905 lines
39 KiB
Python
905 lines
39 KiB
Python
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#!/usr/bin/env python
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#
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# Copyright 2009 Facebook
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#
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# Licensed under the Apache License, Version 2.0 (the "License"); you may
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# not use this file except in compliance with the License. You may obtain
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# a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
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# WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
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# License for the specific language governing permissions and limitations
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# under the License.
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import os
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import re
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import os.path
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import tornado.httpserver
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import tornado.autoreload
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import tornado.ioloop
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import tornado.options
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import tornado.web
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import tornado.escape as escape
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import settings as msettings
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import madapps
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import datetime
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import random
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import csv
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import itertools
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import email.utils
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import json
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import StringIO
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from tornado.options import define, options, logging
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from tornado_addons import ozhandler
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import copy
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from collections import OrderedDict
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define("port", default=msettings.WEB_SERVER_PORT, help="run on the given port", type=int)
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filteredapps=None
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filteredevals=None
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smallgif='GIF89a\1\0\1\0\x80\xff\0\xff\xff\xff\0\0\0,\0\0\0\0\1\0\1\0\0\2\2D\1\0;'
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viswidgetmap={
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'motionchart':'google.visualization.MotionChart',
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'table':'google.visualization.Table',
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'linechart':'google.visualization.LineChart',
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'piechart':'google.visualization.PieChart',
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'scatterchart':'google.visualization.ScatterChart',
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'intensitymap':'google.visualization.IntensityMap',
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'geomap':'google.visualization.GeoMap',
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'columnchart':'google.visualization.ColumnChart',
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'barchart':'google.visualization.BarChart',
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'areachart':'google.visualization.AreaChart',
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'annotatedtimeline':'google.visualization.AnnotatedTimeLine',
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'termcloud':'TermCloud',
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}
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queries = {}
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msettings.viswidgetmap=viswidgetmap
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class Application(tornado.web.Application):
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def __init__(self):
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handlers = [
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(r"/", createUploadProfileHandler),
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(r"/upload-codes", uploadCodesHandler),
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(r"/save-config-controller", profileCreationHandler),
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(r"/download-config-controller", profileServeHandler),
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(r"/configure-profile", configureProfileHandler),
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(r"/save-profile", saveProfileHandler),
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(r"/?$", madAppBarHandler),
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(r"/[^/]+/?$", madAppHandler),
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(r"/[^/]+/.+$", madAppDataHandler)
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]
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settings = dict(
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template_path=os.path.join(os.path.dirname(__file__), "templates"),
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static_path=os.path.join(os.path.dirname(__file__), "static"),
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xsrf_cookies=False,
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cookie_secret=msettings.SECRET_KEY,
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login_url="/auth/login",
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debug=msettings.DEBUG
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)
