def __format_episode_as_timeline_xml(episode, patient):
end = gmTools.bool2subst(
episode['episode_open'],
format_pydt(now),
format_pydt(episode.latest_access_date),
)
return __xml_episode_template % (
format_pydt(episode.best_guess_start_date), # start
end, # end
gmTools.xml_escape_string(episode['description']), # text
gmTools.bool2subst(episode['episode_open'], u'True',
u'False'), # ends_today
_('Episodes'), # category
gmTools.xml_escape_string(
episode.format( # description
patient=patient,
with_summary=True,
with_codes=True,
with_encounters=True,
with_documents=False,
with_hospital_stays=False,
with_procedures=False,
with_family_history=False,
with_tests=False,
with_vaccinations=False,
with_health_issue=True)))
def __format_episode_as_timeline_xml(episode, patient):
end = gmTools.bool2subst (
episode['episode_open'],
format_pydt(now),
format_pydt(episode.latest_access_date),
)
return __xml_episode_template % (
format_pydt(episode.best_guess_start_date), # start
end, # end
gmTools.xml_escape_string(episode['description']), # text
gmTools.bool2subst(episode['episode_open'], u'True', u'False'), # ends_today
_('Episodes'), # category
gmTools.xml_escape_string(episode.format ( # description
patient = patient,
with_summary = True,
with_codes = True,
with_encounters = True,
with_documents = False,
with_hospital_stays = False,
with_procedures = False,
with_family_history = False,
with_tests = False,
with_vaccinations = False,
with_health_issue = True
))
)
def __format_episode_as_timeline_xml(episode, patient):
data = {
'category': _('Episodes'),
'start': format_pydt(episode.best_guess_clinical_start_date),
'container_id': gmTools.coalesce(episode['pk_health_issue'], '', '(%s)'),
'label': gmTools.xml_escape_string (
gmTools.shorten_words_in_line(text = episode['description'], max_length = 20, min_word_length = 5)
),
'ends2day': gmTools.bool2subst(episode['episode_open'], 'True', 'False'),
'progress': gmTools.bool2subst(episode['episode_open'], '0', '100'),
'desc': gmTools.xml_escape_string(episode.format (
patient = patient,
with_summary = True,
with_codes = True,
with_encounters = True,
with_documents = False,
with_hospital_stays = False,
with_procedures = False,
with_family_history = False,
with_tests = False,
with_vaccinations = False,
with_health_issue = True
).strip().strip('\n').strip())
}
end = episode.best_guess_clinical_end_date
if end is None:
data['end'] = format_pydt(now)
else:
data['end'] = format_pydt(end)
return __xml_episode_template % data
def __format_episode_as_timeline_xml(episode, patient):
data = {
'category': _('Episodes'),
'start': format_pydt(episode.best_guess_clinical_start_date),
'container_id': gmTools.coalesce (
value2test = episode['pk_health_issue'],
return_instead = '',
template4value = '(%s)'
),
'label': gmTools.xml_escape_string (
gmTools.shorten_words_in_line(text = episode['description'], max_length = 20, min_word_length = 5)
),
'ends2day': gmTools.bool2subst(episode['episode_open'], 'True', 'False'),
'progress': gmTools.bool2subst(episode['episode_open'], '0', '100'),
'desc': gmTools.xml_escape_string(episode.format (
patient = patient,
with_summary = True,
with_codes = True,
with_encounters = True,
with_documents = False,
with_hospital_stays = False,
with_procedures = False,
with_family_history = False,
with_tests = False,
with_vaccinations = False,
with_health_issue = True
).strip().strip('\n').strip())
}
end = episode.best_guess_clinical_end_date
if end is None:
data['end'] = format_pydt(now)
else:
data['end'] = format_pydt(end)
return __xml_episode_template % data
def __format_document_as_timeline_xml(doc):
desc = gmTools.shorten_words_in_line(text=doc['l10n_type'],
max_length=20,
min_word_length=5)
return __xml_document_template % (
format_pydt(doc['clin_when']), format_pydt(
doc['clin_when']), gmTools.xml_escape_string(desc), _('Documents'),
gmTools.xml_escape_string(doc.format().strip().strip('\n').strip()))
def __format_document_as_timeline_xml(doc):
return __xml_document_template % (
format_pydt(doc['clin_when']),
