Gnumed.business.gmVaccination API documentation
Description: GNUmed vaccination related business objects.

# Module `Gnumed.business.gmVaccination`

GNUmed vaccination related business objects.

Expand source code

    """GNUmed vaccination related business objects.
    """
    #============================================================
    __author__ = "K.Hilbert <Karsten.Hilbert@gmx.net>"
    __license__ = "GPL"

    import sys
    import logging

    if __name__ == '__main__':
            sys.path.insert(0, '../../')
            _ = lambda x:x
    from Gnumed.pycommon import gmBusinessDBObject
    from Gnumed.pycommon import gmPG2

    from Gnumed.pycommon import gmTools
    from Gnumed.pycommon import gmDateTime
    from Gnumed.business import gmMedication

    _log = logging.getLogger('gm.vacc')

    #============================================================
    URL_vaccination_plan = 'http://www.rki.de/DE/Content/Infekt/EpidBull/Archiv/2017/Ausgaben/34_17.pdf?__blob=publicationFile'

    # http://www.pei.de/cln_042/SharedDocs/Downloads/fachkreise/uaw/meldeboegen/b-ifsg-meldebogen,templateId=raw,property=publicationFile.pdf/b-ifsg-meldebogen.pdf
    URL_vaccine_adr_german_default = 'https://nebenwirkungen.pei.de'

    #============================================================
    _SQL_create_substance4vaccine = """-- in case <%(substance_tag)s> already exists: add ATC
    UPDATE ref.substance SET atc = '%(atc)s' WHERE lower(description) = lower('%(desc)s') AND atc IS NULL;

    INSERT INTO ref.substance (description, atc)
            SELECT
                    '%(desc)s',
                    '%(atc)s'
            WHERE NOT EXISTS (
                    SELECT 1 FROM ref.substance WHERE
                            atc = '%(atc)s'
                                    AND
                            description = '%(desc)s'
            );

    -- generic English
    SELECT i18n.upd_tx('en', '%(orig)s', '%(trans)s');
    -- user language, if any, fails if not set
    SELECT i18n.upd_tx('%(orig)s', '%(trans)s');"""

    _SQL_map_indication2substance = """-- old-style "%(v21_ind)s" => "%(desc)s"
    INSERT INTO staging.lnk_vacc_ind2subst_dose (fk_indication, fk_dose, is_live)
            SELECT
                    (SELECT id FROM ref.vacc_indication WHERE description = '%(v21_ind)s'),
                    (SELECT pk_dose FROM ref.v_substance_doses WHERE
                            amount = 1
                                    AND
                            unit = 'dose'
                                    AND
                            dose_unit = 'shot'
                                    AND
                            substance = '%(desc)s'
                    ),
                    %(is_live)s
            WHERE EXISTS (
                    SELECT 1 FROM ref.vacc_indication WHERE description = '%(v21_ind)s'
            );"""

    _SQL_create_vacc_product = """-- --------------------------------------------------------------
    -- in case <%(prod_name)s> exists: add ATC
    UPDATE ref.drug_product SET atc_code = '%(atc_prod)s' WHERE
            atc_code IS NULL
                    AND
            description = '%(prod_name)s'
                    AND
            preparation = '%(prep)s'
                    AND
            is_fake IS TRUE;

    INSERT INTO ref.drug_product (description, preparation, is_fake, atc_code)
            SELECT
                    '%(prod_name)s',
                    '%(prep)s',
                    TRUE,
                    '%(atc_prod)s'
            WHERE NOT EXISTS (
                    SELECT 1 FROM ref.drug_product WHERE
                            description = '%(prod_name)s'
                                    AND
                            preparation = '%(prep)s'
                                    AND
                            is_fake = TRUE
                                    AND
                            atc_code = '%(atc_prod)s'
            );"""

    _SQL_create_vaccine = """-- add vaccine if necessary
    INSERT INTO ref.vaccine (is_live, fk_drug_product)
            SELECT
                    %(is_live)s,
                    (SELECT pk FROM ref.drug_product WHERE
                            description = '%(prod_name)s'
                                    AND
                            preparation = '%(prep)s'
                                    AND
                            is_fake = TRUE
                                    AND
                            atc_code = '%(atc_prod)s'
                    )
            WHERE NOT EXISTS (
                    SELECT 1 FROM ref.vaccine WHERE
                            is_live IS %(is_live)s
                                    AND
                            fk_drug_product = (
                                    SELECT pk FROM ref.drug_product WHERE
                                            description = '%(prod_name)s'
                                                    AND
                                            preparation = '%(prep)s'
                                                    AND
                                            is_fake = TRUE
                                                    AND
                                            atc_code = '%(atc_prod)s'
                            )
            );"""

    _SQL_create_vacc_subst_dose = """-- create dose, assumes substance exists
    INSERT INTO ref.dose (fk_substance, amount, unit, dose_unit)
            SELECT
                    (SELECT pk FROM ref.substance WHERE atc = '%(atc_subst)s' AND description = '%(name_subst)s' LIMIT 1),
                    1,
                    'dose',
                    'shot'
            WHERE NOT EXISTS (
                    SELECT 1 FROM ref.dose WHERE
                            fk_substance = (SELECT pk FROM ref.substance WHERE atc = '%(atc_subst)s' AND description = '%(name_subst)s' LIMIT 1)
                                    AND
                            amount = 1
                                    AND
                            unit = 'dose'
                                    AND
                            dose_unit IS NOT DISTINCT FROM 'shot'
            );"""

    _SQL_link_dose2vacc_prod = """-- link dose to product
    INSERT INTO ref.lnk_dose2drug (fk_dose, fk_drug_product)
            SELECT
                    (SELECT pk from ref.dose WHERE
                            fk_substance = (SELECT pk FROM ref.substance WHERE atc = '%(atc_subst)s' AND description = '%(name_subst)s' LIMIT 1)
                                    AND
                            amount = 1
                                    AND
                            unit = 'dose'
                                    AND
                            dose_unit IS NOT DISTINCT FROM 'shot'
                    ),
                    (SELECT pk FROM ref.drug_product WHERE
                            description = '%(prod_name)s'
                                    AND
                            preparation = '%(prep)s'
                                    AND
                            is_fake = TRUE
                                    AND
                            atc_code = '%(atc_prod)s'
                    )
            WHERE NOT EXISTS (
                    SELECT 1 FROM ref.lnk_dose2drug WHERE
                            fk_dose = (
                                    SELECT PK from ref.dose WHERE
                                            fk_substance = (SELECT pk FROM ref.substance WHERE atc = '%(atc_subst)s' AND description = '%(name_subst)s' LIMIT 1)
                                                    AND
                                            amount = 1
                                                    AND
                                            unit = 'dose'
                                                    AND
                                            dose_unit IS NOT DISTINCT FROM 'shot'
                            )
                                    AND
                            fk_drug_product = (
                                    SELECT pk FROM ref.drug_product WHERE
                                            description = '%(prod_name)s'
                                                    AND
                                            preparation = '%(prep)s'
                                                    AND
                                            is_fake = TRUE
                                                    AND
                                            atc_code = '%(atc_prod)s'
                            )
            );"""

