diff options
Diffstat (limited to 'workflows/tools')
| -rwxr-xr-x | workflows/tools/normalize-yamlfa.py | 6 | ||||
| -rw-r--r-- | workflows/tools/normalize/mapping.py | 59 |
2 files changed, 47 insertions, 18 deletions
diff --git a/workflows/tools/normalize-yamlfa.py b/workflows/tools/normalize-yamlfa.py index 20c2feb..55a8848 100755 --- a/workflows/tools/normalize-yamlfa.py +++ b/workflows/tools/normalize-yamlfa.py @@ -19,10 +19,10 @@ directory are parsed using the state.json file. It is possible to select a subset of IDs. This tool has two modes of operation. It can validate with the -`--validate` switch which stops at a warning and does no rewriting. +--validate switch which stops at a warning and does no rewriting. This mode is typically used in troubleshooting. -The other mode is `--rewrite` which rewrites the JSON files after +The other mode is --rewrite which rewrites the JSON files after making a backup (.bak) of the original. This mode updates files and won't stop - it is used for (automated) uploads. @@ -92,6 +92,6 @@ for id in ids: os.rename(fn,fn+".bak") with open(fn, 'w') as outfile: print(f" Writing {fn}") - json.dump(rec.__dict__, outfile, indent=4) + json.dump(rec.__dict__, outfile, indent=2) else: print(rec) diff --git a/workflows/tools/normalize/mapping.py b/workflows/tools/normalize/mapping.py index bc82fea..3ed09c2 100644 --- a/workflows/tools/normalize/mapping.py +++ b/workflows/tools/normalize/mapping.py @@ -17,14 +17,36 @@ 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 @@ -35,8 +57,10 @@ def specimen_source(sample,mapping): 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" + 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, @@ -44,28 +68,33 @@ def specimen_source(sample,mapping): "\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 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: + 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: |