Module Gnumed.business.gmMedication
Medication handling code.
license: GPL v2 or later
intake regimen:
beim Aufstehen / Frühstück / Mittag / abends / zum Schlafengehen
"19 Uhr"
"Mittwochs" (Alendronsäure)
"1x/Monat" (Alendronsäure)
"Mo Di Mi Do Fr Sa So" (Falithrom)
"Tag 1: 4, Tag 2: 3, Tag 3: 2, Tag 4: 1" (Prednisonstoß)
"1T:4, 1T:3, 2T:2, 3T:1, 4T:1/2" (Prednisonstoß)
"bei Bedarf"
Functions
def calculate_amts_data_check_symbol_v2_0(intakes=None)-
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def calculate_amts_data_check_symbol_v2_0(intakes=None): # first char of generic substance or product name first_chars = [] for intake in intakes: first_chars.append(intake['drug_product'][0]) # add up_per page val_sum = 0 for first_char in first_chars: # ziffer: ascii+7 if first_char.isdigit(): val_sum += (ord(first_char) + 7) # großbuchstabe: ascii # kleinbuchstabe ascii(großbuchstabe) if first_char.isalpha(): val_sum += ord(first_char.upper()) # other: 0 # get remainder of sum mod 36 tmp, remainder = divmod(val_sum, 36) # 0-9 -> '0' - '9' if remainder < 10: return '%s' % remainder # 10-35 -> 'A' - 'Z' return chr(remainder + 55) def create_default_medication_history_episode(pk_health_issue=None, encounter=None, link_obj=None)-
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def create_default_medication_history_episode(pk_health_issue=None, encounter=None, link_obj=None): return gmEpisode.create_episode ( pk_health_issue = pk_health_issue, episode_name = DEFAULT_MEDICATION_HISTORY_EPISODE, is_open = False, allow_dupes = False, encounter = encounter, link_obj = link_obj ) def create_drug_product(product_name=None,
preparation=None,
return_existing=False,
link_obj=None,
doses=None,
pk_doses: list[int] = None)-
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def create_drug_product(product_name=None, preparation=None, return_existing=False, link_obj=None, doses=None, pk_doses:list[int]=None): if preparation is None: preparation = _('units') if preparation.strip() == '': preparation = _('units') if return_existing: drug = get_drug_by_name(product_name = product_name, preparation = preparation, link_obj = link_obj) if drug is not None: return drug if link_obj is None: link_obj = gmPG2.get_connection(readonly = False) conn_commit = link_obj.commit conn_close = link_obj.close else: conn_commit = lambda *x: None conn_close = lambda *x: None cmd = 'INSERT INTO ref.drug_product (description, preparation) VALUES (%(prod_name)s, %(prep)s) RETURNING pk' args = {'prod_name': product_name, 'prep': preparation} rows = gmPG2.run_rw_queries(link_obj = link_obj, queries = [{'sql': cmd, 'args': args}], return_data = True) product = cDrugProduct(aPK_obj = rows[0]['pk'], link_obj = link_obj) if doses or pk_doses: product.set_substance_doses_as_components ( link_obj = link_obj, substance_doses = doses, pk_substance_doses = pk_doses ) conn_commit() conn_close() return product def create_drug_product_by_atc(atc=None, product_name=None, preparation=None, return_existing=False, link_obj=None)-
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def create_drug_product_by_atc(atc=None, product_name=None, preparation=None, return_existing=False, link_obj=None): if atc is None: raise ValueError('cannot create drug product by ATC without ATC') if preparation is None: preparation = _('units') if preparation.strip() == '': preparation = _('units') if return_existing: drug = get_drug_by_atc(atc = atc, preparation = preparation, link_obj = link_obj) if drug is not None: return drug drug = create_drug_product ( link_obj = link_obj, product_name = product_name, preparation = preparation, return_existing = False ) drug['atc'] = atc drug.save(conn = link_obj) return drug def create_intake_regimen(pk_intake: int = None,
started=None,
pk_encounter: int = None,
pk_episode: int = None,
schedule: str = None,
discontinued=None,
amount=None,
unit: str = None,
link_obj=None) ‑> cIntakeRegimen-
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def create_intake_regimen ( pk_intake:int=None, started=None, pk_encounter:int=None, pk_episode:int=None, schedule:str=None, discontinued=None, amount=None, unit:str=None, link_obj=None ) -> cIntakeRegimen: query_args = { 'pk_intake': pk_intake, 'started': started, 'pk_encounter': pk_encounter, 'pk_episode': pk_episode, 'schedule': schedule, 'amount': amount, 'unit': unit } cols = [ 'fk_intake', 'clin_when', 'fk_encounter', 'fk_episode', 'narrative', 'amount', 'unit', ] placeholders = [ '%(pk_intake)s', '%(started)s', '%(pk_encounter)s', '%(pk_episode)s', 'gm.nullify_empty_string(%(schedule)s)', '%(amount)s', '%(unit)s' ] if discontinued: cols.append('discontinued') placeholders.append('%(discontinued)s') query_args['discontinued'] = discontinued SQL = """ INSERT INTO clin.intake_regimen ( %s ) VALUES ( %s ) RETURNING pk """ % (', '.join(cols), ', '.join(placeholders)) rows = gmPG2.run_rw_query(sql = SQL, args = query_args, return_data = True, link_obj = link_obj) return cIntakeRegimen(aPK_obj = rows[0]['pk'], link_obj = link_obj) def create_intake_with_regimen(pk_encounter: int = None,
pk_episode: int = None,
pk_substance: int = None,
started=None,
schedule: str = None,
discontinued=None,
link_obj=None) ‑> cIntakeWithRegimen-
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def create_intake_with_regimen ( # intake: pk_encounter:int=None, pk_episode:int=None, pk_substance:int=None, # regimen: started=None, schedule:str=None, discontinued=None, # other: link_obj=None ) -> cIntakeWithRegimen: intake = create_substance_intake ( pk_encounter = pk_encounter, pk_episode = pk_episode, pk_substance = pk_substance, link_obj = link_obj ) regimen = create_intake_regimen ( pk_intake = intake['pk_intake'], started = started, pk_encounter = pk_encounter, pk_episode = pk_episode, schedule = schedule, discontinued = discontinued, link_obj = link_obj ) return cIntakeWithRegimen ( aPK_obj = {'pk_intake_regimen': regimen['pk_intake_regimen'], 'pk_intake': regimen['pk_intake']}, link_obj = link_obj ) def create_substance(substance=None, atc=None, link_obj=None)-
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def create_substance(substance=None, atc=None, link_obj=None): if atc: atc = atc.strip() args = { 'desc': substance.strip(), 'atc': atc } cmd = "SELECT pk FROM ref.substance WHERE lower(description) = lower(%(desc)s)" rows = gmPG2.run_ro_queries(link_obj = link_obj, queries = [{'sql': cmd, 'args': args}]) if len(rows) == 0: cmd = """ INSERT INTO ref.substance (description, atc) VALUES ( %(desc)s, coalesce ( gm.nullify_empty_string(%(atc)s), (SELECT code FROM ref.atc WHERE term = %(desc)s LIMIT 1) ) ) RETURNING pk""" rows = gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}], return_data = True, link_obj = link_obj) if atc: gmATC.propagate_atc(link_obj = link_obj, substance = substance.strip(), atc = atc) return cSubstance(aPK_obj = rows[0]['pk'], link_obj = link_obj) def create_substance_by_atc(substance=None, atc=None, link_obj=None)-
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def create_substance_by_atc(substance=None, atc=None, link_obj=None): if atc is None: raise ValueError('<atc> must be supplied') atc = atc.strip() if atc == '': raise ValueError('<atc> cannot be empty: [%s]', atc) queries = [] args = { 'desc': substance.strip(), 'atc': atc } # in case the substance already exists: add ATC cmd = "UPDATE ref.substance SET atc = %(atc)s WHERE lower(description) = lower(%(desc)s) AND atc IS NULL" queries.append({'sql': cmd, 'args': args}) # or else INSERT the substance cmd = """ INSERT INTO ref.substance (description, atc) SELECT %(desc)s, %(atc)s WHERE NOT EXISTS ( SELECT 1 FROM ref.substance WHERE atc = %(atc)s ) RETURNING pk""" queries.append({'sql': cmd, 'args': args}) rows = gmPG2.run_rw_queries(link_obj = link_obj, queries = queries, return_data = True) if len(rows) == 0: cmd = "SELECT pk FROM ref.substance WHERE atc = %(atc)s LIMIT 1" rows = gmPG2.run_ro_queries(link_obj = link_obj, queries = [{'sql': cmd, 'args': args}]) return cSubstance(aPK_obj = rows[0]['pk'], link_obj = link_obj) def create_substance_dose(link_obj=None,
pk_substance=None,
substance=None,
atc=None,
amount=None,
unit=None,
dose_unit=None)-
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def create_substance_dose(link_obj=None, pk_substance=None, substance=None, atc=None, amount=None, unit=None, dose_unit=None): if [pk_substance, substance].count(None) != 1: raise ValueError('exctly one of <pk_substance> and <substance> must be None') converted, amount = gmTools.input2decimal(amount) if not converted: raise ValueError('<amount> must be a number: %s (is: %s)', amount, type(amount)) if pk_substance is None: pk_substance = create_substance(link_obj = link_obj, substance = substance, atc = atc)['pk_substance'] args = { 'pk_subst': pk_substance, 'amount': amount, 'unit': unit.strip(), 'dose_unit': dose_unit } cmd = """ SELECT pk FROM ref.dose WHERE fk_substance = %(pk_subst)s AND amount = %(amount)s AND unit = %(unit)s AND dose_unit IS NOT DISTINCT FROM gm.nullify_empty_string(%(dose_unit)s) """ rows = gmPG2.run_ro_queries(link_obj = link_obj, queries = [{'sql': cmd, 'args': args}]) if len(rows) == 0: cmd = """ INSERT INTO ref.dose (fk_substance, amount, unit, dose_unit) VALUES ( %(pk_subst)s, %(amount)s, gm.nullify_empty_string(%(unit)s), gm.nullify_empty_string(%(dose_unit)s) ) RETURNING pk""" rows = gmPG2.run_rw_queries(link_obj = link_obj, queries = [{'sql': cmd, 'args': args}], return_data = True) return cSubstanceDose(aPK_obj = rows[0]['pk'], link_obj = link_obj) def create_substance_dose_by_atc(link_obj=None, substance=None, atc=None, amount=None, unit=None, dose_unit=None)-
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def create_substance_dose_by_atc(link_obj=None, substance=None, atc=None, amount=None, unit=None, dose_unit=None): subst = create_substance_by_atc ( link_obj = link_obj, substance = substance, atc = atc ) return create_substance_dose ( link_obj = link_obj, pk_substance = subst['pk_substance'], amount = amount, unit = unit, dose_unit = dose_unit ) def create_substance_intake(pk_encounter=None, pk_episode=None, pk_substance=None, link_obj=None)-
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def create_substance_intake(pk_encounter=None, pk_episode=None, pk_substance=None, link_obj=None): args = { 'pk_enc': pk_encounter, 'pk_epi': pk_episode, 'pk_subst': pk_substance } cmd = """ INSERT INTO clin.intake ( fk_encounter, fk_episode, fk_substance ) VALUES ( %(pk_enc)s, %(pk_epi)s, %(pk_subst)s ) RETURNING pk """ rows = gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}], return_data = True, link_obj = link_obj) return cSubstanceIntakeEntry(aPK_obj = rows[0][0], link_obj = link_obj) def delete_drug_product(pk_drug_product: int = None) ‑> bool-
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def delete_drug_product(pk_drug_product:int=None) -> bool: args = {'pk': pk_drug_product} SQL = 'SELECT EXISTS(SELECT 1 FROM clin.vaccination WHERE fk_vaccine = (SELECT pk FROM ref.vaccine WHERE fk_drug_product = %(pk)s))' args = {'pk': pk_drug_product} rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}]) if rows and rows[0][0]: _log.error('cannot delete drug product [%s], it is used as a vaccine') return False queries = [] SQL = 'DELETE FROM ref.lnk_dose2drug WHERE fk_drug_product = %(pk)s' queries.append({'sql': SQL, 'args': args}) SQL = 'DELETE FROM ref.drug_product WHERE pk = %(pk)s' queries.append({'sql': SQL, 'args': args}) gmPG2.run_rw_queries(queries = queries) return True def delete_intake_regimen(pk_intake_regimen: int = None, link_obj=None) ‑> bool-
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def delete_intake_regimen(pk_intake_regimen:int=None, link_obj=None) -> bool: SQL = 'DELETE FROM clin.intake_regimen WHERE pk = %(pk)s' args = {'pk': pk_intake_regimen} gmPG2.run_rw_query(sql = SQL, args = args, link_obj = link_obj) return True def delete_intake_with_regimen(pk_intake_regimen: int, pk_intake: int = None, link_obj=None) ‑> bool-
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def delete_intake_with_regimen(pk_intake_regimen:int, pk_intake:int=None, link_obj=None) -> bool: """Delete the given intake regimen. If that had been the only regimen, also delete the intake itself, IF the PK for that is known. """ delete_intake_regimen(pk_intake_regimen = pk_intake_regimen, link_obj = link_obj) if not pk_intake: return True other_regimen4intake = get_intake_regimens(pk_intake = pk_intake, ongoing_only = False, as_instance = False, link_obj = link_obj) if not other_regimen4intake: delete_substance_intake(pk_intake = pk_intake, delete_regimen = False, link_obj = link_obj) return TrueDelete the given intake regimen.
If that had been the only regimen, also delete the intake itself, IF the PK for that is known.
def delete_substance(pk_substance=None)-
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def delete_substance(pk_substance=None): args = {'pk': pk_substance} cmd = """ DELETE FROM ref.substance WHERE pk = %(pk)s AND -- must not currently be used with a patient NOT EXISTS ( SELECT 1 FROM clin.v_intakes WHERE pk_substance = %(pk)s LIMIT 1 ) AND -- must not currently have doses defined for it NOT EXISTS ( SELECT 1 FROM ref.dose WHERE fk_substance = %(pk)s LIMIT 1 ) """ gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}]) return True def delete_substance_dose(pk_dose=None)-
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def delete_substance_dose(pk_dose=None): args = {'pk_dose': pk_dose} cmd = """ DELETE FROM ref.dose WHERE pk = %(pk_dose)s AND -- must not currently be used with a patient NOT EXISTS ( SELECT 1 FROM clin.v_intakes WHERE pk_dose = %(pk_dose)s LIMIT 1 ) AND -- must not currently be linked to a drug NOT EXISTS ( SELECT 1 FROM ref.lnk_dose2drug WHERE fk_dose = %(pk_dose)s LIMIT 1 ) """ gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}]) return True def delete_substance_intake(pk_intake: int = None, delete_regimen: bool = False, link_obj=None) ‑> bool-
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def delete_substance_intake(pk_intake:int=None, delete_regimen:bool=False, link_obj=None) -> bool: args = {'pk_intake': pk_intake} queries = [] if delete_regimen: queries.append ({ 'sql': 'DELETE FROM clin.intake_regimen c_ir WHERE fk_intake = %(pk_intake)s', 'args': args }) queries.append ({ 'sql': 'DELETE FROM clin.intake WHERE pk = %(pk_intake)s', 'args': args }) gmPG2.run_rw_queries(queries = queries, link_obj = link_obj) return True def format_intake_with_regimen_as_amts_data(intake=None, strict=True)-
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def format_intake_with_regimen_as_amts_data(intake=None, strict=True): """ <M a="Handelsname" fd="freie Formangabe" t="freies Dosierschema" dud="freie Dosiereinheit (Stück Tab)" r="reason" i="info"> <W w="Metformin" s="500 mg"/> <W ...> </M> """ if not strict: pass # relax length checks M_fields = [] M_fields.append('a="%s"' % intake['substance']) M_fields.append('fd="Tabl.o.ä."') if intake['schedule']: M_fields.append('t="%s"' % intake['schedule']) #M_fields.append(u'dud="%s"' % intake['dose unit, like Stück']) M_fields.append('r="%s"' % intake['episode']) if intake['notes4patient']: M_fields.append('i="%s"' % intake['notes4patient'].replace('\n', '//').strip('/')) M_line = '<M %s>' % ' '.join(M_fields) W_lines = ['<W w="%s" s="%s %s"/>' % ( intake['substance'], intake['amount'], format_units(intake['unit'], short = True) )] return M_line + ''.join(W_lines) + '</M>' def format_regimen_end_medically(regimen_like: cIntakeWithRegimen | cIntakeRegimen,
terse: bool = False) ‑> str-
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def format_regimen_end_medically(regimen_like:cIntakeWithRegimen|cIntakeRegimen, terse:bool=False) -> str: """Format end of intake regimen suitable for display. Args: regimen_like: cIntakeWithRegimen or cIntakeRegimen """ assert regimen_like, '<regimen_like> must be given' if gmDateTime.pydt_is_today(regimen_like['discontinued']): return _('today') if gmDateTime.pydt_is_yesterday(regimen_like['discontinued']): return '-1/365' if terse else _('yesterday') if not regimen_like['discontinued'] and not regimen_like['planned_duration']: return gmTools.u_ellipsis if not regimen_like['discontinued'] and not regimen_like['started']: return gmTools.u_ellipsis now = gmDateTime.pydt_now_here() if not regimen_like['discontinued']: planned_end = regimen_like['started'] + regimen_like['planned_duration'] - pydt.timedelta(days = 1) intv = max(now, planned_end) - min(now, planned_end) if planned_end.year == now.year: end_template = '%b %d' if planned_end < now: planned_end_from_now_template = ('-%s,%s' % planned_end.year) if terse else _('%s ago, this year') else: planned_end_from_now_template = ('+%s,%s' % planned_end.year) if terse else _('in %s, this year') planned_end_from_now_str = planned_end_from_now_template % gmDateTime.format_interval_medically(intv, terse = terse) else: end_template = '%Y' if planned_end < now: planned_end_from_now_template = '-%s,%s' if terse else _('%s ago: %s') else: planned_end_from_now_template = '+%s,%s' if terse else _('in %s: %s') planned_end_from_now_str = planned_end_from_now_template % ( gmDateTime.format_interval_medically(intv, terse = terse), planned_end.strftime('%b %d') ) return '%s (%s)' % (planned_end.strftime(end_template), planned_end_from_now_str) intv = max(now, regimen_like['discontinued']) - min(now, regimen_like['discontinued']) if regimen_like['discontinued'].year == now.year: end_date_template = '%b %d' if regimen_like['discontinued'] < now: planned_end_from_now_template = ('-%s,%s' % regimen_like['discontinued'].year) if terse else _('%s ago, this year') else: planned_end_from_now_template = ('+%s,%s' % regimen_like['discontinued'].year) if terse else _('in %s, this year') planned_end_from_now_str = planned_end_from_now_template % gmDateTime.format_interval_medically(intv, terse = terse) else: end_date_template = '%Y' if regimen_like['discontinued'] < now: planned_end_from_now_template = '-%s,%s' if terse else _('%s ago: %s') else: planned_end_from_now_template = '+%s,%s' if terse else _('in %s: %s') planned_end_from_now_str = planned_end_from_now_template % ( gmDateTime.format_interval_medically(intv, terse = terse), regimen_like['discontinued'].strftime('%b %d') ) return '%s (%s)' % (regimen_like['discontinued'].strftime(end_date_template), planned_end_from_now_str)Format end of intake regimen suitable for display.
Args
regimen_like- cIntakeWithRegimen or cIntakeRegimen
def format_regimen_like_as_multiple_lines(regimen_like: cIntakeWithRegimen | cIntakeRegimen = None,
left_margin: int = 0,
date_format: str = '%Y %b %d',
allergy=None,
include_loincs: bool = False,
include_metadata: bool = False,
eol: str = None) ‑> str | list-
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def format_regimen_like_as_multiple_lines ( regimen_like:cIntakeRegimen | cIntakeWithRegimen=None, left_margin:int=0, date_format:str='%Y %b %d', allergy=None, include_loincs:bool=False, include_metadata:bool=False, eol:str=None ) -> list | str: """Format the intake regimen into multiple lines. Args: regimen_like: cIntakeRegimen or cIntakeWithRegimen left_margin: number of leading spaces added to each line if <eol> is defined """ assert isinstance(regimen_like, (cIntakeRegimen, cIntakeWithRegimen)), '<regimen_like> must be cIntakeRegimen or cIntakeWithRegimen' lines = [] # header status = _('Ongoing') if regimen_like['discontinued'] and regimen_like['discontinued'] < gmDateTime.pydt_now_here(): status = _('Inactive') lines.append(_('%s intake of "%s"') % (status, regimen_like['substance']) + ' ') # caveat if allergy: certainty = gmTools.bool2subst(allergy['definite'], _('definite'), _('suspected')) lines.append('') lines.append(' !! ---- Cave ---- !!') lines.append(' %s (%s): %s (%s)' % ( allergy['l10n_type'], certainty, allergy['descriptor'], gmTools.coalesce(allergy['reaction'], '')[:40] )) lines.append('') # use type if regimen_like['use_type'] is not None: lines.append(' ' + regimen_like.use_type_string) if regimen_like['amount']: lines.append(' ' + _('Amount: %s %s') % ( regimen_like['amount'], regimen_like._get_formatted_units(short = False) )) if regimen_like['schedule']: lines.append(_(' Regimen: %s') % regimen_like['schedule']) # codes if regimen_like['atc_substance']: lines.append(_(' ATC (substance): %s') % regimen_like['atc_substance']) if include_loincs and regimen_like['loincs']: lines.append('%s %s' % (' ' * left_margin, _('LOINCs to monitor:'))) lines.extend(['%s%s%s%s' % ( ' ' * (left_margin + 1), l['loinc'], gmTools.coalesce(l['max_age_str'], '', ': ' + _('once within %s')), gmTools.coalesce(l['comment'], '', ' (%s)') ) for l in regimen_like['loincs'] ]) lines.append('') lines.append('') # regimen if regimen_like['planned_duration']: duration = ' %s %s' % (gmTools.u_arrow2right, gmDateTime.format_interval(regimen_like['planned_duration'], gmDateTime.ACC_DAYS)) else: duration = '' lines.append(' ' + _('Started: %s%s') % (regimen_like.medically_formatted_start, duration)) if regimen_like['discontinued']: lines.append(' ' + _('Discontinued %s') % regimen_like['discontinued'].strftime(date_format)) if regimen_like['discontinue_reason']: lines.append(_(' Reason: %s') % regimen_like['discontinue_reason']) lines.append('') # further notes lines.append(_(' Episode: %s')% regimen_like['episode']) if regimen_like['health_issue']: lines.append(_(' Health issue: %s') % regimen_like['health_issue']) if regimen_like['notes4patient']: lines.append(_(' Patient advice: %s') % regimen_like['notes4patient']) if regimen_like['intake_instructions']: lines.append(' ' + _('Intake: %s') % regimen_like['intake_instructions']) if regimen_like['notes4provider']: lines.append(_(' Provider notes: %s') % regimen_like['notes4provider']) if regimen_like['notes4us']: lines.append(_(' Own notes: %s') % regimen_like['notes4us']) if include_metadata: lines.append('') lines.append('') lines.append('Substance: #%s' % regimen_like['pk_substance']) lines.append(_('Intake: #%(pk)s, rev %(row_ver)s, %(mod_when)s by %(mod_by)s.') % { 'pk': regimen_like['pk_intake'], 'row_ver': regimen_like['row_version__intake'], 'mod_when': regimen_like['modified_when__intake'].strftime('%Y %b %d %H:%M.%S'), 'mod_by': regimen_like['modified_by__intake'] }) if regimen_like['pk_intake_regimen']: lines.append(_('Regimen: #%(pk)s, rev %(row_ver)s, %(mod_when)s by %(mod_by)s.') % { 'pk': regimen_like['pk_intake_regimen'], 'row_ver': regimen_like['row_version__regimen'], 'mod_when': regimen_like['modified_when__regimen'].strftime('%Y %b %d %H:%M.%S'), 'mod_by': regimen_like['modified_by__regimen'] }) if not eol: return lines eol += (' ' * left_margin) return (' ' * left_margin) + eol.join(lines)Format the intake regimen into multiple lines.
