Upgrade node unit tests (#363)

* added notes to test_collection.py tests

* getter and setter tests
* complex node creation test

* added notes to test_computation.py tests

* added notes to test_computational_process.py tests

* added notes to test_data.py tests

* removed deepcopy for complex_file_node

* added notes to test_inventory.py tests

* added notes to test_process.py tests

* added notes to test_material.py tests

* added notes to test_project.py tests

* added notes to test_file.py tests

* formatted with black

* removed unused import

* fixed test errors

tests/nodes/primary_nodes/test_collection.py

@@ -37,14 +37,9 @@ def test_create_complex_collection(simple_experiment_node, simple_inventory_node
     """
     my_collection_name = "my complex collection name"
     my_cript_doi = "10.1038/1781168a0"
+    my_collection_notes = "test_create_complex_collection notes"
 
-    my_collection = cript.Collection(
-        name=my_collection_name,
-        experiment=[simple_experiment_node],
-        inventory=[simple_inventory_node],
-        doi=my_cript_doi,
-        citation=[complex_citation_node],
-    )
+    my_collection = cript.Collection(name=my_collection_name, experiment=[simple_experiment_node], inventory=[simple_inventory_node], doi=my_cript_doi, citation=[complex_citation_node], notes=my_collection_notes)
 
     # assertions
     assert isinstance(my_collection, cript.Collection)
@@ -53,6 +48,7 @@ def test_create_complex_collection(simple_experiment_node, simple_inventory_node
     assert my_collection.inventory == [simple_inventory_node]
     assert my_collection.doi == my_cript_doi
     assert my_collection.citation == [complex_citation_node]
+    assert my_collection.notes == my_collection_notes
 
 
 def test_collection_getters_and_setters(simple_experiment_node, simple_inventory_node, complex_citation_node) -> None:
@@ -69,13 +65,15 @@ def test_collection_getters_and_setters(simple_experiment_node, simple_inventory
 
     new_collection_name = "my new collection name"
     new_cript_doi = "my new cript doi"
+    new_collection_notes = "my collection getters and setters notes"
 
     # set Collection attributes
     my_collection.name = new_collection_name
     my_collection.experiment = [simple_experiment_node]
     my_collection.inventory = [simple_inventory_node]
     my_collection.doi = new_cript_doi
     my_collection.citation = [complex_citation_node]
+    my_collection.notes = new_collection_notes
 
     # assert getters and setters are the same
     assert isinstance(my_collection, cript.Collection)
@@ -84,19 +82,22 @@ def test_collection_getters_and_setters(simple_experiment_node, simple_inventory
     assert my_collection.inventory == [simple_inventory_node]
     assert my_collection.doi == new_cript_doi
     assert my_collection.citation == [complex_citation_node]
+    assert my_collection.notes == new_collection_notes
 
     # remove Collection attributes
     my_collection.experiment = []
     my_collection.inventory = []
     my_collection.doi = ""
     my_collection.citation = []
+    my_collection.notes = ""
 
     # assert users can remove optional attributes
     assert my_collection.name == new_collection_name
     assert my_collection.experiment == []
     assert my_collection.inventory == []
     assert my_collection.doi == ""
     assert my_collection.citation == []
+    assert my_collection.notes == ""
 
 
 def test_serialize_collection_to_json(complex_user_node) -> None:

tests/nodes/primary_nodes/test_computation.py

@@ -30,6 +30,7 @@ def test_create_complex_computation_node(simple_data_node, complex_software_conf
     test that a complex computation node with all possible arguments can be created
     """
     my_computation_type = "analysis"
+    my_computation_notes = "this is my computation notes"
 
     citation = copy.deepcopy(complex_citation_node)
     condition = copy.deepcopy(complex_condition_node)
@@ -42,6 +43,7 @@ def test_create_complex_computation_node(simple_data_node, complex_software_conf
         condition=[condition],
         prerequisite_computation=simple_computation_node,
         citation=[citation],
+        notes=my_computation_notes,
     )
 
