How can I batch ingest multiple PDFs from AWS S3 into a Pinecone vector store for RAG?

Below is an approach that many n8n users have found effective for batch ingestion without having to roll your own JavaScript solution:

Use the "SplitInBatches" Node

Instead of processing all 100 PDFs at once, consider these steps:

1. List and Fetch Files:
   Use an S3 node (or HTTP Request node if you’re using signed URLs) to list or get the details of all available PDF files.

2. Split the Batch:
   Add a "SplitInBatches" node to break your list of PDFs into smaller groups. This lets you process, for example, 10 files at a time.

3. Process Each File Separately:
   For each file in the batch, perform the following:

   • Download the PDF from S3.
   • Use an "Extract From File" node to convert the downloaded PDF (binary) to JSON or text.
   • Use your embeddings node (such as Embeddings OpenAI, if available) to generate the representation.
   • Upsert the vector into Pinecone using the Pinecone Vector Store node.

4. Loop Through All Batches:
   The workflow will loop through the batches until all files have been processed.

Benefits of This Approach

• No Custom JavaScript Needed:
  By utilizing the built-in looping and batch splitting features, you can remain within the confines of n8n’s core nodes.

• Resource Management:
  Processing files in smaller batches helps avoid memory and performance bottlenecks, especially on a VPS.

• Modularity:
  Each step focuses on a single operation (download, extract, embed, upsert), making debugging easier.

Example Workflow Outline

Below is a rough outline (in pseudo-code style) of how your workflow might look:

MERMAIDCopied
flowchart TD
    A(List PDFs from S3) --> B(SplitInBatches: 10 files per batch)
    B --> C[For each PDF]
    C --> D(Download PDF from S3)
    D --> E(Extract PDF Content)
    E --> F(Generate Embeddings)
    F --> G(Upsert Document to Pinecone)
    G --> H(Loop until complete)

Additional Tips

• Monitoring & Error Handling:
  Consider adding error handling (e.g. try/catch in a Function node) to account for any file download or conversion issues.

• Optimize Batch Size:
  Experiment with the batch size in the "SplitInBatches" node to find the optimal number for your VPS resources.

• Reuse Existing Workflows:
  If you have a working flow for a single PDF, refactor that into a sub-workflow and call it within the batch loop. This promotes reusability and cleaner design.

This approach leverages n8n's native features for batch processing and is well-aligned with the standard RAG flow using embeddings and the Pinecone vector store. It should address the bulk ingestion challenge without needing additional JavaScript customization.