def user_summary(request):
u = request.user
plist = Profile.objects.filter(user = u, status="submitted")
result = ""
r = Json("array")
for p in plist:
ri = Json("object")
ri.add_pair("date", str(p.submitted_date))
ri.add_pair("model", str(p.name))
ri.add_pair("type", str(p.model_type))
ri.add_pair("status", str(p.status))
r.add_item(ri)
result += "{ response: { status : 0, startRows: 0 , endRow: "
if (len(plist) > 0):
result += str(len(plist) - 1)
else:
result += "0"
result += " , totalRows: "
result += str(len(plist))
result += " , data :"
result += repr(r)
result += "} } "
q = request.GET
nq = dict(q)
result = get_callback(nq) + "(" + result + ")"
return HttpResponse(content = result, status = 200, content_type = "text/html")
def user_summary(request):
u = request.user
plist = Profile.objects.filter(user=u, status="submitted")
result = ""
r = Json("array")
for p in plist:
ri = Json("object")
ri.add_pair("date", str(p.submitted_date))
ri.add_pair("model", str(p.name))
ri.add_pair("type", str(p.model_type))
ri.add_pair("status", str(p.status))
r.add_item(ri)
result += "{ response: { status : 0, startRows: 0 , endRow: "
if (len(plist) > 0):
result += str(len(plist) - 1)
else:
result += "0"
result += " , totalRows: "
result += str(len(plist))
result += " , data :"
result += repr(r)
result += "} } "
q = request.GET
nq = dict(q)
result = get_callback(nq) + "(" + result + ")"
return HttpResponse(content=result, status=200, content_type="text/html")
def _process_sv_fetch(pathway): # Merged
sv = pathway.get_sv()
ret = Json("array")
for name in sv:
j = Json()
j.add_pair("c", pathway.get_long_name(name))
j.add_pair("r", ''.join(sv[name]) + " = 0")
ret.add_item(j)
return ret
def _process_object_fetch(pathway):
weights = pathway.get_objective_weights()
ret = Json("array")
public_key = 1
for name in pathway.reactions:
j = Json()
j.add_pair("pk", public_key)
public_key += 1
j.add_pair("r", name)
j.add_pair("w", str(weights[name]))
ret.add_item(j)
return ret
def _process_pathway_fetch(pathway):
public_key = 0
ret = Json("array")
for rname in pathway.reactions:
r = pathway.reactions[rname]
if not r.products or not r.substrates:
continue
json = r.getJson()
json.add_pair("pk", public_key)
public_key += 1
ret.add_item(json)
return ret
def _process_boundary_fetch(pathway):
boundarys = pathway.get_bounds()
ret = Json("array")
public_key = 0
for name in boundarys:
j = Json()
j.add_pair("pk", public_key)
public_key += 1
j.add_pair("r", name)
j.add_pair("l", str(boundarys[name][0]))
j.add_pair("u", str(boundarys[name][1]))
ret.add_item(j)
return ret
def _process_pathway_info(input_params, pathway, cname):
t = map(str, pathway.statistics())
r0 = Json("object")
r0.add_pair("name" , "Name of the pathway")
r0.add_pair("value", cname)
r1 = Json("object")
r1.add_pair("name" , "Name of the organism")
r1.add_pair("value", pathway.name)
r2 = Json("object")
r2.add_pair("name", "Number of all genes/orthologs")
r2.add_pair("value", t[0])
r3 = Json("object")
r3.add_pair("name", "Number of annotated genes/orthologs")
r3.add_pair("value", t[1])
r4 = Json("object")
r4.add_pair("name", "Number of all pathways")
r4.add_pair("value", t[2])
r5 = Json("object")
r5.add_pair("name", "Number of active pathways")
r5.add_pair("value", t[3])
r = Json("array")
r.add_item(r0)
r.add_item(r1)
r.add_item(r2)
r.add_item(r3)
r.add_item(r4)
r.add_item(r5)
return r
def new_get_json(method, input_params, pathway):
r = ""
if method == "pathway_add": # merged
""" Input parameters: pathway, products, reactants"""
