def importGene(filename):
filename = filename or r'C:\work\caida\Dropbox\precon\engineering\Contents\GBM_BN-symbols.txt'
cnt = 0
set = {}
col = mongo.db()['entity']
with open(filename) as f:
content = f.read()
for line in content.split('\n'):
line = line.strip()
sym = line.lower()
if (sym in set): continue
set[sym] = 1
doc = ObjDict()
doc._id = 'enti_sym_%s' % sym
doc.symbol = sym
doc.group = 'protein'
doc.name = line
doc.label = line
if (col.find({'symbol': sym}).count() > 0): continue
col.save(doc, safe=True)
cnt += 1
print "Added # %d: %s" % (cnt, sym)
print "Inserted %d gene" % cnt
def importGene(filename):
filename = filename or r'C:\work\caida\Dropbox\precon\engineering\Contents\GBM_BN-symbols.txt'
cnt = 0
set = {}
col = mongo.db()['entity']
with open(filename) as f:
content = f.read()
for line in content.split('\n'):
line = line.strip()
sym = line.lower()
if(sym in set): continue
set[sym] = 1
doc=ObjDict()
doc._id = 'enti_sym_%s' %sym
doc.symbol = sym
doc.group='protein'
doc.name = line
doc.label = line
if(col.find({'symbol':sym}).count()>0): continue
col.save( doc,safe=True)
cnt += 1
print "Added # %d: %s" %(cnt, sym)
print "Inserted %d gene" %cnt
def mongo_scripts():
mydb = db()
for f in filesInDir("etc/mongo"):
if f.find(".js") < 0: continue
funcname = f.replace(".js", "")
handle = open("etc/mongo/%s" % f, 'r')
funcbody = handle.read()
handle.close()
print "Load function: %s" % funcname
mydb.system.js.save({'_id': funcname, 'value': funcbody}, safe=True)
print "Done"
def mongo_scripts():
mydb= db()
for f in filesInDir("etc/mongo"):
if f.find(".js")<0: continue
funcname = f.replace(".js", "")
handle = open("etc/mongo/%s" %f,'r')
funcbody = handle.read()
handle.close()
print "Load function: %s" %funcname
mydb.system.js.save({'_id':funcname, 'value':funcbody}, safe=True)
print "Done"
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)