def __init__(self):
self._config = Config(os.path.join(PROJECT_ROOT, 'config.json'))
self._db = DrugDatabase(self._config)
self._env = Environment(loader=FileSystemLoader(
[TEMPLATE_ROOT, TRANSLATIONS_ROOT]),
lstrip_blocks=True,
trim_blocks=True)
from combogen.ChartGenerator import ChartGenerator, PROJECT_ROOT, TEMPLATE_ROOT, TRANSLATIONS_ROOT, TOOLS_ROOT
from combogen.Config import Config
import os
import subprocess
RENDER_SCRIPT_PATH = os.path.join(TOOLS_ROOT, 'render.js')
OUTPUT_PATH = os.path.abspath(os.path.join(PROJECT_ROOT, 'output'))
HTML_PATH = os.path.join(OUTPUT_PATH, 'html')
PNG_PATH = os.path.join(OUTPUT_PATH, 'png')
PDF_PATH = os.path.join(OUTPUT_PATH, 'pdf')
config = Config(os.path.join(PROJECT_ROOT, 'config.json'))
try:
os.makedirs(HTML_PATH)
except FileExistsError:
pass
try:
os.makedirs(PNG_PATH)
except FileExistsError:
pass
try:
os.makedirs(PDF_PATH)
except FileExistsError:
pass
try:
chart_generator = ChartGenerator()
chart_generator.debug()
def __init__(self):
self._config = Config(os.path.join(PROJECT_ROOT, 'config.json'))
self._db = DrugDatabase(self._config)
self._env = Environment(loader=PackageLoader('combogen', 'templates'),
lstrip_blocks=True,
trim_blocks=True)
class BackGenerator(object):
def __init__(self):
self._config = Config(os.path.join(PROJECT_ROOT, 'config.json'))
self._db = DrugDatabase(self._config)
self._env = Environment(loader=PackageLoader('combogen', 'templates'),
lstrip_blocks=True,
trim_blocks=True)
def generate(self, lang):
template = self._env.get_template('combo-back-full.html')
time_generated = datetime.now(timezone.utc)
status_msg = "Verze {}<br>".format(self._config.version)
status_msg += "Vygenerováno {} {} UTC".format(
time_generated.strftime("%d. %m. %Y"),
time_generated.strftime("%H:%M"))
return template.render(status=status_msg,
lang=lang,
db=self._db,
cfg=self._config)
def _find_missing_drugs(self):
config_drugs = self._config.all_drugs_in_order
json_drugs = self._db.combos.keys()
missing_from_config = [
drug for drug in json_drugs
if not self._config.is_drug_in_config(drug)
]
missing_from_json = [
drug for drug in config_drugs
if not self._db.is_drug_in_combos(drug)
]
return (missing_from_json, missing_from_config)
def _find_missing_combos(self):
"""
Find missing or asymmetric drug combos
(If DrugA->DrugB combo is defined, but DrugB->DrugA isn't).
It will also return interactions which don't have CSS class defined in config.json
(In "interactionClass" section)
Only checks combos for drugs defined in config
"""
all_drugs = self._config.all_drugs_in_order
missing = set()
unknown_interactions = set()
asymmetric_combos = dict()
for drug_a in all_drugs:
for drug_b in all_drugs:
if drug_a == drug_b:
continue
a_to_b = self._db.interaction(drug_a, drug_b, strict=True)
b_to_a = self._db.interaction(drug_b, drug_a, strict=True)
if a_to_b is None:
missing.add((drug_a, drug_b))
elif self._config.interaction_to_class(a_to_b) == "unknown":
unknown_interactions.add(repr(a_to_b))
if b_to_a is None:
missing.add((drug_b, drug_a))
elif self._config.interaction_to_class(b_to_a) == "unknown":
unknown_interactions.add(repr(b_to_a))
if (a_to_b is not None
and b_to_a is not None) and a_to_b != b_to_a:
if "{}+{}".format(drug_b,
drug_a) not in asymmetric_combos.keys():
asymmetric_combos["{}+{}".format(
drug_a,
drug_b)] = "'{}', '{}'".format(a_to_b, b_to_a)
return (missing, asymmetric_combos, unknown_interactions)
def debug(self):
print("== DRUG GROUPS IN DATABASE (FROM CONFIG) ==\r\n")
for group in self._db.drug_groups:
drug_names = [drug.name for drug in group]
drugs_with_commas = ', '.join(drug_names)
message = "{} ({}): {}".format(group.name, len(group),
drugs_with_commas)
print(message)
print("\r\n== MISSING DRUGS (ASYMMETRIC JSON <-> CONFIG) ==\r\n")
from_json, from_config = self._find_missing_drugs()
print("Missing from JSON ({}): {}".format(len(from_json),
', '.join(from_json)))
print("Missing from Config ({}): {}".format(len(from_config),
', '.join(from_config)))
print(
"\r\n== MISSING DRUG COMBO DEFINITIONS AND UNKNOWN INTERACTIONS ==\r\n"
)
missing_combos, asymmetric_combos, unknown_interactions = self._find_missing_combos(
)
missing_combos = ["{}->{}".format(a, b) for a, b in missing_combos]
print("Combos missing in JSON ({}): {}".format(
len(missing_combos), ', '.join(missing_combos)))