ko = input_params['ko']
reactants = input_params.get("reactants", "")
arrow = input_params['arrow']
products = input_params.get('products')
pathway_name = input_params.get("pathway", "")
new_key = ''
# pk = 0
if pathway_name == "BIOMASS":
""" If user gives us biomass, we have to make sure that
the left side of the equation is updated
reactants --> BIOMASS
"""
# 1. Check if we can find a metabolism that contains USER:BIOMASS pathway
for m in pathway.metabolism:
if m.name == "USER:BIOMASS" and len(m.reactions) > 0:
new_key = m.reactions.keys()[0]
break
# 2.1. If there is already a biomass, we have to update its reactant list
if len(new_key) > 0:
reaction = pathway.reactions[new_key]
ret = ""
for i in reaction.substrates:
ret += str(reaction.stoichiometry[i])
ret += " "
ret += i
ret += " + "
pathway.add_pathway(new_key, False, ret + reactants, arrow,
"BIOMASS", "BIOMASS")
else: # 2.2. If there is no existing BIOMASS pathway, add a new BIOMASS
pathway.user_reaction += 1
new_key = "Biomass" + str(pathway.user_reaction)
pathway.add_pathway(new_key, ko, reactants, arrow, products,
pathway_name)
elif pathway_name == "Inflow":
pathway.user_reaction += 1
new_key = "Inflow" + str(pathway.user_reaction)
pathway.register_user_pathway(new_key)
pathway.add_pathway(new_key, ko, reactants, arrow, products,
pathway_name)
elif pathway_name == "Outflow":
pathway.user_reaction += 1
new_key = "Outflow" + str(pathway.user_reaction)
pathway.register_user_pathway(new_key)
pathway.add_pathway(new_key, ko, reactants, arrow, products,
pathway_name)
elif pathway_name == "Heterologous Pathways":
pathway.user_reaction += 1
new_key = "Heterologous" + str(pathway.user_reaction)
pathway.add_pathway(new_key, ko, reactants, arrow, products,
pathway_name)
else:
pass
j = Json("object")
tpk = digital_pattern.match(new_key)
pk = int(tpk.group(1))
j.add_pair("pk", 100000 + pk)
j.add_pair("reactionid", new_key)
j.add_pair("ko", ko)
j.add_pair("reactants", reactants)
if arrow == '1':
j.add_pair("arrow", "<==>")
else:
j.add_pair("arrow", "===>")
j.add_pair("products", products)
j.add_pair("pathway", pathway_name)
return j
elif method == "pathway_update": # merged
key = input_params["pk"]
new_key = input_params["reactionid"]
ko = input_params['ko']
reactants = input_params.get("reactants", "")
arrow = input_params['arrow']
if arrow == "<==>":
arrow = '1'
else:
arrow = '0'
products = input_params.get('products')
pathway_name = input_params.get("pathway", "")
pathway.update_pathway(new_key, ko, reactants, arrow, products,
pathway_name)
j = Json("object")
j.add_pair("pk", key)
j.add_pair("reactionid", new_key)
j.add_pair("ko", ko)
j.add_pair("reactants", reactants)
if arrow == '1':
j.add_pair("arrow", "<==>")
else:
j.add_pair("arrow", "===>")
j.add_pair("products", products)
j.add_pair("pathway", pathway_name)
return j
elif method == "pathway_info": # merged
t = map(str, pathway.statistics())
r1 = Json("object")
r1.add_pair("name", "Name of the pathway")
r1.add_pair("value", pathway.name)
r2 = Json("object")
r2.add_pair("name", "Number of all genes/orthologs")
r2.add_pair("value", t[0])
r3 = Json("object")
r3.add_pair("name", "Number of annotated genes/orthologs")
r3.add_pair("value", t[1])
r4 = Json("object")
r4.add_pair("name", "Number of all pathways")
r4.add_pair("value", t[2])
r5 = Json("object")
r5.add_pair("name", "Number of active pathways")
r5.add_pair("value", t[3])
r = Json("array")
r.add_item(r1)
r.add_item(r2)
r.add_item(r3)
r.add_item(r4)
