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JR-1991JR-1991
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update model version
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Lines changed: 18 additions & 18 deletions

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‎pyenzyme/versions/v2.py‎

Lines changed: 18 additions & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -33,9 +33,9 @@
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## This is a generated file. Do not modify it manually!
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from __future__ import annotations
36-
from enum import Enum
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from pydantic import BaseModel, Field, ConfigDict
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from typing import Optional, Generic, TypeVar
38+
from enum import Enum
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from uuid import uuid4
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from mdmodels.units.annotation import UnitDefinitionAnnot
4141

@@ -137,8 +137,8 @@ class EnzymeMLDocument(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"name": "schema:title",
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"created": "schema:dateCreated",
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"modified": "schema:dateModified",
@@ -335,7 +335,7 @@ def add_to_creators(
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if "id" in kwargs:
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params["id"] = kwargs["id"]
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338-
self.creators.append(Creator(**params)) # type: ignore
338+
self.creators.append(Creator(**params))
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340340
return self.creators[-1]
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@@ -582,8 +582,8 @@ class Creator(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"given_name": "schema:givenName",
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"family_name": "schema:familyName",
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"mail": "schema:email",
@@ -680,8 +680,8 @@ class Vessel(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -779,14 +779,14 @@ class Protein(BaseModel):
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)
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ld_type: list[str] = Field(
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serialization_alias="@type",
782-
default_factory=lambda: ["enzml:Protein", "schema:Protein"],
782+
default_factory=lambda: ["enzml:Protein", "OBO:PR_000000001"],
783783
)
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ld_context: dict[str, str | dict] = Field(
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
788-
"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -900,8 +900,8 @@ class Complex(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -1012,8 +1012,8 @@ class SmallMolecule(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -1123,8 +1123,8 @@ class Reaction(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -1251,8 +1251,8 @@ class ReactionElement(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
1254-
"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
1255+
"OBO": "http://purl.obolibrary.org/obo/",
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"species_id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -1351,8 +1351,8 @@ class Equation(BaseModel):
13511351
serialization_alias="@context",
13521352
default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
1354-
"OBO": "http://purl.obolibrary.org/obo/",
13551354
"schema": "https://schema.org/",
1355+
"OBO": "http://purl.obolibrary.org/obo/",
13561356
"species_id": {
13571357
"@id": "schema:identifier",
13581358
"@type": "@id",
@@ -1449,7 +1449,7 @@ def add_to_variables(
14491449
if "id" in kwargs:
14501450
params["id"] = kwargs["id"]
14511451

1452-
self.variables.append(Variable(**params)) # type: ignore
1452+
self.variables.append(Variable(**params))
14531453

14541454
return self.variables[-1]
14551455

@@ -1478,8 +1478,8 @@ class Variable(BaseModel):
14781478
serialization_alias="@context",
14791479
default_factory=lambda: {
14801480
"enzml": "http://www.enzymeml.org/v2/",
1481-
"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
1482+
"OBO": "http://purl.obolibrary.org/obo/",
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"id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -1567,7 +1567,7 @@ class Parameter(BaseModel):
15671567
upper_bound: Optional[float] = Field(default=None)
15681568
lower_bound: Optional[float] = Field(default=None)
15691569
stderr: Optional[float] = Field(default=None)
1570-
constant: bool = True
1570+
constant: Optional[bool] = True
15711571

15721572
# JSON-LD fields
15731573
ld_id: str = Field(
@@ -1584,8 +1584,8 @@ class Parameter(BaseModel):
15841584
serialization_alias="@context",
15851585
default_factory=lambda: {
15861586
"enzml": "http://www.enzymeml.org/v2/",
1587-
"OBO": "http://purl.obolibrary.org/obo/",
15881587
"schema": "https://schema.org/",
1588+
"OBO": "http://purl.obolibrary.org/obo/",
15891589
"id": {
15901590
"@id": "schema:identifier",
15911591
"@type": "@id",
@@ -1687,8 +1687,8 @@ class Measurement(BaseModel):
16871687
serialization_alias="@context",
16881688
default_factory=lambda: {
16891689
"enzml": "http://www.enzymeml.org/v2/",
1690-
"OBO": "http://purl.obolibrary.org/obo/",
16911690
"schema": "https://schema.org/",
1691+
"OBO": "http://purl.obolibrary.org/obo/",
16921692
"id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -1839,8 +1839,8 @@ class MeasurementData(BaseModel):
18391839
serialization_alias="@context",
18401840
default_factory=lambda: {
18411841
"enzml": "http://www.enzymeml.org/v2/",
1842-
"OBO": "http://purl.obolibrary.org/obo/",
18431842
"schema": "https://schema.org/",
1843+
"OBO": "http://purl.obolibrary.org/obo/",
18441844
"species_id": {
18451845
"@type": "@id",
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},

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