antarctic 0.3.4

Storing Pandas Data in a MongoDB database

Antarctic

Project to persist Pandas data structures in a MongoDB database.

Installation

pip install antarctic

Usage

This project (unless the popular arctic project which I admire) is based on top of MongoEngine, see MongoEngine. MongoEngine is an ORM for MongoDB. MongoDB stores documents. We introduce new fields and extend the Document class to make Antarctic a convenient choice for storing Pandas (time series) data.

Experiments

We highly recommend to start first with some experiments using the Binder server given above.

Fields

We introduce first two new fields --- one for a Pandas Series and one for a Pandas DataFrame.

from mongoengine import Document, connect
from antarctic.pandas_fields import SeriesField, FrameField

# connect with your existing MongoDB (here I am using a popular interface mocking a MongoDB)
client = connect(db="test", host="mongomock://localhost")


# Define the blueprint for a portfolio document
class Portfolio(Document):
	nav = SeriesField()
	weights = FrameField()
	prices = FrameField()

The portfolio objects works exactly the way you think it works

p = Portfolio()
p.nav = pd.Series(...)
p.prices = pd.DataFrame(...)
p.save()

print(p.nav)
print(p.prices)

Behind the scenes we convert the both Series and Frame objects into json documents and store them in a MongoDB database.

Unfortunately it is rather slow to write json documents to disk. We therefore introduce the ParquteFrameField, the ParquetSeriesField and the PicklePandasField. In our first experiments the PicklePandasField is the fastest option and outperforms arctic. However, further work and experiments are required.

The ParquetFrameField relies on a popular format which should also be readable by R. Here the frame is converted in a bytestream rather than a json document. Users gain speed, save space and it's possible to work with larger frames.

class Maffay(Document):
    # we support the engine and compression argument as in .to_parquet in pandas
    frame = ParquetFrameField(engine="pyarrow", compression=None)

maffay = Maffay()

# the magic happens in the background. The frame is converted in parquet byte stream and stored in the MongoDB.    
maffay.frame = pd.DataFrame(...) # some very large DataFrame, note that column names have to strings.

# reading the frame applies the same magic again.
print(maffay.frame)

Documents

In most cases we have copies of very similar documents, e.g. we store Portfolios and Symbols rather than just a Portfolio or a Symbol. For this purpose we have developed the abstract XDocument class relying on the Document class of MongoEngine. It provides some convenient tools to simplify looping over all or a subset of Documents of the same type, e.g.

from antarctic.document import XDocument
from antarctic.pandas_fields import SeriesField

client = connect(db="test", host="mongomock://localhost")


class Symbol(XDocument):
	price = SeriesField()

We define a bunch of symbols and assign a price for each (or some of it):

s1 = Symbol(name="A", price=pd.Series(...)).save()
s2 = Symbol(name="B", price=pd.Series(...)).save()

# We can access subsets like
for symbol in Symbol.subset(names=["B"]):
	print(symbol)

# often we need a dictionary of Symbols:
Symbol.to_dict(objects=[s1, s2])

# Each XDocument also provides a field for reference data:
s1.reference["MyProp1"] = "ABC"
s2.reference["MyProp2"] = "BCD"

# You can loop over (subsets) of Symbols and extract reference and/or series data
print(Symbol.reference_frame(objects=[s1, s2]))
print(Symbol.series(series="price"))
print(Symbol.apply(func=lambda x: x.price.mean(), default=np.nan))

The XDocument class is exposing DataFrames both for reference and time series data. There is an apply method for using a function on (subset) of documents.

Database vs. Datastore

Storing json or bytestream representations of Pandas objects is not exactly a database. Appending is rather expensive as one would have to extract the original Pandas object, append to it and convert the new object back into a json or bytestream representation. Clever sharding can mitigate such effects but at the end of the day you shouldn't update such objects too often. Often practitioners use a small database for recording (e.g. over the last 24h) and update the MongoDB database once a day. It's extremely fast to read the Pandas objects out of such a construction.

Often such concepts are called DataStores.