data-transport/transport/mongo.py

216 lines
8.0 KiB
Python

"""
Data Transport - 1.0
Steve L. Nyemba, The Phi Technology LLC
This file is a wrapper around mongodb for reading/writing content against a mongodb server and executing views (mapreduce)
"""
from pymongo import MongoClient
from bson.objectid import ObjectId
from bson.binary import Binary
# import nujson as json
from datetime import datetime
import pandas as pd
import numpy as np
import gridfs
# from transport import Reader,Writer
import sys
if sys.version_info[0] > 2 :
from transport.common import Reader, Writer
else:
from common import Reader, Writer
import json
import re
from multiprocessing import Lock, RLock
class Mongo :
lock = RLock()
"""
Basic mongodb functions are captured here
"""
def __init__(self,**args):
"""
:dbname database name/identifier
:host host and port of the database by default localhost:27017
:username username for authentication
:password password for current user
"""
self.mechanism= 'SCRAM-SHA-256' if 'mechanism' not in args else args['mechanism']
# authSource=(args['authSource'] if 'authSource' in args else self.dbname)
self._lock = False if 'lock' not in args else args['lock']
username = password = None
if 'auth_file' in args :
_info = json.loads((open(args['auth_file'])).read())
else:
_info = {}
_args = dict(args,**_info)
for key in _args :
if key in ['username','password'] :
username = _args['username'] if key=='username' else username
password = _args['password'] if key == 'password' else password
continue
value = _args[key]
self.setattr(key,value)
#
# Let us perform aliasing in order to remain backwards compatible
self.dbname = self.db if hasattr(self,'db')else self.dbname
self.uid = _args['table'] if 'table' in _args else (_args['doc'] if 'doc' in _args else (_args['collection'] if 'collection' in _args else None))
if username and password :
self.client = MongoClient(self.host,
username=username,
password=password ,
authSource=self.authSource,
authMechanism=self.mechanism)
else:
self.client = MongoClient(self.host,maxPoolSize=10000)
self.db = self.client[self.dbname]
def isready(self):
p = self.dbname in self.client.list_database_names()
q = self.uid in self.client[self.dbname].list_collection_names()
return p and q
def setattr(self,key,value):
_allowed = ['host','port','db','doc','authSource','mechanism']
if key in _allowed :
setattr(self,key,value)
pass
def close(self):
self.client.close()
def meta(self,**_args):
return []
class MongoReader(Mongo,Reader):
"""
This class will read from a mongodb data store and return the content of a document (not a collection)
"""
def __init__(self,**args):
Mongo.__init__(self,**args)
def read(self,**args):
if 'mongo' in args or 'cmd' in args:
#
# @TODO:
cmd = args['mongo'] if 'mongo' in args else args['cmd']
if "aggregate" in cmd :
if "allowDiskUse" not in cmd :
cmd["allowDiskUse"] = True
if "cursor" not in cmd :
cmd["cursor"] = {}
r = []
out = self.db.command(cmd)
#@TODO: consider using a yield (generator) works wonders
while True :
if 'values' in out :
r += out['values']
if 'cursor' in out :
key = 'firstBatch' if 'firstBatch' in out['cursor'] else 'nextBatch'
else:
key = 'n'
if 'cursor' in out and out['cursor'][key] :
r += list(out['cursor'][key])
elif key in out and out[key]:
r.append (out[key])
# yield out['cursor'][key]
if key not in ['firstBatch','nextBatch'] or ('cursor' in out and out['cursor']['id'] == 0) :
break
else:
out = self.db.command({"getMore":out['cursor']['id'],"collection":out['cursor']['ns'].split(".")[-1]})
return pd.DataFrame(r)
else:
collection = self.db[self.uid]
_filter = args['filter'] if 'filter' in args else {}
_df = pd.DataFrame(collection.find(_filter))
columns = _df.columns.tolist()[1:]
return _df[columns]
def view(self,**args):
"""
This function is designed to execute a view (map/reduce) operation
"""
pass
class MongoWriter(Mongo,Writer):
"""
This class is designed to write to a mongodb collection within a database
"""
def __init__(self,**args):
Mongo.__init__(self,**args)
def upload(self,**args) :
"""
This function will upload a file to the current database (using GridFS)
:param data binary stream/text to be stored
:param filename filename to be used
:param encoding content_encoding (default utf-8)
"""
if 'encoding' not in args :
args['encoding'] = 'utf-8'
gfs = GridFS(self.db)
gfs.put(**args)
def archive(self):
"""
This function will archive documents to the
"""
collection = self.db[self.uid]
rows = list(collection.find())
for row in rows :
if type(row['_id']) == ObjectId :
row['_id'] = str(row['_id'])
stream = Binary(json.dumps(collection).encode())
collection.delete_many({})
now = "-".join([str(datetime.now().year()),str(datetime.now().month), str(datetime.now().day)])
name = ".".join([self.uid,'archive',now])+".json"
description = " ".join([self.uid,'archive',str(len(rows))])
self.upload(filename=name,data=stream,description=description,content_type='application/json')
# gfs = GridFS(self.db)
# gfs.put(filename=name,description=description,data=stream,encoding='utf-8')
# self.write({{"filename":name,"file":stream,"description":descriptions}})
pass
def write(self,info,**_args):
"""
This function will write to a given collection i.e add a record to a collection (no updates)
@param info new record in the collection to be added
"""
# document = self.db[self.uid].find()
#collection = self.db[self.uid]
# if type(info) == list :
# self.db[self.uid].insert_many(info)
# else:
try:
_uid = self.uid if 'doc' not in _args else _args['doc']
if self._lock :
Mongo.lock.acquire()
if type(info) == list or type(info) == pd.DataFrame :
self.db[_uid].insert_many(info if type(info) == list else info.to_dict(orient='records'))
else:
self.db[_uid].insert_one(info)
finally:
if self._lock :
Mongo.lock.release()
def set(self,document):
"""
if no identifier is provided the function will delete the entire collection and set the new document.
Please use this function with great care (archive the content first before using it... for safety)
"""
collection = self.db[self.uid]
if collection.count_document() > 0 and '_id' in document:
id = document['_id']
del document['_id']
collection.find_one_and_replace({'_id':id},document)
else:
collection.delete_many({})
self.write(info)
def close(self):
Mongo.close(self)
# collecton.update_one({"_id":self.uid},document,True)