OMIX3 File Upload and Indexd Script

This repository contains a Python script to upload files to OMIX3 storage and update Indexd records using the Gen3 SDK.

---

Prerequisites

1. Gen3 Credentials: You must have a cred.json file containing your Gen3 API token with appropriate write permissions to the target project.
2. Access to S3 Bucket: Ensure that your Gen3 project is configured with an S3 bucket where files can be uploaded.
3. Python Environment: Python 3.10+ is recommended.

---

Python Environment Setup

Step 1: Create a virtual environment

python3 -m venv ~/gen3_env

Step 2: Activate the environment

Linux/macOS:

source ~/gen3_env/bin/activate

Windows:

gen3_env\Scripts\activate

Step 3: Install required packages

pip install -r requirements.txt

Packages used in the script:

1. gen3.auth and gen3.file (from gen3)
2. requests (for HTTP uploads)
3. PyJWT (for decoding token information)
4. boto3, botocore, jmespath, s3transfer (if using S3 uploads)

Script Usage

Step1: Configure credentials

In the script ( scripts/gen3sdk_upload_file.py ), there is a variable called CREDENTIALS that points to your Gen3 credentials file:

CREDENTIALS = "/path/to/the/cred.json"

➡️ Update this path to point to your actual Gen3 credentials file before running the script.

Step 1: Run the script

python scripts/gen3sdk_upload_file.py <file_to_upload>

Example:

python scripts/gen3sdk_upload_file.py ~/path/to/test_s3_in_01.txt

Step2: File Downloading

Usage:
  Single file:   python gen3sdk_download_file.py <GUID> [output_dir]
  Multiple files: python gen3sdk_download_file.py <GUID1> <GUID2> ... [output_dir]

Examples:

  python gen3sdk_download_file.py 0479c9c6-89bc-4717-8952-763ccb555eba
  python gen3sdk_download_file.py guid1 guid2 guid3 ./my_downloads/