Merge pull request #238 from zekh167/test_uterus_network

Test uterus network

src/scaffoldmaker/annotation/uterus_terms.py

@@ -0,0 +1,44 @@
+"""
+Common resource for uterus annotation terms.
+"""
+
+# convention: preferred name, preferred id, followed by any other ids and alternative names
+uterus_terms = [
+    ("uterus", "UBERON:0000995"),
+    ("serosa of uterus", "UBERON:0001297"),
+    ("body of uterus", "UBERON:0009853"),
+    ("cervix of uterus", "ILX:0745917 "),
+    ("uterine cervix", "UBERON:0000002"),
+    ("uterine wall", "UBERON:0000459"),
+    ("uterine horn", "UBERON:000224"),
+    ("uterine lumen", "UBERON:0013769"),
+    ("left uterine horn", "UBERON:0009020"),
+    ("right uterine horn", "UBERON:0009022"),
+    ("serosa of uerine cervix", "None"),
+    ("lumen of uerine cervix", "None"),
+    ("serosa of right horn", "None"),
+    ("lumen of right horn", "None"),
+    ("serosa of left horn", "None"),
+    ("lumen of left horn", "None"),
+    ("serosa of uterus", "None"),
+    ("lumen of uterus", "None"),
+    ("fundus", "None"),
+    ("ventral cervix junction with vagina", "None"),
+    ("dorsal cervix junction with vagina", "None"),
+    ("dorsal top right horn", "None"),
+    ("ventral top right horn", "None"),
+    ("dorsal top left horn", "None"),
+    ("ventral top left horn", "None"),
+    ("vagina", "None")
+]
+
+def get_uterus_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 uterus_terms:
+        if name in term:
+            return (term[0], term[1])
+    raise NameError("Uterus annotation term '" + name + "' not found.")