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IPython magic for simple, organized, compressed and encrypted: storage & transfer of files between notebooks

Project description

IPython data-vault

|Build Status| |codecov| |CodeQL| |MIT License| |Binder| |DOI|

IPython magic for simple, organized, compressed and encrypted storage & transfer of files between notebooks.

Background and demo

Right tool for a simple job


The ``%vault`` magic provides a reproducible caching mechanism for
variables exchange between notebooks. The cache is compressed,
persistent and safe.

Differently to the builtin ``%store`` magic, the variables are stored in
plain sight, in a zipped archive, so that they can be easily accessed
for manual inspection, or for the use by other tools.

Demonstration by usage:
~~~~~~~~~~~~~~~~~~~~~~~

Let’s open the vault (it will be created if not here yet):

.. code:: python

   %open_vault -p data/storage.zip

Generate some dummy dataset:

.. code:: python

   from pandas import DataFrame
   from random import choice, randint
   cities = ['London', 'Delhi', 'Tokyo', 'Lagos', 'Warsaw', 'Chongqing']
   salaries = DataFrame([
       {'salary': randint(0, 100), 'city': choice(cities)}
       for i in range(10000)
   ])

Store variable in a module
^^^^^^^^^^^^^^^^^^^^^^^^^^

And store it in the vault:

.. code:: python

   %vault store salaries in datasets

..

   Stored salaries (None → 40CA7812) at Sunday, 08. Dec 2019 11:58

A short description is printed out (including a CRC32 hashsum and a
timestamp) by default, but can be disabled by passing
``--timestamp False`` to ``%open_vault`` magic. Even more information
enhancing the reproducibility is `stored in the cell
metadata <#metadata-for-storage-operations>`__.

Import variable from a module
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

We can now load the stored DataFrame in another (or the same) notebook:

.. code:: python

   %vault import salaries from datasets

..

   Imported salaries (40CA7812) at Sunday, 08. Dec 2019 12:02

Thanks to (optional) `memory optimizations <#memory-optimizations>`__ we
saved some RAM (87% as compared to unoptimized ``pd.read_csv()``
result). To track how many MB were saved use ``--report_memory_gain``
setting which will display memory optimization results below imports,
for example:

   Reduced memory usage by 87.28%, from 0.79 MB to 0.10 MB.

Import variable as something else
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

If we already have the salaries variable, we can use ``as``, just like
in the Python import system.

.. code:: python

   %vault import salaries from datasets as salaries_dataset

Store or import with a custom function
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. code:: python

   from pandas import read_csv
   to_csv = lambda df: df.to_csv()
   %vault store salaries in datasets with to_csv as salaries_csv
   %vault import salaries_csv from datasets with read_csv

Import an arbitrary file
^^^^^^^^^^^^^^^^^^^^^^^^

.. code:: python

   from pandas import read_excel
   %vault import 'cars.xlsx' as cars_dataset with read_excel

More examples are available in the
`Examples.ipynb <https://github.com/krassowski/data-vault/blob/master/Example.ipynb>`__
notebook, which can be `run interactively in the
browser <https://mybinder.org/v2/gh/krassowski/data-vault/master?filepath=Example.ipynb>`__.

Goals
~~~~~

Syntax: - easy to understand in plain language (avoid abbreviations when
possible), - while intuitive for Python developers, - …but sufficiently
different so that it would not be mistaken with Python constructs - for
example, we could have ``%from x import y``, but this looks very like
normal Python; having ``%vault from x import y`` makes it sufficiently
easy to distinguish - star imports are better avoided, thus not
supported - as imports may be confusing if there is more than one

Reproducibility: - promote good reproducible and traceable organization
of files: - promote storage in plain text files and the use of DataFrame
> pickling is often an easy solution, but it can cause hurtful problems
in prototyping phase (which is what notebooks are often used for): if
you pickle you objects, then change the class definition and attempt to
load your data again you are likely to fail severly; this is why the
plain text files are the default option in this package (but pickling is
supported too!). - print out a short hashsum and human-readable datetime
(always in UTC), - while providing even more details in cell metadata -
allow to trace instances of the code being modified post execution

Security:

-  think of it as a tool to minimize the damage in case of accidental
   ``git add`` of data files (even if those should have been elsewhere
   and ``.gitignore``\ d in the first place),
-  or, as an additional layer of security for already anonymized data,
-  but this tool is **not** aimed at facilitating the storage of highly
   sensitive data
-  you have to set a password, or explicitly set ``--secure False`` to
   get rid of a security warning

Features overview
-----------------

Metadata for storage operations

Each operation will print out the timestamp and the CRC32 short checksum of the files involved. The timestamp of the operation is reported in the UTC timezone in a human-readable format.

