"""
Iodine Network Object Model.
Original author: RJ Zhou
"Forked" from: https://github.com/zrj26/go-NOM
Adapted by: Gary Geng
TODOs
* Phase out errCode, or at least provide more detalis in error messages.
"""
# from __future__ import annotations
import abc
from re import S, X
from functools import partial
from marshmallow.decorators import post_dump, post_load, pre_load
from marshmallow_polyfield import PolyField
from numpy.lib.npyio import recfromcsv
from .mvc import (ModifierTipStyle, IDNotFoundError, IDRepeatError, NodeNotFreeError, NetIndexError,
ReactionIndexError, NodeIndexError, CompartmentIndexError, StoichError,
StackEmptyError, JSONError, FileError)
from .config import ColorField, Pixel, Dim, Dim2, Color, Font, FontField, get_theme
from .canvas.geometry import Vec2
from .canvas.data import CompositeShapeFactory, PrimitiveFactory, CirclePrim, CompositeShape, Primitive, \
RectanglePrim, HexagonPrim, LinePrim, TrianglePrim, Transform, TextPrim, ChoiceItem,\
FONT_FAMILY_CHOICES, FONT_STYLE_CHOICES, FONT_WEIGHT_CHOICES, TEXT_ALIGNMENT_CHOICES
import copy
from dataclasses import dataclass, field
import json
from typing import Any, DefaultDict, Dict, MutableSet, Optional, Set, Tuple, List, cast
from enum import Enum
from collections import defaultdict
from marshmallow import Schema, fields, validate, missing as missing_, ValidationError, pre_dump
from pprint import pprint
# The current version of the network serialization schema.
SERIAL_VERSION = "1.0.0"
[docs]def get_theme_fn(name):
return partial(get_theme, name, convert_color=False)
# kwargs common to geometric shapes
geometry_kwargs = {
'fill_color': get_theme_fn('node_fill'),
'border_color': get_theme_fn('node_border'),
'border_width': get_theme_fn('node_border_width'),
}
# Default primitive factories
rectFact = PrimitiveFactory(RectanglePrim, **geometry_kwargs)
circleFact = PrimitiveFactory(CirclePrim, **geometry_kwargs)
hexFact = PrimitiveFactory(HexagonPrim, **geometry_kwargs)
lineFact = PrimitiveFactory(LinePrim, **geometry_kwargs)
triangleFact = PrimitiveFactory(TrianglePrim, **geometry_kwargs)
textFact = PrimitiveFactory(TextPrim)
singletonTrans = Transform() # fills the entire bounding box
DEFAULT_SHAPE_FACTORY = CompositeShapeFactory([(rectFact, singletonTrans)],
(textFact, singletonTrans), 'rectangle')
# These are the default shape factories. They should never be modified by the user.
shapeFactories = [
DEFAULT_SHAPE_FACTORY,
CompositeShapeFactory([(circleFact, singletonTrans)], (textFact, singletonTrans), 'circle'),
CompositeShapeFactory([(hexFact, singletonTrans)], (textFact, singletonTrans), 'hexagon'),
CompositeShapeFactory([(lineFact, singletonTrans)], (textFact, singletonTrans), 'line'),
CompositeShapeFactory([(triangleFact, singletonTrans)], (textFact, singletonTrans), 'triangle'),
CompositeShapeFactory([], (textFact, singletonTrans), 'text-only'),
CompositeShapeFactory([(circleFact, singletonTrans)], (textFact, Transform(translation=Vec2(1, 1))), 'text outside'),
CompositeShapeFactory([(circleFact, Transform(scale=Vec2.repeat(0.5))),
(circleFact, Transform(scale=Vec2.repeat(0.5), translation=Vec2.repeat(0.5))),
(PrimitiveFactory(RectanglePrim, fill_color=Color(255, 0, 0, 255)),
Transform(scale=Vec2.repeat(0.5), translation=Vec2.repeat(0.25)))
],
(PrimitiveFactory(TextPrim, font_color=Color(255, 255, 255, 255)), singletonTrans), 'demo combo'),
]
# TODO add lockedNode here too
[docs]class TAbstractNode(abc.ABC):
index: int
position: Vec2
rectSize: Vec2
compi: int
nodeLocked: bool
[docs]@dataclass
class TNode(TAbstractNode):
index: int
id: str
position: Vec2
rectSize: Vec2
floating : bool # If false it means the node is a boundary node
nodeLocked: bool #if false it means the node can be moved
compi: int = -1
shapei: int = 0
shape: CompositeShape = field(default_factory=lambda: shapeFactories[0].produce())
[docs]@dataclass
class TAliasNode(TAbstractNode):
index: int
position: Vec2
rectSize: Vec2
originalIdx: int
nodeLocked: bool
compi: int = -1
[docs]class TNetwork:
'''Represents an entire reaction network.
**NOTE IMPORTANT** whenever any change is made to the code that changes how the network is
serialized/deserialized, one must bump the global variable SERIAL_VERSION to reflect that. See
NetworkSchema::serialVersion for more information.
'''
id: str
nodes: Dict[int, TAbstractNode]
reactions: Dict[int, 'TReaction']
compartments: Dict[int, 'TCompartment']
baseNodes: Set[int] #: Set of node indices not in any compartment
srcMap: DefaultDict[int, MutableSet[int]] #: Map nodes to reactions of which it is a source
destMap: DefaultDict[int, MutableSet[int]] #: Map nodes to reactions of which it is a target
lastNodeIdx: int
lastReactionIdx: int
lastCompartmentIdx: int
def __init__(self, id: str, nodes: Dict[int, TAbstractNode] = None,
reactions: Dict[int, 'TReaction'] = None,
compartments: Dict[int, 'TCompartment'] = None,
):
if nodes is None:
nodes = dict()
if reactions is None:
reactions = dict()
if compartments is None:
compartments = dict()
self.id = id
self.nodes = nodes
self.reactions = reactions
self.compartments = compartments
self.baseNodes = set(index for index, n in nodes.items() if n.compi == -1)
self.srcMap = defaultdict(set)
self.destMap = defaultdict(set)
# Initialize srcMap and destMap
for index, reaction in reactions.items():
for src in reaction.reactants:
self.srcMap[src].add(index)
for dest in reaction.products:
self.destMap[dest].add(index)
self.lastNodeIdx = max(nodes.keys(), default=-1) + 1
self.lastReactionIdx = max(reactions.keys(), default=-1) + 1
self.lastCompartmentIdx = max(compartments.keys(), default=-1) + 1
[docs] def addNode(self, node: TAbstractNode) -> int:
self.nodes[self.lastNodeIdx] = node
self.baseNodes.add(self.lastNodeIdx)
ret = self.lastNodeIdx
self.lastNodeIdx += 1
return ret
[docs] def addReaction(self, rea: 'TReaction'):
self.reactions[self.lastReactionIdx] = rea
# update nodeToReactions
for src in rea.reactants:
self.srcMap[src].add(self.lastReactionIdx)
for dest in rea.products:
self.destMap[dest].add(self.lastReactionIdx)
self.lastReactionIdx += 1
[docs] def addCompartment(self, comp: 'TCompartment') -> int:
ind = self.lastCompartmentIdx
self.compartments[ind] = comp
self.lastCompartmentIdx += 1
return ind
[docs]@dataclass
class TReaction:
id: str
centerPos: Optional[Vec2] = None
rateLaw: str = ""
reactants: Dict[int, 'TSpeciesNode'] = field(default_factory=dict)
products: Dict[int, 'TSpeciesNode'] = field(default_factory=dict)
fillColor: Color = Color(255, 150, 80, 255)
thickness: float = 3.0
centerHandlePos: Vec2 = Vec2()
bezierCurves: bool = True # If false it means a straight line
modifiers: Set[int] = field(default_factory=set)
tipStyle: ModifierTipStyle = ModifierTipStyle.CIRCLE
[docs]@dataclass
class TSpeciesNode:
stoich: float
handlePos: Vec2 = Vec2()
[docs]@dataclass
class TCompartment:
id: str
position: Vec2
rectSize: Vec2
node_indices: Set[int] = field(default_factory=set)
volume: float = 1
fillColor: Color = Color(0, 247, 255, 255)
outlineColor: Color = Color(0, 106, 255, 255)
outlineThickness: float = 2
[docs]class TStack:
items: List['TNetworkDict']
def __init__(self):
self.items = []
[docs] def isEmpty(self):
return self.items == []
[docs] def push(self, netDict: 'TNetworkDict'):
theSet = copy.deepcopy(netDict)
self.items.append(theSet)
[docs] def pop(self):
return self.items.pop()
[docs]class TNetworkDict(Dict[int, TNetwork]):
def __init__(self):
super().__init__()
self.lastNetIndex = 0
[docs]class ErrorCode(Enum):
OK = 0
OTHER = -1
ID_NOT_FOUND = -2
ID_REPEAT = -3
NODE_NOT_FREE = -4
NETI_NOT_FOUND = -5
REAI_NOT_FOUND = -6
NODEI_NOT_FOUND = -7
BAD_STOICH = -8
STACK_EMPTY = -9
JSON_ERROR = -10
FILE_ERROR = -11
OUT_OF_RANGE = -12
COMPI_NOT_FOUND = -13
errorDict = {
0: "ok",
-1: "other",
-2: "id not found",
-3: "id repeat",
-4: "node is not free",
-5: "net index not found",
-6: "reaction index not found",
-7: "node index not found",
-8: "bad stoich: stoich has to be positive",
-9: "undo/redo stack is empty",
-10: "Json convert error",
-11: "File error",
-12: "Variable out of range",
-13: "Compartment index not found",
}
ExceptionDict = {
-2: IDNotFoundError,
-3: IDRepeatError,
-4: NodeNotFreeError,
-5: NetIndexError,
-6: ReactionIndexError,
-7: NodeIndexError,
-8: StoichError,
-9: StackEmptyError,
-10: JSONError,
-11: FileError,
-12: ValueError,
-13: CompartmentIndexError,
}
fontFamilyDict = {
"default": 0,
"decorative": 1,
"roman": 2,
"script": 3,
"swiss": 4,
"modern": 5,
}
fontStyleDict = {
"normal": 0,
"italic": 1,
}
fontWeightDict = {
"default": 0,
"light": 1,
"bold": 2,
}
stackFlag: bool = True
errCode: int = 0
# dict mapping from index to network
networkDict: TNetworkDict = TNetworkDict()
undoStack: TStack = TStack()
redoStack: TStack = TStack()
lastNetIndex: int = 0
[docs]def getErrorCode():
"""get the error code of last function"""
global errCode
return errCode
[docs]def undo():
"""
Undo ge back to last state
errCode: -9: stack is empty
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if undoStack.isEmpty():
errCode = -9
else:
redoStack.push(networkDict)
networkDict = undoStack.pop()
if errCode < 0:
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def redo():
"""
Redo redo
errCode: -9: stack is empty
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
if redoStack.isEmpty():
errCode = -9
else:
undoStack.push(networkDict)
networkDict = redoStack.pop()
if errCode < 0:
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def startGroup():
"""
StartGroup used at the start of a group operaction or secondary function.