    _SQL_create_indications_mapping_table = """-- set up helper table for conversion of vaccines from using
    -- linked indications to using linked substances,
    -- to be dropped after converting vaccines
    DROP TABLE IF EXISTS staging.lnk_vacc_ind2subst_dose CASCADE;

    CREATE UNLOGGED TABLE staging.lnk_vacc_ind2subst_dose (
            fk_indication INTEGER
                    NOT NULL
                    REFERENCES ref.vacc_indication(id)
                            ON UPDATE CASCADE
                            ON DELETE RESTRICT,
            fk_dose INTEGER
                    NOT NULL
                    REFERENCES ref.dose(pk)
                            ON UPDATE CASCADE
                            ON DELETE RESTRICT,
            is_live
                    BOOLEAN
                    NOT NULL
                    DEFAULT false,
            UNIQUE(fk_indication, fk_dose),
            UNIQUE(fk_indication, is_live)
    );

    DROP VIEW IF EXISTS staging.v_lnk_vacc_ind2subst_dose CASCADE;

    CREATE VIEW staging.v_lnk_vacc_ind2subst_dose AS
    SELECT
            s_lvi2sd.is_live
                    as mapping_is_for_live_vaccines,
            r_vi.id
                    as pk_indication,
            r_vi.description
                    as indication,
            r_vi.atcs_single_indication,
            r_vi.atcs_combi_indication,
            r_d.pk
                    as pk_dose,
            r_d.amount,
            r_d.unit,
            r_d.dose_unit,
            r_s.pk
                    as pk_substance,
            r_s.description
                    as substance,
            r_s.atc
                    as atc_substance
    FROM
            staging.lnk_vacc_ind2subst_dose s_lvi2sd
                    inner join ref.vacc_indication r_vi on (r_vi.id = s_lvi2sd.fk_indication)
                    inner join ref.dose r_d on (r_d.pk = s_lvi2sd.fk_dose)
                            inner join ref.substance r_s on (r_s.pk = r_d.fk_substance)
    ;"""

    _SQL_create_generic_vaccines_script = """-- ==============================================================
    -- GNUmed database schema change script
    --
    -- License: GPL v2 or later
    -- Author: karsten.hilbert@gmx.net
    --
    -- THIS IS A GENERATED FILE. DO NOT EDIT.
    --
    -- ==============================================================
    \set ON_ERROR_STOP 1
    --set default_transaction_read_only to off;

    -- --------------------------------------------------------------
    -- indications mapping helper table
    -- --------------------------------------------------------------
    %s

    -- --------------------------------------------------------------
    -- generic vaccine "substances" (= indications)
    -- --------------------------------------------------------------
    %s

    -- --------------------------------------------------------------
    -- generic vaccines
    -- --------------------------------------------------------------
    -- new-style vaccines are not linked to indications, so drop
    -- trigger asserting that condition,
    DROP FUNCTION IF EXISTS clin.trf_sanity_check_vaccine_has_indications() CASCADE;

    -- need to disable trigger before running
    ALTER TABLE ref.drug_product
            DISABLE TRIGGER tr_assert_product_has_components
    ;

    %s

    -- want to re-enable trigger as now all inserted
    -- vaccines satisfy the conditions
    ALTER TABLE ref.drug_product
            ENABLE TRIGGER tr_assert_product_has_components
    ;

    -- --------------------------------------------------------------
    -- indications mapping data
    -- --------------------------------------------------------------
    -- map old style
    --              (clin|ref).vacc_indication.description
    -- to new style
    --              ref.v_substance_doses.substance

    %s

    -- --------------------------------------------------------------
    select gm.log_script_insertion('v%s-ref-create_generic_vaccines.sql', '%s');
    """

    #============================================================
    def write_generic_vaccine_sql(version, include_indications_mapping=False, filename=None):
            if filename is None:
                    filename = gmTools.get_unique_filename(suffix = '.sql')
            _log.debug('writing SQL for creating generic vaccines to: %s', filename)
            sql_file = open(filename, mode = 'wt', encoding = 'utf8')
            sql_file.write(create_generic_vaccine_sql (
                    version,
                    include_indications_mapping = include_indications_mapping
            ))
            sql_file.close()
            return filename

    #------------------------------------------------------------
    def create_generic_vaccine_sql(version, include_indications_mapping=False):

            _log.debug('including indications mapping table with generic vaccines creation SQL: %s', include_indications_mapping)

            from Gnumed.business import gmVaccDefs

            sql_create_substances = []
            sql_populate_ind2subst_map = []
            sql_create_vaccines = []

            for substance_tag in gmVaccDefs._VACCINE_SUBSTANCES:
                    subst = gmVaccDefs._VACCINE_SUBSTANCES[substance_tag]
                    args = {
                            'substance_tag': substance_tag,
                            'atc': subst['atc4target'],
                            'desc': subst['name'],
                            'orig': subst['target'].split('::')[0],
                            'trans': subst['target'].split('::')[-1]
                    }
                    sql_create_substances.append(_SQL_create_substance4vaccine % args)
                    try:
                            for v21_ind in subst['v21_indications']:
                                    args['v21_ind'] = v21_ind
                                    args['is_live'] = 'false'
                                    sql_populate_ind2subst_map.append(_SQL_map_indication2substance % args)
                    except KeyError:
                            pass
                    try:
                            for v21_ind in subst['v21_indications_live']:
                                    args['v21_ind'] = v21_ind
                                    args['is_live'] = 'true'
                                    sql_populate_ind2subst_map.append(_SQL_map_indication2substance % args)
                    except KeyError:
                            pass
                    args = {}

            for key in gmVaccDefs._GENERIC_VACCINES:
                    vaccine_def = gmVaccDefs._GENERIC_VACCINES[key]
                    # create product
                    args = {
                            'atc_prod': vaccine_def['atc'],
                            'prod_name': vaccine_def['name'],
                            # generic vaccines always have the English preparation
                            'prep': 'vaccine',
                            'is_live': vaccine_def['live']
                    }
                    sql_create_vaccines.append(_SQL_create_vacc_product % args)
                    # create doses
                    for ingredient_tag in vaccine_def['ingredients']:
                            vacc_subst_def = gmVaccDefs._VACCINE_SUBSTANCES[ingredient_tag]
                            args['atc_subst'] = vacc_subst_def['atc4target']
                            args['name_subst'] = vacc_subst_def['name']
                            # substance already created, only need to create dose
                            sql_create_vaccines.append(_SQL_create_vacc_subst_dose % args)
                            # link dose to product
                            sql_create_vaccines.append(_SQL_link_dose2vacc_prod % args)
                            # the following does not work because there are mixed vaccines
                            # any live ingredients included ?
    #                       if vacc_subst_def.has_key('v21_indications_live'):
    #                               if vaccine_def['live'] is False:
    #                                       print vaccine_def
    #                                       raise Exception('vaccine def says "NOT live" but ingredients DO map to <v21_indications_LIVE>')
    #                       if vacc_subst_def.has_key('v21_indications'):
    #                               if vaccine_def['live'] is True:
    #                                       print vaccine_def
    #                                       raise Exception('vaccine def says "live" but ingredients do NOT map to v21_indications_LIVE')

