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https://github.com/krassowski/data-vault
IPython magic for simple, organized, compressed and encrypted: storage & transfer of files between notebooks.
https://github.com/krassowski/data-vault
data-storage disk-cache ipython-magic jupyter-notebook persistent-storage
Last synced: about 3 hours ago
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IPython magic for simple, organized, compressed and encrypted: storage & transfer of files between notebooks.
- Host: GitHub
- URL: https://github.com/krassowski/data-vault
- Owner: krassowski
- License: mit
- Created: 2019-12-07T23:35:35.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2022-12-08T15:48:22.000Z (almost 2 years ago)
- Last Synced: 2024-04-26T09:45:27.525Z (7 months ago)
- Topics: data-storage, disk-cache, ipython-magic, jupyter-notebook, persistent-storage
- Language: Python
- Homepage:
- Size: 81.1 KB
- Stars: 13
- Watchers: 3
- Forks: 2
- Open Issues: 11
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# IPython data-vault
[](https://github.com/krassowski/data-vault/actions/workflows/tests.yml)
[](http://choosealicense.com/licenses/mit/)
[](https://mybinder.org/v2/gh/krassowski/data-vault/master?filepath=Example.ipynb)
[](https://zenodo.org/badge/latestdoi/226589892)
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):
```python
%open_vault -p data/storage.zip
```
Generate some dummy dataset:
```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:
```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:
```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.
```python
%vault import salaries from datasets as salaries_dataset
```
#### Store or import with a custom function
```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
```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:
```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.
```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:
```bash
pip3 install data_vault
```
### Installing 7-zip
You can use p7zip packages from the default repositories:
#### Ubuntu
```bash
sudo apt-get install -y p7zip-full
```
#### Mac
```bash
brew install p7zip
```
#### Windows
Installers for Windows can be downloaded from the [7-zip website](https://www.7-zip.org/download.html).
Windows is not supported as it has known issues.