Renal pelvis scaffold

src/scaffoldmaker/annotation/kidney_terms.py

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+"""
+Common resource for kidney annotation terms.
+"""
+
+# convention: preferred name, preferred id, followed by any other ids and alternative names
+kidney_terms = [
+    ("core", ""),
+    ("renal pelvis", "UBERON:0001224", "ILX:0723968"),
+    ("major calyx", "UBERON:0001226", "ILX:0730785"),
+    ("minor calyx", "UBERON:0001227", "ILX:0730473"),
+    ("renal pyramid", "UBERON:0004200", "ILX:0727514"),
+    ("shell", "")
+    ]
+
+def get_kidney_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 kidney_terms:
+        if name in term:
+            return (term[0], term[1])
+    raise NameError("Kidney annotation term '" + name + "' not found.")

src/scaffoldmaker/annotation/ureter_terms.py

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+"""
+Common resource for ureter annotation terms.
+"""
+
+# convention: preferred name, preferred id, followed by any other ids and alternative names
+ureter_terms = [
+    ("ureter", "UBERON:0000056", "ILX:0728080")
+    ]
+
+def get_ureter_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 ureter_terms:
+        if name in term:
+            return (term[0], term[1])
+    raise NameError("Body annotation term '" + name + "' not found.")