Gnumed.business.gmMedication API documentation
Description: Medication handling code …

# 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)`
  Expand source code

      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)`
  Expand source code

      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)`
  Expand source code

      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)`
  Expand source code

      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`
  Expand source code

      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`
  Expand source code

      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)`
  Expand source code

      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)`
  Expand source code

      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)`
  Expand source code

      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)`
  Expand source code

      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)`
  Expand source code

      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`
  Expand source code

      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`
  Expand source code

      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`
  Expand source code

      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 True

  Delete 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)`
  Expand source code

      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)`
  Expand source code

      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`
  Expand source code

      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)`
  Expand source code

      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`
  Expand source code

      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`
  Expand source code

      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')`
  Expand source code

      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)`
  Expand source code

      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)`
  Expand source code

      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`
  Expand source code

      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]`
  Expand source code

      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`
  Expand source code

      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`
  Expand source code

      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`
  Expand source code

      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()`
  Expand source code

      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)`
  Expand source code

      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)`
  Expand source code

      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)`
  Expand source code

      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)`
  Expand source code

      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)`
  Expand source code

      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)`
  Expand source code

      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

  - cBusinessDBObject

  ### Instance variables

  `prop containing_drug`
    Expand source code

        def _get_containing_drug(self):
                return cDrugProduct(aPK_obj = self._payload['pk_drug_product'])

  `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')),
                        self._payload['l10n_preparation'],
                        short = short,
                        none_str = ''
                )

  `prop is_in_use_by_patients`
    Expand source code

        def _get_is_in_use_by_patients(self):
                return self._payload['is_in_use']

  `prop substance`
    Expand source code

        def _get_substance(self):
                return cSubstance(aPK_obj = self._payload['pk_substance'])

  `prop substance_dose`
    Expand source code

        def _get_substance_dose(self):
                return cSubstanceDose(aPK_obj = self._payload['pk_dose'])

  ### 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
                )

  `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

  - `cBusinessDBObject`:
    - `fields_as_dict`
    - `format`
    - `get_fields`
    - `get_patient`
    - `get_updatable_fields`
    - `is_modified`
    - `keys`
    - `patient_pk`
    - `refetch_payload`
    - `same_payload`
    - `save`
    - `save_payload`
    - `staff_id`
`class cDrugComponentMatchProvider (queries=None, context=None)`
  Expand source code

      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

  - cMatchProvider_SQL2
  - cMatchProvider

  ### Inherited members

  - `cMatchProvider_SQL2`:
    - `getAllMatches`
    - `getMatches`
    - `getMatchesByPhrase`
    - `getMatchesBySubstr`
    - `getMatchesByWord`
    - `setThresholds`
    - `set_context`
`class cDrugProduct (aPK_obj: int | dict = None, row: dict = None, link_obj=None)`
  Expand source code

      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

  - cBusinessDBObject

  ### 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`
    Expand source code

        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

  - `cBusinessDBObject`:
    - `fields_as_dict`
    - `format`
    - `get_fields`
    - `get_patient`
    - `get_updatable_fields`
    - `is_modified`
    - `keys`
    - `patient_pk`
    - `refetch_payload`
    - `same_payload`
    - `save`
    - `save_payload`
    - `staff_id`
`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

  - cBusinessDBObject

  ### 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

  - `cBusinessDBObject`:
    - `fields_as_dict`
    - `format`
    - `get_fields`
    - `get_patient`
    - `get_updatable_fields`
    - `is_modified`
    - `keys`
    - `patient_pk`
    - `refetch_payload`
    - `same_payload`
    - `save`
    - `save_payload`
    - `staff_id`
`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

  - cBusinessDBObject

  ### 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

  - `cBusinessDBObject`:
    - `fields_as_dict`
    - `format`
    - `get_fields`
    - `get_patient`
    - `get_updatable_fields`
    - `is_modified`
    - `keys`
    - `patient_pk`
    - `refetch_payload`
    - `same_payload`
    - `save`
    - `save_payload`
    - `staff_id`
`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

  - cMatchProvider_SQL2
  - cMatchProvider

  ### Inherited members

  - `cMatchProvider_SQL2`:
    - `getAllMatches`
    - `getMatches`
    - `getMatchesByPhrase`
    - `getMatchesBySubstr`
    - `getMatchesByWord`
    - `setThresholds`
    - `set_context`
`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

  - cBusinessDBObject

  ### 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

  - `cBusinessDBObject`:
    - `fields_as_dict`
    - `format`
    - `get_fields`
    - `get_patient`
    - `get_updatable_fields`
    - `is_modified`
    - `keys`
    - `patient_pk`
    - `refetch_payload`
    - `same_payload`
    - `save`
    - `save_payload`
    - `staff_id`
`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

  - cBusinessDBObject

  ### 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

  - `cBusinessDBObject`:
    - `fields_as_dict`
    - `format`
    - `get_fields`
    - `get_patient`
    - `get_updatable_fields`
    - `is_modified`
    - `keys`
    - `patient_pk`
    - `refetch_payload`
    - `same_payload`
    - `save`
    - `save_payload`
    - `staff_id`
`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

  - cMatchProvider_SQL2
  - cMatchProvider

  ### 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

  - `cMatchProvider_SQL2`:
    - `getAllMatches`
    - `getMatches`
    - `setThresholds`
    - `set_context`
`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

  - cBusinessDBObject

  ### 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')`
    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_maximum_information(self, patient=None)`
    Expand source code

        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')`
    Expand source code

        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

  - `cBusinessDBObject`:
    - `fields_as_dict`
    - `format`
    - `get_fields`
    - `get_patient`
    - `get_updatable_fields`
    - `is_modified`
    - `keys`
    - `patient_pk`
    - `refetch_payload`
    - `same_payload`
    - `save`
    - `save_payload`
    - `staff_id`
`class cSubstanceIntakeObjectMatchProvider (queries=None, context=None)`
  Expand source code

      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'

  ### Ancestors

  - cMatchProvider_SQL2
  - cMatchProvider

  ### Inherited members

  - `cMatchProvider_SQL2`:
    - `getAllMatches`
    - `getMatches`
    - `getMatchesByPhrase`
    - `getMatchesBySubstr`
    - `getMatchesByWord`
    - `setThresholds`
    - `set_context`