def home_view(request):
settings = request.registry.settings
GUILDifier.set_parameters(settings)
return {
"species_list": BIANAQuery.SPECIES_NAMES,
"species_to_value": BIANAQuery.SPECIES_NAME_TO_VALUE
}
def __init__(self, config_file):
config = ConfigParser.SafeConfigParser()
config.read(config_file)
self.settings = dict(config._defaults)
#self.settings = self.create_settings_dict(db_host, db_user, db_pass, db_name, unification_protocol, guild_excecutable, data_dir, cluster_script, queue_name)
GUILDifier.set_parameters(self.settings)
return
def query_result_view(request):
settings = request.registry.settings
GUILDifier.set_parameters(settings)
if request.method == 'POST':
if request.POST.get('keywords') or request.POST.get('user_entity_ids'):
keywords = request.POST['keywords']
species = request.POST['species']
user_entity_ids = None
genes = None
ue_ids = []
try:
query = BIANAQuery(settings)
except ValueError, e:
if e.message == "biana":
request.session.flash(
'Internal server error, please reload the page and and try again! Contact to the webmaster if the problem persists.'
)
return HTTPFound(location=request.route_url('home'))
#query = BIANAQuery(settings)
#query.reconnect()
try:
query = BIANAQuery(settings)
except ValueError, e:
if e.message == "biana":
request.session.flash(
'Internal server error, please reload the page and and try again! Contact to the webmaster if the problem persists.'
)
return HTTPFound(
location=request.route_url('home'))
if request.POST.get('user_entity_ids'):
user_entity_ids = map(
lambda x: str(x.strip("'\"")),
request.POST['user_entity_ids'].strip("[]").split(", "))
genes = request.POST['genes'].split()
print "added genes:", genes
try:
values, ue_ids, ue_ids_in_network = query.get_associated_user_entities(
keywords, species, user_entity_ids, genes)
if values is None:
request.session.flash('No match for the query!')
return HTTPFound(location=request.route_url('home'))
#values = [('410664',), ('108201',), ('409022',)]
values_in_network = []
values_not_in_network = []
for val in values:
if val[0].endswith("disabled/>"):
values_not_in_network.append(val)
else:
values_in_network.append(val)
except ValueError, e:
# None of the added genes are found
if e.message == "biana":
request.session.flash(
'No match for genes in the query! You can go back and try with other gene symbols.'
)
return HTTPFound(location=request.route_url('home'))
def retrieve_results_view(request):
settings = request.registry.settings
GUILDifier.set_parameters(settings)
if request.method == 'POST':
#!
if request.POST.get('session_id1') and request.POST.get('session_id2'):
session_id = request.POST["session_id1"]
session_id2 = request.POST["session_id2"]
try:
result = GUILDifier(session_id,
species=None,
settings=settings)
result2 = GUILDifier(session_id2,
species=None,
settings=settings)
except: # job(s) not finished / session does not exist
request.session.flash('Provided job id is not valid!')
return HTTPFound(location=request.route_url('home'))
ready_flag = result.create_output_file()
ready_flag2 = result2.create_output_file()
if (ready_flag is None or ready_flag == False) or (
ready_flag2 is None
or ready_flag2 == False): # Error / still running
request.session.flash('Provided job id is not valid!')
return HTTPFound(location=request.route_url('home'))
else:
return HTTPFound(
location=request.route_url('result_overlap',
session_id1=session_id,
session_id2=session_id2,
n_start="1",
n_end="20",
p_top="1"))
if request.POST.get('session_id'):
session_id = request.POST["session_id"]
try:
result = GUILDifier(session_id,
species=None,
settings=settings)
except: # species.txt does not exits - job not finished
request.session.flash('Provided job id is not valid!')
return HTTPFound(location=request.route_url('home'))
ready_flag = result.create_output_file()
if ready_flag is None or ready_flag == False: # Error / still running
request.session.flash('Provided job id is not valid!')
return HTTPFound(location=request.route_url('home'))
else:
return HTTPFound(
location=request.route_url('result',
session_id=session_id,
n_start="1",
n_end="20",
p_top="1"))
request.session.flash('No job id is provided!')