                    # create vaccine
                    sql_create_vaccines.append(_SQL_create_vaccine % args)

            # join
            sql = _SQL_create_generic_vaccines_script % (
                    gmTools.bool2subst (
                            include_indications_mapping,
                            _SQL_create_indications_mapping_table,
                            '-- indications mapping table not included'
                    ),
                    '\n\n'.join(sql_create_substances),
                    '\n\n'.join(sql_create_vaccines),
                    gmTools.bool2subst (
                            include_indications_mapping,
                            '\n\n'.join(sql_populate_ind2subst_map),
                            '-- indications mapping table not populated'
                    ),
                    version,
                    version
            )
            return sql

    #============================================================
    # vaccine related code
    #------------------------------------------------------------
    _SQL_get_vaccine_fields = """SELECT * FROM ref.v_vaccines WHERE %s"""

    class cVaccine(gmBusinessDBObject.cBusinessDBObject):
            """Represents one vaccine."""

            _cmd_fetch_payload = _SQL_get_vaccine_fields % "pk_vaccine = %s"

            _cmds_store_payload = [
                    """UPDATE ref.vaccine SET
                                    --id_route = %(pk_route)s,
                                    is_live = %(is_live)s,
                                    min_age = %(min_age)s,
                                    max_age = %(max_age)s,
                                    comment = gm.nullify_empty_string(%(comment)s),
                                    fk_drug_product = %(pk_drug_product)s
                            WHERE
                                    pk = %(pk_vaccine)s
                                            AND
                                    xmin = %(xmin_vaccine)s
                            RETURNING
                                    xmin as xmin_vaccine
                    """
            ]

            _updatable_fields = [
                    #'pk_route',
                    'is_live',
                    'min_age',
                    'max_age',
                    'comment',
                    'pk_drug_product'
            ]

            #--------------------------------------------------------
            def format(self, *args, **kwargs):
                    lines = []
                    lines.append(_('%s with %s %s     #%s') % (
                            gmTools.bool2subst(self._payload[self._idx['is_live']], _('Live vaccine'), _('Inactive vaccine'), '<liveness error in DB>'),
                            len(self._payload[self._idx['indications']]),
                            gmTools.bool2subst(len(self._payload[self._idx['indications']]) == 1, _('indication'), _('indications'), _('indication(s)')),
                            self._payload[self._idx['pk_vaccine']]
                    ))
                    lines.append(_(' Product: "%s"     #%s') % (
                            self._payload[self._idx['vaccine']],
                            self._payload[self._idx['pk_drug_product']]
                    ))
                    lines.append(_('  %s%s%s%s') % (
                            self._payload[self._idx['l10n_preparation']],
                            gmTools.coalesce(gmTools.bool2subst(self._payload[self._idx['is_fake_vaccine']], _('fake product'), None, None), '', ', %s'),
                            gmTools.coalesce(self._payload[self._idx['atc_code']], '', ' [ATC:%s]'),
                            gmTools.coalesce(self._payload[self._idx['external_code']], '', ' [%s:%%s]' % self._payload[self._idx['external_code_type']])
                    ))
                    #lines.append(_(u' %sage %s - %s') % (
                    #       gmTools.coalesce(self._payload[self._idx['route_description']], u'', u'%s, '),          #route_abbreviation
                    lines.append(_(' Age %s - %s') % (
                            gmTools.coalesce(self._payload[self._idx['min_age']], '?'),
                            gmTools.coalesce(self._payload[self._idx['max_age']], '?')
                    ))
                    if self._payload[self._idx['comment']] is not None:
                            lines.extend([ ' %s' % l for l in self._payload[self._idx['comment']].split('\n')] )
                    lines.append(_(' Indications'))
                    lines.extend( [ '  %s [ATC:%s]' % (i['l10n_indication'], i['atc_indication']) for i in self._payload[self._idx['indications']] ])

                    return lines

            #--------------------------------------------------------
            # properties
            #--------------------------------------------------------
            def _get_product(self):
                    return gmMedication.cDrugProduct(aPK_obj = self._payload[self._idx['pk_drug_product']])

            product = property(_get_product, lambda x:x)

            #--------------------------------------------------------
            def _get_is_in_use(self):
                    cmd = 'SELECT EXISTS(SELECT 1 FROM clin.vaccination WHERE fk_vaccine = %(pk)s)'
                    args = {'pk': self._payload[self._idx['pk_vaccine']]}
                    rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
                    return rows[0][0]

            is_in_use = property(_get_is_in_use, lambda x:x)

    #------------------------------------------------------------
    def create_vaccine(pk_drug_product=None, product_name=None, indications=None, is_live=None):

            assert (is_live is not None), '<is_live> must not be <None>'

            conn = gmPG2.get_connection(readonly = False)
            if pk_drug_product is None:
                    #prep = _('vaccine')
                    prep = 'vaccine'
                    _log.debug('creating vaccine drug product [%s %s]', product_name, prep)
                    vacc_prod = gmMedication.create_drug_product (
                            product_name = product_name,
                            preparation = prep,
                            return_existing = True,
                            # indications are ref.dose rows
                            doses = indications,
                            link_obj = conn
                    )
                    #conn.commit()
                    vacc_prod['atc'] = 'J07'
                    vacc_prod.save(conn = conn)
                    pk_drug_product = vacc_prod['pk_drug_product']
            cmd = 'INSERT INTO ref.vaccine (fk_drug_product, is_live) values (%(pk_drug_product)s, %(live)s) RETURNING pk'
            queries = [{'cmd': cmd, 'args': {'pk_drug_product': pk_drug_product, 'live': is_live}}]
            rows, idx = gmPG2.run_rw_queries(link_obj = conn, queries = queries, get_col_idx = False, return_data = True, end_tx = True)
            conn.close()
            return cVaccine(aPK_obj = rows[0]['pk'])

