New upstream version 1.7.4+dfsg

# rel-1-7-patches

------------------------------------------------

	1.7.4

NEW: placeholders now nest with $2<>2$ $3<>3$ rather than $<<>>$ $<<<>>>$

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: 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

	1.7.3

FIX: failure to merge patients under some conditions [thanks Marc]

# gnumed_v22

------------------------------------------------

	22.4

FIX: LaTeX-Template for Begleitbrief

FIX: 2nd/3rd level placeholders in LaTeX templates

	22.2

FIX: staff/v_staff plausibility check [thanks Marc]

<!-- Thanks to Carsten Grohmann <mail@carstengrohmann.de> -->

<!-- Thanks to Richard Hughes (https://people.freedesktop.org/~hughsient/appdata/) -->

<component type="desktop">

 <id>gnumed-client.desktop</id>

 <id>gnumed_client.desktop</id>

 <metadata_license>CC0-1.0</metadata_license>

 <project_license>GPL-2.0+ and GFDL-1.3</project_license>

 <name>GNUmed EMR</name>

 <summary>An Electronic Medical Record for community care.</summary>

 <summary>An Electronic Medical Record for community care</summary>

 <description>

	<p>

	GNUmed enables doctors to keep a medically sound record

		<caption>http://wiki.gnumed.de</caption>

	</screenshot>

	<!--<screenshot type="default">

			<image>http://www.hughsie.com/en_US/main.png</image>

			<image>https://screenshots.debian.net/screenshots/000/002/117/large.png</image>

			<caption>The main window showing the application in action</caption>

		</screenshot>-->

 </screenshots>

 <url type="homepage">http://www.gnumed.de</url>

 <updatecontact>gnumed-devel_at_gnu.org</updatecontact>

 <!--<project_group>GNOME</project_group>-->

 <update_contact>gnumed-devel_AT_gnu.org</update_contact>

</component>

# -*- coding: utf-8 -*-

"""Manage German AMTS BMP data."""

#============================================================

__author__ = "K.Hilbert <Karsten.Hilbert@gmx.net>"

__license__ = "GPL v2"

# std lib

import sys

import os

import logging

import decimal

import datetime as pyDT

#from xml.etree import ElementTree as py_etree

import typing

# 3rd party

#lxml_etree = None

import lxml.etree as lxml_etree

# GNUmed

if __name__ == '__main__':

	sys.path.insert(0, '../../')

	from Gnumed.pycommon import gmLog2

	from Gnumed.pycommon import gmI18N

	gmI18N.activate_locale()

	gmI18N.install_domain()

from Gnumed.pycommon import gmTools

from Gnumed.pycommon import gmDateTime

from Gnumed.business import gmPerson

AMTS_BMP_ENCODING = 'latin1'

AMTS_BMP_DOB_FORMAT = '%Y%m%d'

AMTS_BMP_DOB_FORMAT_NO_DAY = '%Y%m'

AMTS_BMP_DOB_FORMAT_YEAR_ONLY = '%Y'

AMTS2GMD_GENDER_MAP = {

	'W': 'f',

	'M': 'm',

	'X': None

}

# the attribute

#

#			<xs:attribute name="p" use="prohibited">

#				<xs:annotation>

#					<xs:documentation>Name: Patchnummer 

#

# Beschreibung: Patchnummer des zugrunde liegenden BMP (zusätzlich zum Attribut Version)

# </xs:documentation>

#				</xs:annotation>

#			</xs:attribute>

#

# needs to be removed from the XSDs or else lxml will

# choke on the <use="prohibited"> part

AMTS_BMP_XSDs = {

	'2.5': 'bmp_V2.5.xsd',

	'2.4.1': 'bmp_V2.4.1.xsd',

	'2.3': 'bmp023.xsd'

}

_log = logging.getLogger('AMTS_BMP')

