def persist(req):
jsondata = req.REQUEST.get("data")
initdata = json.loads(jsondata)
logger.debug("Persisting")
logger.debug( "%s" % (initdata) )
fileutil.writeFile("test1", jsondata)
try:
if(initdata['_id'][:4] == 'conn'):
con = Connection(initdata)
con.save()
return SmartResponse(con._id, req)
else:
network = Network(initdata)
network.save()
index(network.name, network)
return SmartResponse(network._id, req)
except Error as e:
logger.error("Error saving data: %s" %traceback.format_exc())
return SmartResponse(e, req)
def persist(req):
jsondata = req.REQUEST.get("data")
initdata = json.loads(jsondata)
logger.debug("Persisting")
logger.debug("%s" % (initdata))
fileutil.writeFile("test1", jsondata)
try:
if (initdata['_id'][:4] == 'conn'):
con = Connection(initdata)
con.save()
return SmartResponse(con._id, req)
else:
network = Network(initdata)
network.save()
index(network.name, network)
return SmartResponse(network._id, req)
except Error as e:
logger.error("Error saving data: %s" % traceback.format_exc())
return SmartResponse(e, req)
def importEdges(filename=None):
"""
import edges, one pair per line
Edge property: - no direction, -> left to right, <- right to left
"""
filename = filename or r'C:\work\caida\Dropbox\precon\engineering\Contents\GBM_BN-Massaged.csv'
# add a network
n = Network.findOne({'name': "GBM Predicted Tumor Network"}) or Network()
n.name = "GBM Predicted Tumor Network"
n.group = "predicted"
n.owner = 'precon'
n.save()
col = mongo.db()['entity']
count = 0
now = time.time()
ec = mongo.getCollection('edge')
with open(filename) as f:
content = f.read()
for line in content.split('\n'):
doc = {}
line = line.strip()
pos = line.find("///")
if pos > 0:
line = line[0:pos].strip()
doc['comment'] = line[pos:]
items = line.split("->")
if (len(items) == 1): items = line.split("<-")
if (len(items) == 1): items = line.split(" - ")
if (len(items) == 1):
error("Ignore invalid line: [%s]" % line)
continue
count += 1
if (count < 8378): continue
tmp = []
tmp.append(items[0].lower().strip())
tmp.append(items[1].lower().strip())
entities = ['', '']
print "!!! %d " % (col.find({'symbol': {'$in': tmp}}).count())
for r in col.find({'symbol': {'$in': tmp}}):
if (r['symbol'] == tmp[0]):
entities[0] = Entity(r)
if (r['symbol'] == tmp[1]):
entities[1] = Entity(r)
if (len(entities) != 2):
raise "Invalid nodes %s, continue" % entities
node1 = Node.findOne({'network': n._id, 'entity': entities[0]._id})
if not node1:
node1 = Node({'network': n._id}, entities[0])
node1.save()
node2 = Node.findOne({'network': n._id, 'entity': entities[1]._id})
if not node2:
node2 = Node({'network': n._id}, entities[1])
node2.save()
con = Connection()
con._id = "conn_%s_%s" % (tmp[0], tmp[1])
con.nodes = [node1._id, node2._id]
con.entities = [entities[0]._id, entities[1]._id]
con.type = 'predicted'
con.network = n._id
con.label = ""
con.save()
print "Saving connection %d %s" % (count, con._id)
finish = time.time()
print "Imported %d edges, time elpased %d seconds" % (count, finish - now)
def importEdges(filename=None):
"""
import edges, one pair per line
Edge property: - no direction, -> left to right, <- right to left
"""
filename = filename or r'C:\work\caida\Dropbox\precon\engineering\Contents\GBM_BN-Massaged.csv'
# add a network
n = Network.findOne({'name': "GBM Predicted Tumor Network"}) or Network()
n.name = "GBM Predicted Tumor Network"
n.group = "predicted"
n.owner = 'precon'
n.save()
col = mongo.db()['entity']
count = 0
now = time.time()
ec = mongo.getCollection('edge')
with open(filename) as f:
content = f.read()
for line in content.split('\n'):
doc = {}
line = line.strip()
pos = line.find("///")
if pos>0:
line = line[0:pos].strip()
doc['comment'] = line[pos:]
items = line.split("->")
if (len(items) == 1): items = line.split("<-")
if (len(items) == 1): items = line.split(" - ")
if (len(items) == 1):
error("Ignore invalid line: [%s]" %line)
continue
count+=1
if(count<8378): continue
tmp =[]
tmp.append( items[0].lower().strip())
tmp.append( items[1].lower().strip())
entities = ['','']
print "!!! %d " %( col.find({'symbol': {'$in': tmp } }).count() )
for r in col.find({'symbol': {'$in': tmp } }):
if(r['symbol'] == tmp[0]):
entities[0] = Entity(r)
if(r['symbol'] == tmp[1]):
entities[1] = Entity(r)
if(len(entities)!=2 ):
raise "Invalid nodes %s, continue" % entities
node1 = Node.findOne({'network': n._id, 'entity': entities[0]._id})
if not node1:
node1 = Node({'network':n._id}, entities[0])
node1.save()
node2 = Node.findOne({'network': n._id, 'entity': entities[1]._id})
if not node2:
node2 = Node({'network':n._id}, entities[1])
node2.save()
con = Connection()
con._id = "conn_%s_%s" %(tmp[0], tmp[1])
con.nodes = [node1._id, node2._id]
con.entities = [ entities[0]._id, entities[1]._id ]
con.type = 'predicted'
con.network = n._id
con.label = ""
con.save()
print "Saving connection %d %s" % (count, con._id)
finish = time.time()
print "Imported %d edges, time elpased %d seconds" %(count, finish - now)