Args
regimen_like- cIntakeRegimen or cIntakeWithRegimen
left_margin- number of leading spaces added to each line if
is defined
def format_regimen_like_as_multiple_lines_abuse(regimen_like: cIntakeWithRegimen | cIntakeRegimen = None,
left_margin=0,
date_format='%Y %b %d',
include_metadata=False,
eol='\n')-
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def format_regimen_like_as_multiple_lines_abuse(regimen_like:cIntakeRegimen | cIntakeWithRegimen=None, left_margin=0, date_format='%Y %b %d', include_metadata=False, eol='\n'): assert isinstance(regimen_like, (cIntakeRegimen, cIntakeWithRegimen)), '<regimen_like> must be cIntakeRegimen or cIntakeWithRegimen' lines = [] if include_metadata: lines.append(_('Substance abuse entry [#%s]') % regimen_like['pk_intake']) lines.append(' ' + _('Substance: %s [#%s]%s') % ( regimen_like['substance'], regimen_like['pk_substance'], gmTools.coalesce(regimen_like['atc_substance'], '', ' ATC %s') )) lines.append(' ' + _('Use type: %s') % regimen_like.use_type_string) lines.append(' ' + _('Last checked: %s') % regimen_like['last_checked_when'].strftime('%Y %b %d')) if regimen_like['discontinued']: lines.append(_(' Discontinued %s') % regimen_like['discontinued'].strftime(date_format)) if regimen_like['notes4provider']: lines.append(_(' Notes: %s') % regimen_like['notes4provider']) lines.append('') if include_metadata: lines.append(_('Intake revision: #%(row_ver)s, %(mod_when)s by %(mod_by)s.') % { 'row_ver': regimen_like['row_version__intake'], 'mod_when': regimen_like['modified_when__intake'].strftime('%Y %b %d %H:%M.%S'), 'mod_by': regimen_like['modified_by__intake'] }) if regimen_like['row_version__regimen']: lines.append(_('Regimen revision: #%(row_ver)s, %(mod_when)s by %(mod_by)s.') % { 'row_ver': regimen_like['row_version__regimen'], 'mod_when': regimen_like['modified_when__regimen'].strftime('%Y %b %d %H:%M.%S'), 'mod_by': regimen_like['modified_by__regimen'] }) if eol is None: return lines return eol.join(lines) def format_regimen_like_as_single_line(regimen_like: cIntakeWithRegimen | cIntakeRegimen = None,
date_format: str = '%Y %b %d',
terse: bool = True,
include_substance_name: bool = False) ‑> str-
Expand source code
def format_regimen_like_as_single_line(regimen_like:cIntakeRegimen|cIntakeWithRegimen=None, date_format:str='%Y %b %d', terse:bool=True, include_substance_name:bool=False) -> str: """Format intake regimen into a single line. start duration end output x x x "planned 14 days, starting 1.3.2020 (cmt), stopped 16.3.2020 (x ago)" "14d, (~)1.3.2020 -> 16.3.2020 (x ago)" x x - "planned 14 days, starting 1.3.2020 (x ago, cmt)" "14d, (~)1.3.2020 (x ago)" x - x "starting 1.3.2020 (cmt), for 16 days, until 16.3.2020 (x ago)" "(~)1.3.2020 -16d->16.3.2020 (x ago)" - x x "planned 14 days, cmt, until 16.3.2020 (x ago)" "14d, (...)->16.3.2020 (x ago)" x - - "since 1.3.2020 (x ago, cmt)" "(~)1.3.2020... (x ago)" - x - "for 14d, (since: cmt)" "14d (...->)" - - x "(since: cmt), until 16.3.2020 (x ago)" "14d (...)->16.3.2020 (x ago)" - - - "(since: cmt)" "?" or "..." Args: regimen: cIntakeRegimen or cIntakeWithRegimen """ assert isinstance(regimen_like, (cIntakeRegimen, cIntakeWithRegimen)), '<regimen> must be cIntakeRegimen or cIntakeWithRegimen' comment_mark = '¹' if regimen_like['comment_on_start'] else '' started = None if regimen_like['start_is_unknown'] else regimen_like['started'] parts_terse = [] parts_verbose = [] if started: if gmDateTime.pydt_is_today(started): parts_terse.append('[%s%s]' % (_('today'), comment_mark)) parts_verbose.append(_('started today')) elif gmDateTime.pydt_is_yesterday(started): parts_terse.append('[%s%s]' % (_('yesterday'), comment_mark)) parts_verbose.append(_('started yesterday')) else: parts_terse.append('[%s%s]' % (started.strftime(date_format), comment_mark)) parts_verbose.append(_('started %s') % started.strftime(date_format)) if regimen_like['comment_on_start']: parts_verbose.append('(%s)' % regimen_like['comment_on_start']) else: parts_terse.append('?%s' % comment_mark) if regimen_like['comment_on_start']: parts_verbose.append(_('started "%s"') % regimen_like['comment_on_start']) if regimen_like['planned_duration']: parts_terse.append('-%s-' % (gmDateTime.format_interval_medically(regimen_like['planned_duration']))) parts_verbose.append(_('planned for %s') % gmDateTime.format_interval_medically(regimen_like['planned_duration'])) if regimen_like['discontinued']: if gmDateTime.pydt_is_today(regimen_like['discontinued']): parts_terse.append('[%s]' % _('today')) parts_verbose.append(_('discontinued today')) elif gmDateTime.pydt_is_yesterday(regimen_like['discontinued']): parts_terse.append('[%s]' % _('yesterday')) parts_verbose.append(_('discontinued yesterday')) else: now = gmDateTime.pydt_now_here() if regimen_like['discontinued'] < now: terse_prefix = '-' verbose_template = '(%s ago)' else: terse_prefix = '+' verbose_template = '(in %s)' parts_terse.append('[%s] (%s%s)' % ( regimen_like['discontinued'].strftime(date_format), terse_prefix, gmDateTime.format_apparent_age_medically(gmDateTime.calculate_apparent_age(start = regimen_like['discontinued'])) )) parts_verbose.append(_('discontinued %s %s') % ( regimen_like['discontinued'].strftime(date_format), verbose_template % gmDateTime.format_apparent_age_medically(gmDateTime.calculate_apparent_age(start = regimen_like['discontinued'])) )) if started: parts_verbose.append(_('after %s') % gmDateTime.format_apparent_age_medically(gmDateTime.calculate_apparent_age ( start = started, end = regimen_like['discontinued'] ))) if regimen_like['discontinue_reason']: parts_verbose.append('"%s"' % regimen_like['discontinue_reason']) else: parts_terse.append('?') if terse: return gmTools.u_arrow2right.join(parts_terse) subst_prefix = '%s%s%s: ' % ( regimen_like['substance'], gmTools.coalesce(regimen_like['amount'], '', ' %s'), format_units(unit = regimen_like['unit'], short = True, none_str = '') ) return subst_prefix + ', '.join(parts_verbose)Format intake regimen into a single line.
start duration end output x x x "planned 14 days, starting 1.3.2020 (cmt), stopped 16.3.2020 (x ago)" "14d, (~)1.3.2020 -> 16.3.2020 (x ago)" x x - "planned 14 days, starting 1.3.2020 (x ago, cmt)" "14d, (~)1.3.2020 (x ago)" x - x "starting 1.3.2020 (cmt), for 16 days, until 16.3.2020 (x ago)" "(~)1.3.2020 -16d->16.3.2020 (x ago)" - x x "planned 14 days, cmt, until 16.3.2020 (x ago)" "14d, (…)->16.3.2020 (x ago)" x - - "since 1.3.2020 (x ago, cmt)" "(~)1.3.2020… (x ago)" - x - "for 14d, (since: cmt)" "14d (…->)" - - x "(since: cmt), until 16.3.2020 (x ago)" "14d (…)->16.3.2020 (x ago)" - - - "(since: cmt)" "?" or "…"
Args
regimen- cIntakeRegimen or cIntakeWithRegimen
def format_regimen_start_medically(regimen_like: cIntakeWithRegimen | cIntakeRegimen,
terse: bool = False) ‑> str-
Expand source code
def format_regimen_start_medically(regimen_like:cIntakeWithRegimen|cIntakeRegimen, terse:bool=False) -> str: """Format start of intake regimen suitable for display. Args: regimen_like: cIntakeWithRegimen or cIntakeRegimen """ assert regimen_like, '<regimen_like> must be given' if regimen_like['start_is_unknown'] or not regimen_like['started']: if not regimen_like['comment_on_start']: return '?' if terse: return '?¹' return regimen_like['comment_on_start'] comment_mark = '¹' if regimen_like['comment_on_start'] else '' # starts today if gmDateTime.pydt_is_today(regimen_like['started']): if terse: return _('today') + comment_mark return _('today%s (%s)') % ( comment_mark, regimen_like['started'].strftime('%Y %b %d') ) start_prefix = gmTools.u_almost_equal_to if regimen_like['comment_on_start'] else '' now = gmDateTime.pydt_now_here() # start in the future if regimen_like['started'] > now: starts_in = regimen_like['started'] - now if terse: return '%s%s (%s+%s)' % ( regimen_like['started'].strftime('%Y %b %d'), comment_mark, gmTools.u_almost_equal_to, gmDateTime.format_interval_medically(starts_in, terse = terse) ) return _('%s%s%s (in %s%s)') % ( start_prefix, regimen_like['started'].strftime('%Y %b %d'), gmTools.coalesce(regimen_like['comment_on_start'], '', ' [%s]'), gmTools.u_almost_equal_to, gmDateTime.format_interval_medically(starts_in, terse = terse) ) # started in the past started_ago = now - regimen_like['started'] three_months = pydt.timedelta(weeks = 13, days = 3) if started_ago < three_months: if terse: return '%s%s (%s-%s,%s)' % ( regimen_like['started'].strftime('%b %d'), comment_mark, gmTools.u_almost_equal_to, gmDateTime.format_interval_medically(started_ago, terse = terse), regimen_like['started'].strftime('%Y') ) return _('%s%s%s (%s%s ago, in %s)') % ( start_prefix, regimen_like['started'].strftime('%b %d'), gmTools.coalesce(regimen_like['comment_on_start'], '', ' [%s]'), gmTools.u_almost_equal_to, gmDateTime.format_interval_medically(started_ago, terse = terse), regimen_like['started'].strftime('%Y') ) five_years = pydt.timedelta(weeks = 265) if started_ago < five_years: if terse: return '%s%s (%s-%s,%s)' % ( regimen_like['started'].strftime('%Y %b'), comment_mark, gmTools.u_almost_equal_to, gmDateTime.format_interval_medically(started_ago, terse = terse), regimen_like['started'].strftime('%b %d') ) return _('%s%s%s (%s%s ago: %s)') % ( start_prefix, regimen_like['started'].strftime('%Y %b'), gmTools.coalesce(regimen_like['comment_on_start'], '', ' [%s]'), gmTools.u_almost_equal_to, gmDateTime.format_interval_medically(started_ago, terse = terse), regimen_like['started'].strftime('%b %d') ) if terse: return '%s%s (%s-%s,%s)' % ( regimen_like['started'].strftime('%Y'), comment_mark, gmTools.u_almost_equal_to, gmDateTime.format_interval_medically(started_ago, terse = terse), regimen_like['started'].strftime('%b %d') ) return _('%s%s%s (%s%s ago: %s)') % ( start_prefix, regimen_like['started'].strftime('%Y'), gmTools.coalesce(regimen_like['comment_on_start'], '', ' [%s]'), gmTools.u_almost_equal_to, gmDateTime.format_interval_medically(started_ago, terse = terse), regimen_like['started'].strftime('%b %d') )Format start of intake regimen suitable for display.
Args
regimen_like- cIntakeWithRegimen or cIntakeRegimen
def format_regimen_timerange_medically(regimen_like: cIntakeWithRegimen | cIntakeRegimen,
terse: bool = False) ‑> str-
Expand source code
def format_regimen_timerange_medically(regimen_like:cIntakeWithRegimen|cIntakeRegimen, terse:bool=False) -> str: """Format start/end of intake regimen suitable for display. Args: regimen_like: cIntakeWithRegimen or cIntakeRegimen """ now = gmDateTime.pydt_now_here() # medications stopped today or before today if regimen_like['discontinued']: if (regimen_like['discontinued'] < now) or (gmDateTime.pydt_is_today(regimen_like['discontinued'])): return format_regimen_timerange_of_stopped_medically(regimen_like, terse = terse) arrow_parts = [] # format start arrow_parts.append(format_regimen_start_medically(regimen_like, terse = terse)) # format durations durations = [] if regimen_like['discontinued']: if regimen_like['started']: duration_documented = regimen_like['discontinued'] - regimen_like['started'] durations.append(_('%s (documented)') % gmDateTime.format_interval(duration_documented, gmDateTime.ACC_DAYS)) if regimen_like['planned_duration'] is not None: durations.append(_('%s (plan)') % gmDateTime.format_interval(regimen_like['planned_duration'], gmDateTime.ACC_DAYS)) spacer = '' if terse else ' ' if len(durations) == 0: duration_str = '' if terse else '?' else: duration_str = (',%s' % spacer).join(durations) arrow_parts.append(duration_str) # format end arrow_parts.append(format_regimen_end_medically(regimen_like, terse = terse)) # assemble return ('%s%s%s' % (spacer, gmTools.u_arrow2right_thick, spacer)).join(arrow_parts)Format start/end of intake regimen suitable for display.
Args
regimen_like- cIntakeWithRegimen or cIntakeRegimen
def format_regimen_timerange_of_stopped_medically(regimen_like: cIntakeWithRegimen | cIntakeRegimen,
terse: bool = False) ‑> str-
Expand source code
def format_regimen_timerange_of_stopped_medically(regimen_like:cIntakeWithRegimen|cIntakeRegimen, terse:bool=False) -> str: """Format start/end of discontinued regiment suitable for display. Args: regimen_like: cIntakeWithRegimen or cIntakeRegimen """ assert regimen_like['discontinued'], '<regimen_like> does not contain discontinued regimen' now = gmDateTime.pydt_now_here() # format intro if gmDateTime.pydt_is_today(regimen_like['discontinued']): intro = _('until today') else: ended_ago = now - regimen_like['discontinued'] intro = _('until %s%s ago') % ( gmTools.u_almost_equal_to, gmDateTime.format_interval_medically(ended_ago, terse = terse) ) # format start if regimen_like['started']: comment = '¹' if terse else gmTools.coalesce(regimen_like['comment_on_start'], '', ' [%s]') start = '%s%s%s' % ( gmTools.bool2subst((regimen_like['comment_on_start'] is None), '', gmTools.u_almost_equal_to), regimen_like['started'].strftime('%Y %b %d'), comment ) else: start = gmTools.coalesce(regimen_like['comment_on_start'], '?') # format duration taken if regimen_like['started']: duration_taken = regimen_like['discontinued'] - regimen_like['started'] + pydt.timedelta(days = 1) duration_taken_str = gmDateTime.format_interval(duration_taken, gmDateTime.ACC_DAYS) else: duration_taken_str = '?' # format duration planned if regimen_like['planned_duration']: duration_planned_str = _(' [planned: %s]') % gmDateTime.format_interval(regimen_like['planned_duration'], gmDateTime.ACC_DAYS) else: duration_planned_str = '' # format end end = regimen_like['discontinued'].strftime('%Y %b %d') # assemble return '%s: %s %s %s%s %s %s' % ( intro, start, gmTools.u_arrow2right_thick, duration_taken_str, duration_planned_str, gmTools.u_arrow2right_thick, end )Format start/end of discontinued regiment suitable for display.
Args
regimen_like- cIntakeWithRegimen or cIntakeRegimen
def format_substance_intake(emr=None, output_format='latex', table_type='by-product')-
Expand source code
def format_substance_intake(emr=None, output_format='latex', table_type='by-product'): # FIXME: add intake_instructions tex = '%s {\\tiny (%s)}\n' % ( gmTools.tex_escape_string(_('Medication list')), gmTools.tex_escape_string(_('ordered by brand')) ) tex += '%% requires "\\usepackage{longtable}"\n' tex += '%% requires "\\usepackage{tabu}"\n' tex += u'\\begin{longtabu} to \\textwidth {|X[-1,L]|X[2.5,L]|}\n' tex += u'\\hline\n' tex += u'%s & %s\\\\\n' % ( gmTools.tex_escape_string(_('Drug')), gmTools.tex_escape_string(_('Regimen / Advice')) ) tex += '\\hline\n' tex += '%s\n' tex += '\\end{longtabu}\n' # aggregate medication data current_meds = emr.get_current_medications ( include_inactive = False, include_unapproved = False, order_by = 'product, substance' ) line_data = {} for med in current_meds: identifier = med['drug_product'] try: line_data[identifier] except KeyError: line_data[identifier] = {'drug_product': '', 'l10n_preparation': '', 'schedule': '', 'notes': [], 'strengths': []} line_data[identifier]['drug_product'] = identifier line_data[identifier]['strengths'].append('%s %s%s' % (med['substance'][:20], med['amount'], med.formatted_units)) if med['l10n_preparation'] not in identifier: line_data[identifier]['l10n_preparation'] = med['l10n_preparation'] sched_parts = [] if med['planned_duration'] is not None: sched_parts.append(gmDateTime.format_interval(med['planned_duration'], gmDateTime.ACC_DAYS, verbose = True)) if med['schedule'] is not None: sched_parts.append(med['schedule']) line_data[identifier]['schedule'] = ': '.join(sched_parts) if med['notes'] is not None: if med['notes'] not in line_data[identifier]['notes']: line_data[identifier]['notes'].append(med['notes']) # format aggregated data already_seen = [] lines = [] #line1_template = u'\\rule{0pt}{3ex}{\\Large %s} %s & %s \\\\' line1_template = u'{\\Large %s} %s & %s\\\\' line2_template = u'{\\tiny %s} & {\\scriptsize %s}\\\\' line3_template = u' & {\\scriptsize %s}\\\\' for med in current_meds: identifier = med['drug_product'] if identifier in already_seen: continue already_seen.append(identifier) lines.append (line1_template % ( gmTools.tex_escape_string(line_data[identifier]['drug_product']), gmTools.tex_escape_string(line_data[identifier]['l10n_preparation']), gmTools.tex_escape_string(line_data[identifier]['schedule']) )) strengths = gmTools.tex_escape_string(' / '.join(line_data[identifier]['strengths'])) if len(line_data[identifier]['notes']) == 0: first_note = '' else: first_note = gmTools.tex_escape_string(line_data[identifier]['notes'][0]) lines.append(line2_template % (strengths, first_note)) if len(line_data[identifier]['notes']) > 1: for note in line_data[identifier]['notes'][1:]: lines.append(line3_template % gmTools.tex_escape_string(note)) lines.append('\\hline') return tex % '\n'.join(lines) def format_substance_intake_as_amts_data(intake=None, strict=True)-
Expand source code
def format_substance_intake_as_amts_data(intake=None, strict=True): """ <M a="Handelsname" fd="freie Formangabe" t="freies Dosierschema" dud="freie Dosiereinheit (Stück Tab)" r="reason" i="info"> <W w="Metformin" s="500 mg"/> <W ...> </M> """ if not strict: pass # relax length checks M_fields = [] #M_fields.append('a="%s"' % intake['drug_product']) M_fields.append('a="%s"' % intake['substance']) #M_fields.append('fd="%s"' % intake['l10n_preparation']) M_fields.append('fd="EINHEIT"') if intake['schedule'] is not None: M_fields.append('t="%s"' % intake['schedule']) #M_fields.append(u'dud="%s"' % intake['dose unit, like Stück']) if intake['aim'] is None: M_fields.append('r="%s"' % intake['episode']) else: M_fields.append('r="%s"' % intake['aim']) if intake['notes'] is not None: M_fields.append('i="%s"' % intake['notes']) M_line = '<M %s>' % ' '.join(M_fields) W_lines = [] for comp in intake.containing_drug['components']: W_lines.append('<W w="%s" s="%s %s"/>' % ( comp['substance'], comp['amount'], format_units(comp['unit'], comp['dose_unit'], short = True) )) return M_line + ''.join(W_lines) + '</M>' def format_substance_intake_as_amts_data_v2_0(intake=None, strict=True)-
Expand source code
def format_substance_intake_as_amts_data_v2_0(intake=None, strict=True): if not strict: pass # relax length checks fields = [] # components components = [ c.split('::') for c in intake.containing_drug['components'] ] if len(components) > 3: fields.append('WS-Kombi.') elif len(components) == 1: c = components[0] fields.append(c[0][:80]) else: fields.append('~'.join([c[0][:80] for c in components])) # product fields.append(intake['drug_product'][:50]) # Wirkstärken if len(components) > 3: fields.append('') elif len(components) == 1: c = components[0] fields.append(('%s%s' % (c[1], c[2]))[:11]) else: fields.append('~'.join([('%s%s' % (c[1], c[2]))[:11] for c in components])) # preparation fields.append(intake['l10n_preparation'][:7]) # schedule - for now be simple - maybe later parse 1-1-1-1 etc fields.append(gmTools.coalesce(intake['schedule'], '')[:20]) # Einheit to take fields.append('')#[:20] # notes fields.append(gmTools.coalesce(intake['notes'], '')[:80]) # aim fields.append(gmTools.coalesce(intake['aim'], '')[:50]) return '|'.join(fields) def format_substance_intake_as_amts_latex(intake=None, strict=True)-
Expand source code
def format_substance_intake_as_amts_latex(intake=None, strict=True): _esc = gmTools.tex_escape_string # %(contains)s & %(product)s & %(amount)s%(unit)s & %(preparation)s & \multicolumn{4}{l|}{%(schedule)s} & Einheit & %(notes)s & %(aim)s \tabularnewline{}\hline cells = [] # components components = intake.containing_drug['components'] if len(components) > 3: cells.append(_esc('WS-Kombi.')) elif len(components) == 1: c = components[0] if strict: cells.append('\\mbox{%s}' % _esc(c['substance'][:80])) else: cells.append('\\mbox{%s}' % _esc(c['substance'])) else: if strict: cells.append('\\fontsize{10pt}{12pt}\selectfont %s ' % '\\newline '.join(['\\mbox{%s}' % _esc(c['substance'][:80]) for c in components])) else: cells.append('\\fontsize{10pt}{12pt}\selectfont %s ' % '\\newline '.join(['\\mbox{%s}' % _esc(c['substance']) for c in components])) # product if strict: cells.append(_esc(intake['drug_product'][:50])) else: cells.append(_esc(intake['drug_product'])) # Wirkstärken if len(components) > 3: cells.append('') elif len(components) == 1: c = components[0] dose = ('%s%s' % (c['amount'], format_units(c['unit'], c['dose_unit'], short = True))).replace('.', ',') if strict: dose = dose[:11] cells.append(_esc(dose)) else: # 2 if strict: doses = '\\fontsize{10pt}{12pt}\selectfont %s ' % '\\newline\\ '.join ([ _esc(('%s%s' % ( ('%s' % c['amount']).replace('.', ','), format_units(c['unit'], c['dose_unit'], short = True) ))[:11]) for c in components ]) else: doses = '\\fontsize{10pt}{12pt}\selectfont %s ' % '\\newline\\ '.join ([ _esc('%s%s' % ( ('%s' % c['amount']).replace('.', ','), format_units(c['unit'], c['dose_unit'], short = True) )) for c in components ]) cells.append(doses) # preparation if strict: cells.append(_esc(intake['l10n_preparation'][:7])) else: cells.append(_esc(intake['l10n_preparation'])) # schedule - for now be simple - maybe later parse 1-1-1-1 etc if intake['schedule'] is None: cells.append('\\multicolumn{4}{p{3.2cm}|}{\\ }') else: # spec says [:20] but implementation guide says: never trim if len(intake['schedule']) > 20: cells.append('\\multicolumn{4}{>{\\RaggedRight}p{3.2cm}|}{\\fontsize{10pt}{12pt}\selectfont %s}' % _esc(intake['schedule'])) else: cells.append('\\multicolumn{4}{>{\\RaggedRight}p{3.2cm}|}{%s}' % _esc(intake['schedule'])) # Einheit to take cells.append('')#[:20] # notes if intake['notes'] is None: cells.append(' ') else: if strict: cells.append(_esc(intake['notes'][:80])) else: cells.append('\\fontsize{10pt}{12pt}\selectfont %s ' % _esc(intake['notes'])) # aim if intake['aim'] is None: #cells.append(' ') cells.append(_esc(intake['episode'][:50])) else: if strict: cells.append(_esc(intake['aim'][:50])) else: cells.append('\\fontsize{10pt}{12pt}\selectfont %s ' % _esc(intake['aim'])) table_row = ' & '.join(cells) table_row += '\\tabularnewline{}\n\\hline' return table_row def format_substance_intake_notes(emr=None, output_format='latex', table_type='by-product')-
Expand source code
def format_substance_intake_notes(emr=None, output_format='latex', table_type=u'by-product'): tex = '%s\n' % _('Additional notes for healthcare professionals') tex += '%%%% requires "\\usepackage{longtable}"\n' tex += '%%%% requires "\\usepackage{tabu}"\n' tex += '\\begin{longtabu} to \\textwidth {|X[,L]|r|X[,L]|}\n' tex += '\\hline\n' tex += '%s {\\scriptsize (%s)} & %s & %s\\\\\n' % (_('Substance'), _('Drug Product'), _('Strength'), _('Aim')) tex += '\\hline\n' tex += '%s\n' # this is where the lines end up tex += '\\end{longtabu}\n' current_meds = emr.get_current_medications ( include_inactive = False, include_unapproved = False, order_by = 'product, substance' ) # create lines lines = [] for med in current_meds: if med['aim'] is None: aim = '' else: aim = '{\\scriptsize %s}' % gmTools.tex_escape_string(med['aim']) lines.append('%s {\\small (%s: {\\tiny %s})} & %s%s & %s\\\\' % ( gmTools.tex_escape_string(med['substance']), gmTools.tex_escape_string(med['l10n_preparation']), gmTools.tex_escape_string(med['drug_product']), med['amount'], gmTools.tex_escape_string(med.formatted_units), aim )) lines.append(u'\\hline') return tex % '\n'.join(lines) def format_units(unit: str = None,
dose_unit: str = None,
preparation: str = None,
short: bool = True,
none_str: str = None) ‑> str-
Expand source code
def format_units(unit:str=None, dose_unit:str=None, preparation:str=None, short:bool=True, none_str:str=None) -> str: """Format units for display. Args: unit: the actual unit, say, "mg" (milligrams) dose_unit: the "delivery unit", say, "ml" (milliliter) preparation: the form factor, say "tablet" none_str: what to return if the unit is None Returns: Formatted unit or None. """ if unit is None: return none_str unit = unit.strip() dose_unit = dose_unit.strip() if dose_unit else None preparation = preparation.strip() if preparation else None if short: if dose_unit: d_u = '/' + dose_unit else: if preparation: d_u = '/' + preparation else: d_u = '' return '%s%s' % (unit, d_u) return '%s / %s' % ( unit, gmTools.coalesce ( dose_unit, _('delivery unit%s') % gmTools.coalesce(preparation, '', ' (%s)'), '%s' ) )Format units for display.