return HTTPFound(location=request.route_url('home'))
def scoring_results_overlap_view(request):
settings = request.registry.settings
GUILDifier.set_parameters(settings)
session_id = request.matchdict["session_id1"]
session_id2 = request.matchdict["session_id2"]
result = GUILDifier(session_id, species=None, settings=settings)
result2 = GUILDifier(session_id2, species=None, settings=settings)
ready_flag = result.create_output_file()
ready_flag2 = result2.create_output_file()
if ready_flag is None or ready_flag2 is None: # Error
request.session["id"] = session_id
request.session["species"] = result.species
request.session["message"] = "error/contact webmaster"
return HTTPFound(location=request.route_url('status'))
elif ready_flag and ready_flag2: # Finished
if "id" in request.session:
del request.session["id"]
del request.session["species"]
del request.session["message"]
n_start = int(request.matchdict["n_start"])
n_end = int(request.matchdict["n_end"])
p_top = request.matchdict["p_top"]
parser = GUILDScoreParser(result.output_file)
parser2 = GUILDScoreParser(result2.output_file)
values, values_stat = parser.overlap_with(parser2, result.n_node,
result.species, int(p_top))
return dict(session_id1=session_id,
session_id2=session_id2,
species=BIANAQuery.TAX_ID_TO_SPECIES_NAME[result.species],
n_start=n_start,
n_end=min(n_end, len(values)),
n_node=len(values),
values=values[(n_start - 1):n_end],
values_stat=values_stat,
output_file_url=result.output_file_url,
seed_file_url=result.seed_file_url,
network_file_url=result.network_file_url,
network_json=result.get_network_json(p_top),
subnetwork_file_url=result.subnetwork_file_url + "." +
p_top,
drug_file_url=result.drug_file_url + "." + p_top,
not_last_page=n_end < result.n_node,
p_top=p_top,
top1=p_top == "1",
top5=p_top == "5",
top10=p_top == "10",
human=result.species == "9606")
request.session["id"] = session_id
request.session["species"] = result.species
request.session["message"] = "queued/running"
return HTTPFound(location=request.route_url('status'))
def run_scoring_method_view(request):
settings = request.registry.settings
GUILDifier.set_parameters(settings)
if request.method == 'POST':
#print request.POST
user_entity_ids = []
for user_entity_id in request.POST:
try:
int(user_entity_id)
except:
continue
user_entity_ids.append(user_entity_id)
print user_entity_ids
session_id = str(uuid.uuid4())
print "Session:", session_id
species = request.POST["species"]
scoring_parameters = {}
if "netscore" in request.POST:
scoring_parameters["ns"] = [
int(request.POST["repetitionSelector"]),
int(request.POST["iterationSelector"])
]
if "netzcore" in request.POST:
scoring_parameters["nz"] = [
int(request.POST["repetitionZelector"])
]
if "netshort" in request.POST:
scoring_parameters["nd"] = None
result = GUILDifier(session_id, species, settings)
result.prepare(user_entity_ids)
result.score(scoring_parameters)
return dict(session_id=session_id,
species=BIANAQuery.TAX_ID_TO_SPECIES_NAME[species],
seed_file_url=result.seed_file_url,
network_file_url=result.network_file_url,
message="submitted",
submitted=True)
elif "id" in request.session:
session_id = request.session["id"]
species = request.session["species"]
message = request.session["message"]
result = GUILDifier(session_id, species, settings)
return dict(session_id=session_id,
species=BIANAQuery.TAX_ID_TO_SPECIES_NAME[species],
seed_file_url=result.seed_file_url,
network_file_url=result.network_file_url,
message=message,
submitted=False)
request.session.flash('Invalid session, please start over!')
return HTTPFound(location=request.route_url('home'))
def results_ajax(request):
settings = request.registry.settings
GUILDifier.set_parameters(settings)
session_id = request.matchdict["session_id"]
n_start = int(request.matchdict["n_start"])
n_end = int(request.matchdict["n_end"])
result = GUILDifier(session_id, species = None, settings = settings)
result.create_output_file()
parser = GUILDScoreParser(result.output_file)
values, ueids = parser.get_user_entity_info_and_scores(n_start, n_end, result.species) #!
