def create_vaccine(pk_drug_product=None, product_name=None, indications=None, is_live=None):
assert (is_live is not None), '<is_live> must not be <None>'
conn = gmPG2.get_connection(readonly = False)
if pk_drug_product is None:
#prep = _('vaccine')
prep = 'vaccine'
_log.debug('creating vaccine drug product [%s %s]', product_name, prep)
vacc_prod = gmMedication.create_drug_product (
product_name = product_name,
preparation = prep,
return_existing = True,
# indications are ref.dose rows
doses = indications,
link_obj = conn
)
#conn.commit()
vacc_prod['atc'] = 'J07'
vacc_prod.save(conn = conn)
pk_drug_product = vacc_prod['pk_drug_product']
cmd = 'INSERT INTO ref.vaccine (fk_drug_product, is_live) values (%(pk_drug_product)s, %(live)s) RETURNING pk'
queries = [{'cmd': cmd, 'args': {'pk_drug_product': pk_drug_product, 'live': is_live}}]
rows, idx = gmPG2.run_rw_queries(link_obj = conn, queries = queries, get_col_idx = False, return_data = True, end_tx = True)
conn.close()
return cVaccine(aPK_obj = rows[0]['pk'])
def create_vaccine(pk_drug_product=None, product_name=None, indications=None):
conn = gmPG2.get_connection(readonly=False)
if pk_drug_product is None:
#prep = _('vaccine')
prep = u'vaccine'
_log.debug('creating vaccine drug product [%s %s]', product_name, prep)
vacc_prod = gmMedication.create_drug_product(
product_name=product_name,
preparation=prep,
return_existing=True,
# indications are ref.dose rows
doses=indications,
link_obj=conn)
#conn.commit()
vacc_prod['atc'] = u'J07'
vacc_prod.save(conn=conn)
pk_drug_product = vacc_prod['pk_drug_product']
cmd = u'INSERT INTO ref.vaccine (fk_drug_product) values (%(pk_drug_product)s) RETURNING pk'
queries = [{'cmd': cmd, 'args': {'pk_drug_product': pk_drug_product}}]
rows, idx = gmPG2.run_rw_queries(link_obj=conn,
queries=queries,
get_col_idx=False,
return_data=True,
end_tx=True)
conn.close()
return cVaccine(aPK_obj=rows[0]['pk'])
def create_vaccine(pk_drug_product=None,
product_name=None,
indications=None,
pk_indications=None):
if pk_drug_product is None:
prep = _('vaccine')
_log.debug('creating drug product [%s %s]', product_name, prep)
prod = gmMedication.create_drug_product(product_name=product_name,
preparation=prep,
return_existing=True)
prod['atc'] = u'J07'
prod.save()
pk_drug_product = prod['pk_drug_product']
cmd = u'INSERT INTO clin.vaccine (fk_drug_product) values (%(pk_drug_product)s) RETURNING pk'
queries = [{'cmd': cmd, 'args': {'pk_drug_product': pk_drug_product}}]
if pk_indications is None:
for indication in indications:
cmd = u"""
INSERT INTO clin.lnk_vaccine2inds (
fk_vaccine,
fk_indication
) VALUES (
currval(pg_get_serial_sequence('clin.vaccine', 'pk')),
(SELECT id
FROM clin.vacc_indication
WHERE
lower(description) = lower(%(ind)s)
LIMIT 1
)
)
RETURNING fk_vaccine
"""
queries.append({'cmd': cmd, 'args': {'ind': indication}})
else:
for pk_indication in pk_indications:
cmd = u"""
INSERT INTO clin.lnk_vaccine2inds (
fk_vaccine,
fk_indication
) VALUES (
currval(pg_get_serial_sequence('clin.vaccine', 'pk')),
%(pk_ind)s
)
RETURNING fk_vaccine
"""
queries.append({'cmd': cmd, 'args': {'pk_ind': pk_indication}})
rows, idx = gmPG2.run_rw_queries(queries=queries,
get_col_idx=False,
return_data=True)
return cVaccine(aPK_obj=rows[0]['fk_vaccine'])
def import_drugs(self):
selected_drugs = self.__let_user_select_drugs()
if selected_drugs is None:
return None
data_src_pk = self.create_data_source_entry()
new_drugs = []
new_substances = []
for entry in selected_drugs:
_log.debug('importing drug: %s %s', entry['name'], entry['darreichungsform'])
if entry['hilfsmittel']:
_log.debug('skipping Hilfsmittel')
continue
if entry['erstattbares_medizinprodukt']:
_log.debug('skipping sonstiges Medizinprodukt')
continue
# create drug product (or get it if it already exists)
drug = gmMedication.create_drug_product(product_name = entry['name'], preparation = entry['darreichungsform'])
if drug is None:
drug = gmMedication.get_drug_by_name(product_name = entry['name'], preparation = entry['darreichungsform'])
new_drugs.append(drug)
# update fields
drug['is_fake_product'] = False
drug['atc'] = entry['atc']
drug['external_code_type'] = 'DE-PZN'
drug['external_code'] = entry['pzn']
drug['fk_data_source'] = data_src_pk
drug.save()
# add components to drug
atc = None # hopefully MMI eventually supports atc-per-substance in a drug...
