two failing tests still trying to debug

src/cript/nodes/core.py

@@ -79,6 +79,15 @@ def shallow_equal(self, other):
 
         self_sorted_json = self.get_json(known_uuid=self_child_map.keys(), sort_keys=True, condense_to_uuid={}).json
         other_sorted_json = other.get_json(known_uuid=other_child_map.keys(), sort_keys=True, condense_to_uuid={}).json
+        # maybe bring back
+        # self_sorted_json_dict = json.loads(self_sorted_json)
+        # other_sorted_json_dict = json.loads(other_sorted_json)
+
+        # del self_sorted_json_dict["uid"]
+        # del other_sorted_json_dict["uid"]
+
+        # self_sorted_json = json.dumps(self_sorted_json_dict)
+        # other_sorted_json = json.dumps(other_sorted_json_dict)
 
         return self_sorted_json == other_sorted_json
 
@@ -429,6 +438,15 @@ def get_expanded_json(self, **kwargs) -> str:
         """
         return self.get_json(handled_ids=None, known_uuid=None, suppress_attributes=None, is_patch=False, condense_to_uuid={}, **kwargs).json
 
+    # @staticmethod
+    # def clean_dict(data):
+    #     if isinstance(data, dict):
+    #         return {key: BaseNode.clean_dict(value) for key, value in data.items() if value != "" and value != [""]}
+    #     elif isinstance(data, list):
+    #         return [BaseNode.clean_dict(item) for item in data if item != "" and item != [""]]
+    #     else:
+    #         return data
+
     def get_json(
         self,
         handled_ids: Optional[Set[str]] = None,
@@ -439,7 +457,7 @@ def get_json(
             "Material": {"parent_material", "component"},
             "Experiment": {"data"},
             "Inventory": {"material"},
-            "Ingredient": {"material"},
+            # "Ingredient": {"material"},
             "Property": {"component"},
             "ComputationProcess": {"material"},
             "Data": {"material"},
@@ -493,9 +511,32 @@ class ReturnTuple:
         try:
             tmp_json = json.dumps(self, cls=NodeEncoder, **kwargs)
             tmp_dict = json.loads(tmp_json)
+            #####
+
+            # try:
+            #     print(tmp_dict)  # ["inventory"])#[0]["experiment"][0]["data"])
+            #     print(f"is_patch: {is_patch}")
+            #     print(f"_no_condense_uuid: {_no_condense_uuid}")
+            #     print(" 🐨🐱🦊 ")
+            # except:
+            #     print(" - ")
+
+            # if tmp_dict["collection"]["experiment"]["data"]:
+            #     print("-----tmp_dict_is_there_a_full data or not")
+            #     print(tmp_dict["collection"]["experiment"]["data"])
+
             if is_patch:
-                del tmp_dict["uuid"]  # patches do not allow UUID is the parent most node
-                del tmp_dict["uid"]
+                # del tmp_dict["uuid"]  # patches do not allow UUID is the parent most node
+
+                # try:  # this should only affect parent
+                #     del tmp_dict["uuid"]
+                # except KeyError:
+                #     pass
+
+                # try:
+                #     del tmp_dict["uid"]
+                # except KeyError:
+                #     pass
 
                 try:
                     del tmp_dict["created_at"]

src/cript/nodes/primary_nodes/computation.py

@@ -212,7 +212,7 @@ def input_data(self) -> List[Any]:
         ...     source="https://criptapp.org",
         ...     type="calibration",
         ...     extension=".csv",
-        ...     data_dictionary="my file's data dictionary"
+        ...     data_dictionary="my files data dictionary"
         ... )
         >>> my_input_data = cript.Data(name="my data name", type="afm_amp", file=[my_file])
         >>> my_computation.input_data = [my_input_data]
@@ -257,7 +257,7 @@ def output_data(self) -> List[Any]:
         ...     source="https://criptapp.org",
         ...     type="calibration",
         ...     extension=".csv",
-        ...     data_dictionary="my file's data dictionary"
+        ...     data_dictionary="my files data dictionary"
         ... )
         >>> my_output_data = cript.Data(name="my data name", type="afm_amp", file=[my_file])
         >>> my_computation.output_data = [my_output_data]

