Pull request for bone scaffold - final

src/scaffoldmaker/annotation/bone_terms.py

@@ -0,0 +1,33 @@
+"""
+Common resource for testing annotation terms.
+"""
+
+# convention: preferred name, preferred id, followed by any other ids and alternative names
+bone_terms = [
+                    #General bones
+                    ("Cancellous bone", "ILX:0491986"),
+                    ("Cortical bone", "ILX:0745808"),
+                    # Geometric markers for bones
+                    ("Olecranon", "UBERON:0006810","ILX:0735843"),
+                    ("Coronoid process of ulna", "UBERON:0010994","ILX:0735423"),
+                    ("Greater tubercle of radius","ILX:0745221"),
+                    ("Medial epicondyle of radius","ILX:0748959"),
+                    ("Lateral epicondyle of radius", "ILX:0748301"),
+                    ("Intercondylar eminence of tibia", "ILX:0743525"),
+                    ("Inferior articular surface of tibia", "ILX:0748099"),
+                    ("Medial surface of tibia", "ILX:0747893"),
+                    ("Lateral surface of tibia", "ILX:0742857"),
+
+]
+
+
+def get_bone_term(name : str):
+    """
+    Find term by matching name to any identifier held for a term.
+    Raise exception if name not found.
+    :return ( preferred name, preferred id )
+    """
+    for term in bone_terms:
+        if name in term:
+            return ( term[0], term[1] )
+    raise NameError("Bone annotation term '" + name + "' not found.")