Args
unit- the actual unit, say, "mg" (milligrams)
dose_unit- the "delivery unit", say, "ml" (milliliter)
preparation- the form factor, say "tablet"
none_str- what to return if the unit is None
Returns
Formatted unit or None.
def generate_amts_data_template_definition_file(work_dir=None, strict=True)-
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def generate_amts_data_template_definition_file(work_dir=None, strict=True): _log.debug('generating AMTS data template definition file(workdir=%s, strict=%s)', work_dir, strict) if not strict: return __generate_enhanced_amts_data_template_definition_file(work_dir = work_dir) amts_lines = [ l for l in ('<MP v="023" U="%s"' % uuid.uuid4().hex + """ l="de-DE"$<<if_not_empty::$<amts_page_idx::::1>$// a="%s"//::>>$$<<if_not_empty::$<amts_page_idx::::>$// z="$<amts_total_pages::::1>$"//::>>$> <P g="$<name::%(firstnames)s::45>$" f="$<name::%(lastnames)s::45>$" b="$<date_of_birth::%Y%m%d::8>$"/> <A n="$<<range_of::$<praxis::%(praxis)s,%(branch)s::>$,$<current_provider::::>$::30>>$" $<praxis_address:: s="%(street)s"::>$ $<praxis_address:: z="%(postcode)s"::>$ $<praxis_address:: c="%(urb)s"::>$ $<praxis_comm::workphone// p="%(url)s"::20>$ $<praxis_comm::email// e="%(url)s"::80>$ t="$<today::%Y%m%d::8>$" /> <O ai="s.S.$<amts_total_pages::::1>$ unten"/> $<amts_intakes_as_data::::9999999>$ </MP>""").split('\n') ] #$<<if_not_empty::$<allergy_list::%(descriptor)s//,::>$//<O ai="%s"/>::>>$ amts_fname = gmTools.get_unique_filename ( prefix = 'gm2amts_data-', suffix = '.txt', tmp_dir = work_dir ) amts_template = open(amts_fname, mode = 'wt', encoding = 'utf8') amts_template.write('[form]\n') amts_template.write('template = $template$\n') amts_template.write(''.join(amts_lines)) amts_template.write('\n') amts_template.write('$template$\n') amts_template.close() return amts_fname def generate_amts_data_template_definition_file_v2_0(work_dir=None, strict=True)-
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def generate_amts_data_template_definition_file_v2_0(work_dir=None, strict=True): if not strict: return __generate_enhanced_amts_data_template_definition_file(work_dir = work_dir) amts_fields = [ 'MP', '020', # Version 'DE', # Land 'DE', # Sprache '1', # Zeichensatz 1 = Ext ASCII (fest) = ISO8859-1 = Latin1 '$<today::%Y%m%d::8>$', '$<amts_page_idx::::1>$', # to be set by code using the template '$<amts_total_pages::::1>$', # to be set by code using the template '0', # Zertifizierungsstatus '$<name::%(firstnames)s::45>$', '$<name::%(lastnames)s::45>$', '', # Patienten-ID '$<date_of_birth::%Y%m%d::8>$', '$<<range_of::$<praxis::%(praxis)s,%(branch)s::>$,$<current_provider::::>$::30>>$', '$<praxis_address::%(street)s %(number)s %(subunit)s|%(postcode)s|%(urb)s::57>$', # 55+2 because of 2 embedded "|"s '$<praxis_comm::workphone::20>$', '$<praxis_comm::email::80>$', #u'264 $<allergy_state::::21>$', # param 1, Allergien 25-4 (4 for "264 ", spec says max of 25) '264 Seite $<amts_total_pages::::1>$ unten', # param 1, Allergien 25-4 (4 for "264 ", spec says max of 25) '', # param 2, not used currently '', # param 3, not used currently # Medikationseinträge '$<amts_intakes_as_data::::9999999>$', '$<amts_check_symbol::::1>$', # Prüfzeichen, value to be set by code using the template, *per page* ! '#@', # Endesymbol ] amts_fname = gmTools.get_unique_filename ( prefix = 'gm2amts_data-', suffix = '.txt', tmp_dir = work_dir ) amts_template = open(amts_fname, mode = 'wt', encoding = 'utf8') amts_template.write('[form]\n') amts_template.write('template = $template$\n') amts_template.write('|'.join(amts_fields)) amts_template.write('\n') amts_template.write('$template$\n') amts_template.close() return amts_fname def generate_failsafe_medication_list_entries(pk_patient: int = None, max_width: int = 80, eol: str = None) ‑> str | list-
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def generate_failsafe_medication_list_entries(pk_patient:int=None, max_width:int=80, eol:str=None) -> str|list: lines = [] iwrs = get_intakes_with_regimens ( pk_patient = pk_patient, include_inactive = False, order_by = 'discontinued NULLS FIRST, substance', exclude_potential_abuses = True, exclude_medications = False ) delim = '#' + '-' * (max_width - 1) for i in iwrs: lines.append(delim) lines.extend(i.format_for_failsafe_output(max_width = max_width)) lines.append(delim) if not eol: return lines return eol.join(lines) def generate_liver_information_urls(search_term: str = None) ‑> list[str]-
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def generate_liver_information_urls(search_term:str=None) -> list[str]: if search_term is None: return [URL_liver] if isinstance(search_term, str): if search_term.strip() == '': return [URL_liver] names = [] if isinstance(search_term, cSubstance): names.append(search_term['substance']) elif isinstance(search_term, cSubstanceDose): names.append(search_term['substance']) elif isinstance(search_term, cSubstanceIntakeEntry): names.append(search_term['substance']) elif isinstance(search_term, cIntakeWithRegimen): names.append(search_term['substance']) elif isinstance(search_term, cIntakeRegimen): names.append(search_term['substance']) else: names.append('%s' % search_term) terms = [] for name in names: terms.append(name) if name.endswith('e'): terms.append(name[:-1]) urls = [ URL_liver__search_template % t for t in terms ] _log.debug('liver information URLs: %s', urls) return urls def generate_pregnancy_information_urls(search_term: str = None) ‑> list-
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def generate_pregnancy_information_urls(search_term:str=None) -> list: if search_term is None: return [URL_pregnancy] if isinstance(search_term, str): if search_term.strip() == '': return [URL_pregnancy] atcs = [] names = [] if isinstance(search_term, cSubstance): names.append(search_term['substance']) if search_term['atc']: atcs.append(search_term['atc']) elif isinstance(search_term, cSubstanceDose): names.append(search_term['substance']) if search_term['atc_substance']: atcs.append(search_term['atc_substance']) elif isinstance(search_term, cSubstanceIntakeEntry): names.append(search_term['substance']) if search_term['atc_substance']: atcs.append(search_term['atc_substance']) elif isinstance(search_term, cIntakeWithRegimen): names.append(search_term['substance']) if search_term['atc_substance']: atcs.append(search_term['atc_substance']) elif isinstance(search_term, cIntakeRegimen): names.append(search_term['substance']) if search_term['atc_substance']: atcs.append(search_term['atc_substance']) else: names.append('%s' % search_term) atcs.extend(gmATC.text2atc(text = '%s' % search_term, fuzzy = True)) terms = [] for name in names: terms.append(name) if name.endswith('e'): terms.append(name[:-1]) terms.extend(atcs) urls = [ URL_pregnancy__search_template % t for t in terms ] _log.debug('pregnancy information URLs: %s', urls) return urls def generate_pulmonary_information_urls(search_term: str = None) ‑> list-
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def generate_pulmonary_information_urls(search_term:str=None) -> list: if search_term is None: return [URL_lungs] if isinstance(search_term, str): if search_term.strip() == '': return [URL_lungs] atcs = [] names = [] if isinstance(search_term, cSubstance): names.append(search_term['substance']) if search_term['atc']: atcs.append(search_term['atc']) elif isinstance(search_term, cSubstanceDose): names.append(search_term['substance']) if search_term['atc_substance']: atcs.append(search_term['atc_substance']) elif isinstance(search_term, cSubstanceIntakeEntry): names.append(search_term['substance']) if search_term['atc_substance']: atcs.append(search_term['atc_substance']) elif isinstance(search_term, cIntakeWithRegimen): names.append(search_term['substance']) if search_term['atc_substance']: atcs.append(search_term['atc_substance']) elif isinstance(search_term, cIntakeRegimen): names.append(search_term['substance']) if search_term['atc_substance']: atcs.append(search_term['atc_substance']) else: names.append('%s' % search_term) atcs.extend(gmATC.text2atc(text = '%s' % search_term, fuzzy = True)) terms = [] for name in names: terms.append(name) if name.endswith('e'): terms.append(name[:-1]) terms.extend(atcs) urls = [ URL_lungs__search_template % t for t in terms ] _log.debug('pulmonary information URLs: %s', urls) return urls def generate_renal_insufficiency_urls(search_term: str = None) ‑> list-
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def generate_renal_insufficiency_urls(search_term:str=None) -> list: if search_term is None: return [URL_renal_insufficiency] if isinstance(search_term, str): if search_term.strip() == '': return [URL_renal_insufficiency] atcs = [] names = [] if isinstance(search_term, cSubstance): names.append(search_term['substance']) if search_term['atc']: atcs.append(search_term['atc']) elif isinstance(search_term, cSubstanceDose): names.append(search_term['substance']) if search_term['atc_substance']: atcs.append(search_term['atc_substance']) elif isinstance(search_term, cSubstanceIntakeEntry): names.append(search_term['substance']) if search_term['atc_substance']: atcs.append(search_term['atc_substance']) elif isinstance(search_term, cIntakeWithRegimen): names.append(search_term['substance']) if search_term['atc_substance']: atcs.append(search_term['atc_substance']) elif isinstance(search_term, cIntakeRegimen): names.append(search_term['substance']) if search_term['atc_substance']: atcs.append(search_term['atc_substance']) else: names.append('%s' % search_term) atcs.extend(gmATC.text2atc(text = '%s' % search_term, fuzzy = True)) terms = [] for name in names: terms.append(name) if name.endswith('e'): terms.append(name[:-1]) terms.extend(atcs) urls = [ URL_renal_insufficiency__search_template % t for t in terms ] _log.debug('renal insufficiency URLs: %s', urls) return urls def get_alcohol()-
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def get_alcohol(): ethanol = create_substance_dose_by_atc ( substance = _('ethanol'), atc = gmATC.ATC_ETHANOL, amount = 1, unit = 'g', dose_unit = 'ml' ) drink = create_drug_product ( product_name = _('alcohol'), preparation = _('liquid'), doses = [ethanol], return_existing = True ) drink['is_fake_product'] = True drink.save() return drink def get_drug_by_atc(atc=None, preparation=None, link_obj=None)-
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def get_drug_by_atc(atc=None, preparation=None, link_obj=None): args = {'atc': atc, 'prep': preparation} cmd = 'SELECT * FROM ref.v_drug_products WHERE lower(atc) = lower(%(atc)s) AND lower(preparation) = lower(%(prep)s)' rows = gmPG2.run_ro_queries(link_obj = link_obj, queries = [{'sql': cmd, 'args': args}]) if len(rows) == 0: return None return cDrugProduct(row = {'data': rows[0], 'pk_field': 'pk_drug_product'}, link_obj = link_obj) def get_drug_by_name(product_name=None, preparation=None, link_obj=None)-
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def get_drug_by_name(product_name=None, preparation=None, link_obj=None): args = {'prod_name': product_name, 'prep': preparation} cmd = 'SELECT * FROM ref.v_drug_products WHERE lower(product) = lower(%(prod_name)s) AND lower(preparation) = lower(%(prep)s)' rows = gmPG2.run_ro_queries(link_obj = link_obj, queries = [{'sql': cmd, 'args': args}]) if len(rows) == 0: return None return cDrugProduct(row = {'data': rows[0], 'pk_field': 'pk_drug_product'}) def get_drug_components(return_pks=False)-
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def get_drug_components(return_pks=False): cmd = _SQL_get_drug_components % 'true ORDER BY product, substance' rows = gmPG2.run_ro_queries(queries = [{'sql': cmd}]) if return_pks: return [ r['pk_component'] for r in rows ] return [ cDrugComponent(row = {'data': r, 'pk_field': 'pk_component'}) for r in rows ] def get_drug_products(return_pks=False)-
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def get_drug_products(return_pks=False): cmd = _SQL_get_drug_product % 'TRUE ORDER BY product' rows = gmPG2.run_ro_queries(queries = [{'sql': cmd}]) if return_pks: return [ r['pk_drug_product'] for r in rows ] return [ cDrugProduct(row = {'data': r, 'pk_field': 'pk_drug_product'}) for r in rows ] def get_intake_regimens(order_by: str = None,
pk_intake: int = None,
ongoing_only: bool = False,
pk_patient: int = None,
pk_substance: int = None,
as_instance: bool = True,
link_obj=None) ‑> list-
Expand source code
def get_intake_regimens(order_by:str=None, pk_intake:int=None, ongoing_only:bool=False, pk_patient:int=None, pk_substance:int=None, as_instance:bool=True, link_obj=None) -> list: """Get intake regimens. Args: order_by: SQL sort criteria pk_intake: constrain by clin.intake PK ongoing_only: True -> only return those which are not discontinued pk_patient: constrain to this patient pk_substance: constrain to this substance """ assert not(pk_intake and pk_patient), 'must not pass <pk_intake> AND <pk_patient>' assert not(pk_intake and pk_substance), 'must not pass <pk_intake> AND <pk_substance>' # FIXME: support most_recent where_parts = ['true'] args = {} if pk_intake: where_parts.append('pk_intake = %(pk_intake)s') args['pk_intake'] = pk_intake if pk_patient: where_parts.append('pk_patient = %(pk_patient)s') args['pk_patient'] = pk_patient if pk_substance: where_parts.append('pk_substance = %(pk_substance)s') args['pk_substance'] = pk_substance if ongoing_only: where_parts.append('discontinued IS NULL') SQL = _SQL_get_intake_regimens % '\nAND '.join(where_parts) if order_by: SQL += ' ORDER BY %s' % order_by rows = gmPG2.run_ro_query(sql = SQL, args = args, link_obj = link_obj) if as_instance: return [ cIntakeRegimen(row = {'data': r, 'pk_field': 'pk_intake_regimen'}, link_obj = link_obj) for r in rows ] return [ r['pk_intake_regimen'] for r in rows ]Get intake regimens.
Args
order_by- SQL sort criteria
pk_intake- constrain by clin.intake PK
ongoing_only- True -> only return those which are not discontinued
pk_patient- constrain to this patient
pk_substance- constrain to this substance
def get_intakes_with_regimens(pk_patient: int = None,
include_inactive: bool = False,
order_by: str = None,
episodes: list[int] = None,
issues: list[int] = None,
exclude_potential_abuses: bool = False,
exclude_medications: bool = False,
pk_substance: int = None) ‑> list[cIntakeWithRegimen]-
Expand source code
def get_intakes_with_regimens ( pk_patient:int=None, include_inactive:bool=False, order_by:str=None, episodes:list[int]=None, issues:list[int]=None, exclude_potential_abuses:bool=False, exclude_medications:bool=False, pk_substance:int=None ) -> list[cIntakeWithRegimen]: """Retrieve intake entries for each regimen.""" where_parts = ['TRUE'] args:dict[str,int|list[int]] = {} if pk_patient: where_parts.append('pk_patient = %(pat)s') args['pat'] = pk_patient if not include_inactive: where_parts.append('((discontinued IS NULL) OR (discontinued > clock_timestamp()))') if exclude_potential_abuses: where_parts.append('use_type IS NULL -- explicit medications only') if exclude_medications: where_parts.append('use_type IS NOT NULL -- no medications') if episodes: where_parts.append('pk_episode = ANY(%(pk_epis)s)') args['pk_epis'] = episodes if issues: where_parts.append('pk_health_issue = ANY(%(pk_issues)s)') args['pk_issues'] = issues if pk_substance: where_parts.append('pk_substance = %(pk_subst)s') args['pk_subst'] = pk_substance if order_by: order_by = 'ORDER BY %s' % order_by else: order_by = '' cmd = _SQL_get_intake_with_regimen % ('%s %s' % ( '\nAND '.join(where_parts), order_by )) rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) return [ cIntakeWithRegimen(row = { 'data': r, 'pk_obj': {'pk_intake_regimen': r['pk_intake_regimen'], 'pk_intake': r['pk_intake']} }) for r in rows ]Retrieve intake entries for each regimen.
def get_other_drug(name=None, pk_dose=None)-
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def get_other_drug(name=None, pk_dose=None): if pk_dose is None: content = create_substance_dose ( substance = name, amount = 1, unit = _('unit'), dose_unit = _('unit') ) else: content = {'pk_dose': pk_dose} #cSubstanceDose(aPK_obj = pk_dose) drug = create_drug_product ( product_name = name, preparation = _('unit'), doses = [content], return_existing = True ) drug['is_fake_product'] = True drug.save() return drug def get_substance_doses(order_by=None, return_pks=False)-
Expand source code
def get_substance_doses(order_by=None, return_pks=False): if order_by is None: order_by = 'true' else: order_by = 'true ORDER BY %s' % order_by cmd = _SQL_get_substance_dose % order_by rows = gmPG2.run_ro_queries(queries = [{'sql': cmd}]) if return_pks: return [ r['pk_dose'] for r in rows ] return [ cSubstanceDose(row = {'data': r, 'pk_field': 'pk_dose'}) for r in rows ] def get_substance_intakes(pk_patient: int = None,
return_pks: bool = False,
pk_substances: list[int] = None,
link_obj=None) ‑> list[cSubstanceIntakeEntry] | list[int]-
Expand source code
def get_substance_intakes(pk_patient:int=None, return_pks:bool=False, pk_substances:list[int]=None, link_obj=None) -> list[cSubstanceIntakeEntry] | list[int]: """Retrieve substance intakes. Args: pk_patient: constrain results by patient pk_substances: constrain by list of substances return_pks: return PKs rather than cSubstanceIntakeEntry's """ args:dict[str,int|list[int]] = {} where_parts = ['true'] if pk_patient: args['pat'] = pk_patient where_parts.append('pk_patient = %(pat)s') if pk_substances: args['pk_substances'] = pk_substances where_parts.append('pk_substance = ANY(%(pk_substances)s)') SQL = _SQL_get_substance_intake % '\nAND '.join(where_parts) rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}], link_obj = link_obj) if return_pks: return [ r['pk_intake'] for r in rows ] return [ cSubstanceIntakeEntry(row = {'data': r, 'pk_field': 'pk_intake'}) for r in rows ]Retrieve substance intakes.
