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Diffstat (limited to 'workflows/tools/normalize/mapping.py')
| -rw-r--r-- | workflows/tools/normalize/mapping.py | 102 |
1 files changed, 0 insertions, 102 deletions
diff --git a/workflows/tools/normalize/mapping.py b/workflows/tools/normalize/mapping.py deleted file mode 100644 index 3ed09c2..0000000 --- a/workflows/tools/normalize/mapping.py +++ /dev/null @@ -1,102 +0,0 @@ -# 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 |