def test_toy_model_fba(self):
m = Metabolism(MODEL_FILE)
flux = 3.0
self.assertEquals(m.fba().Z, flux)
m = JsonModel.from_model(m).to_model()
self.assertEquals(m.fba().Z, flux)
m.get_reaction("reac1").constraint = (0, 5)
flux = 5.5
self.assertEquals(m.fba().Z, flux)
m = JsonModel.from_model(m).to_model()
self.assertEquals(m.fba().Z, flux)
m.get_reaction("reac1").stoic = [[1.5], [2.5]]
flux = 9.25
self.assertEquals(m.fba().Z, flux)
m = JsonModel.from_model(m).to_model()
self.assertEquals(m.fba().Z, flux)
def test_toy_model_fba(self):
m = Metabolism(MODEL_FILE)
flux = 3.0
self.assertEquals(m.fba().Z, flux)
m = JsonModel.from_model(m).to_model()
self.assertEquals(m.fba().Z, flux)
m.get_reaction("reac1").constraint = (0, 5)
flux = 5.5
self.assertEquals(m.fba().Z, flux)
m = JsonModel.from_model(m).to_model()
self.assertEquals(m.fba().Z, flux)
m.get_reaction("reac1").stoic = [[1.5],[2.5]]
flux = 9.25
self.assertEquals(m.fba().Z, flux)
m = JsonModel.from_model(m).to_model()
self.assertEquals(m.fba().Z, flux)
def setUp(self):
self.doLogin()
self.user.profile.assign_perm(ACCESS_PERM)
# Add templates
m = Metabolism(MODEL_FILE)
j = JsonModel.from_model(m)
dt = DesignTemplate(name="Test")
dt.description = "Test"
dt.filename = "ToyModel.txt"
dt.content = j.to_json()
dt.save()
self.pk = dt.pk
m = Metabolism(MODEL_FILE2)
j = JsonModel.from_model(m)
dt = DesignTemplate(name="Test")
dt.description = "Test"
dt.filename = "iSyn.txt"
dt.content = j.to_json()
dt.save()
def setUp(self):
self.doLogin()
self.user.profile.assign_perm(ACCESS_PERM)
# Add templates
m = Metabolism(MODEL_FILE)
j = JsonModel.from_model(m)
dt = DesignTemplate(name="Test")
dt.description = "Test"
dt.filename = "ToyModel.txt"
dt.content = j.to_json()
dt.save()
self.pk = dt.pk
m = Metabolism(MODEL_FILE2)
j = JsonModel.from_model(m)
dt = DesignTemplate(name="Test")
dt.description = "Test"
dt.filename = "iSyn.txt"
dt.content = j.to_json()
dt.save()
def get_reactions(request, pk):
try:
item = DesignModel.objects.get(user=UserProfile.get_profile(
request.user),
pk=pk)
except ObjectDoesNotExist:
return BadRequest("Bad Model")
try:
revision = request.GET["revision"]
try:
revision = Revision.objects.get(model=item, pk=revision)
except ObjectDoesNotExist:
return BadRequest("Bad Revision")
except KeyError:
revision = item.get_latest_revision()
return JsonModel.from_sbml(revision.content).to_json()
def test_isyn_model_sbml(self):
m = Metabolism(MODEL_FILE3)
flux = 0.08940293757452249
self.assertEquals(m.fba().Z, flux)
m = JsonModel.from_model(m).to_model()
self.assertEquals(m.fba().Z, flux)
def upload(request, pk):
data = {}
if request.method == 'POST':
if pk == "1":
# Uploaded model
form = UploadModelForm(request.POST, request.FILES)
if form.is_valid():
name = form.cleaned_data.get('name')
#save to temporary file
freq = request.FILES['file']
filename = freq.name
ss = StringIO()
for chunk in freq.chunks():
try:
ss.write(chunk.decode("utf-8"))
except UnicodeDecodeError:
form.add_error("file", "File does not have UTF-8 encoding")
form_html = render_crispy_form(form, context=request)
return {'success': False, 'form_html': form_html}
try:
model = Metabolism(ss)
except:
form.add_error("file", "Not a valid model")
form_html = render_crispy_form(form, context=request)
return {'success': False, 'form_html': form_html}
dm = DesignModel.objects.create(
user=request.user.profile,
name=name,
filename=filename,
content=ss.getvalue()
)
try:
jm = JsonModel.from_model(model).to_json()
except ValueError:
return BadRequest(str(ValueError))
Revision(
model=dm,
content=jm,
reason="Initial version"
).save()
return {'success': True}
else:
form_html = render_crispy_form(form, context=request)
return {'success': False, 'form_html': form_html}
if pk == "2":
