Calibraton timecourse unity (#19)

* added calibration attributes

* new implementation calibration timecourse diff

* working mode selector

* fixed failing tests

* updated docs

chromatopy/ioutils/enzymeml.py

@@ -240,6 +240,8 @@ def add_measurements_to_enzymeml(
 
     doc.measurements.append(enzml_measurement)
 
+    patch_init_t0(doc)
+
     return doc
 
 
@@ -321,7 +323,7 @@ def add_measurement_to_MeasurementData(
                 add_data(
                     measurement_data=measurement_data_instances[molecule_id],
                     chromatogram=chrom,
-                    reaction_time=measurement.reaction_time,
+                    reaction_time=measurement.data.value,
                     calibrators=calibrators,
                     calibrator_type=strategy,
                     extrapolate=extrapolate,
@@ -513,7 +515,7 @@ def extract_measurement_conditions(
     # extract measurement conditions
     phs = [measurement.ph for measurement in measurements]
     temperatures = [measurement.temperature for measurement in measurements]
-    time_units = [measurement.time_unit.name for measurement in measurements]
+    time_units = [measurement.data.unit.name for measurement in measurements]
     temperature_units = [
         measurement.temperature_unit.name  # type: ignore
         for measurement in measurements  # type: ignore
@@ -534,14 +536,14 @@ def extract_measurement_conditions(
     assert (
         measurements[0].temperature is not None
     ), "The temperature needs to be defined."
-    assert measurements[0].time_unit is not None, "The time unit needs to be defined."
+    assert measurements[0].data.unit is not None, "The time unit needs to be defined."
     assert (
         measurements[0].temperature_unit is not None
     ), "The temperature unit needs to be defined."
 
     ph = measurements[0].ph
     temperature = measurements[0].temperature
-    time_unit = measurements[0].time_unit
+    time_unit = measurements[0].data.unit
     temperature_unit = measurements[0].temperature_unit
 
     return ph, temperature, time_unit, temperature_unit

chromatopy/model.py

@@ -78,8 +78,7 @@ class Measurement(BaseModel):
     )  # type: ignore
 
     id: str
-    reaction_time: float
-    time_unit: UnitDefinition
+    data: Data
     temperature: float
     temperature_unit: UnitDefinition
     ph: float
@@ -212,6 +211,100 @@ def add_to_chromatograms(
         return self.chromatograms[-1]
 
 
+class Data(BaseModel):
+    model_config: ConfigDict = ConfigDict(  # type: ignore
+        validate_assigment=True,
+        use_enum_values=True,
+    )  # type: ignore
+
+    value: float
+    unit: UnitDefinition
+    data_type: DataType
+
+    # JSON-LD fields
+    ld_id: str = Field(
+        serialization_alias="@id",
+        default_factory=lambda: "chromatopy:Data/" + str(uuid4()),
+    )
+    ld_type: list[str] = Field(
+        serialization_alias="@type",
+        default_factory=lambda: [
+            "chromatopy:Data",
+        ],
+    )
+    ld_context: dict[str, str | dict] = Field(
+        serialization_alias="@context",
+        default_factory=lambda: {
+            "chromatopy": "https://github.com/FAIRChemistry/chromatopy",
+        },
+    )
+
+    def set_attr_term(
+        self,
+        attr: str,
+        term: str | dict,
+        prefix: str | None = None,
+        iri: str | None = None,
+    ):
+        """Sets the term for a given attribute in the JSON-LD object
+
+        Example:
+            # Using an IRI term
+            >> obj.set_attr_term("name", "http://schema.org/givenName")
+
+            # Using a prefix and term
+            >> obj.set_attr_term("name", "schema:givenName", "schema", "http://schema.org")
+
+            # Usinng a dictionary term
+            >> obj.set_attr_term("name", {"@id": "http://schema.org/givenName", "@type": "@id"})
+
+        Args:
+            attr (str): The attribute to set the term for
+            term (str | dict): The term to set for the attribute
+
+        Raises:
+            AssertionError: If the attribute is not found in the model
+        """
+
+        assert (
+            attr in self.model_fields
+        ), f"Attribute {attr} not found in {self.__class__.__name__}"
+
+        if prefix:
+            validate_prefix(term, prefix)
+
+        add_namespace(self, prefix, iri)
+        self.ld_context[attr] = term
+
+    def add_type_term(
+        self, term: str, prefix: str | None = None, iri: str | None = None
+    ):
+        """Adds a term to the @type field of the JSON-LD object
+
+        Example:
+            # Using a term
+            >> obj.add_type_term("https://schema.org/Person")
+
+            # Using a prefixed term
+            >> obj.add_type_term("schema:Person", "schema", "https://schema.org/Person")
+
+        Args:
+            term (str): The term to add to the @type field
+            prefix (str, optional): The prefix to use for the term. Defaults to None.
+            iri (str, optional): The IRI to use for the term prefix. Defaults to None.
+
+        Raises:
+            ValueError: If prefix is provided but iri is not
+            ValueError: If iri is provided but prefix is not
+        """
+
+        if prefix:
+            validate_prefix(term, prefix)
+
+        add_namespace(self, prefix, iri)
+        self.ld_type.append(term)
+
+
 class Chromatogram(BaseModel):
     model_config: ConfigDict = ConfigDict(  # type: ignore
         validate_assigment=True,
@@ -466,6 +559,7 @@ def add_type_term(
 class UnitDefinition(BaseModel):
     model_config: ConfigDict = ConfigDict(  # type: ignore
         validate_assigment=True,
+        use_enum_values=True,
     )  # type: ignore
 
     id: Optional[str] = Field(default=None)
@@ -696,6 +790,11 @@ class SignalType(Enum):
     UV = "uv/visible absorbance detector"
 
 
+class DataType(Enum):
+    CALIBRATION = "calibration"
+    TIMECOURSE = "timecourse"
+
+
 class UnitType(Enum):
     AMPERE = "ampere"
     AVOGADRO = "avogadro"