r.add_item(r5)
elif method == "user_obj_update": # changed
key = str(input_params["pk"])
if len(key) < 5:
new_key = 'R' + '0' * (5 - len(key)) + key
else:
new_key = 'R' + key
#w = input_params["w"][0].encode('ascii', 'ignore')
w = input_params["w"]
weight = float(w)
pathway.objective[new_key] = weight
r = Json()
r.add_pair("pk", key)
r.add_pair("r", new_key)
r.add_pair("w", str(weight))
return r
elif method == "user_obj_fetch": # changed
objective_json = pathway.json_objective()
return objective_json
elif method == "model_sv":
""" Output the SV=0 equations """
sv = pathway.json_sv()
# print "In Model SV, Now SV is", len(pathway.sv)
t = len(pathway.sv)
input_params['startRows'] = '0'
input_params['endRow'] = str(t - 1)
input_params['totalRows'] = str(t) # later get_header will use it
return "[" + sv + "]"
elif method == "model_bound_fetch":
bound = pathway.get_bounds_as_json()
# print "In Model bound, Now bound is", len(pathway.bound)
t = len(pathway.reactions)
input_params['startRows'] = '0'
input_params['endRow'] = str(t - 1)
input_params['totalRows'] = str(t) # later get_header will use it
return "[" + bound + "]"
elif method == "model_bound_update":
bound = pathway.get_bounds()
key = str(input_params["pk"][0])
# print "key is", key
if len(key) < 5:
new_key = 'R' + '0' * (5 - len(key)) + key
else:
new_key = 'R' + key
# print new_key
lb = float(input_params["l"][0].encode('ascii', 'ignore'))
ub = float(input_params["u"][0].encode('ascii', 'ignore'))
# print lb, ub
bound[new_key][0] = lb
bound[new_key][1] = ub
r += '"pk":"' + key + '",'
r += '"r":"' + new_key + '",'
r += '"l":"' + str(lb) + '",'
r += '"u":"' + str(ub) + '"'
else:
r = ""
pass
return r
def new_get_json(method, input_params, pathway):
r = ""
if method == "pathway_add": # merged
""" Input parameters: pathway, products, reactants"""
ko = input_params['ko']
reactants = input_params.get("reactants", "")
arrow = input_params['arrow']
products = input_params.get('products')
pathway_name = input_params.get("pathway", "")
new_key = ''
# pk = 0
if pathway_name == "BIOMASS":
""" If user gives us biomass, we have to make sure that
the left side of the equation is updated
reactants --> BIOMASS
"""
# 1. Check if we can find a metabolism that contains USER:BIOMASS pathway
for m in pathway.metabolism:
if m.name == "USER:BIOMASS" and len(m.reactions) > 0:
new_key = m.reactions.keys()[0]
break
# 2.1. If there is already a biomass, we have to update its reactant list
if len(new_key) > 0:
reaction = pathway.reactions[new_key]
ret = ""
for i in reaction.substrates:
ret += str(reaction.stoichiometry[i])
ret += " "
ret += i
ret += " + "
pathway.add_pathway(new_key, False, ret + reactants, arrow, "BIOMASS", "BIOMASS")
else: # 2.2. If there is no existing BIOMASS pathway, add a new BIOMASS
pathway.user_reaction += 1
new_key = "Biomass" + str(pathway.user_reaction)
pathway.add_pathway(new_key, ko, reactants, arrow, products, pathway_name)
elif pathway_name == "Inflow":
pathway.user_reaction += 1
new_key = "Inflow" + str(pathway.user_reaction)
pathway.register_user_pathway(new_key)
pathway.add_pathway(new_key, ko, reactants, arrow, products, pathway_name)
elif pathway_name == "Outflow":
pathway.user_reaction += 1
new_key = "Outflow" + str(pathway.user_reaction)
pathway.register_user_pathway(new_key)
pathway.add_pathway(new_key, ko, reactants, arrow, products, pathway_name)
elif pathway_name == "Heterologous Pathways":
pathway.user_reaction += 1
new_key = "Heterologous" + str(pathway.user_reaction)
