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Tentaclio

CircleCI status Documentation Status

Python library that simplifies:

  • Handling streams from different protocols such as file:, ftp:, sftp:, s3:, ...
  • Opening database connections.
  • Managing the credentials in distributed systems.

Main considerations in the design:

  • Easy to use: all streams are open via tentaclio.open, all database connections through tentaclio.db.
  • URLs are the basic resource locator and db connection string.
  • Automagic authentication for protected resources.
  • Extensible: you can add your own handlers for other schemes.
  • Pandas interaction.

Quick Examples.

Read and write streams.

import tentaclio
contents = "👋 🐙"

with tentaclio.open("ftp://localhost:2021/upload/file.txt", mode="w") as writer:
    writer.write(contents)

# Using boto3 authentication under the hood.
bucket = "s3://my-bucket/octopus/hello.txt"
with tentaclio.open(bucket) as reader:
    print(reader.read())

Copy streams

import tentaclio

tentaclio.copy("/home/constantine/data.csv", "sftp://constantine:[email protected]/uploads/data.csv")

Delete resources

import tentaclio

tentaclio.remove("s3://my-bucket/octopus/the-9th-tentacle.txt")

List resources

import tentaclio

for entry in tentaclio.listdir("s3:://mybucket/path/to/dir"):
    print("Entry", entry)

Authenticated resources.

import os

import tentaclio

print("env ftp credentials", os.getenv("OCTOIO__CONN__OCTOENERGY_FTP"))
# This prints `sftp://constantine:[email protected]/`

# Credentials get automatically injected.

with tentaclio.open("sftp://sftp.octoenergy.com/uploads/data.csv") as reader:
    print(reader.read())

Database connections.

import os

import tentaclio

print("env TENTACLIO__CONN__DB", os.getenv("TENTACLIO__CONN__DB"))

# This prints `postgresql://octopus:tentacle@localhost:5444/example`

# hostname is a wildcard, the credentials get injected.
with tentaclio.db("postgresql://hostname/example") as pg:
    results = pg.query("select * from my_table")

Pandas interaction.

import pandas as pd  # 🐼🐼
import tentaclio  # 🐙

df = pd.DataFrame([[1, 2, 3], [10, 20, 30]], columns=["col_1", "col_2", "col_3"])

bucket = "s3://my-bucket/data/pandas.csv"

with tentaclio.open(bucket, mode="w") as writer:  # supports more pandas readers
    df.to_csv(writer, index=False)

with tentaclio.open(bucket) as reader:
    new_df = pd.read_csv(reader)

# another example: using pandas.DataFrame.to_sql() with tentaclio to upload
with tentaclio.db(
        connection_info,
        connect_args={'options': '-csearch_path=schema_name'}
    ) as client:
    df.to_sql(
        name='observations', # table name
        con=client.conn,
    )

Installation

You can get tentaclio using pip

pip install tentaclio

or pipenv

pipenv install tentaclio

Developing.

Clone this repo and install pipenv:

In the Makefile you'll find some useful targets for linting, testing, etc. i.e.:

make test

How to use

This is how to use tentaclio for your daily data ingestion and storing needs.

Streams

In order to open streams to load or store data the universal function is:

import tentaclio

with tentaclio.open("/path/to/my/file") as reader:
    contents = reader.read()

with tentaclio.open("s3://bucket/file", mode='w') as writer:
    writer.write(contents)

Allowed modes are r, w, rb, and wb. You can use t instead of b to indicate text streams, but that's the default.

In order to keep tentaclio as light as possible, it only includes file, ftp, sftp, http and https schemes by default. However, many more are easily available by installing extra packages:

Default:

  • /local/file
  • file:///local/file
  • ftp://path/to/file
  • sftp://path/to/file
  • http://host.com/path/to/resource
  • https://host.com/path/to/resource

tentaclio-s3

  • s3://bucket/file

tentaclio-gs

  • gs://bucket/file
  • gsc://bucket/file

tentaclio-gdrive

  • gdrive:/My Drive/file
  • googledrive:/My Drive/file

tentaclio-postgres

  • postgresql://host/database::table will allow you to write from a csv format into a database with the same column names (note that the table goes after :: ⚠️).

You can add the credentials for any of the urls in order to access protected resources.

