Extract an archive file (zip file or tar file) stored on AWS S3

Overview

S3 Extract

Extract an archive file (zip file or tar file) stored on AWS S3.

Details

Downloads archive from S3 into memory, then extract and re-upload to given destination.

The following S3 information is expected to be given as Environment Variables:

  • AWS_ENDPOINT_URL
  • AWS_ACCESS_KEY_ID
  • AWS_SECRET_ACCESS_KEY
  • CERT_PATH (optional)
  • CERT_DL_URL (optional)
  • SIGNATURE_VERSION (optional, defaults to "s3v4")
  • REGION_NAME (optional, defaults to "us-east-1")

Additionally, these information needed for ClearML remote execution can also be given as Env Variable (optional, args will override env var):

  • DEFAULT_DOCKER_IMG
  • DEFAULT_QUEUE

For those not familiar, environment variables can be set through various ways, some being:

  • export = in terminal
  • can be set in ~/.bashrc as well for more permanence

Iteratively extracting a folder of zips/tars is supported as well, through --src-is-dir flag.

Usage

usage: run.py [-h] [--src-is-dir] [--dst-bucket DST_BUCKET] [--verbose] [--remote] [--clml-proj CLML_PROJ] [--clml-task-name CLML_TASK_NAME] [--clml-task-type CLML_TASK_TYPE]
              [--docker-img DOCKER_IMG] [--queue QUEUE]
              src_bucket src_path dst_path

positional arguments:
  src_bucket            Source bucket
  src_path              Source path
  dst_path              Destination path

optional arguments:
  -h, --help            show this help message and exit
  --src-is-dir          Flag to indicate that given src path is a directory. Will iteratively extract any files in it ending with .zip or .tar.
  --dst-bucket DST_BUCKET
                        Destination bucket (optional), will default to Source bucket.
  --verbose             print out current upload filename as it progresses
  --remote              use clearml to remotely run job
  --clml-proj CLML_PROJ
                        ClearML Project Name
  --clml-task-name CLML_TASK_NAME
                        ClearML Task Name
  --clml-task-type CLML_TASK_TYPE
                        ClearML Task Type, e.g. training, testing, inference, etc
  --docker-img DOCKER_IMG
                        Base docker image to pull for ClearML remote execution
  --queue QUEUE         ClearML remote execution queue

Example usage:

python run.py my-bucket dataset/coco/images.tar dataset/coco/ --verbose --remote --clml-proj coco --clml-task-name coco_extraction --docker-img ubuntu/20.04 --queue 1xGPU
Owner
Evan
Evan
Uproot is a library for reading and writing ROOT files in pure Python and NumPy.

Uproot is a library for reading and writing ROOT files in pure Python and NumPy. Unlike the standard C++ ROOT implementation, Uproot is only an I/O li

Scikit-HEP Project 164 Dec 31, 2022
Provides a convenient way to append numpy arrays to a file.

Provides a convenient way to append numpy arrays to a file. The NpendWriter and NpendReader classes are used to write and read numpy arrays respective

3 May 14, 2022
Extract the windows major and minor build numbers from an ISO file, and automatically sort the iso files.

WindowsBuildFromISO Extract the windows major and minor build numbers from an ISO file, and automatically sort the iso files. Features Parse multiple

Podalirius 9 Nov 09, 2022
Quick and dirty FAT12 filesystem to ZIP file converter

Quick and Dirty FAT12 Filesystem Converter This is a really crappy Python script I wrote to convert a semi-compatible FAT12 filesystem from my HP150's

Tube Time 2 Feb 12, 2022
Small-File-Explorer - I coded a small file explorer with several options

Petit explorateur de fichier / Small file explorer Pour la première option (création de répertoire) / For the first option (creation of a directory) e

Xerox 1 Jan 03, 2022
Organize the files into the relevant sub-folders

This program can be used to organize files in a directory by their file extension. And move duplicate files to a duplicates folder.

Thushara Thiwanka 2 Dec 15, 2021
Python's Filesystem abstraction layer

PyFilesystem2 Python's Filesystem abstraction layer. Documentation Wiki API Documentation GitHub Repository Blog Introduction Think of PyFilesystem's

pyFilesystem 1.8k Jan 02, 2023
Organizer is a python program that organizes your downloads folder

Organizer Organizer is a python program that organizes your downloads folder, it can run as a service and so will start along with the system, and the

Gustavo 2 Oct 18, 2021
This python project contains a class FileProcessor which allows one to grab a file and get some meta data and header information from it

This python project contains a class FileProcessor which allows one to grab a file and get some meta data and header information from it. In the current state, it outputs a PrettyTable to txt file as

Joshua Wren 1 Nov 09, 2021
Vericopy - This Python script provides various usage modes for secure local file copying and hashing.

Vericopy This Python script provides various usage modes for secure local file copying and hashing. Hash data is captured and logged for paths before

15 Nov 05, 2022
Python file organizer application

Python file organizer application

Pak Maneth 1 Jun 21, 2022
Python virtual filesystem for SQLite to read from and write to S3

Python virtual filesystem for SQLite to read from and write to S3

Department for International Trade 70 Jan 04, 2023
A simple file sharing tool written in python

Share it A simple file sharing tool written in python Installation If you are using Windows os you can directly Run .exe file -- download If you are

Sachit Yadav 7 Dec 16, 2022
A python module to parse text files with contains secret variables.

A python module to parse text files with contains secret variables.

0 Dec 05, 2022
QSynthesis is a Python3 API to perform I/O based program synthesis of bitvector expressions.

QSynthesis is a Python3 API to perform I/O based program synthesis of bitvector expressions. It aims at facilitating code deobfuscation. The algorithm is greybox approach combining both a blackbox I/

Quarkslab 103 Dec 30, 2022
This project is a set of programs that I use to create a README.md file.

🤖 codex-readme 📜 codex-readme What is it? This project is a set of programs that I use to create a README.md file. How does it work? It reads progra

Tom Dörr 224 Jan 07, 2023
Extract longest transcript or longest CDS transcript from GTF annotation file or gencode transcripts fasta file.

Extract longest transcript or longest CDS transcript from GTF annotation file or gencode transcripts fasta file.

laojunjun 13 Nov 23, 2022
A wrapper for DVD file structure and ISO files.

vs-parsedvd DVDs were an error. A wrapper for DVD file structure and ISO files. You can find me in the IEW Discord server

7 Nov 17, 2022
Object-oriented file system path manipulation

path (aka path pie, formerly path.py) implements path objects as first-class entities, allowing common operations on files to be invoked on those path

Jason R. Coombs 1k Dec 28, 2022
Various converters to convert value sets from CSV to JSON, etc.

ValueSet Converters Tools for converting value sets in different formats. Such as converting extensional value sets in CSV format to JSON format able

Health Open Terminology Ecosystem 4 Sep 08, 2022