Finished and Removed TODO (#377)

* removed and fixed some TODO comments

* upgraded `test_complex_process_node` to use fixture, removed unused fixtures, and removed copy.deep_copy()

* removed unused import `copy`

src/cript/api/api.py

@@ -563,7 +563,6 @@ def get_vocab_by_category(self, category: VocabCategories) -> List[dict]:
         response: Dict = requests.get(url=vocabulary_category_url, timeout=_API_TIMEOUT).json()
 
         if response["code"] != 200:
-            # TODO give a better CRIPT custom Exception
             raise APIError(api_error=str(response), http_method="GET", api_url=vocabulary_category_url)
 
         # add to cache

src/cript/api/exceptions.py

@@ -31,7 +31,6 @@ def __str__(self) -> str:
         return error_message
 
 
-# TODO refactor
 class InvalidVocabulary(CRIPTException):
     """
     Raised when the CRIPT controlled vocabulary is invalid

src/cript/api/paginator.py

@@ -163,8 +163,7 @@ def current_page_number(self, new_page_number: int) -> None:
         if new_page_number < 0:
             error_message: str = f"Paginator current page number is invalid because it is negative: " f"{self.current_page_number} please set paginator.current_page_number " f"to a positive page number"
 
-            # TODO replace with custom error
-            raise Exception(error_message)
+            raise RuntimeError(error_message)
 
         else:
             self._current_page_number = new_page_number

src/cript/nodes/primary_nodes/computation_process.py

@@ -199,8 +199,6 @@ def __init__(
         """
         super().__init__(name=name, notes=notes, **kwargs)
 
-        # TODO validate type from vocab
-
         if input_data is None:
             input_data = []
 
@@ -273,7 +271,6 @@ def type(self, new_type: str) -> None:
         -------
         None
         """
-        # TODO check computational_process type with CRIPT controlled vocabulary
         new_attrs = replace(self._json_attrs, type=new_type)
         self._update_json_attrs_if_valid(new_attrs)
 

src/cript/nodes/primary_nodes/data.py

@@ -223,7 +223,6 @@ def type(self, new_data_type: str) -> None:
         -------
         None
         """
-        # TODO validate that the data type is valid from CRIPT controlled vocabulary
         new_attrs = replace(self._json_attrs, type=new_data_type)
         self._update_json_attrs_if_valid(new_attrs)
 

src/cript/nodes/primary_nodes/process.py

@@ -255,8 +255,6 @@ def ingredient(self, new_ingredient_list: List[Any]) -> None:
         -------
         None
         """
-        # TODO need to validate with CRIPT controlled vocabulary
-        #   and if invalid then raise an error immediately
         new_attrs = replace(self._json_attrs, ingredient=new_ingredient_list)
         self._update_json_attrs_if_valid(new_attrs)
 

src/cript/nodes/supporting_nodes/file.py

@@ -177,9 +177,6 @@ def __init__(self, name: str, source: str, type: str, extension: str, data_dicti
 
         super().__init__(name=name, notes=notes, **kwargs)
 
-        # TODO check if vocabulary is valid or not
-        # is_vocab_valid("file type", type)
-
         # setting every attribute except for source, which will be handled via setter
         self._json_attrs = replace(
             self._json_attrs,

tests/fixtures/subobjects.py

@@ -24,7 +24,6 @@ def complex_parameter_dict() -> dict:
     return ret_dict
 
 
-# TODO this fixture should be renamed because it is simple_algorithm_subobject not complex
 @pytest.fixture(scope="function")
 def simple_algorithm_node() -> cript.Algorithm:
     """

tests/nodes/primary_nodes/test_process.py

@@ -1,4 +1,3 @@
-import copy
 import json
 import uuid
 
@@ -30,16 +29,14 @@ def test_simple_process() -> None:
     assert my_process.keyword == my_process_keywords
 
 
-def test_complex_process_node(complex_ingredient_node, simple_equipment_node, complex_citation_node, simple_property_node, simple_condition_node, simple_material_node, simple_process_node, complex_equipment_node, complex_condition_node) -> None:
+def test_complex_process_node(complex_ingredient_node, complex_citation_node, simple_property_node, simple_material_node, simple_process_node, complex_equipment_node, complex_condition_node) -> None:
     """
     create a process node with all possible arguments
 
     Notes
     -----
     * indirectly tests the vocabulary as well, as it gives it valid vocabulary
     """
-    # TODO clean up this test and use fixtures from conftest.py
-
     my_process_name = "my complex process node name"
     my_process_type = "affinity_pure"
     my_process_description = "my simple material description"
@@ -55,10 +52,6 @@ def test_complex_process_node(complex_ingredient_node, simple_equipment_node, co
 
     my_notes = "my complex process notes"
 
-    # create complex process
-    citation = copy.deepcopy(complex_citation_node)
-    prop = cript.Property("n_neighbor", "value", 2.0, None)
-
     my_complex_process = cript.Process(
         name=my_process_name,
         type=my_process_type,
@@ -69,9 +62,9 @@ def test_complex_process_node(complex_ingredient_node, simple_equipment_node, co
         waste=process_waste,
         prerequisite_process=[simple_process_node],
         condition=[complex_condition_node],
-        property=[prop],
+        property=[simple_property_node],
         keyword=my_process_keywords,
-        citation=[citation],
+        citation=[complex_citation_node],
         notes=my_notes,
     )
     # assertions
@@ -83,9 +76,9 @@ def test_complex_process_node(complex_ingredient_node, simple_equipment_node, co
     assert my_complex_process.waste == process_waste
     assert my_complex_process.prerequisite_process[-1] == simple_process_node
     assert my_complex_process.condition[-1] == complex_condition_node
-    assert my_complex_process.property[-1] == prop
+    assert my_complex_process.property[-1] == simple_property_node
     assert my_complex_process.keyword[-1] == my_process_keywords[-1]
-    assert my_complex_process.citation[-1] == citation
+    assert my_complex_process.citation[-1] == complex_citation_node
     assert my_complex_process.notes == my_notes