print("Unknown interactions ({}): {}".format(
len(unknown_interactions), ', '.join(unknown_interactions)))
print("\r\n== ASYMMETRIC DRUG COMBOS ==\r\n")
asymmetric_combos = [
"{} ({})".format(combo, diff)
for combo, diff in asymmetric_combos.items()
]
print("Asymmetric combos ({}): {}".format(
len(asymmetric_combos), ", ".join(asymmetric_combos)))
def __init__(self):
self._config = Config(os.path.join(PROJECT_ROOT, 'config.json'))
self._db = DrugDatabase(self._config)
self._env = Environment(loader=PackageLoader('combogen', 'templates'), lstrip_blocks=True, trim_blocks=True)
class ChartGenerator(object):
def __init__(self):
self._config = Config(os.path.join(PROJECT_ROOT, 'config.json'))
self._db = DrugDatabase(self._config)
self._env = Environment(loader=PackageLoader('combogen', 'templates'), lstrip_blocks=True, trim_blocks=True)
def generate(self, lang):
template = self._env.get_template('combo-chart-full.html')
time_generated = datetime.now(timezone.utc)
status_msg = "Verze {}<br>".format(self._config.version)
status_msg += "Vygenerováno {} {} UTC".format(time_generated.strftime("%d. %m. %Y"), time_generated.strftime("%H:%M"))
return template.render(status=status_msg, lang=lang, db=self._db, cfg=self._config)
def _find_missing_drugs(self):
config_drugs = self._config.all_drugs_in_order
json_drugs = self._db.combos.keys()
missing_from_config = [drug for drug in json_drugs if not self._config.is_drug_in_config(drug)]
missing_from_json = [drug for drug in config_drugs if not self._db.is_drug_in_combos(drug)]
return (missing_from_json, missing_from_config)
def _find_missing_combos(self):
"""
Find missing or asymmetric drug combos
(If DrugA->DrugB combo is defined, but DrugB->DrugA isn't).
It will also return interactions which don't have CSS class defined in config.json
(In "interactionClass" section)
Only checks combos for drugs defined in config
"""
all_drugs = self._config.all_drugs_in_order
missing = set()
unknown_interactions = set()
asymmetric_combos = dict()
for drug_a in all_drugs:
for drug_b in all_drugs:
if drug_a == drug_b:
continue
a_to_b = self._db.interaction(drug_a, drug_b, strict=True)
b_to_a = self._db.interaction(drug_b, drug_a, strict=True)
if a_to_b is None:
missing.add((drug_a, drug_b))
elif self._config.interaction_to_class(a_to_b) == "unknown":
unknown_interactions.add(repr(a_to_b))
if b_to_a is None:
missing.add((drug_b, drug_a))
elif self._config.interaction_to_class(b_to_a) == "unknown":
unknown_interactions.add(repr(b_to_a))
if (a_to_b is not None and b_to_a is not None) and a_to_b != b_to_a:
if "{}+{}".format(drug_b, drug_a) not in asymmetric_combos.keys():
asymmetric_combos["{}+{}".format(drug_a, drug_b)] = "'{}', '{}'".format(a_to_b, b_to_a)
return (missing, asymmetric_combos, unknown_interactions)
def debug(self):
print("== DRUG GROUPS IN DATABASE (FROM CONFIG) ==\r\n")
for group in self._db.drug_groups:
drug_names = [drug.name for drug in group]
drugs_with_commas = ', '.join(drug_names)
message = "{} ({}): {}".format(group.name, len(group), drugs_with_commas)
print(message)
print("\r\n== MISSING DRUGS (ASYMMETRIC JSON <-> CONFIG) ==\r\n")
from_json, from_config = self._find_missing_drugs()
print("Missing from JSON ({}): {}".format(len(from_json), ', '.join(from_json)))
print("Missing from Config ({}): {}".format(len(from_config), ', '.join(from_config)))
print("\r\n== MISSING DRUG COMBO DEFINITIONS AND UNKNOWN INTERACTIONS ==\r\n")
missing_combos, asymmetric_combos, unknown_interactions = self._find_missing_combos()
missing_combos = ["{}->{}".format(a, b) for a, b in missing_combos]
print("Combos missing in JSON ({}): {}".format(len(missing_combos), ', '.join(missing_combos)))
print("Unknown interactions ({}): {}".format(len(unknown_interactions), ', '.join(unknown_interactions)))
print("\r\n== ASYMMETRIC DRUG COMBOS ==\r\n")
asymmetric_combos = ["{} ({})".format(combo, diff) for combo, diff in asymmetric_combos.items()]
print("Asymmetric combos ({}): {}".format(len(asymmetric_combos), ", ".join(asymmetric_combos)))
def __init__(self):
self._config = Config(os.path.join(PROJECT_ROOT, 'config.json'))
self._db = DrugDatabase(self._config)
self._env = Environment(loader=FileSystemLoader([TEMPLATE_ROOT, TRANSLATIONS_ROOT]), lstrip_blocks=True,
trim_blocks=True)
