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# Normalization steps
#
# This library contains generic logic to normalize (string) data and
# transforms strings to URIs. It should be applicable to data from
# any source (GenBank, ENA etc).
#
# Important: missing data should be missing or None! Do not fill
# in data by 'guessing'.
#
# When data is malformed a warning should be logged and added to the
# warning list. Functions should be small enough to return only 1
# warning!
#
# Pjotr Prins (c) 2021
import types
def host_species(host,mapping):
warning = None
host = types.SimpleNamespace(**host)
if not 'obolibrary' in host.host_species:
key = host.host_species
if key in mapping:
host.host_species = mapping[key]
else:
warning = f"No URI mapping for host_species <{key}>"
return host.__dict__,warning
def specimen_source(sample,mapping):
warning = None
sample = types.SimpleNamespace(**sample)
try:
if sample.specimen_source and not 'obolibrary' in sample.specimen_source:
key = sample.specimen_source
if key in mapping:
sample.specimen_source = mapping[key]
else:
sample.specimen_source = None
warning = f"No URI mapping for specimen_source <{key}>"
except AttributeError:
pass
if not sample.specimen_source: del(sample.specimen_source)
return sample.__dict__,warning
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