def test_update_failure(self):
api.add_node(self.neti, id='Zulu')
# empty ID
with self.assertRaises(ValueError):
api.update_node(self.neti, 0, id='')
# nodes don't exist
with self.assertRaises(NetIndexError):
api.update_node(-1, 0, size=Vec2(50, 60))
with self.assertRaises(NodeIndexError):
api.update_node(0, 2, size=Vec2(50, 60))
# out of bounds
with self.assertRaises(ValueError):
api.update_node(self.neti, 0, position=Vec2(-1, 0))
with self.assertRaises(ValueError):
api.update_node(self.neti, 0, position=Vec2(0, -1))
csize = api.canvas_size()
# in bounds
api.update_node(self.neti, 0, position=csize - Vec2(100, 100))
# out of bounds
with self.assertRaises(ValueError):
api.update_node(self.neti, 0, position=csize - Vec2(1, 1))
def test_update_nodes(self):
with run_app():
node = Node('Charles',
pos=Vec2(50, 50),
size=Vec2(40, 12),
fill_color=wx.RED,
border_color=wx.GREEN,
border_width=4)
api.add_node(self.neti, node)
api.update_node(self.neti, 0, 'James')
nodes = api.all_nodes()
self.assertEqual(len(nodes), 1)
self.assertTrue(nodes[0].id_, 'James')
def test_add_nodes(self):
with run_app():
node = Node('Charles',
pos=Vec2(50, 50),
size=Vec2(40, 12),
fill_color=wx.RED,
border_color=wx.GREEN,
border_width=4)
api.add_node(self.neti, node)
nodes = api.all_nodes()
self.assertEqual(len(nodes), 1)
self.assertEqual(0, nodes[0].index)
self.assertTrue(node.props_equal(nodes[0]))
def test_separate_props(self):
'''Test modifying the properties of node and alias that are separate, i.e. not shared.
As in, if the position of an alias is changed, that of the node should remain the same,
and vice versa.
'''
alias_pos = Vec2(100, 100)
alias_size = Vec2(50, 50)
nodei = api.add_node(self.neti, id='Hookie')
aliasi = api.add_alias(self.neti,
nodei,
position=alias_pos,
size=alias_size)
new_pos = Vec2(33, 33)
new_size = Vec2(66, 66)
new_lockNode = True
api.update_node(self.neti,
nodei,
position=Vec2(33, 33),
size=Vec2(66, 66),
lockNode=True)
node = api.get_node_by_index(self.neti, nodei)
alias = api.get_node_by_index(self.neti, aliasi)
# alias remains the same
self.assertEqual(alias_pos, alias.position)
self.assertEqual(alias_size, alias.size)
self.assertEqual(False, alias.lockNode)
# node is updated
self.assertEqual(new_pos, node.position)
self.assertEqual(new_size, node.size)
self.assertEqual(new_lockNode, node.lockNode)
def test_add_basic(self):
node = Node('Charles', self.neti, pos=Vec2(50, 50), size=Vec2(50, 30))
api.add_node(
self.neti,
id=node.id,
position=node.position,
size=node.size,
fill_color=api._to_color(wx.RED), # HACK using API private methods
border_color=api._to_color(wx.BLUE),
border_width=2,
)
nodes = api.get_nodes(self.neti)
self.assertEqual(len(nodes), 1)
self.assertEqual(0, nodes[0].index)
expected = NodeData(id='Charles',
net_index=self.neti,
position=Vec2(50, 50),
size=Vec2(50, 30),
index=0)
self.assertEqual(expected, nodes[0])
def test_add_alias(self):
size = Vec2(60, 60)
nodei = api.add_node(self.neti, id='Hookie', size=size)
api.add_alias(self.neti, nodei, size=size)
nodes = api.get_nodes(self.neti)
self.assertEqual(2, len(nodes))
original = NodeData(net_index=self.neti,
id='Hookie',
index=0,
original_index=-1,
size=size)
alias = NodeData(net_index=self.neti,
id='Hookie',
index=1,
original_index=0,
size=size)
self.assertEqual(original, nodes[0])
self.assertEqual(alias, nodes[1])
def Visualize(self, evt):
"""
Handler for the "Visualize" button.
Visualize the SBML string to a network shown on the canvas.