format_pydt(doc['clin_when']),
gmTools.xml_escape_string(doc['l10n_type']),
_('Documents'),
gmTools.xml_escape_string(doc.format())
)
def __format_vaccination_as_timeline_xml(vacc):
return __xml_vaccination_template % (
format_pydt(vacc['date_given']), format_pydt(vacc['date_given']),
gmTools.xml_escape_string(vacc['vaccine']), _('Vaccinations'),
gmTools.xml_escape_string('\n'.join(
vacc.format(with_indications=True,
with_comment=True,
with_reaction=True,
date_format='%Y %b %d')).strip().strip('\n').strip()))
def __format_document_as_timeline_xml(doc):
desc = gmTools.shorten_words_in_line(text = doc['l10n_type'], max_length = 20, min_word_length = 5)
return __xml_document_template % (
format_pydt(doc['clin_when']),
format_pydt(doc['clin_when']),
gmTools.xml_escape_string(desc),
_('Documents'),
gmTools.xml_escape_string(doc.format().strip().strip('\n').strip())
)
def __format_hospital_stay_as_timeline_xml(stay):
end = stay['discharge']
if end is None:
end = now
return __xml_hospital_stay_template % (
format_pydt(stay['admission']),
format_pydt(end),
gmTools.xml_escape_string(stay['hospital']),
_('Hospital stays'), # category
gmTools.xml_escape_string(stay.format().strip().strip('\n').strip()))
def __format_hospital_stay_as_timeline_xml(stay):
end = stay['discharge']
if end is None:
end = now
return __xml_hospital_stay_template % (
format_pydt(stay['admission']),
format_pydt(end),
gmTools.xml_escape_string(stay['hospital']),
_('Hospital stays'), # category
gmTools.xml_escape_string(stay.format())
)
def __format_health_issue_as_timeline_xml(issue, patient, emr):
# container IDs are supposed to be numeric
# [email protected]
data = {'category': _('Health issues')}
possible_start = issue.possible_start_date
safe_start = issue.safe_start_date
end = issue.clinical_end_date
ends_today = 'False'
if end is None:
# open episode or active
ends_today = 'True'
end = now
# somewhat hacky and not really correct:
start2use = safe_start
if safe_start > end:
if possible_start < end:
start2use = possible_start
else:
start2use = end
data['desc'] = gmTools.xml_escape_string(
issue.format(patient=patient,
with_summary=True,
with_codes=True,
with_episodes=True,
with_encounters=False,
with_medications=False,
with_hospital_stays=False,
with_procedures=False,
with_family_history=False,
with_documents=False,
with_tests=False,
with_vaccinations=False).strip().strip('\n').strip())
label = gmTools.shorten_words_in_line(text=issue['description'],
max_length=25,
min_word_length=5)
xml = ''
# if possible_start < safe_start:
# data['start'] = format_pydt(possible_start)
# data['end'] = format_pydt(safe_start)
# data['ends2day'] = 'False'
# data['fuzzy'] = 'True'
# data['container_id'] = ''
# data['label'] = '?%s?' % gmTools.xml_escape_string(label)
# xml += __xml_issue_template % data
data['start'] = format_pydt(start2use)
data['end'] = format_pydt(end)
data['ends2day'] = ends_today
data['fuzzy'] = 'False'
data['container_id'] = '[%s]' % issue['pk_health_issue']
data['label'] = gmTools.xml_escape_string(label)
xml += __xml_issue_template % data
return xml
def __format_vaccination_as_timeline_xml(vacc):
return __xml_vaccination_template % (
format_pydt(vacc['date_given']),
format_pydt(vacc['date_given']),
gmTools.xml_escape_string(vacc['vaccine']),
_('Vaccinations'),
gmTools.xml_escape_string(u'\n'.join(vacc.format (
with_indications = True,
with_comment = True,
with_reaction = True,
date_format = '%Y %b %d'
)))
)
def __format_procedure_as_timeline_xml(proc):
if proc['is_ongoing']:
end = now
else:
if proc['clin_end'] is None:
end = proc['clin_when']
else:
end = proc['clin_end']
return __xml_procedure_template % (
format_pydt(proc['clin_when']), format_pydt(end),
gmTools.xml_escape_string(
proc['performed_procedure']), _('Procedures'),
gmTools.xml_escape_string(
proc.format(include_episode=True, include_codes=True)))
def __format_procedure_as_timeline_xml(proc):
if proc['is_ongoing']:
end = now
else:
if proc['clin_end'] is None:
end = proc['clin_when']
else:
end = proc['clin_end']
