Reportable clinic events, reference ranges, grading
from dateutil.relativedelta import relativedelta
from edc_base.utils import get_utcnow
from edc_constants.constants import MALE, FEMALE
from edc_reportable import ValueReferenceGroup, NormalReference, GradeReference
from edc_reportable import site_reportables
from edc_reportable.tests.reportables import normal_data, grading_data
Create a group for each test:
neutrophils = ValueReferenceGroup(name='neutrophils')
A normal reference is declared like this:
ref = NormalReference(
name='neutrophils',
lower=2.5,
upper=7.5,
units='10e9/L',
age_lower=18,
age_upper=99,
age_units='years',
gender=[MALE, FEMALE])
ref
>>> NormalReference(neutrophils, 2.5<x<7.5 10e9/L MF, 18<AGE<99 years)
And add to a group like this:
neutrophils.add_normal(ref)
Add as many normal references in a group as you like, just ensure the lower and upper boundaries don't overlap.
Note: If the lower and upper values of a normal reference overlap with another normal reference in the same group, a
BoundaryOverlapexception will be raised when the value is evaluated. Catch this in your tests.
A grading reference is declared like this:
g3 = GradeReference(
name='neutrophils',
grade=3,
lower=0.4,
lower_inclusive=True,
upper=0.59,
upper_inclusive=True,
units='10e9/L',
age_lower=18,
age_upper=99,
age_units='years',
gender=[MALE, FEMALE])
>>> g3
GradeReference(neutrophils, 0.4<=x<=0.59 in 10e9/L GRADE 3, MF, 18<AGE<99 in years) GRADE 3)
And added to the group like this:
neutrophils.add_grading(g3)
Declare and add a GradeReference for each reportable grade of the test.
Note: If the lower and upper values of a grade reference overlap with another grade reference in the same group, a
BoundaryOverlapexception will be raised when the value is evaluated. Catch this in your tests.
Once you have declared all your references, register them
site_reportables.register(
name='my_project',
normal_data=normal_data,
grading_data=grading_data)
Important: Writing out references is prone to error. It is better to declare a dictionary of normal references and grading references. Use the
parsefunction so that you can use a phrase like13.5<=x<=17.5instead of a listing attributes. There are examples of completenormal_dataandgrading_datain the tests. Seeedc_reportable.tests.reportables.
You can export your declared references to CSV for further inspection
>>> site_reportables.to_csv(name='my_project', path='~/')
('/Users/erikvw/my_project_normal_ranges.csv',
'/Users/erikvw/my_project_grading.csv')
In your code, get the references by collection name:
my_project_reportables = site_reportables.get('my_project')
neutrophil = my_project_reportables.get('neutrophil')
report_datetime = get_utcnow()
dob = (report_datetime - relativedelta(years=25)).date()
If a value is normal, get_normal returns the NormalReference instance that matched with the value.
# evaluate a normal value
normal = neutrophil.get_normal(
value=3.5, units='10^9/L',
gender=MALE, dob=dob, report_datetime=report_datetime)
# returns a normal object with information about the range selected
>>> normal.description
'2.5<=3.5<=7.5 10^9/L MF, 18<=AGE years'
If a value is abnormal, get_normal returns None.
# evaluate an abnormal value
opts = dict(
units='10^9/L',
gender=MALE, dob=dob,
report_datetime=report_datetime)
normal = neutrophil.get_normal(value=0.3, **opts)
# returns None
>>> if not normal:
print('abnormal')
'abnormal'
To show which ranges the value was evaluated against
# use same options for units, gender, dob, report_datetime
>>> neutrophil.get_normal_description(**opts)
['2.5<=x<=7.5 10^9/L MF, 18<=AGE years']
grade = neutrophil.get_grade(
value=0.43, units='10^9/L',
gender=MALE, dob=dob, report_datetime=report_datetime)
>>> grade.grade
3
>>> grade.description
'0.4<=0.43<=0.59 10^9/L GRADE 3'
grade = neutrophil.get_grade(
value=0.3, units='10^9/L',
gender=MALE, dob=dob, report_datetime=report_datetime)
>>> grade.grade
4
>>> grade.description
'0.3<0.4 10^9/L GRADE 4'
If the value is not evaluated against any reportable ranges, a NotEvaluated exception is raised
# call with the wrong units
>>> grade = neutrophil.get_grade(
value=0.3, units='mmol/L',
gender=MALE, dob=dob, report_datetime=report_datetime)
NotEvaluated: neutrophil value not graded. No reference range found ...
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