#============================================================

class cDTO_AmtsBmp(gmPerson.cDTO_person):

	def __init__(self):

		super().__init__()

		self.dob_formats = [

			AMTS_BMP_DOB_FORMAT,

			AMTS_BMP_DOB_FORMAT_NO_DAY,

			AMTS_BMP_DOB_FORMAT_YEAR_ONLY

		]

		self.dob_tz = gmDateTime.pydt_now_here().tzinfo

		self.gender_map = AMTS2GMD_GENDER_MAP

	#--------------------------------------------------------

	# internal helpers

	#--------------------------------------------------------

	def _get_unambiguous_identity(self) -> typing.Union[None, gmPerson.cPerson]:

		egk_tag = 'eGK'

		egk_issuer = 'Krankenkasse'

		egk_id = None

		for ext_id in self.external_ids:

			if ext_id['name'] == egk_tag and ext_id['issuer'] == egk_issuer:

				egk_id = ext_id['value']

				break

		if egk_id is None:

			_log.debug('cannot search for patient by eGK ID')

			return None

		candidates = gmPerson.get_persons_by_external_id (

			external_id = egk_id,

			external_id_type = egk_tag,

			issuer = egk_issuer

		)

		if len(candidates) != 1:

			_log.debug('cannot uniquely identify person by eGK ID [%s]', egk_id)

			return None

		return candidates[0]

#============================================================

class cAmtsBmpFile:

	# take up to three filenames (or more, in non-strict mode)

	def __init__(self, filename) -> None:

		self.__filename:str = filename

		self.__xml_schema:lxml_etree.XMLSchema = None

		self.xml_doc = None

		self.bmp_version = None

	#--------------------------------------------------------

	# version=..., strict=True/False

	def valid(self):

		for bmp_version in AMTS_BMP_XSDs:

			xsd_filename = os.path.join(gmTools.gmPaths().system_app_data_dir, 'resources', 'amts', AMTS_BMP_XSDs[bmp_version])

			try:

				self.__xml_schema = lxml_etree.XMLSchema(file = xsd_filename)

			except lxml_etree.XMLSchemaParseError:

				_log.exception('cannot find [%s], trying local base dir', xsd_filename)

				# retry, maybe in dev tree

				xsd_filename = os.path.join(gmTools.gmPaths().local_base_dir, 'resources', 'amts', AMTS_BMP_XSDs[bmp_version])

				self.__xml_schema = lxml_etree.XMLSchema(file = xsd_filename)

			with open(self.__filename, encoding = 'iso-8859-1') as bmp_file:

				try:

					self.xml_doc = lxml_etree.parse(bmp_file)

				except lxml_etree.XMLSyntaxError:

					_log.exception('[%s] does not parse as XML', self.__filename)

					break

			validated = self.__xml_schema.validate(self.xml_doc)

			if validated:

				self.bmp_version = bmp_version

				_log.debug('[%s] validates as AMTS BMP v%s', self.__filename, self.bmp_version)

				# check for second/third file !

				return True

			_log.debug('[%s] does not validate against [%s]', self.__filename, xsd_filename)

		_log.debug('[%s] does not validate as AMTS BMP', self.__filename)

		return False

	#--------------------------------------------------------

	def format(self, eol:str=None, verbose:bool=False) -> typing.Union[str, typing.List[str]]:

		assert (self.xml_doc is not None), 'self.xml_doc is None, forgot to call valid() before'

		lines = []

		lines.append(_('AMTS BMP file: %s') % self.__filename)

		lines.append(_('Created: %s') % self.created_when)

		lines.append(_('Version: %s') % self.bmp_version)

		lines.append(_('UID: %s') % self.uid)

		lines.append(_('Creator:'))

		lines.append(' ' + str(self.originator))

		lines.append(_('Patient:'))

		lines.append(' ' + str(self.patient_as_dto))

		lines.append(_('Clinical data:'))

		lines.append(' ' + str(self.clinical_data))

		if verbose:

			lines.append(_('Raw data:'))

			lines.extend(lxml_etree.tostring(self.xml_doc, encoding = 'unicode', pretty_print = True, method = 'xml').split('\n'))

		if eol is None:

			return lines

		return eol.join(lines)