src/cript/nodes/primary_nodes/computation_process.py

@@ -93,7 +93,7 @@ class ComputationProcess(PrimaryBaseNode):
                    "node":["File"],
                    "source":"https://criptapp.org",
                    "type":"calibration",
-                    "data_dictionary":"my file's data dictionary",
+                    "data_dictionary":"my files data dictionary",
                    "extension":".csv",
                    "uid":"_:ee8153db-4108-49e4-8c5b-ffc26d4e6f71",
                    "uuid":"ee8153db-4108-49e4-8c5b-ffc26d4e6f71"
@@ -150,7 +150,7 @@ def __init__(
         ...     source="https://criptapp.org",
         ...     type="calibration",
         ...     extension=".csv",
-        ...     data_dictionary="my file's data dictionary"
+        ...     data_dictionary="my files data dictionary"
         ... )
         >>> input_data = cript.Data(name="my data name", type="afm_amp", file=[data_files])
         >>> my_material = cript.Material(
@@ -287,7 +287,7 @@ def input_data(self) -> List[Any]:
         ...     name="my file node name",
         ...     source="https://criptapp.org",
         ...     type="calibration",
-        ...     data_dictionary="my file's data dictionary",
+        ...     data_dictionary="my files data dictionary",
         ...     extension=".csv",
         ... )
         >>> my_input_data = cript.Data(name="my input data name", type="afm_amp", file=[my_file])
@@ -331,7 +331,7 @@ def output_data(self) -> List[Any]:
         ...     source="https://criptapp.org",
         ...     type="calibration",
         ...     extension=".csv",
-        ...     data_dictionary="my file's data dictionary"
+        ...     data_dictionary="my files data dictionary"
         ... )
         >>> my_output_data = cript.Data(name="my output data name", type="afm_amp", file=[my_file])
         >>> my_computation_process.output_data = [my_output_data]    # doctest: +SKIP

src/cript/nodes/primary_nodes/data.py

@@ -39,7 +39,7 @@ class Data(PrimaryBaseNode):
     ...    source="https://criptapp.org",
     ...    type="calibration",
     ...    extension=".csv",
-    ...    data_dictionary="my file's data dictionary"
+    ...    data_dictionary="my files data dictionary"
     ... )
     >>> my_data = cript.Data(name="my data name", type="afm_amp", file=[my_file])
 
@@ -60,7 +60,7 @@ class Data(PrimaryBaseNode):
              "type":"calibration",
              "source":"https://criptapp.org",
              "extension":".csv",
-             "data_dictionary":"my file's data dictionary",
+             "data_dictionary":"my files data dictionary",
           }
        ]
     }
@@ -195,7 +195,7 @@ def type(self) -> str:
         ...    source="https://criptapp.org",
         ...    type="calibration",
         ...    extension=".csv",
-        ...    data_dictionary="my file's data dictionary"
+        ...    data_dictionary="my files data dictionary"
         ... )
         >>> my_data = cript.Data(name="my data name", type="afm_amp", file=[my_file])
         >>> my_data.type = "nmr_h1"
@@ -240,15 +240,15 @@ def file(self) -> List[Any]:
         ...    source="https://criptapp.org",
         ...    type="calibration",
         ...    extension=".csv",
-        ...    data_dictionary="my file's data dictionary"
+        ...    data_dictionary="my files data dictionary"
         ... )
         >>> my_data = cript.Data(name="my data name", type="afm_amp", file=[my_file])
         >>> my_new_file = cript.File(
         ...    name="my new file node name",
         ...    source="path/to/local/file",
         ...    type="calibration",
         ...    extension=".csv",
-        ...    data_dictionary="my file's data dictionary"
+        ...    data_dictionary="my files data dictionary"
         ... )
         >>> my_data.file += [my_new_file]
 