     # assertions
@@ -53,6 +55,7 @@ def test_create_complex_computation_node(simple_data_node, complex_software_conf
     assert my_computation_node.condition == [condition]
     assert my_computation_node.prerequisite_computation == simple_computation_node
     assert my_computation_node.citation == [citation]
+    assert my_computation_node.notes == my_computation_notes
 
 
 def test_computation_type_invalid_vocabulary() -> None:

tests/nodes/primary_nodes/test_computational_process.py

@@ -41,6 +41,7 @@ def test_create_complex_computational_process(
     """
 
     computational_process_name = "my computational process name"
+    computational_process_notes = "my computational process notes"
     computational_process_type = "cross_linking"
 
     ingredient = complex_ingredient_node
@@ -55,6 +56,7 @@ def test_create_complex_computational_process(
         condition=[complex_condition_node],
         property=[simple_property_node],
         citation=[complex_citation_node],
+        notes=computational_process_notes,
     )
 
     # assertions
@@ -68,6 +70,7 @@ def test_create_complex_computational_process(
     assert my_computational_process.condition == [complex_condition_node]
     assert my_computational_process.property == [simple_property_node]
     assert my_computational_process.citation == [complex_citation_node]
+    assert my_computational_process.notes == computational_process_notes
 
 
 def test_computational_process_getters_and_setters(simple_computation_process_node, simple_data_node, simple_ingredient_node, simple_software_configuration, simple_condition_node, simple_property_node, complex_citation_node) -> None:

tests/nodes/primary_nodes/test_data.py

@@ -1,4 +1,3 @@
-import copy
 import json
 import uuid
 
@@ -36,29 +35,32 @@ def test_create_complex_data_node(
     create a complex data node with all possible arguments
     """
 
-    file_node = copy.deepcopy(complex_file_node)
+    my_notes = "my complex data node notes"
+
     my_complex_data = cript.Data(
         name="my complex data node name",
         type="afm_amp",
-        file=[file_node],
+        file=[complex_file_node],
         sample_preparation=simple_process_node,
         computation=[simple_computation_node],
         computation_process=[simple_computational_process_node],
         material=[simple_material_node],
         process=[simple_process_node],
         # citation=[complex_citation_node],
+        notes=my_notes,
     )
 
     # assertions
     assert isinstance(my_complex_data, cript.Data)
     assert my_complex_data.type == "afm_amp"
-    assert my_complex_data.file == [file_node]
+    assert my_complex_data.file == [complex_file_node]
     assert my_complex_data.sample_preparation == simple_process_node
     assert my_complex_data.computation == [simple_computation_node]
     assert my_complex_data.computation_process == [simple_computational_process_node]
     assert my_complex_data.material == [simple_material_node]
     assert my_complex_data.process == [simple_process_node]
     # assert my_complex_data.citation == [complex_citation_node]
+    assert my_complex_data.notes == my_notes
 
 
 def test_data_getters_and_setters(
@@ -83,6 +85,7 @@ def test_data_getters_and_setters(
     None
     """
     my_data_type = "afm_height"
+    my_data_notes = "my data getter setter notes"
 
     my_new_files = [
         complex_file_node,
@@ -105,6 +108,7 @@ def test_data_getters_and_setters(
     simple_data_node.material = [simple_material_node]
     simple_data_node.process = [simple_process_node]
     simple_data_node.citation = [complex_citation_node]
+    simple_data_node.notes = my_data_notes
 
     # assertions check getters and setters
     assert simple_data_node.type == my_data_type
@@ -115,6 +119,7 @@ def test_data_getters_and_setters(
     assert simple_data_node.material == [simple_material_node]
     assert simple_data_node.process == [simple_process_node]
     assert simple_data_node.citation == [complex_citation_node]
+    assert simple_data_node.notes == my_data_notes
 
     # remove optional attributes
     simple_data_node.sample_preparation = []
@@ -123,6 +128,7 @@ def test_data_getters_and_setters(
     simple_data_node.material = []
     simple_data_node.process = []
     simple_data_node.citation = []
+    simple_data_node.notes = ""
 
     # assert that optional attributes have been removed from data node
     assert simple_data_node.sample_preparation == []
@@ -131,6 +137,7 @@ def test_data_getters_and_setters(
     assert simple_data_node.material == []
     assert simple_data_node.process == []
     assert simple_data_node.citation == []
+    assert simple_data_node.notes == ""
 
 
 def test_serialize_data_to_json(simple_data_node) -> None:

tests/nodes/primary_nodes/test_inventory.py

@@ -21,19 +21,24 @@ def test_get_and_set_inventory(simple_inventory_node) -> None:
     """
     # create new materials
     material_1 = cript.Material(name="new material 1", identifier=[{"names": ["new material 1 alternative name"]}])
+    my_notes = "my inventory notes"
 