desc = gmTools.shorten_words_in_line(text=proc['performed_procedure'],
max_length=20,
min_word_length=5)
return __xml_procedure_template % (
format_pydt(proc['clin_when']), format_pydt(end),
gmTools.xml_escape_string(desc), _('Procedures'),
gmTools.xml_escape_string(
proc.format(include_episode=True,
include_codes=True).strip().strip('\n').strip()))
def __format_encounter_as_timeline_xml(encounter, patient):
return __xml_encounter_template % (
format_pydt(encounter['started']),
format_pydt(encounter['last_affirmed']),
#u'(%s)' % encounter['pk_episode'],
gmTools.xml_escape_string(
format_pydt(encounter['started'], format='%b %d')),
_('Encounters'), # category
gmTools.xml_escape_string(
encounter.format(patient=patient,
with_soap=True,
with_docs=False,
with_tests=False,
fancy_header=False,
with_vaccinations=False,
with_co_encountlet_hints=False,
with_rfe_aoe=True,
with_family_history=False)))
def __format_procedure_as_timeline_xml(proc):
if proc['is_ongoing']:
end = now
else:
if proc['clin_end'] is None:
end = proc['clin_when']
else:
end = proc['clin_end']
return __xml_procedure_template % (
format_pydt(proc['clin_when']),
format_pydt(end),
gmTools.xml_escape_string(proc['performed_procedure']),
_('Procedures'),
gmTools.xml_escape_string(proc.format (
include_episode = True,
include_codes = True
))
)
def __format_intake_as_timeline_xml(intake):
if intake['discontinued'] is None:
if intake['duration'] is None:
if intake['seems_inactive']:
end = intake['started']
else:
end = now
else:
end = intake['started'] + intake['duration']
else:
end = intake['discontinued']
return __xml_intake_template % (
format_pydt(intake['started']), format_pydt(end),
gmTools.xml_escape_string(intake['substance']), _('Substances'),
gmTools.xml_escape_string(
intake.format(single_line=False, show_all_product_components=False
).strip().strip('\n').strip()))
def __format_health_issue_as_timeline_xml(issue, patient, emr): # container IDs are supposed to be numeric # [email protected] data = {'category': _('Health issues')} possible_start = issue.possible_start_date safe_start = issue.safe_start_date end = issue.clinical_end_date ends_today = 'False' if end is None: # open episode or active ends_today = 'True' end = now data['desc'] = gmTools.xml_escape_string(issue.format ( patient = patient, with_summary = True, with_codes = True, with_episodes = True, with_encounters = False, with_medications = False, with_hospital_stays = False, with_procedures = False, with_family_history = False, with_documents = False, with_tests = False, with_vaccinations = False ).strip().strip('\n').strip()) label = gmTools.shorten_words_in_line(text = issue['description'], max_length = 25, min_word_length = 5) xml = '' # if possible_start < safe_start: # data['start'] = format_pydt(possible_start) # data['end'] = format_pydt(safe_start) # data['ends2day'] = 'False' # data['fuzzy'] = 'True' # data['container_id'] = '' # data['label'] = '?%s?' % gmTools.xml_escape_string(label) # xml += __xml_issue_template % data data['start'] = format_pydt(safe_start) data['end'] = format_pydt(end) data['ends2day'] = ends_today data['fuzzy'] = 'False' data['container_id'] = '[%s]' % issue['pk_health_issue'] data['label'] = gmTools.xml_escape_string(label) xml += __xml_issue_template % data return xml
def __format_encounter_as_timeline_xml(encounter, patient):
return __xml_encounter_template % (
format_pydt(encounter['started']),
format_pydt(encounter['last_affirmed']),
#u'(%s)' % encounter['pk_episode'],
gmTools.xml_escape_string(format_pydt(encounter['started'], format = '%b %d')),
_('Encounters'), # category
gmTools.xml_escape_string(encounter.format (
patient = patient,
with_soap = True,
with_docs = False,
with_tests = False,
fancy_header = False,
with_vaccinations = False,
with_co_encountlet_hints = False,
with_rfe_aoe = True,
with_family_history = False
))
)
def __format_procedure_as_timeline_xml(proc):
if proc['is_ongoing']:
end = now
else:
if proc['clin_end'] is None:
end = proc['clin_when']
else:
