[med-svn] [Git][med-team/gnumed-server][upstream] New upstream version 22.6
Andreas Tille
gitlab at salsa.debian.org
Tue Aug 20 11:54:51 BST 2019
Andreas Tille pushed to branch upstream at Debian Med / gnumed-server
Commits:
23f40043 by Andreas Tille at 2019-08-20T10:44:22Z
New upstream version 22.6
- - - - -
9 changed files:
- server/bootstrap/update_db-v21_v22.conf
- server/doc/schema/gnumed-entire_schema.html
- server/gm-backup.sh
- server/sql/v21-v22/data/v22-Begleitbrief.tex
- server/sql/v21-v22/data/v22-Begleitbrief_mit_Diagnosen.tex
- server/sql/v21-v22/fixups/v22-ref-paperwork_templates-fixups.sql
- server/sql/v21-v22/fixups/v22-release_notes-fixup.sql
- server/sql/v21-v22/python/v22-2-fixup-form-templates.py
- server/sql/v21-v22/python/v22-import-form-templates.py
Changes:
=====================================
server/bootstrap/update_db-v21_v22.conf
=====================================
@@ -28,6 +28,7 @@ bundles = $bundles$
v21_fixups-pre_v22
v21-v22-static
v21-v22-dynamic
+v22-fixups
$bundles$
#----------------------------------
@@ -259,7 +260,7 @@ 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
+messages::::select count(1) + 3 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
@@ -315,7 +316,7 @@ requests on results::::select count(1) from clin.test_result where fk_request is
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
+paperwork templates::::select count(1) + 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
=====================================
server/doc/schema/gnumed-entire_schema.html
=====================================
@@ -112,7 +112,7 @@
<body>
<!-- Primary Index -->
- <p><br><br>Dumped on 2019-01-25</p>
+ <p><br><br>Dumped on 2019-07-28</p>
<h1><a name="index">Index of database - gnumed_v22</a></h1>
<ul>
=====================================
server/gm-backup.sh
=====================================
@@ -117,21 +117,33 @@ TS=$(date +%Y-%m-%d-%H-%M-%S)
BACKUP_FILENAME="${BACKUP_BASENAME}-${TS}"
-# taken from config file
-cd "${BACKUP_DIR}"
+# generate scratch dir
+SCRATCH_DIR="/tmp/${BACKUP_FILENAME}"
+mkdir -p ${SCRATCH_DIR}
RESULT="$?"
if test "${RESULT}" != "0" ; then
- echo "Cannot change into backup directory [${BACKUP_DIR}] (${RESULT}). Aborting."
+ echo "Cannot create backup scratch directory [${SCRATCH_DIR}] (${RESULT}). Aborting."
+ exit ${RESULT}
+fi
+cd ${SCRATCH_DIR}
+RESULT="$?"
+if test "${RESULT}" != "0" ; then
+ echo "Cannot change into scratch backup directory [${SCRATCH_DIR}] (${RESULT}). Aborting."
exit ${RESULT}
fi
+# create backup timestamp tag file
+TS_FILE="${BACKUP_BASENAME}-timestamp.txt"
+echo "backup: ${TS}" > ${TS_FILE}
+
+
# create dumps
-BACKUP_DATA_DIR="${BACKUP_FILENAME}.dir"
+BACKUP_DATA_DIR="${BACKUP_BASENAME}.dir"
# database
pg_dump --verbose --format=directory --compress=0 --column-inserts --clean --if-exists --serializable-deferrable ${_PG_HOST_ARG} ${_PG_PORT_ARG} --username="${GM_DBO}" -f "${BACKUP_DATA_DIR}" "${GM_DATABASE}" 2> /dev/null
# roles
-ROLES_FILE="${BACKUP_FILENAME}-roles.sql"
+ROLES_FILE="${BACKUP_BASENAME}-roles.sql"
# -r -> -g for older versions
ROLES=`psql --no-psqlrc --no-align --tuples-only --dbname="${GM_DATABASE}" ${_PG_HOST_ARG} ${_PG_PORT_ARG} --username="${GM_DBO}" --command="select gm.get_users('${GM_DATABASE}');"`
{
@@ -179,6 +191,26 @@ if test "${RESULT}" != "0" ; then
fi
+# move "untested" tar archive to final directory
+# so the compression script can pick it up if needed
+mv --force "${TAR_UNTESTED}" "${BACKUP_DIR}/"
+RESULT="$?"
+if test "${RESULT}" != "0" ; then
+ echo "cannot move TAR archive: ${TAR_UNTESTED} => ${BACKUP_DIR}/"
+ exit ${RESULT}
+fi
+
+
+# taken from config file
+cd "${BACKUP_DIR}"
+RESULT="$?"
+if test "${RESULT}" != "0" ; then
+ echo "Cannot change into backup directory [${BACKUP_DIR}] (${RESULT}). Aborting."