-    # set inventory materials
+    # set inventory
     simple_inventory_node.material = [material_1]
+    simple_inventory_node.notes = my_notes
 
     # get and check inventory materials
     assert isinstance(simple_inventory_node, cript.Inventory)
     assert simple_inventory_node.material[-1] == material_1
+    assert simple_inventory_node.notes == my_notes
 
     # remove optional attributes
     simple_inventory_node.material = []
+    simple_inventory_node.notes = ""
 
     # assert that optional attributes have been removed
     assert simple_inventory_node.material == []
+    assert simple_inventory_node.notes == ""
 
 
 def test_inventory_serialization(simple_inventory_node, simple_material_dict) -> None:

tests/nodes/primary_nodes/test_material.py

@@ -17,13 +17,14 @@ def test_create_complex_material(simple_material_node, simple_computational_forc
     material_name = "my material name"
     identifier = [{"bigsmiles": "1234"}, {"bigsmiles": "4567"}]
     keyword = ["acetylene"]
+    material_notes = "my material notes"
 
     component = [simple_material_node]
     forcefield = [simple_computational_forcefield_node]
 
     my_property = [cript.Property(key="modulus_shear", type="min", value=1.23, unit="gram")]
 
-    my_material = cript.Material(name=material_name, identifier=identifier, keyword=keyword, component=component, process=simple_process_node, property=my_property, computational_forcefield=forcefield)
+    my_material = cript.Material(name=material_name, identifier=identifier, keyword=keyword, component=component, process=simple_process_node, property=my_property, computational_forcefield=forcefield, notes=material_notes)
 
     assert isinstance(my_material, cript.Material)
     assert my_material.name == material_name
@@ -33,6 +34,7 @@ def test_create_complex_material(simple_material_node, simple_computational_forc
     assert my_material.process == simple_process_node
     assert my_material.property == my_property
     assert my_material.computational_forcefield == forcefield
+    assert my_material.notes == material_notes
 
 
 def test_invalid_material_keywords() -> None:
@@ -53,6 +55,7 @@ def test_all_getters_and_setters(simple_material_node, simple_property_node, sim
     """
     # new attributes
     new_name = "new material name"
+    new_notes = "new material notes"
 
     new_identifier = [{"bigsmiles": "6789"}]
 
@@ -82,6 +85,7 @@ def test_all_getters_and_setters(simple_material_node, simple_property_node, sim
     simple_material_node.computational_forcefield = simple_computational_forcefield_node
     simple_material_node.keyword = new_material_keywords
     simple_material_node.component = new_components
+    simple_material_node.notes = new_notes
 
     # get all attributes and assert that they are equal to the setter
     assert simple_material_node.name == new_name
@@ -91,18 +95,21 @@ def test_all_getters_and_setters(simple_material_node, simple_property_node, sim
     assert simple_material_node.computational_forcefield == simple_computational_forcefield_node
     assert simple_material_node.keyword == new_material_keywords
     assert simple_material_node.component == new_components
+    assert simple_material_node.notes == new_notes
 
     # remove optional attributes
     simple_material_node.property = []
     simple_material_node.parent_material = None
     simple_material_node.computational_forcefield = None
     simple_material_node.component = []
+    simple_material_node.notes = ""
 
     # assert optional attributes have been removed
     assert simple_material_node.property == []
     assert simple_material_node.parent_material is None
     assert simple_material_node.computational_forcefield is None
     assert simple_material_node.component == []
+    assert simple_material_node.notes == ""
 
 
 def test_serialize_material_to_json(complex_material_dict, complex_material_node) -> None:

tests/nodes/primary_nodes/test_process.py

@@ -53,6 +53,8 @@ def test_complex_process_node(complex_ingredient_node, simple_equipment_node, co
         "annealing_sol",
     ]
 