end = proc['clin_end']
desc = gmTools.shorten_words_in_line(text = proc['performed_procedure'], max_length = 20, min_word_length = 5)
return __xml_procedure_template % (
format_pydt(proc['clin_when']),
format_pydt(end),
gmTools.xml_escape_string(desc),
_('Procedures'),
gmTools.xml_escape_string(proc.format (
include_episode = True,
include_codes = True
).strip().strip('\n').strip())
)
def __format_intake_as_timeline_xml(intake):
if intake['discontinued'] is None:
if intake['duration'] is None:
if intake['seems_inactive']:
end = intake['started']
else:
end = now
else:
end = intake['started'] + intake['duration']
else:
end = intake['discontinued']
return __xml_intake_template % (
format_pydt(intake['started']),
format_pydt(end),
gmTools.xml_escape_string(intake['substance']),
_('Substances'),
gmTools.xml_escape_string(intake.format (
one_line = False,
show_all_brand_components = False
))
)
def __format_health_issue_as_timeline_xml(issue, patient, emr):
tooltip = issue.format (
patient = patient,
with_summary = True,
with_codes = True,
with_episodes = True,
with_encounters = False,
with_medications = False,
with_hospital_stays = False,
with_procedures = False,
with_family_history = False,
with_documents = False,
with_tests = False,
with_vaccinations = False
)
safe_start = issue.safe_start_date
possible_start = issue.possible_start_date
txt = u''
if possible_start < safe_start:
txt += __xml_issue_template % (
format_pydt(possible_start), # start
format_pydt(safe_start), # end
gmTools.xml_escape_string(u'?[%s]?' % issue['description']), # text
u'False', # ends_today
_('Health issues'), # category
gmTools.xml_escape_string(tooltip) # description
)
txt += __xml_issue_template % (
format_pydt(safe_start), # start
format_pydt(issue.end_date), # end
gmTools.xml_escape_string(issue['description']), # text
gmTools.bool2subst(issue['is_active'], u'True', u'False'), # ends_today
_('Health issues'), # category
gmTools.xml_escape_string(tooltip) # description
)
return txt
def __format_health_issue_as_timeline_xml(issue, patient, emr):
tooltip = issue.format(patient=patient,
with_summary=True,
with_codes=True,
with_episodes=True,
with_encounters=False,
with_medications=False,
with_hospital_stays=False,
with_procedures=False,
with_family_history=False,
with_documents=False,
with_tests=False,
with_vaccinations=False)
safe_start = issue.safe_start_date
possible_start = issue.possible_start_date
txt = u''
if possible_start < safe_start:
txt += __xml_issue_template % (
format_pydt(possible_start), # start
format_pydt(safe_start), # end
gmTools.xml_escape_string(
u'?[%s]?' % issue['description']), # text
u'False', # ends_today
_('Health issues'), # category
gmTools.xml_escape_string(tooltip) # description
)
txt += __xml_issue_template % (
format_pydt(safe_start), # start
format_pydt(issue.end_date), # end
gmTools.xml_escape_string(issue['description']), # text
gmTools.bool2subst(issue['is_active'], u'True',
u'False'), # ends_today
_('Health issues'), # category
gmTools.xml_escape_string(tooltip) # description
)
return txt
def __format_document_as_timeline_xml(doc):
return __xml_document_template % (
format_pydt(doc['clin_when']), format_pydt(
doc['clin_when']), gmTools.xml_escape_string(doc['l10n_type']),
_('Documents'), gmTools.xml_escape_string(doc.format()))
def __create_prescription_file(self, substance_intakes=None):
"""FreeDiams calls this exchange-out or prescription file.
CIS stands for Unique Speciality Identifier (eg bisoprolol 5 mg, gel).
CIS is AFSSAPS specific, but pharmacist can retreive drug name with the CIS.
AFSSAPS is the French FDA.
CIP stands for Unique Presentation Identifier (eg 30 pills plaq)
CIP if you want to specify the packaging of the drug (30 pills
thermoformed tablet...) -- actually not really usefull for french
doctors.
# .external_code_type: u'FR-CIS'
# .external_cod: the CIS value
OnlyForTest:
OnlyForTest drugs will be processed by the IA Engine but
not printed (regardless of FreeDiams mode). They are shown
in gray in the prescription view.