"""
def hex_to_rgb(value):
value = value.lstrip('#')
return tuple(int(value[i:i+2], 16) for i in (0, 2, 4))
if len(self.sbmlStr) == 0:
wx.MessageBox("Please import an SBML file.", "Message", wx.OK | wx.ICON_INFORMATION)
else:
net_index = 0
api.clear_network(net_index)
comp_id_list = []
comp_dimension_list = []
comp_position_list = []
spec_id_list =[]
spec_dimension_list =[]
spec_position_list = []
#set the default values without render info:
comp_fill_color = (158, 169, 255)
comp_border_color = (0, 29, 255)
comp_border_width = 2.0
spec_fill_color = (255, 204, 153)
spec_border_color = (255, 108, 9)
spec_border_width = 2.0
reaction_line_color = (129, 123, 255)
reaction_line_width = 3.0
### from here for layout ###
document = readSBMLFromString(self.sbmlStr)
model_layout = document.getModel()
mplugin = (model_layout.getPlugin("layout"))
if mplugin is None:
wx.MessageBox("There is no layout information, so positions are randomly assigned.", "Message", wx.OK | wx.ICON_INFORMATION)
#
# Get the first Layout object via LayoutModelPlugin object.
#
else:
layout = mplugin.getLayout(0)
if layout is None:
wx.MessageBox("There is no layout information, so positions are randomly assigned.", "Message", wx.OK | wx.ICON_INFORMATION)
else:
numCompGlyphs = layout.getNumCompartmentGlyphs()
numSpecGlyphs = layout.getNumSpeciesGlyphs()
for i in range(numCompGlyphs):
compGlyph = layout.getCompartmentGlyph(i)
temp_id = compGlyph.getCompartmentId()
comp_id_list.append(temp_id)
boundingbox = compGlyph.getBoundingBox()
height = boundingbox.getHeight()
width = boundingbox.getWidth()
pos_x = boundingbox.getX()
pos_y = boundingbox.getY()
comp_dimension_list.append([width,height])
comp_position_list.append([pos_x,pos_y])
for i in range(numSpecGlyphs):
specGlyph = layout.getSpeciesGlyph(i)
spec_id = specGlyph.getSpeciesId()
spec_id_list.append(spec_id)
boundingbox = specGlyph.getBoundingBox()
height = boundingbox.getHeight()
width = boundingbox.getWidth()
pos_x = boundingbox.getX()
pos_y = boundingbox.getY()
spec_dimension_list.append([width,height])
spec_position_list.append([pos_x,pos_y])
rPlugin = layout.getPlugin("render")
if (rPlugin != None and rPlugin.getNumLocalRenderInformationObjects() > 0):
info = rPlugin.getRenderInformation(0)
color_list = []
for j in range ( 0, info.getNumColorDefinitions()):
color = info.getColorDefinition(j)
color_list.append([color.getId(),color.createValueString()])
for j in range (0, info.getNumStyles()):
style = info.getStyle(j)
group = style.getGroup()
typeList = style.createTypeString()
if 'COMPARTMENTGLYPH' in typeList:
for k in range(len(color_list)):
if color_list[k][0] == group.getFill():
comp_fill_color = hex_to_rgb(color_list[k][1])
if color_list[k][0] == group.getStroke():
comp_border_color = hex_to_rgb(color_list[k][1])
comp_border_width = group.getStrokeWidth()
elif 'SPECIESGLYPH' in typeList:
for k in range(len(color_list)):
if color_list[k][0] == group.getFill():
spec_fill_color = hex_to_rgb(color_list[k][1])
if color_list[k][0] == group.getStroke():
spec_border_color = hex_to_rgb(color_list[k][1])
spec_border_width = group.getStrokeWidth()
elif 'REACTIONGLYPH' in typeList:
for k in range(len(color_list)):
if color_list[k][0] == group.getStroke():
reaction_line_color = hex_to_rgb(color_list[k][1])
reaction_line_width = group.getStrokeWidth()
model = simplesbml.loadSBMLStr(self.sbmlStr)
numFloatingNodes = model.getNumFloatingSpecies()
FloatingNodes_ids = model.getListOfFloatingSpecies()
numBoundaryNodes = model.getNumBoundarySpecies()
BoundaryNodes_ids = model.getListOfBoundarySpecies()
numRxns = model.getNumReactions()
Rxns_ids = model.getListOfReactionIds()
numComps = model.getNumCompartments()
Comps_ids = model.getListOfCompartmentIds()
numNodes = numFloatingNodes + numBoundaryNodes
for i in range(numComps):
temp_id = Comps_ids[i]
vol= model.getCompartmentVolume(i)
if len(comp_id_list) != 0:
#if mplugin is not None:
for j in range(numComps):
if comp_id_list[j] == temp_id:
dimension = comp_dimension_list[j]
position = comp_position_list[j]
else:# no layout info about compartment,
# then the whole size of the canvas is the compartment size
dimension = [4000,2500]
position = [0,0]
api.add_compartment(net_index, id=temp_id, volume = vol,
size=Vec2(dimension[0],dimension[1]),position=Vec2(position[0],position[1]),
