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 test_reaction(self):
print "\nTest | ReactionObject | GetJson\t",
r = Reaction("Test")
r.reversible = False
r.products = ["A", "B"]
r.substrates = ["C", "D"]
r.stoichiometry = {"A":1, "B":2, "C":3, "D":4}
r.longname_map = {"A":"LongA", "B":"LongB", "C":"LongC", "D":"LongD"}
r.ko = False
expected = '{"reactionid":"Test","reactants":"3 LongC + 4 LongD","products":"1 LongA + 2 LongB","arrow":"===>","ko":false}'
json = Json("object")
r.get_json(json)
result = json.__repr__()
self.assertEquals(expected, result)
def getJson(self):
""" Return a JSON object """
r = Json("object")
r.add_pair("reactionid", self.name)
s = []
for t in self.substrates:
s.append(str(self.stoichiometry[t]) + ' ' + self._get_long_name(t))
r.add_pair("reactants", " + ".join(s))
s = []
for t in self.products:
s.append(str(self.stoichiometry[t]) + ' ' + self._get_long_name(t))
r.add_pair("products", " + ".join(s))
if self.reversible:
r.add_pair("arrow", "<==>")
else:
r.add_pair("arrow", "===>")
ko_label = Json()
ko_label.set_label('"ko"')
ko_value = Json()
if self.ko:
ko_value.set_label("true")
else:
ko_value.set_label("false")
r.add_pair(ko_label, ko_value)
if self.metabolism:
r.add_pair("pathway", self.metabolism)
return r
def setUp(self):
self.json = Json()
class JsonTest(TestCase):
def setUp(self):
self.json = Json()
def test_json_bool(self):
print "\nTest | JsonObject | bool as json value\t",
self.json.set_value(True)
self.assertEquals("true", repr(self.json))
self.json.set_value(False)
self.assertEquals("false", repr(self.json))
def test_json_number(self):
print "\nTest | JsonObject | number as json value\t",
self.json.set_value(2.5)
self.assertEquals("2.5", repr(self.json))
def test_json_obj(self):
print "\nTest | JsonObject | object pairs\t",
self.json.type = "object"
self.json.add_pair("eric", 123)
self.json.add_pair("gretchen", True)
self.json.add_pair("random", "random")
self.assertEquals ("""{"eric":123,"gretchen":true,"random":"random"}""", repr(self.json))
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 newfn(arg):
response = Json("object")
status_label = Json()
status_label.set_label("status")
status_indicate_label = Json()
status_indicate_label.set_label("0")
data_label = Json()
data_label.set_label("data")
response_label = Json()
response_label.set_label("response")
response.add_pair(status_label, status_indicate_label)
response.add_pair(data_label, f(arg))
result = Json("object")
result.add_pair(response_label, response)
return result
def newfn(arg):
tempresult = f(arg)
startRow = int(arg.GET['_startRow'])
endRow = int(arg.GET['_endRow'])
totalRow = len(tempresult.array_container)
if endRow >= totalRow:
endRow = totalRow - 1
response = Json("object")
status_label = Json()
status_label.set_label("status")
status_indicate_label = Json()
status_indicate_label.set_label("0")
response.add_pair(status_label, status_indicate_label)
startrow_label = Json()
startrow_label.set_label("startRow")
startrow_value = Json()
startrow_value.set_label(str(startRow))
response.add_pair(startrow_label, startrow_value)
endrow_label = Json()
endrow_label.set_label("endRow")
endrow_value = Json()
endrow_value.set_label(str(endRow))
response.add_pair(endrow_label, endrow_value)
totalrow_label = Json() # note here might be a bug that those labels are not out
totalrow_label.set_label("totalRows")
totalrow_value = Json()
totalrow_value.set_label(str(totalRow))
response.add_pair(totalrow_label, totalrow_value)
jarray = tempresult.array_container[startRow:endRow + 1]
newjson = Json("array")
newjson.array_container = jarray
data_label = Json()
data_label.set_label("data")
response.add_pair(data_label, newjson)
result = Json("object")
response_label = Json()
response_label.set_label("response")
result.add_pair(response_label, response)
return result
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 _process_pathway_add(input_params, pathway):
public_key = len(pathway.reactions)
ko = input_params['ko']
print "Input ko value is ", ko
reactants = input_params.get("reactants", "")
arrow = input_params['arrow']
products = input_params.get('products')
pathway_name = input_params.get("pathway", "")
if pathway_name == "BIOMASS":
if pathway.reactions.has_key("BIOMASS0"): # Already there
reaction = pathway.reactions["BIOMASS0"]
ret = ""
for i in reaction.substrates:
ret += str(reaction.stoichiometry[i])
ret += " "
ret += i
ret += " + "
pathway.update_pathway("BIOMASS0", False, ret + reactants, arrow, "BIOMASS", "BIOMASS") # update
new_key = "BIOMASS0"
else:
new_key = "BIOMASS0"
pathway.add_pathway("BIOMASS0", ko, reactants, arrow, "BIOMASS", "BIOMASS")
elif pathway_name == "Inflow":
pathway.user_reaction_index += 1
new_key = "Inflow" + str(pathway.user_reaction_index)
reactants = _attach_suffix( reactants, ".ext" )
pathway.register_user_pathway(new_key)
pathway.add_pathway(new_key, ko, reactants, arrow, products, pathway_name)
elif pathway_name == "Outflow":
pathway.user_reaction_index += 1
new_key = "Outflow" + str(pathway.user_reaction_index)
products = _attach_suffix( products, ".ext" )
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_index += 1
new_key = "Heterologous" + str(pathway.user_reaction_index)
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", public_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
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 _process_pathway_update(input_params, pathway):
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)
# Pack results into a JSON object
j = Json("object")
j.add_pair("pk", key) # respect input pathway
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
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")