Select-only is a mode where FreeDiams creates a list of drugs
not a full prescription. In this list, users can add ForTestOnly
drug if they want to
1. print the list without some drugs
2. but including these drugs in the IA engine calculation
Select-Only mode does not have any relation with the ForTestOnly drugs.
IsTextual:
What is the use and significance of the
<IsTextual>true/false</IsTextual>
flag when both <DrugName> and <TextualDrugName> exist ?
This tag must be setted even if it sounds like a duplicated
data. This tag is needed inside FreeDiams code.
INN:
GNUmed will pass the substance in <TextualDrugName
and will also pass <INN>True</INN>.
Eric: Nop, this is not usefull because pure textual drugs
are not processed but just shown.
"""
# virginize file
open(self.__fd2gm_filename, 'wb').close()
# make sure we've got something to do
if substance_intakes is None:
if self.patient is None:
_log.warning('cannot create prescription file because there is neither a patient nor a substance intake list')
# do fail because __export_latest_prescription() should not have been called without patient
return False
emr = self.patient.emr
substance_intakes = emr.get_current_medications (
include_inactive = False,
include_unapproved = True
)
drug_snippets = []
# process FD drugs
fd_intakes = [ i for i in substance_intakes if (
(i['intake_is_approved_of'] is True)
and
(i['external_code_type_product'] is not None)
and
(i['external_code_type_product'].startswith('FreeDiams::'))
)]
intakes_pooled_by_product = {}
for intake in fd_intakes:
# this will leave only one entry per drug
# but FreeDiams knows the components ...
intakes_pooled_by_product[intake['product']] = intake
del fd_intakes
drug_snippet = """<Prescription>
<Drug u1="%s" u2="" old="%s" u3="" db="%s"> <!-- "old" needs to be the same as "u1" if not known -->
<DrugName>%s</DrugName> <!-- just for identification when reading XML files -->
</Drug>
</Prescription>"""
last_db_id = 'CA_HCDPD'
for intake in intakes_pooled_by_product.values():
last_db_id = gmTools.xml_escape_string(text = intake['external_code_type_product'].replace('FreeDiams::', '').split('::')[0])
drug_snippets.append(drug_snippet % (
gmTools.xml_escape_string(text = intake['external_code_product'].strip()),
gmTools.xml_escape_string(text = intake['external_code_product'].strip()),
last_db_id,
gmTools.xml_escape_string(text = intake['product'].strip())
))
# process non-FD drugs
non_fd_intakes = [ i for i in substance_intakes if (
(i['intake_is_approved_of'] is True)
and (
(i['external_code_type_product'] is None)
or
(not i['external_code_type_product'].startswith('FreeDiams::'))
)
)]
non_fd_product_intakes = [ i for i in non_fd_intakes if i['product'] is not None ]
non_fd_substance_intakes = [ i for i in non_fd_intakes if i['product'] is None ]
del non_fd_intakes
drug_snippet = """<Prescription>
<Drug u1="-1" u2="" old="" u3="" db="">
<DrugName>%s</DrugName>
</Drug>
<Dose Note="%s" IsTextual="true" IsAld="false"/>
</Prescription>"""
# <DrugUidName></DrugUidName>
# <DrugForm></DrugForm>
# <DrugRoute></DrugRoute>
# <DrugStrength/>
for intake in non_fd_substance_intakes:
drug_name = '%s %s%s (%s)' % (
intake['substance'],
intake['amount'],
intake['unit'],
intake['l10n_preparation']
)
drug_snippets.append(drug_snippet % (
gmTools.xml_escape_string(text = drug_name.strip()),
gmTools.xml_escape_string(text = gmTools.coalesce(intake['schedule'], ''))
))
intakes_pooled_by_product = {}
for intake in non_fd_product_intakes:
prod = '%s %s' % (intake['product'], intake['l10n_preparation'])
try:
intakes_pooled_by_product[prod].append(intake)
except KeyError:
intakes_pooled_by_product[prod] = [intake]
for product, comps in intakes_pooled_by_product.items():
drug_name = '%s\n' % product
for comp in comps:
drug_name += ' %s %s%s\n' % (
comp['substance'],
comp['amount'],