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
redoStack = TStack()
undoStack.push(networkDict)
stackFlag = False
[docs]def endGroup():
"""
EndGroup used at the end of a group operaction or secondary function.
"""
global stackFlag
stackFlag = True
[docs]def newNetwork(netID: str):
"""
newNetwork Create a new network
errCode -3: id repeat, 0 :ok
"""
global stackFlag, errCode, networkDict, undoStack, redoStack, lastNetIndex
errCode = 0
for network in networkDict.values():
if network.id == netID:
errCode = -3
break
if errCode < 0:
raise ExceptionDict[errCode](errorDict[errCode])
else:
_pushUndoStack()
newNetwork = TNetwork(netID)
networkDict[lastNetIndex] = newNetwork
lastNetIndex += 1
[docs]def getNetworkIndex(netID: str) -> int:
"""
getNetworkIndex
return: -2: net id can't find
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = -2
for i, net in networkDict.items():
if net.id == netID:
errCode = 0
return i
raise ExceptionDict[errCode](errorDict[errCode])
# def saveNetworkAsJSON(neti: int, fileName: str):
# """
# SaveNetworkAsJSON SaveNetworkAsJSON
# errCode: -5: net index out of range
# -10: "Json convert error", -11: "File error"
# """
# global stackFlag, errCode, networkDict, undoStack, redoStack
# errCode = 0
# if neti not in networkDict:
# errCode = -5
# raise ExceptionDict[errCode](errorDict[errCode])
# else:
# data2 = json.dumps(networkDict[neti],
# sort_keys=True, indent=4, separators=(',', ': '))
# print(data2)
# #ReadNetworkFromJSON ReadNetworkFromJSON
# #errCode -3: id repeat, 0 :ok
# #-10: "Json convert error", -11: "File error",
# def ReadNetworkFromJSON(filePath string) int :
# errCode = 0
# file, err1 = ioutil.ReadFile(filePath)
# if err1 != nil :
# errCode = -11
# addErrorMessage(errCode, "(\"" + filePath + "\")", "", "")
# return errCode
# newNet = TNetwork{
# err2 = json.Unmarshal([]byte(file), &newNet)
# if err2 != nil :
# errCode = -10
# addErrorMessage(errCode, "(\"" + filePath + "\")", "", "")
# return errCode
# for i = range networkDict :
# if newNet.id == networkDict[i].id :
# errCode = -3
# addErrorMessage(errCode, ("(\"" + filePath + "\")"), newNet.id, "")
# return errCode
# if stackFlag :
# redoStack = TundoStack{
# undoStack.push(networkDict)
# networkDict = append(networkDict, newNet)
# # fmt.Println(networkDict)
# return errCode
[docs]def deleteNetwork(neti: int):
"""
DeleteNetwork DeleteNetwork
errCode: -5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
if errCode < 0:
raise ExceptionDict[errCode](errorDict[errCode])
else:
_pushUndoStack()
del networkDict[neti]
[docs]def clearNetworks():
global stackFlag, errCode, networkDict, undoStack, redoStack, lastNetIndex
errCode = 0
_pushUndoStack()
networkDict = TNetworkDict()
lastNetIndex = 0
[docs]def getNumberOfNetworks():
return len(networkDict)
[docs]def getNetworkID(neti: int):
"""
GetNetworkID GetID of network
errCode: -5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
if errCode < 0:
raise ExceptionDict[errCode](errorDict[errCode])
else:
return networkDict[neti].id
[docs]def getListOfNetworks() -> List[int]:
return list(networkDict.keys())
def _raiseError(eCode: int):
global errCode
assert eCode < 0
errCode = eCode
raise ExceptionDict[errCode](errorDict[errCode])
def _addNetwork(network: TNetwork) -> int:
"""Helper function that adds a network object."""
global lastNetIndex
for net in networkDict.values():
if net.id == network.id:
_raiseError(-3)
_pushUndoStack()
networkDict[lastNetIndex] = network
lastNetIndex += 1
return lastNetIndex - 1
def _getNetwork(neti: int) -> TNetwork:
if neti not in networkDict:
errCode = -5
raise ExceptionDict[errCode](errorDict[errCode])
return networkDict[neti]
def _getNodeOrAlias(neti: int, nodei: int) -> TAbstractNode:
net = _getNetwork(neti)
if nodei not in net.nodes:
_raiseError(-7)
return net.nodes[nodei]
def _getConcreteNode(neti: int, nodei: int) -> TNode:
net = _getNetwork(neti)
node = _getNodeOrAlias(neti, nodei)
if isinstance(node, TAliasNode):
# get the original node
originalIdx = node.originalIdx
assert originalIdx in net.nodes
node = net.nodes[originalIdx]
assert isinstance(node, TNode)
return node
def _getReaction(neti: int, reai: int) -> TReaction:
net = _getNetwork(neti)
if reai not in net.reactions:
_raiseError(-6)
return net.reactions[reai]
def _getCompartment(neti: int, compi: int) -> TCompartment:
global errCode
net = _getNetwork(neti)
if compi not in net.compartments:
errCode = -13
raise CompartmentIndexError('Unknown index: {}'.format(compi))
return net.compartments[compi]
def _pushUndoStack():
global stackFlag, errCode, networkDict, undoStack, redoStack
if stackFlag:
redoStack = TStack()
undoStack.push(networkDict)
[docs]def addNode(neti: int, nodeID: str, x: float, y: float, w: float, h: float, floatingNode: bool = True, nodeLocked: bool = False) -> int:
"""
AddNode adds a node to the network
errCode - 3: id repeat, 0: ok
-5: net index out of range
-12: Variable out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
n = _getNetwork(neti)
for node in n.nodes.values():
if isinstance(node, TNode) and node.id == nodeID:
_raiseError(-3)
if x < 0 or y < 0 or w <= 0 or h <= 0:
_raiseError(-12)
_pushUndoStack()
newNode = TNode(n.lastNodeIdx, nodeID, Vec2(x, y), Vec2(w, h), floatingNode, nodeLocked)
return n.addNode(newNode)
[docs]def addAliasNode(neti: int, originalIdx: int, x: float, y: float, w: float, h: float) -> int:
net = _getNetwork(neti)
# make sure we can get it
original_node = _getConcreteNode(neti, originalIdx)
_pushUndoStack()
# Refer to the original node's index, whether 'original_index' is a TNode or a TAliasNode
anode = TAliasNode(net.lastNodeIdx, Vec2(x, y), Vec2(w, h), original_node.index,
nodeLocked=False)
anodei = net.addNode(anode)
setCompartmentOfNode(neti, anodei, original_node.compi)
return anodei
[docs]def aliasForReaction(neti: int, reai: int, nodei: int, x: float, y: float, w: float, h: float):
'''Create an alias for nodei, and replace each instance of nodei in reai with the alias
'''
# ensure that the original node exists
_getConcreteNode(neti, nodei)
_pushUndoStack()
aliasi = addAliasNode(neti, nodei, x, y, w, h)
reaction = _getReaction(neti, reai)
net = _getNetwork(neti)
# update reactants and srcMap
if nodei in reaction.reactants:
reaction.reactants[aliasi] = reaction.reactants[nodei]
del reaction.reactants[nodei]
net.srcMap[nodei].remove(reai)
net.srcMap[aliasi].add(reai)
# update products and destMap
if nodei in reaction.products:
reaction.products[aliasi] = reaction.products[nodei]
del reaction.products[nodei]
net.destMap[nodei].remove(reai)
net.destMap[aliasi].add(reai)
[docs]def getNodeIndex(neti: int, nodeID: str):
"""
GetNodeIndex get node index by id
errCode: -2: node id not found,
-5: net index out of range
return: >=0
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = -2
if neti not in networkDict:
errCode = -5
else:
n = networkDict[neti]
for i, node, in n.nodes.items():
if isinstance(node, TNode) and node.id == nodeID:
errCode = 0
return i
assert errCode < 0
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def deleteNode(neti: int, nodei: int) -> bool:
"""
DeleteNode deletes the node with index. Returns whether there was a node with the given index,
i.e. whether a node was deleted.