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tornado.web.Application.__init__(self, handlers, **settings)
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def auth_callback(request, realm, username, password):
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if username==msettings.USERNAME and password == msettings.PASSWORD:
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request.user_id = 1
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return True
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else:
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return False
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def numberOfGrantsUploaded(user_id, cookie_set):
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if cookie_set and user_id:
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file_name = "/tmp/p%s.tsv" % (user_id)
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if os.path.isfile(file_name):
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num_lines = sum(1 for line in open(file_name))
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if str(num_lines) == cookie_set:
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return num_lines
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return 0
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def numberOfDocsUploaded(user_id):
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if user_id:
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file_name = "/tmp/docs%s.json" % (user_id)
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if os.path.isfile(file_name):
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num_lines = sum(1 for line in open(file_name))
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return num_lines
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return 0
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class BaseHandler(ozhandler.DjangoErrorMixin, ozhandler.BasicAuthMixin, tornado.web.RequestHandler):
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def __init__(self, *args):
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tornado.web.RequestHandler.__init__(self, *args)
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if msettings.USERNAME!='':
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self.hiddenauthget=self.get
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self.get=self.authget
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if msettings.RESTRICT_IPS:
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self.hiddenget=self.get
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self.get=self.checkwhitelistget
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def authget(self, *args):
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try:
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if self.passwordless:
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self.hiddenauthget(*args)
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return
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except:
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pass
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if not self.get_authenticated_user(auth_callback, 'stats'):
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return False
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self.hiddenauthget(*args)
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def checkwhitelistget(self, *args):
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if self.request.remote_ip not in msettings.RESTRICT_IP_WHITELIST:
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raise tornado.web.HTTPError(403)
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return self.hiddenget(*args)
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def get_current_user(self):
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return 'anonymous'
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def executequery(self, query, bindings=None):
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def latinnum(x):
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x=int(x)
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lx=""
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while x>25:
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lx+=chr( ord('A')+int(x/25) )
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x%=25
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lx+=chr(ord('A')+x)
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return lx
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query=query.rstrip(';\n\s ')
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try:
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origvars=msettings.madis.functions.variables
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c=msettings.Connection.cursor().execute(query, localbindings=bindings)
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except Exception, e:
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try:
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c.close()
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except:
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pass
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msettings.madis.functions.variables=origvars
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self.finish(str(e))
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if msettings.DEBUG:
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raise e
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return
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# Schema from query's description
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try:
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schema=c.getdescription()
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except:
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c.close()
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msettings.madis.functions.variables=origvars
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self.finish()
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return
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colnames=[]
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coltypes=[]
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for cname, ctype in schema:
