mapping sample_species using regex

1 files changed, 24 insertions, 4 deletions

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