Module Gnumed.business.gmVaccDefs

# -*- coding: utf-8 -*-

"""GNUmed vaccination related definitions (only).

Based on WHO ATC data.

Interestingly, WHO does not list ATC codes for a few
vaccination indications, such as Q-fever. It also misses some
common multi-component vaccines, such as TdaP."""

#============================================================
__author__ = "K.Hilbert <Karsten.Hilbert@gmx.net>"
__license__ = "GPL v2"

import sys
import logging


if __name__ == '__main__':
        sys.path.insert(0, '../../')
        _ = lambda x:x
else:
        try:
                _
        except NameError:
                from Gnumed.pycommon import gmI18N
                gmI18N.activate_locale()
                gmI18N.install_domain()


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

#============================================================
__VACCINATION__SINGLE_TARGET_ATCS = {
        # -- non-viral -------------------------------
        'anthrax (bacillus anthracis)': {'atc': 'J07AC01'},
        'brucellosis (brucella)': {'atc': 'J07AD01'},
        'cholera (vibrio cholerae)': {'atc': 'J07AE0'},
        'diphtheria (corynebacterium diphtheriae)': {'atc': 'J07AF01'},
        'HiB (hemophilus influenzae B)': {'atc': 'J07AG01'},
        'MenA (meningococcus A)': {'atc': 'J07AH01'},
        'MenB (meningococcus B)': {'atc': 'J07AH06'},
        'MenC (meningococcus C)': {'atc': 'J07AH07'},
        'MenY (meningococcus Y)': {'atc': 'J07AH0Y'},
        'MenW (meningococcus W)': {'atc': 'J07AH0W'},
        'pertussis (bordetella pertussis)': {'atc': 'J07AJ0'},
        'plague (yersinia pestis)': {'atc': 'J07AK01'},
        'pneumococcal infection (streptococcus pneumoniae)': {'atc': 'J07AL0'},
        'tetanus (clostridium tetani)': {'atc': 'J07AM01'},
        'tuberculosis (mycobacterium tuberculosis)': {'atc': 'J07AN01'},
        'typhoid (salmonella typhi)': {'atc': 'J07AP0'},
        'parathypoid (salmonella typhi)': {'atc': 'J07AP1'},
        'typhus exanthematicus (rickettsia prowazekii)': {'atc': 'J07AR01'},
        'Q fever (coxiella burnetii)': {'atc': 'J07AXQF'},
        # -- viral ------------------------------------------------
        'tick-borne meningoencephalitis (flavivirus)': {'atc': 'J07BA01'},
        'japanese B encephalitis (flavivirus)': {'atc': 'J07BA0J'},
        'influenza (seasonal, H3N2, H1N1)': {'atc': 'J07BB0'},
        'hepatitis B (HBV)': {'atc': 'J07BC01'},
        'hepatitis A (HAV)': {'atc': 'J07BC02'},
        'measles (morbillivirus hominis)': {'atc': 'J07BD01'},
        'mumps (Mumps orthorubolavirus)': {'atc': 'J07BE01'},
        'chickenpox, shingles (varicella zoster virus)': {'atc': 'J07BK0'},
        'rubella (rubivirus rubellae)': {'atc': 'J07BJ01'},
        'poliomyelitis (polio virus)': {'atc': 'J07BF0'},
        'rabies (rabies lyssavirus)': {'atc': 'J07BG01'},
        'rotavirus': {'atc': 'J07BH0'},
        'yellow fever (yellow fever virus)': {'atc': 'J07BL01'},
        'smallpox, mpox (variola virus)': {'atc': 'J07BX01'},
        'dengue fever (flavivirus)': {'atc': 'J07BX04'},
        'RSV (human respiratory syncytial virus)': {'atc': 'J07BX05'},
        'HPV (generic)': {'atc': 'J07BM0'},
        'HPV (6,11,16,18)': {'atc': 'J07BM01'},
        'HPV (16,18)': {'atc': 'J07BM02'},
        'HPV (6,11,16,18,31,33,45,52,58)': {'atc': 'J07BM03'},
        'CoViD-2019 (SARS-CoV-2)': {'atc': 'J07BX03'}
}

#============================================================
__SQL_v23_insert_vaccination_target = """-- v23: single-target vaccination indication "%(target)s"
INSERT INTO ref.vacc_indication (target, atc)
SELECT '%(target)s', '%(atc)s' WHERE NOT EXISTS (
        SELECT 1 FROM ref.vacc_indication
        WHERE target = '%(target)s' OR atc = '%(atc)s'
);
"""

# useful for creating a bootstrapper script
def v23_generate_vaccination_targets_SQL():
        lines = []
        for target, data in __VACCINATION__SINGLE_TARGET_ATCS.items():
                lines.append(__SQL_v23_insert_vaccination_target % {
                        'target': target,
                        'atc': data['atc']
                })
        return '\n'.join(lines)

#============================================================
__SQL_v23_insert_generic_vaccine = """-- v23: single-target generic vaccine for indication "%(target)s"
INSERT INTO ref.vaccine (atc, comment, is_live)
        SELECT '%(atc)s', 'generic vaccine for %(target)s', False
        WHERE NOT EXISTS (
                SELECT 1 FROM ref.vaccine WHERE atc = '%(atc)s'
        );

INSERT INTO ref.lnk_indic2vaccine (fk_vaccine, fk_indication)
        SELECT
                (SELECT pk FROM ref.vaccine WHERE atc = '%(atc)s' AND fk_drug_product IS NULL),
                (SELECT pk FROM ref.vacc_indication WHERE atc = '%(atc)s')
        WHERE NOT EXISTS (
                SELECT 1 FROM ref.lnk_indic2vaccine
                WHERE
                        (fk_vaccine = (SELECT pk FROM ref.vaccine WHERE atc = '%(atc)s' AND fk_drug_product IS NULL))
                                AND
                        (fk_indication = (SELECT pk FROM ref.vacc_indication WHERE atc = '%(atc)s'))
        );
"""

def v23_generate_generic_vaccines_SQL():
        lines = []
        for target, data in __VACCINATION__SINGLE_TARGET_ATCS.items():
                lines.append(__SQL_v23_insert_generic_vaccine % {
                        'target': target,
                        'atc': data['atc']
                })
        return '\n'.join(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()

        #-----------------------------------------------------
        def test_v23_generate_vaccination_targets_SQL():
                print(v23_generate_vaccination_targets_SQL())

        #-----------------------------------------------------
        def test_v23_generate_generic_vaccines_SQL():
                print(v23_generate_generic_vaccines_SQL())

        #-----------------------------------------------------
        #test_v23_generate_vaccination_targets_SQL()
        test_v23_generate_generic_vaccines_SQL()