fill_color = api.Color(comp_fill_color[0],comp_fill_color[1],comp_fill_color[2]),
border_color = api.Color(comp_border_color[0],comp_border_color[1],comp_border_color[2]),
border_width = comp_border_width)
comp_node_list = [0]*numComps
for i in range(numComps):
comp_node_list[i] = []
if len(comp_id_list) != 0:
#if mplugin is not None:
for i in range (numFloatingNodes):
temp_id = FloatingNodes_ids[i]
comp_id = model.getCompartmentIdSpeciesIsIn(temp_id)
for j in range(numNodes):
if temp_id == spec_id_list[j]:
dimension = spec_dimension_list[j]
position = spec_position_list[j]
nodeIdx_temp = api.add_node(net_index, id=temp_id, floatingNode = True,
size=Vec2(dimension[0],dimension[1]), position=Vec2(position[0],position[1]),
fill_color=api.Color(spec_fill_color[0],spec_fill_color[1],spec_fill_color[2]),
border_color=api.Color(spec_border_color[0],spec_border_color[1],spec_border_color[2]),
border_width=spec_border_width)
for j in range(numComps):
if comp_id == comp_id_list[j]:
comp_node_list[j].append(nodeIdx_temp)
for i in range (numBoundaryNodes):
temp_id = BoundaryNodes_ids[i]
comp_id = model.getCompartmentIdSpeciesIsIn(temp_id)
for j in range(numNodes):
if temp_id == spec_id_list[j]:
dimension = spec_dimension_list[j]
position = spec_position_list[j]
nodeIdx_temp = api.add_node(net_index, id=temp_id, floatingNode = False,
size=Vec2(dimension[0],dimension[1]), position=Vec2(position[0],position[1]),
fill_color=api.Color(spec_fill_color[0],spec_fill_color[1],spec_fill_color[2]),
border_color=api.Color(spec_border_color[0],spec_border_color[1],spec_border_color[2]),
border_width=spec_border_width)
for j in range(numComps):
if comp_id == comp_id_list[j]:
comp_node_list[j].append(nodeIdx_temp)
else: # there is no layout information, assign position randomly and size as default
comp_id_list = Comps_ids
for i in range (numFloatingNodes):
temp_id = FloatingNodes_ids[i]
comp_id = model.getCompartmentIdSpeciesIsIn(temp_id)
nodeIdx_temp = api.add_node(net_index, id=temp_id, size=Vec2(60,40), floatingNode = True,
position=Vec2(40 + math.trunc (_random.random()*800), 40 + math.trunc (_random.random()*800)),
fill_color=api.Color(spec_fill_color[0],spec_fill_color[1],spec_fill_color[2]),
border_color=api.Color(spec_border_color[0],spec_border_color[1],spec_border_color[2]),
border_width=spec_border_width)
for j in range(numComps):
if comp_id == comp_id_list[j]:
comp_node_list[j].append(nodeIdx_temp)
for i in range (numBoundaryNodes):
temp_id = BoundaryNodes_ids[i]
comp_id = model.getCompartmentIdSpeciesIsIn(temp_id)
nodeIdx_temp = api.add_node(net_index, id=temp_id, size=Vec2(60,40), floatingNode = False,
position=Vec2(40 + math.trunc (_random.random()*800), 40 + math.trunc (_random.random()*800)),
fill_color=api.Color(spec_fill_color[0],spec_fill_color[1],spec_fill_color[2]),
border_color=api.Color(spec_border_color[0],spec_border_color[1],spec_border_color[2]),
border_width=spec_border_width)
for j in range(numComps):
if comp_id == comp_id_list[j]:
comp_node_list[j].append(nodeIdx_temp)
for i in range(numComps):
temp_id = Comps_ids[i]
for j in range(numComps):
if comp_id_list[j] == temp_id:
node_list_temp = comp_node_list[j]
for j in range(len(node_list_temp)):
api.set_compartment_of_node(net_index=net_index, node_index=node_list_temp[j], comp_index=i)
#handle_positions, center_pos was set as the default
numNodes = api.node_count(net_index)
allNodes = api.get_nodes(net_index)
for i in range (numRxns):
src = []
dst = []
temp_id = Rxns_ids[i]
kinetics = model.getRateLaw(i)
rct_num = model.getNumReactants(i)
prd_num = model.getNumProducts(i)
for j in range(rct_num):
rct_id = model.getReactant(temp_id,j)
for k in range(numNodes):
if allNodes[k].id == rct_id:
src.append(allNodes[k].index)
for j in range(prd_num):
prd_id = model.getProduct(temp_id,j)
for k in range(numNodes):
if allNodes[k].id == prd_id:
dst.append(allNodes[k].index)
api.add_reaction(net_index, id=temp_id, reactants=src, products=dst, rate_law = kinetics,
fill_color=api.Color(reaction_line_color[0],reaction_line_color[1],reaction_line_color[2]),
line_thickness=reaction_line_width)
def setUp(self):
api.add_node(self.neti, 'Alice')
api.add_node(self.neti, 'Bob')
api.add_node(self.neti, 'Charlie')
def Apply(self, evt):
"""
Handler for the "apply" button. apply the random network.
