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-rw-r--r--workflows/pull-data/genbank/ref.py19
-rw-r--r--workflows/tools/normalize/mapping.py28
2 files changed, 24 insertions, 23 deletions
diff --git a/workflows/pull-data/genbank/ref.py b/workflows/pull-data/genbank/ref.py
index 4d4df48..d2a377e 100644
--- a/workflows/pull-data/genbank/ref.py
+++ b/workflows/pull-data/genbank/ref.py
@@ -21,22 +21,3 @@ elif GBQualifier_name_text == 'collected_by':
elif GBQualifier_name_text == 'isolation_source':
if GBQualifier_value_text.upper() in field_to_term_to_uri_dict['ncbi_speciesman_source']:
GBQualifier_value_text = GBQualifier_value_text.upper() # For example, in case of 'usa: wa'
-
-# Little cleaning
-GBQualifier_value_text = GBQualifier_value_text.strip("/'")
-
-if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_speciesman_source']:
- sample['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source'][GBQualifier_value_text]]
-else:
- if GBQualifier_value_text.lower() in ['np/op', 'np-op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'combined nasopharyngeal and oropharyngeal swab', 'naso and/or oropharyngeal swab']:
- sample['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['oropharyngeal swab']]
- elif GBQualifier_value_text.lower() in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab', 'nasopharyngeal swab and throat swab', 'nasal swab and throat swab', 'nasopharyngeal aspirate/throat swab', 'Nasopharyngeal/Throat']:
- sample['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']]
- elif GBQualifier_value_text.lower() in ['nasopharyngeal aspirate & throat swab', 'nasopharyngeal aspirate and throat swab']:
- sample['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal aspirate'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']]
- elif GBQualifier_value_text.lower() in ['nasal swab and throat swab']:
- sample['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']]
- elif GBQualifier_value_text.lower() in ['nasal-swab and oro-pharyngeal swab']:
- sample['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['oropharyngeal swab']]
- else:
- missing_value_list.append('\t'.join([accession_version, 'specimen_source', GBQualifier_value_text]))
diff --git a/workflows/tools/normalize/mapping.py b/workflows/tools/normalize/mapping.py
index 1d52b03..d2af3b5 100644
--- a/workflows/tools/normalize/mapping.py
+++ b/workflows/tools/normalize/mapping.py
@@ -13,6 +13,7 @@
#
# Pjotr Prins (c) 2021
+import re
import types
def host_species(host,mapping):
@@ -26,18 +27,37 @@ def host_species(host,mapping):
warning = f"No URI mapping for host_species <{key}>"
return host.__dict__,warning
+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"
+
def specimen_source(sample,mapping):
+ SPECIMEN_TERMS = {
+ r".*swab": Nasal_Swab,
+ "saliva": Saliva,
+ "seafood": Frozen_Food,
+ "packaging": Frozen_Food
+ }
warning = None
sample = types.SimpleNamespace(**sample)
+
try:
- if sample.specimen_source and not 'obolibrary' in sample.specimen_source:
+ 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:
- sample.specimen_source = None
- warning = f"No URI mapping for specimen_source <{key}>"
+ 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 == None: del(sample.specimen_source)
except AttributeError:
pass
- if not sample.specimen_source: del(sample.specimen_source)
return sample.__dict__,warning