def save(request, pk):
if not all(x in request.POST for x in ["changes", "objectives"]):
raise BadRequest("Request incomplete")
try:
model = DesignModel.objects.get(user=UserProfile.get_profile(request.user), pk=pk)
except ObjectDoesNotExist:
raise BadRequest("Bad Model")
try:
revision = request.POST["revision"]
try:
revision = Revision.objects.get(model=model, pk=revision)
except ObjectDoesNotExist:
raise BadRequest("Bad Revision")
except KeyError:
revision = model.get_latest_revision()
org = model_from_string(revision.content)
try:
changes = json.loads(request.POST["changes"])
objectives = json.loads(request.POST["objectives"])
except ValueError:
return BadRequest("Invalid JSON data")
summary = request.POST.get("summary")
try:
apply_commandlist(org, changes)
org = model_from_string(revision.content)
changes = compress_command_list(changes)
apply_commandlist(org, changes)
if objectives:
org.objectives = []
for obj in objectives:
if len(obj["name"]) > 0:
obj_reac = org.get_reaction(obj["name"])
if obj_reac is None:
raise BadRequest("Objective not in model: " + obj["name"])
org.objectives.append(JsonModel.Objective(**obj))
except ValueError as e:
raise BadRequest("Model error: " + str(e))
if len(changes) == 0:
raise BadRequest("Model not saved: No changes found")
Revision(
model=model,
content=org.to_json(),
changes=dict(changes=changes,objectives=objectives),
reason=summary
).save()
return {}
def export(request, pk):
form = request.GET.get("format", "bioopt")
if form not in ["bioopt", "sbml"]:
return HttpResponseBadRequest("Bad format")
try:
model = DesignModel.objects.get(user=UserProfile.get_profile(request.user), pk=pk)
content = model.get_latest_revision().content
except ObjectDoesNotExist:
return HttpResponseBadRequest("Bad Model")
org = model_from_string(content)
ss = StringIO()
org.to_model().dump(fileout=ss, filetype="opt" if form == "bioopt" else "sbml")
response = HttpResponse(
ss.getvalue(),
content_type="application/x-bioopt" if form=="bioopt" else "application/sbml+xml"
)
ss.close()
response['Content-Disposition'] = "attachment; filename=" + model.filename
return response
def simulate(request, pk):
if not all(x in request.POST for x in ["changes", "objectives", "display", "auto_flux"]):
return HttpResponseBadRequest("Request incomplete")
output_format = request.POST.get("format", "json")
dry_run = request.POST.get("dry_run", False)
try:
model = DesignModel.objects.get(user=UserProfile.get_profile(request.user), pk=pk)
except ObjectDoesNotExist:
return HttpResponseBadRequest("Bad Model")
try:
revision = request.POST["revision"]
try:
revision = Revision.objects.get(model=model, pk=revision)
except ObjectDoesNotExist:
return HttpResponseBadRequest("Bad Revision")
except KeyError:
revision = model.get_latest_revision()
org = model_from_string(revision.content)
try:
changes = json.loads(request.POST["changes"])
objectives = json.loads(request.POST["objectives"])
display = json.loads(request.POST["display"])
auto_flux = json.loads(request.POST["auto_flux"])
except ValueError:
return HttpResponseBadRequest("Invalid JSON data")
try:
auto_flux = bool(auto_flux)
except ValueError:
return HttpResponseBadRequest("Invalid data type")
try:
apply_commandlist(org, changes)
org = model_from_string(revision.content)
changes = compress_command_list(changes)
apply_commandlist(org, changes)
if not objectives:
raise ValueError("No objective specified")
org.objectives = []
for obj in objectives:
if len(obj["name"]) > 0:
obj_reac = org.get_reaction(obj["name"])
if obj_reac is None:
raise ValueError("Objective not in model: " + obj["name"])
if obj_reac.disabled:
return HttpResponseBadRequest("Objective disabled: " + obj_reac.name)
org.objectives.append(JsonModel.Objective(**obj))
else:
raise ValueError("No objective specified")
except ValueError as e:
return HttpResponseBadRequest("Model error: " + str(e))
display = filter(lambda x: not len(x) == 0, display)
for item in display:
if not org.has_reaction(item):
return HttpResponseBadRequest("Unknown reaction in display list: " + item)
org = org.to_model()
try:
fba = org.fba()
except ValueError as e:
return HttpResponseBadRequest("FBA error: " + str(e))
if dry_run:
return HttpResponse(
json.dumps({"solution": fba.get_status()}),
content_type="application/json")
full_g, nodeIDs = calc_reactions(org, fba)
display = json.loads(request.POST["display"])
display = list(filter(lambda x: len(x) > 0 and org.has_reaction(x), display))
dflux = {}
for reac, flux in zip(map(lambda x: x.name, fba.reacs), fba.flux):
dflux[reac] = flux
# Auto filter by FBA
if auto_flux:
if len(full_g.edges()) <= 30:
full_eg = full_g
else:
full_eg = nx.ego_graph(full_g.reverse(), nodeIDs[org.obj[0][0]], radius=3, center=False, undirected=False)
full_g.remove_edges_from(full_g.in_edges(nodeIDs[org.obj[0][0]]) + full_g.out_edges(nodeIDs[org.obj[0][0]]))
all_edges = map(lambda x: full_eg.get_edge_data(*x)["object"].name, full_eg.edges())
# Get fluxes of "edges"
flux = []
for reac in all_edges:
flux.append([reac, dflux[reac]])
flux = sorted(flux, key=lambda x: -x[1])
display = list(map(lambda x: x[0], flux[:30]))
else:
full_g.remove_edges_from(full_g.in_edges(nodeIDs[org.obj[0][0]]) + full_g.out_edges(nodeIDs[org.obj[0][0]]))
display.append(org.obj[0][0])
g = get_selected_reaction(json_graph.node_link_data(full_g), nodeIDs, display, org)
graph = nx.to_agraph(g)
graph.graph_attr.update(splines=True, overlap=False, rankdir="LR")
graph.node_attr.update(style="filled", colorscheme="pastel19")
outgraph = str(graph.to_string())
outgraph = pygraphviz.AGraph(outgraph)
outgraph = outgraph.draw(format="svg", prog="dot")
if output_format == "json":
return HttpResponse(json.dumps(
{"graph": outgraph.decode("utf-8"),
"solution": fba.get_status(),
"flux": dflux
}),
content_type="application/json"
)
elif output_format == "png":
import wand.image
with wand.image.Image(blob=outgraph, format="svg") as image:
png_image = image.make_blob("png")
r = HttpResponse(png_image, content_type="image/png")
r['Content-Disposition'] = 'attachment; filename={}.png'.format(model.filename)
return r
elif output_format == "svg":
r = HttpResponse(outgraph.decode("utf-8"), content_type="image/svg+xml")
r['Content-Disposition'] = 'attachment; filename={}.svg'.format(model.filename)
return r
elif output_format == "csv":
s = StringIO()
for reac, flux in zip(fba.reacs, fba.flux):
s.write(reac.name)
s.write("\t")
s.write(str(flux))
s.write("\r\n")
r = HttpResponse(s.getvalue(), content_type="text/csv")
r['Content-Disposition'] = 'attachment; filename={}.csv'.format(model.filename)
return r
else:
return HttpResponseBadRequest("Unknown format")