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if ctype==None:
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colnames+=[cname]
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coltypes+=[ctype]
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continue
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ctypehead3=ctype.lower()[0:3]
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if ctypehead3 in ('int', 'rea', 'flo', 'dou', 'num'):
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ctype='number'
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else:
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ctype='string'
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colnames+=[cname]
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coltypes+=[ctype]
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try:
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firstrow=c.next()
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except StopIteration:
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c.close()
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msettings.madis.functions.variables=origvars
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self.finish()
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return
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except Exception, e:
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c.close()
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msettings.madis.functions.variables=origvars
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self.finish(str(e))
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return
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# Merge with guessed schema from query's first row
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for cname, ctype, i in zip(colnames, coltypes, xrange(len(colnames))):
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if ctype==None:
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frtype=type(firstrow[i])
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if frtype in (int, float):
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coltypes[i]='number'
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else:
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coltypes[i]='string'
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# Write responce's header
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response={"cols":[]}
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for name, ctype,num in zip(colnames, coltypes, xrange(len(colnames))):
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id=latinnum(num)
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response["cols"]+=[{"id":id, "label":name,"type":ctype}]
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# Write header
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self.write(json.dumps(response, separators=(',', ':'), sort_keys=True, ensure_ascii=False)[0:-1] + ',"rows":[')
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# Write first line
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response=json.dumps({"c":[{"v":x} for x in firstrow]}, separators=(',', ':'), sort_keys=True, ensure_ascii=False)
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self.write(response)
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self.executequeryrow(c, msettings.madis.functions.variables)
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msettings.madis.functions.variables=origvars
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def executequeryrow(self, cursor, vars):
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try:
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try:
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origvars=msettings.madis.functions.variables
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msettings.madis.functions.variables=vars
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buffer=StringIO.StringIO()
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while buffer.len<30000:
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buffer.write(','+json.dumps({"c":[{"v":x} for x in cursor.next()]}, separators=(',', ':'), sort_keys=True, ensure_ascii=False))
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self.write(buffer.getvalue())
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self.flush(callback=lambda : self.executequeryrow(cursor, msettings.madis.functions.variables))
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except StopIteration:
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cursor.close()
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self.finish(buffer.getvalue()+']}')
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finally:
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msettings.madis.functions.variables=origvars
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except IOError:
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msettings.madis.functions.variables=origvars
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cursor.close()
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pass
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def serveimage(self, path, mime_type=None):
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if os.path.sep != "/":
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path = path.replace("/", os.path.sep)
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abspath = os.path.abspath(os.path.join(self.settings['static_path'], path))
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if mime_type==None:
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mime_type='image/'+path[-3:]
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self.set_header("Content-Type", mime_type)
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# Check the If-Modified-Since, and don't send the result if the
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# content has not been modified
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ims_value = self.request.headers.get("If-Modified-Since")
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if ims_value is not None:
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date_tuple = email.utils.parsedate(ims_value)