Args
pk_patient- constrain results by patient
pk_substances- constrain by list of substances
return_pks- return PKs rather than cSubstanceIntakeEntry's
def get_substances(order_by: str = '', return_pks: bool = False, substance: str = None) ‑> list[cSubstance] | list[int]-
Expand source code
def get_substances(order_by:str='', return_pks:bool=False, substance:str=None) -> list[cSubstance] | list[int]: args = {} where_parts = [] if substance: args['substance'] = substance.strip() where_parts.append('substance = %(substance)s') if where_parts: WHERE = '\nAND '.join(where_parts) else: WHERE = 'true' if order_by: order_by = ' ORDER BY %s' % order_by SQL = _SQL_get_substance % WHERE SQL += order_by rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}]) if return_pks: return [ r['pk_substance'] for r in rows ] return [ cSubstance(row = {'data': r, 'pk_field': 'pk_substance'}) for r in rows ] def get_tobacco()-
Expand source code
def get_tobacco(): nicotine = create_substance_dose_by_atc ( substance = _('nicotine'), atc = gmATC.ATC_NICOTINE, amount = 1, unit = 'pack', dose_unit = 'year' ) tobacco = create_drug_product ( product_name = _('nicotine'), preparation = _('tobacco'), doses = [nicotine], return_existing = True ) tobacco['is_fake_product'] = True tobacco.save() return tobacco def substance_intake_exists(pk_identity: int = None, pk_substance: int = None, substance: str = None) ‑> bool-
Expand source code
def substance_intake_exists(pk_identity:int=None, pk_substance:int=None, substance:str=None) -> bool: """Check for existence of substance intakes. Args: pk_identity: constrain by person pk_substance: constrain by substance """ assert not ((pk_substance is None) and (substance is None)), 'either <pk_substance> or <substance> must be given' assert not ((pk_substance is not None) and (substance is not None)), 'only one of <pk_substance> or <substance> may be given' where_parts = [] args:dict[str, int|str] = {} if pk_identity: args['pk_pat'] = pk_identity where_parts.append('fk_encounter IN (SELECT pk FROM clin.encounter WHERE fk_patient = %(pk_pat)s)') if pk_substance: args['pk_subst'] = pk_substance where_parts.append('fk_substance = %(pk_subst)s') if substance: args['subst'] = substance.strip() where_parts.append('fk_substance = (select pk from ref.substance r_s where r_s.description = %(subst)s)') cmd = """SELECT EXISTS ( SELECT 1 FROM clin.intake WHERE %s LIMIT 1 )""" % '\nAND\n'.join(where_parts) rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) return rows[0][0]Check for existence of substance intakes.
Args
pk_identity- constrain by person
pk_substance- constrain by substance
def substance_intake_exists_by_atc(pk_identity=None, atc=None)-
Expand source code
def substance_intake_exists_by_atc(pk_identity=None, atc=None): if (atc is None) or (pk_identity is None): raise ValueError('atc and pk_identity cannot be None') args = { 'pat': pk_identity, 'atc': atc } where_parts = [ 'pk_patient = %(pat)s', '((atc_substance = %(atc)s) OR (atc_drug = %(atc)s))' ] cmd = """ SELECT EXISTS ( SELECT 1 FROM clin.v_intakes WHERE %s LIMIT 1 ) """ % '\nAND\n'.join(where_parts) rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) return rows[0][0] def use_type2str(use_type: int) ‑> str-
Expand source code
def use_type2str(use_type:int) -> str: try: return USE_TYPE_NAMES[use_type] except KeyError: _log.error('unknown medication use type') return _('unknown use type [%s]' % use_type)
Classes
class cDrugComponent (aPK_obj: int | dict = None, row: dict = None, link_obj=None)-
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class cDrugComponent(gmBusinessDBObject.cBusinessDBObject): _cmd_fetch_payload = _SQL_get_drug_components % 'pk_component = %s' _cmds_store_payload = [ """UPDATE ref.lnk_dose2drug SET fk_drug_product = %(pk_drug_product)s, fk_dose = %(pk_dose)s WHERE pk = %(pk_component)s AND NOT EXISTS ( SELECT 1 FROM clin.substance_intake WHERE fk_drug_component = %(pk_component)s LIMIT 1 ) AND xmin = %(xmin_lnk_dose2drug)s RETURNING xmin AS xmin_lnk_dose2drug """ ] _updatable_fields = [ 'pk_drug_product', 'pk_dose' ] #-------------------------------------------------------- def format(self, left_margin=0, include_loincs=False): lines = [] lines.append('%s %s%s' % ( self._payload['substance'], self._payload['amount'], self.formatted_units )) lines.append(_('Component of %s (%s)') % ( self._payload['drug_product'], self._payload['l10n_preparation'] )) if self._payload['is_fake_product']: lines.append(' ' + _('(not a real drug product)')) if self._payload['intake_instructions'] is not None: lines.append(_('Instructions: %s') % self._payload['intake_instructions']) if self._payload['atc_substance'] is not None: lines.append(_('ATC (substance): %s') % self._payload['atc_substance']) if self._payload['atc_drug'] is not None: lines.append(_('ATC (drug): %s') % self._payload['atc_drug']) if self._payload['external_code'] is not None: lines.append('%s: %s' % ( self._payload['external_code_type'], self._payload['external_code'] )) if include_loincs: if len(self._payload['loincs']) > 0: lines.append(_('LOINCs to monitor:')) lines.extend ([ ' %s%s%s' % ( loinc['loinc'], gmTools.coalesce(loinc['max_age_str'], '', ': ' + _('once within %s')), gmTools.coalesce(loinc['comment'], '', ' (%s)') ) for loinc in self._payload['loincs'] ]) return (' ' * left_margin) + ('\n' + (' ' * left_margin)).join(lines) #-------------------------------------------------------- def exists_as_intake(self, pk_patient=None): return substance_intake_exists ( pk_substance = -1, # FIXME pk_identity = pk_patient ) #-------------------------------------------------------- def turn_into_intake(self, emr=None, encounter=None, episode=None): return create_substance_intake ( pk_substance = -1, # FIXME pk_encounter = encounter, pk_episode = episode ) #-------------------------------------------------------- # properties #-------------------------------------------------------- def _get_containing_drug(self): return cDrugProduct(aPK_obj = self._payload['pk_drug_product']) containing_drug = property(_get_containing_drug) #-------------------------------------------------------- def _get_is_in_use_by_patients(self): return self._payload['is_in_use'] is_in_use_by_patients = property(_get_is_in_use_by_patients) #-------------------------------------------------------- def _get_substance_dose(self): return cSubstanceDose(aPK_obj = self._payload['pk_dose']) substance_dose = property(_get_substance_dose) #-------------------------------------------------------- def _get_substance(self): return cSubstance(aPK_obj = self._payload['pk_substance']) substance = property(_get_substance) #-------------------------------------------------------- def _get_formatted_units(self, short=True): return format_units ( self._payload['unit'], gmTools.coalesce(self._payload['dose_unit'], _('delivery unit')), self._payload['l10n_preparation'], short = short, none_str = '' ) formatted_units = property(_get_formatted_units)Represents business objects in the database.
Rules
- instances ARE ASSUMED TO EXIST in the database
- PK construction (aPK_obj): DOES verify its existence on instantiation (fetching data fails)
- Row construction (row): allowed by using a dict of pairs of field name: field value (PERFORMANCE improvement)
- does NOT verify FK target existence
- does NOT create new entries in the database
- does NOT lazy-fetch fields on access
Class scope SQL commands and variables:
_cmd_fetch_payload:
- must return exactly one row
- WHERE clause argument values are expected in self.pk_obj (taken from init(aPK_obj))
- must return xmin of all rows that _cmds_store_payload will be updating, so views must support the xmin columns of their underlying tables
_cmds_store_payload:
- one or multiple "update … set … where xmin_ = … and pk = …" statements which actually update the database from the data in self._payload,
- the last query must refetch at least the XMIN values needed to detect concurrent updates, their field names had better be the same as in _cmd_fetch_payload,
- the last query CAN return other fields which is particularly useful when those other fields are computed in the backend and may thus change upon save but will not have been set by the client code explicitly - this is only really of concern if the saved subclass is to be reused after saving rather than re-instantiated
- when subclasses tend to live a while after save_payload() was called and they support computed fields (say, _(some_column) you need to return all columns (see cEncounter)
_updatable_fields:
- a list of fields available for update via object['field']
Call init from child classes like so:
super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)Args
aPK_obj- retrieve data from backend
- an scalar value the ._cmd_fetch_payload WHERE condition must be a simple column: "… WHERE pk_col = %s"
- a dictionary of values the ._cmd_fetch_payload WHERE condition must consume the dictionary and produce a unique row
row- must hold the fields
- data: list of column values for the row selected by ._cmd_fetch_payload (as returned by cursor.fetchone() in the DB-API)
- pk_field: the name of the primary key column OR
- pk_obj: a dictionary suitable for being passed to cursor.execute and holding the primary key values, used for composite PKs
- for example:
row = { 'data': rows[0], 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) objects = [ cChildClass(row = {'data': r, 'pk_field': 'the PK column name'}) for r in rows ]
Ancestors
Instance variables
prop containing_drug-
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def _get_containing_drug(self): return cDrugProduct(aPK_obj = self._payload['pk_drug_product']) prop formatted_units-
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def _get_formatted_units(self, short=True): return format_units ( self._payload['unit'], gmTools.coalesce(self._payload['dose_unit'], _('delivery unit')), self._payload['l10n_preparation'], short = short, none_str = '' ) prop is_in_use_by_patients-
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def _get_is_in_use_by_patients(self): return self._payload['is_in_use'] prop substance-
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def _get_substance(self): return cSubstance(aPK_obj = self._payload['pk_substance']) prop substance_dose-
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def _get_substance_dose(self): return cSubstanceDose(aPK_obj = self._payload['pk_dose'])
Methods
def exists_as_intake(self, pk_patient=None)-
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def exists_as_intake(self, pk_patient=None): return substance_intake_exists ( pk_substance = -1, # FIXME pk_identity = pk_patient ) def turn_into_intake(self, emr=None, encounter=None, episode=None)-
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def turn_into_intake(self, emr=None, encounter=None, episode=None): return create_substance_intake ( pk_substance = -1, # FIXME pk_encounter = encounter, pk_episode = episode )
Inherited members
class cDrugComponentMatchProvider (queries=None, context=None)-
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class cDrugComponentMatchProvider(gmMatchProvider.cMatchProvider_SQL2): _pattern = regex.compile(r'^\D+\s*\d+$', regex.UNICODE) _query_desc_only = """ SELECT DISTINCT ON (list_label) r_vdc1.pk_component AS data, (r_vdc1.substance || ' ' || r_vdc1.amount || r_vdc1.unit || ' ' || r_vdc1.preparation || ' (' || r_vdc1.product || ' [' || ( SELECT array_to_string(array_agg(r_vdc2.amount), ' / ') FROM ref.v_drug_components r_vdc2 WHERE r_vdc2.pk_drug_product = r_vdc1.pk_drug_product ) || ']' || ')' ) AS field_label, (r_vdc1.substance || ' ' || r_vdc1.amount || r_vdc1.unit || ' ' || r_vdc1.preparation || ' (' || r_vdc1.product || ' [' || ( SELECT array_to_string(array_agg(r_vdc2.amount), ' / ') FROM ref.v_drug_components r_vdc2 WHERE r_vdc2.pk_drug_product = r_vdc1.pk_drug_product ) || ']' || ')' ) AS list_label FROM ref.v_drug_components r_vdc1 WHERE r_vdc1.substance %(fragment_condition)s OR r_vdc1.product %(fragment_condition)s ORDER BY list_label LIMIT 50""" _query_desc_and_amount = """ SELECT DISTINCT ON (list_label) pk_component AS data, (r_vdc1.substance || ' ' || r_vdc1.amount || r_vdc1.unit || ' ' || r_vdc1.preparation || ' (' || r_vdc1.product || ' [' || ( SELECT array_to_string(array_agg(r_vdc2.amount), ' / ') FROM ref.v_drug_components r_vdc2 WHERE r_vdc2.pk_drug_product = r_vdc1.pk_drug_product ) || ']' || ')' ) AS field_label, (r_vdc1.substance || ' ' || r_vdc1.amount || r_vdc1.unit || ' ' || r_vdc1.preparation || ' (' || r_vdc1.product || ' [' || ( SELECT array_to_string(array_agg(r_vdc2.amount), ' / ') FROM ref.v_drug_components r_vdc2 WHERE r_vdc2.pk_drug_product = r_vdc1.pk_drug_product ) || ']' || ')' ) AS list_label FROM ref.v_drug_components WHERE %(fragment_condition)s ORDER BY list_label LIMIT 50""" #-------------------------------------------------------- def getMatchesByPhrase(self, aFragment): """Return matches for aFragment at start of phrases.""" if cDrugComponentMatchProvider._pattern.match(aFragment): self._queries = [cDrugComponentMatchProvider._query_desc_and_amount] fragment_condition = """(substance ILIKE %(desc)s OR product ILIKE %(desc)s) AND amount::text ILIKE %(amount)s""" self._args['desc'] = '%s%%' % regex.sub(r'\s*\d+$', '', aFragment) self._args['amount'] = '%s%%' % regex.sub(r'^\D+\s*', '', aFragment) else: self._queries = [cDrugComponentMatchProvider._query_desc_only] fragment_condition = "ILIKE %(fragment)s" self._args['fragment'] = "%s%%" % aFragment return self._find_matches(fragment_condition) #-------------------------------------------------------- def getMatchesByWord(self, aFragment): """Return matches for aFragment at start of words inside phrases.""" if cDrugComponentMatchProvider._pattern.match(aFragment): self._queries = [cDrugComponentMatchProvider._query_desc_and_amount] desc = regex.sub(r'\s*\d+$', '', aFragment) desc = gmPG2.sanitize_pg_regex(expression = desc, escape_all = False) fragment_condition = """(substance ~* %(desc)s OR product ~* %(desc)s) AND amount::text ILIKE %(amount)s""" self._args['desc'] = "( %s)|(^%s)" % (desc, desc) self._args['amount'] = '%s%%' % regex.sub(r'^\D+\s*', '', aFragment) else: self._queries = [cDrugComponentMatchProvider._query_desc_only] fragment_condition = "~* %(fragment)s" aFragment = gmPG2.sanitize_pg_regex(expression = aFragment, escape_all = False) self._args['fragment'] = "( %s)|(^%s)" % (aFragment, aFragment) return self._find_matches(fragment_condition) #-------------------------------------------------------- def getMatchesBySubstr(self, aFragment): """Return matches for aFragment as a true substring.""" if cDrugComponentMatchProvider._pattern.match(aFragment): self._queries = [cDrugComponentMatchProvider._query_desc_and_amount] fragment_condition = """(substance ILIKE %(desc)s OR product ILIKE %(desc)s) AND amount::text ILIKE %(amount)s""" self._args['desc'] = '%%%s%%' % regex.sub(r'\s*\d+$', '', aFragment) self._args['amount'] = '%s%%' % regex.sub(r'^\D+\s*', '', aFragment) else: self._queries = [cDrugComponentMatchProvider._query_desc_only] fragment_condition = "ILIKE %(fragment)s" self._args['fragment'] = "%%%s%%" % aFragment return self._find_matches(fragment_condition)Match provider which searches matches in possibly several database tables.
queries: - a list of unicode strings - each string is a query - each string must contain: "… WHERE
%(fragment_condition)s …" - each string can contain in the where clause: "… %( )s …" - each query must return (data, list_label, field_label) context definitions to be used in the queries, example: {'ctxt_key1': {'where_part': 'AND country = %(country)s', 'placeholder': 'country'}}
client code using .set_context() must use the 'placeholder':
/ .set_context('country', 'Germany') full example query:
query = u" " " SELECT DISTINCT ON (list_label) pk_encounter AS data, to_char(started, 'YYYY Mon DD (HH24:MI)') || ': ' || l10n_type || ' [#' || pk_encounter || ']' AS list_label, to_char(started, 'YYYY Mon DD') || ': ' || l10n_type AS field_label FROM clin.v_pat_encounters WHERE ( l10n_type %(fragment_condition)s OR type %(fragment_condition)s ) %(ctxt_patient)s ORDER BY list_label LIMIT 30 " " " context = {'ctxt_patient': { 'where_part': u'AND pk_patient = %(PLACEHOLDER)s', 'placeholder': u'PLACEHOLDER' }} self.mp = gmMatchProvider.cMatchProvider_SQL2(queries = query, context = context) self.set_context(context = 'PLACEHOLDER', val = '<THE VALUE>')_SQL_data2match: SQL to retrieve a match by, say, primary key wherein the only keyword argument is 'pk'
Ancestors
Inherited members
class cDrugProduct (aPK_obj: int | dict = None, row: dict = None, link_obj=None)-
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class cDrugProduct(gmBusinessDBObject.cBusinessDBObject): """Represents a drug as marketed by a manufacturer or a generic drug product.""" _cmd_fetch_payload = _SQL_get_drug_product % 'pk_drug_product = %s' _cmds_store_payload = [ """UPDATE ref.drug_product SET description = %(product)s, preparation = %(preparation)s, atc_code = gm.nullify_empty_string(%(atc)s), external_code = gm.nullify_empty_string(%(external_code)s), external_code_type = gm.nullify_empty_string(%(external_code_type)s), is_fake = %(is_fake_product)s, fk_data_source = %(pk_data_source)s WHERE pk = %(pk_drug_product)s AND xmin = %(xmin_drug_product)s RETURNING xmin AS xmin_drug_product """ ] _updatable_fields = [ 'product', 'preparation', 'atc', 'is_fake_product', 'external_code', 'external_code_type', 'pk_data_source' ] #-------------------------------------------------------- def format(self, left_margin=0, include_component_details=False): lines = [] lines.append('%s (%s)' % ( self._payload['drug_product'], self._payload['l10n_preparation'] ) ) if self._payload['atc'] is not None: lines.append('ATC: %s' % self._payload['atc']) if self._payload['external_code'] is not None: lines.append('%s: %s' % (self._payload['external_code_type'], self._payload['external_code'])) if len(self._payload['components']) > 0: lines.append(_('Components:')) for comp in self._payload['components']: lines.append(' %s %s %s' % ( comp['substance'], comp['amount'], format_units(comp['unit'], comp['dose_unit'], short = False) )) if include_component_details: if comp['intake_instructions'] is not None: lines.append(comp['intake_instructions']) lines.extend([ '%s%s%s' % ( l['loinc'], gmTools.coalesce(l['max_age_str'], '', ': ' + _('once within %s')), gmTools.coalesce(l['comment'], '', ' (%s)') ) for l in comp['loincs'] ]) if self._payload['is_fake_product']: lines.append('') lines.append(_('this is a fake drug product')) if self.is_vaccine: lines.append(_('this is a vaccine')) return (' ' * left_margin) + ('\n' + (' ' * left_margin)).join(lines) #-------------------------------------------------------- def save_payload(self, conn=None): success, data = super().save_payload(conn = conn) if not success: return (success, data) if self._payload['atc'] is not None: atc = self._payload['atc'].strip() if atc != '': gmATC.propagate_atc ( link_obj = conn, substance = self._payload['product'].strip(), atc = atc ) return (success, data) #-------------------------------------------------------- def set_substance_doses_as_components(self, substance_doses:list=None, pk_substance_doses:list[int]=None, link_obj=None): if self.is_in_use: return False if pk_substance_doses: pk_doses2keep = pk_substance_doses else: pk_doses2keep = [ s['pk_dose'] for s in substance_doses ] _log.debug('setting components of "%s" from doses: %s', self._payload['product'], pk_doses2keep) args = {'pk_drug_product': self._payload['pk_drug_product']} queries = [] # INSERT those which are not there yet cmd = """ INSERT INTO ref.lnk_dose2drug ( fk_drug_product, fk_dose ) SELECT %(pk_drug_product)s, %(pk_dose)s WHERE NOT EXISTS ( SELECT 1 FROM ref.lnk_dose2drug WHERE fk_drug_product = %(pk_drug_product)s AND fk_dose = %(pk_dose)s )""" for pk_dose in pk_doses2keep: args['pk_dose'] = pk_dose queries.append({'sql': cmd, 'args': args.copy()}) # DELETE those that don't belong anymore args['doses2keep'] = pk_doses2keep cmd = """ DELETE FROM ref.lnk_dose2drug WHERE fk_drug_product = %(pk_drug_product)s AND fk_dose <> ALL(%(doses2keep)s)""" queries.append({'sql': cmd, 'args': args}) gmPG2.run_rw_queries(link_obj = link_obj, queries = queries) self.refetch_payload(link_obj = link_obj) return True #-------------------------------------------------------- def add_component(self, substance=None, atc=None, amount=None, unit=None, dose_unit=None, pk_dose=None, pk_substance=None): if pk_dose is None: if pk_substance is None: pk_dose = create_substance_dose(substance = substance, atc = atc, amount = amount, unit = unit, dose_unit = dose_unit)['pk_dose'] else: pk_dose = create_substance_dose(pk_substance = pk_substance, atc = atc, amount = amount, unit = unit, dose_unit = dose_unit)['pk_dose'] args = { 'pk_dose': pk_dose, 'pk_drug_product': self.pk_obj } cmd = """ INSERT INTO ref.lnk_dose2drug (fk_drug_product, fk_dose) SELECT %(pk_drug_product)s, %(pk_dose)s WHERE NOT EXISTS ( SELECT 1 FROM ref.lnk_dose2drug WHERE fk_drug_product = %(pk_drug_product)s AND fk_dose = %(pk_dose)s )""" gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}]) self.refetch_payload() #------------------------------------------------------------ def remove_component(self, pk_dose=None, pk_component=None): if len(self._payload['components']) == 1: _log.error('will not remove the only component of a drug') return False args = {'pk_drug_product': self.pk_obj, 'pk_dose': pk_dose, 'pk_component': pk_component} if pk_component is None: cmd = """DELETE FROM ref.lnk_dose2drug WHERE fk_drug_product = %(pk_drug_product)s AND fk_dose = %(pk_dose)s AND NOT EXISTS ( SELECT 1 FROM clin.v_intakes WHERE pk_dose = %(pk_dose)s LIMIT 1 )""" else: cmd = """DELETE FROM ref.lnk_dose2drug WHERE pk = %(pk_component)s AND NOT EXISTS ( SELECT 1 FROM clin.substance_intake WHERE fk_drug_component = %(pk_component)s LIMIT 1 )""" gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}]) self.refetch_payload() return True #-------------------------------------------------------- def exists_as_intake(self, pk_patient=None): return substance_intake_exists ( pk_substance = -1, # FIXME pk_identity = pk_patient ) #-------------------------------------------------------- def turn_into_intake(self, emr=None, encounter=None, episode=None): return create_substance_intake ( pk_substance = -1, # FIXME pk_encounter = encounter, pk_episode = episode ) #-------------------------------------------------------- def delete_associated_vaccine(self): if self._payload['is_vaccine'] is False: return True args = {'pk_product': self._payload['pk_drug_product']} cmd = """DELETE FROM ref.vaccine WHERE fk_drug_product = %(pk_product)s AND -- not in use: NOT EXISTS ( SELECT 1 FROM clin.vaccination WHERE fk_vaccine = ( select pk from ref.vaccine where fk_drug_product = %(pk_product)s ) ) RETURNING *""" rows = gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}], return_data = True) if len(rows) == 0: _log.debug('cannot delete vaccine on: %s', self) return False return True #-------------------------------------------------------- # properties #-------------------------------------------------------- def _get_external_code(self): return self._payload['external_code'] external_code = property(_get_external_code) #-------------------------------------------------------- def _get_external_code_type(self): # FIXME: maybe evaluate fk_data_source ? return self._payload['external_code_type'] external_code_type = property(_get_external_code_type) #-------------------------------------------------------- def _get_components(self): SQL = _SQL_get_drug_components % 'pk_drug_product = %(pk_product)s' args = {'pk_product': self._payload['pk_drug_product']} rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}]) return [ cDrugComponent(row = {'data': r, 'pk_field': 'pk_component'}) for r in rows ] components = property(_get_components) #-------------------------------------------------------- def _get_components_as_doses(self): pk_doses = [ c['pk_dose'] for c in self._payload['components'] ] if len(pk_doses) == 0: return [] cmd = _SQL_get_substance_dose % 'pk_dose = ANY(%(pks)s)' args = {'pks': pk_doses} rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) return [ cSubstanceDose(row = {'data': r, 'pk_field': 'pk_dose'}) for r in rows ] components_as_doses = property(_get_components_as_doses) #-------------------------------------------------------- def _get_components_as_substances(self): pk_substances = [ c['pk_substance'] for c in self._payload['components'] ] if len(pk_substances) == 0: return [] cmd = _SQL_get_substance % 'pk_substance = ANY(%(pks)s)' args = {'pks': pk_substances} rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) return [ cSubstance(row = {'data': r, 'pk_field': 'pk_substance'}) for r in rows ] components_as_substances = property(_get_components_as_substances) #-------------------------------------------------------- def _get_is_fake_product(self): return self._payload['is_fake_product'] is_fake_product = property(_get_is_fake_product) #-------------------------------------------------------- def _get_is_vaccine(self): return self._payload['is_vaccine'] is_vaccine = property(_get_is_vaccine) #-------------------------------------------------------- def _get_is_in_use(self): # as of v23 drug products are not linked to intakes return self.is_in_use_as_vaccine is_in_use = property(_get_is_in_use) #-------------------------------------------------------- def _get_is_in_use_as_vaccine(self): if self._payload['is_vaccine'] is False: return False SQL = 'SELECT EXISTS(SELECT 1 FROM clin.vaccination WHERE fk_vaccine = (SELECT pk FROM ref.vaccine WHERE fk_drug_product = %(pk)s))' args = {'pk': self.pk_obj} rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}]) return rows[0][0] is_in_use_as_vaccine = property(_get_is_in_use_as_vaccine)Represents a drug as marketed by a manufacturer or a generic drug product.