+ exit ${RESULT}
+fi
+rm --dir --recursive --one-file-system "${SCRATCH_DIR:?}"/
+
+
# test tar archive
tar --extract --to-stdout --file="${TAR_UNTESTED}" > /dev/null
RESULT="$?"
@@ -187,8 +219,6 @@ if test "${RESULT}" != "0" ; then
rm --force "${TAR_UNTESTED}"
exit ${RESULT}
fi
-rm --dir --recursive --one-file-system "${BACKUP_DATA_DIR:?}"/
-rm --force "${ROLES_FILE}"
# rename to final archive name which
@@ -201,4 +231,5 @@ if test "${RESULT}" != "0" ; then
fi
chown "${BACKUP_OWNER}" "${TAR_FILE}"
+
exit 0
=====================================
server/sql/v21-v22/data/v22-Begleitbrief.tex
=====================================
@@ -118,7 +118,7 @@ $<if_debugging:://%::>$\renewcommand*\ShowFrameColor{\color{red}} % configure s
$3<ph_cfg::argumentsdivider//#3#//%% <%(name)s> set to [%(value)s]::>3$
$2<ph_cfg::argumentsdivider//#2#//%% <%(name)s> set to [%(value)s]::>2$
$1<ph_cfg::argumentsdivider//#1#//%% <%(name)s> set to [%(value)s]::>1$
- $3<if_not_empty::$<data_snippet::praxis-logo#1#%s#1#image/png#1#.png::>$#3#$2<if_not_empty::$<praxis_comm::web::>$#2#\href{http://%s}{$1<data_snippet::praxis-logo#1#\includegraphics[width=20mm]{%s}#1#image/png#1#.png::250>1$}#2#$1<data_snippet::praxis-logo#1#\includegraphics[width=20mm]{%s}#1#image/png#1#.png::250>1$::>2$#3#\href{http://www.gnumed.de}{$<qrcode::http://www.gnumed.de#1#\includegraphics[width=15mm]{%s}} %% no praxis logo available::>$::>3$
+ $3<if_not_empty::$<data_snippet::praxis-logo#1#%s#1#image/png#1#.png::>$#3#$2<if_not_empty::$<praxis_comm::web::>$#2#\href{http://%s}{$1<data_snippet::praxis-logo#1#\includegraphics[width=20mm]{%s}#1#image/png#1#.png::250>1$}#2#$1<data_snippet::praxis-logo#1#\includegraphics[width=20mm]{%s}#1#image/png#1#.png::250>1$::>2$#3#\href{https://www.scan2pay.info}{\includegraphics[width=15mm]{$<praxis_scan2pay::fmt=qr::>$}} %% no praxis logo available::>3$
$1<ph_cfg::argumentsdivider//DEFAULT//%% <%(name)s> set to [%(value)s]::>1$
$2<ph_cfg::argumentsdivider//DEFAULT//%% <%(name)s> set to [%(value)s]::>2$
$3<ph_cfg::argumentsdivider//DEFAULT//%% <%(name)s> set to [%(value)s]::>3$
=====================================
server/sql/v21-v22/data/v22-Begleitbrief_mit_Diagnosen.tex
=====================================
@@ -118,7 +118,7 @@ $<if_debugging:://%::>$\renewcommand*\ShowFrameColor{\color{red}} % configure s
$3<ph_cfg::argumentsdivider//#3#//%% <%(name)s> set to [%(value)s]::>3$
$2<ph_cfg::argumentsdivider//#2#//%% <%(name)s> set to [%(value)s]::>2$
$1<ph_cfg::argumentsdivider//#1#//%% <%(name)s> set to [%(value)s]::>1$
- $3<if_not_empty::$<data_snippet::praxis-logo#1#%s#1#image/png#1#.png::>$#3#$2<if_not_empty::$<praxis_comm::web::>$#2#\href{http://%s}{$1<data_snippet::praxis-logo#1#\includegraphics[width=20mm]{%s}#1#image/png#1#.png::250>1$}#2#$1<data_snippet::praxis-logo#1#\includegraphics[width=20mm]{%s}#1#image/png#1#.png::250>1$::>2$#3#\href{http://www.gnumed.de}{$<qrcode::http://www.gnumed.de#1#\includegraphics[width=15mm]{%s}} %% no praxis logo available::>$::>3$
+ $3<if_not_empty::$<data_snippet::praxis-logo#1#%s#1#image/png#1#.png::>$#3#$2<if_not_empty::$<praxis_comm::web::>$#2#\href{http://%s}{$1<data_snippet::praxis-logo#1#\includegraphics[width=20mm]{%s}#1#image/png#1#.png::250>1$}#2#$1<data_snippet::praxis-logo#1#\includegraphics[width=20mm]{%s}#1#image/png#1#.png::250>1$::>2$#3#\href{https://www.scan2pay.info}{\includegraphics[width=15mm]{$<praxis_scan2pay::fmt=qr::>$}} %% no praxis logo available::>3$
$1<ph_cfg::argumentsdivider//DEFAULT//%% <%(name)s> set to [%(value)s]::>1$
$2<ph_cfg::argumentsdivider//DEFAULT//%% <%(name)s> set to [%(value)s]::>2$
$3<ph_cfg::argumentsdivider//DEFAULT//%% <%(name)s> set to [%(value)s]::>3$
=====================================
server/sql/v21-v22/fixups/v22-ref-paperwork_templates-fixups.sql
=====================================