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if_since = datetime.datetime.fromtimestamp(time.mktime(date_tuple))
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if if_since >= modified:
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self.set_status(304)
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return
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file = open(abspath, "rb")
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try:
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self.write(file.read())
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finally:
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file.close()
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class HomeHandler(BaseHandler):
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def get(self):
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self.render("home.html", settings=msettings)
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class madAppBarHandler(BaseHandler):
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def get(self):
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self.render('madappbar.html', apps=filteredapps, evals=filteredevals, settings=msettings)
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trueset = set([1 , 'on', 'true', 'TRUE'])
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URIdemultiplex = {r"/" + msettings.APPDIRNAME + "/analyze":'projects'
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, r"/" + msettings.APPDIRNAME + "/datacitations":'datacitations'
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, r"/" + msettings.APPDIRNAME + "/classifier":'classification'
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, r"/" + msettings.APPDIRNAME + "/pdbs":'pdb'
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, r"/" + msettings.APPDIRNAME + "/interactivemining":'interactivemining'}
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class createUploadProfileHandler(BaseHandler):
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passwordless=True
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# When loading the page first time and every refresh
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def get(self):
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if 'data' in self.request.arguments:
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return
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elif 'reset' in self.request.arguments:
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# TODO RESET everything
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print "TODO RESET everything"
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else:
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# check if we already gave client a user_id
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user_id = self.get_secure_cookie('madgikmining')
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if not user_id:
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# give him a unique user_id
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user_id = 'user{0}'.format(datetime.datetime.now().microsecond + (random.randrange(1, 100+1) * 100000))
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self.set_secure_cookie('madgikmining', user_id)
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self.render('create_upload_profile.html', settings=msettings)
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# TODO Upload profile post
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def post(self):
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try:
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user_id = self.get_secure_cookie('madgikmining')
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if user_id is None:
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return
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if 'upload' in self.request.files:
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# get file info and body from post data
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fileinfo = self.request.files['upload'][0]
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fname = fileinfo['filename']
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extn = os.path.splitext(fname)[1]
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# must be .pdf or .json
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if extn != ".oamp":
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self.write(json.dumps({'respond': "<b style=\"color: red\">File must be .oamp compatible profile</b>"}))
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return
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# write data to physical file
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cname = "/tmp/profile{0}.oamp".format(user_id)
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fh = open(cname, 'w')
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fh.write(fileinfo['body'])
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fh.close()
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# extract data from profile file
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import sys
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sys.path.append(msettings.MADIS_PATH)
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import madis
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# get the profile database cursor
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cursor=madis.functions.Connection(cname).cursor()
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# data to be sent
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data = {}
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# Write to csv file the grants ids
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if len([r for r in cursor.execute("SELECT name FROM sqlite_master WHERE type='table' AND name='grants'")]):
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cursor.execute("output '/tmp/p{0}.csv' select * from grants".format(user_id))
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numberOfGrants = numberOfGrantsUploaded(user_id, "puppet_value")
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self.set_secure_cookie('madgikmining_grantsuploaded', str(numberOfGrants))
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data['grants'] = numberOfGrants