Call init from child classes like so:
super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)Args
aPK_obj- retrieve data from backend
- an scalar value the ._cmd_fetch_payload WHERE condition must be a simple column: "… WHERE pk_col = %s"
- a dictionary of values the ._cmd_fetch_payload WHERE condition must consume the dictionary and produce a unique row
row- must hold the fields
- data: list of column values for the row selected by ._cmd_fetch_payload (as returned by cursor.fetchone() in the DB-API)
- pk_field: the name of the primary key column OR
- pk_obj: a dictionary suitable for being passed to cursor.execute and holding the primary key values, used for composite PKs
- for example:
row = { 'data': rows[0], 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) objects = [ cChildClass(row = {'data': r, 'pk_field': 'the PK column name'}) for r in rows ]
Ancestors
Instance variables
prop components-
Expand source code
def _get_components(self): SQL = _SQL_get_drug_components % 'pk_drug_product = %(pk_product)s' args = {'pk_product': self._payload['pk_drug_product']} rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}]) return [ cDrugComponent(row = {'data': r, 'pk_field': 'pk_component'}) for r in rows ] prop components_as_doses-
Expand source code
def _get_components_as_doses(self): pk_doses = [ c['pk_dose'] for c in self._payload['components'] ] if len(pk_doses) == 0: return [] cmd = _SQL_get_substance_dose % 'pk_dose = ANY(%(pks)s)' args = {'pks': pk_doses} rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) return [ cSubstanceDose(row = {'data': r, 'pk_field': 'pk_dose'}) for r in rows ] prop components_as_substances-
Expand source code
def _get_components_as_substances(self): pk_substances = [ c['pk_substance'] for c in self._payload['components'] ] if len(pk_substances) == 0: return [] cmd = _SQL_get_substance % 'pk_substance = ANY(%(pks)s)' args = {'pks': pk_substances} rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) return [ cSubstance(row = {'data': r, 'pk_field': 'pk_substance'}) for r in rows ] prop external_code-
Expand source code
def _get_external_code(self): return self._payload['external_code'] prop external_code_type-
Expand source code
def _get_external_code_type(self): # FIXME: maybe evaluate fk_data_source ? return self._payload['external_code_type'] prop is_fake_product-
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def _get_is_fake_product(self): return self._payload['is_fake_product'] prop is_in_use-
Expand source code
def _get_is_in_use(self): # as of v23 drug products are not linked to intakes return self.is_in_use_as_vaccine prop is_in_use_as_vaccine-
Expand source code
def _get_is_in_use_as_vaccine(self): if self._payload['is_vaccine'] is False: return False SQL = 'SELECT EXISTS(SELECT 1 FROM clin.vaccination WHERE fk_vaccine = (SELECT pk FROM ref.vaccine WHERE fk_drug_product = %(pk)s))' args = {'pk': self.pk_obj} rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}]) return rows[0][0] prop is_vaccine-
Expand source code
def _get_is_vaccine(self): return self._payload['is_vaccine']
Methods
def add_component(self,
substance=None,
atc=None,
amount=None,
unit=None,
dose_unit=None,
pk_dose=None,
pk_substance=None)-
Expand source code
def add_component(self, substance=None, atc=None, amount=None, unit=None, dose_unit=None, pk_dose=None, pk_substance=None): if pk_dose is None: if pk_substance is None: pk_dose = create_substance_dose(substance = substance, atc = atc, amount = amount, unit = unit, dose_unit = dose_unit)['pk_dose'] else: pk_dose = create_substance_dose(pk_substance = pk_substance, atc = atc, amount = amount, unit = unit, dose_unit = dose_unit)['pk_dose'] args = { 'pk_dose': pk_dose, 'pk_drug_product': self.pk_obj } cmd = """ INSERT INTO ref.lnk_dose2drug (fk_drug_product, fk_dose) SELECT %(pk_drug_product)s, %(pk_dose)s WHERE NOT EXISTS ( SELECT 1 FROM ref.lnk_dose2drug WHERE fk_drug_product = %(pk_drug_product)s AND fk_dose = %(pk_dose)s )""" gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}]) self.refetch_payload() def delete_associated_vaccine(self)-
Expand source code
def delete_associated_vaccine(self): if self._payload['is_vaccine'] is False: return True args = {'pk_product': self._payload['pk_drug_product']} cmd = """DELETE FROM ref.vaccine WHERE fk_drug_product = %(pk_product)s AND -- not in use: NOT EXISTS ( SELECT 1 FROM clin.vaccination WHERE fk_vaccine = ( select pk from ref.vaccine where fk_drug_product = %(pk_product)s ) ) RETURNING *""" rows = gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}], return_data = True) if len(rows) == 0: _log.debug('cannot delete vaccine on: %s', self) return False return True def exists_as_intake(self, pk_patient=None)-
Expand source code
def exists_as_intake(self, pk_patient=None): return substance_intake_exists ( pk_substance = -1, # FIXME pk_identity = pk_patient ) def remove_component(self, pk_dose=None, pk_component=None)-
Expand source code
def remove_component(self, pk_dose=None, pk_component=None): if len(self._payload['components']) == 1: _log.error('will not remove the only component of a drug') return False args = {'pk_drug_product': self.pk_obj, 'pk_dose': pk_dose, 'pk_component': pk_component} if pk_component is None: cmd = """DELETE FROM ref.lnk_dose2drug WHERE fk_drug_product = %(pk_drug_product)s AND fk_dose = %(pk_dose)s AND NOT EXISTS ( SELECT 1 FROM clin.v_intakes WHERE pk_dose = %(pk_dose)s LIMIT 1 )""" else: cmd = """DELETE FROM ref.lnk_dose2drug WHERE pk = %(pk_component)s AND NOT EXISTS ( SELECT 1 FROM clin.substance_intake WHERE fk_drug_component = %(pk_component)s LIMIT 1 )""" gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}]) self.refetch_payload() return True def set_substance_doses_as_components(self,
substance_doses: list = None,
pk_substance_doses: list[int] = None,
link_obj=None)-
Expand source code
def set_substance_doses_as_components(self, substance_doses:list=None, pk_substance_doses:list[int]=None, link_obj=None): if self.is_in_use: return False if pk_substance_doses: pk_doses2keep = pk_substance_doses else: pk_doses2keep = [ s['pk_dose'] for s in substance_doses ] _log.debug('setting components of "%s" from doses: %s', self._payload['product'], pk_doses2keep) args = {'pk_drug_product': self._payload['pk_drug_product']} queries = [] # INSERT those which are not there yet cmd = """ INSERT INTO ref.lnk_dose2drug ( fk_drug_product, fk_dose ) SELECT %(pk_drug_product)s, %(pk_dose)s WHERE NOT EXISTS ( SELECT 1 FROM ref.lnk_dose2drug WHERE fk_drug_product = %(pk_drug_product)s AND fk_dose = %(pk_dose)s )""" for pk_dose in pk_doses2keep: args['pk_dose'] = pk_dose queries.append({'sql': cmd, 'args': args.copy()}) # DELETE those that don't belong anymore args['doses2keep'] = pk_doses2keep cmd = """ DELETE FROM ref.lnk_dose2drug WHERE fk_drug_product = %(pk_drug_product)s AND fk_dose <> ALL(%(doses2keep)s)""" queries.append({'sql': cmd, 'args': args}) gmPG2.run_rw_queries(link_obj = link_obj, queries = queries) self.refetch_payload(link_obj = link_obj) return True def turn_into_intake(self, emr=None, encounter=None, episode=None)-
Expand source code
def turn_into_intake(self, emr=None, encounter=None, episode=None): return create_substance_intake ( pk_substance = -1, # FIXME pk_encounter = encounter, pk_episode = episode )
Inherited members
class cIntakeRegimen (aPK_obj: int | dict = None, row: dict = None, link_obj=None)-
Expand source code
class cIntakeRegimen(gmBusinessDBObject.cBusinessDBObject): """Represents a (real) intake regimen, either active or inactive.""" _cmd_fetch_payload = _SQL_get_intake_regimens % 'pk_intake_regimen = %s' _cmds_store_payload = [ """ UPDATE clin.intake_regimen SET clin_when = %(started)s, start_is_unknown = %(start_is_unknown)s, comment_on_start = gm.nullify_empty_string(%(comment_on_start)s), planned_duration = %(planned_duration)s, discontinued = %(discontinued)s, discontinue_reason = gm.nullify_empty_string(%(discontinue_reason)s), narrative = gm.nullify_empty_string(%(schedule)s), fk_encounter = %(pk_encounter)s, fk_episode = %(pk_episode)s, fk_intake = %(pk_intake)s WHERE pk = %(pk_intake_regimen)s AND xmin = %(xmin_intake_regimen)s RETURNING xmin AS xmin_intake_regimen -- also return columns which are calculated in the view used by -- the initial SELECT such that they will further on contain their -- updated value: --, ... """ ] # view columns that can be updated: _updatable_fields = [ 'started', 'start_is_unknown', 'comment_on_start', 'planned_duration', 'discontinued', 'discontinue_reason', 'pk_encounter', 'pk_episode', 'pk_intake', 'schedule' ] #-------------------------------------------------------- def format(self, left_margin=0, date_format:str='%Y %b %d', single_line:bool=True, terse:bool=True, eol:str=None, allergy=None): if single_line: return '%s%s' % ( ' ' * left_margin, format_regimen_like_as_single_line(self, date_format = date_format, terse = terse) ) return self.format_as_multiple_lines ( left_margin = left_margin, date_format = date_format, allergy = allergy, eol = eol ) #-------------------------------------------------------- def format_as_single_line_abuse(self, left_margin=0, date_format='%Y %b %d'): return '%s%s: %s (%s)' % ( ' ' * left_margin, self._payload['substance'], self.use_type_string, self._payload['modified_when'].strftime('%b %Y') ) #-------------------------------------------------------- def format_as_multiple_lines(self, left_margin:int=0, date_format:str='%Y %b %d', allergy=None, include_loincs:bool=False, eol:str='\n'): return format_regimen_like_as_multiple_lines ( regimen_like = self, left_margin = left_margin, date_format = date_format, allergy = allergy, include_loincs = include_loincs, eol = eol ) #-------------------------------------------------------- def _get_is_ongoing(self): if self._payload['discontinued'] is None: return True now = gmDateTime.pydt_now_here() if self._payload['discontinued'] < now: return False return True is_ongoing = property(_get_is_ongoing) #-------------------------------------------------------- def __get_as_intake_with_regimen(self): return cIntakeWithRegimen(aPK_obj = {'pk_intake_regimen': self['pk_intake_regimen'], 'pk_intake': self['pk_intake']}) as_intake_with_regimen = property(__get_as_intake_with_regimen) #-------------------------------------------------------- def _get_use_type_string(self): return use_type2str(self._payload['use_type']) use_type_string = property(_get_use_type_string) #-------------------------------------------------------- def _get_formatted_units(self, short=True): return format_units(self._payload['unit'], short = short, none_str = '') formatted_units = property(_get_formatted_units) #-------------------------------------------------------- def _get_medically_formatted_start(self): return format_regimen_start_medically(self) medically_formatted_start = property(_get_medically_formatted_start) #-------------------------------------------------------- def _get_medically_formatted_timerange(self, terse:bool=False): return format_regimen_timerange_medically(self, terse = terse) medically_formatted_timerange = property(_get_medically_formatted_timerange) #-------------------------------------------------------- def _get_parsed_schedule(self): tests = [ # lead, trail ' 1-1-1-1 ', # leading dose '1-1-1-1', '22-1-1-1', '1/3-1-1-1', '/4-1-1-1' ] pattern = "^(\d\d|/\d|\d/\d|\d)[\s-]{1,5}\d{0,2}[\s-]{1,5}\d{0,2}[\s-]{1,5}\d{0,2}$" for test in tests: print(test.strip(), ":", regex.match(pattern, test.strip()))Represents a (real) intake regimen, either active or inactive.
Call init from child classes like so:
super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)Args
aPK_obj- retrieve data from backend
- an scalar value the ._cmd_fetch_payload WHERE condition must be a simple column: "… WHERE pk_col = %s"
- a dictionary of values the ._cmd_fetch_payload WHERE condition must consume the dictionary and produce a unique row
row- must hold the fields
- data: list of column values for the row selected by ._cmd_fetch_payload (as returned by cursor.fetchone() in the DB-API)
- pk_field: the name of the primary key column OR
- pk_obj: a dictionary suitable for being passed to cursor.execute and holding the primary key values, used for composite PKs
- for example:
row = { 'data': rows[0], 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) objects = [ cChildClass(row = {'data': r, 'pk_field': 'the PK column name'}) for r in rows ]
Ancestors
Instance variables
prop as_intake_with_regimen-
Expand source code
def __get_as_intake_with_regimen(self): return cIntakeWithRegimen(aPK_obj = {'pk_intake_regimen': self['pk_intake_regimen'], 'pk_intake': self['pk_intake']}) prop formatted_units-
Expand source code
def _get_formatted_units(self, short=True): return format_units(self._payload['unit'], short = short, none_str = '') prop is_ongoing-
Expand source code
def _get_is_ongoing(self): if self._payload['discontinued'] is None: return True now = gmDateTime.pydt_now_here() if self._payload['discontinued'] < now: return False return True prop medically_formatted_start-
Expand source code
def _get_medically_formatted_start(self): return format_regimen_start_medically(self) prop medically_formatted_timerange-
Expand source code
def _get_medically_formatted_timerange(self, terse:bool=False): return format_regimen_timerange_medically(self, terse = terse) prop use_type_string-
Expand source code
def _get_use_type_string(self): return use_type2str(self._payload['use_type'])
Methods
def format_as_multiple_lines(self,
left_margin: int = 0,
date_format: str = '%Y %b %d',
allergy=None,
include_loincs: bool = False,
eol: str = '\n')-
Expand source code
def format_as_multiple_lines(self, left_margin:int=0, date_format:str='%Y %b %d', allergy=None, include_loincs:bool=False, eol:str='\n'): return format_regimen_like_as_multiple_lines ( regimen_like = self, left_margin = left_margin, date_format = date_format, allergy = allergy, include_loincs = include_loincs, eol = eol ) def format_as_single_line_abuse(self, left_margin=0, date_format='%Y %b %d')-
Expand source code
def format_as_single_line_abuse(self, left_margin=0, date_format='%Y %b %d'): return '%s%s: %s (%s)' % ( ' ' * left_margin, self._payload['substance'], self.use_type_string, self._payload['modified_when'].strftime('%b %Y') )
Inherited members
class cIntakeWithRegimen (aPK_obj: int | dict = None, row: dict = None, link_obj=None)-
Expand source code
class cIntakeWithRegimen(gmBusinessDBObject.cBusinessDBObject): """A substance intake with regimen. There may be several concurrent ongoing regimens for any given substance intake. Intakes without any regimen will show empty regimen fields, IOW a pseudo-regimen. To be intialized with a dictionary like { 'pk_intake': INT, 'pk_intake_regimen': INT } where pk_intake_regimen can be None. """ _cmd_fetch_payload = _SQL_get_intake_with_regimen % 'pk_intake = %(pk_intake)s AND pk_intake_regimen IS NOT DISTINCT FROM %(pk_intake_regimen)s' _cmds_store_payload = [ """ -- cIntakeWithRegimen: clin.intake UPDATE clin.intake SET clin_when = %(last_checked_when)s, narrative = gm.nullify_empty_string(%(notes4provider)s), notes4patient = gm.nullify_empty_string(%(notes4patient)s), notes4us = gm.nullify_empty_string(%(notes4us)s), use_type = %(use_type)s, -- only update episode when there's no regimen fk_episode = CASE WHEN %(pk_intake_regimen)s IS DISTINCT FROM NULL THEN fk_episode ELSE %(pk_episode)s END WHERE pk = %(pk_intake)s AND xmin = %(xmin_intake)s """, """ -- cIntakeWithRegimen: clin.intake_regimen UPDATE clin.intake_regimen SET narrative = gm.nullify_empty_string(%(schedule)s), clin_when = %(started)s, start_is_unknown = %(start_is_unknown)s, comment_on_start = gm.nullify_empty_string(%(comment_on_start)s), discontinued = %(discontinued)s, discontinue_reason = gm.nullify_empty_string(%(discontinue_reason)s), planned_duration = %(planned_duration)s, fk_episode = %(pk_episode)s -- , fk_encounter = %(pk_encounter)s WHERE -- pseudo-regimen will have pk_intake_regimen=NULL while rows in clin.intake_regimen will never do pk = %(pk_intake_regimen)s AND xmin = %(xmin_regimen)s """, _cmd_fetch_payload ] _updatable_fields = [ # intake fields: 'last_checked_when', 'notes4provider', 'notes4patient', 'notes4us', 'use_type', # regimen fields: 'schedule', 'started', 'start_is_unknown', 'comment_on_start', 'discontinued', 'discontinue_reason', 'planned_duration', 'pk_encounter', 'pk_episode' ] #-------------------------------------------------------- def format_maximum_information(self, allergy=None, left_margin=0, date_format='%Y %b %d'): return self.format ( single_line = False, left_margin = left_margin, date_format = date_format, allergy = allergy, include_metadata = True, include_instructions = True, include_loincs = True, eol = None ) #-------------------------------------------------------- def format(self, left_margin=0, date_format='%Y %b %d', single_line=False, allergy=None, include_instructions=False, include_loincs=False, include_metadata:bool=False, terse:bool=False, eol=None): # medication if self._payload['use_type'] is None: if single_line: return '%s%s' % ( ' ' * left_margin, format_regimen_like_as_single_line(self, date_format = date_format, terse = terse) ) return self.format_as_multiple_lines ( left_margin = left_margin, date_format = date_format, allergy = allergy, include_metadata = include_metadata, eol = eol ) # misuse if self._payload['use_type'] in [0, 1, 2, 3]: if single_line: return self.format_as_single_line_abuse(left_margin = left_margin, date_format = date_format) return self.format_as_multiple_lines_abuse ( left_margin = left_margin, date_format = date_format, include_metadata = include_metadata, eol = eol ) #-------------------------------------------------------- def format_as_multiple_lines(self, left_margin:int=0, date_format:str='%Y %b %d', allergy=None, include_loincs:bool=False, include_metadata:bool=False, eol:str=None): return format_regimen_like_as_multiple_lines ( regimen_like = self, left_margin = left_margin, date_format = date_format, allergy = allergy, include_loincs = include_loincs, include_metadata = include_metadata, eol = eol ) #-------------------------------------------------------- def format_as_single_line_abuse(self, left_margin=0, date_format='%Y %b %d'): return '%s%s: %s (%s)' % ( ' ' * left_margin, self._payload['substance'], self.use_type_string, self._payload['last_checked_when'].strftime('%b %Y') ) #-------------------------------------------------------- def format_as_multiple_lines_abuse(self, left_margin=0, date_format='%Y %b %d', include_metadata:bool=False, eol:str=None): return format_regimen_like_as_multiple_lines_abuse ( regimen_like = self, left_margin = left_margin, date_format = date_format, include_metadata = include_metadata, eol = eol ) #-------------------------------------------------------- def format_for_failsafe_output(self, max_width:int=80) -> list[str]: lines = [_('Substance: %s %s') % ( self['substance'], self.formatted_units )] if self['schedule']: lines.append(' ' + _('Regimen: %s') % self['schedule']) lines.append(' ' + _('Timerange: %s') % self.medically_formatted_timerange) if self['notes4patient']: lines.append(gmTools.wrap ( _('Patient notes: %s') % self['notes4patient'], width = max_width, initial_indent = ' ', subsequent_indent = ' ' )) if self['intake_instructions']: lines.append(gmTools.wrap ( _('Instructions: %s') % self['intake_instructions'], width = max_width, initial_indent = ' ', subsequent_indent = ' ' )) if self['notes4provider']: lines.append(gmTools.wrap ( _('Provider notes: %s') % self['notes4provider'], width = max_width, initial_indent = ' ', subsequent_indent = ' ' )) lines.append(' ' + _('Episode: %s%s') % ( self['episode'], gmTools.coalesce(self['health_issue'], '', ' (%s: %%s)' % _('Issue')) )) return lines #-------------------------------------------------------- def _get_as_amts_data(self, strict=True): return format_intake_with_regimen_as_amts_data(intake = self, strict = strict) as_amts_data = property(_get_as_amts_data) #-------------------------------------------------------- def _get_use_type_string(self): return use_type2str(self._payload['use_type']) use_type_string = property(_get_use_type_string) #-------------------------------------------------------- def __get_as_intake_with_regimen(self): return self as_intake_with_regimen = property(__get_as_intake_with_regimen) #-------------------------------------------------------- def _get_intake(self): return cSubstanceIntakeEntry(aPK_obj = self._payload['pk_intake']) intake = property(_get_intake) #-------------------------------------------------------- def _get_regimen(self): if self._payload['pk_intake_regimen']: return cIntakeRegimen(aPK_obj = self._payload['pk_intake_regimen']) return None regimen = property(_get_regimen) #-------------------------------------------------------- def get_regimens_for_substance(self, ongoing_only:bool=False) -> list: return get_intake_regimens ( pk_substance = self._payload['pk_substance'], pk_patient = self._payload['pk_patient'], ongoing_only = ongoing_only ) regimens_for_substance = property(get_regimens_for_substance) #-------------------------------------------------------- def _get_containing_drug(self): return None containing_drug = property(_get_containing_drug) #-------------------------------------------------------- def _get_medically_formatted_start(self): return format_regimen_start_medically(self) medically_formatted_start = property(_get_medically_formatted_start) #-------------------------------------------------------- def _get_medically_formatted_timerange(self, terse:bool=False): return format_regimen_timerange_medically(self, terse = terse) medically_formatted_timerange = property(_get_medically_formatted_timerange) #-------------------------------------------------------- def _get_is_ongoing(self): if self._payload['discontinued'] is None: return True now = gmDateTime.pydt_now_here() if self._payload['discontinued'] < now: return False return True is_ongoing = property(_get_is_ongoing) #-------------------------------------------------------- def _get_formatted_units(self, short=True): return format_units(self._payload['unit'], short = short, none_str = '') formatted_units = property(_get_formatted_units) #-------------------------------------------------------- def turn_into_allergy(self, encounter_id=None, allergy_type='allergy'): return self.intake.turn_into_allergy ( encounter_id = encounter_id, allergy_type = allergy_type )A substance intake with regimen.
