Insert a Pandas Dataframe into mongodb using PyMongo
PythonMongodbPython 2.7PandasPymongoPython Problem Overview
What is the quickest way to insert a pandas DataFrame into mongodb using PyMongo?
Attempts
db.myCollection.insert(df.to_dict())
gave an error
> InvalidDocument: documents must have only string keys, the key was > Timestamp('2013-11-23 13:31:00', tz=None)
>
db.myCollection.insert(df.to_json())
gave an error
> TypeError: 'str' object does not support item assignment
>
db.myCollection.insert({id: df.to_json()})
gave an error
InvalidDocument: documents must have only string a keys, key was <built-in function id>
df
<class 'pandas.core.frame.DataFrame'>
DatetimeIndex: 150 entries, 2013-11-23 13:31:26 to 2013-11-23 13:24:07
Data columns (total 3 columns):
amount 150 non-null values
price 150 non-null values
tid 150 non-null values
dtypes: float64(2), int64(1)
Python Solutions
Solution 1 - Python
Here you have the very quickest way. Using the insert_many method from pymongo 3 and 'records' parameter of to_dict method.
db.collection.insert_many(df.to_dict('records'))
Solution 2 - Python
I doubt there is a both quickest and simple method. If you don't worry about data conversion, you can do
>>> import json
>>> df = pd.DataFrame.from_dict({'A': {1: datetime.datetime.now()}})
>>> df
A
1 2013-11-23 21:14:34.118531
>>> records = json.loads(df.T.to_json()).values()
>>> db.myCollection.insert(records)
But in case you try to load data back, you'll get:
>>> df = read_mongo(db, 'myCollection')
>>> df
A
0 1385241274118531000
>>> df.dtypes
A int64
dtype: object
so you'll have to convert 'A' columnt back to datetimes, as well as all not int, float or str fields in your DataFrame. For this example:
>>> df['A'] = pd.to_datetime(df['A'])
>>> df
A
0 2013-11-23 21:14:34.118531
Solution 3 - Python
odo can do it using
odo(df, db.myCollection)
Solution 4 - Python
If your dataframe has missing data (i.e None,nan) and you don't want null key values in your documents:
db.insert_many(df.to_dict("records")) will insert keys with null values. If you don't want the empty key values in your documents you can use a modified version of pandas .to_dict("records") code below:
from pandas.core.common import _maybe_box_datetimelike
my_list = [dict((k, _maybe_box_datetimelike(v)) for k, v in zip(df.columns, row) if v != None and v == v) for row in df.values]
db.insert_many(my_list)
where the if v != None and v == v I've added checks to make sure the value is not None or nan before putting it in the row's dictionary. Now your .insert_many will only include keys with values in the documents (and no null data types).
Solution 5 - Python
I think there is cool ideas in this question. In my case I have been spending time more taking care of the movement of large dataframes. In those case pandas tends to allow you the option of chunksize (for examples in the pandas.DataFrame.to_sql). So I think I con contribute here by adding the function I am using in this direction.
def write_df_to_mongoDB( my_df,\
database_name = 'mydatabasename' ,\
collection_name = 'mycollectionname',
server = 'localhost',\
mongodb_port = 27017,\
chunk_size = 100):
#"""
#This function take a list and create a collection in MongoDB (you should
#provide the database name, collection, port to connect to the remoete database,
#server of the remote database, local port to tunnel to the other machine)
#
#---------------------------------------------------------------------------
#Parameters / Input
# my_list: the list to send to MongoDB
# database_name: database name
#
# collection_name: collection name (to create)
# server: the server of where the MongoDB database is hosted
# Example: server = 'XXX.XXX.XX.XX'
# this_machine_port: local machine port.
# For example: this_machine_port = '27017'
# remote_port: the port where the database is operating
# For example: remote_port = '27017'
# chunk_size: The number of items of the list that will be send at the
# some time to the database. Default is 100.
#
#Output
# When finished will print "Done"
#----------------------------------------------------------------------------
#FUTURE modifications.
#1. Write to SQL
#2. Write to csv
#----------------------------------------------------------------------------
#30/11/2017: Rafael Valero-Fernandez. Documentation
#"""
#To connect
# import os
# import pandas as pd
# import pymongo
# from pymongo import MongoClient
client = MongoClient('localhost',int(mongodb_port))
db = client[database_name]
collection = db[collection_name]
# To write
collection.delete_many({}) # Destroy the collection
#aux_df=aux_df.drop_duplicates(subset=None, keep='last') # To avoid repetitions
my_list = my_df.to_dict('records')
l = len(my_list)
ran = range(l)
steps=ran[chunk_size::chunk_size]
steps.extend([l])
# Inser chunks of the dataframe
i = 0
for j in steps:
print j
collection.insert_many(my_list[i:j]) # fill de collection
i = j
print('Done')
return
Solution 6 - Python
how about this:
db.myCollection.insert({id: df.to_json()})
id will be a unique string for that df
Solution 7 - Python
I use the following part to insert the dataframe to a collection in the database.
df.reset_index(inplace=True)
data_dict = df.to_dict("records")
myCollection.insert_many(data_dict)
Solution 8 - Python
Just make string keys!
import json
dfData = json.dumps(df.to_dict('records'))
savaData = {'_id': 'a8e42ed79f9dae1cefe8781760231ec0', 'df': dfData}
res = client.insert_one(savaData)
##### load dfData
data = client.find_one({'_id': 'a8e42ed79f9dae1cefe8781760231ec0'}).get('df')
dfData = json.loads(data)
df = pd.DataFrame.from_dict(dfData)
Solution 9 - Python
If you want to send several at one time:
db.myCollection.insert_many(df.apply(lambda x: x.to_dict(), axis=1).to_list())
Solution 10 - Python
If you want to make sure that you're not raising InvalidDocument errors, then something like the following is a good idea. This is because mongo does not recognize types such as np.int64, np.float64, etc.
from pymongo import MongoClient
client = MongoClient()
db = client.test
col = db.col
def createDocsFromDF(df, collection = None, insertToDB=False):
docs = []
fields = [col for col in df.columns]
for i in range(len(df)):
doc = {col:df[col][i] for col in df.columns if col != 'index'}
for key, val in doc.items():
# we have to do this, because mongo does not recognize these np. types
if type(val) == np.int64:
doc[key] = int(val)
if type(val) == np.float64:
doc[key] = float(val)
if type(val) == np.bool_:
doc[key] = bool(val)
docs.append(doc)
if insertToDB and collection:
db.collection.insert_many(docs)
return docs
Solution 11 - Python
For upserts this worked.
for r in df2.to_dict(orient="records"):
db['utest-pd'].update_one({'a':r['a']},{'$set':r})
Does it one record at a time but it didn't seem upsert_many was able to work with more than one filter value for different records.