This does not throw an error due to the possibility of someone deleting nodes in a loop, in
which case an original copy may be deleted before its alias, and so when the alias is reached,
it no longer exists.
"""
def deleteHelper(net: TNetwork, node: TAbstractNode, neti: int, nodei: int, is_alias: bool):
# to delete an alias, remove it from the compartment
# modify the reactions that it is in, so that previous references now point to the original
# node. Also modify the modifiers to do the same
if is_alias:
# swap all occurrences of alias with the original node, since we're deleting the alias
assert isinstance(node, TAliasNode)
srcReactions = net.srcMap[nodei]
destReactions = net.destMap[nodei]
# put the original node in the reaction in the place of the alias node
for reai in srcReactions:
rxn = net.reactions[reai]
rxn.reactants[node.originalIdx] = rxn.reactants[nodei]
# I'm not sure what should happen if both a node and its alias are reactants of
# the same reaction. Originally I thought of adding up the stoich of the deleted
# alias to that of the original node, but frankly this is such a nonsensical case
# that I think doing so would be making it unncessarily complicated.
# So now I'm just deleting it and doing nothing
# if original_species:
# new_species = rxn.reactants[node.originalIdx]
# new_species.stoich += original_species.stoich
# new_species.handlePos = original_species.handlePos
del rxn.reactants[nodei]
for reai in destReactions:
rxn = net.reactions[reai]
# see above for explanation
rxn.products[node.originalIdx] = rxn.products[nodei]
# if original_species:
# new_species = rxn.products[node.originalIdx]
# new_species.stoich += original_species.stoich
# new_species.handlePos = original_species.handlePos
del rxn.products[nodei]
# update srcMap and destMap
net.srcMap[node.originalIdx] |= net.srcMap[nodei]
net.destMap[node.originalIdx] |= net.destMap[nodei]
del net.srcMap[nodei]
del net.destMap[nodei]
# replace occurrences in modifiers
for rxn in net.reactions.values():
if nodei in rxn.modifiers:
rxn.modifiers.remove(nodei)
rxn.modifiers.add(node.originalIdx)
else:
# for now, disallow removing concrete nodes that are part of a reaction
if len(net.srcMap[nodei]) != 0 or len(net.destMap[nodei]) != 0:
_raiseError(-4)
# remove self from modifiers list
for rxn in net.reactions.values():
rxn.modifiers.discard(nodei)
# remove from compartment
compi = getCompartmentOfNode(neti, nodei)
if compi == -1:
net.baseNodes.remove(nodei)
else:
net.compartments[compi].node_indices.remove(nodei)
# remove from 'nodes'
del net.nodes[nodei]
net = _getNetwork(neti)
try:
node = _getNodeOrAlias(neti, nodei)
except NodeIndexError:
return False
# validate that node is not part of a reaction
if isinstance(node, TNode) and (len(net.srcMap[nodei]) != 0 or len(net.destMap[nodei]) != 0):
_raiseError(-4)
_pushUndoStack()
is_alias = isinstance(node, TAliasNode)
if is_alias:
deleteHelper(net, node, neti, nodei, True)
else:
# delete all the aliases of node if node is an original node
alias_indices = [i for i, n in net.nodes.items() if isinstance(n, TAliasNode) and cast(TAliasNode, n).originalIdx == nodei]
for alias_idx in alias_indices:
deleteHelper(net, net.nodes[alias_idx], neti, alias_idx, True)
# delete original node
deleteHelper(net, node, neti, nodei, False)
return True
[docs]def clearNetwork(neti: int):
"""
ClearNetwork clear all nodes and reactions in this network
errCode: -5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
if errCode < 0:
raise ExceptionDict[errCode](errorDict[errCode])
else:
_pushUndoStack()
# networkDict[neti].nodes.clear()
# networkDict[neti].reactions.clear()
# networkDict[neti].compartments.clear()
networkDict[neti] = TNetwork(networkDict[neti].id)
[docs]def getNumberOfNodes(neti: int):
"""
GetNumberOfNodes get the number of nodes in the current network
num: >= -5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
if errCode < 0:
raise ExceptionDict[errCode](errorDict[errCode])
else:
n = networkDict[neti]
return len(n.nodes)
[docs]def getNodeCenter(neti: int, nodei: int):
"""
GetNodeCenter Get the X and Y coordinate of the Center of node
errCode: -7: node index out of range
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
n = networkDict[neti]
if nodei not in n.nodes:
errCode = -7
else:
X = round(n.nodes[nodei].position.x + n.nodes[nodei].rectSize.x*0.5, 2)
Y = round(n.nodes[nodei].position.y + n.nodes[nodei].rectSize.y*0.5, 2)
return (X, Y)
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def getNodeID(neti: int, nodei: int):
"""
GetNodeID Get the id of the node
errCode: -7: node index out of range
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
node = _getConcreteNode(neti, nodei)
return node.id
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def getOriginalIndex(neti: int, nodei: int) -> int:
'''Return -1 if the node is an original, or if this is an alias, return the original index.'''
node = _getNodeOrAlias(neti, nodei)
if isinstance(node, TNode):
return -1
else:
assert isinstance(node, TAliasNode)
return node.originalIdx
[docs]def IsFloatingNode(neti : int, nodei : int):
return _getConcreteNode(neti, nodei).floating
[docs]def IsBoundaryNode(neti : int, nodei : int):
return not IsFloatingNode(neti, nodei)
[docs]def IsNodeLocked(neti: int, nodei: int):
return _getNodeOrAlias(neti, nodei).nodeLocked
[docs]def getListOfNodeIDs(neti: int) -> List[str]:
if neti not in networkDict:
errCode = -5
raise ExceptionDict[errCode](errorDict[errCode])
return [n.id for n in networkDict[neti].nodes.values() if isinstance(n, TNode)]
[docs]def getListOfNodeIndices(neti: int) -> Set[int]:
return cast(Set[int], _getNetwork(neti).nodes.keys())
[docs]def getListOfReactionIndices(neti: int) -> Set[int]:
return cast(Set[int], _getNetwork(neti).reactions.keys())
[docs]def getListOfCompartmentIndices(neti: int) -> Set[int]:
return cast(Set[int], _getNetwork(neti).compartments.keys())
[docs]def getSrcReactions(neti: int, nodei: int) -> Set[int]:
return set(_getNetwork(neti).srcMap[nodei])
[docs]def getDestReactions(neti: int, nodei: int) -> Set[int]:
return set(_getNetwork(neti).destMap[nodei])
[docs]def getNodeCoordinateAndSize(neti: int, nodei: int):
"""
getNodeCoordinateAndSize get the x,y,w,h of the node
errCode:-7: node index out of range
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
n = networkDict[neti]
if nodei not in n.nodes:
errCode = -7
else:
X = round(n.nodes[nodei].position.x, 2)
Y = round(n.nodes[nodei].position.y, 2)
W = round(n.nodes[nodei].rectSize.x, 2)
H = round(n.nodes[nodei].rectSize.y, 2)
return (X, Y, W, H)
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def colorToRGB(color: Color):
color1 = color.r
color1 = (color1 << 8) | color.g
color1 = (color1 << 8) | color.b
return color1
[docs]def getNodeFillColor(neti: int, nodei: int):
"""
Return the 'fill_color' property of the first primitive in the given node's composite shape, if
there is such a primitive. Otherwise, return None.
