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submitModel2.py
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# -*- coding: utf-8 -*-
"""
Created on Wed Jul 17 15:42:26 2013
@author: proto
"""
from __future__ import with_statement
import webapp2
import jinja2
import os
from google.appengine.ext.webapp import blobstore_handlers
from google.appengine.ext import blobstore
from google.appengine.ext import ndb
import xmlrpclib
import urllib
from google.appengine.api import files
from google.appengine.api import urlfetch
urlfetch.set_default_fetch_deadline(60)
import logging
class GAEXMLRPCTransport(object):
"""taken directly from http://brizzled.clapper.org/blog/2008/08/25/making-xmlrpc-calls-from-a-google-app-engine-application/"""
"""Handles an HTTP transaction to an XML-RPC server."""
def __init__(self):
pass
def request(self, host, handler, request_body, verbose=0):
result = None
url = 'http://%s%s' % (host, handler)
try:
response = urlfetch.fetch(url,
payload=request_body,
method=urlfetch.POST,
headers={'Content-Type': 'text/xml'},
deadline=60)
except:
msg = 'Failed to fetch %s' % url
logging.error(msg)
raise xmlrpclib.ProtocolError(host + handler, 500, msg, {})
if response.status_code != 200:
logging.error('%s returned status code %s' %
(url, response.status_code))
raise xmlrpclib.ProtocolError(host + handler,
response.status_code,
"",
response.headers)
else:
result = self.__parse_response(response.content)
return result
def __parse_response(self, response_body):
p, u = xmlrpclib.getparser(use_datetime=False)
p.feed(response_body)
return u.close()
JINJA_ENVIRONMENT = jinja2.Environment(
loader=jinja2.FileSystemLoader(os.path.dirname(__file__)),
extensions=['jinja2.ext.autoescape'])
DATABASE_NAME = 'models'
class ModelInfo(ndb.Model):
"""Models an individual Guestbook entry with author, content, and date."""
content = ndb.BlobKeyProperty() #BlobInfo(blobkey)
class MainPage(webapp2.RequestHandler):
def get(self):
template_values = {
}
template =JINJA_ENVIRONMENT.get_template('index.html')
self.response.write(template.render(template_values))
def dbmodel_key(model_name=DATABASE_NAME):
"""Constructs a Datastore key for a ModelDB entity with model_name."""
return ndb.Key('ModelDB', model_name)
class Translate(webapp2.RequestHandler):
def get(self):
upload_url = blobstore.create_upload_url('/process')
s = xmlrpclib.ServerProxy('http://54.214.249.43:9000',GAEXMLRPCTransport())
#s = xmlrpclib.ServerProxy('http://127.0.0.1:9000')
#reactionFiles,speciesFiles = s.getSpeciesConventions()
#print '-----',reactionFiles,speciesFiles
template_values={
'action' : upload_url,
#'reactionDefinition' : ['1','2','3','4','5','6','7','8','9','10','a','b','c']
#'reactionDefinition' : reactionFiles,
#'speciesDefinition': speciesFiles
}
template =JINJA_ENVIRONMENT.get_template('translate.html')
self.response.write(template.render(template_values))
class ProcessFile(blobstore_handlers.BlobstoreUploadHandler):
def post(self):
upload_files = self.get_uploads('file')
blob_info = upload_files[0]
reader = blob_info.open()
sbmlContent = xmlrpclib.Binary(reader.read())
atomizeString = self.request.get('atomize')
reaction = self.request.get('reaction')
species = self.request.get('species')
#print 'fsdgsdgsd',atomize
#https://developers.google.com/appengine/docs/python/urlfetch/fetchfunction
#https://groups.google.com/forum/#!topic/google-appengine/XbrJvt9LfuI
s = xmlrpclib.ServerProxy('http://54.214.249.43:9000',GAEXMLRPCTransport())
#s = xmlrpclib.ServerProxy('http://127.0.0.1:9000',GAEXMLRPCTransport())
result = s.atomize(sbmlContent,atomizeString,reaction,species)
#self.response.write(result)
file_name = files.blobstore.create(mime_type='application/octet-stream')
# Open the file and write to it
with files.open(file_name, 'a') as f:
f.write(result)
# Finalize the file. Do this before attempting to read it.
files.finalize(file_name)
# Get the file's blob key
blob_key = files.blobstore.get_blob_key(file_name)
###
#blob_info = blobstore.BlobInfo.get(blob_key)
#output = blob_info.open()
###
printStatement = '<a href="/serve/{1}.bngl?key={0}">{1}.bngl</a>'.format(blob_key,blob_info.filename)
#p2 = output.read()
self.response.write(printStatement)
#modelSubmission.put()
class Graph(webapp2.RequestHandler):
def get(self):
upload_url = blobstore.create_upload_url('/graphp')
#s = xmlrpclib.ServerProxy('http://127.0.0.1:9100')
template_values={
'action' : upload_url,
#'reactionDefinition' : ['1','2','3','4','5','6','7','8','9','10','a','b','c']
}
template =JINJA_ENVIRONMENT.get_template('graph.html')
self.response.write(template.render(template_values))
class GraphFile(blobstore_handlers.BlobstoreUploadHandler):
def post(self):
upload_files = self.get_uploads('file')
blob_info = upload_files[0]
reader = blob_info.open()
bnglContent = xmlrpclib.Binary(reader.read())
returnType = self.request.get('return')
reactionCenter = True if self.request.get('center') else False
context = True if self.request.get('context') else False
product = True if self.request.get('products') else False
#atomizeString = self.request.get('atomize')
#print 'fsdgsdgsd',atomize
urlfetch.set_default_fetch_deadline(blob_info.size/300)
s = xmlrpclib.ServerProxy('http://54.214.249.43:9100')
#s = xmlrpclib.ServerProxy('http://127.0.0.1:9100')
dotResult = s.bipartite(bnglContent,returnType,reactionCenter,context,product).data
'''
rpc = urlfetch.create_rpc(deadline= 10)
urlfetch.make_fetch_call(rpc, "http://54.214.249.43:9100",method='bipartite',headers=[bnglContent,returnType])
try:
result = rpc.get_result()
if result.status_code == 200:
dotResult = result.content
# ...
except urlfetch.DownloadError:
dotResult = None
'''
# Request timed out or failed.
# ...
#self.response.write(result)
file_name = files.blobstore.create(mime_type='application/octet-stream')
# Open the file and write to it
with files.open(file_name, 'a') as f:
f.write(dotResult)
# Finalize the file. Do this before attempting to read it.
files.finalize(file_name)
# Get the file's blob key
blob_key = files.blobstore.get_blob_key(file_name)
###
#blob_info = blobstore.BlobInfo.get(blob_key)
#output = blob_info.open()
###
printStatement = '<a href="/serve/{1}.{2}?key={0}">{1}.{2}</a>'.format(blob_key,blob_info.filename,returnType)
#p2 = output.read()
self.response.write(printStatement)
class ServeHandler(blobstore_handlers.BlobstoreDownloadHandler):
def get(self, resource):
resource = str(urllib.unquote(self.request.get('key')))
blob_info = blobstore.BlobInfo.get(resource)
self.send_blob(blob_info)
app = webapp2.WSGIApplication([
('/', MainPage),
('/translate',Translate),
('/serve/([^/]+)?', ServeHandler),
('/process',ProcessFile),
('/graphp',GraphFile),
('/graph',Graph)
], debug=True)