Merge branch 'enzymeml-2' of https://github.com/EnzymeML/enzymeml-spe…

…cifications into enzymeml-2
EnzymeML · Aug 14, 2024 · 2fe8aea · 2fe8aea
2 parents 88ca1d8 + 602b177
commit 2fe8aea
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Showing 7 changed files with 164 additions and 164 deletions.
diff --git a/docs/model.md b/docs/model.md
@@ -75,8 +75,8 @@ This page provides comprehensive information about the structure and components
 
 
 ## Ontologies
-- [schema](https://schema.org/)
 - [OBO](http://purl.obolibrary.org/obo/)
+- [schema](https://schema.org/)
 
 
 ## Types
@@ -497,12 +497,7 @@ __species_id__* `string`
 - The identifier for the described reactant.
 
 
-__init_conc__* `float`
-
-- Initial concentration of the measurement data. This must be the same as the first data point in the
-
-
-__conc_unit__* [`UnitDefinition`](#unitdefinition)
+__data_unit__* [`UnitDefinition`](#unitdefinition)
 
 - SI unit of the data that was measured.
 
@@ -517,9 +512,14 @@ __data_type__* `string`
 - Type of data that was measured (e.g. concentration)
 
 
-__prep_conc__ `float`
+__prepared__ `float`
+
+- Amount of the reactant before the measurement. This field should be used for specifying the prepared amount of a species in the reaction mix. Not to be confused with
+
+
+__initial__ `float`
 
-- Concentration of the reactant before the measurement. This field should be used for specifying the prepared concentration of a species in the reaction mix. Not to be confused with init_conc, specifying the concentration at the first data point from the
+- Initial amount of the measurement data. This must be the same as the first data point in the
 
 
 __data__* `list[float]`

diff --git a/python/pyenzyme/dataclass_models.py b/python/pyenzyme/dataclass_models.py
@@ -721,23 +721,23 @@ class Measurement:
     def add_to_species_data(
         self,
         species_id: str,
-        init_conc: float,
-        conc_unit: UnitDefinition,
+        data_unit: UnitDefinition,
         time_unit: UnitDefinition,
         data_type: str,
-        prep_conc: Optional[float] = None,
+        prepared: Optional[float] = None,
+        initial: Optional[float] = None,
         data: list[float] = [],
         time: list[float] = [],
         is_simulated: bool = False,
         **kwargs,
     ):
         params = {
             "species_id": species_id,
-            "init_conc": init_conc,
-            "conc_unit": conc_unit,
+            "data_unit": data_unit,
             "time_unit": time_unit,
             "data_type": data_type,
-            "prep_conc": prep_conc,
+            "prepared": prepared,
+            "initial": initial,
             "data": data,
             "time": time,
             "is_simulated": is_simulated,
@@ -755,11 +755,13 @@ def add_to_species_data(
 @dataclass
 class MeasurementData:
     species_id: str
-    init_conc: float
-    conc_unit: UnitDefinition
+    data_unit: UnitDefinition
     time_unit: UnitDefinition
     data_type: str
-    prep_conc: Optional[float] = field(
+    prepared: Optional[float] = field(
+        default=None, metadata=config(exclude=lambda x: x is None)
+    )
+    initial: Optional[float] = field(
         default=None, metadata=config(exclude=lambda x: x is None)
     )
     data: List[float] = field(default_factory=list)