    #------------------------------------------------------------
    def delete_vaccine(vaccine=None):

            cmd = 'DELETE FROM ref.vaccine WHERE pk = %(pk)s'
            args = {'pk': vaccine}

            try:
                    gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
            except gmPG2.dbapi.IntegrityError:
                    _log.exception('cannot delete vaccine [%s]', vaccine)
                    return False

            return True

    #------------------------------------------------------------
    def get_vaccines(order_by=None, return_pks=False):

            if order_by is None:
                    cmd = _SQL_get_vaccine_fields % 'TRUE'
            else:
                    cmd = _SQL_get_vaccine_fields % ('TRUE\nORDER BY %s' % order_by)

            rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd}], get_col_idx = True)
            if return_pks:
                    return [ r['pk_vaccine'] for r in rows ]
            return [ cVaccine(row = {'data': r, 'idx': idx, 'pk_field': 'pk_vaccine'}) for r in rows ]

    #============================================================
    # vaccination related classes
    #============================================================
    _SQL_get_vaccination_fields = """SELECT * FROM clin.v_vaccinations WHERE %s"""

    class cVaccination(gmBusinessDBObject.cBusinessDBObject):

            _cmd_fetch_payload = _SQL_get_vaccination_fields % "pk_vaccination = %s"

            _cmds_store_payload = [
                    """UPDATE clin.vaccination SET
                                    soap_cat = %(soap_cat)s,
                                    clin_when = %(date_given)s,
                                    site = gm.nullify_empty_string(%(site)s),
                                    batch_no = gm.nullify_empty_string(%(batch_no)s),
                                    reaction = gm.nullify_empty_string(%(reaction)s),
                                    narrative = gm.nullify_empty_string(%(comment)s),
                                    fk_vaccine = %(pk_vaccine)s,
                                    fk_provider = %(pk_provider)s,
                                    fk_encounter = %(pk_encounter)s,
                                    fk_episode = %(pk_episode)s
                            WHERE
                                    pk = %(pk_vaccination)s
                                            AND
                                    xmin = %(xmin_vaccination)s
                            RETURNING
                                    xmin as xmin_vaccination
                    """
            ]

            _updatable_fields = [
                    'soap_cat',
                    'date_given',
                    'site',
                    'batch_no',
                    'reaction',
                    'comment',
                    'pk_vaccine',
                    'pk_provider',
                    'pk_encounter',
                    'pk_episode'
            ]

            #--------------------------------------------------------
            def format_maximum_information(self, patient=None):
                    return self.format (
                            with_indications = True,
                            with_comment = True,
                            with_reaction = True,
                            date_format = '%Y %b %d'
                    )

            #--------------------------------------------------------
            def format(self, with_indications=False, with_comment=False, with_reaction=False, date_format='%Y-%m-%d'):

                    lines = []

                    lines.append (' %s: %s [%s]%s' % (
                            self._payload[self._idx['date_given']].strftime(date_format),
                            self._payload[self._idx['vaccine']],
                            self._payload[self._idx['batch_no']],
                            gmTools.coalesce(self._payload[self._idx['site']], '', ' (%s)')
                    ))

                    if with_comment:
                            if self._payload[self._idx['comment']] is not None:
                                    lines.append('   %s' % self._payload[self._idx['comment']])

                    if with_reaction:
                            if self._payload[self._idx['reaction']] is not None:
                                    lines.append('   %s' % self._payload[self._idx['reaction']])

                    if with_indications:
                            lines.append('   %s' % ' / '.join([ i['l10n_indication'] for i in self._payload[self._idx['indications']] ]))

                    return lines

            #--------------------------------------------------------
            def _get_vaccine(self):
                    return cVaccine(aPK_obj = self._payload[self._idx['pk_vaccine']])

            vaccine = property(_get_vaccine, lambda x:x)

    #------------------------------------------------------------
    def get_vaccinations(pk_identity=None, pk_episodes=None, pk_health_issues=None, pk_encounters=None, order_by=None, return_pks=False):

            args = {}
            where_parts = []

            if pk_identity is not None:
                    args = {'pk_identity': pk_identity}
                    where_parts.append('pk_patient = %(pk_identity)s')

            if (pk_episodes is not None) and (len(pk_episodes) > 0):
                    where_parts.append('pk_episode = ANY(%(pk_epis)s)')
                    args['pk_epis'] = pk_episodes

            if (pk_health_issues is not None) and (len(pk_health_issues) > 0):
                    where_parts.append('pk_episode = ANY(SELECT pk FROM clin.episode WHERE fk_health_issue = ANY(%(pk_issues)s))')
                    args['pk_issues'] = pk_health_issues

            if (pk_encounters is not None) and (len(pk_encounters) > 0):
                    where_parts.append('pk_encounter = ANY(%(pk_encs)s)')
                    args['pk_encs'] = pk_encounters

            ORDER_BY = gmTools.coalesce (
                    value2test = order_by,
                    return_instead = '',
                    value2return = 'ORDER BY %s' % order_by
            )
            if len(where_parts) == 0:
                    WHERE = 'True'
            else:
                    WHERE = '\nAND '.join(where_parts)

            SQL = '%s %s' % (
                    _SQL_get_vaccination_fields % WHERE,
                    ORDER_BY
            )
            rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': SQL, 'args': args}], get_col_idx = True)
            if return_pks:
                    return [ r['pk_vaccination'] for r in rows ]
            vaccs = [ cVaccination(row = {'idx': idx, 'data': r, 'pk_field': 'pk_vaccination'})  for r in rows ]
            return vaccs

    #------------------------------------------------------------
    def create_vaccination(encounter=None, episode=None, vaccine=None, batch_no=None):

            cmd = """
                    INSERT INTO clin.vaccination (
                            fk_encounter,
                            fk_episode,
                            fk_vaccine,
                            batch_no
                    ) VALUES (
                            %(enc)s,
                            %(epi)s,
                            %(vacc)s,
                            %(batch)s
                    ) RETURNING pk;
            """
            args = {
                    'enc': encounter,
                    'epi': episode,
                    'vacc': vaccine,
                    'batch': batch_no
            }

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

            return cVaccination(aPK_obj = rows[0][0])

    #------------------------------------------------------------
    def delete_vaccination(vaccination=None):
            cmd = """DELETE FROM clin.vaccination WHERE pk = %(pk)s"""
            args = {'pk': vaccination}

            gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])

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

    def format_latest_vaccinations(output_format='latex', emr=None):

            _log.debug('formatting latest vaccinations into [%s]', output_format)

            vaccs = emr.get_latest_vaccinations()

            if output_format == 'latex':
                    return __format_latest_vaccinations_latex(vaccinations = vaccs)

            msg = _('unknown vaccinations output format [%s]') % output_format
            _log.error(msg)
            return msg