if len(entry['wirkstoffe']) == 1:
atc = entry['atc']
for wirkstoff in entry['wirkstoffe']:
drug.add_component(substance = wirkstoff, atc = atc)
# create as substance doses, too
atc = None # hopefully MMI eventually supports atc-per-substance in a drug...
if len(entry['wirkstoffe']) == 1:
atc = entry['atc']
for wirkstoff in entry['wirkstoffe']:
#new_substances.append(gmMedication.create_substance_dose(substance = wirkstoff, atc = atc, amount = amount, unit = unit))
pass
return new_drugs, new_substances
def import_drugs(self):
selected_drugs = self.__let_user_select_drugs()
if selected_drugs is None:
return None
data_src_pk = self.create_data_source_entry()
new_drugs = []
new_substances = []
for entry in selected_drugs:
_log.debug('importing drug: %s %s', entry['name'], entry['darreichungsform'])
if entry['hilfsmittel']:
_log.debug('skipping Hilfsmittel')
continue
if entry['erstattbares_medizinprodukt']:
_log.debug('skipping sonstiges Medizinprodukt')
continue
# create drug product (or get it if it already exists)
drug = gmMedication.create_drug_product(product_name = entry['name'], preparation = entry['darreichungsform'])
if drug is None:
drug = gmMedication.get_drug_by_name(product_name = entry['name'], preparation = entry['darreichungsform'])
new_drugs.append(drug)
# update fields
drug['is_fake_product'] = False
drug['atc'] = entry['atc']
drug['external_code_type'] = 'DE-PZN'
drug['external_code'] = entry['pzn']
drug['fk_data_source'] = data_src_pk
drug.save()
# add components to drug
atc = None # hopefully MMI eventually supports atc-per-substance in a drug...
if len(entry['wirkstoffe']) == 1:
atc = entry['atc']
for wirkstoff in entry['wirkstoffe']:
drug.add_component(substance = wirkstoff, atc = atc)
# create as substance doses, too
atc = None # hopefully MMI eventually supports atc-per-substance in a drug...