This function exists for backwards-compatibility and convenience reasons.
errCode: -7: node index out of range
-5: net index out of range
"""
node = _getConcreteNode(neti, nodei)
for prim, _ in node.shape.items:
if 'fill_color' in prim.__dataclass_fields__:
ret = getattr(prim, 'fill_color')
assert isinstance(ret, Color)
return ret
return None
[docs]def getNodeFillColorRGB(neti: int, nodei: int):
"""
See getNodeFillColor(), except only returns the RGB values
errCode: -7: node index out of range
-5: net index out of range
"""
color = getNodeFillColor(neti, nodei)
if color is None:
return None
return colorToRGB(color)
[docs]def getNodeFillColorAlpha(neti: int, nodei: int):
"""
getNodeFillColorAlpha getNodeFillColor alpha value(float)
errCode: -7: node index out of range
-5: net index out of range
"""
color = getNodeFillColor(neti, nodei)
if color is None:
return None
return float(color.a) / 255
[docs]def getNodeBorderColor(neti: int, nodei: int):
"""
getNodeBorderColor rgba tulple format, rgb range int[0,255] alpha range float[0,1]
errCode: -7: node index out of range
-5: net index out of range
"""
node = _getConcreteNode(neti, nodei)
for prim, _ in node.shape.items:
if 'border_color' in prim.__dataclass_fields__:
ret = getattr(prim, 'border_color')
assert isinstance(ret, Color)
return ret
return None
[docs]def getNodeBorderColorRGB(neti: int, nodei: int):
"""
getNodeBorderColorRGB getNodeBorderColor rgb int format
errCode: -7: node index out of range
-5: net index out of range
"""
color = getNodeBorderColor(neti, nodei)
if color is None:
return None
return colorToRGB(color)
[docs]def getNodeBorderColorAlpha(neti: int, nodei: int):
"""
getNodeBorderColorAlpha getNodeBorderColor alpha value(float)
errCode: -7: node index out of range
-5: net index out of range
"""
color = getNodeBorderColor(neti, nodei)
if color is None:
return None
return float(color.a) / 255
[docs]def getNodeBorderWidth(neti: int, nodei: int):
"""
getNodeBorderWidth
errCode: -7: node index out of range
-5: net index out of range
"""
node = _getConcreteNode(neti, nodei)
for prim, _ in node.shape.items:
if 'border_width' in prim.__dataclass_fields__:
return getattr(prim, 'border_width')
return None
[docs]def setNodeID(neti: int, nodei: int, newID: str):
"""
setNodeID set the id of a node
errCode -3: id repeat
-5: net index out of range
-7: node index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
net = networkDict[neti]
if nodei not in net.nodes.keys():
errCode = -7
else:
if any((n.id == newID for n in net.nodes.values() if isinstance(n, TNode))):
errCode = -3
else:
_pushUndoStack()
_getConcreteNode(neti, nodei).id = newID
return
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def setNodeCoordinate(neti: int, nodei: int, x: float, y: float, allowNegativeCoordinates: bool = False):
"""
setNodeCoordinate setNodeCoordinate
errCode: -7: node index out of range
-5: net index out of range
-12: Variable out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if allowNegativeCoordinates:
lowerLimit = -1E12
else:
lowerLimit = 0
if neti not in networkDict:
errCode = -5
else:
if x < lowerLimit or y < lowerLimit:
_raiseError(-12)
n = _getNodeOrAlias(neti, nodei)
# only move if node is locked
if not n.nodeLocked:
_pushUndoStack()
n.position = Vec2(x, y)
return
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def setNodeSize(neti: int, nodei: int, w: float, h: float):
"""
setNodeSize setNodeSize
errCode: -7: node index out of range
-5: net index out of range
-12: Variable out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
n = networkDict[neti]
if nodei not in n.nodes:
errCode = -7
elif w <= 0 or h <= 0:
errCode = -12
else:
_pushUndoStack()
n.nodes[nodei].rectSize = Vec2(w, h)
return
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def setNodeFloatingStatus (neti: int, nodei: int, floatingStatus : bool):
"""
setNodeFloatingStatus setNodeFloatingStatus
errCode: -7: node index out of range
-5: net index out of range
-12: Variable out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
n = networkDict[neti]
if nodei not in n.nodes:
errCode = -7
else:
_pushUndoStack()
_getConcreteNode(neti, nodei).floating = floatingStatus
return
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def setNodeLockedStatus (neti: int, nodei: int, lockedNode: bool):
"""
setNodeLockedStatus setNodeLockedStatus
errCode: -7: node index out of range
-5: net index out of range
-12: Variable out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
n = networkDict[neti]
if nodei not in n.nodes:
errCode = -7
else:
_pushUndoStack()
_getNodeOrAlias(neti, nodei).nodeLocked = lockedNode
return
[docs]def setNodeFillColorRGB(neti: int, nodei: int, r: int, g: int, b: int):
"""
setNodeFillColorRGB setNodeFillColorRGB
errCode: -7: node index out of range
-5: net index out of range
-12: Variable out of range
"""
if r < 0 or r > 255 or g < 0 or g > 255 or b < 0 or b > 255:
_raiseError(-12)
node = _getConcreteNode(neti, nodei)
for prim, _ in node.shape.items:
if 'fill_color' in prim.__dataclass_fields__:
old_color = getattr(prim, 'fill_color')
assert isinstance(old_color, Color)
setattr(prim, 'fill_color', old_color.swapped(r, g, b))
[docs]def setNodeFillColorAlpha(neti: int, nodei: int, a: float):
"""
setNodeFillColorAlpha setNodeFillColorAlpha
errCode: -7: node index out of range
-5: net index out of range
-12: Variable out of range
"""
if a < 0 or a > 1:
_raiseError(-12)
node = _getConcreteNode(neti, nodei)
for prim, _ in node.shape.items:
if 'fill_color' in prim.__dataclass_fields__:
a_int = int(a * 255)
old_color = getattr(prim, 'fill_color')
assert isinstance(old_color, Color)
setattr(prim, 'fill_color', old_color.swapped(a=a_int))
[docs]def setNodeBorderColorRGB(neti: int, nodei: int, r: int, g: int, b: int):
"""
setNodeBorderColorRGB setNodeBorderColorRGB
errCode: -7: node index out of range
-5: net index out of range
-12: Variable out of range
"""
if r < 0 or r > 255 or g < 0 or g > 255 or b < 0 or b > 255:
_raiseError(-12)
node = _getConcreteNode(neti, nodei)
for prim, _ in node.shape.items:
if 'border_color' in prim.__dataclass_fields__:
old_color = getattr(prim, 'border_color')
assert isinstance(old_color, Color)
setattr(prim, 'border_color', old_color.swapped(r, g, b))
[docs]def setNodeBorderColorAlpha(neti: int, nodei: int, a: float):
"""
setNodeBorderColorAlpha setNodeBorderColorAlpha, alpha is a float between 0 and 1
errCode: -7: node index out of range
-5: net index out of range
-12: Variable out of range
"""
if a < 0 or a > 1:
_raiseError(-12)
node = _getConcreteNode(neti, nodei)
for prim, _ in node.shape.items:
if 'border_color' in prim.__dataclass_fields__:
a_int = int(a * 255)
old_color = getattr(prim, 'border_color')
assert isinstance(old_color, Color)
setattr(prim, 'border_color', old_color.swapped(a=a_int))
[docs]def setNodeBorderWidth(neti: int, nodei: int, width: float):
"""
setNodeBorderWidth setNodeBorderWidth
errCode: -7: node index out of range
-5: net index out of range
-12: Variable out of range
"""
if width <= 0:
_raiseError(-12)
node = _getConcreteNode(neti, nodei)
for prim, _ in node.shape.items:
if 'border_width' in prim.__dataclass_fields__:
setattr(prim, 'border_width', width)
[docs]def createReaction(neti: int, reaID: str, sources: List[int], targets: List[int]):
"""
createReaction create an empty reacton
errCode: -3: id repeat
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if len(sources) == 0 or len(targets) == 0:
raise ValueError("Reaction '{}' has no reactants or it has no products".format(reaID))
net = _getNetwork(neti)
# duplicate ID?
if any((r.id == reaID for r in net.reactions.values())):
errCode = -3
else:
# ensure nodes exist
if any(nodei not in net.nodes.keys() for nodei in sources):
_raiseError(-7)
if any(nodei not in net.nodes.keys() for nodei in targets):
_raiseError(-7)
if set(sources) == set(targets):
raise ValueError('Reaction source node set and target node set cannot be identical.')