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

    def __format_latest_vaccinations_latex(vaccinations=None):

            if len(vaccinations) == 0:
                    return '\\noindent %s' % _('No vaccinations recorded.')

            tex =  '\\noindent %s {\\tiny (%s)\\par}\n' % (_('Latest vaccinations'), _('per target condition'))
            tex += '\n'
            tex += '\\noindent \\begin{tabular}{|l|l|l|l|l|l|}\n'
            tex += '\\hline\n'
            tex += '%s & %s & {\\footnotesize %s} & {\\footnotesize %s} & {\\footnotesize %s\\footnotemark} & {\\footnotesize $\\Sigma$\\footnotemark}\\\\\n' % (
                    _('Target'),
                    _('Last given'),
                    _('Vaccine'),
                    _('Lot \#'),
                    _('SoaP')
            )
            tex += '\\hline\n'
            tex += '\n'
            tex += '\\hline\n'
            tex += '%s'                     # this is where the actual vaccination rows end up
            tex += '\n'
            tex += '\\end{tabular}\n'
            tex += '\n'
            tex += '\\addtocounter{footnote}{-1}\n'
            tex += '\\footnotetext{%s}\n' % _('SoaP -- "S"ubjective: vaccination was remembered by patient. "P"lan: vaccination was administered in the practice or copied from trustworthy records.')
            tex += '\\addtocounter{footnote}{1}\n'
            tex += '\\footnotetext{$\\Sigma$ -- %s}\n' % _('Total number of vaccinations recorded for the corresponding target condition.')
            tex += '\n'

            row_template = '%s & %s & {\\scriptsize %s} & {\\scriptsize %s} & {\\scriptsize %s} & {\\scriptsize %s}\\\\\n'
            lines = ''
            targets = sorted(vaccinations)
            for target in targets:
                    target_count, vacc = vaccinations[target]
                    lines += row_template % (
                            target,
                            gmDateTime.pydt_strftime(vacc['date_given'], '%Y %b %d'),
                            vacc['vaccine'],
                            gmTools.tex_escape_string(vacc['batch_no'].strip()),
                            vacc['soap_cat'].upper(),
                            target_count
                    )
                    if vacc['site'] is not None:
                            lines += ' & \\multicolumn{5}{l|}{\\scriptsize %s: %s\\par}\\\\\n' % (_('Injection site'), vacc['site'].strip())
                    if vacc['reaction'] is not None:
                            lines += ' & \\multicolumn{5}{l|}{\\scriptsize %s: %s\\par}\\\\\n' % (_('Reaction'), vacc['reaction'].strip())
                    if vacc['comment'] is not None:
                            lines += ' & \\multicolumn{5}{l|}{\\scriptsize %s: %s\\par}\\\\\n' % (_('Comment'), vacc['comment'].strip())
                    lines += '\\hline\n'

            return tex % lines

    #============================================================
    # main - unit testing
    #------------------------------------------------------------
    if __name__ == '__main__':

            if len(sys.argv) < 2:
                    sys.exit()

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

            del _
            from Gnumed.pycommon import gmI18N
            gmI18N.activate_locale()
            gmI18N.install_domain()

    #       from Gnumed.pycommon import gmPG
            #--------------------------------------------------------
            def test_vacc():
                    vacc = cVaccination(aPK_obj=1)
                    print(vacc)
                    fields = vacc.get_fields()
                    for field in fields:
                            print(field, ':', vacc[field])
                    print("updatable:", vacc.get_updatable_fields())

    #       #--------------------------------------------------------
    #       def test_due_vacc():
    #               # Test for a due vaccination
    #               pk_args = {
    #                       'pat_id': 12,
    #                       'indication': 'meningococcus C',
    #                       'seq_no': 1
    #               }
    #               missing_vacc = cMissingVaccination(aPK_obj=pk_args)
    #               fields = missing_vacc.get_fields()
    #               print("\nDue vaccination:")
    #               print(missing_vacc)
    #               for field in fields:
    #                       print(field, ':', missing_vacc[field])
    #               # Test for an overdue vaccination
    #               pk_args = {
    #                       'pat_id': 12,
    #                       'indication': 'haemophilus influenzae b',
    #                       'seq_no': 2
    #               }
    #               missing_vacc = cMissingVaccination(aPK_obj=pk_args)
    #               fields = missing_vacc.get_fields()
    #               print("\nOverdue vaccination (?):")
    #               print(missing_vacc)
    #               for field in fields:
    #                       print(field, ':', missing_vacc[field])

    #       #--------------------------------------------------------
    #       def test_due_booster():
    #               pk_args = {
    #                       'pat_id': 12,
    #                       'indication': 'tetanus'
    #               }
    #               missing_booster = cMissingBooster(aPK_obj=pk_args)
    #               fields = missing_booster.get_fields()
    #               print("\nDue booster:")
    #               print(missing_booster)
    #               for field in fields:
    #                       print(field, ':', missing_booster[field])

            #--------------------------------------------------------
    #       def test_scheduled_vacc():
    #               scheduled_vacc = cScheduledVaccination(aPK_obj=20)
    #               print("\nScheduled vaccination:")
    #               print(scheduled_vacc)
    #               fields = scheduled_vacc.get_fields()
    #               for field in fields:
    #                       print(field, ':', scheduled_vacc[field])
    #               print("updatable:", scheduled_vacc.get_updatable_fields())

    #       #--------------------------------------------------------
    #       def test_vaccination_course():
    #               vaccination_course = cVaccinationCourse(aPK_obj=7)
    #               print("\nVaccination course:")
    #               print(vaccination_course)
    #               fields = vaccination_course.get_fields()
    #               for field in fields:
    #                       print(field, ':', vaccination_course[field])
    #               print("updatable:", vaccination_course.get_updatable_fields())

            #--------------------------------------------------------
    #       def test_put_patient_on_schedule():
    #               result, msg = put_patient_on_schedule(patient_id=12, course_id=1)
    #               print('\nPutting patient id 12 on schedule id 1... %s (%s)' % (result, msg))

            #--------------------------------------------------------
            def test_get_vaccines():
                    for vaccine in get_vaccines():
                            print('--------------------------------')
                            #print u'%s' % vaccine
                            print('\n'.join(vaccine.format()))

            #--------------------------------------------------------
            def test_get_vaccinations():
                    v1 = get_vaccinations(return_pks = True, order_by = 'date_given')
                    print(v1)

            #--------------------------------------------------------
            def test_create_generic_vaccine_sql():
                    print(create_generic_vaccine_sql('22.0'))

