debian/NEWS.Debian

+gnumed-server (22.0-1) unstable; urgency=medium
+
+  If you are using postgresql-common version < 122 you need to
+  install the file
+    /usr/share/doc/gnumed-server/gm-pg_upgradecluster-helper
+  into the directory
+    /etc/postgresql-common/pg_upgradecluster.d/
+  This script modifies the GNUmed databases such that an upgrade
+  using pg_upgradecluster of earlier versions of postgresql-common
+  will succeed.
+
+ -- Andreas Tille <tille@debian.org>  Mon, 26 Mar 2018 14:48:43 +0200
+
 gnumed-server (19.0-1) unstable; urgency=low
 
   Before upgrading your existing GNUmed database v18 to the v19 schema it

debian/changelog

+gnumed-server (22.0-1) UNRELEASED; urgency=medium
+
+  * New upstream feature release
+  * Depends: flock
+  * Standards-Version: 4.1.3
+  * debhelper 11
+  * debian/cron.daily: gm-backup_database is deprecated and replaced by
+    gm-backup
+  * debian/NEWS.Debian: Mention need of gm-pg_upgradecluster-helper
+
+ -- Andreas Tille <tille@debian.org>  Mon, 26 Mar 2018 14:48:43 +0200
+
 gnumed-server (21.15-1) unstable; urgency=medium
 
   * New upstream version

debian/compat

-10
+11

debian/control

@@ -4,10 +4,10 @@ Uploaders: Andreas Tille <tille@debian.org>,
            Sebastian Hilbert <sebastian.hilbert@gmx.net>
 Section: misc
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                python
 Build-Depends-Indep: po-debconf
-Standards-Version: 4.1.1
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/gnumed-server.git
 Vcs-Git: https://anonscm.debian.org/debian-med/gnumed-server.git
 Homepage: http://www.gnumed.de
@@ -23,6 +23,7 @@ Depends: ${misc:Depends},
          openssl,
          bzip2,
          cron | anacron,
+         flock,
          sudo,
          gnupg | gnupg2,
          rsync,

debian/cron.daily

@@ -6,7 +6,7 @@
 # DATA=/usr/sbin/gm-backup_data
 
 # Backup of data and table structure
-DATABASE=/usr/sbin/gm-backup_database
+DATABASE=/usr/sbin/gm-backup
 
 # Compress and sign backup
 ZIPSIGN=/usr/sbin/gm-zip+sign_backups

debian/patches/make_sure_user_has_set_organisation_in_v18.patch

-Author: Andreas Tille <tille@debian.org>
-LastChanged: Fri, 08 Nov 2013 15:25:40 +0100
-Description: We want to make really sure that the user has
- set organisation + unit in his old database (v18) before we
- are upgrading to v19.  The patch can be droped again for
- later (major) versions.
- 
---- a/server/gm-bootstrap_server
-+++ b/server/gm-bootstrap_server
-@@ -1,4 +1,28 @@
--#!/bin/sh
-+#!/bin/bash
-+
-+# if any GNUmed database is available ...
-+if psql -l | grep -qi gnumed ; then
-+  # ... ask user whether he has injected organisation + unit
-+  cat <<EOT
-+========================================================================
-+
-+Before upgrading your existing GNUmed database v18 to the v19 schema it
-+is very advisable to make sure you have created (by using the 1.3
-+client) -- an organization and a unit thereof to serve as your praxis
-+and praxis location. During the very first start of the 1.4 client you
-+will be asked which organization/unit represents your praxis/location.
-+
-+Did you have definte organization and unit thereof?
-+
-+EOT
-+  read -e -p "[y / N]: "
-+  if test "${REPLY}" = "y" ; then
-+    echo "OK. Start upgrading server."
-+  else
-+    echo "Upgrading aborted by user."
-+    exit 1
-+  fi
-+fi
- 
- #==============================================================
- # This wrapper is intended to be installed into a systemwide

debian/patches/series

-make_sure_user_has_set_organisation_in_v18.patch

server/bootstrap/bootstrap-latest.bat

@@ -5,9 +5,9 @@ cd /d %~dp0
 REM command line options:
 REM quiet
 
-SET VER=21
-SET PREV_VER=20
-SET LASTVERSIONSTODROP=19
+SET VER=22
+SET PREV_VER=21
+SET LASTVERSIONSTODROP=20
 SET QUIET=%1
 
 SET PYTHONPATH="%PYTHONPATH%;../../"

server/bootstrap/bootstrap-latest.conf

@@ -38,6 +38,7 @@ update_db-v17_v18.conf
 update_db-v18_v19.conf
 update_db-v19_v20.conf
 update_db-v20_v21.conf
+update_db-v21_v22.conf
 $config files$
 
 interactive = no

server/bootstrap/bootstrap-latest.sh

@@ -4,9 +4,9 @@
 # - command line options:
 #   - "quiet"
 
