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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):
Homo_sapiens = "http://purl.obolibrary.org/obo/NCBITaxon_9606"
SPECIES_TERMS = { # since Python 3.7 dict is ordered! Note that re is allowed
"human": Homo_sapiens,
"sapiens": Homo_sapiens,
"Mustela lutreola": "http://purl.obolibrary.org/obo/NCBITaxon_9666",
"Manis javanica": "http://purl.obolibrary.org/obo/NCBITaxon_9974",
"Felis catus": "http://purl.obolibrary.org/obo/NCBITaxon_9685",
"Panthera tigris": "http://purl.obolibrary.org/obo/NCBITaxon_419130",
"Canis lupus": "http://purl.obolibrary.org/obo/NCBITaxon_9615",
# Mink:
"vison": "http://purl.obolibrary.org/obo/NCBITaxon_452646"
}
warning = None
host = types.SimpleNamespace(**host)
if not 'obolibrary' in host.host_species:
key = host.host_species
host.host_species = None
if key in mapping:
host.host_species = mapping[key]
else:
for term in SPECIES_TERMS:
p = re.compile(".*?"+term,re.IGNORECASE)
m = p.match(key)
if m: host.host_species = SPECIES_TERMS[term]
if not host.host_species:
warning = f"No URI mapping for host_species <{key}>"
if host.host_species == Unknown or host.host_species == None:
del(host.host_species)
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 = Nasopharyngeal # "http://purl.obolibrary.org/obo/NCIT_C132119"
Frozen_Food = "https://www.wikidata.org/wiki/Q751728"
Bronchoalveolar_Lavage = "http://purl.obolibrary.org/obo/NCIT_C13195",
Biospecimen = "http://purl.obolibrary.org/obo/NCIT_C70699"
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,
"broncho": Bronchoalveolar_Lavage,
"seafood": Frozen_Food,
"packaging": Frozen_Food,
"specimen": Biospecimen,
"patient": Biospecimen,
"uknown": Unknown,
"unknown": Unknown
}
warning = None
sample = types.SimpleNamespace(**sample)
try:
if sample.specimen_source:
keys = sample.specimen_source
sample.specimen_source = []
for key in keys:
if 'obolibrary' in key:
sample.specimen_source.append(key)
continue
if key in mapping:
sample.specimen_source.append(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 len(sample.specimen_source)==0:
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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