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That sounds like it will almost certainly require custom scripting because your use case is unique. You can probably break down the problem into multiple steps which are easier to address. There is some decent pdf software out there that can handle OCR (optical character recognition) though barcodes specifically are a bit harder to get opensource solutions for - the main one being tesseract (https://github.com/tesseract-ocr/tesseract) from google I do not believe handles barcodes out the gate.
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