	#--------------------------------------------------------

	# properties

	#--------------------------------------------------------

	def _patient_as_dto(self) -> cDTO_AmtsBmp:

		assert (self.xml_doc is not None), 'self.xml_doc is None, forgot to call valid() before'

		pat = self.xml_doc.find('P').attrib

		dto = cDTO_AmtsBmp()

		# lastname parts

		dto.lastnames = pat['f']

		try:

			dto.lastnames = u'%s %s' % (pat['v'], dto.lastnames)

		except KeyError:

			pass

		try:

			dto.lastnames = u'%s %s' % (pat['z'], dto.lastnames)

		except KeyError:

			pass

		# firstnames

		dto.firstnames = pat['g']

		# title

		try:

			dto.title = pat['t']

		except KeyError:

			pass

		# gender

		try:

			dto.gender = pat['s']

		except KeyError:

			pass

		# DOB

		dob_str = pat['b']

		while dob_str.endswith('00'):

			dto.dob_is_estimated = True

			dob_str = dob_str[:-2]

		dto.dob = dob_str

		source = 'AMTS BMP v%s [uid=%s]' % (self.bmp_version, self.uid)

		# eGK

		try:

			dto.remember_external_id(name = 'eGK', value = pat['egk'], issuer = 'Krankenkasse', comment = source)

		except KeyError:

			pass

		dto.source = source

		return dto

	patient_as_dto = property(_patient_as_dto)

	#--------------------------------------------------------

	def _get_clinical_data(self) -> dict:

		assert (self.xml_doc is not None), 'self.xml_doc is None, forgot to call valid() before'

		O_tag = self.xml_doc.find('O')

		if O_tag is None:

			return {}

		clinical_data = {'valid_when': self.created_when}

		O = O_tag.attrib

		try:

			clinical_data['allergies'] = O['ai'].split(',')

		except KeyError:

			pass

		try:

			clinical_data['pregnant'] = (O['p'] == '1')

		except KeyError:

			pass

		try:

			clinical_data['breast_feeding'] = (O['b'] == '1')

		except KeyError:

			pass

		try:

			clinical_data['weight'] = (decimal.Decimal(O['w']), 'kg')

		except KeyError:

			pass

		try:

			clinical_data['height'] = (int(O['h']), 'cm')

		except KeyError:

			pass

		try:

			clinical_data['creatinine'] = (decimal.Decimal(O['c']), 'mg/dl')

		except KeyError:

			pass

		try:

			clinical_data['comment'] = O['x'].strip()

		except KeyError:

			pass

		return clinical_data

	clinical_data = property(_get_clinical_data)

	#--------------------------------------------------------

	def _get_created_when(self) -> pyDT.datetime:

		assert (self.xml_doc is not None), 'self.xml_doc is None, forgot to call valid() before'

		return pyDT.datetime.strptime (

			self.xml_doc.find('A').attrib['t'],

			'%Y-%m-%dT%H:%M:%S'

		)

	created_when = property(_get_created_when)

	#--------------------------------------------------------

	def _get_uid(self) -> str:

		assert (self.xml_doc is not None), 'self.xml_doc is None, forgot to call valid() before'

		return self.xml_doc.getroot().attrib['U']

	uid = property(_get_uid)

	#--------------------------------------------------------

	#dto.remember_comm_channel(channel=None, url=None):

	#dto.remember_address(number=None, street=None, urb=None, region_code=None, zip=None, country_code=None, adr_type=None, subunit=None)

	def _get_originator(self) -> dict:

		assert (self.xml_doc is not None), 'self.xml_doc is None, forgot to call valid() before'