            #--------------------------------------------------------
            def test_write_generic_vaccine_sql(version, filename):
                    print(write_generic_vaccine_sql (
                            version,
                            include_indications_mapping = True,
                            filename = filename
                    ))

            #--------------------------------------------------------
            #test_vaccination_course()
            #test_put_patient_on_schedule()
            #test_scheduled_vacc()
            #test_vacc()
            #test_due_vacc()
            #test_due_booster()

            #test_get_vaccines()
            test_get_vaccinations()
            #test_create_generic_vaccine_sql()
            #test_write_generic_vaccine_sql(sys.argv[2], sys.argv[3])

## Functions

`def create_generic_vaccine_sql(version, include_indications_mapping=False)`
  Expand source code

      def create_generic_vaccine_sql(version, include_indications_mapping=False):

              _log.debug('including indications mapping table with generic vaccines creation SQL: %s', include_indications_mapping)

              from Gnumed.business import gmVaccDefs

              sql_create_substances = []
              sql_populate_ind2subst_map = []
              sql_create_vaccines = []

              for substance_tag in gmVaccDefs._VACCINE_SUBSTANCES:
                      subst = gmVaccDefs._VACCINE_SUBSTANCES[substance_tag]
                      args = {
                              'substance_tag': substance_tag,
                              'atc': subst['atc4target'],
                              'desc': subst['name'],
                              'orig': subst['target'].split('::')[0],
                              'trans': subst['target'].split('::')[-1]
                      }
                      sql_create_substances.append(_SQL_create_substance4vaccine % args)
                      try:
                              for v21_ind in subst['v21_indications']:
                                      args['v21_ind'] = v21_ind
                                      args['is_live'] = 'false'
                                      sql_populate_ind2subst_map.append(_SQL_map_indication2substance % args)
                      except KeyError:
                              pass
                      try:
                              for v21_ind in subst['v21_indications_live']:
                                      args['v21_ind'] = v21_ind
                                      args['is_live'] = 'true'
                                      sql_populate_ind2subst_map.append(_SQL_map_indication2substance % args)
                      except KeyError:
                              pass
                      args = {}

              for key in gmVaccDefs._GENERIC_VACCINES:
                      vaccine_def = gmVaccDefs._GENERIC_VACCINES[key]
                      # create product
                      args = {
                              'atc_prod': vaccine_def['atc'],
                              'prod_name': vaccine_def['name'],
                              # generic vaccines always have the English preparation
                              'prep': 'vaccine',
                              'is_live': vaccine_def['live']
                      }
                      sql_create_vaccines.append(_SQL_create_vacc_product % args)
                      # create doses
                      for ingredient_tag in vaccine_def['ingredients']:
                              vacc_subst_def = gmVaccDefs._VACCINE_SUBSTANCES[ingredient_tag]
                              args['atc_subst'] = vacc_subst_def['atc4target']
                              args['name_subst'] = vacc_subst_def['name']
                              # substance already created, only need to create dose
                              sql_create_vaccines.append(_SQL_create_vacc_subst_dose % args)
                              # link dose to product
                              sql_create_vaccines.append(_SQL_link_dose2vacc_prod % args)
                              # the following does not work because there are mixed vaccines
                              # any live ingredients included ?
      #                       if vacc_subst_def.has_key('v21_indications_live'):
      #                               if vaccine_def['live'] is False:
      #                                       print vaccine_def
      #                                       raise Exception('vaccine def says "NOT live" but ingredients DO map to <v21_indications_LIVE>')
      #                       if vacc_subst_def.has_key('v21_indications'):
      #                               if vaccine_def['live'] is True:
      #                                       print vaccine_def
      #                                       raise Exception('vaccine def says "live" but ingredients do NOT map to v21_indications_LIVE')

                      # create vaccine
                      sql_create_vaccines.append(_SQL_create_vaccine % args)

              # join
              sql = _SQL_create_generic_vaccines_script % (
                      gmTools.bool2subst (
                              include_indications_mapping,
                              _SQL_create_indications_mapping_table,
                              '-- indications mapping table not included'
                      ),
                      '\n\n'.join(sql_create_substances),
                      '\n\n'.join(sql_create_vaccines),
                      gmTools.bool2subst (
                              include_indications_mapping,
                              '\n\n'.join(sql_populate_ind2subst_map),
                              '-- indications mapping table not populated'
                      ),
                      version,
                      version
              )
              return sql

`def create_vaccination(encounter=None, episode=None, vaccine=None, batch_no=None)`
  Expand source code

      def create_vaccination(encounter=None, episode=None, vaccine=None, batch_no=None):

              cmd = """
                      INSERT INTO clin.vaccination (
                              fk_encounter,
                              fk_episode,
                              fk_vaccine,
                              batch_no
                      ) VALUES (
                              %(enc)s,
                              %(epi)s,
                              %(vacc)s,
                              %(batch)s
                      ) RETURNING pk;
              """
              args = {
                      'enc': encounter,
                      'epi': episode,
                      'vacc': vaccine,
                      'batch': batch_no
              }

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

              return cVaccination(aPK_obj = rows[0][0])

`def create_vaccine(pk_drug_product=None, product_name=None, indications=None, is_live=None)`
  Expand source code

      def create_vaccine(pk_drug_product=None, product_name=None, indications=None, is_live=None):

              assert (is_live is not None), '<is_live> must not be <None>'

              conn = gmPG2.get_connection(readonly = False)
              if pk_drug_product is None:
                      #prep = _('vaccine')
                      prep = 'vaccine'
                      _log.debug('creating vaccine drug product [%s %s]', product_name, prep)
                      vacc_prod = gmMedication.create_drug_product (
                              product_name = product_name,
                              preparation = prep,
                              return_existing = True,
                              # indications are ref.dose rows
                              doses = indications,
                              link_obj = conn
                      )
                      #conn.commit()
                      vacc_prod['atc'] = 'J07'
                      vacc_prod.save(conn = conn)
                      pk_drug_product = vacc_prod['pk_drug_product']
              cmd = 'INSERT INTO ref.vaccine (fk_drug_product, is_live) values (%(pk_drug_product)s, %(live)s) RETURNING pk'
              queries = [{'cmd': cmd, 'args': {'pk_drug_product': pk_drug_product, 'live': is_live}}]
              rows, idx = gmPG2.run_rw_queries(link_obj = conn, queries = queries, get_col_idx = False, return_data = True, end_tx = True)
              conn.close()
              return cVaccine(aPK_obj = rows[0]['pk'])

`def delete_vaccination(vaccination=None)`
  Expand source code

      def delete_vaccination(vaccination=None):
              cmd = """DELETE FROM clin.vaccination WHERE pk = %(pk)s"""
              args = {'pk': vaccination}

              gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])

