PDF Fingerprinting

The Hypothesis web annotation client uses PDF fingerprints to identify PDFs independent of their URLs. Hypothesis knows when it’s looking at the same PDF, even if that PDF appears at two different URLs, or appears as a local file on your computer and then later online, and even if the file has been edited and then re-uploaded. This enables a “magic” Hypothesis feature where, for example, you can annotate a local PDF file on your computer and then later publish that file online and Hypothesis will still find your annotations of the file when you view it online.

Hypothesis knows that it’s looking at the same PDF because it looks at the PDF’s fingerprint. Computing the fingerprint of a PDF turns out to be a simple algorithm, implemented by PDF.js, based on top of standard identifiers that PDFs contain.

This post explains what PDF file identifiers and fingerprints are, and re-implements the PDF.js fingerprint algorithm in Python.

PDF file identifiers

PDFs can contain file identifiers that are intended to be used to allow one PDF to contain a filename-independent link to another PDF, although applications may also use them to identify files for other purposes.

A file identifier looks something like this, inside the PDF file:

/ID [<6426256F1EF8F6A9CC257A60F3D3BA57> <27efe497bd0ec74687a46771aa54f25b>]

Some variation on the format is possible.

Section 14.4 of the PDF spec (this is ISO 32000-1, the PDF 1.7 spec, there’s now a newer ISO 32000-2 PDF 2.0 spec but you have to pay to download it) describes PDF file identifiers as an “optional ID entry in the PDF file’s trailer dictionary.”

(The trailer of a PDF is a dictionary at the end of the file that PDF readers use to find certain parts of the file, see section 7.5.5 in ISO 32000-1.)

The ID entry is an array of two byte strings. The first byte string in the array is a “permanent identifier” that’s “based on the contents of the file at the time it was originally created” and “shall not change when the file is incrementally updated”. This is the identifier that we’re interested in.

The second byte string is a secondary identifier that should also be based on the contents of the file, and should initially have the same value as the first identifier, but that should be re-computed based on the new file contents each time the file is updated. It enables you to identify a different version of the same file. Hypothesis doesn’t use this second identifier.

Section 14.4 of ISO 32000-1 goes on to say that file identifiers “should be computed by means of a message digest algorithm such as MD5” using the current time, the file’s pathname, the size of the file in bytes, and the contents of the file. There’s of course no guarantee that every program that creates PDFs computes the IDs in this way.

PDF identifiers aren’t guaranteed to be unique. The spec emphasises that the algorithm a program uses to generate IDs should ensure that they’re “likely to be unique” but nothing guarantees this.

Not all valid PDFs contain a file identifier. The spec says “The ID entry is optional but should be used.”

In practice most but not all PDFs do contain an ID. Of 3594 real-world PDFs that I tested below, 5% had no file identifier.

PDF.js’s PDF “fingerprints”

PDF.js, the JavaScript PDF viewer that Hypothesis uses, provides access to a fingerprint for any PDF based on PDF file identifiers and MD5 message digests. This fingerprint is what Hypothesis actually uses to identify PDFs independent of their URLs and make annotations magically follow their PDFs from one location to another.

The fingerprint for a PDF is computed by PDF.js’s fingerprint() function. What this fingerprint() function does is:

  1. Extract the file identifier from the PDF’s trailer, if it has one
  2. If the ID can’t be extracted (because the PDF doesn’t contain a trailer, the trailer doesn’t contain a valid ID array, etc) then use an MD5 digest of the first 1024 bytes of the file instead
  3. Either way, convert the bytes of the ID or digest to a hex string and that’s your fingerprint

This turns out to be a pretty nice fingerprint algorithm:

This fingerprint is described by PDF.js’s API docs as “A unique ID to identify a PDF. Not guaranteed to be unique.” It’s possible for two different PDFs to contain the same identifier, or for two PDFs without identifiers to contain the same first 1024 bytes. But in practice the fingerprint is likely to be unique almost always.

PDF fingerprinting in Python

At Hypothesis we thought we had a need to compute these PDF.js fingerprints server-side. We got this to work but didn’t actually end up using it. It might be useful to record what we did anyway.

