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Nanopub Setup Guide

Initial Setup

Before you can publish nanopublications, you need to set up your profile with RSA keys and your ORCID iD.

Step 1: Set Up Nanopub Profile

Run the interactive setup command:

python3 -m nanopub setup --newkeys

This will:

  1. Ask for your ORCID iD (e.g., https://orcid.org/0000-0000-0000-0000)
  2. Ask for your name
  3. Generate new RSA keys automatically (with --newkeys flag)
  4. Store the configuration in ~/.nanopub/

Important: Make sure to use the --newkeys flag so it generates the RSA keys for you!

Step 2: Verify Setup

Check that your profile is configured correctly:

python3 -m nanopub profile

This should show your ORCID iD and key paths.

Alternative: Manual Key Generation

If you prefer to generate keys manually first:

# Create the directory
mkdir -p ~/.nanopub

# Generate RSA key pair
ssh-keygen -t rsa -b 4096 -f ~/.nanopub/id_rsa -N ""

# Then run setup pointing to these keys
python3 -m nanopub setup \
    --orcid-id "https://orcid.org/YOUR-ORCID-ID" \
    --name "Your Name" \
    --keypair ~/.nanopub/id_rsa.pub ~/.nanopub/id_rsa

Troubleshooting

Error: FileNotFoundError for id_rsa.pub

If you see this error, it means the RSA keys haven't been generated yet. Run:

python3 -m nanopub setup --newkeys

Error: Permission denied

Make sure the ~/.nanopub/ directory has the correct permissions:

chmod 700 ~/.nanopub
chmod 600 ~/.nanopub/id_rsa  # Private key should be read-only by owner
chmod 644 ~/.nanopub/id_rsa.pub  # Public key can be readable

After Setup

Once setup is complete, you can use the batch publishing scripts:

# Preview what would be published
./publish_batch.sh --dry-run

# Publish to test server
./publish_batch.sh --test

# Publish to production
./publish_batch.sh --prod