		A_tag = self.xml_doc.find('A')

		if A_tag is None:

			return {}

		originator = {}

		A = A_tag.attrib

		try:

			originator['id'] = (A['lanr'].strip(), 'lanr')

		except KeyError:

			pass

		try:

			originator['id'] = (A['idf'].strip(), 'idf')

		except KeyError:

			pass

		try:

			originator['id'] = (A['kik'].strip(), 'kik')

		except KeyError:

			pass

		try:

			originator['name'] = A['n'].strip()

		except KeyError:

			pass

		try:

			originator['street'] = A['s'].strip()

		except KeyError:

			pass

		try:

			originator['zip'] = A['z'].strip()

		except KeyError:

			pass

		try:

			originator['city'] = A['c'].strip()

		except KeyError:

			pass

		try:

			originator['phone'] = A['p'].strip()

		except KeyError:

			pass

		try:

			originator['email'] = A['e'].strip()

		except KeyError:

			pass

		return originator

	originator = property(_get_originator)

#============================================================

#============================================================

#============================================================

#============================================================

# main/testing

#============================================================

if __name__ == '__main__':

	if len(sys.argv) == 1:

		sys.exit()

	if sys.argv[1] != 'test':

		sys.exit()

	print('log file:', gmLog2._logfile_name)

	gmDateTime.init()

	#-------------------------------------------------------

	def test_validate_files():

		for fname in sys.argv[2:]:

			print(fname)

			bmp = cAmtsBmpFile(fname)

			if not bmp.valid():

				print('-> failed')

				continue

			print('-> conformant with version', bmp.bmp_version)

	#-------------------------------------------------------

	def test():

		print(sys.argv[2])

		print()

		bmp = cAmtsBmpFile(sys.argv[2])

		if not bmp.valid():

			print('failed')

			return

		print('validated as version', bmp.bmp_version)

		print(lxml_etree.tostring(bmp.xml_doc, encoding = 'unicode', pretty_print = True, method = 'xml'))

		dto = bmp.patient_as_dto

		print(dto)

		print(dto.external_ids)

		print(bmp.created_when)

		print('clinical data:', bmp.clinical_data)

		print('originator:', bmp.originator)

#		print('exists:', dto.exists)

#		cands = dto.get_candidate_identities(can_create=False)

#		print('candidates:')

#		for cand in cands:

#			print(cand)

	#-------------------------------------------------------

	test_validate_files()

	#test()

#============================================================

# bill items

#------------------------------------------------------------

_SQL_fetch_bill_item_fields = u"SELECT * FROM bill.v_bill_items WHERE %s"

_SQL_get_bill_item_fields = u"SELECT * FROM bill.v_bill_items WHERE %s"

class cBillItem(gmBusinessDBObject.cBusinessDBObject):

	_cmd_fetch_payload = _SQL_fetch_bill_item_fields % u"pk_bill_item = %s"

	_cmd_fetch_payload = _SQL_get_bill_item_fields % u"pk_bill_item = %s"

	_cmds_store_payload = [

		u"""UPDATE bill.bill_item SET

				fk_provider = %(pk_provider)s,

#------------------------------------------------------------

def get_bill_items(pk_patient=None, non_invoiced_only=False):

	if non_invoiced_only:

		cmd = _SQL_fetch_bill_item_fields % u"pk_patient = %(pat)s AND pk_bill IS NULL"

		cmd = _SQL_get_bill_item_fields % u"pk_patient = %(pat)s AND pk_bill IS NULL"

	else:

		cmd = _SQL_fetch_bill_item_fields % u"pk_patient = %(pat)s"

		cmd = _SQL_get_bill_item_fields % u"pk_patient = %(pat)s"

	args = {'pat': pk_patient}

	rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)

	return [ cBillItem(row = {'data': r, 'idx': idx, 'pk_field': 'pk_bill_item'}) for r in rows ]

			args['encs'] = tuple(encounters)

		cmd = u'%s %s' % (

			gmVaccination.sql_fetch_vaccination % u'\nAND '.join(where_parts),

			gmVaccination._SQL_get_vaccination_fields % u'\nAND '.join(where_parts),

			order_by

		)

		rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)