return dict(n_start = n_start,
n_end = n_end,
n_node = result.n_node,
values = [ ";".join(map(lambda x: str(x), value)) for value in values ])
def scoring_results_view(request):
settings = request.registry.settings
GUILDifier.set_parameters(settings)
session_id = request.matchdict["session_id"]
result = GUILDifier(session_id, species=None, settings=settings)
ready_flag = result.create_output_file()
if ready_flag is None: # Error
request.session["id"] = session_id
request.session["species"] = result.species
request.session["message"] = "error/contact webmaster"
return HTTPFound(location=request.route_url('status'))
elif ready_flag: # Finished
if "id" in request.session:
del request.session["id"]
del request.session["species"]
del request.session["message"]
n_start = int(request.matchdict["n_start"])
n_end = int(request.matchdict["n_end"])
p_top = request.matchdict["p_top"]
parser = GUILDScoreParser(result.output_file)
values = parser.get_user_entity_info_and_scores(
n_start, n_end, result.species)
return dict(session_id=session_id,
species=BIANAQuery.TAX_ID_TO_SPECIES_NAME[result.species],
n_start=n_start,
n_end=n_end,
n_node=result.n_node,
values=values,
output_file_url=result.output_file_url,
seed_file_url=result.seed_file_url,
network_file_url=result.network_file_url,
network_json=result.get_network_json(p_top),
subnetwork_file_url=result.subnetwork_file_url + "." +
p_top,
drug_file_url=result.drug_file_url + "." + p_top,
not_last_page=n_end < result.n_node,
top1=p_top == "1",
top5=p_top == "5",
top10=p_top == "10",
human=result.species == "9606")
request.session["id"] = session_id
request.session["species"] = result.species
request.session["message"] = "queued/running"
return HTTPFound(location=request.route_url('status'))
def results_overlap_ajax(request):
settings = request.registry.settings
GUILDifier.set_parameters(settings)
session_id = request.matchdict["session_id1"]
session_id2 = request.matchdict["session_id2"]
n_start = int(request.matchdict["n_start"])
n_end = int(request.matchdict["n_end"])
p_top = request.matchdict["p_top"]
result = GUILDifier(session_id, species = None, settings = settings)
result.create_output_file()
parser = GUILDScoreParser(result.output_file)
result2 = GUILDifier(session_id2, species = None, settings = settings)
result2.create_output_file()
parser2 = GUILDScoreParser(result2.output_file)
values, values_stat, values_chart, ueids = parser.overlap_with(parser2, result.n_node, result.species, int(p_top))
return dict(n_start = n_start,
n_end = n_end,
n_node = result.n_node,
p_top = p_top,
values = [ ";".join(map(lambda x: str(x), value)) for value in values[(n_start-1):n_end] ])
def genes_to_scores(self, query_ids, species, parameters):
"""
parameters containing scoring parameters
"""
#g = get_guildify()
settings = self.get_settings()
GUILDifier.set_parameters(settings)
user_entity_ids = []
for user_entity_id in query_ids:
try:
int(user_entity_id)
except:
continue
user_entity_ids.append(user_entity_id)
print user_entity_ids
session_id = str(uuid.uuid4())
print "Session:", session_id
scoring_parameters = {}
if "netscore" in parameters:
scoring_parameters["ns"] = [
int(parameters["repetitionSelector"]),
int(parameters["iterationSelector"])
]
if "netzcore" in parameters:
scoring_parameters["nz"] = [int(parameters["repetitionZelector"])]
if "netshort" in parameters:
scoring_parameters["nd"] = None
result = GUILDifier(session_id, species, settings)
result.prepare(user_entity_ids)
result.score(scoring_parameters)
return dict(session_id=session_id,
species=BIANAQuery.TAX_ID_TO_SPECIES_NAME[species],
seed_file_url=result.seed_file_url,
network_file_url=result.network_file_url,
message="submitted",
submitted=True)