_pushUndoStack()
newReact = TReaction(reaID)
# Add src/target nodes
for srcNodeIdx in sources:
newReact.reactants[srcNodeIdx] = TSpeciesNode(1) # default stoich to 1
for destNodeIdx in targets:
newReact.products[destNodeIdx] = TSpeciesNode(1) # default stoich to 1
net.addReaction(newReact)
return
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def getReactionIndex(neti: int, reaID: str):
"""
getReactionIndex get reaction index by id
return: -2: id can't find, >=0: ok
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
errCode = -2
for i, r in networkDict[neti].reactions.items():
if r.id == reaID:
errCode = 0
return i
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def deleteReaction(neti: int, reai: int):
"""
deleteReaction delete the reaction with index
errCode: -6: reaction index out of range
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
if reai not in networkDict[neti].reactions:
errCode = -6
else:
_pushUndoStack()
net = _getNetwork(neti)
reaction = _getReaction(neti, reai)
for src in reaction.reactants:
net.srcMap[src].remove(reai)
for dest in reaction.products:
net.destMap[dest].remove(reai)
del networkDict[neti].reactions[reai]
return
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def clearReactions(neti: int):
"""
clearReactions clear all reactions in this network
errCode: -5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
if errCode < 0:
raise ExceptionDict[errCode](errorDict[errCode])
else:
_pushUndoStack()
net = _getNetwork(neti)
net.reactions.clear()
net.srcMap.clear()
net.destMap.clear()
[docs]def getNumberOfReactions(neti: int):
"""
getNumberOfReactions get the number of reactions in the current Reactionset
return: >=0: ok, -5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
if neti not in networkDict:
errCode = -5
if errCode < 0:
raise ExceptionDict[errCode](errorDict[errCode])
else:
r = networkDict[neti].reactions
return len(r)
[docs]def getReactionID(neti: int, reai: int):
"""
getReactionID get the id of Reaction
errCode: -6: reaction index out of range
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
else:
return r[reai].id
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def getListOfReactionIDs(neti: int) -> List[str]:
if neti not in networkDict:
errCode = -5
raise ExceptionDict[errCode](errorDict[errCode])
return [r.id for r in networkDict[neti].reactions.values()]
[docs]def getReactionRateLaw(neti: int, reai: int):
"""
getReactionRateLaw get the ratelaw of Reaction
errCode: -6: reaction index out of range
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
else:
return r[reai].rateLaw
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def getReactionCenterPos(neti: int, reai: int):
"""
getReactionCenterPos get the center position of the Reaction
"""
r = _getReaction(neti, reai)
return r.centerPos
[docs]def getReactionFillColor(neti: int, reai: int):
"""
getReactionFillColor rgba tulple format, rgb range int[0,255] alpha range float[0,1]
errCode: -6: reaction index out of range
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
else:
return (r[reai].fillColor.r, r[reai].fillColor.g, r[reai].fillColor.b, float(r[reai].fillColor.a)/255)
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def getReactionFillColorRGB(neti: int, reai: int):
"""
getReactionFillColorRGB getReactionFillColorRGB
errCode: -6: reaction index out of range
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
else:
color1 = r[reai].fillColor.r
color1 = (color1 << 8) | r[reai].fillColor.g
color1 = (color1 << 8) | r[reai].fillColor.b
return color1
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def getReactionFillColorAlpha(neti: int, reai: int):
"""
getReactionFillColorAlpha getReactionFillColorAlpha
errCode: -6: reaction index out of range
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
else:
alpha1 = float(r[reai].fillColor.a) / 255
return alpha1
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def getReactionLineThickness(neti: int, reai: int):
"""
getReactionLineThickness getReactionLineThickness
errCode: -6: reaction index out of range
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
else:
return r[reai].thickness
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def getReactionCenterHandlePosition(neti: int, reai: int):
"""
getReactionCenterHandlePosition getReactionCenterHandlePosition
errCode: -6: reaction index out of range
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
else:
return (round(r[reai].centerHandlePos.x, 2), round(r[reai].centerHandlePos.y, 2))
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def getReactionSrcNodeStoich(neti: int, reai: int, srcNodeIdx: int):
"""
getReactionSrcNodeStoich get the SrcNode stoichiometry of Reaction
errCode: -6: reaction index out of range,
-5: net index out of range, -7: node index not found
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
elif srcNodeIdx not in networkDict[neti].nodes:
errCode = -7
elif srcNodeIdx not in r[reai].reactants:
raise ValueError('The given node index "{}" is not a reactant node of "{}"'.format(
srcNodeIdx, reai))
else:
return r[reai].reactants[srcNodeIdx].stoich
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def getReactionDestNodeStoich(neti: int, reai: int, destNodeIdx: int):
"""
getReactionDestNodeStoich get the DestNode stoichiometry of Reaction
return: positive float : ok, -6: reaction index out of range, -7: node index out of range
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
elif destNodeIdx not in networkDict[neti].nodes:
errCode = -7
elif destNodeIdx not in r[reai].products:
raise ValueError('The given node index "{}" is not a product node of "{}"'.format(
destNodeIdx, reai))
else:
s = r[reai].products[destNodeIdx]
return s.stoich
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def getReactionSrcNodeHandlePosition(neti: int, reai: int, srcNodeIdx: int):
"""
getReactionSrcNodeHandlePosition get the SrcNode HandlePosition of Reaction
errCode: -6: reaction index out of range,
-5: net index out of range, -7: node index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
elif srcNodeIdx not in networkDict[neti].nodes:
errCode = -7
elif srcNodeIdx not in r[reai].reactants:
raise ValueError('The given node index "{}" is not a reactant node of "{}"'.format(
srcNodeIdx, reai))
else:
return (round(r[reai].reactants[srcNodeIdx].handlePos.x, 2),
round(r[reai].reactants[srcNodeIdx].handlePos.y, 2))
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def getReactionDestNodeHandlePosition(neti: int, reai: int, destNodeIdx: int):
"""
getReactionDestNodeStoich get the DestNode HandlePosition of Reaction
return: positive float : ok, -6: reaction index out of range, -7: node index out of range
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
elif destNodeIdx not in networkDict[neti].nodes:
errCode = -7
elif destNodeIdx not in r[reai].products:
raise ValueError('The given node index "{}" is not a product node of "{}"'.format(
destNodeIdx, reai))
else:
return (round(r[reai].products[destNodeIdx].handlePos.x, 2),
round(r[reai].products[destNodeIdx].handlePos.y, 2))
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def getNumberOfSrcNodes(neti: int, reai: int):
"""
getNumberOfSrcNodes get the SrcNode length of Reaction
return: non-negative int: ok, -6: reaction index out of range
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
else:
return len(r[reai].reactants)
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def getNumberOfDestNodes(neti: int, reai: int):
"""
getNumberOfDestNodes get the DestNode length of Reaction
return: non-negative int: ok, -6: reaction index out of range
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
else:
return len(r[reai].products)
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def getListOfReactionSrcNodes(neti: int, reai: int) -> List[int]:
"""
getListOfReactionSrcNodes getListOfReactionSrcNodes in alphabetical order
return: non-empty slice : ok, -6: reaction index out of range
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
reactions = networkDict[neti].reactions
if reai not in reactions:
errCode = -6
else:
list1 = []
for k in reactions[reai].reactants:
list1.append(k)
list1.sort()
return list1
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def getListOfReactionDestNodes(neti: int, reai: int) -> List[int]:
"""
getListOfReactionDestNodes getListOfReactionDestNodes in alphabetical order
return: non-empty slice : ok, -6: reaction index out of range
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
else:
list1 = []
for k in r[reai].products:
list1.append(k)
list1.sort()
return list1
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def getListOfReactionSrcStoich(neti: int, reai: int) -> List[float]:
n = getListOfReactionSrcNodes(neti, reai)
srcStoichList = []
for srcNodeID in n:
srcStoichList.append(getReactionSrcNodeStoich(neti, reai, srcNodeID))
return srcStoichList
[docs]def getListOfReactionDestStoich(neti: int, reai: int) -> List[float]:
n = getListOfReactionDestNodes(neti, reai)
destStoichList = []
for destNodeID in n:
destStoichList.append(getReactionDestNodeStoich(neti, reai, destNodeID))
return destStoichList
[docs]def printReactionInfo(neti: int, reai: int):
print("id:", getReactionID(neti, reai))
print("rateLaw:", getReactionRateLaw(neti, reai))
print("SrcNodes:", getListOfReactionSrcNodes(neti, reai))
print("DestNodes:", getListOfReactionDestNodes(neti, reai))
print("SrcNodeStoichs:", getListOfReactionSrcStoich(neti, reai))
print("DestNodeStoichs:", getListOfReactionDestStoich(neti, reai))
