def get_sensibility_percentages(df):
microorganisms = dict()
antibiotics = helper.get_all_antibiotics(df)
for index, row in df.iterrows():
if helper.get(row, 'microorganismo') in microorganisms:
microorganism_record = microorganisms.get(
helper.get(row, 'microorganismo'))
else:
microorganism_record = initialize_microorganism_record(
row, antibiotics)
microorganisms[helper.get(row,
'microorganismo')] = microorganism_record
for antibiotic in antibiotics:
antibiotic_resistance = helper.get(row, antibiotic)
if antibiotic_resistance != 'nan':
microorganism_record.sensibility[antibiotic].total += 1
if antibiotic_resistance == 'sensible' or antibiotic_resistance == 'intermedio':
microorganism_record.sensibility[antibiotic].sensible += 1
if microorganism_record.sensibility[antibiotic].total != 0:
microorganism_record.sensibility[antibiotic].percentage = \
microorganism_record.sensibility[antibiotic].sensible / microorganism_record.sensibility[antibiotic].total
microorganism_record.frequency += 1
return microorganisms
def initialize_microorganism_record(row, antibiotics):
microorganism_record = Microorganism(helper.get(row, 'microorganismo'))
microorganism_sensibility = dict()
for antibiotic in antibiotics:
microorganism_sensibility[antibiotic] = SensibilityRecord()
microorganism_record.sensibility = microorganism_sensibility
return microorganism_record
def is_fqr(row):
microorganismo_name = helper.get(row, "microorganismo")
if helper.get_key_matches(['pseudomonas aeruginosa'], microorganismo_name):
return helper.is_resistant_to_all(
row, pseudomonas_aeruginosa_fqr_antibiotics)
if helper.get_key_matches(watched_microorganisms, microorganismo_name):
return helper.is_resistant_to_all(row, enterobacter_fqr_antibiotics)
def fourth_criteria(df):
"""
DTR > CR > ECR > FQR
:param df:
:return:
"""
microorganisms = dict()
for index, row in df.iterrows():
microorganism = Microorganismo()
microorganism.last_register = helper.get(row, 'fechapeticion')
microorganism.last_nhc = helper.get(row, 'nhc')
if is_dtr(row):
microorganism.last_fenotype = ('dtr', 3)
microorganism.dtr_frequency += 1
elif is_cr(row):
microorganism.last_fenotype = ('cr', 2)
microorganism.cr_frequency += 1
elif is_ecr(row):
microorganism.last_fenotype = ('ecr', 1)
microorganism.ecr_frequency += 1
elif is_fqr(row):
microorganism.last_fenotype = ('fqr', 0)
microorganism.fqr_frequency += 1
else:
microorganism.last_fenotype = ('none', -1)
if helper.get(row, 'microorganismo') in microorganisms:
saved_record = microorganisms.get(helper.get(row, 'microorganismo'))
current_date = pd.to_datetime(microorganism.last_register, dayfirst=True)
last_date = pd.to_datetime(saved_record.last_register, dayfirst=True)
if (current_date - last_date).days < 30 and saved_record.last_nhc == microorganism.last_nhc:
if microorganism.last_fenotype[1] >= saved_record.last_fenotype[1]:
helper.decrement_frequency(saved_record, saved_record.last_fenotype[0])
helper.increment_frequency(saved_record, microorganism.last_fenotype[0])
saved_record.last_fenotype = microorganism.last_fenotype
else:
helper.increment_frequency(saved_record, microorganism.last_fenotype[0])
saved_record.frequency += 1
saved_record.last_nhc = microorganism.last_nhc
saved_record.last_fenotype = microorganism.last_fenotype
saved_record.last_register = microorganism.last_register
else:
microorganism.frequency = 1
microorganisms[helper.get(row, 'microorganismo')] = microorganism
return microorganisms
def is_dtr(row):
microorganismo_name = helper.get(row, "microorganismo")
if helper.get_key_matches(acinetobacter_baumannii_complex,
microorganismo_name):
return helper.is_resistant_to_all(
row, acinetobacter_baumannii_complex_dtr_antibiotics)
if helper.get_key_matches(watched_microorganisms, microorganismo_name):
return helper.is_resistant_to_all(row, dtr_antibiotics)
def is_cr(row):
microorganismo_name = helper.get(row, "microorganismo")
if helper.get_key_matches(
acinetobacter_baumannii_complex + ['pseudomonas aeruginosa'],
microorganismo_name):
return helper.is_resistant_to_all(
row, pseudomonas_aeruginosa_cr_antibiotics)
if helper.get_key_matches(watched_microorganisms, microorganismo_name):
return helper.is_resistant_to_all(row, enterobacter_cr_antibiotics)
def matches_criteria(dataframe, antibiotics, excluded=None, included=None):
microorganismos = dict()
for index, row in dataframe.iterrows():
microorganismo_name = helper.get(row, "microorganismo")
if (excluded is not None) and helper.get_key_matches(
excluded, microorganismo_name):
continue
if (included is not None) and not helper.get_key_matches(
included, microorganismo_name):
continue
if helper.is_resistant_to_all(row, antibiotics):
if microorganismo_name in microorganismos:
microorganismo = microorganismos.get(microorganismo_name)
microorganismo.frequency += 1
else:
microorganismo = Microorganism(resistant_to=antibiotics)
microorganismo.frequency += 1
microorganismos[microorganismo_name] = microorganismo
return microorganismos