This can be disabled by setting -t False or --timestamp False, however for the sake of reproducibility it is encouraged to keep this information visible in the notebook.

More precise information including the SHA256 cheksum (with a lower probability of collisions), and a full timestamp (to detect potential race condition errors in file write operations) are embedded in the metadata of the cell. You can disable this by setting –metadata False.

The exact command line is also stored in the metadata, so that if you accidentally modify the code cell without re-running the code, the change can be tracked down.

Storage


In order to enforce interoperability plain text files are used for
pandas DataFrame and Series objects. Other variables are stores as
pickle objects. The location of the storage archive on the disk defaults
to ``storage.zip`` in the current directory, and can changed using
``%open_vault`` magic:

.. code:: python

   %open_vault -p custom_storage.zip

Encryption
^^^^^^^^^^

   **The encryption is not intended as a high security mechanism, but
   only as an additional layer of protection for already anonymized
   data.**

The password to encrypt the storage archive is retrieved from the
environmental variable, using a name provided in ``encryption_variable``
during the setup.

.. code:: python

   %open_vault -e ENV_STORAGE_KEY

Memory optimizations

Pandas DataFrames are by-default memory optimized by conversion of string variables to (ordered) categorical columns (pandas equivalent of R’s factors/levels). Each string column will be tested for the memory improvement and the optimization will be only applied if it does reduce the memory usage.

Why ZIP and not HDF?


The storage archive is conceptually similar to Hierarchical Data Format
(e.g. HDF5) object - it contains: - a hierarchy of files, and - a
metadata files

I believe that HDF may be the future, but this future is not here yet -
numerous issues with the packages handling the HDF files, as well as low
performance and compression rate prompted me to stay with a simple zip
format now.

ZIP is a popular file format with known features and limitations - files
can be password encrypted, while the file list is always accessible.
This is okay given that the code of the project is assumed to be public,
and only the files in the storage area are assumed to be of encrypted,
increasing the security in case of unauthorized access.

As the limitations of the ZIP encryption are assumed to be a common
knowledge, I hope that managing expectations of the level of security
offered by this package will be easier.

Installation and requirements
-----------------------------

Pre-requirements: - Python 3.6+ - 7zip (16.02+) (see
`below <#installing-7-zip>`__ for Ubuntu and Mac commands)

Installation:
~~~~~~~~~~~~~

.. code:: bash

   pip3 install data_vault

Installing 7-zip
~~~~~~~~~~~~~~~~

Installers for Windows can be downloaded from the `7-zip
website <https://www.7-zip.org/download.html>`__.

For other systems you can use packages from the default repositories:

Ubuntu
^^^^^^

.. code:: bash

   sudo apt-get install -y p7zip-full

Mac
^^^

.. code:: bash

   brew install p7zip

.. |Build Status| image:: https://travis-ci.org/krassowski/data-vault.svg?branch=master
   :target: https://travis-ci.org/krassowski/data-vault
.. |codecov| image:: https://codecov.io/gh/krassowski/data-vault/branch/master/graph/badge.svg
   :target: https://codecov.io/gh/krassowski/data-vault
.. |CodeQL| image:: https://github.com/krassowski/data-vault/workflows/CodeQL/badge.svg
.. |MIT License| image:: https://img.shields.io/badge/license-MIT-blue.svg?style=flat
   :target: http://choosealicense.com/licenses/mit/
.. |Binder| image:: https://mybinder.org/badge_logo.svg
   :target: https://mybinder.org/v2/gh/krassowski/data-vault/master?filepath=Example.ipynb
.. |DOI| image:: https://zenodo.org/badge/226589892.svg
   :target: https://zenodo.org/badge/latestdoi/226589892


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