = False
 	if len(keys_d1) != len(keys_d2):
 		_log.info('different number of keys: %s vs %s', len(keys_d1), len(keys_d2))
@@ -1487,8 +1487,8 @@ def format_dict_likes_comparison(d1, d2, title_left=None, title_right=None, left
 	except TypeError: pass
 	try: d2 = dict(d2)
 	except TypeError: pass
-	keys_d1 = d1.keys()
-	keys_d2 = d2.keys()
+	keys_d1 = list(d1)
+	keys_d2 = list(d2)
 	data = {}
 	for key in keys_d1:
 		data[key] = [d1[key], ' ']
@@ -1586,7 +1586,7 @@ def format_dict_like(d, relevant_keys=None, template=None, missing_key_template=
 			return template % d
 
 	if relevant_keys is None:
-		relevant_keys = list(d.keys())
+		relevant_keys = list(d)
 	lines = []
 	if value_delimiters is None:
 		delim_left = ''
@@ -1636,7 +1636,7 @@ def dicts2table(dict_list, left_margin=0, eol='\n', keys2ignore=None, column_lab
 			d[col_label_key] = max(column_labels[dict_idx].split('\n'), key = len)
 		field_lengths = []
 		# loop over all keys in this dict
-		for key in d.keys():
+		for key in d:
 			# ignore this key
 			if key in keys2ignore:
 				continue


=====================================
server/sql/v21-v22/fixups/v22-release_notes-fixup.sql
=====================================
@@ -17,25 +17,28 @@ INSERT INTO dem.message_inbox (
 ) VALUES (
 	(select pk from dem.staff where db_user = 'any-doc'),
 	(select pk_type from dem.v_inbox_item_type where type = 'memo' and category = 'administrative'),
-	'Release Notes for GNUmed 1.8.1 (database v22.12)',
-	'GNUmed 1.8.1 Release Notes:
+	'Release Notes for GNUmed 1.8.3 (database v22.13)',
+	'GNUmed 1.8.3 Release Notes:
 
-	1.8.1
+	1.8.3
 
-NEW: tool: read_all_rows_of_table
+NEW: tool: fingerprint_db
 
-FIX: bills: failure to generate bill PDFs [thanks Marc]
-FIX: bills: failure to edit bill item date [thanks Marc]
-FIX: bills: failure to edit billable [thanks Marc]
-FIX: export area: fails to load when gm-burn.sh not found [thanks Marc]
-FIX: demographics: failure to edit type of address [thanks Marc]
-FIX: forms: failure to archive generated forms [thanks Marc]
-FIX: demographics: faulty display of patient addresses [thanks Marc]
+IMPROVED: forms: log pdflatex version
 
-	22.12
+FIX: meds: drug data source selection [thanks bganglia892]
+FIX: meds: ADR URL configuration [thanks bganglia892]
+FIX: vaccs: ADR URL configuration [thanks bganglia892]
+FIX: tests: LOINC import fixup [thanks bganglia892]
+FIX: db: whitespace in connection parameters [thanks kikiruz]
+FIX: startup: startup without console fails [thanks Marc]
+FIX: top panel: incorrect age-at-birthday display
+FIX: i18n: locale activation
 
-IMPROVED: robustify backup script
+	22.13
+
+IMPROVED: bootstrapper logging
 ');
 
 -- --------------------------------------------------------------
-select gm.log_script_insertion('v22-release_notes-fixup.sql', '22.12');
+select gm.log_script_insertion('v22-release_notes-fixup.sql', '22.13 at 1.8.3');



View it on GitLab: https://salsa.debian.org/med-team/gnumed-server/-/compare/f3240512fe25d261fd5f7de852611d6ba749f5b3...3700d97352a66ac4ba41a3450fadc5e9935a6c05

-- 
View it on GitLab: https://salsa.debian.org/med-team/gnumed-server/-/compare/f3240512fe25d261fd5f7de852611d6ba749f5b3...3700d97352a66ac4ba41a3450fadc5e9935a6c05
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