Unit dictionary is now pseudo-private

This is done to remove it from the REST API since it is not part of the actual request body

pyenzyme/enzymeml/core/abstract_classes.py

@@ -54,7 +54,7 @@ def unitdef(self):
         if not self.unit:
             return None
 
-        return self._enzmldoc.unit_dict[self._unit_id]
+        return self._enzmldoc._unit_dict[self._unit_id]
 
 
 class AbstractSpeciesFactory(ABC):

pyenzyme/enzymeml/core/enzymemlbase.py

@@ -25,7 +25,6 @@ def json(self, indent: int = 2, **kwargs):
             exclude_none=True,
             exclude={
                 "log": ...,
-                "unit_dict": ...,
                 "file_dict": ...,
                 "protein_dict": {"Protein": {"__all__": {"_unit_id"}}},
             },
@@ -57,7 +56,7 @@ def __setattr__(self, name, value):
 
                 # Create a new UnitDef and get the ID
                 new_unit_id = self._enzmldoc._convertToUnitDef(value)
-                value = self._enzmldoc.unit_dict[new_unit_id]._get_unit_name()
+                value = self._enzmldoc._unit_dict[new_unit_id]._get_unit_name()
 
                 # Set the unit ID to the object
                 attr_name = f"_{name}_id"
@@ -69,7 +68,7 @@ def __setattr__(self, name, value):
         # Whenever a new ID is assigned, make sure the names are compliant with our standards
         if "unit_id" in name and hasattr(self, "_enzmldoc"):
             if self._enzmldoc:
-                unit_name = self._enzmldoc.unit_dict[value]._get_unit_name()
+                unit_name = self._enzmldoc._unit_dict[value]._get_unit_name()
                 attr_name = name.replace("_id", "")[1::]
                 super().__setattr__(attr_name, unit_name)
 

pyenzyme/enzymeml/core/enzymemldocument.py

@@ -14,7 +14,7 @@
 import seaborn as sns
 import plotly.express as px
 
-from pydantic import Field, validator, validate_arguments
+from pydantic import Field, PrivateAttr, validator, validate_arguments
 from typing import Dict, List, Tuple, TYPE_CHECKING, Optional, Union
 from dataclasses import dataclass
 from io import StringIO
@@ -134,12 +134,6 @@ class EnzymeMLDocument(EnzymeMLBase):
         description="Dictionary mapping from reaction IDs to reaction describing objects.",
     )
 
-    unit_dict: Dict[str, UnitDef] = Field(
-        alias="units",
-        default_factory=dict,
-        description="Dictionary mapping from unit IDs to unit describing objects.",
-    )
-
     measurement_dict: Dict[str, Measurement] = Field(
         alias="measurements",
         default_factory=dict,
@@ -162,6 +156,9 @@ class EnzymeMLDocument(EnzymeMLBase):
         default="",
     )
 
+    # * Private attributes
+    _unit_dict: Dict[str, UnitDef] = PrivateAttr(default_factory=dict)
+
     # ! Validators
     @validator("log")
     def start_logger(cls, logs: str, values: dict):
@@ -648,7 +645,7 @@ def _generateID(prefix: str, dictionary: dict) -> str:
 
         return prefix + str(0)
 
-    def validate(self, yaml_path: str) -> Tuple[Dict, bool]:
+    def validateDocument(self, yaml_path: str) -> Tuple[Dict, bool]:
         """Validates an EnzymeML based on a given YAML file.
 
         The YAML file should be compliant with PyEnzymes template found on Github
@@ -729,7 +726,7 @@ def generate_lines(dictionary: dict) -> None:
 
         if units:
             fin_string.append(">>> Units")
-            generate_lines(self.unit_dict)
+            generate_lines(self._unit_dict)
 
         fin_string.append(">>> Reactants")
         generate_lines(self.reactant_dict)
@@ -931,7 +928,7 @@ def addGlobalParameter(
 
         if param.unit:
             param._unit_id = self._convertToUnitDef(param.unit)
-            param.unit = self.unit_dict[param._unit_id]._get_unit_name()
+            param.unit = self._unit_dict[param._unit_id]._get_unit_name()
 
         # Assign the current EnzymeMLDocument
         param._enzmldoc = self
@@ -1094,12 +1091,12 @@ def _addSpecies(
         if species.unit and use_parser:
             unit_id = self._convertToUnitDef(species.unit)
             species._unit_id = unit_id
-            species.unit = self.unit_dict[species._unit_id]._get_unit_name()
+            species.unit = self._unit_dict[species._unit_id]._get_unit_name()
 
         elif species.unit and use_parser is False:
             species._unit_id = species.unit
             species.unit = self.getUnitString(species._unit_id)
-            species.unit = self.unit_dict[species._unit_id]._get_unit_name()
+            species.unit = self._unit_dict[species._unit_id]._get_unit_name()
 