if len(entry['wirkstoffe']) == 1:
atc = entry['atc']
for wirkstoff in entry['wirkstoffe']:
new_substances.append(gmMedication.create_substance_dose(substance = wirkstoff, atc = atc, amount = amount, unit = unit))
return new_drugs, new_substances
def __import_fd2gm_file_as_drugs_0_6_0(self, fd2gm_xml=None, pk_data_source=None):
# drug_id_name = db_def.attrib['drugUidName']
fd_xml_prescriptions = fd2gm_xml.findall('FullPrescription/Prescription')
self.__imported_drugs = []
for fd_xml_prescription in fd_xml_prescriptions:
drug_uid = fd_xml_prescription.find('Drug').attrib['u1'].strip()
if drug_uid == '-1':
_log.debug('skipping textual drug')
continue
drug_db = fd_xml_prescription.find('Drug').attrib['db'].strip()
drug_uid_name = fd_xml_prescription.find('Drug/DrugUidName').text.strip()
#drug_uid_name = u'<%s>' % drug_db
drug_name = fd_xml_prescription.find('Drug/DrugName').text.replace(', )', ')').strip()
drug_form = fd_xml_prescription.find('Drug/DrugForm').text.strip()
# drug_atc = fd_xml_prescription.find('DrugATC')
# if drug_atc is None:
# drug_atc = u''
# else:
# if drug_atc.text is None:
# drug_atc = u''
# else:
# drug_atc = drug_atc.text.strip()
# create new drug product
new_drug = gmMedication.create_drug_product(product_name = drug_name, preparation = drug_form, return_existing = True)
self.__imported_drugs.append(new_drug)
new_drug['is_fake_product'] = False
# new_drug['atc'] = drug_atc
new_drug['external_code_type'] = 'FreeDiams::%s::%s' % (drug_db, drug_uid_name)
new_drug['external_code'] = drug_uid
new_drug['pk_data_source'] = pk_data_source
new_drug.save()
# parse XML for composition records
fd_xml_components = fd_xml_prescription.getiterator('Composition')
comp_data = {}
for fd_xml_comp in fd_xml_components:
data = {}
xml_strength = fd_xml_comp.attrib['strength'].strip()
amount = regex.match(r'^\d+[.,]{0,1}\d*', xml_strength)
if amount is None:
amount = 99999
else:
amount = amount.group()
data['amount'] = amount
#unit = regex.sub(r'\d+[.,]{0,1}\d*', u'', xml_strength).strip()
unit = (xml_strength[len(amount):]).strip()
if unit == '':
unit = '*?*'
data['unit'] = unit
# hopefully, FreeDiams gets their act together, eventually:
atc = regex.match(r'[A-Za-z]\d\d[A-Za-z]{2}\d\d', fd_xml_comp.attrib['atc'].strip())
if atc is None:
data['atc'] = None
else:
atc = atc.group()
data['atc'] = atc
molecule_name = fd_xml_comp.attrib['molecularName'].strip()
if molecule_name != '':
gmMedication.create_substance_dose(substance = molecule_name, atc = atc, amount = amount, unit = unit)
data['molecule_name'] = molecule_name
inn_name = fd_xml_comp.attrib['inn'].strip()
if inn_name != '':
gmMedication.create_substance_dose(substance = inn_name, atc = atc, amount = amount, unit = unit)
#data['inn_name'] = molecule_name
data['inn_name'] = inn_name
if molecule_name == '':
data['substance'] = inn_name
_log.info('linking INN [%s] rather than molecularName as component', inn_name)
else:
data['substance'] = molecule_name
data['nature'] = fd_xml_comp.attrib['nature'].strip()
data['nature_ID'] = fd_xml_comp.attrib['natureLink'].strip()
# merge composition records of SA/FT nature
try:
old_data = comp_data[data['nature_ID']]
# normalize INN
if old_data['inn_name'] == '':
old_data['inn_name'] = data['inn_name']
if data['inn_name'] == '':
data['inn_name'] = old_data['inn_name']
# normalize molecule
if old_data['molecule_name'] == '':
old_data['molecule_name'] = data['molecule_name']
if data['molecule_name'] == '':
data['molecule_name'] = old_data['molecule_name']
# normalize ATC
if old_data['atc'] == '':
old_data['atc'] = data['atc']
if data['atc'] == '':
data['atc'] = old_data['atc']
# FT: transformed form
# SA: active substance
# it would be preferable to use the SA record because that's what's *actually*
# contained in the drug, however FreeDiams does not list the amount thereof
# (rather that of the INN)
# FT and SA records of the same component carry the same nature_ID
if data['nature'] == 'FT':
