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Simiotics integration with AWS S3
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README.md

simiotics-s3

This repository contains the code for the simiotics_s3 tool, which you can use to sanely share datasets with your friends - both human and machine (especially machine)!

It does so using AWS S3 in combination with a Simiotics data registry.

Installation

We recommend you use virtual environments. If you are using a recent Python3, you can create a virtual environment wherever you would like:

python3 -m venv <desired-venv-directory>

Then, to activate:

. <desired-venv-directory>/bin/activate

Installation from PyPI

simiotics_s3 can be installed from PyPI:

pip3 install simiotics-s3

Installation from source code

From the root of this repository:

pip3 install -e .

Usage

Simiotics data registry

To use this tool, you will need to specify a Simiotics data registry in which you will register your data and your datasets. Our customers use private registries hosted on their own infrastructure. If you don't have access to such a private registry and would like to experiment with our tool, you can use our public alpha registry. Just set the SIMIOTICS_DATA_REGISTRY environment variable:

export SIMIOTICS_DATA_REGISTRY=registry-alpha.simiotics.com:7010

S3

The simiotics_s3 tool is BYOB (bring your own bucket). The data will be hosted on your own S3 bucket. The tool will use a Simiotics data registry to index your S3 blobs and share them with others in the form of datasets.

simiotics_s3 uses the boto3 library under the hood and you will have to provide it with credentials that it can use to authenticate against the bucket. One way to do this is to export the AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY environment variables, which can be populated with values from your AWS credentials file (on Linux or Mac, try less ~/.aws/credentials).

Run:

export AWS_ACCESS_KEY_ID=<COPYPASTA YOUR ACCCESS KEY ID HERE>
export AWS_SECRET_ACCESS_KEY=<COPYPASTA YOUR SECRET ACCCESS KEY HERE>

Workflow

In the commands below, replace:

  1. <UNIQUE SOURCE ID> with a name that you would like to give your source
  2. <SOURCE S3 ROOT> with an S3 path of the form s3://<BUCKET>/<KEY_PREFIX> (e.g. s3://simiotics-is-awesome/source/goes/here)
  3. <DOWNLOAD DIR> with the path to the directory into which you'd like to download data

Register a source (which you can also think of as a dataset). It will be empty at first. This is okay. After all, sources change over time.

simiotics_s3 sources create --id <UNIQUE SOURCE ID> --s3-path <SOURCE S3 ROOT>

If your ID was truly unique, you should see a response like this:

*** Source registered ***
id: "first-source"
source_type: SOURCE_S3
data_access_spec: "s3://simiotics-test/first-source"
created_at {
  seconds: 1568050335
  nanos: 766883136
}

Register a bunch of data files against the source like this:

simiotics_s3 data register --source <UNIQUE SOURCE ID> <FILE PATHS>

To download all the data registered under a given source, you can use the simiotics_s3 data download command. Anyone that has access to both the S3 bucket hosting the data and the Simiotics data registry can do this. Humans, servers, docker containers -- Simiotics has no prejudices and neither does S3!

simiotics_s3 data download --source <UNIQUE SOURCE ID> --dir <DOWNLOAD DIR>

Check that the data has been downloaded:

ls <DOWNLOAD DIR>

Model away. :)

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