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 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 = Metabolism(StringIO(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 = Metabolism(StringIO(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.obj = []
org.obj.append(
[obj_reac.id, "1" if obj["maximize"] else "-1"])
except ValueError as e:
raise BadRequest("Model error: " + str(e))
if len(changes) == 0:
raise BadRequest("Model not saved: No changes found")
sio = StringIO()
org.write_sbml(fileout=sio)
Revision(model=model,
content=sio.getvalue(),
changes=dict(changes=changes, objectives=objectives),
reason=summary).save()
return {}
def simulate(request, pk):
if not all(x in request.POST for x in [
"changes", "objectives", "design_objectives", "target_reactions",
"display", "auto_flux", "type"
]):
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 = Metabolism(StringIO(revision.content))
try:
changes = json.loads(request.POST["changes"])
objectives = json.loads(request.POST["objectives"])
design_objectives = json.loads(request.POST["design_objectives"])
target_reactions = json.loads(request.POST["target_reactions"])
display = json.loads(request.POST["display"])
auto_flux = json.loads(request.POST["auto_flux"])
simtype = json.loads(request.POST["type"])
except ValueError:
return HttpResponseBadRequest("Invalid JSON data")
try:
auto_flux = bool(auto_flux)
except ValueError:
return HttpResponseBadRequest("Invalid data type")
if str(simtype) not in ["fba", "mba", "sa"]:
return HttpResponseBadRequest(
"Unsupported simulation type: {}".format(simtype))
try:
apply_commandlist(org, changes)
org = Metabolism(StringIO(revision.content))
changes = compress_command_list(changes)
apply_commandlist(org, changes)
if not objectives:
raise ValueError("No objective specified")
org.obj = []
for obj in objectives:
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.obj.append([obj["name"], "1" if obj["maximize"] else "0"])
if simtype == "mba" or simtype == "sa":
org.design_obj = []
for obj in design_objectives:
obj_reac = org.get_reaction(obj["name"])
if obj_reac is None:
raise ValueError("Design objective not in model: " +
obj["name"])
if obj_reac.disabled:
return HttpResponseBadRequest(
"Design objective disabled: " + obj_reac.name)
org.design_obj.append(
[obj["name"], "1" if obj["maximize"] else "0"])
org.target_reactions = []
if simtype == "sa":
for obj in target_reactions:
obj_reac = org.get_reaction(obj["name"])
if obj_reac is None:
raise ValueError("Target reaction not in model: " +
obj["name"])
if obj_reac.disabled:
return HttpResponseBadRequest(
"Target reaction disabled: " + obj_reac.name)
org.target_reactions.append(
[obj["name"], "1" if obj["maximize"] else "0"])
except ValueError as e:
return HttpResponseBadRequest("Model error: " + str(e))
try:
fba = org.fba()
except ValueError as e:
return HttpResponseBadRequest("FBA error: " + str(e))
if simtype == "fba":
if dry_run:
return HttpResponse(json.dumps({"solution": fba.get_status()}),
content_type="application/json")
full_g, nodeIDs = calc_reactions(org, fba)
display = list(
filter(lambda x: len(x) > 0 and org.has_reaction(x), display))
dflux = {}
for reac, flux in zip(map(lambda x: x, fba.reacs), fba.flux):
dflux[reac.id] = 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"]["id"],
full_eg.edges())
# Get fluxes of "edges"
flux = []
for reac in set(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)
# Work around a bug in nx 1.11 breaking nx.to_agraph function
graph = nx.drawing.nx_agraph.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": None,
"graphstr": str(graph.to_string()),
"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")
elif simtype == "mba":
# Determine optimal steps
obj = org.obj[:]
dobj = org.design_obj[:]
# Absolute
design_result = [["x"], [dobj[0][0]]]
#design_result[0] += [0, 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.1]
sim_result = fba.design_fba()
#dflux = [list(str(x[fba.reac_names.index(obj[0][0])]) for x in sim_result),
# list(x[fba.reac_names.index(dobj[0][0])] for x in sim_result)]
dflux = list([x[0]] for x in sim_result)
for lst, sim_res in zip(dflux, sim_result):
lst.append({})
for name, flux in zip(fba.reac_names, sim_res[1]):
lst[1][name] = flux
graph = [["x"], [dobj[0][0]]]
for d in dflux:
graph[0].append(d[0])
graph[1].append(d[1][dobj[0][0]])
if output_format == "json":
return HttpResponse(json.dumps({
"solution": fba.get_status(),
"flux": dflux,
"graph": graph
}),
content_type="application/json")
else:
return HttpResponseBadRequest("Unknown format")
elif simtype == "sa":
# Percentage
# 1. WT conditions
obj = org.obj[:]
dobj = org.design_obj[:]
tobj = target_reactions[0]["name"]
obj_r = org.get_reaction(obj[0][0])
target = org.get_reaction(tobj)
target_flux = fba.flux[fba.reac_names.index(target.id)]
design_result = [["x"], [obj[0][0]], [dobj[0][0]], ["Yield"]]
dflux = list([x] for x in [1.0, 0.8, 0.6, 0.4, 0.2, 0.0])
# 2. Limit target reaction
for i, limit in enumerate([1.0, 0.8, 0.6, 0.4, 0.2, 0.0]):
# Limit to a % of the target flux
target.constraint = (target.constraint[0], target_flux * limit)
# Optimize limited growth
org.obj = obj
fba = org.fba()
growth = fba.Z
# Optimize production
obj_r.constraint = (growth, growth)
org.obj = dobj
fba = org.fba()
production = fba.Z
# Reset production constraint
obj_r.constraint = (0, None)
design_result[0].append(str(int(limit * 100)) + "%")
design_result[1].append(round(growth, 4))
design_result[2].append(round(production, 4))
design_result[3].append(round(growth * production, 4))
dflux[i].append({})
for reac, flux in zip(map(lambda x: x.name, fba.reacs), fba.flux):
dflux[i][-1][reac] = flux
dflux.append(target_flux)
if output_format == "json":
return HttpResponse(json.dumps({
"solution": fba.get_status(),
"flux": dflux,
"graph": design_result
}),
content_type="application/json")
else:
return HttpResponseBadRequest("Unknown format")
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")