comp_data[data['nature_ID']] = data
else:
comp_data[data['nature_ID']] = old_data
# or create new record
except KeyError:
comp_data[data['nature_ID']] = data
# actually create components from (possibly merged) composition records
for key, data in comp_data.items():
new_drug.add_component (
substance = data['substance'],
atc = data['atc'],
amount = data['amount'],
unit = data['unit']
)
def __import_fd2gm_file_as_drugs_0_5(self, fd2gm_xml=None, pk_data_source=None):
db_def = fd2gm_xml.find('DrugsDatabaseName')
db_id = db_def.text.strip()
drug_id_name = db_def.attrib['drugUidName']
fd_xml_drug_entries = fd2gm_xml.findall('FullPrescription/Prescription')
self.__imported_drugs = []
for fd_xml_drug in fd_xml_drug_entries:
drug_uid = fd_xml_drug.find('Drug_UID').text.strip()
if drug_uid == '-1':
_log.debug('skipping textual drug')
continue # it's a TextualDrug, skip it
drug_name = fd_xml_drug.find('DrugName').text.replace(', )', ')').strip()
drug_form = fd_xml_drug.find('DrugForm').text.strip()
drug_atc = fd_xml_drug.find('DrugATC')
if drug_atc is None:
drug_atc = ''
else:
if drug_atc.text is None:
drug_atc = ''
else:
drug_atc = drug_atc.text.strip()
# create new drug product
new_drug = gmMedication.create_drug_product(product_name = drug_name, preparation = drug_form, return_existing = True)
self.__imported_drugs.append(new_drug)
new_drug['is_fake_product'] = False
new_drug['atc'] = drug_atc
new_drug['external_code_type'] = 'FreeDiams::%s::%s' % (db_id, drug_id_name)
new_drug['external_code'] = drug_uid
new_drug['pk_data_source'] = pk_data_source
new_drug.save()
# parse XML for composition records
fd_xml_components = fd_xml_drug.getiterator('Composition')
comp_data = {}
for fd_xml_comp in fd_xml_components:
data = {}
amount = regex.match(r'\d+[.,]{0,1}\d*', fd_xml_comp.attrib['strenght'].strip()) # sic, typo
if amount is None:
amount = 99999
else:
amount = amount.group()
data['amount'] = amount
unit = regex.sub(r'\d+[.,]{0,1}\d*', '', fd_xml_comp.attrib['strenght'].strip()).strip() # sic, typo
if unit == '':
unit = '*?*'
data['unit'] = unit
molecule_name = fd_xml_comp.attrib['molecularName'].strip()
if molecule_name != '':
gmMedication.create_substance_dose(substance = molecule_name, atc = None, amount = amount, unit = unit)
data['molecule_name'] = molecule_name
inn_name = fd_xml_comp.attrib['inn'].strip()
if inn_name != '':
gmMedication.create_substance_dose(substance = inn_name, atc = None, amount = amount, unit = unit)
data['inn_name'] = molecule_name
if molecule_name == '':
data['substance'] = inn_name
_log.info('linking INN [%s] rather than molecularName as component', inn_name)
else:
data['substance'] = molecule_name
data['nature'] = fd_xml_comp.attrib['nature'].strip()
data['nature_ID'] = fd_xml_comp.attrib['natureLink'].strip()
# merge composition records of SA/FT nature
try:
old_data = comp_data[data['nature_ID']]
# normalize INN
if old_data['inn_name'] == '':
old_data['inn_name'] = data['inn_name']
if data['inn_name'] == '':
data['inn_name'] = old_data['inn_name']
# normalize molecule
if old_data['molecule_name'] == '':
old_data['molecule_name'] = data['molecule_name']
if data['molecule_name'] == '':
data['molecule_name'] = old_data['molecule_name']
# FT: transformed form
# SA: active substance
# it would be preferable to use the SA record because that's what's *actually*
# contained in the drug, however FreeDiams does not list the amount thereof
# (rather that of the INN)
if data['nature'] == 'FT':
comp_data[data['nature_ID']] = data
else:
comp_data[data['nature_ID']] = old_data
# or create new record
except KeyError:
comp_data[data['nature_ID']] = data
# actually create components from (possibly merged) composition records
for key, data in comp_data.items():
new_drug.add_component (
substance = data['substance'],
amount = data['amount'],
unit = data['unit']
)
def __import_fd2gm_file_as_drugs_0_6_0(self, fd2gm_xml=None, pk_data_source=None):
# drug_id_name = db_def.attrib['drugUidName']
fd_xml_prescriptions = fd2gm_xml.findall('FullPrescription/Prescription')
self.__imported_drugs = []
for fd_xml_prescription in fd_xml_prescriptions:
drug_uid = fd_xml_prescription.find('Drug').attrib['u1'].strip()
if drug_uid == '-1':
_log.debug('skipping textual drug')
continue
drug_db = fd_xml_prescription.find('Drug').attrib['db'].strip()
drug_uid_name = fd_xml_prescription.find('Drug/DrugUidName').text.strip()
#drug_uid_name = u'<%s>' % drug_db
drug_name = fd_xml_prescription.find('Drug/DrugName').text.replace(', )', ')').strip()
drug_form = fd_xml_prescription.find('Drug/DrugForm').text.strip()
# drug_atc = fd_xml_prescription.find('DrugATC')
# if drug_atc is None:
# drug_atc = u''
# else:
# if drug_atc.text is None:
# drug_atc = u''
# else:
# drug_atc = drug_atc.text.strip()
# create new drug product
new_drug = gmMedication.create_drug_product(product_name = drug_name, preparation = drug_form, return_existing = True)
self.__imported_drugs.append(new_drug)
new_drug['is_fake_product'] = False
# new_drug['atc'] = drug_atc
new_drug['external_code_type'] = 'FreeDiams::%s::%s' % (drug_db, drug_uid_name)
new_drug['external_code'] = drug_uid
new_drug['pk_data_source'] = pk_data_source
new_drug.save()
# parse XML for composition records
fd_xml_components = fd_xml_prescription.getiterator('Composition')
comp_data = {}
for fd_xml_comp in fd_xml_components:
data = {}
xml_strength = fd_xml_comp.attrib['strength'].strip()
amount = regex.match(r'^\d+[.,]{0,1}\d*', xml_strength)
if amount is None:
amount = 99999
else:
amount = amount.group()
data['amount'] = amount
#unit = regex.sub(r'\d+[.,]{0,1}\d*', u'', xml_strength).strip()
unit = (xml_strength[len(amount):]).strip()
if unit == '':
unit = '*?*'
data['unit'] = unit
# hopefully, FreeDiams gets their act together, eventually:
atc = regex.match(r'[A-Za-z]\d\d[A-Za-z]{2}\d\d', fd_xml_comp.attrib['atc'].strip())
if atc is None:
data['atc'] = None
else:
atc = atc.group()
data['atc'] = atc
molecule_name = fd_xml_comp.attrib['molecularName'].strip()
if molecule_name != '':
gmMedication.create_substance_dose(substance = molecule_name, atc = atc, amount = amount, unit = unit)
data['molecule_name'] = molecule_name
inn_name = fd_xml_comp.attrib['inn'].strip()
if inn_name != '':
gmMedication.create_substance_dose(substance = inn_name, atc = atc, amount = amount, unit = unit)
#data['inn_name'] = molecule_name
data['inn_name'] = inn_name
if molecule_name == '':
data['substance'] = inn_name
_log.info('linking INN [%s] rather than molecularName as component', inn_name)
else:
data['substance'] = molecule_name
data['nature'] = fd_xml_comp.attrib['nature'].strip()
data['nature_ID'] = fd_xml_comp.attrib['natureLink'].strip()
# merge composition records of SA/FT nature
try:
old_data = comp_data[data['nature_ID']]
# normalize INN
if old_data['inn_name'] == '':
old_data['inn_name'] = data['inn_name']
if data['inn_name'] == '':
data['inn_name'] = old_data['inn_name']
# normalize molecule
if old_data['molecule_name'] == '':
old_data['molecule_name'] = data['molecule_name']
if data['molecule_name'] == '':
data['molecule_name'] = old_data['molecule_name']
# normalize ATC
if old_data['atc'] == '':
old_data['atc'] = data['atc']
if data['atc'] == '':
data['atc'] = old_data['atc']
# FT: transformed form
# SA: active substance
# it would be preferable to use the SA record because that's what's *actually*
# contained in the drug, however FreeDiams does not list the amount thereof
# (rather that of the INN)
# FT and SA records of the same component carry the same nature_ID
if data['nature'] == 'FT':