         # Log creation of the object
         log_object(logger, species)
@@ -1261,7 +1258,9 @@ def _convert_kinetic_model_units(
         for parameter in parameters:
             if parameter.unit:
                 parameter._unit_id = enzmldoc._convertToUnitDef(parameter.unit)
-                parameter.unit = enzmldoc.unit_dict[parameter._unit_id]._get_unit_name()
+                parameter.unit = enzmldoc._unit_dict[
+                    parameter._unit_id
+                ]._get_unit_name()
                 parameter._enzmldoc = enzmldoc
 
     def addReactions(self, reactions: List[EnzymeReaction]):
@@ -1360,7 +1359,7 @@ def _convertMeasurementUnits(self, measurement: Measurement) -> None:
             )
 
             # Set correct string
-            measurement.global_time_unit = self.unit_dict[
+            measurement.global_time_unit = self._unit_dict[
                 measurement._global_time_unit_id
             ]._get_unit_name()
 
@@ -1371,7 +1370,7 @@ def _convertMeasurementUnits(self, measurement: Measurement) -> None:
             )
 
             # Set correct string
-            measurement.temperature_unit = self.unit_dict[
+            measurement.temperature_unit = self._unit_dict[
                 measurement._temperature_unit_id
             ]._get_unit_name()
 
@@ -1489,7 +1488,7 @@ def _convertToUnitDef(self, unit: Optional[str]) -> str:
 
         if unit is None:
             raise TypeError("No unit given.")
-        elif unit in self.unit_dict.keys():
+        elif unit in self._unit_dict.keys():
             return unit
 
         return UnitCreator().getUnit(unit, self)
@@ -1517,7 +1516,7 @@ def getUnitString(self, unit_id: Optional[str]) -> str:
             raise TypeError("No unit given.")
 
         try:
-            return self.unit_dict[unit_id].name
+            return self._unit_dict[unit_id].name
         except KeyError:
             raise SpeciesNotFoundError(species_id=unit_id, enzymeml_part="Units")
 
@@ -1536,7 +1535,7 @@ def getUnitDef(self, id: str) -> UnitDef:
 
         return self._getSpecies(
             id=id,
-            dictionary=self.unit_dict,
+            dictionary=self._unit_dict,
             element_type="Units",
         )
 
@@ -1669,7 +1668,7 @@ def getAny(self, id: str) -> AbstractSpecies:
         """
 
         all_dicts = {
-            **self.unit_dict,
+            **self._unit_dict,
             **self.vessel_dict,
             **self.reactant_dict,
             **self.protein_dict,
@@ -1829,7 +1828,7 @@ def getMeasurementDict(self):
 
     @deprecated_getter("unit_dict")
     def getUnitDict(self):
-        return self.unit_dict
+        return self._unit_dict
 
     @deprecated_getter("file_dict")
     def getFileDict(self):

pyenzyme/enzymeml/core/enzymereaction.py

@@ -688,7 +688,7 @@ def unitdef(self):
         if not self._enzmldoc:
             return None
 
-        return self._enzmldoc.unit_dict[self._temperature_unit_id]
+        return self._enzmldoc._unit_dict[self._temperature_unit_id]
 
     def getTemperature(self) -> float:
         raise NotImplementedError("Temperature is now part of measurements.")

pyenzyme/enzymeml/core/measurement.py

@@ -396,7 +396,7 @@ def temperature_unitdef(self):
         if not self._enzmldoc:
             return None
 
-        return self._enzmldoc.unit_dict[self._temperature_unit_id]
+        return self._enzmldoc._unit_dict[self._temperature_unit_id]
 
     @validate_arguments
     def getReactant(self, reactant_id: str) -> MeasurementData:

pyenzyme/enzymeml/core/measurementData.py

@@ -86,7 +86,7 @@ def unifyUnits(self, kind: str, scale: int, enzmldoc) -> Optional[str]:
         unit_id = None
 