-VERSIONS_TO_DROP="2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19"
-PREV_VER="20"
-VER="21"
+VERSIONS_TO_DROP="2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20"
+PREV_VER="21"
+VER="22"
 QUIET="$1"
 
 

server/bootstrap/bootstrap_gm_db_system.py

@@ -652,6 +652,10 @@ class database:
 			_log.error(u'cannot REINDEX cloned target database')
 			return False
 
+		if not self.revalidate_constraints():
+			_log.error(u'cannot VALIDATE CONSTRAINTs in cloned target database')
+			return False
+
 		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):
@@ -732,12 +736,14 @@ class database:
 		curs.close()
 		self.conn.commit()
 
-		# we need inheritance or else things will fail miserably
+		# we need inheritance or else things will fail miserably but:
+		# default now ON and PG10.0 hardwired to ON
+		# so remove database specific setting
 		curs = self.conn.cursor()
 		try:
 			curs.execute("alter database %s set sql_inheritance to DEFAULT" % self.name)
 		except:
-			_log.exception(u'PG 10 hardwired for sql_inheritance')
+			_log.exception('PostgreSQL 10 onwards: <sql_inheritance> hardwired')
 		curs.close()
 		self.conn.commit()
 
@@ -798,6 +804,7 @@ class database:
 
 		_log.info(u"Database [%s] does not exist." % self.name)
 		return None
+
 	#--------------------------------------------------------------
 	def __create_db(self):
 
@@ -821,14 +828,11 @@ class database:
 				print_msg("==> dropping pre-existing target database [%s] ..." % self.name)
 				_log.info(u'trying to drop target database')
 				cmd = 'DROP DATABASE "%s"' % self.name
-				_log.debug(u'committing existing connection before setting autocommit')
+				# DROP DATABASE must be run outside transactions
 				self.conn.commit()
-				_log.debug(u'setting autocommit to TRUE')
-				self.conn.autocommit = True
-				self.conn.readonly = False
+				self.conn.set_session(readonly = False, autocommit = True)
 				cursor = self.conn.cursor()
 				try:
-					cursor.execute(u'SET default_transaction_read_only TO OFF')
 					_log.debug(u'running SQL: %s', cmd)
 					cursor.execute(cmd)
 				except:
@@ -875,13 +879,11 @@ class database:
 
 		# create database by cloning
 		print_msg("==> cloning [%s] (%s) as target database [%s] ..." % (self.template_db, size, self.name))
-		# create DB must be run outside transactions
+		# CREATE DATABASE must be run outside transactions
 		self.conn.commit()
-		self.conn.autocommit = True
-		self.conn.readonly = False
+		self.conn.set_session(readonly = False, autocommit = True)
 		cursor = self.conn.cursor()
 		try:
-			cursor.execute(u'SET default_transaction_read_only TO OFF')
 			cursor.execute(create_db_cmd)
 		except:
 			_log.exception(u">>>[%s]<<< failed" % create_db_cmd)
@@ -1155,10 +1157,10 @@ class database:
 		_log.info(u'this may potentially take "quite a long time" depending on how much data there is in the database')
 		_log.info(u'you may want to monitor the PostgreSQL log for signs of progress')
 
+		# REINDEX must be run outside transactions
 		self.conn.commit()
 		self.conn.set_session(readonly = False, autocommit = True)
 		curs_outer = self.conn.cursor()
-		curs_outer.execute(u'SET default_transaction_read_only TO OFF')
 		cmd = 'REINDEX (VERBOSE) DATABASE %s' % self.name
 		try:
 			curs_outer.execute(cmd)
@@ -1182,6 +1184,52 @@ class database:
 