@@ -336,7 +336,7 @@ def computation(self) -> List[Any]:
         ...    source="https://criptapp.org",
         ...    type="calibration",
         ...    extension=".csv",
-        ...    data_dictionary="my file's data dictionary"
+        ...    data_dictionary="my files data dictionary"
         ... )
         >>> my_data = cript.Data(name="my data name", type="afm_amp", file=[my_file])
         >>> my_computation = cript.Computation(name="my computation name", type="analysis")
@@ -381,7 +381,7 @@ def computation_process(self) -> Union[Any, None]:
         ...     source="https://criptapp.org",
         ...     type="calibration",
         ...     extension=".csv",
-        ...     data_dictionary="my file's data dictionary"
+        ...     data_dictionary="my files data dictionary"
         ... )
         >>> my_data = cript.Data(
         ...     name="my data name",
@@ -393,7 +393,7 @@ def computation_process(self) -> Union[Any, None]:
         ...     source="https://criptapp.org",
         ...     type="calibration",
         ...     extension=".csv",
-        ...     data_dictionary="my file's data dictionary"
+        ...     data_dictionary="my files data dictionary"
         ... )
         >>> my_second_data_node = cript.Data(
         ...     name="my data name",
@@ -457,7 +457,7 @@ def material(self) -> List[Any]:
         ...    source="https://criptapp.org",
         ...    type="calibration",
         ...    extension=".csv",
-        ...    data_dictionary="my file's data dictionary"
+        ...    data_dictionary="my files data dictionary"
         ... )
         >>> my_data = cript.Data(name="my data name", type="afm_amp", file=[my_file])
         >>> my_material = cript.Material(name="my material name", bigsmiles = "123456")
@@ -501,7 +501,7 @@ def process(self) -> List[Any]:
         ...    source="https://criptapp.org",
         ...    type="calibration",
         ...    extension=".csv",
-        ...    data_dictionary="my file's data dictionary"
+        ...    data_dictionary="my files data dictionary"
         ... )
         >>> my_data = cript.Data(name="my data name", type="afm_amp", file=[my_file])
         >>> my_process = cript.Process(name="my process name", type="affinity_pure")
@@ -553,7 +553,7 @@ def citation(self) -> List[Any]:
         ...    source="https://criptapp.org",
         ...    type="calibration",
         ...    extension=".csv",
-        ...    data_dictionary="my file's data dictionary"
+        ...    data_dictionary="my files data dictionary"
         ... )
         >>> my_data = cript.Data(name="my data name", type="afm_amp", file=[my_file])
         >>> my_reference = cript.Reference(type="journal_article", title="'Living' Polymers")

src/cript/nodes/primary_nodes/experiment.py

@@ -241,7 +241,7 @@ def computation_process(self) -> List[Any]:
         ...     source="https://criptapp.org",
         ...     type="calibration",
         ...     extension=".csv",
-        ...     data_dictionary="my file's data dictionary",
+        ...     data_dictionary="my files data dictionary",
         ... )
         >>> my_data = cript.Data(name="my data name", type="afm_amp", file=[my_file])
         >>> my_material = cript.Material(
@@ -301,7 +301,7 @@ def data(self) -> List[Any]:
         ...    source="https://criptapp.org",
         ...    type="calibration",
         ...    extension=".csv",
-        ...    data_dictionary="my file's data dictionary",
+        ...    data_dictionary="my files data dictionary",
         ... )
         >>> my_data = cript.Data(name="my data name", type="afm_amp", file=[my_file])
         >>> my_experiment.data = [my_data]

src/cript/nodes/primary_nodes/primary_base_node.py

@@ -57,6 +57,17 @@ def __str__(self) -> str:
         """
         return super().__str__()
 
+    @classmethod
+    def _from_json(cls, json_dict: dict):
+        # GOOD CHANGE - ALI
+        # TODO: remove this temporary fix, once back end is working correctly
+        try:
+            if json_dict["model_version"] == "1.0.0":
+                json_dict["model_version"] = "1.0.1"
+        except KeyError:
+            pass
+        return super(PrimaryBaseNode, cls)._from_json(json_dict)
+
     @property
     @beartype
     def locked(self):

src/cript/nodes/subobjects/computational_forcefield.py

@@ -54,7 +54,7 @@ class ComputationalForcefield(UUIDBaseNode):
                     "type":"calibration",
                     "source":"https://criptapp.org",
                     "extension":".csv",
-                    "data_dictionary":"my file's data dictionary"
+                    "data_dictionary":"my files data dictionary"
                 }
             ]
         },

src/cript/nodes/subobjects/condition.py

@@ -68,7 +68,7 @@ class Condition(UUIDBaseNode):
                     "type":"calibration",
                     "source":"https://criptapp.org",
                     "extension":".csv",
-                    "data_dictionary":"my file's data dictionary"
+                    "data_dictionary":"my files data dictionary"
                 }
             ]
         }],