`def delete_vaccine(vaccine=None)`
  Expand source code

      def delete_vaccine(vaccine=None):

              cmd = 'DELETE FROM ref.vaccine WHERE pk = %(pk)s'
              args = {'pk': vaccine}

              try:
                      gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
              except gmPG2.dbapi.IntegrityError:
                      _log.exception('cannot delete vaccine [%s]', vaccine)
                      return False

              return True

`def format_latest_vaccinations(output_format='latex', emr=None)`
  Expand source code

      def format_latest_vaccinations(output_format='latex', emr=None):

              _log.debug('formatting latest vaccinations into [%s]', output_format)

              vaccs = emr.get_latest_vaccinations()

              if output_format == 'latex':
                      return __format_latest_vaccinations_latex(vaccinations = vaccs)

              msg = _('unknown vaccinations output format [%s]') % output_format
              _log.error(msg)
              return msg

`def get_vaccinations(pk_identity=None, pk_episodes=None, pk_health_issues=None, pk_encounters=None, order_by=None, return_pks=False)`
  Expand source code

      def get_vaccinations(pk_identity=None, pk_episodes=None, pk_health_issues=None, pk_encounters=None, order_by=None, return_pks=False):

              args = {}
              where_parts = []

              if pk_identity is not None:
                      args = {'pk_identity': pk_identity}
                      where_parts.append('pk_patient = %(pk_identity)s')

              if (pk_episodes is not None) and (len(pk_episodes) > 0):
                      where_parts.append('pk_episode = ANY(%(pk_epis)s)')
                      args['pk_epis'] = pk_episodes

              if (pk_health_issues is not None) and (len(pk_health_issues) > 0):
                      where_parts.append('pk_episode = ANY(SELECT pk FROM clin.episode WHERE fk_health_issue = ANY(%(pk_issues)s))')
                      args['pk_issues'] = pk_health_issues

              if (pk_encounters is not None) and (len(pk_encounters) > 0):
                      where_parts.append('pk_encounter = ANY(%(pk_encs)s)')
                      args['pk_encs'] = pk_encounters

              ORDER_BY = gmTools.coalesce (
                      value2test = order_by,
                      return_instead = '',
                      value2return = 'ORDER BY %s' % order_by
              )
              if len(where_parts) == 0:
                      WHERE = 'True'
              else:
                      WHERE = '\nAND '.join(where_parts)

              SQL = '%s %s' % (
                      _SQL_get_vaccination_fields % WHERE,
                      ORDER_BY
              )
              rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': SQL, 'args': args}], get_col_idx = True)
              if return_pks:
                      return [ r['pk_vaccination'] for r in rows ]
              vaccs = [ cVaccination(row = {'idx': idx, 'data': r, 'pk_field': 'pk_vaccination'})  for r in rows ]
              return vaccs

`def get_vaccines(order_by=None, return_pks=False)`
  Expand source code

      def get_vaccines(order_by=None, return_pks=False):

              if order_by is None:
                      cmd = _SQL_get_vaccine_fields % 'TRUE'
              else:
                      cmd = _SQL_get_vaccine_fields % ('TRUE\nORDER BY %s' % order_by)

              rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd}], get_col_idx = True)
              if return_pks:
                      return [ r['pk_vaccine'] for r in rows ]
              return [ cVaccine(row = {'data': r, 'idx': idx, 'pk_field': 'pk_vaccine'}) for r in rows ]

`def write_generic_vaccine_sql(version, include_indications_mapping=False, filename=None)`
  Expand source code

      def write_generic_vaccine_sql(version, include_indications_mapping=False, filename=None):
              if filename is None:
                      filename = gmTools.get_unique_filename(suffix = '.sql')
              _log.debug('writing SQL for creating generic vaccines to: %s', filename)
              sql_file = open(filename, mode = 'wt', encoding = 'utf8')
              sql_file.write(create_generic_vaccine_sql (
                      version,
                      include_indications_mapping = include_indications_mapping
              ))
              sql_file.close()
              return filename

## Classes

`class cVaccination (aPK_obj=None, row: dict = None, link_obj=None)`

  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']

  Init business object.

  Call from child classes like so:

          super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)

  ## Args

  `aPK_obj`
    retrieve data from backend * a simple value the primary key WHERE condition must be a simple column * a dictionary of values the primary key WHERE condition must be a subselect consuming the dict and producing the single-value primary key
  `row`
    must hold the fields * idx: a dict mapping field names to position * data: the field values in a list (as returned by cursor.fetchone() in the DB-API) * pk_field: the name of the primary key field OR * pk_obj: a dictionary suitable for passed to cursor.execute and holding the primary key values, used for composite PKs

  ## Examples

  row = { 'data': rows[0], 'idx': idx, 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) objects = [ cChildClass(row = {'data': r, 'idx': idx, 'pk_field': 'the PK column name'}) for r in rows ]

  Expand source code

      class cVaccination(gmBusinessDBObject.cBusinessDBObject):

              _cmd_fetch_payload = _SQL_get_vaccination_fields % "pk_vaccination = %s"

              _cmds_store_payload = [
                      """UPDATE clin.vaccination SET
                                      soap_cat = %(soap_cat)s,
                                      clin_when = %(date_given)s,
                                      site = gm.nullify_empty_string(%(site)s),
                                      batch_no = gm.nullify_empty_string(%(batch_no)s),
                                      reaction = gm.nullify_empty_string(%(reaction)s),
                                      narrative = gm.nullify_empty_string(%(comment)s),
                                      fk_vaccine = %(pk_vaccine)s,
                                      fk_provider = %(pk_provider)s,
                                      fk_encounter = %(pk_encounter)s,
                                      fk_episode = %(pk_episode)s
                              WHERE
                                      pk = %(pk_vaccination)s
                                              AND
                                      xmin = %(xmin_vaccination)s
                              RETURNING
                                      xmin as xmin_vaccination
                      """
              ]

              _updatable_fields = [
                      'soap_cat',
                      'date_given',
                      'site',
                      'batch_no',
                      'reaction',
                      'comment',
                      'pk_vaccine',
                      'pk_provider',
                      'pk_encounter',
                      'pk_episode'
              ]

              #--------------------------------------------------------
              def format_maximum_information(self, patient=None):
                      return self.format (
                              with_indications = True,
                              with_comment = True,
                              with_reaction = True,
                              date_format = '%Y %b %d'
                      )