 		return True
 
+	#--------------------------------------------------------------
+	def revalidate_constraints(self):
+
+		print_msg("==> revalidating constraints in target database (can take a while) ...")
+
+		do_revalidate = cfg_get(self.section, 'revalidate')
+		if do_revalidate is None:
+			do_revalidate = True		# default: do it
+		else:
+			do_revalidate = (int(do_revalidate) == 1)
+		if not do_revalidate:
+			_log.warning('skipping VALIDATE CONSTRAINT')
+			print_msg("    ... skipped")
+			return True
+
+		_log.info(u'reVALIDATing CONSTRAINTs in cloned target database so upgrade does not fail due to broken data')
+		_log.info(u'this may potentially take "quite a long time" depending on how much data there is in the database')
+		_log.info(u'you may want to monitor the PostgreSQL log for signs of progress')
+
+		curs = self.conn.cursor()
+		cmd = u"""do $$
+			DECLARE
+				r record;
+			BEGIN
+				FOR r IN (
+					select con.connamespace, nsp.nspname, con.conname, con.conrelid, rel.relname
+					from pg_constraint con
+						join pg_namespace nsp on nsp.oid = con.connamespace
+						join pg_class rel on rel.oid = con.conrelid
+					where contype in ('c','f')
+				) LOOP
+					RAISE NOTICE 'validating [%] on [%.%]', r.conname, r.nspname, r.relname;
+					EXECUTE 'UPDATE pg_constraint SET convalidated=false WHERE conname=$1 AND connamespace=$2 AND conrelid=$3' USING r.conname, r.connamespace, r.conrelid;
+					EXECUTE 'ALTER TABLE ' || r.nspname || '.' || r.relname || ' VALIDATE CONSTRAINT "' || r.conname || '"';
+				END LOOP;
+			END
+		$$;"""
+		try:
+			curs.execute(cmd)
+		except:
+			_log.exception(u">>>[VALIDATE CONSTRAINT]<<< failed")
+			return False
+		finally:
+			curs.close()
+		return True
+
 	#--------------------------------------------------------------
 	def transfer_users(self):
 		print_msg("==> transferring users ...")
@@ -1806,8 +1854,6 @@ finally:
 			_log.warning(u'%s', conn)
 			_log.warning(u'closing connection')
 			conn.close()
-		del conn
-	del conn_ref_count
 
 _log.info(u'after main, before sys.exit(0)')
 

server/bootstrap/fixup_db-v22.conf

+# GNUmed database system bootstrapping config file
+#-------------------------------------------------
+# license: GPL v2 or later
+# author: Karsten Hilbert@gmx.net
+
+#----------------------------------
+[installation]
+interactive = yes
+
+keep temp files = no
+
+description = $description$
+This will update an existing GNUmed database.
+
+It does so by applying all fixup SQL scripts
+appropriate to the version of the database.
+
+$description$
+
+bundles = $bundles$
+v22-fixups
+$bundles$
+
+#----------------------------------
+[bundle v22-fixups]
+database alias = gnumed_v22
+minimum postgresql version = 9.2
+schema base directory = ../sql/v21-v22/fixups/
+schema = $schema$
+../dynamic/v22-release_notes-dynamic.sql
+$schema$
+
+#----------------------------------
+[database gnumed_v22]
+name = gnumed_v22
+override name by = GM_CORE_DB
+drop target database = 0
+use existing target database = 1
+target version = v22
+transfer users = 0
+
+template database = template1
+server alias = local host
+audit disable = 1
+audit trail parent table = audit.audit_trail
+audit trail table prefix = log_
+audit fields table = audit.audit_fields
+schema base directory = ../sql/v21-v22/
+schema = $schema$
+$schema$
+
+superuser schema = $superuser schema$
+$superuser schema$
+
+upgrade plausibility checks = $upgrade plausibility checks$
+$upgrade plausibility checks$
+
+script base directory = ../sql/v21-v22/python/
+data import scripts = $data import scripts$
+$data import scripts$
+
+#----------------------------------
+[server local host]
+name = 
+port = 5432
+template database = template1
+super user alias = postgres
+schema base directory = ../sql/v21-v22/
+schema = $schema$
+$schema$
+
+#----------------------------------
+[user GNUmed owner]
+name = gm-dbo
+password = 
+
+[user postgres]
+name = postgres
+#password =
+
+#----------------------------------
+# these really shouldn't be changed
+#----------------------------------
+[GnuMed defaults]
+
+database owner alias = GNUmed owner
+
+groups = $groups$
+$groups$
+
+#----------------------------------

server/bootstrap/update_db-v21_v22.conf

+# GNUmed database system bootstrapping config file
+#-------------------------------------------------
+# license: GPL v2 or later
+# author: Karsten Hilbert@gmx.net
+
+#----------------------------------
+[revision control]
+file = /home/ncq/Projekte/cvs2git/vcs-mirror/gnumed/gnumed/server/bootstrap/update_db-v21_v22.conf
+version = 1.0
+
+#----------------------------------
+[installation]
+interactive = yes
+
+keep temp files = no
+
+description = $description$
+This will update an existing GNUmed version 21
+database to the version 22 schema. It does not do
+any harm to the data contained within.
+
+The existing database will be cloned first. The copy is
+then modified. The original database remains unchanged.
+$description$
+
+
+bundles = $bundles$
+v21_fixups-pre_v22
+v21-v22-static
+v21-v22-dynamic
+$bundles$
+
+#----------------------------------
+[bundle v21_fixups-pre_v22]
+database alias = gnumed_v22
+minimum postgresql version = 9.2
+schema base directory = ../sql/v20-v21/fixups/
+schema = $schema$
+v21-db-sql_inheritance-fixup.sql
+v21-previously-missing-array_agg-fixup.sql
+v21-dem-view_grants-fixup.sql
+../dynamic/v21-release_notes-dynamic.sql
+v21-ref-auto_hint-tetanus_STIKO.sql
+v21-ref-auto_hint-klug_entscheiden_pulmo.sql
+v21-ref-auto_hint-klug_entscheiden_endokrino.sql
+v21-CD_DVD-sleeve.sql
+v21-AMTS_Medikationsplan-fixup.sql
+v21-ref-auto_hint-smoking_status-fixup.sql
+v21-ref-GKV_CU-fixup.sql
+v21-clin-get_hints_for_patient-fixup.sql
+v21-notifications-dynamic.sql
+v21-clin-uppercase_soap_cat-fixup.sql
+v21-dem-identity-fixup.sql
+v21-Constans-TVT-OE.sql
+$schema$
+
+#----------------------------------
+[bundle v21-v22-static]
+database alias = gnumed_v22
+minimum postgresql version = 9.2
+schema base directory = ../sql/v21-v22/static/
+schema = $schema$
+v22-ref-substance-static.sql
+v22-ref-lnk_loinc2substance-static.sql
+v22-ref-dose-static.sql
+v22-ref-drug_product-static.sql
+v22-ref-lnk_dose2drug-static.sql
+v22-ref-auto_hint-static.sql
+v22-clin-vaccine-static.sql
+v22-clin-lnk_loinc2test_panel-static.sql
+v22-clin-procedure-static.sql
+v22-clin-external_care-static.sql
+v22-blobs-doc_med-static.sql
+$schema$
+
+#----------------------------------
+[bundle v21-v22-dynamic]
+database alias = gnumed_v22
+minimum postgresql version = 9.2
+schema base directory = ../sql/v21-v22/dynamic/
+schema = $schema$
+v22-i18n-v_missing_translations.sql
+v22-notifications-dynamic.sql
+v22-blobs-doc_med-dynamic.sql
+v22-blobs-v_doc_med.sql
+v22-blobs-v_doc_desc.sql
+v22-blobs-v_obj4doc_no_data.sql
+v22-blobs-v_reviewed_doc_objects.sql
+v22-blobs-v_latest_mugshot.sql
+v22-ref-auto_hint-dynamic.sql
+# conversion of drug products
+v22-ref-substance-dynamic.sql
+v22-ref-lnk_loinc2substance-dynamic.sql
+v22-ref-dose-dynamic.sql
+v22-ref-lnk_dose2drug-dynamic.sql
+v22-ref-v_drug_products.sql
+# convert vaccines
+v22-clin-move_vacc_objects_to_ref.sql
+v22-ref-remove_unused_vaccines.sql
+v22-ref-create_generic_vaccines.sql
+v22-ref-convert_vaccines.sql
+v22-ref-remove_unused_vaccines.sql
+v22-ref-create_generic_vaccines.sql
+v22-ref-vacc_indication-drop.sql
+v22-ref-v_vaccines.sql
+v22-ref-v_indications4vaccine.sql
+# done with vaccines, now vaccinations
+v22-clin-v_vaccinations.sql
+v22-clin-v_pat_vaccs4indication.sql
+v22-clin-v_pat_last_vacc4indication.sql
+v22-clin-v_vaccinations_journal.sql
+# done with vaccinations
+# test panel conversion
+v22-clin-lnk_loinc2test_panel-dynamic.sql
+v22-clin-convert_test_panels.sql
+v22-clin-v_test_panels.sql
+v22-clin-v_test_types4test_panel.sql
+v22-clin-v_test_types.sql
+v22-clin-v_test_results.sql
+v22-clin-v_test_results_journal.sql
+# with test panel conversion
+v22-dem-unique_named_identity.sql
+v22-dem-v_person_names.sql
+v22-dem-v_message_inbox.sql
+v22-dem-v_pat_addresses.sql
+v22-clin-lowercase_soap_cat.sql
+v22-clin-remove_old_empty_encounters.sql
+v22-clin-v_hospital_stays.sql
+v22-clin-procedure-dynamic.sql
+v22-clin-export_item-dynamic.sql
+v22-clin-v_export_items.sql
+v22-clin-v_external_care.sql
+v22-clin-substance_intake-dynamic-run_once.sql
+v22-clin-substance_intake-dynamic.sql
+v22-clin-substance_intake-insert_triggers.sql
+v22-clin-substance_intake-update_triggers.sql
+v22-clin-substance_intake-delete_triggers.sql
+v22-clin-transfer_all_encounter_data.sql
+v22-clin-vaccine_batches-dynamic.sql
+v22-clin-v_suppressed_hints.sql
+v22-clin-v_suppressed_hints_journal.sql
+v22-blobs-v_doc_med_journal.sql
+v22-clin-v_procedures_journal.sql
+v22-clin-v_substance_intake_journal.sql
+v22-clin-v_external_care_journal.sql
+v22-clin-v_emr_journal.sql
+v22-clin-get_hints_for_patient.sql
+v22-clin-v_candidate_diagnoses.sql
+v22-ref-auto_hints.sql
+v22-i18n-German.sql
+v22-kwd-patient_media_export_icon.sql
+v22-release_notes-dynamic.sql
+$schema$
+
+#----------------------------------
+[bundle v22-fixups]
+database alias = gnumed_v22
+minimum postgresql version = 9.2
+schema base directory = ../sql/v21-v22/fixups/
+schema = $schema$
+$schema$
+
+#----------------------------------
+[bundle v22-test_data]
+database alias = gnumed_v22
+minimum postgresql version = 9.2
+schema base directory = ../sql/test-data/
+schema = $schema$
+$schema$
+
+#----------------------------------
+[database gnumed_v22]
+name = gnumed_v22
+override name by = GM_CORE_DB
+drop target database = 1
+target version = v22
+reindex = 1
+revalidate = 1
+transfer users = 1
+template database = gnumed_v21
+template version = v21
+server alias = local host
+audit disable = 0
+audit trail parent table = audit.audit_trail
+audit trail table prefix = log_
+audit fields table = audit.audit_fields
+schema base directory = ../sql/v21-v22/
+schema = $schema$
+$schema$
+
+superuser schema = $superuser schema$
+$superuser schema$
+
+script base directory = ../sql/v21-v22/python/
+data import scripts = $data import scripts$
+v22-import-form-templates.py
+$data import scripts$
+
+
+
+
+# line 1: old database
+# line 2: new database
+upgrade plausibility checks = $upgrade plausibility checks$
+identities::::select count(1) from dem.identity
+	select count(1) from dem.identity			-- new
+names::::select count(1) from dem.names
+	select count(1) from dem.names	-- new
+v_all_persons::::select count(1) from dem.v_persons
+	select count(1) from dem.v_all_persons	-- new
+v_active_persons::::select count(1) from dem.v_active_persons
+	select count(1) from dem.v_active_persons	-- new
+staff::::select count(1) from dem.staff								-- old
+	select count(1) from dem.v_staff where not person_is_deleted	-- new
+v_staff::::select count(1) from dem.v_staff
+	select count(1) from dem.v_staff	-- new
+addresses::::select count(1) from dem.address
+	select count(1) from dem.address	-- new
+unique URBs with ZIP::::select count(1) from dem.v_uniq_zipped_urbs		-- old
+	select count(1) from dem.v_uniq_zipped_urbs							-- new
+patient addresses view::::select count(1) from dem.v_pat_addresses		-- old
+	select count(1) from dem.v_pat_addresses							-- new
+episodes::::select count(1) from clin.episode where not summary ilike '%[substance use]%'
+	select count(1) from clin.episode where not summary ilike '%[substance use]%'
+denormalized episodes::::select count(1) from clin.v_pat_episodes where not summary ilike '%[substance use]%'
+	select count(1) from clin.v_pat_episodes where not summary ilike '%[substance use]%'
+encounters::::select count(1) from clin.encounter
+	select count(1) from clin.v_pat_encounters
+issues::::select count(1) from clin.health_issue
+	select count(1) from clin.health_issue
+issues view::::select count(1) from clin.v_health_issues
+	select count(1) from clin.v_health_issues
+procedures::::select count(1) from clin.procedure
+	select count(1) from clin.procedure
+documents::::select count(1) from blobs.doc_med
+	select count(1) from blobs.doc_med
+document pages::::select count(1) from blobs.doc_obj
+	select count(1) from blobs.doc_obj
+allergies::::select count(1) from clin.allergy
+	select count(1) from clin.allergy
+communication channels::::select count(1) from dem.lnk_identity2comm
+	select count(1) from dem.lnk_identity2comm
+test results::::select count(1) from clin.test_result
+	select count(1) from clin.test_result
+unmatched test results::::select count(1) from clin.incoming_data_unmatched
+	select count(1) from clin.incoming_data_unmatched
+unmatchable test results::::select count(1) from clin.incoming_data_unmatchable
+	select count(1) from clin.incoming_data_unmatchable
+denormalized test results::::select count(1) from clin.v_test_results
+	select count(1) from clin.v_test_results
+allergy states::::select count(1) from clin.allergy_state
+	select count(1) from clin.allergy_state
+waiting list entries::::select count(1) from clin.waiting_list
+	select count(1) from clin.waiting_list
+waiting list view entries::::select count(1) from clin.v_waiting_list
+	select count(1) from clin.v_waiting_list
+waiting list integrity::::select((select count(1) from clin.v_waiting_list) = (select count(1) from clin.waiting_list))
+	select((select count(1) from clin.v_waiting_list) = (select count(1) from clin.waiting_list))
+messages::::select count(1) + 2 from dem.message_inbox
+	select count(1) from dem.message_inbox
+test orgs::::select count(1) from clin.test_org
+	select count(1) from clin.test_org
+--substance transfer - name::::select count(1) from (select distinct on (description) description from ref.consumable_substance WHERE atc_code NOT LIKE 'J07%') as d
+--	select count(1) from ref.substance WHERE atc NOT LIKE 'J07%'
+--substance transfer - dose::::select count(1) from ref.consumable_substance WHERE atc_code NOT LIKE 'J07%'
+--	select count(1) from ref.v_substance_doses where atc_substance NOT LIKE 'J07%'
+--dose view consistency::::select count(1) from ref.consumable_substance
+--	select count(1) from ref.v_substance_doses
+substance view -- correctness::::select True
+	select (select count(1) from ref.substance) = (select count(1) from ref.v_substances)
+dose view -- correctness::::select True
+	select (select count(1) from ref.dose) = (select count(1) from ref.v_substance_doses)
+substance intakes (tables)::::select count(1) from clin.substance_intake
+	select count(1) from clin.substance_intake
+substance intakes (views)::::select count(1) from clin.v_substance_intakes
+	select count(1) from clin.v_substance_intakes
+substance intakes (table vs view)::::select count(1) from clin.substance_intake
+	select count(1) from clin.v_substance_intakes
+--brands consistency::::select (select count(1) from ref.branded_drug) + (select count(1) from (select distinct on (substance, amount, unit) substance from clin.v_nonbrand_intakes) as d)
+--	select count(1) from ref.drug_product
+--vaccines::::select count(1) from clin.vaccine where pk in (select fk_vaccine from clin.vaccination)
+--	select count(1) from ref.vaccine
+vaccines view (existence)::::select TRUE from clin.v_vaccines
+	select TRUE from ref.v_vaccines
+--vaccines (indication count)::::select count(1) from clin.v_indications4vaccine where pk_vaccine in (select fk_vaccine from clin.vaccination)
+--	select count(1) from ref.v_indications4vaccine
+vaccinations (total count)::::select count(1) from clin.vaccination
+	select count(1) from clin.vaccination
+--vaccinations-by-indication (total count)::::select count(1) from clin.v_pat_vaccs4indication
+--	select count(1) from clin.v_pat_vaccs4indication
+vaccinations-by-indication (patient count)::::select count(1) from (select distinct on (pk_patient) pk_patient from clin.v_pat_vaccs4indication) as distinct_pats
+	select count(1) from (select distinct on (pk_patient) pk_patient from clin.v_pat_vaccs4indication) as distinct_pats
+vaccinations-by-indication (shots count)::::select count(1) from (select distinct on (pk_vaccination) pk_vaccination from clin.v_pat_vaccs4indication) as distinct_shots
+	select count(1) from (select distinct on (pk_vaccination) pk_vaccination from clin.v_pat_vaccs4indication) as distinct_shots
+--vaccinations-by-indication (indications count)::::select count(1) from clin.v_pat_vaccs4indication group by pk_indication
+--	select count(1) from clin.v_pat_vaccs4indication group by atc_indication
+--vaccinations-by-indication (vaccine count)::::select count(1) from (select distinct on (pk_vaccine) pk_vaccine clin.v_pat_vaccs4indication) as distinct_vaccines
+--	select count(1) from (select distinct on (pk_vaccine) pk_vaccine clin.v_pat_vaccs4indication) as distinct_vaccines
+vaccinations-by-indication (consistency)::::select count(1) from clin.vaccination
+	select count(1) from (select distinct on (pk_vaccination) pk_vaccination from clin.v_pat_vaccs4indication) as distinct_shots
+latest vaccinations (total count)::::select count(1) from clin.v_pat_last_vacc4indication where indication NOT ILIKE '%influenza%'
+	select count(1) from clin.v_pat_last_vacc4indication where indication NOT ILIKE '%influenza%'
+latest vaccinations (patient count)::::select count(1) from clin.v_pat_last_vacc4indication where indication NOT ILIKE '%influenza%' group by pk_patient
+	select count(1) from clin.v_pat_last_vacc4indication where indication NOT ILIKE '%influenza%' group by pk_patient
+latest vaccinations (shots count)::::select count(1) from clin.v_pat_last_vacc4indication group by pk_vaccination
+	select count(1) from clin.v_pat_last_vacc4indication group by pk_vaccination
+latest vaccinations (indications count)::::select count(1) from clin.v_pat_last_vacc4indication group by pk_indication
+	select count(1) from clin.v_pat_last_vacc4indication group by atc_indication
+latest vaccinations (vaccine count)::::select count(1) from clin.v_pat_last_vacc4indication group by pk_vaccine