# def deleteSrcNode(neti: int, reai: int, srcNodeIdx: int):
# """
# deleteSrcNode delete src nodes by id(ID).
# errCode: -6: reaction index out of range,
# -5: net index out of range
# -2: id not found
# """
# global stackFlag, errCode, networkDict, undoStack, redoStack
# errCode = 0
# if neti not in networkDict:
# errCode = -5
# else:
# r = networkDict[neti].reactions
# if reai not in networkDict[neti].reactions:
# errCode = -6
# else:
# rea = r[reai]
# if srcNodeIdx not in rea.reactants:
# errCode = -2
# else:
# _pushUndoStack()
# del rea.reactants[srcNodeIdx]
# networkDict[neti].reactions[reai] = rea
# return
# raise ExceptionDict[errCode](errorDict[errCode])
# def deleteDestNode(neti: int, reai: int, destNodeIdx: int):
# """
# deleteDestNode delete all dest nodes by id
# errCode: -6: reaction index out of range,
# -5: net index out of range
# -2: id not found
# """
# global stackFlag, errCode, networkDict, undoStack, redoStack
# errCode = 0
# if neti not in networkDict:
# errCode = -5
# else:
# r = networkDict[neti].reactions
# if reai not in networkDict[neti].reactions:
# errCode = -6
# else:
# rea = r[reai]
# if destNodeIdx not in rea.products:
# errCode = -2
# else:
# _pushUndoStack()
# del rea.products[destNodeIdx]
# return
# raise ExceptionDict[errCode](errorDict[errCode])
[docs]def setReactionID(neti: int, reai: int, newID: str):
"""
setReactionID edit id of reaction
errCode: 0:ok, -6: reaction index out of range
-5: net index out of range
-3: id repeat
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
reactions = networkDict[neti].reactions
if reai not in reactions:
errCode = -6
else:
if any((r.id == newID for r in reactions.values())):
errCode = -3
else:
_pushUndoStack()
networkDict[neti].reactions[reai].id = newID
return
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def setRateLaw(neti: int, reai: int, rateLaw: str):
"""
setRateLaw edit rate law of reaction
errCode: -6: reaction index out of range
-5: net index out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
if reai not in networkDict[neti].reactions:
errCode = -6
else:
_pushUndoStack()
networkDict[neti].reactions[reai].rateLaw = rateLaw
return
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def setReactionCenterPos(neti: int, reai: int, centerPos: Optional[Vec2]):
"""
setReactionCenterPos set the center position of the Reaction
"""
r = _getReaction(neti, reai)
r.centerPos = centerPos
[docs]def setReactionSrcNodeStoich(neti: int, reai: int, srcNodeIdx: int, newStoich: float):
"""
setReactionSrcNodeStoich edit Stoich by Reaction srcNodeID
errCode: -6: reaction index not found,
-5: net index not found
-7: node index not found,
-8: wrong stoich
raises ValueError if given node index not a dest node
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
elif srcNodeIdx not in networkDict[neti].nodes:
errCode = -7
elif srcNodeIdx not in r[reai].reactants:
raise ValueError('The given node index "{}" is not a reactant node of "{}"'.format(
srcNodeIdx, reai))
elif newStoich <= 0.0:
errCode = -8
else:
_pushUndoStack()
networkDict[neti].reactions[reai].reactants[srcNodeIdx].stoich = newStoich
return
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def setReactionDestNodeStoich(neti: int, reai: int, destNodeIdx: int, newStoich: float):
"""
setReactionDestNodeStoich edit Stoich by Reaction destNodeID
errCode: -6: reaction index out of range,
-5: net index out of range,
-7: node index not found,
-8: wrong stoich
raises ValueError if given node index not a dest node
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
elif destNodeIdx not in networkDict[neti].nodes:
errCode = -7
elif destNodeIdx not in r[reai].products:
raise ValueError('The given node index "{}" is not a product node of "{}"'.format(
destNodeIdx, reai))
elif newStoich <= 0.0:
errCode = -8
else:
_pushUndoStack()
networkDict[neti].reactions[reai].products[destNodeIdx].stoich = newStoich
return
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def setReactionSrcNodeHandlePosition(neti: int, reai: int, srcNodeIdx: int, handlePosX: float, handlePosY: float):
"""
setReactionSrcNodeHandlePosition edit HandlePosition by Reaction srcNodeID
errCode: -6: reaction index out of range,
-5: net index out of range, -7: node index not found
-12: Variable out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
elif srcNodeIdx not in networkDict[neti].nodes:
_raiseError(-7)
elif srcNodeIdx not in r[reai].reactants:
raise ValueError('The given node index "{}" is not a reactant node of "{}"'.format(
srcNodeIdx, reai))
else:
_pushUndoStack()
networkDict[neti].reactions[reai].reactants[srcNodeIdx].handlePos = Vec2(
handlePosX, handlePosY)
return
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def setReactionDestNodeHandlePosition(neti: int, reai: int, destNodeIdx: int, handlePosX: float, handlePosY: float):
"""
setReactionDestNodeHandlePosition edit HandlePosition by Reaction destNodeID
errCode: -6: reaction index out of range,
-5: net index out of range, -2: id not found
-12: Variable out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
elif destNodeIdx not in networkDict[neti].nodes:
_raiseError(-7)
elif destNodeIdx not in r[reai].products:
raise ValueError('The given node index "{}" is not a product node of "{}"'.format(
destNodeIdx, reai))
else:
_pushUndoStack()
networkDict[neti].reactions[reai].products[destNodeIdx].handlePos = Vec2(
handlePosX, handlePosY)
return
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def setReactionFillColorRGB(neti: int, reai: int, R: int, G: int, B: int):
"""
setReactionFillColorRGB setReactionFillColorRGB
errCode: -6: reaction index out of range
-5: net index out of range
-12: Variable out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
elif R < 0 or R > 255 or G < 0 or G > 255 or B < 0 or B > 255:
errCode = -12
else:
_pushUndoStack()
r[reai].fillColor = r[reai].fillColor.swapped(R, G, B)
return
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def setReactionFillColorAlpha(neti: int, reai: int, a: float):
"""
setReactionFillColorAlpha setReactionFillColorAlpha
errCode: -6: reaction index out of range
-5: net index out of range
-12: Variable out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
elif a < 0 or a > 1:
errCode = -12
else:
_pushUndoStack()
A1 = int(a * 255)
r[reai].fillColor = r[reai].fillColor.swapped(a=A1)
return
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def setReactionLineThickness(neti: int, reai: int, thickness: float):
"""
setReactionLineThickness setReactionLineThickness
errCode: -6: reaction index out of range
-5: net index out of range
-12: Variable out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
if reai not in networkDict[neti].reactions:
errCode = -6
elif thickness <= 0:
errCode = -12
else:
_pushUndoStack()
networkDict[neti].reactions[reai].thickness = thickness
return
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def bezier_curves(neti: int, reai: int):
n = _getNetwork(neti)
return n.reactions[reai].bezierCurves
[docs]def setReactionBezierCurves(neti: int, reai: int, bezierCurves: bool):
"""
setReactionBezierCurves setReactionBezierCurves
errCode: -6: reaction index out of range
-5: net index out of range
-12: Variable out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
r = networkDict[neti].reactions
if reai not in networkDict[neti].reactions:
errCode = -6
else:
_pushUndoStack()
r[reai].bezierCurves = bezierCurves
return
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def setReactionModifiers(neti: int, reai: int, modifiers: Set[int]):
r = _getReaction(neti, reai)
r.modifiers = copy.copy(set(modifiers))
[docs]def getReactionModifiers(neti: int, reai: int) -> Set[int]:
r = _getReaction(neti, reai)
return copy.copy(r.modifiers)
[docs]def setModifierTipStyle(neti: int, reai: int, tipStyle: ModifierTipStyle):
r = _getReaction(neti, reai)
r.tipStyle = tipStyle
[docs]def getModifierTipStyle(neti: int, reai: int) -> ModifierTipStyle:
r = _getReaction(neti, reai)
return r.tipStyle
[docs]def setReactionCenterHandlePosition(neti: int, reai: int, centerHandlePosX: float, centerHandlePosY: float):
"""
setReactionCenterHandlePosition setReactionCenterHandlePosition
errCode: -6: reaction index out of range
-5: net index out of range
-12: Variable out of range
"""
global stackFlag, errCode, networkDict, undoStack, redoStack
errCode = 0
if neti not in networkDict:
errCode = -5
else:
if reai not in networkDict[neti].reactions:
errCode = -6
else:
_pushUndoStack()
networkDict[neti].reactions[reai].centerHandlePos = Vec2(
centerHandlePosX, centerHandlePosY)
return
raise ExceptionDict[errCode](errorDict[errCode])
[docs]def addCompartment(neti: int, compID: str, x: float, y: float, w: float, h: float) -> int:
"""
Create a compartment and add to canvas. Return the index of the compartment added.
Args:
neti: network index.
compID: ID of the compartment.
x: x coordinate of top-left corner
y: y coordinate of top-left corner
w: width
h: height
"""
if x < 0 or y < 0 or w < 0 or h < 0:
_raiseError(-12)
net = _getNetwork(neti)
comp = TCompartment(compID, Vec2(x, y), Vec2(w, h))
if any((compID == c.id for c in net.compartments.values())):
_raiseError(-3)
_pushUndoStack()
return net.addCompartment(comp)
[docs]def deleteCompartment(neti: int, compi: int):
"""Delete the compartment of the given index in the given network."""
net = _getNetwork(neti)
if compi not in net.compartments:
_raiseError(-13)
_pushUndoStack()
# Put all nodes in compartment in base compartment (-1)
for nodei in net.compartments[compi].node_indices:
assert net.nodes[nodei].compi == compi
# move to base compartment
net.nodes[nodei].compi = -1
net.baseNodes.add(nodei)
del net.compartments[compi]
[docs]def getListOfCompartments(neti: int) -> List[int]:
return list(_getNetwork(neti).compartments.keys())
[docs]def getNodesInCompartment(neti: int, compi: int) -> List[int]:
"""Return the list of node indices in the given compartment."""
if compi == -1:
return list(_getNetwork(neti).baseNodes)
return list(_getCompartment(neti, compi).node_indices) # Make copy in the process
[docs]def getCompartmentOfNode(neti: int, nodei: int) -> int:
"""Return the compartment index that the given node is in, or -1 if it is not in any."""
return _getNodeOrAlias(neti, nodei).compi
[docs]def setCompartmentOfNode(neti: int, nodei: int, compi: int):
"""Set the compartment of the node, or remove it from any compartment if -1 is given."""