              #--------------------------------------------------------
              def format(self, with_indications=False, with_comment=False, with_reaction=False, date_format='%Y-%m-%d'):

                      lines = []

                      lines.append (' %s: %s [%s]%s' % (
                              self._payload[self._idx['date_given']].strftime(date_format),
                              self._payload[self._idx['vaccine']],
                              self._payload[self._idx['batch_no']],
                              gmTools.coalesce(self._payload[self._idx['site']], '', ' (%s)')
                      ))

                      if with_comment:
                              if self._payload[self._idx['comment']] is not None:
                                      lines.append('   %s' % self._payload[self._idx['comment']])

                      if with_reaction:
                              if self._payload[self._idx['reaction']] is not None:
                                      lines.append('   %s' % self._payload[self._idx['reaction']])

                      if with_indications:
                              lines.append('   %s' % ' / '.join([ i['l10n_indication'] for i in self._payload[self._idx['indications']] ]))

                      return lines

              #--------------------------------------------------------
              def _get_vaccine(self):
                      return cVaccine(aPK_obj = self._payload[self._idx['pk_vaccine']])

              vaccine = property(_get_vaccine, lambda x:x)

  ### Ancestors

  - cBusinessDBObject

  ### Instance variables

  `var vaccine`
    Expand source code

        def _get_vaccine(self):
                return cVaccine(aPK_obj = self._payload[self._idx['pk_vaccine']])

  ### Methods

  `def format_maximum_information(self, patient=None)`
    Expand source code

        def format_maximum_information(self, patient=None):
                return self.format (
                        with_indications = True,
                        with_comment = True,
                        with_reaction = True,
                        date_format = '%Y %b %d'
                )

  ### Inherited members

  - `cBusinessDBObject`:
    - `fields_as_dict`
    - `format`
    - `get_fields`
    - `get_patient`
    - `get_updatable_fields`
    - `is_modified`
    - `patient_pk`
    - `refetch_payload`
    - `same_payload`
    - `save`
    - `save_payload`
    - `staff_id`
`class cVaccine (aPK_obj=None, row: dict = None, link_obj=None)`

  Represents one vaccine.

  Init business object.

  Call from child classes like so:

          super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)

  ## Args

  `aPK_obj`
    retrieve data from backend * a simple value the primary key WHERE condition must be a simple column * a dictionary of values the primary key WHERE condition must be a subselect consuming the dict and producing the single-value primary key
  `row`
    must hold the fields * idx: a dict mapping field names to position * data: the field values in a list (as returned by cursor.fetchone() in the DB-API) * pk_field: the name of the primary key field OR * pk_obj: a dictionary suitable for passed to cursor.execute and holding the primary key values, used for composite PKs

  ## Examples

  row = { 'data': rows[0], 'idx': idx, 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) objects = [ cChildClass(row = {'data': r, 'idx': idx, 'pk_field': 'the PK column name'}) for r in rows ]

  Expand source code

      class cVaccine(gmBusinessDBObject.cBusinessDBObject):
              """Represents one vaccine."""

              _cmd_fetch_payload = _SQL_get_vaccine_fields % "pk_vaccine = %s"

              _cmds_store_payload = [
                      """UPDATE ref.vaccine SET
                                      --id_route = %(pk_route)s,
                                      is_live = %(is_live)s,
                                      min_age = %(min_age)s,
                                      max_age = %(max_age)s,
                                      comment = gm.nullify_empty_string(%(comment)s),
                                      fk_drug_product = %(pk_drug_product)s
                              WHERE
                                      pk = %(pk_vaccine)s
                                              AND
                                      xmin = %(xmin_vaccine)s
                              RETURNING
                                      xmin as xmin_vaccine
                      """
              ]

              _updatable_fields = [
                      #'pk_route',
                      'is_live',
                      'min_age',
                      'max_age',
                      'comment',
                      'pk_drug_product'
              ]

              #--------------------------------------------------------
              def format(self, *args, **kwargs):
                      lines = []
                      lines.append(_('%s with %s %s     #%s') % (
                              gmTools.bool2subst(self._payload[self._idx['is_live']], _('Live vaccine'), _('Inactive vaccine'), '<liveness error in DB>'),
                              len(self._payload[self._idx['indications']]),
                              gmTools.bool2subst(len(self._payload[self._idx['indications']]) == 1, _('indication'), _('indications'), _('indication(s)')),
                              self._payload[self._idx['pk_vaccine']]
                      ))
                      lines.append(_(' Product: "%s"     #%s') % (
                              self._payload[self._idx['vaccine']],
                              self._payload[self._idx['pk_drug_product']]
                      ))
                      lines.append(_('  %s%s%s%s') % (
                              self._payload[self._idx['l10n_preparation']],
                              gmTools.coalesce(gmTools.bool2subst(self._payload[self._idx['is_fake_vaccine']], _('fake product'), None, None), '', ', %s'),
                              gmTools.coalesce(self._payload[self._idx['atc_code']], '', ' [ATC:%s]'),
                              gmTools.coalesce(self._payload[self._idx['external_code']], '', ' [%s:%%s]' % self._payload[self._idx['external_code_type']])
                      ))
                      #lines.append(_(u' %sage %s - %s') % (
                      #       gmTools.coalesce(self._payload[self._idx['route_description']], u'', u'%s, '),          #route_abbreviation
                      lines.append(_(' Age %s - %s') % (
                              gmTools.coalesce(self._payload[self._idx['min_age']], '?'),
                              gmTools.coalesce(self._payload[self._idx['max_age']], '?')
                      ))
                      if self._payload[self._idx['comment']] is not None:
                              lines.extend([ ' %s' % l for l in self._payload[self._idx['comment']].split('\n')] )
                      lines.append(_(' Indications'))
                      lines.extend( [ '  %s [ATC:%s]' % (i['l10n_indication'], i['atc_indication']) for i in self._payload[self._idx['indications']] ])

                      return lines

              #--------------------------------------------------------
              # properties
              #--------------------------------------------------------
              def _get_product(self):
                      return gmMedication.cDrugProduct(aPK_obj = self._payload[self._idx['pk_drug_product']])

              product = property(_get_product, lambda x:x)

              #--------------------------------------------------------
              def _get_is_in_use(self):
                      cmd = 'SELECT EXISTS(SELECT 1 FROM clin.vaccination WHERE fk_vaccine = %(pk)s)'
                      args = {'pk': self._payload[self._idx['pk_vaccine']]}
                      rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
                      return rows[0][0]

              is_in_use = property(_get_is_in_use, lambda x:x)

  ### Ancestors

  - cBusinessDBObject

  ### Instance variables

  `var is_in_use`
    Expand source code

        def _get_is_in_use(self):
                cmd = 'SELECT EXISTS(SELECT 1 FROM clin.vaccination WHERE fk_vaccine = %(pk)s)'
                args = {'pk': self._payload[self._idx['pk_vaccine']]}
                rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
                return rows[0][0]

  `var product`
    Expand source code

        def _get_product(self):
                return gmMedication.cDrugProduct(aPK_obj = self._payload[self._idx['pk_drug_product']])

  ### Inherited members

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