@@ -25,7 +25,7 @@ insert into ref.paperwork_templates (
'sonstiger Arztbrief',
'Begleitbrf m.Dg.[KH]',
'Begleitbrief mit Diagnosen [K.Hilbert]',
- '22.4',
+ '22.6',
'L',
'begleitbrief.tex',
'real template missing'::bytea
@@ -89,4 +89,4 @@ update ref.paperwork_templates r_pt_u set
;
-- --------------------------------------------------------------
-select gm.log_script_insertion('v22-ref-paperwork_templates-fixups.sql', '22.4');
+select gm.log_script_insertion('v22-ref-paperwork_templates-fixups.sql', '22.6');
=====================================
server/sql/v21-v22/fixups/v22-release_notes-fixup.sql
=====================================
@@ -17,41 +17,25 @@ 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 1.7.5 (database v22.5)',
- 'GNUmed 1.7.5 Release Notes:
+ 'Release Notes for GNUmed 1.7.6 (database v22.6)',
+ 'GNUmed 1.7.6 Release Notes:
- 1.7.5
+ 1.7.6
-FIX: exception on following vaccs reminder from provider inbox
+FIX: application metadata files
+FIX: searching across all EMRs
+FIX: constrain document PRW to current patient
+FIX: lab/table: exception on double-clicking empty cell in row w/o meta test type
+FIX: lab/result EA: failure to show test type on edit
- 1.7.4
+NEW: stub out $praxis_scan2pay$
-NEW: placeholders now nest with $2<>2$ $3<>3$ rather than $<<>>$ $<<<>>>$
+ 22.6
-NEW: placeholder $<patient_mcf>$
-NEW: placeholder $<praxis_mcf>$
-NEW: placehodler $<qrcode>$
-NEW: placeholder $<if_debugging>$
-NEW: LaTeX letter template example
-NEW: Begleitbrief mit Diagnosen (LaTeX)
+FIX: properly include fixups in v21-v22 upgrade
-FIX: map None to '' in address parts placeholder
-FIX: export area export-to-media
-FIX: $<vaccination_history::%(l10n_indications)s::>$ field
-FIX: vaccine creation
-FIX: error in closing expired episodes
-FIX: date formatting in document tree
-
-IMPROVED: AppStream and desktop metadata
-IMPROVED: add "preset" option to $<free_text>$ placeholder
-IMPROVED: include MCF in export area metadata
-IMPROVED: Begleitbrief template
-
- 22.4
-
-FIX: LaTeX-Template for Begleitbrief
-FIX: 2nd/3rd level placeholders in LaTeX templates
+IMPROVED: database backup script
');
-- --------------------------------------------------------------
-select gm.log_script_insertion('v22-release_notes-fixup.sql', '22.4');
+select gm.log_script_insertion('v22-release_notes-fixup.sql', '22.6');
=====================================
server/sql/v21-v22/python/v22-2-fixup-form-templates.py
=====================================
@@ -20,7 +20,7 @@ def run(conn=None):
query = u"""
UPDATE ref.paperwork_templates SET
data = %(data)s::bytea,
- external_version = '22.4'
+ external_version = '22.6'
WHERE
name_long = 'Begleitbrief ohne medizinische Daten [K.Hilbert]'""",
filename = os.path.join('..', 'sql', 'v21-v22', 'data', 'v22-Begleitbrief.tex'),
=====================================
server/sql/v21-v22/python/v22-import-form-templates.py
=====================================
@@ -19,7 +19,7 @@ def run(conn=None):
query = u"""
UPDATE ref.paperwork_templates SET
data = %(data)s::bytea,
- external_version = '22.4'
+ external_version = '22.6'
WHERE
name_long = 'Begleitbrief ohne medizinische Daten [K.Hilbert]'""",
filename = os.path.join('..', 'sql', 'v21-v22', 'data', 'v22-Begleitbrief.tex'),
@@ -66,7 +66,7 @@ def run(conn=None):
query = u"""
UPDATE ref.paperwork_templates SET
data = %(data)s::bytea,
- external_version = '22.4'
+ external_version = '22.6'
WHERE
name_long = 'Begleitbrief mit Diagnosen [K.Hilbert]'""",
filename = os.path.join('..', 'sql', 'v21-v22', 'data', 'v22-Begleitbrief_mit_Diagnosen.tex'),
View it on GitLab: https://salsa.debian.org/med-team/gnumed-server/commit/23f40043d97fc466e8883eaacf5bb7026c054407
--
View it on GitLab: https://salsa.debian.org/med-team/gnumed-server/commit/23f40043d97fc466e8883eaacf5bb7026c054407
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