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-rw-r--r--workflows/tools/normalize/mapping.py102
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diff --git a/workflows/tools/normalize/mapping.py b/workflows/tools/normalize/mapping.py
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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