+    my_notes = "my complex process notes"
+
     # create complex process
     citation = copy.deepcopy(complex_citation_node)
     prop = cript.Property("n_neighbor", "value", 2.0, None)
@@ -70,6 +72,7 @@ def test_complex_process_node(complex_ingredient_node, simple_equipment_node, co
         property=[prop],
         keyword=my_process_keywords,
         citation=[citation],
+        notes=my_notes,
     )
     # assertions
     assert my_complex_process.type == my_process_type
@@ -83,6 +86,7 @@ def test_complex_process_node(complex_ingredient_node, simple_equipment_node, co
     assert my_complex_process.property[-1] == prop
     assert my_complex_process.keyword[-1] == my_process_keywords[-1]
     assert my_complex_process.citation[-1] == citation
+    assert my_complex_process.notes == my_notes
 
 
 def test_process_getters_and_setters(
@@ -107,36 +111,35 @@ def test_process_getters_and_setters(
     new_process_type = "blow_molding"
     new_process_description = "my new process description"
     new_process_keywords = "annealing_sol"
+    new_process_notes = "new process notes"
 
     # test setters
     simple_process_node.type = new_process_type
     simple_process_node.ingredient = [complex_ingredient_node]
     simple_process_node.description = new_process_description
-    equipment = complex_equipment_node
-    simple_process_node.equipment = [equipment]
-    product = simple_material_node
-    simple_process_node.product = [product]
+    simple_process_node.equipment = [complex_equipment_node]
+    simple_process_node.product = [simple_material_node]
     simple_process_node.waste = [simple_material_node]
     simple_process_node.prerequisite_process = [simple_process_node]
     simple_process_node.condition = [complex_condition_node]
-    prop = cript.Property("n_neighbor", "value", 2.0, None)
-    simple_process_node.property += [prop]
+    simple_process_node.property += [simple_property_node]
     simple_process_node.keyword = [new_process_keywords]
-    citation = copy.deepcopy(complex_citation_node)
-    simple_process_node.citation = [citation]
+    simple_process_node.citation = [complex_citation_node]
+    simple_process_node.notes = new_process_notes
 
     # test getters
     assert simple_process_node.type == new_process_type
     assert simple_process_node.ingredient == [complex_ingredient_node]
     assert simple_process_node.description == new_process_description
-    assert simple_process_node.equipment[-1] == equipment
-    assert simple_process_node.product[-1] == product
+    assert simple_process_node.equipment[-1] == complex_equipment_node
+    assert simple_process_node.product[-1] == simple_material_node
     assert simple_process_node.waste == [simple_material_node]
     assert simple_process_node.prerequisite_process == [simple_process_node]
     assert simple_process_node.condition == [complex_condition_node]
-    assert simple_process_node.property[-1] == prop
+    assert simple_process_node.property[-1] == simple_property_node
     assert simple_process_node.keyword == [new_process_keywords]
-    assert simple_process_node.citation[-1] == citation
+    assert simple_process_node.citation[-1] == complex_citation_node
+    assert simple_process_node.notes == new_process_notes
 
     # test that optional attributes can be successfully removed
     simple_process_node.ingredient = []
@@ -149,6 +152,7 @@ def test_process_getters_and_setters(
     simple_process_node.property = []
     simple_process_node.keyword = []
     simple_process_node.citation = []
+    simple_process_node.notes = ""
 
     # assert that optional attributes have been removed
     assert simple_process_node.ingredient == []
@@ -161,6 +165,7 @@ def test_process_getters_and_setters(
     assert simple_process_node.property == []
     assert simple_process_node.keyword == []
     assert simple_process_node.citation == []
+    assert simple_process_node.notes == ""
 
 
 def test_serialize_process_to_json(simple_process_node) -> None:

tests/nodes/primary_nodes/test_project.py

@@ -33,24 +33,29 @@ def test_project_getters_and_setters(simple_project_node, simple_collection_node
     4. what was set and what was gotten should be equivalent
     """
     new_project_name = "my new project name"
+    new_project_notes = "my new project notes"
 
     # set attributes
     simple_project_node.name = new_project_name
     simple_project_node.collection = [complex_collection_node]
     simple_project_node.material = [simple_material_node]
+    simple_project_node.notes = new_project_notes
 
     # get attributes and assert that they are the same
     assert simple_project_node.name == new_project_name
     assert simple_project_node.collection == [complex_collection_node]
     assert simple_project_node.material == [simple_material_node]
+    assert simple_project_node.notes == new_project_notes
 
     # remove optional attributes
     simple_project_node.collection = []
     simple_project_node.material = []
+    simple_project_node.notes = ""
 
     # assert optional attributes have been removed
     assert simple_project_node.collection == []
     assert simple_project_node.material == []
+    assert simple_project_node.notes == ""
 
 
 def test_serialize_project_to_json(complex_project_node, complex_project_dict) -> None: