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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 re
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
Unknown = "Not found" # So as not to create a warning
def specimen_source(sample,mapping):
Oronasopharynx = "http://purl.obolibrary.org/obo/NCIT_C155835"
Oropharyngeal = "http://purl.obolibrary.org/obo/NCIT_C155835"
Nasopharyngeal = "http://purl.obolibrary.org/obo/NCIT_C155831"
Bronchoalveolar_Lavage_Fluid = "http://purl.obolibrary.org/obo/NCIT_C13195"
Saliva = "http://purl.obolibrary.org/obo/NCIT_C13275"
Nasal_Swab = "http://purl.obolibrary.org/obo/NCIT_C132119"
Frozen_Food = "https://www.wikidata.org/wiki/Q751728"
SPECIMEN_TERMS = { # since Python 3.7 dict is ordered! Note that re is allowed
"Oronasopharynx": Oronasopharynx,
"orophar": Oropharyngeal,
"pharyngeal": Nasopharyngeal,
"\snares": Nasal_Swab,
"saliva": Saliva,
"swab": Nasal_Swab,
"seafood": Frozen_Food,
"packaging": Frozen_Food,
"uknown": Unknown,
"unknown": Unknown
}
warning = None
sample = types.SimpleNamespace(**sample)
try:
if sample.specimen_source and \
not 'obolibrary' in sample.specimen_source and \
not 'wikidata' in sample.specimen_source:
key = sample.specimen_source
sample.specimen_source = None
if key in mapping:
sample.specimen_source = mapping[key]
else:
for term in SPECIMEN_TERMS:
p = re.compile(".*?"+term,re.IGNORECASE)
m = p.match(key)
if m: sample.specimen_source = SPECIMEN_TERMS[term]
if not sample.specimen_source:
warning = f"No URI mapping for specimen_source <{key}>"
if sample.specimen_source == Unknown or sample.specimen_source == None:
del(sample.specimen_source)
except AttributeError:
pass
return sample.__dict__,warning
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