"""
if self.randomSeedValue != 0:
_random.seed(self.randomSeedValue)
class _TReactionType:
UNIUNI = 0
BIUNI = 1
UNIBI = 2
BIBI = 3
def _pickReactionType():
rt = _random.random()
if rt < self.probUniUniValue:
return _TReactionType.UNIUNI
elif rt < self.probUniUniValue + self.probBiUniValue:
return _TReactionType.BIUNI
elif rt < self.probUniUniValue + self.probBiUniValue + self.probUniBiValue:
return _TReactionType.UNIBI
else:
return _TReactionType.BIBI
# Generates a reaction network in the form of a reaction list
# reactionList = [nSpecies, reaction, reaction, ....]
# reaction = [reactionType, [list of reactants], [list of products], rateConsta>
# Disallowed reactions:
# S1 -> S1
# S1 + S2 -> S2 # Can't have the same reactant and product
# S1 + S1 -> S1
def _generateReactionList (nSpecies, nReactions):
reactionList = []
for r in range(nReactions):
rateConstant = _random.random()
rt = _pickReactionType()
if rt == _TReactionType.UNIUNI:
# UniUni
reactant = _random.randint (0, nSpecies-1)
product = _random.randint (0, nSpecies-1)
# Disallow S1 -> S1 type of reaction
while product == reactant:
product = _random.randint (0, nSpecies-1)
reactionList.append ([rt, [reactant], [product], rateConstant])
if rt == _TReactionType.BIUNI:
# BiUni
# Pick two reactants
reactant1 = _random.randint (0, nSpecies-1)
reactant2 = _random.randint (0, nSpecies-1)
# pick a product but only products that don't include the reactants
species = range (nSpecies)
# Remove reactant1 and 2 from the species list
species = _np.delete (species, [reactant1, reactant2], axis=0)
# Then pick a product from the reactants that are left
product = species[_random.randint (0, len (species)-1)]
reactionList.append ([rt, [reactant1, reactant2], [product], rateConstant])
if rt == _TReactionType.UNIBI:
# UniBi
reactant1 = _random.randint (0, nSpecies-1)
# pick a product but only products that don't include the reactant
species = range (nSpecies)
# Remove reactant1 from the species list
species = _np.delete (species, [reactant1], axis=0)
# Then pick a product from the reactants that are left
product1 = species[_random.randint (0, len (species)-1)]
product2 = species[_random.randint (0, len (species)-1)]
reactionList.append ([rt, [reactant1], [product1, product2], rateConstant])
if rt == _TReactionType.BIBI:
# BiBi
reactant1 = _random.randint (0, nSpecies-1)
reactant2= _random.randint (0, nSpecies-1)
# pick a product but only products that don't include the reactant
species = range (nSpecies)
# Remove reactant1 and 2 from the species list
species = _np.delete (species, [reactant1, reactant2], axis=0)
# Then pick a product from the reactants that are left
product1 = species[_random.randint (0, len (species)-1)]
product2 = species[_random.randint (0, len (species)-1)]
element = [rt, [reactant1, reactant2], [product1, product2], rateConstant]
reactionList.append (element)
reactionList.insert (0, nSpecies)
return reactionList
# Includes boundary and floating species
# Returns a list:
# [New Stoichiometry matrix, list of floatingIds, list of boundaryIds]
def _getFullStoichiometryMatrix (reactionList):
nSpecies = reactionList[0]
reactionListCopy = _copy.deepcopy (reactionList)
reactionListCopy.pop (0)
st = _np.zeros ((nSpecies, len(reactionListCopy)))
for index, r in enumerate (reactionListCopy):
if r[0] == _TReactionType.UNIUNI:
# UniUni
reactant = reactionListCopy[index][1][0]
st[reactant, index] = -1
product = reactionListCopy[index][2][0]
st[product, index] = 1
if r[0] == _TReactionType.BIUNI:
# BiUni
reactant1 = reactionListCopy[index][1][0]
st[reactant1, index] = -1
reactant2 = reactionListCopy[index][1][1]