diff --git a/python/pyenzyme/pydantic_models.py b/python/pyenzyme/pydantic_models.py
@@ -104,8 +104,8 @@ class EnzymeMLDocument(BaseModel):
         serialization_alias="@context",
         default_factory=lambda: {
             "enzml": "http://www.enzymeml.org/v2/",
-            "schema": "https://schema.org/",
             "OBO": "http://purl.obolibrary.org/obo/",
+            "schema": "https://schema.org/",
             "name": "schema:title",
             "references": {
                 "@id": "schema:citation",
@@ -505,8 +505,8 @@ class Creator(BaseModel):
         serialization_alias="@context",
         default_factory=lambda: {
             "enzml": "http://www.enzymeml.org/v2/",
-            "schema": "https://schema.org/",
             "OBO": "http://purl.obolibrary.org/obo/",
+            "schema": "https://schema.org/",
             "given_name": "schema:givenName",
             "family_name": "schema:familyName",
             "mail": "schema:email",
@@ -603,8 +603,8 @@ class Vessel(BaseModel):
         serialization_alias="@context",
         default_factory=lambda: {
             "enzml": "http://www.enzymeml.org/v2/",
-            "schema": "https://schema.org/",
             "OBO": "http://purl.obolibrary.org/obo/",
+            "schema": "https://schema.org/",
             "id": {
                 "@id": "schema:identifier",
                 "@type": "@id",
@@ -708,8 +708,8 @@ class Protein(BaseModel):
         serialization_alias="@context",
         default_factory=lambda: {
             "enzml": "http://www.enzymeml.org/v2/",
-            "schema": "https://schema.org/",
             "OBO": "http://purl.obolibrary.org/obo/",
+            "schema": "https://schema.org/",
             "id": {
                 "@type": "@id",
             },
@@ -821,8 +821,8 @@ class Complex(BaseModel):
         serialization_alias="@context",
         default_factory=lambda: {
             "enzml": "http://www.enzymeml.org/v2/",
-            "schema": "https://schema.org/",
             "OBO": "http://purl.obolibrary.org/obo/",
+            "schema": "https://schema.org/",
             "id": {
                 "@id": "schema:identifier",
                 "@type": "@id",
@@ -929,8 +929,8 @@ class SmallMolecule(BaseModel):
         serialization_alias="@context",
         default_factory=lambda: {
             "enzml": "http://www.enzymeml.org/v2/",
-            "schema": "https://schema.org/",
             "OBO": "http://purl.obolibrary.org/obo/",
+            "schema": "https://schema.org/",
             "id": {
                 "@id": "schema:identifier",
                 "@type": "@id",
@@ -1040,8 +1040,8 @@ class Reaction(BaseModel):
         serialization_alias="@context",
         default_factory=lambda: {
             "enzml": "http://www.enzymeml.org/v2/",
-            "schema": "https://schema.org/",
             "OBO": "http://purl.obolibrary.org/obo/",
+            "schema": "https://schema.org/",
             "id": {
                 "@id": "schema:identifier",
                 "@type": "@id",
@@ -1168,8 +1168,8 @@ class ReactionElement(BaseModel):
         serialization_alias="@context",
         default_factory=lambda: {
             "enzml": "http://www.enzymeml.org/v2/",
-            "schema": "https://schema.org/",
             "OBO": "http://purl.obolibrary.org/obo/",
+            "schema": "https://schema.org/",
             "species_id": {
                 "@type": "@id",
             },
@@ -1269,8 +1269,8 @@ class Equation(BaseModel):
         serialization_alias="@context",
         default_factory=lambda: {
             "enzml": "http://www.enzymeml.org/v2/",
-            "schema": "https://schema.org/",
             "OBO": "http://purl.obolibrary.org/obo/",
+            "schema": "https://schema.org/",
             "species_id": {
                 "@type": "@id",
             },
@@ -1430,8 +1430,8 @@ class Parameter(BaseModel):
         serialization_alias="@context",
         default_factory=lambda: {
             "enzml": "http://www.enzymeml.org/v2/",
-            "schema": "https://schema.org/",
             "OBO": "http://purl.obolibrary.org/obo/",
+            "schema": "https://schema.org/",
             "id": {
                 "@id": "schema:identifier",
                 "@type": "@id",
@@ -1533,8 +1533,8 @@ class Measurement(BaseModel):
         serialization_alias="@context",
         default_factory=lambda: {
             "enzml": "http://www.enzymeml.org/v2/",
-            "schema": "https://schema.org/",
             "OBO": "http://purl.obolibrary.org/obo/",
+            "schema": "https://schema.org/",
             "id": {
                 "@id": "schema:identifier",
                 "@type": "@id",
@@ -1625,23 +1625,23 @@ def add_type_term(
     def add_to_species_data(
         self,
         species_id: str,
-        init_conc: float,
-        conc_unit: UnitDefinition,
+        data_unit: UnitDefinition,
         time_unit: UnitDefinition,
         data_type: str,
-        prep_conc: Optional[float] = None,
+        prepared: Optional[float] = None,
+        initial: Optional[float] = None,
         data: list[float] = [],
         time: list[float] = [],
         is_simulated: bool = False,
         **kwargs,
     ):
         params = {
             "species_id": species_id,
-            "init_conc": init_conc,
-            "conc_unit": conc_unit,
+            "data_unit": data_unit,
             "time_unit": time_unit,
             "data_type": data_type,
-            "prep_conc": prep_conc,
+            "prepared": prepared,
+            "initial": initial,
             "data": data,
             "time": time,
             "is_simulated": is_simulated,
@@ -1661,11 +1661,11 @@ class MeasurementData(BaseModel):
     )  # type: ignore
 
     species_id: str
-    init_conc: float
-    conc_unit: UnitDefinition
+    data_unit: UnitDefinition
     time_unit: UnitDefinition
     data_type: str
-    prep_conc: Optional[float] = Field(default=None)
+    prepared: Optional[float] = Field(default=None)
+    initial: Optional[float] = Field(default=None)
     data: list[float] = Field(default_factory=list)
     time: list[float] = Field(default_factory=list)
     is_simulated: bool = False
@@ -1685,8 +1685,8 @@ class MeasurementData(BaseModel):
         serialization_alias="@context",
         default_factory=lambda: {
             "enzml": "http://www.enzymeml.org/v2/",
-            "schema": "https://schema.org/",
             "OBO": "http://purl.obolibrary.org/obo/",
+            "schema": "https://schema.org/",
             "species_id": {
                 "@type": "@id",
             },
@@ -1786,8 +1786,8 @@ class UnitDefinition(BaseModel):
         serialization_alias="@context",
         default_factory=lambda: {
             "enzml": "http://www.enzymeml.org/v2/",
-            "schema": "https://schema.org/",
             "OBO": "http://purl.obolibrary.org/obo/",
+            "schema": "https://schema.org/",
         },
     )
 
@@ -1916,8 +1916,8 @@ class BaseUnit(BaseModel):
         serialization_alias="@context",
         default_factory=lambda: {
             "enzml": "http://www.enzymeml.org/v2/",
-            "schema": "https://schema.org/",
             "OBO": "http://purl.obolibrary.org/obo/",
+            "schema": "https://schema.org/",
         },
     )
 
@@ -2011,8 +2011,8 @@ class EqVariable(BaseModel):
         serialization_alias="@context",
         default_factory=lambda: {
             "enzml": "http://www.enzymeml.org/v2/",
-            "schema": "https://schema.org/",
             "OBO": "http://purl.obolibrary.org/obo/",
+            "schema": "https://schema.org/",
             "id": {
                 "@type": "@id",
             },
@@ -2110,8 +2110,8 @@ class EqParameter(BaseModel):
         serialization_alias="@context",
         default_factory=lambda: {
             "enzml": "http://www.enzymeml.org/v2/",
-            "schema": "https://schema.org/",
             "OBO": "http://purl.obolibrary.org/obo/",
+            "schema": "https://schema.org/",
             "id": {
                 "@type": "@id",
             },