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 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 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)