net = _getNetwork(neti)
node = _getNodeOrAlias(neti, nodei)
_pushUndoStack()
if node.compi != -1:
net.compartments[node.compi].node_indices.remove(nodei)
else:
net.baseNodes.remove(nodei)
if compi != -1:
newComp = _getCompartment(neti, compi)
newComp.node_indices.add(nodei)
else:
net.baseNodes.add(nodei)
node.compi = compi
[docs]def setCompartmentPosition(neti: int, compi: int, x: float, y: float):
if x < 0 or y < 0:
_raiseError(-12)
_pushUndoStack()
comp = _getCompartment(neti, compi)
comp.position = Vec2(x, y)
[docs]def getCompartmentPosition(neti: int, compi: int) -> Tuple[float, float]:
comp = _getCompartment(neti, compi)
return (comp.position.x, comp.position.y)
[docs]def setCompartmentSize(neti: int, compi: int, w: float, h: float):
if w < 0 or h < 0:
_raiseError(-12)
_pushUndoStack()
comp = _getCompartment(neti, compi)
comp.rectSize = Vec2(w, h)
[docs]def getCompartmentSize(neti: int, compi: int) -> Tuple[float, float]:
comp = _getCompartment(neti, compi)
return (comp.rectSize.x, comp.rectSize.y)
[docs]def setCompartmentVolume(neti: int, compi: int, volume: float):
_pushUndoStack()
_getCompartment(neti, compi).volume = volume
[docs]def getCompartmentVolume(neti: int, compi: int) -> float:
return _getCompartment(neti, compi).volume
[docs]def setCompartmentID(neti: int, compi: int, id: str):
_pushUndoStack()
_getCompartment(neti, compi).id = id
[docs]def getCompartmentID(neti: int, compi: int) -> str:
return _getCompartment(neti, compi).id
# TODO note that this returns a Color instead of tuples of numbers. Should change the node &
# reaction color functions to do the same.
[docs]def setCompartmentFillColor(neti: int, compi: int, color: Color):
_pushUndoStack()
_getCompartment(neti, compi).fillColor = color
[docs]def getCompartmentFillColor(neti: int, compi: int) -> Color:
return _getCompartment(neti, compi).fillColor
[docs]def setCompartmentOutlineColor(neti: int, compi: int, color: Color):
_pushUndoStack()
_getCompartment(neti, compi).outlineColor = color
[docs]def getCompartmentOutlineColor(neti: int, compi: int) -> Color:
return _getCompartment(neti, compi).outlineColor
[docs]def setCompartmentOutlineThickness(neti: int, compi: int, thickness: float):
_pushUndoStack()
_getCompartment(neti, compi).outlineThickness = thickness
[docs]def getCompartmentOutlineThickness(neti: int, compi: int) -> float:
return _getCompartment(neti, compi).outlineThickness
[docs]def createUniUni(neti: int, reaID: str, rateLaw: str, srci: int, desti: int, srcStoich: float, destStoich: float):
startGroup()
createReaction(neti, reaID, [srci], [desti])
reai = getReactionIndex(neti, reaID)
setReactionSrcNodeStoich(neti, reai, srci, srcStoich)
setReactionDestNodeStoich(neti, reai, desti, destStoich)
setRateLaw(neti, reai, rateLaw)
endGroup()
# TODO allow modification of this list later
# TODO make note that neti is useless here. Probably just remove the argument later
# Also need to change getCompositeShapeAt
[docs]def getListOfCompositeShapes(neti: int):
return [f.produce() for f in shapeFactories]
[docs]def getCompositeShapeAt(neti: int, shapei: int):
return shapeFactories[shapei].produce()
[docs]def getNodeShape(neti: int, nodei: int) -> CompositeShape:
return copy.copy(_getConcreteNode(neti, nodei).shape)
[docs]def getNodeShapeIndex(neti: int, nodei: int) -> int:
return _getConcreteNode(neti, nodei).shapei
[docs]def setNodeShapeIndex(neti: int, nodei: int, shapei: int, preserve_common_fields=True):
'''If preserve_common_fields is True, then preserve common field values such as fill_color,
if applicable. (Not implemented)
'''
net = _getNetwork(neti)
node = _getConcreteNode(neti, nodei)
node.shapei = shapei
node.shape = shapeFactories[shapei].produce()
[docs]def setNodePrimitiveProperty(neti: int, nodei: int, prim_index: int, prop_name: str, prop_value: Any):
'''Set an individual property of a node's primitive.
Args:
neti: The network index
nodei: The node index
prim_index: The index of the primitive, in the node's shape. If -1, then update the text
primitive instead.
prop_name: The name of the primitive's property.
prop_value: The value of the primitives's property
'''
node = _getConcreteNode(neti, nodei)
if prim_index >= len(node.shape.items) or prim_index < -1:
raise ValueError('Primitive index out of range for the shape of node {} in network {}'.format(nodei, neti))
if prim_index == -1:
primitive, _transform = node.shape.text_item
else:
primitive, _transform = node.shape.items[prim_index]
if prop_name not in primitive.__dataclass_fields__:
raise ValueError('`{}` is not a property of primitive `{}`'.format(
prop_name, primitive.__class__.__name__))
field = primitive.__dataclass_fields__[prop_name]
# ensure that the assigned type is correct
if not isinstance(prop_value, field.type):
raise ValueError(f'Could not set primitive property `{prop_name}` of node {nodei} at '
f'primitive index {prim_index}. Expected object of type `{field.type.__name__}`; got '
f'`{prop_value}`(`{type(prop_value).__name__}`) instead. Note: the primitive '
f'is of type `{type(primitive).__name__}`.')
# This is not very safe, but this is very simple to implement, so it shall be like this for now
setattr(primitive, prop_name, prop_value)
[docs]def CreateUniBi(neti: int, reaID: str, rateLaw: str, srci: int, dest1i: int, dest2i: int, srcStoich: float, dest1Stoich: float, dest2Stoich: float):
startGroup()
createReaction(neti, reaID, [srci], [dest1i, dest2i])
reai = getReactionIndex(neti, reaID)
setReactionSrcNodeStoich(neti, reai, srci, srcStoich)
setReactionDestNodeStoich(neti, reai, dest1i, dest1Stoich)
setReactionDestNodeStoich(neti, reai, dest2i, dest2Stoich)
setRateLaw(neti, reai, rateLaw)
endGroup()
[docs]def CreateBiUni(neti: int, reaID: str, rateLaw: str, src1i: int, src2i: int, desti: int, src1Stoich: float, src2Stoich: float, destStoich: float):
startGroup()
createReaction(neti, reaID, [src1i, src2i], [desti])
reai = getReactionIndex(neti, reaID)
setReactionSrcNodeStoich(neti, reai, src1i, src1Stoich)
setReactionSrcNodeStoich(neti, reai, src2i, src2Stoich)
setReactionDestNodeStoich(neti, reai, desti, destStoich)
setRateLaw(neti, reai, rateLaw)
endGroup()
[docs]def CreateBiBi(neti: int, reaID: str, rateLaw: str, src1i: int, src2i: int, dest1i: int, dest2i: int, src1Stoich: float, src2Stoich: float, dest1Stoich: float, dest2Stoich: float):
startGroup()
createReaction(neti, reaID, [src1i, src2i], [dest1i, dest2i])
reai = getReactionIndex(neti, reaID)
setReactionSrcNodeStoich(neti, reai, src1i, src1Stoich)
setReactionSrcNodeStoich(neti, reai, src2i, src2Stoich)
setReactionDestNodeStoich(neti, reai, dest1i, dest1Stoich)
setReactionDestNodeStoich(neti, reai, dest2i, dest2Stoich)
setRateLaw(neti, reai, rateLaw)
endGroup()
[docs]def reset():
global stackFlag, errCode, networkDict, undoStack, redoStack, lastNetIndex
stackFlag = True
errCode = 0
networkDict = TNetworkDict()
undoStack = TStack()
redoStack = TStack()
lastNetIndex = 0
'''Code for serialization/deserialization.'''
[docs]class EnumField(fields.Field):
def __init__(self, enum_class):
super().__init__()
choices = [entry.value for entry in enum_class]
for choice in choices:
if not isinstance(choice, str):
raise ValueError('The enum class given to EnumField must have string values!')
