[med-svn] [Git][med-team/gnumed-server][master] 10 commits: routine-update: New upstream version
Andreas Tille
gitlab at salsa.debian.org
Thu Feb 27 10:59:13 GMT 2020
Andreas Tille pushed to branch master at Debian Med / gnumed-server
Commits:
24564961 by Andreas Tille at 2020-02-27T11:44:16+01:00
routine-update: New upstream version
- - - - -
4078e714 by Andreas Tille at 2020-02-27T11:44:17+01:00
New upstream version 22.9
- - - - -
b120122c by Andreas Tille at 2020-02-27T11:45:07+01:00
Update upstream source from tag 'upstream/22.9'
Update to upstream version '22.9'
with Debian dir 4fd849999cb9cf4cd008784bbac8e6a97ea5f894
- - - - -
db869230 by Andreas Tille at 2020-02-27T11:45:08+01:00
routine-update: Standards-Version: 4.5.0
- - - - -
a3b64b9a by Andreas Tille at 2020-02-27T11:45:15+01:00
routine-update: Add salsa-ci file
- - - - -
a476880a by Andreas Tille at 2020-02-27T11:45:18+01:00
Use secure URI in Homepage field.
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html
- - - - -
bf270800 by Andreas Tille at 2020-02-27T11:45:25+01:00
Set upstream metadata fields: Repository, Repository-Browse.
Fixes: lintian: upstream-metadata-file-is-missing
See-also: https://lintian.debian.org/tags/upstream-metadata-file-is-missing.html
- - - - -
b385eb41 by Andreas Tille at 2020-02-27T11:52:40+01:00
Switch to Python3
- - - - -
039828a8 by Andreas Tille at 2020-02-27T11:54:23+01:00
Upload to unstable
- - - - -
f45fe88f by Andreas Tille at 2020-02-27T11:58:48+01:00
Rename debian/NEWS.Debian to debian/NEWS
- - - - -
17 changed files:
- debian/NEWS.Debian → debian/NEWS
- debian/changelog
- debian/control
- debian/docs
- debian/rules
- + debian/salsa-ci.yml
- + debian/upstream/metadata
- server/bootstrap/fixup_db-v22.conf
- server/bootstrap/update_db-v21_v22.conf
- server/doc/schema/gnumed-entire_schema.html
- server/sql/v21-v22/data/v22-Begleitbrief.tex
- server/sql/v21-v22/data/v22-Begleitbrief_mit_Diagnosen.tex
- server/sql/v21-v22/dynamic/v22-clin-v_candidate_diagnoses.sql
- + server/sql/v21-v22/fixups/v22-clin-v_candidate_diagnoses-fixup.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:
=====================================
debian/NEWS.Debian → debian/NEWS
=====================================
=====================================
debian/changelog
=====================================
@@ -1,3 +1,21 @@
+gnumed-server (22.9-2) UNRELEASED; urgency=medium
+
+ * Rename debian/NEWS.Debian to debian/NEWS
+
+ -- Andreas Tille <tille at debian.org> Thu, 27 Feb 2020 11:58:18 +0100
+
+gnumed-server (22.9-1) unstable; urgency=medium
+
+ * New upstream version
+ * Standards-Version: 4.5.0 (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Use secure URI in Homepage field.
+ * Set upstream metadata fields: Repository, Repository-Browse.
+ * Switch to Python3
+ Closes: #936631
+
+ -- Andreas Tille <tille at debian.org> Thu, 27 Feb 2020 11:52:51 +0100
+
gnumed-server (22.8-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -5,19 +5,20 @@ Uploaders: Andreas Tille <tille at debian.org>,
Section: misc
Priority: optional
Build-Depends: debhelper-compat (= 12),
- python
+ dh-python,
+ python3
Build-Depends-Indep: po-debconf
-Standards-Version: 4.4.1
+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: http://www.gnumed.de
+Homepage: https://www.gnumed.de
Package: gnumed-server
Architecture: all
-Depends: ${misc:Depends},
+Depends: ${python3:Depends},
+ ${misc:Depends},
postgresql,
postgresql-client,
- python,
debconf,
bsd-mailx | mail-reader,
openssl,
@@ -26,8 +27,7 @@ Depends: ${misc:Depends},
sudo,
gnupg | gnupg2,
rsync,
- python-psycopg2,
- python-egenix-mxdatetime
+ python3-psycopg2
Recommends: barman
Suggests: postgresql-contrib,
postgresql-plr,
=====================================
debian/docs
=====================================
@@ -1,2 +1 @@
server/doc/README
-debian/NEWS.Debian
=====================================
debian/rules
=====================================
@@ -3,7 +3,7 @@
include /usr/share/dpkg/default.mk
%:
- dh $@ --with python2
+ dh $@ --with python3
override_dh_install:
dh_install
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/upstream/metadata
=====================================