src/cript/nodes/subobjects/property.py

@@ -576,7 +576,7 @@ def data(self) -> List[Union[Data, UIDProxy]]:
         ...     source="https://criptapp.org",
         ...     type="calibration",
         ...     extension=".csv",
-        ...     data_dictionary="my file's data dictionary",
+        ...     data_dictionary="my files data dictionary",
         ... )
         >>> my_data = cript.Data(name="my data name", type="afm_amp", file=[my_file])
         >>> my_property.data = [my_data]

src/cript/nodes/supporting_nodes/file.py

@@ -108,7 +108,7 @@ class File(PrimaryBaseNode):
         "source": "https://criptapp.org",
         "type": "calibration",
         "extension": ".csv",
-        "data_dictionary": "my file's data dictionary",
+        "data_dictionary": "my files data dictionary",
     }
     ```
     """
@@ -159,7 +159,7 @@ def __init__(self, name: str, source: str, type: str, extension: str, data_dicti
         ...     source="https://pubs.acs.org/doi/suppl/10.1021/acscentsci.3c00011/suppl_file/oc3c00011_si_001.pdf",
         ...     type="calibration",
         ...     extension=".pdf",
-        ...     data_dictionary="my file's data dictionary",
+        ...     data_dictionary="my files data dictionary",
         ...     notes="my notes for this file",
         ... )
 
@@ -170,7 +170,7 @@ def __init__(self, name: str, source: str, type: str, extension: str, data_dicti
         ...     source="/home/user/MIT/project/my_file.csv",
         ...     type="calibration",
         ...     extension=".csv",
-        ...     data_dictionary="my file's data dictionary",
+        ...     data_dictionary="my files data dictionary",
         ...     notes="my notes for this file",
         ... )
         """

src/cript/nodes/supporting_nodes/user.py

@@ -77,6 +77,17 @@ def __init__(self, username: str, email: Optional[str] = "", orcid: Optional[str
         new_json_attrs = replace(self._json_attrs, username=username, email=email, orcid=orcid)
         self._update_json_attrs_if_valid(new_json_attrs)
 
+    @classmethod
+    def _from_json(cls, json_dict: dict):
+        # GOOD CHANGE - ALI
+        # TODO: remove this temporary fix, once back end is working correctly
+        try:
+            if json_dict["model_version"] == "1.0.0":
+                json_dict["model_version"] = "1.0.1"
+        except KeyError:
+            pass
+        return super(User, cls)._from_json(json_dict)
+
     @property
     @beartype
     def created_at(self) -> str:

src/cript/nodes/util/json.py

@@ -1,6 +1,7 @@
 """
 This module contains classes and functions that help with the json serialization and deserialization of nodes.
 """
+
 import dataclasses
 import inspect
 import json
@@ -183,10 +184,15 @@ def strip_to_edge_uuid(element):
                 except AttributeError:
                     uid = element["uid"]
 
-                if self.no_condense_uuid:
-                    element = ""
-                else:
+                # old___
+                # if self.no_condense_uuid:
+                #     element = ""
+                # else:
+                #     element = {"uuid": str(uuid)}
+                # GOOD CHANGE - ALI
+                if self.no_condense_uuid is False:
                     element = {"uuid": str(uuid)}
+
                 return element, uid
 
             # Processes an attribute based on its type (list or single element)

tests/nodes/primary_nodes/test_reference.py

@@ -211,7 +211,12 @@ def test_integration_reference(cript_api, simple_project_node, complex_citation_
     simple_project_node.name = f"test_integration_reference_name_{uuid.uuid4().hex}"
 
     simple_project_node.collection[0].citation = [complex_citation_node]
+    print("PRINTING_citation_INFO 1")
+    print(simple_project_node.collection[0].citation)
 
+    """
+    right now this test is failing when you try to add citation
+    """
     save_integration_node_helper(cript_api=cript_api, project_node=simple_project_node)
 
     # TODO deserialization with citation in collection is wrong
@@ -222,6 +227,10 @@ def test_integration_reference(cript_api, simple_project_node, complex_citation_
     # change simple attribute to trigger update
     #   TODO can enable this later
     #  complex_reference_node.type = "book"
+
+    print("PRINTING_citation_INFO 2")
+    print(simple_project_node.collection[0].citation)
+
     simple_project_node.collection[0].citation[0].reference.title = "reference title UPDATED"
 
     save_integration_node_helper(cript_api=cript_api, project_node=simple_project_node)