comp['unit']
)
drug_snippets.append(drug_snippet % (
gmTools.xml_escape_string(text = drug_name.strip()),
gmTools.xml_escape_string(text = gmTools.coalesce(comps[0]['schedule'], ''))
))
# assemble XML file
xml = """<?xml version = "1.0" encoding = "UTF-8"?>
<!DOCTYPE FreeMedForms>
<FreeDiams>
<FullPrescription version="0.7.2">
%s
</FullPrescription>
</FreeDiams>
"""
xml_file = io.open(self.__fd2gm_filename, mode = 'wt', encoding = 'utf8')
xml_file.write(xml % '\n\t\t'.join(drug_snippets))
xml_file.close()
return True
def __create_gm2fd_file(self, mode='interactions'): if mode == 'interactions': mode = 'select-only' elif mode == 'prescription': mode = 'prescriber' else: mode = 'select-only' xml_file = io.open(self.__gm2fd_filename, mode = 'wt', encoding = 'utf8') xml = """<?xml version="1.0" encoding="UTF-8"?> <FreeDiams_In version="0.5.0"> <EMR name="GNUmed" uid="unused"/> <ConfigFile value="%s"/> <ExchangeOut value="%s" format="xml"/> <!-- <DrugsDatabase uid="can be set to a specific DB"/> --> <Ui editmode="%s" blockPatientDatas="1"/> %%s </FreeDiams_In> """ % ( self.__fd4gm_config_file, self.__fd2gm_filename, mode ) if self.patient is None: xml_file.write(xml % '') xml_file.close() return name = self.patient.get_active_name() if self.patient['dob'] is None: dob = '' else: dob = self.patient['dob'].strftime(cFreeDiamsInterface.default_dob_format) emr = self.patient.emr allgs = emr.get_allergies() atc_allgs = [ a['atc_code'] for a in allgs if ((a['atc_code'] is not None) and (a['type'] == 'allergy')) ] atc_sens = [ a['atc_code'] for a in allgs if ((a['atc_code'] is not None) and (a['type'] == 'sensitivity')) ] inn_allgs = [ a['allergene'] for a in allgs if ((a['allergene'] is not None) and (a['type'] == 'allergy')) ] inn_sens = [ a['allergene'] for a in allgs if ((a['allergene'] is not None) and (a['type'] == 'sensitivity')) ] # this is rather fragile: FreeDiams won't know what type of UID this is # (but it will assume it is of the type of the drug database in use) # but eventually FreeDiams puts all drugs into one database :-) uid_allgs = [ a['substance_code'] for a in allgs if ((a['substance_code'] is not None) and (a['type'] == 'allergy')) ] uid_sens = [ a['substance_code'] for a in allgs if ((a['substance_code'] is not None) and (a['type'] == 'sensitivity')) ] patient_xml = """<Patient> <Identity lastnames="%s" firstnames="%s" uid="%s" dob="%s" gender="%s" /> <!-- can be <7 characters class codes: --> <ATCAllergies value="%s"/> <ATCIntolerances value="%s"/> <InnAllergies value="%s"/> <InnIntolerances value="%s"/> <DrugsUidAllergies value="%s"/> <DrugsUidIntolerances value="%s"/> <!-- # FIXME: search by LOINC code and add (as soon as supported by FreeDiams ...) <Creatinine value="12" unit="mg/l or mmol/l"/> <Weight value="70" unit="kg or pd" /> <WeightInGrams value="70"/> <Height value="170" unit="cm or "/> <HeightInCentimeters value="170"/> <ICD10 value="J11.0;A22;Z23"/> --> </Patient> """ % ( gmTools.xml_escape_string(text = name['lastnames']), gmTools.xml_escape_string(text = name['firstnames']), self.patient.ID, dob, cFreeDiamsInterface.map_gender2mf[self.patient['gender']], gmTools.xml_escape_string(text = ';'.join(atc_allgs)), gmTools.xml_escape_string(text = ';'.join(atc_sens)), gmTools.xml_escape_string(text = ';'.join(inn_allgs)), gmTools.xml_escape_string(text = ';'.join(inn_sens)), gmTools.xml_escape_string(text = ';'.join(uid_allgs)), gmTools.xml_escape_string(text = ';'.join(uid_sens)) ) xml_file.write(xml % patient_xml) xml_file.close()
def __create_prescription_file(self, substance_intakes=None):
"""FreeDiams calls this exchange-out or prescription file.
CIS stands for Unique Speciality Identifier (eg bisoprolol 5 mg, gel).
CIS is AFSSAPS specific, but pharmacist can retrieve drug name with the CIS.
AFSSAPS is the French FDA.
CIP stands for Unique Presentation Identifier (eg 30 pills plaq)
CIP if you want to specify the packaging of the drug (30 pills
thermoformed tablet...) -- actually not really usefull for french
doctors.
# .external_code_type: u'FR-CIS'
# .external_cod: the CIS value
OnlyForTest:
OnlyForTest drugs will be processed by the IA Engine but
not printed (regardless of FreeDiams mode). They are shown
in gray in the prescription view.
Select-only is a mode where FreeDiams creates a list of drugs
not a full prescription. In this list, users can add ForTestOnly
drug if they want to
1. print the list without some drugs
2. but including these drugs in the IA engine calculation
Select-Only mode does not have any relation with the ForTestOnly drugs.
IsTextual:
What is the use and significance of the
<IsTextual>true/false</IsTextual>
flag when both <DrugName> and <TextualDrugName> exist ?
This tag must be setted even if it sounds like a duplicated
data. This tag is needed inside FreeDiams code.
INN:
GNUmed will pass the substance in <TextualDrugName
and will also pass <INN>True</INN>.
Eric: Nop, this is not useful because pure textual drugs
are not processed but just shown.
"""
# virginize file
open(self.__fd2gm_filename, 'wb').close()
# make sure we've got something to do
if substance_intakes is None:
if self.patient is None:
_log.warning('cannot create prescription file because there is neither a patient nor a substance intake list')
# do fail because __export_latest_prescription() should not have been called without patient
return False
emr = self.patient.emr
substance_intakes = emr.get_current_medications (
include_inactive = False
)
drug_snippets = []
# process FD drugs
fd_intakes = [ i for i in substance_intakes if (
(i['external_code_type_product'] is not None)
and
(i['external_code_type_product'].startswith('FreeDiams::'))
)]
intakes_pooled_by_product = {}
for intake in fd_intakes:
# this will leave only one entry per drug
# but FreeDiams knows the components ...
intakes_pooled_by_product[intake['drug_product']] = intake
del fd_intakes
drug_snippet = """<Prescription>
<Drug u1="%s" u2="" old="%s" u3="" db="%s"> <!-- "old" needs to be the same as "u1" if not known -->
<DrugName>%s</DrugName> <!-- just for identification when reading XML files -->
</Drug>
</Prescription>"""
last_db_id = 'CA_HCDPD'
for intake in intakes_pooled_by_product.values():
last_db_id = gmTools.xml_escape_string(text = intake['external_code_type_product'].replace('FreeDiams::', '').split('::')[0])
drug_snippets.append(drug_snippet % (
gmTools.xml_escape_string(text = intake['external_code_product'].strip()),
gmTools.xml_escape_string(text = intake['external_code_product'].strip()),
last_db_id,
gmTools.xml_escape_string(text = intake['drug_product'].strip())
))
# process non-FD drugs
non_fd_intakes = [ i for i in substance_intakes if (
(
(i['external_code_type_product'] is None)
or
(not i['external_code_type_product'].startswith('FreeDiams::'))
)
)]
non_fd_product_intakes = [ i for i in non_fd_intakes if i['drug_product'] is not None ]
non_fd_substance_intakes = [ i for i in non_fd_intakes if i['drug_product'] is None ]
del non_fd_intakes
drug_snippet = """<Prescription>
<Drug u1="-1" u2="" old="" u3="" db="">
<DrugName>%s</DrugName>
</Drug>
<Dose Note="%s" IsTextual="true" IsAld="false"/>
</Prescription>"""
# <DrugUidName></DrugUidName>
# <DrugForm></DrugForm>
# <DrugRoute></DrugRoute>
# <DrugStrength/>
for intake in non_fd_substance_intakes:
drug_name = '%s %s%s (%s)' % (
intake['substance'],
intake['amount'],
intake['unit'],
intake['l10n_preparation']
)
drug_snippets.append(drug_snippet % (
gmTools.xml_escape_string(text = drug_name.strip()),
gmTools.xml_escape_string(text = gmTools.coalesce(intake['schedule'], ''))
))
intakes_pooled_by_product = {}
for intake in non_fd_product_intakes:
prod = '%s %s' % (intake['drug_product'], intake['l10n_preparation'])
try:
intakes_pooled_by_product[prod].append(intake)
except KeyError:
intakes_pooled_by_product[prod] = [intake]
for product, comps in intakes_pooled_by_product.items():
drug_name = '%s\n' % product
for comp in comps:
drug_name += ' %s %s%s\n' % (
comp['substance'],
comp['amount'],
comp['unit']
)
drug_snippets.append(drug_snippet % (
gmTools.xml_escape_string(text = drug_name.strip()),
gmTools.xml_escape_string(text = gmTools.coalesce(comps[0]['schedule'], ''))
))
# assemble XML file
xml = """<?xml version = "1.0" encoding = "UTF-8"?>
<!DOCTYPE FreeMedForms>
<FreeDiams>
<FullPrescription version="0.7.2">
%s
</FullPrescription>
</FreeDiams>
"""
xml_file = io.open(self.__fd2gm_filename, mode = 'wt', encoding = 'utf8')
xml_file.write(xml % '\n\t\t'.join(drug_snippets))
xml_file.close()
return True
def __create_gm2fd_file(self, mode='interactions'): if mode == 'interactions': mode = 'select-only' elif mode == 'prescription': mode = 'prescriber' else: mode = 'select-only' xml_file = io.open(self.__gm2fd_filename, mode = 'wt', encoding = 'utf8') xml = """<?xml version="1.0" encoding="UTF-8"?> <FreeDiams_In version="0.5.0"> <EMR name="GNUmed" uid="unused"/> <ConfigFile value="%s"/> <ExchangeOut value="%s" format="xml"/> <!-- <DrugsDatabase uid="can be set to a specific DB"/> --> <Ui editmode="%s" blockPatientDatas="1"/> %%s </FreeDiams_In> """ % ( self.__fd4gm_config_file, self.__fd2gm_filename, mode ) if self.patient is None: xml_file.write(xml % '') xml_file.close() return name = self.patient.get_active_name() if self.patient['dob'] is None: dob = '' else: dob = self.patient['dob'].strftime(cFreeDiamsInterface.default_dob_format) emr = self.patient.emr allgs = emr.get_allergies() atc_allgs = [ a['atc_code'] for a in allgs if ((a['atc_code'] is not None) and (a['type'] == 'allergy')) ] atc_sens = [ a['atc_code'] for a in allgs if ((a['atc_code'] is not None) and (a['type'] == 'sensitivity')) ] inn_allgs = [ a['allergene'] for a in allgs if ((a['allergene'] is not None) and (a['type'] == 'allergy')) ] inn_sens = [ a['allergene'] for a in allgs if ((a['allergene'] is not None) and (a['type'] == 'sensitivity')) ] # this is rather fragile: FreeDiams won't know what type of UID this is # (but it will assume it is of the type of the drug database in use) # but eventually FreeDiams puts all drugs into one database :-) uid_allgs = [ a['substance_code'] for a in allgs if ((a['substance_code'] is not None) and (a['type'] == 'allergy')) ] uid_sens = [ a['substance_code'] for a in allgs if ((a['substance_code'] is not None) and (a['type'] == 'sensitivity')) ] patient_xml = """<Patient> <Identity lastnames="%s" firstnames="%s" uid="%s" dob="%s" gender="%s" /> <!-- can be <7 characters class codes: --> <ATCAllergies value="%s"/> <ATCIntolerances value="%s"/> <InnAllergies value="%s"/> <InnIntolerances value="%s"/> <DrugsUidAllergies value="%s"/> <DrugsUidIntolerances value="%s"/> <!-- # FIXME: search by LOINC code and add (as soon as supported by FreeDiams ...) <Creatinine value="12" unit="mg/l or mmol/l"/> <Weight value="70" unit="kg or pd" /> <WeightInGrams value="70"/> <Height value="170" unit="cm or "/> <HeightInCentimeters value="170"/> <ICD10 value="J11.0;A22;Z23"/> --> </Patient> """ % ( gmTools.xml_escape_string(text = name['lastnames']), gmTools.xml_escape_string(text = name['firstnames']), self.patient.ID, dob, cFreeDiamsInterface.map_gender2mf[self.patient['gender']], gmTools.xml_escape_string(text = ';'.join(atc_allgs)), gmTools.xml_escape_string(text = ';'.join(atc_sens)), gmTools.xml_escape_string(text = ';'.join(inn_allgs)), gmTools.xml_escape_string(text = ';'.join(inn_sens)), gmTools.xml_escape_string(text = ';'.join(uid_allgs)), gmTools.xml_escape_string(text = ';'.join(uid_sens)) ) xml_file.write(xml % patient_xml) xml_file.close()