@@ -0,0 +1,2 @@
+Repository: https://github.com/ncqgm/gnumed.git
+Repository-Browse: https://github.com/ncqgm/gnumed
=====================================
server/bootstrap/fixup_db-v22.conf
=====================================
@@ -30,6 +30,7 @@ schema = $schema$
v22-ref-paperwork_templates-fixups.sql
v22-invoice_id_grants-fixup.sql
v22-i18n-lang_funcs-fixup.sql
+v22-clin-v_candidate_diagnoses-fixup.sql
v22-release_notes-fixup.sql
$schema$
=====================================
server/bootstrap/update_db-v21_v22.conf
=====================================
@@ -162,6 +162,7 @@ schema = $schema$
v22-ref-paperwork_templates-fixups.sql
v22-invoice_id_grants-fixup.sql
v22-i18n-lang_funcs-fixup.sql
+v22-clin-v_candidate_diagnoses-fixup.sql
v22-release_notes-fixup.sql
$schema$
=====================================
server/doc/schema/gnumed-entire_schema.html
=====================================
@@ -112,7 +112,7 @@
<body>
<!-- Primary Index -->
- <p><br><br>Dumped on 2019-11-10</p>
+ <p><br><br>Dumped on 2019-12-05</p>
<h1><a name="index">Index of database - gnumed_v22</a></h1>
<ul>
=====================================
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$#3#\href{https://www.scan2pay.info}{\includegraphics[width=15mm]{$<praxis_scan2pay::fmt=qr::>$}} %% no praxis logo available::>3$
+ $3<if_not_empty::$1<data_snippet::praxis-logo#1#%s#1#image/png#1#.png::>1$#3#$2<if_not_empty::$1<praxis_comm::web::>1$#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#$2<if_not_empty::$1<praxis_scan2pay::fmt=txt::>1$#2#\href{https://www.scan2pay.info}{\includegraphics[width=15mm]{$1<praxis_scan2pay::fmt=qr::>1$}} %% no praxis logo available#2#% no praxis logo available::>2$::>3$
$1<ph_cfg::argumentsdivider//DEFAULT//%% <%(name)s> set to [%(value)s]::>1$
$2<ph_cfg::argumentsdivider//DEFAULT//%% <%(name)s> set to [%(value)s]::>2$
$3<ph_cfg::argumentsdivider//DEFAULT//%% <%(name)s> set to [%(value)s]::>3$
=====================================
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$#3#\href{https://www.scan2pay.info}{\includegraphics[width=15mm]{$<praxis_scan2pay::fmt=qr::>$}} %% no praxis logo available::>3$
+ $3<if_not_empty::$1<data_snippet::praxis-logo#1#%s#1#image/png#1#.png::>1$#3#$2<if_not_empty::$1<praxis_comm::web::>1$#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#$2<if_not_empty::$1<praxis_scan2pay::fmt=txt::>1$#2#\href{https://www.scan2pay.info}{\includegraphics[width=15mm]{$1<praxis_scan2pay::fmt=qr::>1$}} %% no praxis logo available#2#% no praxis logo available::>2$::>3$
$1<ph_cfg::argumentsdivider//DEFAULT//%% <%(name)s> set to [%(value)s]::>1$
$2<ph_cfg::argumentsdivider//DEFAULT//%% <%(name)s> set to [%(value)s]::>2$
$3<ph_cfg::argumentsdivider//DEFAULT//%% <%(name)s> set to [%(value)s]::>3$
=====================================
server/sql/v21-v22/dynamic/v22-clin-v_candidate_diagnoses.sql
=====================================
@@ -17,7 +17,7 @@ create view clin.v_candidate_diagnoses as
-- health issues
select
(select c_enc.fk_patient from clin.encounter c_enc where c_enc.pk = c_hi.fk_encounter) as pk_patient,
- c_hi.description || ' (' || c_hi.laterality || ')' as diagnosis,
+ c_hi.description || coalesce(' (' || c_hi.laterality || ')' ,'') as diagnosis,
c_hi.is_confidential AS explicitely_confidential,
c_hi.diagnostic_certainty_classification,
'clin.health_issue' AS source
@@ -86,4 +86,4 @@ comment on view clin.v_candidate_diagnoses is
grant select on clin.v_candidate_diagnoses to group "gm-doctors";
-- --------------------------------------------------------------
-select gm.log_script_insertion('v22-clin-v_candidate_diagnoses.sql', '22.0');
+select gm.log_script_insertion('v22-clin-v_candidate_diagnoses.sql', '22.9');
=====================================
server/sql/v21-v22/fixups/v22-clin-v_candidate_diagnoses-fixup.sql
=====================================
@@ -0,0 +1,89 @@
+-- ==============================================================
+-- GNUmed database schema change script
+--
+-- License: GPL v2 or later
+-- Author: Karsten.Hilbert at gmx.net
+--
+-- ==============================================================
+\set ON_ERROR_STOP 1
+--set default_transaction_read_only to off;
+
+-- --------------------------------------------------------------
+drop view if exists clin.v_candidate_diagnoses cascade ;
+
+
+create view clin.v_candidate_diagnoses as
+
+ -- health issues
+ select
+ (select c_enc.fk_patient from clin.encounter c_enc where c_enc.pk = c_hi.fk_encounter) as pk_patient,
+ c_hi.description || coalesce(' (' || c_hi.laterality || ')' ,'') as diagnosis,
+ c_hi.is_confidential AS explicitely_confidential,
+ c_hi.diagnostic_certainty_classification,
+ 'clin.health_issue' AS source
+ from clin.health_issue c_hi
+
+union all
+
+ -- open episodes
+ select
+ (select c_enc.fk_patient from clin.encounter c_enc where c_enc.pk = c_epi.fk_encounter) as pk_patient,
+ c_epi.description as diagnosis,
+ coalesce (
+ (select c_hi.is_confidential from clin.health_issue c_hi where c_hi.pk = c_epi.fk_health_issue),
+ FALSE
+ ) AS explicitely_confidential,
+ c_epi.diagnostic_certainty_classification,
+ 'clin.episode' AS source
+ from clin.episode c_epi
+ where c_epi.is_open IS TRUE
+
+union all
+
+ -- AOE from encounters of open episodes
+ select
+ c_enc.fk_patient as pk_patient,
+ c_enc.assessment_of_encounter as diagnosis,
+ -- coalesce into issue
+ FALSE::bool AS explicitely_confidential,
+ NULL::text AS diagnostic_certainty_classification,
+ 'clin.encounter' AS source
+ from clin.encounter c_enc
+ where
+ c_enc.assessment_of_encounter IS NOT NULL
+ and
+ c_enc.pk IN (
+ select c_cri.fk_encounter from clin.clin_root_item c_cri where c_cri.fk_episode in (
+ select c_epi.pk from clin.episode c_epi where c_epi.is_open IS TRUE
+ )
+ )
+
+union all
+
+ -- soAp from narrative in open episodes
+ select
+ (select c_enc.fk_patient from clin.encounter c_enc where c_enc.pk = c_cn.fk_encounter) as pk_patient,
+ c_cn.narrative as diagnosis,
+ -- coalesce into issue
+ FALSE::bool AS explicitely_confidential,
+ NULL::text as diagnostic_certainty_classification,
+ 'clin.clin_narrative' as source
+ from clin.clin_narrative c_cn
+ where
+ c_cn.soap_cat = 'a'
+ and
+ c_cn.fk_episode in (
+ select c_epi.pk from clin.episode c_epi where c_epi.is_open IS TRUE
+ )
+
+;
+
+
+comment on view clin.v_candidate_diagnoses is
+ 'Candidates for diagnoses.';
+
+
+grant select on clin.v_candidate_diagnoses to group "gm-doctors";
+
+-- --------------------------------------------------------------
+select gm.log_script_insertion('v22-clin-v_candidate_diagnoses-fixup.sql', '22.9');
=====================================
server/sql/v21-v22/fixups/v22-release_notes-fixup.sql
=====================================
@@ -17,19 +17,21 @@ 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 1.7.8 (database v22.8)',
- 'GNUmed 1.7.8 Release Notes:
+ 'Release Notes for GNUmed 1.7.9 (database v22.9)',
+ 'GNUmed 1.7.9 Release Notes:
- 1.7.8
+ 1.7.9
-FIX: billing: invoice ID template configuration [thanks Marc]
-FIX: config: top pane lab panel setting [thanks Jelle Mous]
-FIX: searching across active EMR [thanks Eberhard]
+FIX: billing: invoice ID generation [thanks Marc]
+FIX: dist: GNUmed Manual d/l URL
+FIX: template: letter w/ & w/o Dx-s
+FIX: paperwork: letter receiver dlg address selection
+FIX: EMR/tree: exception on loading visual progress notes
- 22.8
+ 22.9
-FIX: i18n.set_curr/force_curr_lang()
+FIX: clin.v_candidate_diagnoses: missing coalesce()
');
-- --------------------------------------------------------------
-select gm.log_script_insertion('v22-release_notes-fixup.sql', '22.8');
+select gm.log_script_insertion('v22-release_notes-fixup.sql', '22.9');
=====================================
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 = '22.6'
+ external_version = '22.9'
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 = '22.6'
+ external_version = '22.9'
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 = '22.6'
+ external_version = '22.9'
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/-/compare/a485529c7b3679114a0dffdc8b995f2a87a95018...f45fe88f907b72f25879aee9fe3183d5bb31d6f2
--
View it on GitLab: https://salsa.debian.org/med-team/gnumed-server/-/compare/a485529c7b3679114a0dffdc8b995f2a87a95018...f45fe88f907b72f25879aee9fe3183d5bb31d6f2
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