def test_read_notes():
sbgn = libsbgn.sbgn()
map = libsbgn.map()
map.set_language(Language.PD)
sbgn.set_map(map)
text = """
<body xmlns="http://www.w3.org/1999/xhtml">
This is an example note describing the map.
</body>
"""
notes = Notes(text)
map.set_notes(notes)
assert map.get_notes() is not None
f = tempfile.NamedTemporaryFile(suffix=".sbgn")
utils.write_to_file(sbgn, f.name)
del map, sbgn, notes
sbgn2 = utils.read_from_file(f.name)
print(utils.write_to_string(sbgn2))
map2 = sbgn2.get_map()
notes2 = map2.get_notes()
assert notes2 is not None
assert "<body" in str(notes2)
def test_read_extension():
sbgn = libsbgn.sbgn()
map = libsbgn.map()
map.set_language(Language.PD)
sbgn.set_map(map)
extension = Extension(
"""<renderInformation id="example" programName="SBML Layout" programVersion="3.0"
xmlns="http://projects.eml.org/bcb/sbml/render/level2">
<listOfColorDefinitions>
<colorDefinition id="yelloComp" value="#ffffccff" />
<colorDefinition id="grayComp" value="#e0e0e0ff" />
<colorDefinition id="orange" value="#fa9e2fff" />
<colorDefinition id="blue" value="#2958acff" />
<colorDefinition id="green" value="#378f5cff" />
<colorDefinition id="Color_0" value="#969696" />
<colorDefinition id="Color_1" value="#ff9900" />
<colorDefinition id="Color_2" value="#000000" />
</listOfColorDefinitions>
</renderInformation>"""
)
map.set_extension(extension)
assert map.get_extension() is not None
f = tempfile.NamedTemporaryFile(suffix=".sbgn")
utils.write_to_file(sbgn, f.name)
del map, sbgn, extension
sbgn = utils.read_from_file(f.name)
map = sbgn.get_map()
extension = map.get_extension()
assert extension is not None
assert "<colorDefinition" in str(extension)
def read_glyph_notes(f):
"""Read notes from glyphs.
:return: None
"""
sbgn = utils.read_from_file(f=f)
# map is a container for the glyphs and arcs
map = sbgn.get_map()
glyphs = map.get_glyph()
for g in glyphs:
notes = g.get_notes()
if notes:
print(g.get_id())
print(notes)
def read_glyph_notes(f):
""" Read notes from glyphs.
:return:
"""
sbgn = utils.read_from_file(f=f)
# map is a container for the glyphs and arcs
map = sbgn.get_map()
glyphs = map.get_glyph()
for g in glyphs:
notes = g.get_notes()
if notes:
print(g.get_id())
print(notes)
def __init__(self,sbgnPath,nodeBindings,edgeBindings,timeCourse=None):
self.sbgn = utils.read_from_file(sbgnPath)
self.map = sbgn.get_map()
self.map.set_language(Language.PD)
glyphs = self.map.get_glyph()
validIDs = [g.get_id() for g in glyphs]
processes = {g.get_id():[p.get_id() for p in g.get_port()] for
g in glyphs if g.get_class()=="process"}
arcs = self.map.get_arc()
self.edges = {g:[a.get_id() for a in arcs
if (a.get_source() in p) or (a.get_target() in p)]
for g, p in processes.items()}
self.edges = {reaction:self.edges[sbgnID] for reaction, sbgnID in
edgeBindings if sbgnID in self.edges.keys()}
self.nodes = {metabolite:sbgnID for metabolite, sbgnID in
nodeBindings if sbgnID in validIDs}
self.timeCourse = timeCourse
###RENDER SBGN FILE###
from libsbgnpy import render, utils
import os.path
filename = raw_input("Enter the name of the existing SBGN file: ")
if ".sbgn" not in filename:
filename = filename + ".sbgn"
exist = os.path.isfile(filename)
while exist == False:
filename = raw_input("The file does not exist, please try again: ")
if ".sbgn" not in filename:
filename = filename + ".sbgn"
exist = os.path.isfile(filename)
sbgn = utils.read_from_file(filename)
pngname = ""
for w in filename:
if w == '.':
break
else:
pngname += w
pngname += ".png"
render.render_sbgn(sbgn, pngname)
def test_write_to_string(f_adh):
sbgn = utils.read_from_file(f_adh)
sbgn_str = utils.write_to_string(sbgn)
assert sbgn_str is not None
assert "xml" in sbgn_str
def test_write_to_file(f_adh):
sbgn = utils.read_from_file(f_adh)
f_out = tempfile.NamedTemporaryFile(suffix=".sbgn")
utils.write_to_file(sbgn, f_out.name)
sbgn2 = utils.read_from_file(f_out)
assert sbgn2 is not None
def test_read_from_file(f_adh):
sbgn = utils.read_from_file(f_adh)
assert sbgn is not None
def test_render_sbgn(f_adh):
sbgn = utils.read_from_file(f_adh)
tmp_file = tempfile.NamedTemporaryFile(suffix=".png")
render.render_sbgn(sbgn, image_file=tmp_file.name, file_format="png")
value) + "\n"
styleStr = styleStr + """</listOfStyles>
</renderInformation>"""
extension = Extension(extString)
self.map.set_extension(extension)
render.render_sbgn(self.sbgn, image_file=fPath, file_format="png")
myModel = modelRunner(test_string,os.path.join(working_dir, 'copasiRuns',
'testRun6'))
myModel.genReactionAntString()
data = myModel.runTimeCourse(1)
data2 = myModel.runTimeCourse(1,genReactions=True)
sbgn = utils.read_from_file(os.path.join(working_dir, "test6.sbgn"))
map = sbgn.get_map()
map.set_language(Language.PD)
extString = """<renderInformation id="example" programName="SBML Layout" programVersion="3.0"
xmlns="http://projects.eml.org/bcb/sbml/render/level2">
<listOfStyles>
"""
extString = (extString +"\n"+sbgnLineStyle("R2-react0",0.5) +"\n"+
sbgnFillStyle("sa0",0.5) +"\n"+ """</listOfStyles>
</renderInformation>""")
extension = Extension(extString)
map.set_extension(extension)
def test_render_sbgn(f_adh):
sbgn = utils.read_from_file(f_adh)
tmp_file = tempfile.NamedTemporaryFile(suffix=".png")
render.render_sbgn(sbgn, image_file=tmp_file.name, file_format="png")