self.enum_class = enum_class
self.str_field = fields.Str(validate=validate.OneOf(choices))
def _serialize(self, entry, attr, obj, **kwargs):
return entry.value
def _deserialize(self, value, attr, data, **kwargs):
self.str_field.validate(value)
for entry in self.enum_class:
if entry.value == value:
return entry
assert False, "Not supposed to reach here"
[docs]class ChoiceField(fields.Field):
def __init__(self, choice_list):
super().__init__()
for choice in choice_list:
if not isinstance(choice, ChoiceItem):
raise ValueError("not choice item")
self.choice_list = choice_list
def _serialize(self, entry, attr, obj, **kwargs):
for choice in self.choice_list:
if entry == choice.value:
return choice.text
def _deserialize(self, value, attr, data, **kwargs):
for choice in self.choice_list:
if value == choice.text:
return choice.value
assert False, "No choice found"
[docs]class FontSchema(Schema):
# TODO use this after implemented
pointSize = Pixel()
family = str # TODO change to enum
style: str
weight: str
name: str
color: Color
[docs]class PrimitiveSchema(Schema):
name = fields.Str()
fill_color = ColorField()
border_color = ColorField()
border_width = Dim()
[docs]class RectangleSchema(PrimitiveSchema):
corner_radius = Dim()
[docs] @post_load
def post_load(self, data: Any, **kwargs) -> RectanglePrim:
del data['name']
return RectanglePrim(**data)
[docs]class CircleSchema(PrimitiveSchema):
[docs] @post_load
def post_load(self, data: Any, **kwargs) -> CirclePrim:
del data['name']
return CirclePrim(**data)
[docs]class PolygonSchema(PrimitiveSchema):
#name = fields.Str()
fill_color = ColorField()
border_color = ColorField()
border_width = Dim()
corner_radius = Dim()
radius = Dim()
[docs]class LineSchema(PrimitiveSchema):
points = fields.Tuple(([Dim2()]*2))
[docs] @post_load
def post_load(self, data: Any, **kwargs) -> LinePrim:
del data['name']
return LinePrim(**data)
[docs]class TriangleSchema(PolygonSchema):
points = fields.Tuple(((Dim2(),)*4))
[docs] @post_load
def post_load(self, data: Any, **kwargs) -> TrianglePrim:
del data['name']
return TrianglePrim(**data)
[docs]class HexagonSchema(PolygonSchema):
points = fields.Tuple((Dim2(),)*7)
[docs] @post_load
def post_load(self, data: Any, **kwargs) -> HexagonPrim:
del data['name']
return HexagonPrim(**data)
[docs]def primitive_dump(base_obj, parent_obj):
ret = {
RectanglePrim.__name__: RectangleSchema,
CirclePrim.__name__: CircleSchema,
LinePrim.__name__: LineSchema,
TrianglePrim.__name__: TriangleSchema,
HexagonPrim.__name__: HexagonSchema
}[base_obj.__class__.__name__]()
return ret
primitive_schemas = {'rectangle':RectangleSchema(),
'circle': CircleSchema(),
'triangle': TriangleSchema(),
'line': LineSchema(),
'hexagon': HexagonSchema()}
[docs]def primitive_load(base_dict, parent_dict):
return primitive_schemas[base_dict['name']]
primitiveField = PolyField(
serialization_schema_selector=primitive_dump,
deserialization_schema_selector=primitive_load,
required=True,
)
[docs]class TextSchema(Schema):
#name = fields.Str()
bg_color = ColorField()
font_color = ColorField()
font_size = fields.Int()
font_family = ChoiceField(FONT_FAMILY_CHOICES)
font_style = ChoiceField(FONT_STYLE_CHOICES)
font_weight = ChoiceField(FONT_WEIGHT_CHOICES)
alignment = ChoiceField(TEXT_ALIGNMENT_CHOICES)
[docs] @post_load
def post_load(self, data: Any, **kwargs) -> TextPrim:
return TextPrim(**data)
[docs]class CompositeShapeSchema(Schema):
name = fields.Str()
text_item = fields.Tuple((fields.Nested(TextSchema), fields.Nested(TransformSchema)))
items = fields.List(fields.Tuple((primitiveField, fields.Nested(TransformSchema))))
[docs] @post_load
def post_load(self, data: Any, **kwargs) -> CompositeShape:
return CompositeShape(**data)
[docs]class AbstractNodeSchema(Schema):
index = fields.Int()
id = fields.Str()
position = Dim2()
rectSize = Dim2()
nodeLocked = fields.Bool()
[docs] @post_dump
def post_dump(self, data: Any, **kwargs):
del data['index']
return data
[docs]class NodeSchema(AbstractNodeSchema):
floating = fields.Bool()
compi = fields.Int(missing=-1)
shape = fields.Nested(CompositeShapeSchema)
[docs] @post_load
def post_load(self, data: Any, **kwargs) -> TNode:
shape_name = data['shape'].name
# get shape index manually
# If this fails, then somebody modified the shape name
shapei = [s.name for s in shapeFactories].index(shape_name)
data['shapei'] = shapei
return TNode(**data)
[docs]class AliasSchema(AbstractNodeSchema):
originalIdx = fields.Int()
[docs] @post_load
def post_load(self, data: Any, **kwargs):
return TAliasNode(**data)
[docs]class SpeciesNode(Schema):
"""Represents a species in a reaction."""
stoich = fields.Float()
handlePos = Dim2()
[docs] @post_load
def post_load(self, data: Any, **kwargs) -> TSpeciesNode:
return TSpeciesNode(**data)
[docs]class ReactionSchema(Schema):
id = fields.Str()
centerPos = Dim2(missing=None)
rateLaw = fields.Str()
reactants = fields.Dict(fields.Int(), fields.Nested(SpeciesNode))
products = fields.Dict(fields.Int(), fields.Nested(SpeciesNode))
fillColor = ColorField()
thickness = Dim()
centerHandlePos = Dim2()
bezierCurves = fields.Bool()
modifiers = fields.List(fields.Int())
tipStyle = EnumField(ModifierTipStyle)
[docs] @post_load
def post_load(self, data: Any, **kwargs) -> TReaction:
if 'modifiers' in data:
data['modifiers'] = set(data['modifiers'])
return TReaction(**data)
[docs]class CompartmentSchema(Schema):
id = fields.Str()
position = Dim2()
rectSize = Dim2()
nodes = fields.List(fields.Int())
volume = Dim()
fillColor = ColorField()
outlineColor = ColorField()
outlineThickness = Dim()
[docs] @post_load
def post_load(self, data: Any, **kwargs) -> TCompartment:
return TCompartment(**data)
[docs]def node_or_alias_dump(base_obj, parent_obj):
ret = {
TNode.__name__: NodeSchema,
TAliasNode.__name__: AliasSchema,
}[base_obj.__class__.__name__]()
return ret
[docs]def node_or_alias_load(base_dict, parent_dict):
if 'originalIdx' not in base_dict:
return NodeSchema()
else:
return AliasSchema()
nodeOrAliasField = PolyField(
serialization_schema_selector=node_or_alias_dump,
deserialization_schema_selector=node_or_alias_load,
required=True,
)
[docs]class NetworkSchema(Schema):
id = fields.Str()
nodes = fields.Mapping(fields.Int(), nodeOrAliasField)
reactions = fields.Mapping(fields.Int(), fields.Nested(ReactionSchema))
compartments = fields.Mapping(fields.Int(), fields.Nested(CompartmentSchema))
[docs] @pre_load
def pre_load(self, data: Any, **kwargs):
# load serialization version
# this records the version of the serialization. Whenever the serialization scheme is changed,
# we update the version number, so that if a user is trying to load a network with an
# older serialization version than the current application (or vice versa), we can either fail
# to try to do some conversion.
serial_version = data.get('serialVersion', 'pre-release')
if serial_version != SERIAL_VERSION:
# we have a mismatch
print(("Warning: loaded network has serial version '{}', which does not match that of "
"the application: '{}'").format(serial_version, SERIAL_VERSION))
if 'serialVersion' in data:
del data['serialVersion']
# populate the index field of nodes. This is a redundancy, so we don't expect this field
# to be serialized/deserialized
for nodei, nodedata in data['nodes'].items():
nodedata['index'] = int(nodei)
return data
[docs] @post_load
def post_load(self, data: Any, **kwargs) -> TNetwork:
return TNetwork(**data)
[docs] @post_dump
def post_dump(self, data, **kwargs):
data['serialVersion'] = SERIAL_VERSION
return data
net_schema = NetworkSchema()
[docs]def dumpNetwork(neti: int):
"""Dump the network into an object and return it."""
# TODO don't construct NetworkSchema every time.
net = _getNetwork(neti)
return net_schema.dump(net)
[docs]def loadNetwork(net_object) -> int:
"""Load the network object (laoded directly from JSON) and add it, returning the network index.
Note:
For now this overwrites the network at index 0.
"""
# NOTE marshmallow::load does not guarantee that the input object is not modified. Therefore,
# we need to make a deepcopy
obj_copy = copy.deepcopy(net_object)
net = net_schema.load(obj_copy)
clearNetworks()
_addNetwork(net)
return 0
[docs]def validateState():
assert undoStack is not None
assert redoStack is not None
net_ids = [net.id for net in networkDict.values()]
assert len(net_ids) == len(set(net_ids)), "duplicate network IDs"
assert isinstance(networkDict, dict)
for neti, net in networkDict.items():
assert isinstance(neti, int)
assert isinstance(net, TNetwork)
validateNodes(net.nodes)
# TODO validate reactions, compartments, and cross-validate
[docs]def validateNodes(nodes: Dict[int, TAbstractNode]):
assert isinstance(nodes, dict)
for nodei, node in nodes.items():
assert isinstance(nodei, int)
assert isinstance(node, TNode) or isinstance(node, TAliasNode)
assert isinstance(node, TNode) or isinstance(node, TAliasNode), 'unexpected type: ' + type(node)
cnodes = [n for n in nodes.values() if isinstance(n, TNode)]
aliases = [n for n in nodes.values() if isinstance(n, TAliasNode)]
node_ids = [n.id for n in cnodes]
assert len(node_ids) == len(set(node_ids)), "duplicate node IDs"
# assert alias references are good
for alias in aliases:
assert isinstance(alias.originalIdx, int) and alias.originalIdx >= 0
assert alias.originalIdx in nodes and isinstance(nodes[alias.originalIdx], TNode)
for cnode in cnodes:
assert isinstance(cnode.floating, bool)
for node in nodes.values():
node: TAbstractNode
assert isinstance(node.nodeLocked, bool)
assert isinstance(node.compi, int)
assert isinstance(node.position, Vec2) and node.position.x >= 0 and node.position.y >= 0
assert isinstance(node.rectSize, Vec2) and node.rectSize.x >= 0 and node.rectSize.y >= 0
# TODO assert node.compi in net.compartments OUTSIDE of this function
# TODO assert more properties