# from template
templates = DesignTemplate.objects.values_list("pk", "name")
form = ModelFromTemplateForm(templates, request.POST, request.FILES)
if form.is_valid():
name = form.cleaned_data.get('name')
choice = form.cleaned_data.get('choice')
template = DesignTemplate.objects.get(pk=choice)
dm = DesignModel.objects.create(
user=UserProfile.get_profile(request.user),
name=name,
filename=template.filename,
content=""
)
Revision(
model=dm,
content=template.content,
reason="Initial version"
).save()
return {'success': True}
else:
form_html = render_crispy_form(form, context=request)
return {'success': False, 'form_html': form_html}
return BadRequest()
def model_from_string(model_str):
return JsonModel.from_json(model_str)
def apply_commandlist(model, commandlist):
"""
:type model: PyNetMet2.Metabolism
"""
for command in commandlist:
try:
op = command["op"]
typ = command["type"]
name = command["id"]
cid = create_sid(name)
obj = command["object"]
except KeyError:
raise ValueError("Bad command " + str(command))
if typ == "reaction":
enzyme = model.get_reaction(name)
if op in ["add", "edit"]:
if "id" not in obj:
raise ValueError("Bad command " + str(command))
if op == "add":
if "name" not in obj:
raise ValueError("Bad command " + str(command))
if enzyme is not None:
raise ValueError("Reaction already in model: " + name)
if name != obj["id"]:
raise ValueError("Reaction name mismatch: " + name)
if "reversible" not in obj:
raise ValueError("Bad command " + str(command))
model.add_reaction(JsonModel.Reaction(**obj))
elif op == "edit":
if enzyme is None:
raise ValueError("Reaction not in model: " + name)
if obj["id"] != enzyme.id and model.has_reaction(obj["id"]):
raise ValueError("Reaction already in model: " +
obj["name"])
enzyme.id = obj["id"]
if name in obj:
enzyme.name = obj["name"]
if "substrates" in obj and "products" in obj:
enzyme.substrates = list(
map(lambda x: JsonModel.Compound(**x).name,
obj["substrates"]))
enzyme.products = list(
map(lambda x: JsonModel.Compound(**x).name,
obj["products"]))
enzyme.stoic = [
list(
map(
lambda x: JsonModel.Compound(**x).
stoichiometry, obj["substrates"])),
list(
map(
lambda x: JsonModel.Compound(**x).
stoichiometry, obj["products"]))
]
try:
enzyme.reversible = obj["reversible"]
except KeyError:
pass
try:
enzyme.constraint = obj["constraints"]
except KeyError:
pass
try:
enzyme.pathway = obj["pathway"]
except KeyError:
pass
try:
enzyme.disabled = obj["disabled"]
except KeyError:
pass
elif op == "delete":
if enzyme is None:
raise ValueError("Reaction not in model: " + name)
idd = enzyme.id
model.remove_reaction(idd)
continue
else:
raise ValueError("Invalid operation " + op)
elif typ == "metabolite":
if op in ["add", "edit"] and "id" not in obj:
raise ValueError("Bad command " + str(command))
if op == "add":
if name != obj["id"]:
raise ValueError("Metabolite name mismatch: " + name)
model.add_metabolite(obj["id"], obj.get("external", False))
elif op == "edit":
if "external" in obj:
if obj["external"]:
model.make_metabolite_external(name)
else:
model.make_metabolite_internal(name)
if name != obj["name"]:
model.rename_metabolite(name, obj["name"])
elif op == "delete":
model.remove_metabolite(name)
else:
raise ValueError("Invalid operation " + op)
elif typ == "pathway":
if "id" not in obj:
raise ValueError("Bad command " + str(command))
if op == "edit":
for reac in model.enzymes:
if reac.pathway == name:
reac.pathway = obj["id"]
else:
raise ValueError("Invalid operation " + op)
else:
raise ValueError("Invalid command " + typ)
return model
def model_from_string(model_str):
return JsonModel.from_json(model_str)
def test_isyn_model_sbml(self):
m = Metabolism(MODEL_FILE3)
flux = 0.08940293757452249
self.assertEquals(m.fba().Z, flux)
m = JsonModel.from_model(m).to_model()
self.assertEquals(m.fba().Z, flux)