It’s possible to run PDF.js server-side using Node and get the fingerprints from it. But we didn’t want to do that. We have a Python web app, and it’d be easier if we could do the fingerprinting in Python.

The challenge was to implement a Python PDF fingerprinter that would produce the same fingerprints as PDF.js does for almost any PDF file. Failing to parse a small portion of PDFs and erroring out on those files would be acceptable, even if PDF.js could parse them. What I really wanted to avoid was successfully producing a fingerprint that didn’t match PDF.js’s fingerprint for the same file. This could lead to silent failures and incorrect behaviour only noticed too late, in a system that depended on the Python fingerprinter’s results matching PDF.js’s.

This turns out to be doable but tricky.

Python PDF parsers

While the fingerprint algorithm itself is pretty straightforward, it sits on top of a PDF parser that’s needed to extract the file identifier byte string or to decide that the file doesn’t contain an identifier. Any differences between the Python PDF parser and PDF.js’s parser could result in different fingerprints being produced.

Not wanting to write my own PDF parser I went looking for Python libraries. I ran into problems with both PyPDF2 and pdfrw. They’d return a different file ID than PDF.js for a lot of PDFs, either by doing unwanted interpretation of the file ID’s bytes, or parsing the PDF incorrectly, etc.

I had better luck using PDFMiner, with which I was able to extract the same ID as PDF.js for almost all PDFs that I tested. The PDFs that failed were ones that PDFMiner failed to parse entirely and crashed. Unlike with PyPDF2 and pdfrw, whenever PDFMiner did extract an ID it would always be the same as PDF.js’s.

PDF fingerprinting in Python using PDFMiner

Here’s a Python script, fingerprint.py, that prints out the fingerprint of a given PDF, using PDFMiner:

#!/usr/bin/env python2
Print out the fingerprint of the given PDF file.

Exit with non-zero status code if fingerprinting the file fails.


1. Create a new Python virtual environment

2. Install PDFMiner from git (because the version on PyPI is out of date and
   missing AES v2 decryption support):

   pip install git+https://github.com/euske/pdfminer.git


    ./fingerprint.py /path/to/file.pdf

import hashlib
import sys

import pdfminer.pdfparser
import pdfminer.pdfdocument

def hexify(byte_string):
    ba = bytearray(byte_string)

    def byte_to_hex(b):
        hex_string = hex(b)

        if hex_string.startswith('0x'):
            hex_string = hex_string[2:]

        if len(hex_string) == 1:
            hex_string = '0' + hex_string

        return hex_string

    return ''.join([byte_to_hex(b) for b in ba])

def hash_of_first_kilobyte(path):
    f = open(path, 'rb')
    h = hashlib.md5()
    return h.hexdigest()

def file_id_from(path):
    Return the PDF file identifier from the given file as a hex string.

    Returns None if the document doesn't contain a file identifier.

    parser = pdfminer.pdfparser.PDFParser(open(path, 'rb'))
    document = pdfminer.pdfdocument.PDFDocument(parser)

    for xref in document.xrefs:
        if xref.trailer:
            trailer = xref.trailer

                id_array = trailer["ID"]
            except KeyError:

            # Resolve indirect object references.
                id_array = id_array.resolve()
            except AttributeError:

                file_id = id_array[0]
            except TypeError:

            return hexify(file_id)

def fingerprint(path):
    return file_id_from(path) or hash_of_first_kilobyte(path)

if __name__ == '__main__':
    print fingerprint(sys.argv[1])

A few notes about this code:

  1. You’ll notice the install instructions at the top of the file say to install PDFMiner from GitHub instead of from PyPI. The version on PyPI is very out of date, and lacks support for AES v2 encryption which a lot of PDF files use.

  2. The hexify() function is turning the file ID byte string into a hexadecimal string using Python’s built in hex() function, but then it has to do a little work of its own (removing 0x from the start of some hex characters, appending 0 to the beginning of some) to make the output match PDF.js’s hex strings.

  3. When the file doesn’t contain an ID we don’t need to pass the MD5 digest through hexify() (as PDF.js does) because Python’s hexdigest() function returns a hexadecimal digest directly.