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# write to json the poswords
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if len([r for r in cursor.execute("SELECT name FROM sqlite_master WHERE type='table' AND name='poswords'")]):
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results = [r for r in cursor.execute("select c1, c2 from poswords")]
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data['poswords'] = {value:key for value, key in results}
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# write to json the negwords
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if len([r for r in cursor.execute("SELECT name FROM sqlite_master WHERE type='table' AND name='negwords'")]):
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results = [r for r in cursor.execute("select c1, c2 from negwords")]
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data['negwords'] = {value:key for value, key in results}
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# write to json the filters
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if len([r for r in cursor.execute("SELECT name FROM sqlite_master WHERE type='table' AND name='filters'")]):
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results = [r for r in cursor.execute("select c1, c2 from filters")]
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data['filters'] = {value:key for value, key in results}
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cursor.close()
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self.write(json.dumps(data))
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|
self.finish()
|
||
|
|
|
||
|
|
except Exception as ints:
|
||
|
|
self.write(json.dumps({'respond': "<b style=\"color: red\">Something went very wrong!</b>"}))
|
||
|
|
print ints
|
||
|
|
return
|
||
|
|
|
||
|
|
|
||
|
|
class uploadCodesHandler(BaseHandler):
|
||
|
|
passwordless=True
|
||
|
|
# When loading the page first time and every refresh
|
||
|
|
def get(self):
|
||
|
|
if 'data' in self.request.arguments:
|
||
|
|
return
|
||
|
|
else:
|
||
|
|
# check if we already gave client a user_id
|
||
|
|
user_id = self.get_secure_cookie('madgikmining')
|
||
|
|
if user_id is None:
|
||
|
|
return
|
||
|
|
# check if he already uploaded his grants ids and inform him via a message
|
||
|
|
self.render('upload_codes.html', settings=msettings)
|
||
|
|
def post(self):
|
||
|
|
try:
|
||
|
|
# get user id from cookie. Must have
|
||
|
|
user_id = self.get_secure_cookie('madgikmining')
|
||
|
|
if user_id is None:
|
||
|
|
return
|
||
|
|
if 'upload' in self.request.files:
|
||
|
|
# get file info and body from post data
|
||
|
|
fileinfo = self.request.files['upload'][0]
|
||
|
|
fname = fileinfo['filename']
|
||
|
|
extn = os.path.splitext(fname)[1]
|
||
|
|
# must be .pdf or .json
|
||
|
|
if extn != ".tsv" and extn != ".txt":
|
||
|
|
self.write(json.dumps({'respond': "<b style=\"color: red\">File must be .tsv or .txt</b>"}))
|
||
|
|
return
|
||
|
|
codes = {}
|
||
|
|
lines = fileinfo['body'].splitlines()
|
||
|
|
for line in lines:
|
||
|
|
columns = re.split(r'\t+', line.rstrip('\t'))
|
||
|
|
if len(columns) and columns[0] == '':
|
||
|
|
continue
|
||
|
|
elif len(columns) > 1:
|
||
|
|
codes[columns[0]] = columns[1]
|
||
|
|
elif len(columns) == 1:
|
||
|
|
codes[columns[0]] = ''
|
||
|
|
# data to be sent
|
||
|
|
data = {}
|
||
|
|
if len(lines) == 1:
|
||
|
|
data['error'] = "File <b>{0}</b> uploaded.<br><b>1 Code</b> loaded! <i>Please make sure that you separate each code with newline!</i>".format(fname)
|
||
|
|
else:
|
||
|
|
data['data'] = codes
|
||
|
|
data['respond'] = "<b>{0} Codes</b> loaded successfully!".format(len(lines))
|
||
|
|
self.set_secure_cookie('madgikmining_grantsuploaded', str(len(lines)))
|
||
|
|
self.write(json.dumps(data))
|
||
|
|
self.finish()
|
||
|
|
elif 'concepts' in self.request.arguments and self.request.arguments['concepts'][0] != '{}':
|
||
|
|
# write data to physical file
|
||
|
|
cname = "/tmp/p{0}.tsv".format(user_id)
|
||
|
|
fh = open(cname, 'w')
|
||
|
|
concepts = json.loads(self.request.arguments['concepts'][0])
|
||
|
|
for key, value in concepts.iteritems():
|
||
|
|
fh.write("{0}\t{1}\n".format(key,value))
|
||
|
|
fh.close()
|
||
|
|
# data to be sent
|
||
|
|
data = {}
|
||
|
|
if len(concepts) == 0:
|
||
|
|
data['error'] = "You have to provide at least one concept to continue"
|
||
|
|
else:
|
||
|
|
data['respond'] = "<b>{0} Codes</b> loaded successfully!".format(len(concepts))
|
||
|
|
self.set_secure_cookie('madgikmining_grantsuploaded', str(len(concepts)))
|
||
|
|
self.write(json.dumps(data))
|
||
|
|
self.finish()
|
||
|
|
|
||
|
|
except Exception as ints:
|
||
|
|
data = {}
|
||
|
|
data['error'] = "<b style=\"color: red\">File Failed to Upload!</b>"
|
||
|
|
self.write(json.dumps(data))
|
||
|
|
self.finish()
|
||
|
|
print ints
|
||
|
|
return
|
||
|
|
|
||
|
|
|
||
|
|
class configureProfileHandler(BaseHandler):
|
||
|
|
passwordless=True
|
||
|
|
# When loading the page first time and evry refresh
|
||
|
|
def get(self):
|
||
|
|
if 'data' in self.request.arguments:
|
||
|
|
return
|
||
|
|
else:
|
||
|
|
# check if we already gave client a user_id
|
||
|
|
user_id = self.get_secure_cookie('madgikmining')
|
||
|
|
if user_id is None:
|
||
|
|
return
|
||
|
|
# check if he already uploaded his grants ids and inform him via a message
|
||
|
|
self.render('configure_profile.html', settings=msettings)
|
||
|
|
def post(self):
|
||
|
|
try:
|
||
|
|
# get user id from cookie. Must have
|
||
|
|
user_id = self.get_secure_cookie('madgikmining')
|
||
|
|
if user_id is None:
|
||
|
|
return
|
||
|
|
# post case where the user uploads his own documents
|
||
|
|
if 'upload' in self.request.files:
|
||
|
|
# get file info and body from post data
|
||
|
|
fileinfo = self.request.files['upload'][0]
|
||
|
|
fname = fileinfo['filename']
|
||
|
|
extn = os.path.splitext(fname)[1]
|
||
|
|
# data to be sent
|
||
|
|
data = {}
|
||
|
|
# must be .pdf, .txt or .json
|
||
|
|
if extn != ".pdf" and extn != ".txt" and extn != ".json":
|
||
|
|
data['error'] = "<b style=\"color: red\">File must be .pdf, .json or .txt</b>"
|
||
|
|
return
|
||
|
|
# write data to physical file
|
||
|
|
cname = "/tmp/docs{0}{1}".format(user_id, extn)
|
||
|
|
fh = open(cname, 'w')
|
||
|
|