There may be several concurrent ongoing regimens for any given substance intake.
Intakes without any regimen will show empty regimen fields, IOW a pseudo-regimen.
To be intialized with a dictionary like
{ 'pk_intake': INT, 'pk_intake_regimen': INT }where pk_intake_regimen can be None.
Call init from child classes like so:
super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)Args
aPK_obj- retrieve data from backend
- an scalar value the ._cmd_fetch_payload WHERE condition must be a simple column: "… WHERE pk_col = %s"
- a dictionary of values the ._cmd_fetch_payload WHERE condition must consume the dictionary and produce a unique row
row- must hold the fields
- data: list of column values for the row selected by ._cmd_fetch_payload (as returned by cursor.fetchone() in the DB-API)
- pk_field: the name of the primary key column OR
- pk_obj: a dictionary suitable for being passed to cursor.execute and holding the primary key values, used for composite PKs
- for example:
row = { 'data': rows[0], 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) objects = [ cChildClass(row = {'data': r, 'pk_field': 'the PK column name'}) for r in rows ]
Ancestors
Instance variables
prop as_amts_data-
Expand source code
def _get_as_amts_data(self, strict=True): return format_intake_with_regimen_as_amts_data(intake = self, strict = strict) prop as_intake_with_regimen-
Expand source code
def __get_as_intake_with_regimen(self): return self prop containing_drug-
Expand source code
def _get_containing_drug(self): return None prop formatted_units-
Expand source code
def _get_formatted_units(self, short=True): return format_units(self._payload['unit'], short = short, none_str = '') prop intake-
Expand source code
def _get_intake(self): return cSubstanceIntakeEntry(aPK_obj = self._payload['pk_intake']) prop is_ongoing-
Expand source code
def _get_is_ongoing(self): if self._payload['discontinued'] is None: return True now = gmDateTime.pydt_now_here() if self._payload['discontinued'] < now: return False return True prop medically_formatted_start-
Expand source code
def _get_medically_formatted_start(self): return format_regimen_start_medically(self) prop medically_formatted_timerange-
Expand source code
def _get_medically_formatted_timerange(self, terse:bool=False): return format_regimen_timerange_medically(self, terse = terse) prop regimen-
Expand source code
def _get_regimen(self): if self._payload['pk_intake_regimen']: return cIntakeRegimen(aPK_obj = self._payload['pk_intake_regimen']) return None prop regimens_for_substance : list-
Expand source code
def get_regimens_for_substance(self, ongoing_only:bool=False) -> list: return get_intake_regimens ( pk_substance = self._payload['pk_substance'], pk_patient = self._payload['pk_patient'], ongoing_only = ongoing_only ) prop use_type_string-
Expand source code
def _get_use_type_string(self): return use_type2str(self._payload['use_type'])
Methods
def format_as_multiple_lines(self,
left_margin: int = 0,
date_format: str = '%Y %b %d',
allergy=None,
include_loincs: bool = False,
include_metadata: bool = False,
eol: str = None)-
Expand source code
def format_as_multiple_lines(self, left_margin:int=0, date_format:str='%Y %b %d', allergy=None, include_loincs:bool=False, include_metadata:bool=False, eol:str=None): return format_regimen_like_as_multiple_lines ( regimen_like = self, left_margin = left_margin, date_format = date_format, allergy = allergy, include_loincs = include_loincs, include_metadata = include_metadata, eol = eol ) def format_as_multiple_lines_abuse(self,
left_margin=0,
date_format='%Y %b %d',
include_metadata: bool = False,
eol: str = None)-
Expand source code
def format_as_multiple_lines_abuse(self, left_margin=0, date_format='%Y %b %d', include_metadata:bool=False, eol:str=None): return format_regimen_like_as_multiple_lines_abuse ( regimen_like = self, left_margin = left_margin, date_format = date_format, include_metadata = include_metadata, eol = eol ) def format_as_single_line_abuse(self, left_margin=0, date_format='%Y %b %d')-
Expand source code
def format_as_single_line_abuse(self, left_margin=0, date_format='%Y %b %d'): return '%s%s: %s (%s)' % ( ' ' * left_margin, self._payload['substance'], self.use_type_string, self._payload['last_checked_when'].strftime('%b %Y') ) def format_for_failsafe_output(self, max_width: int = 80) ‑> list[str]-
Expand source code
def format_for_failsafe_output(self, max_width:int=80) -> list[str]: lines = [_('Substance: %s %s') % ( self['substance'], self.formatted_units )] if self['schedule']: lines.append(' ' + _('Regimen: %s') % self['schedule']) lines.append(' ' + _('Timerange: %s') % self.medically_formatted_timerange) if self['notes4patient']: lines.append(gmTools.wrap ( _('Patient notes: %s') % self['notes4patient'], width = max_width, initial_indent = ' ', subsequent_indent = ' ' )) if self['intake_instructions']: lines.append(gmTools.wrap ( _('Instructions: %s') % self['intake_instructions'], width = max_width, initial_indent = ' ', subsequent_indent = ' ' )) if self['notes4provider']: lines.append(gmTools.wrap ( _('Provider notes: %s') % self['notes4provider'], width = max_width, initial_indent = ' ', subsequent_indent = ' ' )) lines.append(' ' + _('Episode: %s%s') % ( self['episode'], gmTools.coalesce(self['health_issue'], '', ' (%s: %%s)' % _('Issue')) )) return lines def format_maximum_information(self, allergy=None, left_margin=0, date_format='%Y %b %d')-
Expand source code
def format_maximum_information(self, allergy=None, left_margin=0, date_format='%Y %b %d'): return self.format ( single_line = False, left_margin = left_margin, date_format = date_format, allergy = allergy, include_metadata = True, include_instructions = True, include_loincs = True, eol = None ) def get_regimens_for_substance(self, ongoing_only: bool = False) ‑> list-
Expand source code
def get_regimens_for_substance(self, ongoing_only:bool=False) -> list: return get_intake_regimens ( pk_substance = self._payload['pk_substance'], pk_patient = self._payload['pk_patient'], ongoing_only = ongoing_only ) def turn_into_allergy(self, encounter_id=None, allergy_type='allergy')-
Expand source code
def turn_into_allergy(self, encounter_id=None, allergy_type='allergy'): return self.intake.turn_into_allergy ( encounter_id = encounter_id, allergy_type = allergy_type )
Inherited members
class cProductOrSubstanceMatchProvider (queries=None, context=None)-
Expand source code
class cProductOrSubstanceMatchProvider(gmMatchProvider.cMatchProvider_SQL2): # by product name _query_drug_product_by_name = """ SELECT ARRAY[1, pk]::INTEGER[] AS data, (description || ' (' || preparation || ')' || coalesce(' [' || atc_code || ']', '')) AS list_label, (description || ' (' || preparation || ')' || coalesce(' [' || atc_code || ']', '')) AS field_label, 1 AS rank FROM ref.drug_product WHERE description %(fragment_condition)s LIMIT 50 """ _query_drug_product_by_name_and_strength = """ SELECT ARRAY[1, pk_drug_product]::INTEGER[] AS data, (product || ' (' || preparation || ' %s ' || amount || unit || coalesce('/' || dose_unit, '') || ' ' || substance || ')' || coalesce(' [' || atc_drug || ']', '')) AS list_label, (product || ' (' || preparation || ' %s ' || amount || unit || coalesce('/' || dose_unit, '') || ' ' || substance || ')' || coalesce(' [' || atc_drug || ']', '')) AS field_label, 1 AS rank FROM (SELECT *, product AS description FROM ref.v_drug_components) AS _components WHERE %%(fragment_condition)s LIMIT 50 """ % ( _('w/'), _('w/') ) # by component # _query_component_by_name = u""" # SELECT # ARRAY[3, r_vdc1.pk_component]::INTEGER[] # AS data, # (r_vdc1.substance || ' ' || r_vdc1.amount || r_vdc1.unit || ' ' || r_vdc1.preparation || ' (' # || r_vdc1.product || ' [' # || ( # SELECT array_to_string(array_agg(r_vdc2.amount), ' / ') # FROM ref.v_drug_components r_vdc2 # WHERE r_vdc2.pk_drug_product = r_vdc1.pk_drug_product # ) # || ']' # || ')' # ) AS field_label, # (r_vdc1.substance || ' ' || r_vdc1.amount || r_vdc1.unit || ' ' || r_vdc1.preparation || ' (' # || r_vdc1.product || ' [' # || ( # SELECT array_to_string(array_agg(r_vdc2.amount), ' / ') # FROM ref.v_drug_components r_vdc2 # WHERE r_vdc2.pk_drug_product = r_vdc1.pk_drug_product # ) # || ']' # || ')' # ) AS list_label, # 1 AS rank # FROM # (SELECT *, product AS description FROM ref.v_drug_components) AS r_vdc1 # WHERE # r_vdc1.substance %(fragment_condition)s # LIMIT 50""" # _query_component_by_name_and_strength = u""" # SELECT # ARRAY[3, r_vdc1.pk_component]::INTEGER[] # AS data, # (r_vdc1.substance || ' ' || r_vdc1.amount || r_vdc1.unit || ' ' || r_vdc1.preparation || ' (' # || r_vdc1.product || ' [' # || ( # SELECT array_to_string(array_agg(r_vdc2.amount), ' / ') # FROM ref.v_drug_components r_vdc2 # WHERE r_vdc2.pk_drug_product = r_vdc1.pk_drug_product # ) # || ']' # || ')' # ) AS field_label, # (r_vdc1.substance || ' ' || r_vdc1.amount || r_vdc1.unit || ' ' || r_vdc1.preparation || ' (' # || r_vdc1.product || ' [' # || ( # SELECT array_to_string(array_agg(r_vdc2.amount), ' / ') # FROM ref.v_drug_components r_vdc2 # WHERE r_vdc2.pk_drug_product = r_vdc1.pk_drug_product # ) # || ']' # || ')' # ) AS list_label, # 1 AS rank # FROM (SELECT *, substance AS description FROM ref.v_drug_components) AS r_vdc1 # WHERE # %(fragment_condition)s # ORDER BY list_label # LIMIT 50""" # by substance name in doses _query_substance_by_name = """ SELECT data, field_label, list_label, rank FROM (( -- first: substance intakes which match, because we tend to reuse them often SELECT ARRAY[2, pk_substance]::INTEGER[] AS data, (description || ' ' || amount || unit || coalesce('/' || dose_unit, '')) AS field_label, (description || ' ' || amount || unit || coalesce('/' || dose_unit, '') || ' (%s)') AS list_label, 1 AS rank FROM ( SELECT DISTINCT ON (description, amount, unit, dose_unit) pk_substance, substance AS description, amount, unit, dose_unit FROM clin.v_intakes ) AS normalized_intakes WHERE description %%(fragment_condition)s ) UNION ALL ( xxxxxxxxxxxxxxxxxxxxxxxxxxxx -- second: consumable substances which match but are not intakes SELECT ARRAY[2, pk]::INTEGER[] AS data, (description || ' ' || amount || ' ' || unit) AS field_label, (description || ' ' || amount || ' ' || unit) AS list_label, 2 AS rank FROM ref.consumable_substance WHERE description %%(fragment_condition)s AND pk NOT IN ( SELECT fk_substance FROM clin.substance_intake WHERE fk_substance IS NOT NULL ) )) AS candidates --ORDER BY rank, list_label LIMIT 50""" % _('in use') _query_substance_by_name_and_strength = """ SELECT data, field_label, list_label, rank FROM (( SELECT ARRAY[2, pk_substance]::INTEGER[] AS data, (description || ' ' || amount || ' ' || unit) AS field_label, (description || ' ' || amount || ' ' || unit || ' (%s)') AS list_label, 1 AS rank FROM ( SELECT DISTINCT ON (description, amount, unit) pk_substance, substance AS description, amount, unit FROM clin.v_nonbraXXXnd_intakes ) AS normalized_intakes WHERE %%(fragment_condition)s ) UNION ALL ( -- matching substances which are not in intakes SELECT ARRAY[2, pk]::INTEGER[] AS data, (description || ' ' || amount || ' ' || unit) AS field_label, (description || ' ' || amount || ' ' || unit) AS list_label, 2 AS rank FROM ref.consumable_substance WHERE %%(fragment_condition)s AND pk NOT IN ( SELECT fk_substance FROM clin.substance_intake WHERE fk_substance IS NOT NULL ) )) AS candidates --ORDER BY rank, list_label LIMIT 50""" % _('in use') _pattern = regex.compile(r'^\D+\s*\d+$', regex.UNICODE) _master_query = """ SELECT data, field_label, list_label, rank FROM ((%s) UNION (%s) UNION (%s)) AS _union ORDER BY rank, list_label LIMIT 50 """ #-------------------------------------------------------- def getMatchesByPhrase(self, aFragment): """Return matches for aFragment at start of phrases.""" if cProductOrSubstanceMatchProvider._pattern.match(aFragment): self._queries = [ cProductOrSubstanceMatchProvider._master_query % ( cProductOrSubstanceMatchProvider._query_drug_product_by_name_and_strength, cProductOrSubstanceMatchProvider._query_substance_by_name_and_strength, cProductOrSubstanceMatchProvider._query_component_by_name_and_strength ) ] #self._queries = [cProductOrSubstanceMatchProvider._query_substance_by_name_and_strength] fragment_condition = """description ILIKE %(desc)s AND amount::text ILIKE %(amount)s""" self._args['desc'] = '%s%%' % regex.sub(r'\s*\d+$', '', aFragment) self._args['amount'] = '%s%%' % regex.sub(r'^\D+\s*', '', aFragment) else: self._queries = [ cProductOrSubstanceMatchProvider._master_query % ( cProductOrSubstanceMatchProvider._query_drug_product_by_name, cProductOrSubstanceMatchProvider._query_substance_by_name, cProductOrSubstanceMatchProvider._query_component_by_name ) ] #self._queries = [cProductOrSubstanceMatchProvider._query_substance_by_name] fragment_condition = "ILIKE %(fragment)s" self._args['fragment'] = "%s%%" % aFragment return self._find_matches(fragment_condition) #-------------------------------------------------------- def getMatchesByWord(self, aFragment): """Return matches for aFragment at start of words inside phrases.""" if cProductOrSubstanceMatchProvider._pattern.match(aFragment): self._queries = [ cProductOrSubstanceMatchProvider._master_query % ( cProductOrSubstanceMatchProvider._query_drug_product_by_name_and_strength, cProductOrSubstanceMatchProvider._query_substance_by_name_and_strength, cProductOrSubstanceMatchProvider._query_component_by_name_and_strength ) ] #self._queries = [cProductOrSubstanceMatchProvider._query_substance_by_name_and_strength] desc = regex.sub(r'\s*\d+$', '', aFragment) desc = gmPG2.sanitize_pg_regex(expression = desc, escape_all = False) fragment_condition = """description ~* %(desc)s AND amount::text ILIKE %(amount)s""" self._args['desc'] = "( %s)|(^%s)" % (desc, desc) self._args['amount'] = '%s%%' % regex.sub(r'^\D+\s*', '', aFragment) else: self._queries = [ cProductOrSubstanceMatchProvider._master_query % ( cProductOrSubstanceMatchProvider._query_drug_product_by_name, cProductOrSubstanceMatchProvider._query_substance_by_name, cProductOrSubstanceMatchProvider._query_component_by_name ) ] #self._queries = [cProductOrSubstanceMatchProvider._query_substance_by_name] fragment_condition = "~* %(fragment)s" aFragment = gmPG2.sanitize_pg_regex(expression = aFragment, escape_all = False) self._args['fragment'] = "( %s)|(^%s)" % (aFragment, aFragment) return self._find_matches(fragment_condition) #-------------------------------------------------------- def getMatchesBySubstr(self, aFragment): """Return matches for aFragment as a true substring.""" if cProductOrSubstanceMatchProvider._pattern.match(aFragment): self._queries = [ cProductOrSubstanceMatchProvider._master_query % ( cProductOrSubstanceMatchProvider._query_drug_product_by_name_and_strength, cProductOrSubstanceMatchProvider._query_substance_by_name_and_strength, cProductOrSubstanceMatchProvider._query_component_by_name_and_strength ) ] #self._queries = [cProductOrSubstanceMatchProvider._query_substance_by_name_and_strength] fragment_condition = """description ILIKE %(desc)s AND amount::text ILIKE %(amount)s""" self._args['desc'] = '%%%s%%' % regex.sub(r'\s*\d+$', '', aFragment) self._args['amount'] = '%s%%' % regex.sub(r'^\D+\s*', '', aFragment) else: self._queries = [ cProductOrSubstanceMatchProvider._master_query % ( cProductOrSubstanceMatchProvider._query_drug_product_by_name, cProductOrSubstanceMatchProvider._query_substance_by_name, cProductOrSubstanceMatchProvider._query_component_by_name ) ] #self._queries = [cProductOrSubstanceMatchProvider._query_substance_by_name] fragment_condition = "ILIKE %(fragment)s" self._args['fragment'] = "%%%s%%" % aFragment return self._find_matches(fragment_condition)Match provider which searches matches in possibly several database tables.
queries: - a list of unicode strings - each string is a query - each string must contain: "… WHERE
%(fragment_condition)s …" - each string can contain in the where clause: "… %( )s …" - each query must return (data, list_label, field_label) context definitions to be used in the queries, example: {'ctxt_key1': {'where_part': 'AND country = %(country)s', 'placeholder': 'country'}}
client code using .set_context() must use the 'placeholder':
/ .set_context('country', 'Germany') full example query:
query = u" " " SELECT DISTINCT ON (list_label) pk_encounter AS data, to_char(started, 'YYYY Mon DD (HH24:MI)') || ': ' || l10n_type || ' [#' || pk_encounter || ']' AS list_label, to_char(started, 'YYYY Mon DD') || ': ' || l10n_type AS field_label FROM clin.v_pat_encounters WHERE ( l10n_type %(fragment_condition)s OR type %(fragment_condition)s ) %(ctxt_patient)s ORDER BY list_label LIMIT 30 " " " context = {'ctxt_patient': { 'where_part': u'AND pk_patient = %(PLACEHOLDER)s', 'placeholder': u'PLACEHOLDER' }} self.mp = gmMatchProvider.cMatchProvider_SQL2(queries = query, context = context) self.set_context(context = 'PLACEHOLDER', val = '<THE VALUE>')_SQL_data2match: SQL to retrieve a match by, say, primary key wherein the only keyword argument is 'pk'
Ancestors
Inherited members
class cSubstance (aPK_obj: int | dict = None, row: dict = None, link_obj=None)-
Expand source code
class cSubstance(gmBusinessDBObject.cBusinessDBObject): _cmd_fetch_payload = _SQL_get_substance % "pk_substance = %s" _cmds_store_payload = [ """UPDATE ref.substance SET description = %(substance)s, atc = gm.nullify_empty_string(%(atc)s), intake_instructions = gm.nullify_empty_string(%(intake_instructions)s) WHERE pk = %(pk_substance)s AND xmin = %(xmin_substance)s RETURNING xmin AS xmin_substance """ ] _updatable_fields = [ 'substance', 'atc', 'intake_instructions' ] #-------------------------------------------------------- def format(self, left_margin=0): if len(self._payload['loincs']) == 0: loincs = '' else: loincs = """ %s %s %s %s""" % ( (' ' * left_margin), _('LOINCs to monitor:'), (' ' * left_margin), ('\n' + (' ' * (left_margin + 1))).join ([ '%s%s%s' % ( l['loinc'], gmTools.coalesce(l['max_age_str'], '', ': ' + _('once within %s')), gmTools.coalesce(l['comment'], '', ' (%s)') ) for l in self._payload['loincs'] ]) ) return (' ' * left_margin) + '%s: %s%s%s%s' % ( _('Substance'), self._payload['substance'], gmTools.coalesce(self._payload['atc'], '', ' [%s]'), gmTools.coalesce(self._payload['intake_instructions'], '', _('\n Instructions: %s')), loincs ) #-------------------------------------------------------- def save_payload(self, conn=None): success, data = super().save_payload(conn = conn) if not success: return (success, data) if self._payload['atc'] is not None: atc = self._payload['atc'].strip() if atc != '': gmATC.propagate_atc ( substance = self._payload['substance'].strip(), atc = atc ) return (success, data) #-------------------------------------------------------- def exists_as_intake(self, pk_patient=None): return substance_intake_exists ( pk_substance = self.pk_obj, pk_identity = pk_patient ) #-------------------------------------------------------- def get_regimens(self, pk_patient:int=None, ongoing_only:bool=False, order_by:str=None) -> list: assert pk_patient is not None, '<pk_patient> must be given' return get_intake_regimens ( order_by = order_by, pk_patient = pk_patient, ongoing_only = ongoing_only ) #-------------------------------------------------------- # properties #-------------------------------------------------------- def _set_loincs(self, loincs): args = {'pk_subst': self.pk_obj, 'loincs': loincs} # insert new entries for loinc in loincs: cmd = """INSERT INTO ref.lnk_loinc2substance (fk_substance, loinc) SELECT %(pk_subst)s, %(loinc)s WHERE NOT EXISTS ( SELECT 1 from ref.lnk_loinc2substance WHERE fk_substance = %(pk_subst)s AND loinc = %(loinc)s )""" args['loinc'] = loinc gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}]) # delete old entries cmd = 'DELETE FROM ref.lnk_loinc2substance WHERE fk_substance = %(pk_subst)s AND loinc <> ALL(%(loincs)s)' gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}]) loincs = property(lambda x:x, _set_loincs) #-------------------------------------------------------- def _get_is_in_use_by_patients(self): cmd = """ SELECT EXISTS ( SELECT 1 FROM clin.v_intakes WHERE pk_substance = %(pk)s LIMIT 1 )""" args = {'pk': self.pk_obj} rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) return rows[0][0] is_in_use_by_patients = property(_get_is_in_use_by_patients) #-------------------------------------------------------- def _get_is_drug_component(self): cmd = """ SELECT EXISTS ( SELECT 1 FROM ref.v_drug_components WHERE pk_substance = %(pk)s LIMIT 1 )""" args = {'pk': self.pk_obj} rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) return rows[0][0] is_drug_component = property(_get_is_drug_component)Represents business objects in the database.
