def parse_sample(row, dayfirst_dict, source=None):
"""Parse a row into a Sample.
Parameters
----------
row : dict-like
Object whose keys are column headings and values are the row values.
dayfirst_dict : dict
Dictionary whose keys are names of columns containing date/time data
and values are boolean indicating whether the dates in that column
should be interpreted as having a day as the first component (True)
or a month or year as the first component (False).
source : model.Source
Source for the returned sample.
Returns
-------
Sample
"""
sample = Sample()
sample.age_units = get_age_units(row, ureg.years)
sample.age = get_age(row)
sample.latitude = get_latitude(row)
sample.longitude = get_longitude(row)
sample.elevation = get_elevation(row)
sample.height_units = get_height_units(row, ureg.metres)
sample.height = get_height(row)
sample.weight_units = get_weight_units(row, ureg.kilograms)
sample.weight = get_weight(row)
sample.bmi = get_bmi(row)
(d, t) = get_collection_datetime(row, dayfirst_dict)
sample.sample_date = d
sample.sample_time = t
sample.sampling_time = parse_sampling_time(sample)
sample.sampling_site = parse_sampling_site(row)
# Initialize equality attrs
if not source:
sample.source = parse_source(row)
elif isinstance(source, Source):
sample.source = source
else:
raise TypeError(f'Given source was not of type {type(Source())!r}.')
sample.orig_study_id = get_study_id(row)
sample.orig_subject_id = get_subject_id(row)
sample.orig_sample_id = get_sample_id(row)
return sample
def parse_sample(row, attr_map, site_attrs_map=None, time_attr=None):
"""Parse a row of an indexable collection into a Sample.
Parameters
----------
row : indexable collection
A row to be parsed into a Sample.
attr_map : dict
A dictionary mapping indexes for the indexable collection `row` to
attribute names of the Sample object.
"""
sample = Sample()
# print(row)
for index, attr in attr_map.items():
setattr(sample, attr, row[index])
if site_attrs_map:
sample.sampling_site = parse_sample_site(row, site_attrs_map)
if time_attr:
sample.sampling_time = parse_sample_time(row, time_attr)
return sample