fh.write(fileinfo['body'])
|
||
|
|
fh.close()
|
||
|
|
# Convert pdf to txt and then to json format
|
||
|
|
if extn == ".pdf":
|
||
|
|
import subprocess as sub
|
||
|
|
p = sub.Popen(['pdftotext', '-enc', 'UTF-8', cname],stdout=sub.PIPE,stderr=sub.PIPE)
|
||
|
|
output, errors = p.communicate()
|
||
|
|
if errors:
|
||
|
|
data['error'] = "<b style=\"color: red\">Cannot convert .pdf to .txt</b>"
|
||
|
|
return
|
||
|
|
os.remove(cname)
|
||
|
|
cname = "/tmp/docs{0}.txt".format(user_id)
|
||
|
|
with open(cname, 'r') as fin:
|
||
|
|
docData=fin.read().replace('\n', ' ')
|
||
|
|
if len(docData)==0:
|
||
|
|
data['error'] = "<b style=\"color: red\">Cannot convert .pdf to .txt</b>"
|
||
|
|
return
|
||
|
|
with open("/tmp/docs{0}.json".format(user_id), "wb") as fout:
|
||
|
|
json.dump({"text":docData,"id":os.path.splitext(fname)[0]}, fout)
|
||
|
|
os.remove(cname)
|
||
|
|
# else check if txt is in correct json format
|
||
|
|
elif extn == ".txt" or extn == ".json":
|
||
|
|
try:
|
||
|
|
jsonlist = []
|
||
|
|
for line in open(cname, 'r'):
|
||
|
|
jsonlist.append(json.loads(line))
|
||
|
|
os.rename(cname, "/tmp/docs{0}.json".format(user_id))
|
||
|
|
except ValueError, e:
|
||
|
|
data['error'] = "<b style=\"color: red\">File is not in a valid json format</b>"
|
||
|
|
os.remove(cname)
|
||
|
|
print e
|
||
|
|
return
|
||
|
|
data['respond'] = "<b>File {0}</b> uploaded successfully!".format(fname)
|
||
|
|
self.write(json.dumps(data))
|
||
|
|
self.finish()
|
||
|
|
# post case where the user selects form preset documents samples
|
||
|
|
elif 'doc_sample' in self.request.arguments and self.request.arguments['doc_sample'][0] != '':
|
||
|
|
|
||
|
|
sample_file_name = ""
|
||
|
|
if self.request.arguments['doc_sample'][0] == "nih_sample":
|
||
|
|
sample_file_name = "static/nih_sample.tsv"
|
||
|
|
elif self.request.arguments['doc_sample'][0] == "rcuk_sample":
|
||
|
|
sample_file_name = "static/rcuk_sample.tsv"
|
||
|
|
elif self.request.arguments['doc_sample'][0] == "arxiv_sample":
|
||
|
|
sample_file_name = "static/arxiv_sample.tsv"
|
||
|
|
sample_file = open(sample_file_name, 'r')
|
||
|
|
|
||
|
|
# write data to physical file
|
||
|
|
cname = "/tmp/docs{0}/json".format(user_id)
|
||
|
|
fh = open(cname, 'w')
|
||
|
|
while 1:
|
||
|
|
copy_buffer = sample_file.read(1048576)
|
||
|
|
if not copy_buffer:
|
||
|
|
break
|
||
|
|
fh.write(copy_buffer)
|
||
|
|
fh.close()
|
||
|
|
|
||
|
|
# data to be sent
|
||
|
|
data = {}
|
||
|
|
if len(concepts) == 0:
|
||
|
|
data['error'] = "You have to provide at least one concept to continue"
|
||
|
|
else:
|
||
|
|
data['respond'] = "<b>{0} Codes</b> loaded successfully!".format(len(concepts))
|
||
|
|
self.set_secure_cookie('madgikmining_grantsuploaded', str(len(concepts)))
|
||
|
|
self.write(json.dumps(data))
|
||
|
|
self.finish()
|
||
|
|
# post case for the actual mining proccess
|
||
|
|
else:
|
||
|
|
# data to be sent
|
||
|
|
data = {}
|
||
|
|
# create positive and negative words weighted regex text
|
||
|
|
pos_set = neg_set = conf = whr_conf = ''
|
||
|
|
if 'poswords' in self.request.arguments and self.request.arguments['poswords'][0] != '{}':
|
||
|
|
# construct math string for positive words matching calculation with weights
|
||
|
|
pos_words = json.loads(self.request.arguments['poswords'][0])
|
||
|
|
for key, value in pos_words.iteritems():
|
||
|
|
pos_set += r'regexpcountuniquematches("(?:\b)%s(?:\b)",j2s(prev,middle,next))*%s + ' % (key,value)
|
||
|
|
pos_set += "0"
|
||
|
|
if 'negwords' in self.request.arguments and self.request.arguments['negwords'][0] != '{}':
|
||
|
|
# construct math string for negative words matching calculation with weights
|
||
|
|
neg_words = json.loads(self.request.arguments['negwords'][0])
|
||
|
|
for key, value in neg_words.iteritems():
|
||
|
|
neg_set += r'regexpcountuniquematches("(?:\b)%s(?:\b)",j2s(prev,middle,next))*%s - ' % (key,value)
|
||
|
|
neg_set += "0"
|
||
|
|
if pos_set != '' and neg_set != '':
|
||
|
|
conf = ", ({0} - {1})".format(pos_set, neg_set)
|
||
|
|
elif pos_set != '':
|
||
|
|
conf = ", {0}".format(pos_set)
|
||
|
|
elif neg_set != '':
|
||
|
|
conf = ", -{0}".format(neg_set)
|
||
|
|
if conf != '':
|
||
|
|
conf += ' as conf'
|
||
|
|
whr_conf = 'and conf>=0'
|
||
|
|
|
||
|
|
# get the database cursor
|
||
|
|
cursor=msettings.Connection.cursor()
|
||
|
|
|
||
|
|
if numberOfDocsUploaded(user_id) != 0:
|
||
|
|
doc_filters = "regexpr('[\n|\r]',c2,' ')"
|
||
|
|
ackn_filters = "regexpr(\"\\'\", c2,'')"
|
||
|
|
if 'punctuation' in self.request.arguments and self.request.arguments['punctuation'][0] == "1":
|
||
|
|
doc_filters = 'keywords('+doc_filters+')'
|
||
|
|
ackn_filters = 'keywords('+ackn_filters+')'
|
||
|
|
if 'lettercase' in self.request.arguments and self.request.arguments['lettercase'][0] != '' and self.request.arguments['lettercase'][0] != 'None':
|
||
|
|
if self.request.arguments['lettercase'][0] == 'Lowercase':
|
||
|
|
doc_filters = 'lower('+doc_filters+')'
|
||
|
|
ackn_filters = 'lower('+ackn_filters+')'
|
||
|
|
elif self.request.arguments['lettercase'][0] == 'Uppercase':
|
||
|
|
doc_filters = 'upper('+doc_filters+')'
|
||
|
|
ackn_filters = 'upper('+ackn_filters+')'
|
||
|
|
if 'stopwords' in self.request.arguments and self.request.arguments['stopwords'][0] == "1":
|
||
|
|
doc_filters = 'filterstopwords('+doc_filters+')'
|
||
|
|
ackn_filters = 'filterstopwords('+ackn_filters+')'
|
||
|
|
list(cursor.execute("drop table if exists grantstemp"+user_id, parse=False))
|
||
|
|
query_pre_grants = "create temp table grantstemp{0} as select stripchars(c1) as c1, case when c2 is null then null else {1} end as c2 from (setschema 'c1,c2' file '/tmp/p{0}.tsv' dialect:tsv)".format(user_id, ackn_filters)
|
||
|
|
cursor.execute(query_pre_grants)
|
||
|
|
list(cursor.execute("drop table if exists docs"+user_id, parse=False))
|
||
|
|
query1 = "create temp table docs{0} as select c1, {1} as c2 from (setschema 'c1,c2' select jsonpath(c1, '$.id', '$.text') from (file '/tmp/docs{0}.json'))".format(user_id, doc_filters)
|
||
|
|
cursor.execute(query1)
|
||
|
|
else:
|
||
|
|
data['error'] = "You have to provide at least one concept to continue"
|
||
|
|
self.write(json.dumps(data))
|
||
|
|
self.finish()
|
||
|
|
return
|
||
|
|
|
||
|
|
list(cursor.execute("drop table if exists grants"+user_id, parse=False))