         # Transform initial concentration
-        unitdef: UnitDef = enzmldoc.unit_dict[self._unit_id].copy()
+        unitdef: UnitDef = enzmldoc._unit_dict[self._unit_id].copy()
         transform_value, new_unit_name, unit_id = self._getTransformation(
             unitdef, kind, scale, enzmldoc
         )
@@ -134,7 +134,7 @@ def _rescaleReplicateUnits(
         """
 
         data_unit_id = replicate._data_unit_id
-        unitdef: UnitDef = enzmldoc.unit_dict[data_unit_id].copy()
+        unitdef: UnitDef = enzmldoc._unit_dict[data_unit_id].copy()
 
         # Calculate the scale to transform the unit
         transform_value, new_unit_name, unit_id = self._getTransformation(
@@ -172,7 +172,7 @@ def unitdef(self):
         if not self._enzmldoc:
             return None
 
-        return self._enzmldoc.unit_dict[self._unit_id]
+        return self._enzmldoc._unit_dict[self._unit_id]
 
     @deprecated_getter("reactant_id")
     def getReactantID(self) -> Optional[str]:

pyenzyme/enzymeml/core/replicate.py

@@ -109,15 +109,15 @@ def data_unitdef(self):
         if not self._enzmldoc:
             return None
 
-        return self._enzmldoc.unit_dict[self._data_unit_id]
+        return self._enzmldoc._unit_dict[self._data_unit_id]
 
     def time_unitdef(self):
         """Returns the appropriate unitdef if an enzmldoc is given"""
 
         if not self._enzmldoc:
             return None
 
-        return self._enzmldoc.unit_dict[self._time_unit_id]
+        return self._enzmldoc._unit_dict[self._time_unit_id]
 
     @deprecated_getter("measurement_id")
     def getMeasurement(self):

pyenzyme/enzymeml/core/vessel.py

@@ -83,7 +83,7 @@ def unitdef(self):
         if not self._enzmldoc:
             return None
 
-        return self._enzmldoc.unit_dict[self._unit_id]
+        return self._enzmldoc._unit_dict[self._unit_id]
 
     @deprecated_getter("name")
     def getName(self):

pyenzyme/enzymeml/models/kineticmodel.py

@@ -89,7 +89,7 @@ def unitdef(self):
         if not self._enzmldoc:
             return None
 
-        return self._enzmldoc.unit_dict[self._unit_id]
+        return self._enzmldoc._unit_dict[self._unit_id]
 
 
 @static_check_init_args

pyenzyme/enzymeml/tools/enzymemlreader.py

@@ -147,7 +147,7 @@ def readFromFile(self, path: str) -> EnzymeMLDocument:
 
         # Fetch units
         unitDict = self._getUnits(model)
-        self.enzmldoc.unit_dict = unitDict
+        self.enzmldoc._unit_dict = unitDict
 
         # Fetch Vessel
         vessel = self._getVessel(model, self.enzmldoc)
@@ -728,8 +728,8 @@ def _getData(
                         species_id=reactant_id,
                         data_type=data_type,
                         measurement_id=measurement_id,
-                        data_unit=enzmldoc.unit_dict[data_unit_id].name,
-                        time_unit=enzmldoc.unit_dict[time_unit_id].name,
+                        data_unit=enzmldoc._unit_dict[data_unit_id].name,
+                        time_unit=enzmldoc._unit_dict[time_unit_id].name,
                         data=data,
                         time=time,
                         is_calculated=is_calculated,
@@ -879,7 +879,7 @@ def _parse_init_conc_element(element: ET.Element, enzmldoc):
 
         # Convert the unit ID to the corresponding SI string
         unit_id = element.attrib["unit"]
-        unit = enzmldoc.unit_dict[unit_id].name
+        unit = enzmldoc._unit_dict[unit_id].name
 
         reactant_id = None
         protein_id = None

pyenzyme/enzymeml/tools/enzymemlwriter.py

@@ -153,7 +153,7 @@ def convertEnzymeMLToSBML(self, model: libsbml.Model, enzmldoc):
         self._addReactants(model, enzmldoc.reactant_dict)
         self._addGlobalParameters(model, enzmldoc.global_parameters)
         self._addReactions(model, enzmldoc.reaction_dict)
-        self._addUnits(model, enzmldoc.unit_dict)
+        self._addUnits(model, enzmldoc._unit_dict)
 
     def _createArchive(self, enzmldoc, listofPaths, name: str = None):
 

pyenzyme/enzymeml/tools/unitcreator.py

@@ -55,7 +55,7 @@ def getUnit(self, unit_string, enzmldoc) -> str:
             )
 