You can use these readers and writers with pandas functions like:

import pandas as pd
import tentaclio

with tentaclio.open("/path/to/my/file") as reader:
    df = pd.read_csv(reader)

[...]

with tentaclio.open("s3::/path/to/my/file", mode='w') as writer:
    df.to_parquet(writer)

Readers, Writers and their closeable versions can be used anywhere expecting a file-like object; pandas or pickle are examples of such functions.

Notes on writing files for Spark, Presto, and similar downstream systems

The default behaviour for the open context manager in python is to create an empty file when opening it in writable mode. This can be annoying if the process that creates the data within the with clause yields empty dataframes and nothing gets written. This will make Spark and Presto panic.

To avoid this we can make the stream empty safe so the empty buffer won't be flushed if no writes have been performed so no empty file will be created.

with tio.make_empty_safe(tio.open("s3://bucket/file.parquet", mode="wb")) as writer:
    if not df.empty:
        df.to_parquet(writer)

File system like operations to resources

Listing resources

Some URL schemes allow listing resources in a pythonnic way:

import tentaclio

for entry in tentaclio.listdir("s3:://mybucket/path/to/dir"):
    print("Entry", entry)

Whereas listdir might be convinient we also offer scandir, which returns a list of DirEntrys, and, walk. All functions follow as closely as possible their standard library definitions.

Database access

In order to open db connections you can use tentaclio.db and have instant access to postgres, sqlite, athena and mssql.

import tentaclio

[...]

query = "select 1";
with tentaclio.db(POSTGRES_TEST_URL) as client:
    result =client.query(query)
[...]

The supported db schemes are:

Default:

  • sqlite://
  • mssql://
    • Any other scheme supported by sqlalchemy.

tentaclio-postgres

  • postgresql://

tentaclio-athena

  • awsathena+rest://

tentaclio-databricks

  • databricks+thrift://

tentaclio-snowflake

  • snowflake://

Extras for databases

For postgres you can set the variable TENTACLIO__PG_APPLICATION_NAME and the value will be injected when connecting to the database.

Automatic credentials injection

  1. Configure credentials by using environmental variables prefixed with TENTACLIO__CONN__ (i.e. TENTACLIO__CONN__DATA_FTP=sfpt://real_user:[email protected]).

  2. Open a stream:

with tentaclio.open("sftp://ftp.octoenergy.com/file.csv") as reader:
    reader.read()

The credentials get injected into the url.

  1. Open a db client:
import tentaclio

with tentaclio.db("postgresql://hostname/my_data_base") as client:
    client.query("select 1")

Note that hostname in the url to be authenticated is a wildcard that will match any hostname. So authenticate("http://hostname/file.txt") will be injected to http://user:[email protected]/file.txt if the credential for http://user:[email protected]/ exists.

Different components of the URL are set differently:

  • Scheme and path will be set from the URL, and null if missing.
  • Username, password and hostname will be set from the stored credentials.
  • Port will be set from the stored credentials if it exists, otherwise from the URL.
  • Query will be set from the URL if it exists, otherwise from the stored credentials (so it can be overriden)

Credentials file

You can also set a credentials file that looks like:

secrets:
    db_1: postgresql://user1:[email protected]/database_1
    db_2: mssql://user2:[email protected]/database_2?driver=ODBC+Driver+17+for+SQL+Server
    ftp_server: ftp://fuser:[email protected]

And make it accessible to tentaclio by setting the environmental variable TENTACLIO__SECRETS_FILE. The actual name of each url is for traceability and has no effect in the functionality.

(Note that you may need to add ?driver={driver from /usr/local/etc/odbcinst.ini} for mssql database connection strings; see above example)

Alternatively you can run curl https://raw.githubusercontent.com/octoenergy/tentaclio/master/extras/init_tentaclio.sh to create a secrets file in ~/.tentaclio.yml and automatically configure your environment.

Environment variables can be included in the credentials file by using ${ENV_VARIABLE} as it follows:

secrets:
    db: postgresql://${DB_USER}:${DB_PASS}@myhost.com/database

Tentaclio will search DB_USER and DB_PASS in the environment and will interpolate their values with the secrets file content.

Quick note on protocols structural subtyping.

In order to abstract concrete dependencies from the implementation of data related functions (or in any part of the system really) we use typed protocols. This allows a more flexible dependency injection than using subclassing or more complex approches. This idea is heavily inspired by how this exact thing is done in go. Learn more about this principle in our tech blog.