Improve Term string formatting and obsoleted-term messaging (#53)

Author: ubyndr

pandasaurus/resources/term.py

@@ -102,9 +102,12 @@ def __eq__(self, other):
         return False
 
     def __str__(self):
-        msg = f"IRI: {self.__iri}, Label: {self.__label}, Valid: {self.__is_valid}"
+        label = self.__label or "Unknown label"
+        msg = f"IRI: {self.__iri}, Label: {label}, Valid: {self.__is_valid}"
         if self.__is_valid:
             msg += f", Obsoleted: {self.__is_obsolete}"
         if self.__is_obsolete:
-            msg += f", New term label: {self.__new_label}, New term IRI: {self.__new_iri}"
+            new_label = self.__new_label or "Unknown label"
+            new_iri = self.__new_iri or "Unknown IRI"
+            msg += f", New term label: {new_label}, New term IRI: {new_iri}"
         return msg

pandasaurus/utils/pandasaurus_exceptions.py

@@ -23,9 +23,16 @@ def __init__(self, term_list: List[Term]):
         Args:
             term_list (List[Term]): A list of obsoleted Term objects.
         """
+        obsolete_ids = [term.get_iri() for term in term_list]
+        replacement_descriptions = []
+        for term in term_list:
+            replacement = term.get_new_iri() or "unknown replacement"
+            replacement_descriptions.append(f"{term.get_iri()} -> {replacement}")
+
+        replacement_message = ", ".join(replacement_descriptions)
         self.message = (
-            f"The following terms are obsoleted: {', '.join([term.get_iri() for term in term_list])}, "
-            f"and replaced by following terms: {', '.join([term.get_new_iri() for term in term_list])}. "
+            f"The following terms are obsoleted: {', '.join(obsolete_ids)}. "
+            f"Replacement suggestions: {replacement_message}. "
             f"Please consider using the new terms"
         )
         super().__init__(self.message)

test/test_curie_validator.py

@@ -126,7 +126,8 @@ def test_get_validation_report():
         CurieValidator.get_validation_report(term_list)
 
     expected_message = (
-        "The following terms are obsoleted: CL:0011107, and replaced by following terms: CL:0000636. "
+        "The following terms are obsoleted: CL:0011107. "
+        "Replacement suggestions: CL:0011107 -> CL:0000636. "
         "Please consider using the new terms"
     )
     assert str(exc_info.value) == expected_message

test/utils/test_pandasaurus_exceptions.py

@@ -23,7 +23,21 @@ def test_obsoleted_term_exception():
         raise ObsoletedTerm(term_list)
 
     expected_message = (
-        "The following terms are obsoleted: CL:0011107, and replaced by following terms: CL:0000636. "
+        "The following terms are obsoleted: CL:0011107. "
+        "Replacement suggestions: CL:0011107 -> CL:0000636. "
+        "Please consider using the new terms"
+    )
+    assert str(exc_info.value) == expected_message
+
+
+def test_obsoleted_term_exception_with_missing_replacement():
+    term_list = [Term("obsolete Muller cell", "CL:0011107", True, None, None)]
+    with pytest.raises(ObsoletedTerm) as exc_info:
+        raise ObsoletedTerm(term_list)
+
+    expected_message = (
+        "The following terms are obsoleted: CL:0011107. "
+        "Replacement suggestions: CL:0011107 -> unknown replacement. "
         "Please consider using the new terms"
     )
     assert str(exc_info.value) == expected_message