         # Generate ID
-        id = enzmldoc._generateID(prefix="u", dictionary=enzmldoc.unit_dict)
+        id = enzmldoc._generateID(prefix="u", dictionary=enzmldoc._unit_dict)
 
         # Call unit parser to identify units
         parser = UnitParser()
@@ -101,13 +101,13 @@ def getUnit(self, unit_string, enzmldoc) -> str:
         if self.__checkFootprints(enzmldoc, unitdef.getFootprint()) != "NEW":
             return self.__checkFootprints(enzmldoc, unitdef.getFootprint())
 
-        enzmldoc.unit_dict[unitdef.id] = unitdef
+        enzmldoc._unit_dict[unitdef.id] = unitdef
 
         return unitdef.id
 
     def __checkFootprints(self, enzmldoc, footprint):
 
-        for unit_id, unitdef in enzmldoc.unit_dict.items():
+        for unit_id, unitdef in enzmldoc._unit_dict.items():
             if DeepDiff(unitdef.getFootprint(), footprint) == {}:
                 return unit_id
 
@@ -198,7 +198,6 @@ def __Dimensionless(self, unitdef, prefix=None, exponent=1):
 
     def __getPrefix(self, prefix):
 
-
         if prefix == "f":
             return -15
         elif prefix == "p":

tests/enzymeml/core/test_enzymemldocument.py

@@ -36,7 +36,7 @@ def test_content(self):
         assert not enzmldoc.complex_dict
         assert not enzmldoc.reactant_dict
         assert not enzmldoc.reaction_dict
-        assert not enzmldoc.unit_dict
+        assert not enzmldoc._unit_dict
         assert not enzmldoc.file_dict
         assert not enzmldoc.global_parameters
 
@@ -60,7 +60,7 @@ def test_defaults(self):
         assert not enzmldoc.complex_dict
         assert not enzmldoc.reactant_dict
         assert not enzmldoc.reaction_dict
-        assert not enzmldoc.unit_dict
+        assert not enzmldoc._unit_dict
         assert not enzmldoc.file_dict
         assert not enzmldoc.global_parameters
 
@@ -228,7 +228,7 @@ def test_unit_attribute_change(self, enzmldoc):
         def check_consistency(unit, unit_id, kind):
             # Helper function
             assert (
-                enzmldoc.unit_dict[unit_id].name == unit
+                enzmldoc._unit_dict[unit_id].name == unit
             ), f"Unit change for {kind} inconsistent"
 
         # Test unit change vessel

tests/enzymeml/core/test_enzymereaction.py

@@ -347,7 +347,7 @@ def test_set_model(self, enzmldoc, correct_model, faulty_model):
         assert parameter.name == "x"
         assert parameter.value == 10.0
         assert parameter.unit == "mmole / l"
-        assert enzmldoc.unit_dict[parameter._unit_id].name == "mmole / l"
+        assert enzmldoc._unit_dict[parameter._unit_id].name == "mmole / l"
 
         # Faulty case
         with pytest.raises(SpeciesNotFoundError):

tests/enzymeml/core/test_measurement.py

@@ -201,15 +201,15 @@ def test_unit_unification(self, enzmldoc):
 
         assert replicate.data == [1000.0, 1000.0, 1000.0, 1000.0]
         assert replicate.time == [1.0, 2.0, 3.0, 4.0]
-        assert enzmldoc.unit_dict[nu_unit_id].name == "umole / l"
+        assert enzmldoc._unit_dict[nu_unit_id].name == "umole / l"
 
         # Check for proteins
         replicate = measurement.species_dict["proteins"]["p0"].replicates[0]
         nu_unit_id = replicate._data_unit_id
 
         assert replicate.data == [1000.0, 1000.0, 1000.0, 1000.0]
         assert replicate.time == [1.0, 2.0, 3.0, 4.0]
-        assert enzmldoc.unit_dict[nu_unit_id].name == "umole / l"
+        assert enzmldoc._unit_dict[nu_unit_id].name == "umole / l"
 
         # Test for not supported unit kinds
         with pytest.raises(ValueError):

tests/enzymeml/core/test_measurement_data.py

@@ -62,7 +62,7 @@ def test_unify_units(self, enzmldoc):
 
         assert replicate.data == [1000.0, 1000.0, 1000.0, 1000.0]
         assert replicate.data_unit == "umole / l"
-        assert enzmldoc.unit_dict[replicate._data_unit_id].name == "umole / l"
+        assert enzmldoc._unit_dict[replicate._data_unit_id].name == "umole / l"
 
         assert data.init_conc == 10000.0
         assert data.unit == "umole / l"