+	select count(1) from clin.v_pat_last_vacc4indication group by pk_vaccine
+requests on results::::select count(1) from clin.test_result where fk_request is not NULL
+	select count(1) from clin.test_result where fk_request is not NULL
+clinical code links (total) - internal consistency::::select True
+	select ((select count(1) from clin.lnk_code2item_root) = (select ((select count(1) from clin.lnk_code2procedure) + (select count(1) from clin.lnk_code2rfe) + (select count(1) from clin.lnk_code2aoe) + (select count(1) from clin.lnk_code2episode) + (select count(1) from clin.lnk_code2h_issue) + (select count(1) from clin.lnk_code2narrative))))
+paperwork templates::::select count(1) from ref.paperwork_templates
+	select count(1) from ref.paperwork_templates
+automatic hints::::select count(1) from ref.auto_hint
+	select count(1) - 1 from ref.auto_hint
+-- do NOT try to check the number of suppressed hints because
+-- even though we do know the number of *hints* that will have
+-- changed we simply cannot know the number of suppressions that
+-- will be lifted by those changes
+--suppressed hints::::select count(1) from clin.suppressed_hint
+--	select count(1) from clin.suppressed_hint
+raw keyword expansions::::select count(1) from ref.keyword_expansion
+	select count(1) - 2 from ref.keyword_expansion
+mapped keyword expansions::::select count(1) from ref.v_keyword_expansions
+	select count(1) - 2 from ref.v_keyword_expansions
+organisations::::select count(1) from dem.org
+	select count(1) from dem.org
+organisational units::::select count(1) from dem.org_unit
+	select count(1) from dem.org_unit
+data sources::::select count(1) from ref.data_source
+	select count(1) from ref.data_source
+bills with invoices but without VAT status::::select 0
+	select count(1) from bill.bill where (apply_vat is null) and (fk_doc is not null)
+clinical items::::select count(1) from clin.clin_root_item
+	select count(1) from clin.clin_root_item
+export items::::select count(1) from clin.export_item
+	select count(1) from clin.export_item
+export items view::::select count(1) from clin.v_export_items
+	select count(1) from clin.v_export_items
+export items integrity::::select ((select count(1) from clin.export_item) = (select count(1) from clin.v_export_items))
+	select ((select count(1) from clin.export_item) = (select count(1) from clin.v_export_items))
+external care::::select count(1) from clin.external_care
+	select count(1) from clin.external_care
+external care view integrity::::select TRUE
+	select ((select count(1) from clin.external_care) = (select count(1) from clin.v_external_care))
+-- ------------------
+-- commented out:
+--ATC codes::::select count(1) from (select distinct on (code, term, fk_data_source) 1 from ref.atc) as uniq_atc
+--	select count(1) from ref.atc
+--ATC vs generic codes - internal consistency::::select 0
+--	select code, term, fk_data_source from ref.atc except select code, term, fk_data_source from ref.generic_coding_system
+--LOINC codes::::select count(1) from ref.loinc
+--	select count(1) from ref.loinc
+--LOINC vs generic codes - internal consistency::::select 0
+--	select code, term, fk_data_source from ref.loinc except select code, term, fk_data_source from ref.generic_coding_system
+--generic codes (total) - internal consistency::::select True
+--	select ((select count(1) from ref.coding_system_root) = (select ((select count(1) from ref.atc) + (select count(1) from ref.loinc))))
+-- ------------------
+-- for debugging:
+--skipped check::::select 'skipped in old'		-- old
+--	select 'skipped in new'						-- new
+--check definition error::select 1				-- old
+--	select 1									-- new
+--syntax error (old)::::selec 1 				-- old
+--	select 1									-- new
+--syntax error (new)::::select 1 				-- old
+--	selec 1										-- new
+--data mismatch error::::select 1 				-- old
+--	select 2 -- new
+$upgrade plausibility checks$
+
+#----------------------------------
+[server local host]
+name = 
+port = 5432
+template database = template1
+super user alias = postgres
+schema base directory = ../sql/v21-v22/
+schema = $schema$
+$schema$
+
+#----------------------------------
+[user GNUmed owner]
+name = gm-dbo
+password = 
+
+[user postgres]
+name = postgres
+#password =
+
+#----------------------------------
+# these really shouldn't be changed
+#----------------------------------
+[GnuMed defaults]
+
+database owner alias = GNUmed owner
+
+groups = $groups$
+$groups$
+
+#----------------------------------