pathway.add_pathway(new_key, ko, reactants, arrow, products, pathway_name)
else:
pass
j = Json("object")
tpk = digital_pattern.match(new_key)
pk = int(tpk.group(1))
j.add_pair("pk", 100000 + pk)
j.add_pair("reactionid", new_key)
j.add_pair("ko", ko)
j.add_pair("reactants", reactants)
if arrow == '1':
j.add_pair("arrow", "<==>")
else:
j.add_pair("arrow", "===>")
j.add_pair("products", products)
j.add_pair("pathway", pathway_name)
return j
elif method == "pathway_update": # merged
key = input_params["pk"]
new_key = input_params["reactionid"]
ko = input_params['ko']
reactants = input_params.get("reactants", "")
arrow = input_params['arrow']
if arrow == "<==>":
arrow = '1'
else:
arrow = '0'
products = input_params.get('products')
pathway_name = input_params.get("pathway", "")
pathway.update_pathway(new_key, ko, reactants, arrow, products, pathway_name)
j = Json("object")
j.add_pair("pk", key)
j.add_pair("reactionid", new_key)
j.add_pair("ko", ko)
j.add_pair("reactants", reactants)
if arrow == '1':
j.add_pair("arrow", "<==>")
else:
j.add_pair("arrow", "===>")
j.add_pair("products", products)
j.add_pair("pathway", pathway_name)
return j
elif method == "pathway_info": # merged
t = map(str, pathway.statistics())
r1 = Json("object")
r1.add_pair("name" , "Name of the pathway")
r1.add_pair("value", pathway.name)
r2 = Json("object")
r2.add_pair("name", "Number of all genes/orthologs")
r2.add_pair("value", t[0])
r3 = Json("object")
r3.add_pair("name", "Number of annotated genes/orthologs")
r3.add_pair("value", t[1])
r4 = Json("object")
r4.add_pair("name", "Number of all pathways")
r4.add_pair("value", t[2])
r5 = Json("object")
r5.add_pair("name", "Number of active pathways")
r5.add_pair("value", t[3])
r = Json("array")
r.add_item(r1)
r.add_item(r2)
r.add_item(r3)
r.add_item(r4)
r.add_item(r5)
elif method == "user_obj_update": # changed
key = str(input_params["pk"])
if len(key) < 5:
new_key = 'R' + '0' * (5 - len(key)) + key
else:
new_key = 'R' + key
#w = input_params["w"][0].encode('ascii', 'ignore')
w = input_params["w"]
weight = float(w)
pathway.objective[new_key] = weight
r = Json()
r.add_pair("pk", key)
r.add_pair("r", new_key)
r.add_pair("w", str(weight))
return r
elif method == "user_obj_fetch": # changed
objective_json = pathway.json_objective()
return objective_json
elif method == "model_sv":
""" Output the SV=0 equations """
sv = pathway.json_sv()
# print "In Model SV, Now SV is", len(pathway.sv)
t = len(pathway.sv)
input_params['startRows'] = '0'
input_params['endRow'] = str(t - 1)
input_params['totalRows'] = str(t) # later get_header will use it
return "[" + sv + "]"
elif method == "model_bound_fetch":
bound = pathway.get_bounds_as_json()
# print "In Model bound, Now bound is", len(pathway.bound)
t = len(pathway.reactions)
input_params['startRows'] = '0'
input_params['endRow'] = str(t - 1)
input_params['totalRows'] = str(t) # later get_header will use it
return "[" + bound + "]"
elif method == "model_bound_update":
bound = pathway.get_bounds()
key = str(input_params["pk"][0])
# print "key is", key
if len(key) < 5:
new_key = 'R' + '0' * (5 - len(key)) + key
else:
new_key = 'R' + key
# print new_key
lb = float(input_params["l"][0].encode('ascii', 'ignore'))
ub = float(input_params["u"][0].encode('ascii', 'ignore'))
# print lb, ub
bound[new_key][0] = lb
bound[new_key][1] = ub
r += '"pk":"' + key + '",'
r += '"r":"' + new_key + '",'
r += '"l":"' + str(lb) + '",'
r += '"u":"' + str(ub) + '"'
else:
r = ""
pass
return r