|
||
|
|
# string concatenation workaround because of the special characters conflicts
|
||
|
|
if 'wordssplitnum' in self.request.arguments and self.request.arguments['wordssplitnum'][0] != '':
|
||
|
|
words_split = int(self.request.arguments['wordssplitnum'][0])
|
||
|
|
if 0 < words_split and words_split <= 10:
|
||
|
|
acknowledgment_split = r'textwindow2s(regexpr("([\-\[\]\/\{\}\(\)\*\+\?\.\\\^\$\|])", c2, "\\\1"),0,'+str(words_split)+r',0)'
|
||
|
|
else:
|
||
|
|
acknowledgment_split = r'"prev" as prev, regexpr("([\-\[\]\/\{\}\(\)\*\+\?\.\\\^\$\|])", c2, "\\\1") as middle, "next" as next'
|
||
|
|
query0 = r"create temp table grants"+user_id+r' as select c1 as c3, jmergeregexp(jgroup("(?<=[\s\b])"||middle||"(?=[\s\b])")) as c4 from '+r"(setschema 'c1,prev,middle,next' select c1, "+acknowledgment_split+r' from grantstemp'+user_id+r' where (c1 or c1!="") and c2 not null) group by c1 union all select distinct c1 as c3, "(?!.*)" as c4 from grantstemp'+user_id+r" where (c1 or c1!='') and c2 is null"
|
||
|
|
cursor.execute(query0)
|
||
|
|
|
||
|
|
query2 = "select c1, c3, max(confidence) as confidence from (select c1, c3, regexpcountuniquematches(c4, j2s(prev,middle,next)) as confidence {0} from (select c1, textwindow2s(c2,10,1,5) from (select * from docs{1})), (select c3, c4 from grants{1}) T where middle = T.c3 {2}) group by c1".format(conf, user_id, whr_conf)
|
||
|
|
# query2 = "select c1, c3 {0} from (select c1, textwindow2s(c2,10,1,5) from (select * from docs{1})), (select c3 from grants{1}) T where middle = T.c3 {2}".format(conf, user_id, whr_conf)
|
||
|
|
results = [r for r in cursor.execute(query2)]
|
||
|
|
data['funding_info'] = [{"code": r[1]} for r in results]
|
||
|
|
self.write(json.dumps(data))
|
||
|
|
self.flush()
|
||
|
|
self.finish()
|
||
|
|
|
||
|
|
except Exception as ints:
|
||
|
|
data = {}
|
||
|
|
data['error'] = "<b style=\"color: red\">File Failed to Upload!</b>"
|
||
|
|
self.write(json.dumps(data))
|
||
|
|
self.finish()
|
||
|
|
print ints
|
||
|
|
|
||
|
|
try:
|
||
|
|
cursor.close()
|
||
|
|
except:
|
||
|
|
pass
|
||
|
|
|
||
|
|
|
||
|
|
class saveProfileHandler(BaseHandler):
|
||
|
|
passwordless=True
|
||
|
|
# When loading the page first time and evry refresh
|
||
|
|
def get(self):
|
||
|
|
if 'data' in self.request.arguments:
|
||
|
|
return
|
||
|
|
else:
|
||
|
|
# check if we already gave client a user_id
|
||
|
|
user_id = self.get_secure_cookie('madgikmining')
|
||
|
|
if user_id is None:
|
||
|
|
return
|
||
|
|
# check if he already uploaded his grants ids and inform him via a message
|
||
|
|
self.render('save_profile.html', settings=msettings)
|
||
|
|
|
||
|
|
|
||
|
|
class profileCreationHandler(BaseHandler):
|
||
|
|
def post(self):
|
||
|
|
try:
|
||
|
|
user_id = self.get_secure_cookie('madgikmining')
|
||
|
|
if user_id is None:
|
||
|
|
return
|
||
|
|
|
||
|
|
import sys
|
||
|
|
sys.path.append(msettings.MADIS_PATH)
|
||
|
|
import madis
|
||
|
|
# get the database cursor
|
||
|
|
# profile file name
|
||
|
|
profile_file_name = "/tmp/OAMiningProfile_{0}.oamp".format(user_id)
|
||
|
|
cursor=madis.functions.Connection(profile_file_name).cursor()
|
||
|
|
# Create poswords table
|
||
|
|
cursor.execute("drop table if exists poswords", parse=False)
|
||
|
|
cursor.execute("create table poswords(c1,c2)", parse=False)
|
||
|
|
# Create negwords table
|
||
|
|
cursor.execute("drop table if exists negwords", parse=False)
|
||
|
|
cursor.execute("create table negwords(c1,c2)", parse=False)
|
||
|
|
# Create filters table
|
||
|
|
cursor.execute("drop table if exists filters", parse=False)
|
||
|
|
cursor.execute("create table filters(c1,c2)", parse=False)
|
||
|
|
# Create grants table
|
||
|
|
cursor.execute("drop table if exists grants", parse=False)
|
||
|
|
cursor.execute("create table grants(c1)", parse=False)
|
||
|
|
if 'poswords' in self.request.arguments and self.request.arguments['poswords'][0] != '{}':
|
||
|
|
# construct math string for positive words matching calculation with weights
|
||
|
|
pos_words = json.loads(self.request.arguments['poswords'][0])
|
||
|
|
cursor.executemany("insert into poswords(c1,c2) values(?,?)",
|
||
|
|
(
|
||
|
|
(key, value,) for key, value in pos_words.iteritems()
|
||
|
|
)
|
||
|
|
)
|
||
|
|
if 'negwords' in self.request.arguments and self.request.arguments['negwords'][0] != '{}':
|
||
|
|
# construct math string for negative words matching calculation with weights
|
||
|
|
neg_words = json.loads(self.request.arguments['negwords'][0])
|
||
|
|
cursor.executemany("insert into negwords(c1,c2) values(?,?)",
|
||
|
|
(
|
||
|
|
(key, value,) for key, value in neg_words.iteritems()
|
||
|
|
)
|
||
|
|
)
|
||
|
|
if 'filters' in self.request.arguments and self.request.arguments['filters'][0] != '{}':
|
||
|
|
# construct math string for negative words matching calculation with weights
|
||
|
|
filters = json.loads(self.request.arguments['filters'][0])
|
||
|
|
cursor.executemany("insert into filters(c1,c2) values(?,?)",
|
||
|
|
(
|
||
|
|
(key, value,) for key, value in filters.iteritems()
|
||
|
|
)
|
||
|
|
)
|
||
|
|
if numberOfGrantsUploaded(user_id, self.get_secure_cookie('madgikmining_grantsuploaded')) != 0:
|
||
|
|
cursor.execute("insert into grants select stripchars(c1) as c1 from (file '/tmp/p{0}.csv')".format(user_id))
|
||
|
|
cursor.close()
|
||
|
|
|
||
|
|
self.write(json.dumps({'respond': "File ploaded.<br><b>1 Code</b> loaded! <i>Please make sure that you separate each code with newline!</i>"}))
|
||
|
|
|
||
|
|
except Exception as ints:
|
||
|
|
self.write(json.dumps({'respond': "<b style=\"color: red\">Mining profile couldn't be saved!</b>"}))
|
||
|
|
print ints
|
||
|
|
return
|
||
|
|
self.finish()
|
||
|
|
|
||
|
|
|
||
|
|
class profileServeHandler(BaseHandler):
|
||
|
|
passwordless=True
|
||
|
|
def get(self):
|
||
|
|
try:
|
||
|
|
user_id = self.get_secure_cookie('madgikmining')
|
||
|
|
if user_id is None:
|
||
|
|
return
|
||
|
|
if 'saveprofile' in self.request.arguments:
|
||
|
|
print "asda"
|
||
|
|
profile_file_name = "/tmp/OAMiningProfile_{0}.oamp".format(user_id)
|
||
|
|
buf_size = 4096
|
||
|
|
self.set_header('Content-Type', 'application/octet-stream')
|
||
|
|
self.set_header('Content-Disposition', 'attachment; filename=' + "OAMiningProfile_{0}.oamp".format(user_id))
|
||
|
|
self.flush()
|
