def test_with_libsbml_draw(self):
from collections import OrderedDict
opt = OrderedDict(
k=20.0, # k
boundary=1, # boundary
magnatism=50, # magnatism
grav=5, # grav, has to be > 5 for effect
baryx=500.0, # baryx
baryy=500.0, # baryy
autobary=1, # autobary
enable_comps=0, # enable compartments // breaks the algorithm
prerandomize=0, # pre-randomize
padding=20.0 # padding
)
s = Style()
# edge attributes
# s.edge.edgecolor = 'grey'
# s.edge.fillcolor = 'grey'
# s.edge.width = 15
# font attributes
# s.font.color = 'black'
# s.font.size = 35
# s.font.weight = 'bold'
# node attributes
# s.node.edgecolor = '#b36b00'
# s.node.fillcolor = '#ffcc80'
# s.node.edgewidth = 5
# compartment attributes
# s.compartment.edgecolor = 'black'
# s.compartment.fillcolor = '#ffebcc'
# s.compartment.linewidth = 20
# arrow attributes
# s.arrow.scale = 50
sl = SBMLlayout(self.sbml_fname, autoComputeLayout=True,
# style=s,
layout_alg_options=opt)
# for i in range(10):
# sl.regenerateLayout()
sl.drawNetwork(self.image_fname, show=False, scaling_factor=1.0)
sl.writeSBML(self.sbml_with_layout)
print('saved to {}'.format(self.image_fname))
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
from pathlib import Path
import pkg_resources
from libsbml_draw import SBMLlayout
model_file_name = "model.xml"
model_file = Path(
pkg_resources.resource_filename("libsbml_draw",
"model/libs/" + model_file_name))
sl = SBMLlayout(str(model_file))
sl.describeModel()
fname = r'C:\Users\cwelsh\Downloads\graphfavb\BIO64_layout.xml'
fname = r'D:\ReproduciblePaper\BIOMD64\diagram\Teusink_layout.xml'
fname = r'D:\ReproduciblePaper\BIOMD64\model\JWSOnline_Teusink.xml'
fnameimg = r'D:\ReproduciblePaper\BIOMD64\model\image.png'
if os.path.isfile(fnameimg):
os.remove(fnameimg)
style = Style()
style.font.size = 35
style.edge.edgecolor = '#808080'
style.edge.fillcolor = '#4d4d4d'
style.edge.width = 8
style.node.edgecolor = '#ff8c1a'
style.node.fillcolor = '#ffe6cc'
style.node.edgewidth = 8
style.arrow.scale = 75
s = SBMLlayout(fname, style=style)
for i in range(1):
fnameimg = fr'D:\ReproduciblePaper\BIOMD64\model\image{i}.pdf'
s.regenerateLayout()
# s.setReactionColor('all', 'black')
# s.setReactionCurveWidth('all', 25)
s.apply_style()
s.drawNetwork(show=False, save_file_name=fnameimg)
s.writeSBML()
def test_with_libsbml_draw2(self):
sl = SBMLlayout(self.sbml_with_layout, autoComputeLayout=True)
# sl.drawNetwork(self.image_fname, show=False, scaling_factor=1.0)
sl.writeSBML(self.sbml_with_layout2)
return s import os from libsbml_draw import SBMLlayout, biomodels_download model_id = 'BIOMD0000000001' fname = model_id + '.xml' # download the model biomodels_download(model_id, fname) s = SBMLlayout(fname) s.drawNetwork(model_id + ".png") s.writeSBMLFile(model_id + 'layout.xml') # x = s.getBoundarySpeciesIds() # print(x) # ''' # <species boundaryCondition="true" compartment="cell" hasOnlySubstanceUnits="true" id="R5P" # initialAmount="18" metaid="metaid_0000020" name="ribose-5-phosphate"> # ''' # expected = ['ribose-5-phosphate'] # # # # draw the network
def setUp(self) -> None:
self.sbml = self.get_model_from_url()
self.sl = SBMLlayout(self.sbml_fname, applyRender=True)
class TestWorksWithBioModels(unittest.TestCase):
base_url = "https://www.ebi.ac.uk/biomodels-main/download?mid"
model_id = 'BIOMD0000000091'
sbml_fname = os.path.join(os.path.dirname(__file__), 'sbmlmodel.xml')
sbml_layout_fname = os.path.join(os.path.dirname(__file__), 'sbmlmodel_with_layout.xml')
image_fname = os.path.join(os.path.dirname(__file__), 'network.png')
expected_number_of_compartments = 0
expected_number_of_nodes = 16
expected_number_of_reactions = 23
tear_down = False
def get_model_from_url(self):
self.model_file_name = f"{self.model_id}_url.xml"
model_url = f'{self.base_url}={self.model_id}'
# get the model directly from url
sbml = requests.get(model_url).content.decode('utf-8')
with codecs.open(self.sbml_fname, 'w', 'utf-8') as f:
f.write(sbml)
return sbml
def tearDown(self) -> None:
if self.tear_down:
for i in [self.sbml_fname, self.image_fname, self.sbml_layout_fname]:
if os.path.isfile(i):
os.remove(i)
def setUp(self) -> None:
self.sbml = self.get_model_from_url()
self.sl = SBMLlayout(self.sbml_fname, applyRender=True)
def test_setup(self):
self.get_model_from_url()
self.assertTrue(os.path.isfile(self.sbml_fname))
def test_load_from_biomodels(self):
self.assertIsInstance(self.sl, SBMLlayout)
def do_describe(self):
desc = self.sl.describeModel()
return desc
def test_number_of_nodes(self):
described = self.do_describe()
self.assertEqual(self.expected_number_of_nodes, described['number_of_nodes'])
def test_number_of_compartments(self):
described = self.do_describe()
self.assertEqual(self.expected_number_of_compartments, described['number_of_compartments'])
def test_number_of_reactions(self):
described = self.do_describe()
self.assertEqual(self.expected_number_of_reactions, described['number_of_reactions'])
def test_draw_network_and_save_to_pdf(self):
self.sl.drawNetwork(self.image_fname, show=False, scaling_factor=1.0)
self.assertTrue(os.path.isfile(self.image_fname))
def test_save_sbml_to_file(self):
self.sl.drawNetwork(self.image_fname, show=False, scaling_factor=1.0)
self.sl.writeSBML(self.sbml_layout_fname)
self.assertTrue(os.path.isfile(self.sbml_layout_fname))