comp_data[data['nature_ID']] = data
else:
comp_data[data['nature_ID']] = old_data
# or create new record
except KeyError:
comp_data[data['nature_ID']] = data
# actually create components from (possibly merged) composition records
for key, data in comp_data.items():
new_drug.add_component (
substance = data['substance'],
atc = data['atc'],
amount = data['amount'],
unit = data['unit']
)
def __import_fd2gm_file_as_drugs_0_5(self, fd2gm_xml=None, pk_data_source=None):
db_def = fd2gm_xml.find('DrugsDatabaseName')
db_id = db_def.text.strip()
drug_id_name = db_def.attrib['drugUidName']
fd_xml_drug_entries = fd2gm_xml.findall('FullPrescription/Prescription')
self.__imported_drugs = []
for fd_xml_drug in fd_xml_drug_entries:
drug_uid = fd_xml_drug.find('Drug_UID').text.strip()
if drug_uid == '-1':
_log.debug('skipping textual drug')
continue # it's a TextualDrug, skip it
drug_name = fd_xml_drug.find('DrugName').text.replace(', )', ')').strip()
drug_form = fd_xml_drug.find('DrugForm').text.strip()
drug_atc = fd_xml_drug.find('DrugATC')
if drug_atc is None:
drug_atc = ''
else:
if drug_atc.text is None:
drug_atc = ''
else:
drug_atc = drug_atc.text.strip()
# create new drug product
new_drug = gmMedication.create_drug_product(product_name = drug_name, preparation = drug_form, return_existing = True)
self.__imported_drugs.append(new_drug)
new_drug['is_fake_product'] = False
new_drug['atc'] = drug_atc
new_drug['external_code_type'] = 'FreeDiams::%s::%s' % (db_id, drug_id_name)
new_drug['external_code'] = drug_uid
new_drug['pk_data_source'] = pk_data_source
new_drug.save()
# parse XML for composition records
fd_xml_components = fd_xml_drug.getiterator('Composition')
comp_data = {}
for fd_xml_comp in fd_xml_components:
data = {}
amount = regex.match(r'\d+[.,]{0,1}\d*', fd_xml_comp.attrib['strenght'].strip()) # sic, typo
if amount is None:
amount = 99999
else:
amount = amount.group()
data['amount'] = amount
unit = regex.sub(r'\d+[.,]{0,1}\d*', '', fd_xml_comp.attrib['strenght'].strip()).strip() # sic, typo
if unit == '':
unit = '*?*'
data['unit'] = unit
molecule_name = fd_xml_comp.attrib['molecularName'].strip()
if molecule_name != '':
gmMedication.create_substance_dose(substance = molecule_name, atc = None, amount = amount, unit = unit)
data['molecule_name'] = molecule_name
inn_name = fd_xml_comp.attrib['inn'].strip()
if inn_name != '':
gmMedication.create_substance_dose(substance = inn_name, atc = None, amount = amount, unit = unit)
data['inn_name'] = molecule_name
if molecule_name == '':
data['substance'] = inn_name
_log.info('linking INN [%s] rather than molecularName as component', inn_name)
else:
data['substance'] = molecule_name
data['nature'] = fd_xml_comp.attrib['nature'].strip()
data['nature_ID'] = fd_xml_comp.attrib['natureLink'].strip()
# merge composition records of SA/FT nature
try:
old_data = comp_data[data['nature_ID']]
# normalize INN
if old_data['inn_name'] == '':
old_data['inn_name'] = data['inn_name']
if data['inn_name'] == '':
data['inn_name'] = old_data['inn_name']
# normalize molecule
if old_data['molecule_name'] == '':
old_data['molecule_name'] = data['molecule_name']
if data['molecule_name'] == '':
data['molecule_name'] = old_data['molecule_name']
# FT: transformed form
# SA: active substance
# it would be preferable to use the SA record because that's what's *actually*
# contained in the drug, however FreeDiams does not list the amount thereof
# (rather that of the INN)
if data['nature'] == 'FT':
comp_data[data['nature_ID']] = data
else:
comp_data[data['nature_ID']] = old_data
# or create new record
except KeyError:
comp_data[data['nature_ID']] = data
# actually create components from (possibly merged) composition records
for key, data in comp_data.items():
new_drug.add_component (
substance = data['substance'],
amount = data['amount'],
unit = data['unit']
)