  4. The file_id_from(path) function is finding the file ID using PDFMiner by looping over all “xref”s in the PDF, looking for the first xref that contains a trailer that contains a non-empty ID array.

    One tricky thing here is the id_array = id_array.resolve() call. This resolves PDF “indirect references” (see ISO 3200-1 section 7.3.10). Any object in a PDF file, including the file ID array in the trailer, can be an “indirect object” which is just an identifier that the PDF reader has to use to look up the actual document elsewhere in the file. In some PDF files the file ID array is an indirect object, and PDFMiner’s resolve() does the lookup for us.

Testing the fingerprinter

I used a couple of scripts to test the above code, comparing its fingerprints to those of PDF.js, using 3594 public PDFs that have been annotated by Hypothesis users. Of the 3594 PDFs tested:

The comparison of the fingerprinting algorithms was done using a couple of command line scripts that you can find over in my fork of PDF.js.

First, here’s a Node.js script, fingerprint.js, that prints out the PDF.js fingerprint of a given PDF:

#!/usr/bin/env node
 * Print out the fingerprint of the given PDF file.
 * Exit with non-zero status code if fingerprinting the file fails.
 * Installation:
 *   git clone git@github.com:seanh/pdf.js.git
 *   cd pdf.js
 *   git checkout fingerprint
 *   npm install
 *   npm install estraverse
 *   gulp dist-install
 * Usage:
 *   ./fingerprint.js /path/to/file.pdf
let pdfjs = require('pdfjs-dist');
let pdf = process.argv[2];

pdfjs.getDocument(pdf).then((doc) => {
}).catch((error) => {

Now here’s a Python script, compare-fingerprints, that takes one or more PDF files as command-line arguments, runs both fingerprint.py and fingerprint.js on each file, and prints out which fingerprints match and which don’t. For example to compare results for an entire directory of PDFs, run: ./compare-fingerprints my_files/*.pdf.

#!/usr/bin/env python2
Compare fingerprints from fingerprint.js and fingerprint.py.


1. git clone git@github.com:seanh/pdf.js.git
2. cd pdf.js
3. git checkout fingerprint
4. npm install
5. npm install estraverse
6. gulp dist-install
7. Create a new Python virtual environment
8. Install PDFMiner from git (because the version on PyPI is out of date and
   missing AES v2 decryption support):

     pip install git+https://github.com/euske/pdfminer.git


    ./compare-fingerprints files_to_compare/*.pdf

import subprocess
import sys

for pdf in sys.argv[1:]:

    # Get the fingerprint from PDF.js.
        js_fingerprint = subprocess.check_output(['./fingerprint.js', pdf])
    except subprocess.CalledProcessError:
        # Skip files that PDF.js can't parse.

    # Get the fingerprint from Python.
        py_fingerprint = subprocess.check_output(['./fingerprint.py', pdf])
    except subprocess.CalledProcessError:
        print "Fail: " + pdf

    matches = js_fingerprint == py_fingerprint

    # Strip newlines before printing.
    js_fingerprint = js_fingerprint.strip()
    py_fingerprint = py_fingerprint.strip()

    if matches:
        print "Match: " + js_fingerprint
        print "Mismatch. File: " + pdf + " PDF.js: " + js_fingerprint + " Python: " + py_fingerprint


It turns out not to be the case that “all PDFs contains a unique fingerprint”. PDF fingerprints are actually just a function implemented in PDF.js, one particular PDF reader. They’re based on standard identifiers that PDF files do contain, but these identifiers aren’t guaranteed to be unique and not every valid PDF contains one. When a PDF doesn’t contain an identifier the fingerprint function falls back on a digest of the first part of the file, which is also not guaranteed to be unique.

Changes to PDF.js’s fingerprint code over time may also be a concern to Hypothesis, given that we store the fingerprints from this function in our database and rely on them being stable.

In practice, though, these pseudo-unique fingerprints can be robustly computed for almost any PDF file and aren’t likely to have collisions. Separate implementations of the fingerprint algorithm in different languages turn out to be possible, with very high agreement in the results.