Rules
- instances ARE ASSUMED TO EXIST in the database
- PK construction (aPK_obj): DOES verify its existence on instantiation (fetching data fails)
- Row construction (row): allowed by using a dict of pairs of field name: field value (PERFORMANCE improvement)
- does NOT verify FK target existence
- does NOT create new entries in the database
- does NOT lazy-fetch fields on access
Class scope SQL commands and variables:
_cmd_fetch_payload:
- must return exactly one row
- WHERE clause argument values are expected in self.pk_obj (taken from init(aPK_obj))
- must return xmin of all rows that _cmds_store_payload will be updating, so views must support the xmin columns of their underlying tables
_cmds_store_payload:
- one or multiple "update … set … where xmin_ = … and pk = …" statements which actually update the database from the data in self._payload,
- the last query must refetch at least the XMIN values needed to detect concurrent updates, their field names had better be the same as in _cmd_fetch_payload,
- the last query CAN return other fields which is particularly useful when those other fields are computed in the backend and may thus change upon save but will not have been set by the client code explicitly - this is only really of concern if the saved subclass is to be reused after saving rather than re-instantiated
- when subclasses tend to live a while after save_payload() was called and they support computed fields (say, _(some_column) you need to return all columns (see cEncounter)
_updatable_fields:
- a list of fields available for update via object['field']
Call init from child classes like so:
super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)Args
aPK_obj- retrieve data from backend
- an scalar value the ._cmd_fetch_payload WHERE condition must be a simple column: "… WHERE pk_col = %s"
- a dictionary of values the ._cmd_fetch_payload WHERE condition must consume the dictionary and produce a unique row
row- must hold the fields
- data: list of column values for the row selected by ._cmd_fetch_payload (as returned by cursor.fetchone() in the DB-API)
- pk_field: the name of the primary key column OR
- pk_obj: a dictionary suitable for being passed to cursor.execute and holding the primary key values, used for composite PKs
- for example:
row = { 'data': rows[0], 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) objects = [ cChildClass(row = {'data': r, 'pk_field': 'the PK column name'}) for r in rows ]
Ancestors
Instance variables
prop is_drug_component-
Expand source code
def _get_is_drug_component(self): cmd = """ SELECT EXISTS ( SELECT 1 FROM ref.v_drug_components WHERE pk_substance = %(pk)s LIMIT 1 )""" args = {'pk': self.pk_obj} rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) return rows[0][0] prop is_in_use_by_patients-
Expand source code
def _get_is_in_use_by_patients(self): cmd = """ SELECT EXISTS ( SELECT 1 FROM clin.v_intakes WHERE pk_substance = %(pk)s LIMIT 1 )""" args = {'pk': self.pk_obj} rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) return rows[0][0] prop loincs-
Expand source code
loincs = property(lambda x:x, _set_loincs)
Methods
def exists_as_intake(self, pk_patient=None)-
Expand source code
def exists_as_intake(self, pk_patient=None): return substance_intake_exists ( pk_substance = self.pk_obj, pk_identity = pk_patient ) def get_regimens(self, pk_patient: int = None, ongoing_only: bool = False, order_by: str = None) ‑> list-
Expand source code
def get_regimens(self, pk_patient:int=None, ongoing_only:bool=False, order_by:str=None) -> list: assert pk_patient is not None, '<pk_patient> must be given' return get_intake_regimens ( order_by = order_by, pk_patient = pk_patient, ongoing_only = ongoing_only )
Inherited members
class cSubstanceDose (aPK_obj: int | dict = None, row: dict = None, link_obj=None)-
Expand source code
class cSubstanceDose(gmBusinessDBObject.cBusinessDBObject): _cmd_fetch_payload = _SQL_get_substance_dose % "pk_dose = %s" _cmds_store_payload = [ """UPDATE ref.dose SET amount = %(amount)s, unit = %(unit)s, dose_unit = gm.nullify_empty_string(%(dose_unit)s) WHERE pk = %(pk_dose)s AND xmin = %(xmin_dose)s RETURNING xmin as xmin_dose, pk as pk_dose """ ] _updatable_fields = [ 'amount', 'unit', 'dose_unit' ] #-------------------------------------------------------- def format(self, left_margin=0, include_loincs=False): loincs = '' if include_loincs and (len(self._payload['loincs']) > 0): loincs = """ %s %s %s %s""" % ( (' ' * left_margin), _('LOINCs to monitor:'), (' ' * left_margin), ('\n' + (' ' * (left_margin + 1))).join ([ '%s%s%s' % ( l['loinc'], gmTools.coalesce(l['max_age_str'], '', ': ' + _('once within %s')), gmTools.coalesce(l['comment'], '', ' (%s)') ) for l in self._payload['loincs'] ]) ) return (' ' * left_margin) + '%s: %s %s%s%s%s%s' % ( _('Substance dose'), self._payload['substance'], self._payload['amount'], self.formatted_units, gmTools.coalesce(self._payload['atc_substance'], '', ' [%s]'), gmTools.coalesce(self._payload['intake_instructions'], '', '\n' + (' ' * left_margin) + ' ' + _('Instructions: %s')), loincs ) #-------------------------------------------------------- def exists_as_intake(self, pk_patient=None): return substance_intake_exists ( pk_substance = -1, # FIXME pk_identity = pk_patient ) #-------------------------------------------------------- # properties #-------------------------------------------------------- def _get_is_in_use_by_patients(self): cmd = """ SELECT EXISTS ( SELECT 1 FROM clin.v_intakes WHERE pk_dose = %(pk)s LIMIT 1 )""" args = {'pk': self.pk_obj} rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) return rows[0][0] is_in_use_by_patients = property(_get_is_in_use_by_patients) #-------------------------------------------------------- def _get_is_drug_component(self): cmd = """ SELECT EXISTS ( SELECT 1 FROM ref.v_drug_components WHERE pk_dose = %(pk)s LIMIT 1 )""" args = {'pk': self.pk_obj} rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) return rows[0][0] is_drug_component = property(_get_is_drug_component) #-------------------------------------------------------- def _get_formatted_units(self, short=True): return format_units ( self._payload['unit'], gmTools.coalesce(self._payload['dose_unit'], _('delivery unit')), short = short, none_str = '' ) formatted_units = property(_get_formatted_units) #-------------------------------------------------------- def _get_as_substance(self): return cSubstance(aPK_obj = self._payload['pk_substance']) as_substance = property(_get_as_substance)Represents business objects in the database.
Rules
- instances ARE ASSUMED TO EXIST in the database
- PK construction (aPK_obj): DOES verify its existence on instantiation (fetching data fails)
- Row construction (row): allowed by using a dict of pairs of field name: field value (PERFORMANCE improvement)
- does NOT verify FK target existence
- does NOT create new entries in the database
- does NOT lazy-fetch fields on access
Class scope SQL commands and variables:
_cmd_fetch_payload:
- must return exactly one row
- WHERE clause argument values are expected in self.pk_obj (taken from init(aPK_obj))
- must return xmin of all rows that _cmds_store_payload will be updating, so views must support the xmin columns of their underlying tables
_cmds_store_payload:
- one or multiple "update … set … where xmin_ = … and pk = …" statements which actually update the database from the data in self._payload,
- the last query must refetch at least the XMIN values needed to detect concurrent updates, their field names had better be the same as in _cmd_fetch_payload,
- the last query CAN return other fields which is particularly useful when those other fields are computed in the backend and may thus change upon save but will not have been set by the client code explicitly - this is only really of concern if the saved subclass is to be reused after saving rather than re-instantiated
- when subclasses tend to live a while after save_payload() was called and they support computed fields (say, _(some_column) you need to return all columns (see cEncounter)
_updatable_fields:
- a list of fields available for update via object['field']
Call init from child classes like so:
super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)Args
aPK_obj- retrieve data from backend
- an scalar value the ._cmd_fetch_payload WHERE condition must be a simple column: "… WHERE pk_col = %s"
- a dictionary of values the ._cmd_fetch_payload WHERE condition must consume the dictionary and produce a unique row
row- must hold the fields
- data: list of column values for the row selected by ._cmd_fetch_payload (as returned by cursor.fetchone() in the DB-API)
- pk_field: the name of the primary key column OR
- pk_obj: a dictionary suitable for being passed to cursor.execute and holding the primary key values, used for composite PKs
- for example:
row = { 'data': rows[0], 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) objects = [ cChildClass(row = {'data': r, 'pk_field': 'the PK column name'}) for r in rows ]
Ancestors
Instance variables
prop as_substance-
Expand source code
def _get_as_substance(self): return cSubstance(aPK_obj = self._payload['pk_substance']) prop formatted_units-
Expand source code
def _get_formatted_units(self, short=True): return format_units ( self._payload['unit'], gmTools.coalesce(self._payload['dose_unit'], _('delivery unit')), short = short, none_str = '' ) prop is_drug_component-
Expand source code
def _get_is_drug_component(self): cmd = """ SELECT EXISTS ( SELECT 1 FROM ref.v_drug_components WHERE pk_dose = %(pk)s LIMIT 1 )""" args = {'pk': self.pk_obj} rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) return rows[0][0] prop is_in_use_by_patients-
Expand source code
def _get_is_in_use_by_patients(self): cmd = """ SELECT EXISTS ( SELECT 1 FROM clin.v_intakes WHERE pk_dose = %(pk)s LIMIT 1 )""" args = {'pk': self.pk_obj} rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) return rows[0][0]
Methods
def exists_as_intake(self, pk_patient=None)-
Expand source code
def exists_as_intake(self, pk_patient=None): return substance_intake_exists ( pk_substance = -1, # FIXME pk_identity = pk_patient )
Inherited members
class cSubstanceDoseMatchProvider (queries=None, context=None)-
Expand source code
class cSubstanceDoseMatchProvider(gmMatchProvider.cMatchProvider_SQL2): _pattern = regex.compile(r'^\D+\s*\d+$', regex.UNICODE) # match candidates are subjected to .strip() # the "substance query" is run when the search fragment # does NOT match the regex ._pattern (which is: "chars SPACE digits") # IOW, when a name-only fragment has been entered _substance_query = """-- substance dose match provider: search by substance only SELECT ARRAY[comb.pk_substance, comb.pk_dose]::INTEGER[] AS data, comb.substance -- || coalesce(' (' || comb.amount || ' ' || comb.unit || coalesce(' / ' || comb.dose_unit, '') || ')', '') AS field_label, comb.substance || coalesce(' ' || comb.amount || ' ' || comb.unit || coalesce(' / ' || comb.dose_unit, ''), '') AS list_label FROM (( SELECT -- plain substances w/o any doses available pk AS pk_substance, NULL AS pk_dose, description AS substance, NULL AS amount, NULL AS unit, NULL AS dose_unit FROM ref.substance ) UNION ALL ( SELECT -- substance doses pk_substance, pk_dose, substance, amount, unit, dose_unit FROM ref.v_substance_doses )) AS comb WHERE %(fragment_condition)s ORDER BY list_label LIMIT 50""" # the "dose query" is run when the search fragment # DOES match the regex ._pattern (which is: "chars SPACE digits") # which may make it a substance dose _dose_query = """-- substance dose match provider: search by substance and strength SELECT ARRAY[r_vsd.pk_substance, r_vsd.pk_dose]::INTEGER[] AS data, r_vsd.substance -- || ' (' || r_vsd.amount || ' ' || r_vsd.unit || coalesce(' / ' || r_vsd.dose_unit, '') || ')' AS field_label, r_vsd.substance || ' ' || r_vsd.amount || ' ' || r_vsd.unit || coalesce(' / ' || r_vsd.dose_unit, '') AS list_label FROM ref.v_substance_doses r_vsd WHERE %(fragment_condition)s ORDER BY list_label LIMIT 50""" #-------------------------------------------------------- def __init__(self, queries = None, context = None): super().__init__() #self._SQL_data2match = cSubstanceDoseMatchProvider._dose_query % {'fragment_condition': 'pk_dose = %(pk)s'} #-------------------------------------------------------- def getMatchesByPhrase(self, search_term): """Return matches for search_term at start of phrases.""" if cSubstanceDoseMatchProvider._pattern.match(search_term): self._queries = [cSubstanceDoseMatchProvider._dose_query] search_condition = """r_vsd.substance ILIKE %(subst)s AND r_vsd.amount::text ILIKE %(amount)s""" self._args['subst'] = '%s%%' % regex.sub(r'\s*\d+$', '', search_term) self._args['amount'] = '%s%%' % regex.sub(r'^\D+\s*', '', search_term) else: self._queries = [cSubstanceDoseMatchProvider._substance_query] search_condition = "comb.substance ILIKE %(fragment)s" self._args['fragment'] = "%s%%" % search_term return self._find_matches(search_condition) #-------------------------------------------------------- def getMatchesByWord(self, search_term): """Return matches for search_term at start of words inside phrases.""" if cSubstanceDoseMatchProvider._pattern.match(search_term): self._queries = [cSubstanceDoseMatchProvider._dose_query] subst = regex.sub(r'\s*\d+$', '', search_term) subst = gmPG2.sanitize_pg_regex(expression = subst, escape_all = False) search_condition = """r_vsd.substance ~* %(subst)s AND r_vsd.amount::text ILIKE %(amount)s""" self._args['subst'] = '\m%s' % subst self._args['amount'] = '%s%%' % regex.sub(r'^\D+\s*', '', search_term) else: self._queries = [cSubstanceDoseMatchProvider._substance_query] search_condition = "comb.substance ~* %(fragment)s" search_term = gmPG2.sanitize_pg_regex(expression = search_term, escape_all = False) self._args['fragment'] = r'\m%s' % search_term return self._find_matches(search_condition) #-------------------------------------------------------- def getMatchesBySubstr(self, search_term): """Return matches for search_term as a true substring.""" if cSubstanceDoseMatchProvider._pattern.match(search_term): self._queries = [cSubstanceDoseMatchProvider._dose_query] search_condition = """substance ILIKE %(subst)s AND amount::text ILIKE %(amount)s""" self._args['subst'] = '%%%s%%' % regex.sub(r'\s*\d+$', '', search_term) self._args['amount'] = '%s%%' % regex.sub(r'^\D+\s*', '', search_term) else: self._queries = [cSubstanceDoseMatchProvider._substance_query] search_condition = "comb.substance ILIKE %(fragment)s" self._args['fragment'] = "%%%s%%" % search_term return self._find_matches(search_condition)Match provider which searches matches in possibly several database tables.
queries: - a list of unicode strings - each string is a query - each string must contain: "… WHERE
%(fragment_condition)s …" - each string can contain in the where clause: "… %( )s …" - each query must return (data, list_label, field_label) context definitions to be used in the queries, example: {'ctxt_key1': {'where_part': 'AND country = %(country)s', 'placeholder': 'country'}}
client code using .set_context() must use the 'placeholder':
/ .set_context('country', 'Germany') full example query:
query = u" " " SELECT DISTINCT ON (list_label) pk_encounter AS data, to_char(started, 'YYYY Mon DD (HH24:MI)') || ': ' || l10n_type || ' [#' || pk_encounter || ']' AS list_label, to_char(started, 'YYYY Mon DD') || ': ' || l10n_type AS field_label FROM clin.v_pat_encounters WHERE ( l10n_type %(fragment_condition)s OR type %(fragment_condition)s ) %(ctxt_patient)s ORDER BY list_label LIMIT 30 " " " context = {'ctxt_patient': { 'where_part': u'AND pk_patient = %(PLACEHOLDER)s', 'placeholder': u'PLACEHOLDER' }} self.mp = gmMatchProvider.cMatchProvider_SQL2(queries = query, context = context) self.set_context(context = 'PLACEHOLDER', val = '<THE VALUE>')_SQL_data2match: SQL to retrieve a match by, say, primary key wherein the only keyword argument is 'pk'
Ancestors
Methods
def getMatchesByPhrase(self, search_term)-
Expand source code
def getMatchesByPhrase(self, search_term): """Return matches for search_term at start of phrases.""" if cSubstanceDoseMatchProvider._pattern.match(search_term): self._queries = [cSubstanceDoseMatchProvider._dose_query] search_condition = """r_vsd.substance ILIKE %(subst)s AND r_vsd.amount::text ILIKE %(amount)s""" self._args['subst'] = '%s%%' % regex.sub(r'\s*\d+$', '', search_term) self._args['amount'] = '%s%%' % regex.sub(r'^\D+\s*', '', search_term) else: self._queries = [cSubstanceDoseMatchProvider._substance_query] search_condition = "comb.substance ILIKE %(fragment)s" self._args['fragment'] = "%s%%" % search_term return self._find_matches(search_condition)Return matches for search_term at start of phrases.
def getMatchesBySubstr(self, search_term)-
Expand source code
def getMatchesBySubstr(self, search_term): """Return matches for search_term as a true substring.""" if cSubstanceDoseMatchProvider._pattern.match(search_term): self._queries = [cSubstanceDoseMatchProvider._dose_query] search_condition = """substance ILIKE %(subst)s AND amount::text ILIKE %(amount)s""" self._args['subst'] = '%%%s%%' % regex.sub(r'\s*\d+$', '', search_term) self._args['amount'] = '%s%%' % regex.sub(r'^\D+\s*', '', search_term) else: self._queries = [cSubstanceDoseMatchProvider._substance_query] search_condition = "comb.substance ILIKE %(fragment)s" self._args['fragment'] = "%%%s%%" % search_term return self._find_matches(search_condition)Return matches for search_term as a true substring.
def getMatchesByWord(self, search_term)-
Expand source code
def getMatchesByWord(self, search_term): """Return matches for search_term at start of words inside phrases.""" if cSubstanceDoseMatchProvider._pattern.match(search_term): self._queries = [cSubstanceDoseMatchProvider._dose_query] subst = regex.sub(r'\s*\d+$', '', search_term) subst = gmPG2.sanitize_pg_regex(expression = subst, escape_all = False) search_condition = """r_vsd.substance ~* %(subst)s AND r_vsd.amount::text ILIKE %(amount)s""" self._args['subst'] = '\m%s' % subst self._args['amount'] = '%s%%' % regex.sub(r'^\D+\s*', '', search_term) else: self._queries = [cSubstanceDoseMatchProvider._substance_query] search_condition = "comb.substance ~* %(fragment)s" search_term = gmPG2.sanitize_pg_regex(expression = search_term, escape_all = False) self._args['fragment'] = r'\m%s' % search_term return self._find_matches(search_condition)Return matches for search_term at start of words inside phrases.
Inherited members
class cSubstanceIntakeEntry (aPK_obj: int | dict = None, row: dict = None, link_obj=None)-
Expand source code
class cSubstanceIntakeEntry(gmBusinessDBObject.cBusinessDBObject): """Represents a substance having been/being taken by a patient.""" _cmd_fetch_payload = _SQL_get_substance_intake % 'pk_intake = %s' _cmds_store_payload = [ """UPDATE clin.intake SET clin_when = %(last_checked_when)s, notes4patient = gm.nullify_empty_string(%(notes4patient)s), narrative = gm.nullify_empty_string(%(notes4provider)s), use_type = %(use_type)s, fk_episode = %(pk_episode)s, fk_encounter = %(pk_encounter)s WHERE pk = %(pk_intake)s AND xmin = %(xmin_intake)s RETURNING xmin as xmin_intake """ ] _updatable_fields = [ 'last_checked_when', 'notes4patient', 'notes4provider', 'notes4us', 'use_type', 'pk_episode', 'pk_encounter' ] #-------------------------------------------------------- def format_maximum_information(self, patient=None): return self.format ( single_line = False, show_all_product_components = True, include_metadata = True, date_format = '%Y %b %d', include_instructions = True, include_loincs = True ).split('\n') #-------------------------------------------------------- def format(self, left_margin=0, date_format='%Y %b %d', single_line=True, allergy=None, show_all_product_components=False, include_metadata=True, include_instructions=False, include_loincs=False, eol='\n'): # medication if self._payload['use_type'] is None: if single_line: return self.format_as_single_line(left_margin = left_margin, date_format = date_format) return self.format_as_multiple_lines ( left_margin = left_margin, date_format = date_format, allergy = allergy, show_all_product_components = show_all_product_components, include_instructions = include_instructions, eol = eol ) # abuse if single_line: return self.format_as_single_line_abuse(left_margin = left_margin, date_format = date_format) return self.format_as_multiple_lines_abuse(left_margin = left_margin, date_format = date_format, include_metadata = include_metadata, eol = eol) #-------------------------------------------------------- def format_as_single_line_abuse(self, left_margin=0, date_format='%Y %b %d'): return '%s%s: %s (%s)' % ( ' ' * left_margin, self._payload['substance'], self.use_type_string, self._payload['last_checked_when'].strftime('%b %Y') ) #-------------------------------------------------------- def format_as_single_line(self, left_margin=0, date_format='%Y %b %d'): return '%s: %s (%s)' % ( ' ' * left_margin, self._payload['substance'], self._payload['last_checked_when'].strftime(date_format) ) #-------------------------------------------------------- def format_as_multiple_lines_abuse(self, left_margin=0, date_format='%Y %b %d', include_metadata=True, eol='\n'): lines = [] if include_metadata: lines.append(_('Substance abuse entry [#%s]') % self._payload['pk_intake']) lines.append(' ' + _('Substance: %s [#%s]%s') % ( self._payload['substance'], self._payload['pk_substance'], gmTools.coalesce(self._payload['atc_substance'], '', ' ATC %s') )) lines.append(' ' + _('Use type: %s') % self.use_type_string) lines.append(' ' + _('Last checked: %s') % self._payload['last_checked_when'].strftime('%Y %b %d')) if self._payload['discontinued']: lines.append(_(' Discontinued %s') % self._payload['discontinued'].strftime(date_format)) if self._payload['notes4provider']: lines.append(_(' Notes: %s') % self._payload['notes4provider']) if include_metadata: lines.append('') lines.append(_('Revision: #%(row_ver)s, %(mod_when)s by %(mod_by)s.') % { 'row_ver': self._payload['row_version'], 'mod_when': self._payload['modified_when'].strftime('%Y %b %d %H:%M.%S'), 'mod_by': self._payload['modified_by'] }) if eol is None: return lines return eol.join(lines) #-------------------------------------------------------- def format_as_multiple_lines(self, left_margin:int=0, date_format:str='%Y %b %d', allergy=None, show_all_product_components:bool=False, include_instructions:bool=False, include_loincs:bool=False, eol='\n'):# -> list | str: lines = [] # header lines.append(_('Substance intake [#%s] ') % ( self._payload['pk_intake'] )) # caveat if allergy: certainty = gmTools.bool2subst(allergy['definite'], _('definite'), _('suspected')) lines.append('') lines.append(' !! ---- Cave ---- !!') lines.append(' %s (%s): %s (%s)' % ( allergy['l10n_type'], certainty, allergy['descriptor'], gmTools.coalesce(allergy['reaction'], '')[:40] )) lines.append('') # what lines.append(' ' + _('Substance: %s [#%s]') % (self._payload['substance'], self._payload['pk_substance'])) # codes if self._payload['atc_substance']: lines.append(_(' ATC (substance): %s') % self._payload['atc_substance']) if include_loincs and self._payload['loincs']: lines.append('%s %s' % (' ' * left_margin, _('LOINCs to monitor:'))) lines.extend(['%s%s%s%s' % ( ' ' * (left_margin + 1), l['loinc'], gmTools.coalesce(l['max_age_str'], '', ': ' + _('once within %s')), gmTools.coalesce(l['comment'], '', ' (%s)') ) for l in self._payload['loincs'] ]) lines.append('') lines.append('') lines.append(_(' Last checked %s') % self._payload['last_checked_when'].strftime(date_format)) lines.append('') # further notes lines.append(_(' Episode: %s')% self._payload['episode']) if self._payload['health_issue']: lines.append(_(' Health issue: %s') % self._payload['health_issue']) if self._payload['notes4provider']: lines.append(_(' Provider notes: %s') % self._payload['notes4provider']) if self._payload['notes4patient']: lines.append(_(' Patient advice: %s') % self._payload['notes4patient']) if self._payload['intake_instructions']: lines.append(' ' + _('Intake: %s') % self._payload['intake_instructions']) lines.append('') lines.append(_('Revision: #%(row_ver)s, %(mod_when)s by %(mod_by)s.') % { 'row_ver': self._payload['row_version'], 'mod_when': self._payload['modified_when'].strftime('%Y %b %d %H:%M.%S'), 'mod_by': self._payload['modified_by'] }) if eol is None: return lines return eol.join(lines) #-------------------------------------------------------- def turn_into_allergy(self, encounter_id=None, allergy_type='allergy'): allg = gmAllergy.create_allergy ( allergene = self._payload['substance'], allg_type = allergy_type, episode_id = self._payload['pk_episode'], encounter_id = encounter_id ) allg['substance'] = self._payload['substance'] allg['reaction'] = self._payload['discontinue_reason'] allg['atc_code'] = gmTools.coalesce(self._payload['atc_substance']) allg['generics'] = self._payload['substance'] allg.save() return allg #-------------------------------------------------------- def delete(self): return delete_substance_intake(pk_intake = self._payload['pk_intake']) #-------------------------------------------------------- # properties #-------------------------------------------------------- def __get_as_intake_with_regimen(self): regimens = self.regimens if len(regimens) > 1: # ambigous, cannot turn into intake with regimen return None if not regimens: pk_regimen = None else: pk_regimen = regimens[0]['pk_intake_regimen'] return cIntakeWithRegimen(aPK_obj = {'pk_intake': self['pk_intake'], 'pk_intake_regimen': pk_regimen}) as_intake_with_regimen = property(__get_as_intake_with_regimen) #-------------------------------------------------------- def _get_regimens(self, ongoing_only=False): return get_intake_regimens ( pk_intake = self._payload['pk_intake'], ongoing_only = ongoing_only ) regimens = property(_get_regimens) #-------------------------------------------------------- def _get_ongoing_regimens(self): return self._get_regimens(ongoing_only = True) ongoing_regimens = property(_get_ongoing_regimens) #-------------------------------------------------------- def _get_use_type_string(self): return use_type2str(self._payload['use_type']) use_type_string = property(_get_use_type_string) #-------------------------------------------------------- def _get_external_code(self): drug = self.containing_drug if drug is None: return None return drug.external_code external_code = property(_get_external_code) #-------------------------------------------------------- def _get_external_code_type(self): drug = self.containing_drug if drug is None: return None return drug.external_code_type external_code_type = property(_get_external_code_type) #-------------------------------------------------------- def _get_containing_drug(self): return None containing_drug = property(_get_containing_drug) #-------------------------------------------------------- def _get_as_amts_latex(self, strict=True): return format_substance_intake_as_amts_latex(intake = self, strict=strict) as_amts_latex = property(_get_as_amts_latex) #-------------------------------------------------------- def _get_as_amts_data(self, strict=True): return format_substance_intake_as_amts_data(intake = self, strict = strict) as_amts_data = property(_get_as_amts_data)Represents a substance having been/being taken by a patient.
Call init from child classes like so:
super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)Args
aPK_obj- retrieve data from backend
- an scalar value the ._cmd_fetch_payload WHERE condition must be a simple column: "… WHERE pk_col = %s"
- a dictionary of values the ._cmd_fetch_payload WHERE condition must consume the dictionary and produce a unique row
row- must hold the fields
- data: list of column values for the row selected by ._cmd_fetch_payload (as returned by cursor.fetchone() in the DB-API)
- pk_field: the name of the primary key column OR
- pk_obj: a dictionary suitable for being passed to cursor.execute and holding the primary key values, used for composite PKs
- for example:
row = { 'data': rows[0], 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}]) objects = [ cChildClass(row = {'data': r, 'pk_field': 'the PK column name'}) for r in rows ]
Ancestors
Instance variables
prop as_amts_data-
Expand source code
def _get_as_amts_data(self, strict=True): return format_substance_intake_as_amts_data(intake = self, strict = strict) prop as_amts_latex-
Expand source code
def _get_as_amts_latex(self, strict=True): return format_substance_intake_as_amts_latex(intake = self, strict=strict) prop as_intake_with_regimen-
Expand source code
def __get_as_intake_with_regimen(self): regimens = self.regimens if len(regimens) > 1: # ambigous, cannot turn into intake with regimen return None if not regimens: pk_regimen = None else: pk_regimen = regimens[0]['pk_intake_regimen'] return cIntakeWithRegimen(aPK_obj = {'pk_intake': self['pk_intake'], 'pk_intake_regimen': pk_regimen}) prop containing_drug-
Expand source code
def _get_containing_drug(self): return None prop external_code-
Expand source code
def _get_external_code(self): drug = self.containing_drug if drug is None: return None return drug.external_code prop external_code_type-
Expand source code
def _get_external_code_type(self): drug = self.containing_drug if drug is None: return None return drug.external_code_type prop ongoing_regimens-
Expand source code
def _get_ongoing_regimens(self): return self._get_regimens(ongoing_only = True) prop regimens-
Expand source code
def _get_regimens(self, ongoing_only=False): return get_intake_regimens ( pk_intake = self._payload['pk_intake'], ongoing_only = ongoing_only ) prop use_type_string-
Expand source code
def _get_use_type_string(self): return use_type2str(self._payload['use_type'])
Methods
def delete(self)-
Expand source code
def delete(self): return delete_substance_intake(pk_intake = self._payload['pk_intake']) def format_as_multiple_lines(self,
left_margin: int = 0,
date_format: str = '%Y %b %d',
allergy=None,
show_all_product_components: bool = False,
include_instructions: bool = False,
include_loincs: bool = False,
eol='\n')-
Expand source code
def format_as_multiple_lines(self, left_margin:int=0, date_format:str='%Y %b %d', allergy=None, show_all_product_components:bool=False, include_instructions:bool=False, include_loincs:bool=False, eol='\n'):# -> list | str: lines = [] # header lines.append(_('Substance intake [#%s] ') % ( self._payload['pk_intake'] )) # caveat if allergy: certainty = gmTools.bool2subst(allergy['definite'], _('definite'), _('suspected')) lines.append('') lines.append(' !! ---- Cave ---- !!') lines.append(' %s (%s): %s (%s)' % ( allergy['l10n_type'], certainty, allergy['descriptor'], gmTools.coalesce(allergy['reaction'], '')[:40] )) lines.append('') # what lines.append(' ' + _('Substance: %s [#%s]') % (self._payload['substance'], self._payload['pk_substance'])) # codes if self._payload['atc_substance']: lines.append(_(' ATC (substance): %s') % self._payload['atc_substance']) if include_loincs and self._payload['loincs']: lines.append('%s %s' % (' ' * left_margin, _('LOINCs to monitor:'))) lines.extend(['%s%s%s%s' % ( ' ' * (left_margin + 1), l['loinc'], gmTools.coalesce(l['max_age_str'], '', ': ' + _('once within %s')), gmTools.coalesce(l['comment'], '', ' (%s)') ) for l in self._payload['loincs'] ]) lines.append('') lines.append('') lines.append(_(' Last checked %s') % self._payload['last_checked_when'].strftime(date_format)) lines.append('') # further notes lines.append(_(' Episode: %s')% self._payload['episode']) if self._payload['health_issue']: lines.append(_(' Health issue: %s') % self._payload['health_issue']) if self._payload['notes4provider']: lines.append(_(' Provider notes: %s') % self._payload['notes4provider']) if self._payload['notes4patient']: lines.append(_(' Patient advice: %s') % self._payload['notes4patient']) if self._payload['intake_instructions']: lines.append(' ' + _('Intake: %s') % self._payload['intake_instructions']) lines.append('') lines.append(_('Revision: #%(row_ver)s, %(mod_when)s by %(mod_by)s.') % { 'row_ver': self._payload['row_version'], 'mod_when': self._payload['modified_when'].strftime('%Y %b %d %H:%M.%S'), 'mod_by': self._payload['modified_by'] }) if eol is None: return lines return eol.join(lines) def format_as_multiple_lines_abuse(self, left_margin=0, date_format='%Y %b %d', include_metadata=True, eol='\n')-
Expand source code
def format_as_multiple_lines_abuse(self, left_margin=0, date_format='%Y %b %d', include_metadata=True, eol='\n'): lines = [] if include_metadata: lines.append(_('Substance abuse entry [#%s]') % self._payload['pk_intake']) lines.append(' ' + _('Substance: %s [#%s]%s') % ( self._payload['substance'], self._payload['pk_substance'], gmTools.coalesce(self._payload['atc_substance'], '', ' ATC %s') )) lines.append(' ' + _('Use type: %s') % self.use_type_string) lines.append(' ' + _('Last checked: %s') % self._payload['last_checked_when'].strftime('%Y %b %d')) if self._payload['discontinued']: lines.append(_(' Discontinued %s') % self._payload['discontinued'].strftime(date_format)) if self._payload['notes4provider']: lines.append(_(' Notes: %s') % self._payload['notes4provider']) if include_metadata: lines.append('') lines.append(_('Revision: #%(row_ver)s, %(mod_when)s by %(mod_by)s.') % { 'row_ver': self._payload['row_version'], 'mod_when': self._payload['modified_when'].strftime('%Y %b %d %H:%M.%S'), 'mod_by': self._payload['modified_by'] }) if eol is None: return lines return eol.join(lines) def format_as_single_line(self, left_margin=0, date_format='%Y %b %d')-
Expand source code
def format_as_single_line(self, left_margin=0, date_format='%Y %b %d'): return '%s: %s (%s)' % ( ' ' * left_margin, self._payload['substance'], self._payload['last_checked_when'].strftime(date_format) ) def format_as_single_line_abuse(self, left_margin=0, date_format='%Y %b %d')-
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def format_as_single_line_abuse(self, left_margin=0, date_format='%Y %b %d'): return '%s%s: %s (%s)' % ( ' ' * left_margin, self._payload['substance'], self.use_type_string, self._payload['last_checked_when'].strftime('%b %Y') ) def format_maximum_information(self, patient=None)-
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def format_maximum_information(self, patient=None): return self.format ( single_line = False, show_all_product_components = True, include_metadata = True, date_format = '%Y %b %d', include_instructions = True, include_loincs = True ).split('\n') def turn_into_allergy(self, encounter_id=None, allergy_type='allergy')-
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def turn_into_allergy(self, encounter_id=None, allergy_type='allergy'): allg = gmAllergy.create_allergy ( allergene = self._payload['substance'], allg_type = allergy_type, episode_id = self._payload['pk_episode'], encounter_id = encounter_id ) allg['substance'] = self._payload['substance'] allg['reaction'] = self._payload['discontinue_reason'] allg['atc_code'] = gmTools.coalesce(self._payload['atc_substance']) allg['generics'] = self._payload['substance'] allg.save() return allg
Inherited members
class cSubstanceIntakeObjectMatchProvider (queries=None, context=None)-
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class cSubstanceIntakeObjectMatchProvider(gmMatchProvider.cMatchProvider_SQL2): # (product name) -> product _SQL_drug_product_by_name = """ SELECT pk_drug_product AS data, (product || ' (' || preparation || ')' || coalesce(' [' || atc || ']', '')) AS list_label, (product || ' (' || preparation || ')' || coalesce(' [' || atc || ']', '')) AS field_label FROM ref.v_drug_products WHERE is_vaccine IS FALSE AND product %(fragment_condition)s LIMIT 50 """ # (component name) -> product _SQL_drug_product_by_component_name = """ SELECT pk_drug_product AS data, (product || ' (' || preparation || ' %s ' || amount || unit || coalesce('/' || dose_unit, '') || ' ' || substance || ')' || coalesce(' [' || atc_drug || ']', '')) AS list_label, (product || ' (' || preparation || ' %s ' || amount || unit || coalesce('/' || dose_unit, '') || ' ' || substance || ')' || coalesce(' [' || atc_drug || ']', '')) AS field_label FROM ref.v_drug_components WHERE substance %%(fragment_condition)s LIMIT 50 """ % ( _('w/'), _('w/') ) # (product name + component strength) -> product _SQL_drug_product_by_name_and_strength = """ SELECT pk_drug_product AS data, (product || ' (' || preparation || ' %s ' || amount || unit || coalesce('/' || dose_unit, '') || ' ' || substance || ')' || coalesce(' [' || atc_drug || ']', '')) AS list_label, (product || ' (' || preparation || ' %s ' || amount || unit || coalesce('/' || dose_unit, '') || ' ' || substance || ')' || coalesce(' [' || atc_drug || ']', '')) AS field_label FROM (SELECT *, product AS description FROM ref.v_drug_components) AS _components WHERE %%(fragment_condition)s LIMIT 50 """ % ( _('w/'), _('w/') ) # (component name + component strength) -> product _SQL_drug_product_by_component_name_and_strength = """ SELECT pk_drug_product AS data, (product || ' (' || preparation || ' %s ' || amount || unit || coalesce('/' || dose_unit, '') || ' ' || substance || ')' || coalesce(' [' || atc_drug || ']', '')) AS list_label, (product || ' (' || preparation || ' %s ' || amount || unit || coalesce('/' || dose_unit, '') || ' ' || substance || ')' || coalesce(' [' || atc_drug || ']', '')) AS field_label FROM (SELECT *, substance AS description FROM ref.v_drug_components) AS _components WHERE %%(fragment_condition)s LIMIT 50 """ % ( _('w/'), _('w/') ) # non-drug substance name _SQL_substance_name = """ SELECT DISTINCT ON (field_label) data, list_label, field_label FROM ( SELECT DISTINCT ON (term) NULL::integer AS data, term || ' (ATC: ' || code || ')' AS list_label, term AS field_label FROM ref.atc WHERE lower(term) %(fragment_condition)s UNION ALL SELECT DISTINCT ON (description) NULL::integer AS data, description || coalesce(' (ATC: ' || atc || ')', '') AS list_label, description AS field_label FROM ref.substance WHERE lower(description) %(fragment_condition)s ) AS nondrug_substances WHERE NOT EXISTS ( SELECT 1 FROM ref.v_drug_components WHERE lower(substance) = lower(nondrug_substances.field_label) ) LIMIT 30 """ # this query UNIONs together individual queries _SQL_regex_master_query = """ SELECT data, field_label, list_label FROM ((%s) UNION (%s)) AS _union ORDER BY list_label LIMIT 50 """ % ( _SQL_drug_product_by_name_and_strength, _SQL_drug_product_by_component_name_and_strength ) _SQL_nonregex_master_query = """ SELECT data, field_label, list_label FROM ((%s) UNION (%s) UNION (%s)) AS _union ORDER BY list_label LIMIT 50 """ % ( _SQL_drug_product_by_name, _SQL_drug_product_by_component_name, _SQL_substance_name ) _REGEX_name_and_strength = regex.compile(r'^\D+\s*\d+$', regex.UNICODE) #-------------------------------------------------------- def getMatchesByPhrase(self, aFragment): """Return matches for aFragment at start of phrases.""" if cSubstanceIntakeObjectMatchProvider._REGEX_name_and_strength.match(aFragment): self._queries = [cSubstanceIntakeObjectMatchProvider._SQL_regex_master_query] fragment_condition = """description ILIKE %(desc)s AND amount::text ILIKE %(amount)s""" self._args['desc'] = '%s%%' % regex.sub(r'\s*\d+$', '', aFragment) self._args['amount'] = '%s%%' % regex.sub(r'^\D+\s*', '', aFragment) else: self._queries = [ cSubstanceIntakeObjectMatchProvider._SQL_nonregex_master_query ] fragment_condition = "ILIKE %(fragment)s" self._args['fragment'] = "%s%%" % aFragment return self._find_matches(fragment_condition) #-------------------------------------------------------- def getMatchesByWord(self, aFragment): """Return matches for aFragment at start of words inside phrases.""" if cSubstanceIntakeObjectMatchProvider._REGEX_name_and_strength.match(aFragment): self._queries = [cSubstanceIntakeObjectMatchProvider._SQL_regex_master_query] desc = regex.sub(r'\s*\d+$', '', aFragment) desc = gmPG2.sanitize_pg_regex(expression = desc, escape_all = False) fragment_condition = """description ~* %(desc)s AND amount::text ILIKE %(amount)s""" self._args['desc'] = "( %s)|(^%s)" % (desc, desc) self._args['amount'] = '%s%%' % regex.sub(r'^\D+\s*', '', aFragment) else: self._queries = [ cSubstanceIntakeObjectMatchProvider._SQL_nonregex_master_query ] fragment_condition = "~* %(fragment)s" aFragment = gmPG2.sanitize_pg_regex(expression = aFragment, escape_all = False) self._args['fragment'] = "( %s)|(^%s)" % (aFragment, aFragment) return self._find_matches(fragment_condition) #-------------------------------------------------------- def getMatchesBySubstr(self, aFragment): """Return matches for aFragment as a true substring.""" if cSubstanceIntakeObjectMatchProvider._REGEX_name_and_strength.match(aFragment): self._queries = [cSubstanceIntakeObjectMatchProvider._SQL_regex_master_query] fragment_condition = """description ILIKE %(desc)s AND amount::text ILIKE %(amount)s""" self._args['desc'] = '%%%s%%' % regex.sub(r'\s*\d+$', '', aFragment) self._args['amount'] = '%s%%' % regex.sub(r'^\D+\s*', '', aFragment) else: self._queries = [ cSubstanceIntakeObjectMatchProvider._SQL_nonregex_master_query ] fragment_condition = "ILIKE %(fragment)s" self._args['fragment'] = "%%%s%%" % aFragment return self._find_matches(fragment_condition)Match provider which searches matches in possibly several database tables.
queries: - a list of unicode strings - each string is a query - each string must contain: "… WHERE
%(fragment_condition)s …" - each string can contain in the where clause: "… %( )s …" - each query must return (data, list_label, field_label) context definitions to be used in the queries, example: {'ctxt_key1': {'where_part': 'AND country = %(country)s', 'placeholder': 'country'}}
client code using .set_context() must use the 'placeholder':
/ .set_context('country', 'Germany') full example query:
query = u" " " SELECT DISTINCT ON (list_label) pk_encounter AS data, to_char(started, 'YYYY Mon DD (HH24:MI)') || ': ' || l10n_type || ' [#' || pk_encounter || ']' AS list_label, to_char(started, 'YYYY Mon DD') || ': ' || l10n_type AS field_label FROM clin.v_pat_encounters WHERE ( l10n_type %(fragment_condition)s OR type %(fragment_condition)s ) %(ctxt_patient)s ORDER BY list_label LIMIT 30 " " " context = {'ctxt_patient': { 'where_part': u'AND pk_patient = %(PLACEHOLDER)s', 'placeholder': u'PLACEHOLDER' }} self.mp = gmMatchProvider.cMatchProvider_SQL2(queries = query, context = context) self.set_context(context = 'PLACEHOLDER', val = '<THE VALUE>')_SQL_data2match: SQL to retrieve a match by, say, primary key wherein the only keyword argument is 'pk'
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