||
|
|
with open(profile_file_name, 'r') as f:
|
||
|
|
while True:
|
||
|
|
data = f.read(buf_size)
|
||
|
|
if not data:
|
||
|
|
break
|
||
|
|
self.write(data)
|
||
|
|
self.finish()
|
||
|
|
# TODO delete file after sending if needed
|
||
|
|
|
||
|
|
except Exception as ints:
|
||
|
|
self.write(json.dumps({'respond': "<b style=\"color: red\">Something went very wrong!</b>"}))
|
||
|
|
print ints
|
||
|
|
return
|
||
|
|
|
||
|
|
|
||
|
|
class madAppHandler(BaseHandler):
|
||
|
|
def get(self):
|
||
|
|
try:
|
||
|
|
appname=re.match(r'.+/([^/]+)/?$', self.request.uri).groups()[0].lower()
|
||
|
|
except AttributeError:
|
||
|
|
raise tornado.web.HTTPError(404)
|
||
|
|
|
||
|
|
appobj=None
|
||
|
|
for ap in madapps.apps:
|
||
|
|
if ap['link']==appname:
|
||
|
|
appobj=ap
|
||
|
|
break
|
||
|
|
|
||
|
|
if appobj==None:
|
||
|
|
raise tornado.web.HTTPError(404)
|
||
|
|
|
||
|
|
self.render('madappview.html', app=appobj, apps=filteredapps, evals=filteredevals, settings=msettings)
|
||
|
|
|
||
|
|
class madAppDataHandler(BaseHandler):
|
||
|
|
|
||
|
|
@tornado.web.asynchronous
|
||
|
|
def post(self):
|
||
|
|
try:
|
||
|
|
appname, queryname=[x.lower() for x in re.match(r'.+/([^/]+)/(.+)$', self.request.uri).groups()]
|
||
|
|
except AttributeError:
|
||
|
|
raise tornado.web.HTTPError(404)
|
||
|
|
|
||
|
|
appobj=None
|
||
|
|
query=''
|
||
|
|
for ap in madapps.apps:
|
||
|
|
if ap['link']==appname:
|
||
|
|
if queryname in ap:
|
||
|
|
appobj=ap
|
||
|
|
if queryname=='query':
|
||
|
|
query=appobj['query']
|
||
|
|
else:
|
||
|
|
query=appobj[queryname]['query']
|
||
|
|
break
|
||
|
|
|
||
|
|
if appobj==None:
|
||
|
|
raise tornado.web.HTTPError(404)
|
||
|
|
|
||
|
|
params=dict(((x.replace(' ','_'),y[0].replace('\n','')) for x,y in self.request.arguments.iteritems()) )
|
||
|
|
self.executequery(query, params)
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
def main():
|
||
|
|
global filteredapps, filteredevals
|
||
|
|
|
||
|
|
def getqtext(query,params):
|
||
|
|
query=query.strip('\n \s')
|
||
|
|
query=escape.xhtml_escape(query)
|
||
|
|
for i in params:
|
||
|
|
i=i.replace(' ','_')
|
||
|
|
query=re.sub(':'+i, '<b><i>'+escape.xhtml_escape(i)+'</i></b>', query)
|
||
|
|
query=re.sub('$'+i, '<b><i>'+escape.xhtml_escape(i)+'</i></b>', query)
|
||
|
|
query=re.sub('@'+i, '<b><i>'+escape.xhtml_escape(i)+'</i></b>', query)
|
||
|
|
return query.replace("\n","<br/>")
|
||
|
|
|
||
|
|
def getparams(app):
|
||
|
|
qparams=re.findall('%{(.*?)}',app['query'], re.UNICODE )
|
||
|
|
return set(qparams)
|
||
|
|
|
||
|
|
def getqueries():
|
||
|
|
query_dir = os.path.abspath(os.path.join(os.path.dirname(__file__),'queries'))
|
||
|
|
for dir, _, files in os.walk(query_dir):
|
||
|
|
for file in files:
|
||
|
|
if file.endswith('.sql'):
|
||
|
|
queries[os.path.splitext(file)[0]] = open(os.path.join(dir,file), 'r').read()
|
||
|
|
if msettings.DEBUG:
|
||
|
|
tornado.autoreload.watch(os.path.join(dir,file))
|
||
|
|
|
||
|
|
def getexamples(app):
|
||
|
|
if "examples" not in app:
|
||
|
|
return []
|
||
|
|
fullexamples=[]
|
||
|
|
if type(app["examples"])==list:
|
||
|
|
i=0
|
||
|
|
for el in app["examples"]:
|
||
|
|
i+=1
|
||
|
|
d={}
|
||
|
|
d["name"]='ex'+str(i)
|
||
|
|
d["paramstring"]=str(el).replace('{','').replace('}','').replace("'",'')
|
||
|
|
d["paramarray"]=json.dumps(el)
|
||
|
|
fullexamples.append(d)
|
||
|
|
else:
|
||
|
|
for el in app["examples"]:
|
||
|
|
d={}
|
||
|
|
d["name"]=el
|
||
|
|
d["paramstring"]=str(app["examples"][el]).replace('{','').replace('}','').replace("'",'')
|
||
|
|
d["paramarray"]=json.dumps(app["examples"][el])
|
||
|
|
fullexamples.append(d)
|
||
|
|
fullexamples.sort(key=lambda x:x["name"])
|
||
|
|
return fullexamples
|
||
|
|
|
||
|
|
def processtemplate(app):
|
||
|
|
if 'template' not in app:
|
||
|
|
return
|
||
|
|
|
||
|
|
getqueries()
|
||
|
|
|
||
|
|
if 'initial_queries' in queries:
|
||
|
|
try:
|
||
|
|
list(msettings.Connection.cursor().execute(queries['initial_queries']))
|
||
|
|
except Exception, e:
|
||
|
|
raise Exception("Error when executing DB_INITIAL_EXECUTE:\n"+queries['initial_queries']+"\nThe error was:\n"+ str(e))
|
||
|
|
|
||
|
|
tornado.options.parse_command_line()
|
||
|
|
|
||
|
|
# Restructure applications
|
||
|
|
logging.info('Running madApp startup scripts')
|
||
|
|
|
||
|
|
for app in madapps.apps:
|
||
|
|
|
||
|
|
app['link']=app['link'].lower()
|
||
|
|
if "title" not in app:
|
||
|
|
app["title"]=app['link']
|
||
|
|
if "linktitle" not in app:
|
||
|
|
app["linktitle"]=app["title"]
|
||
|
|
|
||
|
|
if 'startup' in app:
|
||
|
|
c=msettings.Connection.cursor()
|
||
|
|
logging.info('Running startup queries for app'+app['linktitle']+' :\n'+app['startup'])
|
||
|
|
c.execute(app['startup'])
|
||
|
|
c.close()
|
||
|
|
|
||
|
|
app["qtext"]=getqtext(app["query"], [p['name'] for p in app['params']])
|
||
|
|
app["examples"]=getexamples(app)
|
||
|
|
app['datavisualizations']=dict([(x,[y['visualizations']] if type(y['visualizations'])==dict else y['visualizations']) for x,y in app.iteritems() if type(y)==dict and 'query' in y])
|
||
|
|
if 'query' in app:
|
||
|
|
app['datavisualizations']['query']=copy.deepcopy(app['visualisations'])
|
||
|
|
for vis in app['visualisations']:
|
||
|
|
vis['viswidgetmap']=viswidgetmap[vis['name'].lower()]
|
||
|
|
|
||
|
|
logging.info('Completed madApp startup scripts')
|
||
|
|
|
||
|
|
filteredapps=filter(lambda x:("eval" not in x),madapps.apps)
|
||
|
|
filteredevals=filter(lambda x:("eval" in x),madapps.apps)
|
||
|
|
|
||
|
|
if not msettings.DEBUG:
|
||
|
|
sockets = tornado.netutil.bind_sockets(options.port)
|
||
|
|
tornado.process.fork_processes(0)
|
||
|
|
server = tornado.httpserver.HTTPServer(Application())
|
||
|
|
# ssl_options = {
|
||
|
|
#"certfile": os.path.join("/home/openaire/ssl/certificate.crt"),
|
||
|
|
#"keyfile": os.path.join("/home/openaire/ssl/privateKey.key"),
|
||
|
|
#})
|
||
|
|
server.add_sockets(sockets)
|
||
|
|
tornado.ioloop.IOLoop.instance().start()
|
||
|
|
else:
|
||
|
|
# debug case
|
||
|
|
http_server = tornado.httpserver.HTTPServer(Application())
|
||
|
|
http_server.bind(options.port)
|
||
|
|
http_server.start(1)
|
||
|
|
tornado.ioloop.IOLoop.instance().start()
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
if __name__ == "__main__":
|
||
|
|
main()
|