st[reactant2, index] = -1
product = reactionListCopy[index][2][0]
st[product, index] = 1
if r[0] == _TReactionType.UNIBI:
# UniBi
reactant1 = reactionListCopy[index][1][0]
st[reactant1, index] = -1
product1 = reactionListCopy[index][2][0]
st[product1, index] = 1
product2 = reactionListCopy[index][2][1]
st[product2, index] = 1
if r[0] == _TReactionType.BIBI:
# BiBi
reactant1 = reactionListCopy[index][1][0]
st[reactant1, index] = -1
reactant2 = reactionListCopy[index][1][1]
st[reactant2, index] = -1
product1 = reactionListCopy[index][2][0]
st[product1, index] = 1
product2 = reactionListCopy[index][2][1]
st[product2, index] = 1
return st
def _getRateLaw (floatingIds, boundaryIds, reactionList, isReversible):
nSpecies = reactionList[0]
# Remove the first element which is the nSpecies
reactionListCopy = _copy.deepcopy (reactionList)
reactionListCopy.pop (0)
antStr_tot = []
for index, r in enumerate (reactionListCopy):
antStr= ''
antStr = antStr + 'J' + str (index) + ': '
if r[0] == _TReactionType.UNIUNI:
# UniUni
antStr = antStr + '(k' + str (index) + '*S' + str (reactionListCopy[index][1][0])
if isReversible:
antStr = antStr + ' - k' + str (index) + 'r' + '*S' + str (reactionListCopy[index][2][0])
antStr = antStr + ')'
if r[0] == _TReactionType.BIUNI:
# BiUni
antStr = antStr + '(k' + str (index) + '*S' + str (reactionListCopy[index][1][0]) + '*S' + str (reactionListCopy[index][1][1])
if isReversible:
antStr = antStr + ' - k' + str (index) + 'r' + '*S' + str (reactionListCopy[index][2][0])
antStr = antStr + ')'
if r[0] == _TReactionType.UNIBI:
# UniBi
antStr = antStr + '(k' + str (index) + '*S' + str (reactionListCopy[index][1][0])
if isReversible:
antStr = antStr + ' - k' + str (index) + 'r' + '*S' + str (reactionListCopy[index][2][0]) + '*S' + str (reactionListCopy[index][2][1])
antStr = antStr + ')'
if r[0] == _TReactionType.BIBI:
# BiBi
antStr = antStr + '(k' + str (index) + '*S' + str (reactionListCopy[index][1][0]) + '*S' + str (reactionListCopy[index][1][1])
if isReversible:
antStr = antStr + ' - k' + str (index) + 'r' + '*S' + str (reactionListCopy[index][2][0]) + '*S' + str (reactionListCopy[index][2][1])
antStr = antStr + ')'
antStr_tot.append(antStr)
return antStr_tot
test_prob = self.probUniUniValue + self.probBiUniValue + self.probUniBiValue + self.probBiBiValue
if test_prob != 1:
wx.MessageBox("The sum of probabilities should be one!", "Message", wx.OK | wx.ICON_INFORMATION)
else:
net_index = 0
api.clear_network(net_index)
rl = _generateReactionList (self.numSpecsValue, self.numRxnsValue)
st = _getFullStoichiometryMatrix (rl)
antStr = _getRateLaw (st[1], st[2], rl, isReversible=True)
numNodes = st.shape[0]
numRxns = st.shape[1]
nodeIdx = []
for i in range (numNodes):
nodeIdx.append (api.add_node(net_index, 'node_{}'.format(i), size=Vec2(60,40), fill_color=api.Color(255, 204, 153),
border_color=api.Color(255, 108, 9),
position=Vec2(40 + math.trunc (_random.random()*800), 40 + math.trunc (_random.random()*800))))
for i in range (numRxns):
src = []
dest = []
for j in range(numNodes):
if (st.item(j,i) == -1):
src.append(nodeIdx[j])
if (st.item(j,i) == 1):
dest.append(nodeIdx[j])
r_idx = api.add_reaction(net_index, 'reaction_{}'.format(i), src, dest, fill_color=api.Color(91, 176, 253))
# Need to remove orphan nodes
for i in range (numNodes):
if _np.array_equal(st[i,:], _np.zeros(numRxns)):
api.delete_node(net_index, nodeIdx[i])
def test_update_basic(self):
api.add_node(self.neti, id="Eric")
api.update_node(self.neti, 0, 'James')
nodes = api.get_nodes(self.neti)
self.assertEqual(len(nodes), 1)
self.assertEqual(nodes[0].id, 'James')