def start(self,params):
#p = PlosGenerator(u'AVWZBXMiftO65ug')
#d = p.populateNodeFromCustomId('10.1371/journal.pmed.0020124')
self.searcher = PlosSearchStrategy(params['entry_id'],self)
start = self.searcher.start()
start.addCallback(self._send,params = params)
self.params = params
class Maintainer(object):
def __init__(self):
self.searcher = None
self.uuid = uuid.uuid4()
def start(self,params):
#p = PlosGenerator(u'AVWZBXMiftO65ug')
#d = p.populateNodeFromCustomId('10.1371/journal.pmed.0020124')
self.searcher = PlosSearchStrategy(params['entry_id'],self)
start = self.searcher.start()
start.addCallback(self._send,params = params)
self.params = params
def stop(self):
print "ending: %s" %(self.searcher._opennodes,)
self.grapher()
#reactor.stop()
def grapher(self):
print "results length : %s",(len(self.searcher.generator.results), )
grapher = Grapher()
newg = nx.Graph()
for path in self.searcher.useful_paths:
print '%s - %s' % (self.uuid,path)
newg.add_path(path)
grapher.paths.append(path)
grapher.graph = newg
#writer = nx.readwrite.graphml.GraphMLWriter(encoding='utf-8')
#writer.add_graph_element(grapher.graph)
#output = StringIO.StringIO()
#writer.dump(self.request)
from networkx.readwrite import d3_js
# mikedewar = nx.read_graphml('mikedewar_rec.graphml')
mikedewar = newg
# We need to relabel nodes as Twitter name if we want to show the names in the plot
#def gen_label(node):
# label = ""
# label = "%s::%s::%s::%d" %(node.path_index,node.publication_date.absdate,node.id,node.hasMatchingAuthorsName(self.searcher.core_authors()))
# print label
# return label
#label_dict = dict(map(lambda i : (mikedewar.nodes()[i], gen_label(mikedewar.nodes()[i])), xrange(mikedewar.number_of_nodes())))
#mikedewar_d3 = nx.relabel_nodes(mikedewar, label_dict)
# Export
#d3_js.export_d3_js(mikedewar_d3, files_dir="mikedewar", graphname="mikedewar", group=None)
graph_json = d3_js.d3_json(mikedewar, group=None, searcher=self.searcher)
import json
#self.request.write(json.dumps(graph_json, indent=2))
params = self.params
params['network_graph'] = json.dumps(graph_json, indent=2)
self.updateDatabase(params)
#self.request.finish()
#output.close()
#grapher.render(self.searcher,self.searcher.core_node)
def _send(self,result,params):
#self.send("Run finished","Run finished", "dbuschho@localhost",[params['dbResult'][0][1]])
pass
def send(self,message=None, subject=None, sender=None, recipients=None, host=None):
"""
Send email to one or more addresses.
"""
from email.mime.text import MIMEText
from twisted.python import log
import warnings
warnings.filterwarnings('ignore','.*MimeWriter*.',DeprecationWarning,'twisted' )
from twisted.mail.smtp import sendmail
message = 'This is the message body'
subject = 'This is the message subject'
host = 'localhost'
sender = 'dbuschho'
msg = MIMEText(message)
msg['Subject'] = subject
msg['From'] = sender
msg['To'] = ', '.join(recipients)
dfr = sendmail(host, sender, recipients, msg.as_string())
def success(r):
return
def error(e):
print "error:115"
print e
dfr.addCallback(success)
dfr.addErrback(error)
def getUserDataFromDatabase(self,code,entry_id):
from twisted.enterprise import adbapi
try:
dbpool = adbapi.ConnectionPool("psycopg2",
database='drmoon', user='******', password='******', host='localhost', port='5432')
result = dbpool.runQuery("SELECT auth_user.id,auth_user.email from auth_user LEFT JOIN drmoon_userprofile ON drmoon_userprofile.user_id = auth_user.id WHERE drmoon_userprofile.request_code = %s ",(code,))
result.addCallback(self.createNewNetworkEntry,code=code,entry_id=entry_id)
result.addErrback(self.printresult)
#result.addErrback
except Exception as e:
print e
return result
def createNewNetworkEntry(self,dbResult,code,entry_id):
from twisted.enterprise import adbapi
dbpool = adbapi.ConnectionPool("psycopg2",
database='drmoon', user='******', password='******', host='localhost', port='5432')
result = dbpool.runInteraction(self._createNewNetworkEntry,dbResult=dbResult,code=entry_id)
result.addCallback(self._handleStartActions,entry_id=entry_id,dbResult=dbResult,code=entry_id)
result.addErrback(self.printresult)
def _createNewNetworkEntry(self,txn,dbResult,code):
user_id = dbResult[0][0]
txn.execute("INSERT INTO drmoon_networkgraph( \
user_id, created, modified, unique_id, graph_data, shared, complete) \
VALUES (%s, NOW(), NOW(), %s, %s ,false,false)",(user_id,code,' '))
txn.execute("SELECT lastval()")
result = txn.fetchall()
return result[0][0]
def _handleStartActions(self,result,entry_id,dbResult,code):
params = {'entry_id':entry_id,'dbResult':dbResult,'code':code,'id':result}
self.start(params)
import json
self.request.write(json.dumps(params))
self.request.finish()
def updateDatabase(self,params):
# Using the "dbmodule" from the previous example, create a ConnectionPool
from twisted.enterprise import adbapi
dbpool = adbapi.ConnectionPool("psycopg2",
database='drmoon', user='******', password='******', host='localhost', port='5432')
# equivalent of cursor.execute(statement), return cursor.fetchall():
dbpool.runInteraction(self._updateDatabase,params)
def _updateDatabase(self,txn,params):
print "--params--"
print params
id = params['id']
txn.execute(
"SELECT id FROM drmoon_networkgraph WHERE id = %s",
(id,)
)
result = txn.fetchone()
print result
if(result):
txn.execute(
"UPDATE drmoon_networkgraph SET unique_id = %s, graph_data = %s, complete = %s WHERE id = %s",
(params['entry_id'],params['network_graph'], True, id)
)
else:
raise Exception("Database Exception")
def printresult(self,x):
print x
return x