server/doc/gm-backup.8

@@ -21,10 +21,10 @@ loss.  The Debian GNU/Linux packaged version of the GNUmed
 server installs such a cron job by default.
 
 .SH SEE ALSO
-gm-backup_database(8)
+gm-restore(8)
 
 /etc/gnumed/gnumed-backup.conf
 
 .SH AUTHOR
-This manual page was written by Andreas Tille <tille@debian.org>,
+This manual page was written by Andreas Tille <tille@debian.org>
 for the Debian GNU/Linux system (but may be used by others).

server/doc/gm-backup_data.8

 .TH GM-BACKUP_DATA 8 "2009 January 8th" "GNUmed server data backup"
 
+.SH NOTE
+
+.I Deprecated in favour of gm-backup(8).
+
 .SH NAME
 .B gm-backup_data
 - backup of GNUmed data
@@ -19,8 +23,12 @@ If you really know what you are doing and want to
 care for database schema  and roles yourself this
 script might suffice to backup the raw data.
 
+It is recommended to use
+.B gm-backup
+instead.
+
 .SH SEE ALSO
-.B gm-backup_database(8)
+.B gm-backup(8)
 
 .B /etc/gnumed/gnumed-backup.conf
 

server/doc/gm-backup_database.8

 .TH GM-BACKUP_DATABASE 8 "2009 January 8th" "GNUmed server database backup"
 
+.SH NOTE
+
+.I Deprecated in favour of gm-backup(8).
+
 .SH NAME
 .B gm-backup_database
 - complete backup of GNUmed database
@@ -19,10 +23,14 @@ job to ensure that GNUmed patient data are safe against data
 loss.  The Debian GNU/Linux packaged version of the GNUmed
 server installs such a cron job by default.
 
+It is recommended to use
+.B gm-backup
+instead.
+
 .SH SEE ALSO
-gm-backup_data(8)
+.B  gm-backup_data(8)
 
-/etc/gnumed/gnumed-backup.conf
+.B /etc/gnumed/gnumed-backup.conf
 
 .SH AUTHOR
 This manual page was written by Andreas Tille <tille@debian.org>,

server/doc/gm-fingerprint_db.8

@@ -14,7 +14,7 @@
 a GNUmed database (such as "gnumed_VERSION")
 
 .I <gm-dbo password>
-the password for the databse owner <gm-dbo>
+the password for the database owner <gm-dbo>
 
 .I [--with-dump]
 if this option is given a dump of the database schema structure

server/doc/gm-restore_database_from_archive.8 → server/doc/gm-restore.8

-.TH GM-RESTORE_DATABASE_FROM_ARCHIVE 8 "2016 March 13th" "GNUmed server database restore"
+.TH GM-RESTORE 8 "2016 March 13th" "GNUmed server database restore"
 
 .SH NAME
-.B gm-restore_database_from_archive
+.B gm-restore
 - restoring a GNUmed database
 
 .SH SYNOPSIS
-.B gm-restore_database_from_archive
+.B gm-restore
 .I <backup>
 
 .I <backup>:
@@ -13,11 +13,12 @@ a database backup file ("backup-gnumed_vX-*.tar.bz2") created by gm-backup
 
 .SH DESCRIPTION
 The
-.B gm-restore_database_from_archive
+.B gm-restore
 script attempts to recreate from scratch the backed up GNUmed
-database. It tries to be very conservative. It is intended
-for interactive use by root and may have to be adjusted to
-your needs.
+database. It tries to be very conservative.
+
+It is intended for interactive use by root and may have to be
+adjusted to your needs.
 
 .SH KNOWN PROBLEMS
 

server/doc/gm-restore_data.8

 .TH GM-RESTORE_DATA 8 "2011 May 10th" "GNUmed server data-only restore"
 
+.SH NOTE
+
+.I Deprecated in favour of gm-restore(8).
+
 .SH NAME
 .B gm-restore_data
 - restoring data into an empty GNUmed database
@@ -30,7 +34,9 @@ the backup file you intend to restore is a link to the
 actual backup. Use the full path instead.
 
 .SH SEE ALSO
-gm-backup_database(8)
+gm-restore(8)
+
+gm-backup(8)
 
 /etc/gnumed/gnumed-restore.conf