FlowRepository Dataset Downloader

A simple Python script to download dataset files from FlowRepository.org. FlowRepository's built-in ZIP download is often broken, so this tool downloads each file individually instead.

What does this do?

If you have a FlowRepository dataset ID (like FR-FCM-Z2SS), this script will:

1. Log in to FlowRepository with your account
2. Find all the files in that dataset
3. Download them to a folder on your computer
4. Skip files you've already downloaded (safe to re-run if interrupted)

Prerequisites

• Python 3.6+ — Download Python if you don't have it
• A FlowRepository account — Create a free account if you don't have one

Installation

1. Download or clone this repository:

   git clone https://github.com/YOUR_USERNAME/flowRep.git
   cd flowRep
   

2. Create a conda environment and install dependencies:

   conda create -n flowrep python=3.10 -y
   conda activate flowrep
   pip install -r requirements.txt
   

   What is conda? Conda is a tool that creates isolated Python environments so packages don't conflict with each other. If you don't have conda installed, get it from Miniconda (the lightweight option) or Anaconda.

3. Every time you open a new terminal to use this script, activate the environment first:

   conda activate flowrep
   

Usage

Easy mode (interactive)

Just run the script with no arguments and it will walk you through everything:

python download_flowrepo.py

You'll be prompted for:

• The dataset ID (e.g., FR-FCM-Z2SS)
• Where to save the files
• Your FlowRepository email and password

Command-line mode

For more control, you can pass arguments directly:

python download_flowrepo.py FR-FCM-Z2SS
python download_flowrepo.py FR-FCM-Z2SS --output-dir ./my_data
python download_flowrepo.py FR-FCM-Z2SS --email you@example.com

All options

Option	Description
dataset_id	The dataset ID from FlowRepository (e.g., FR-FCM-Z2SS)
--output-dir	Folder to save files to (default: uses the dataset ID as folder name)
--email	Your FlowRepository email (will be prompted if not provided)
--password	Your FlowRepository password (will be prompted if not provided)
--max-retries	Number of times to retry a failed download (default: 3)

Saved credentials

The first time you enter your credentials, you'll be asked if you want to save them for next time. If you choose yes, they are stored in ~/.flowrepo_credentials.

To clear saved credentials, simply delete that file:

rm ~/.flowrepo_credentials

How it works

1. Login — The script logs in to FlowRepository using your email and password via their web login form
2. Resolve dataset — It converts the dataset ID (e.g., FR-FCM-Z2SS) to an internal experiment number
3. Find files — It scrapes the download page to find links to each individual file (FCS files, attachments, etc.)
4. Download — Each file is downloaded one at a time, with automatic retries on failure. Files that already exist are skipped.

Troubleshooting

"Could not find login form" — FlowRepository may have changed their website. Please open an issue.

"Login may have failed" — Double-check your email and password. Make sure you can log in at flowrepository.org in your browser.

"No files found to download" — The dataset may be empty, private, or the ID may be incorrect. Verify the dataset exists by visiting https://flowrepository.org/id/YOUR-DATASET-ID in your browser.

Downloads keep failing — Try increasing retries: --max-retries 5. If the site is slow, you can just re-run the script — it will skip files that were already downloaded successfully.