PDF Data Extraction

Extract text and structured data from PDF documents using a multi-backend approach with automatic fallback.

Overview

This skill provides PDF text extraction with 9 different backends, automatic GPU detection, and intelligent backend selection. The extraction system tries backends in order until one succeeds, producing markdown output optimized for further processing.

Quick Start Workflow

To extract text from PDFs:

1. Single file extraction (installed CLI - recommended):

   extract-pdfs /path/to/document.pdf
   

   Output: Creates document.md in the same directory.

2. Batch extraction (directory):

   extract-pdfs /path/to/pdfs/ /path/to/output/
   

   Output: Creates .md files for all PDFs in output directory.

3. Custom output file:

   extract-pdfs document.pdf output.md
   

4. Specific backends:

   extract-pdfs document.pdf --backends markitdown pdfplumber
   

5. List available backends:

   extract-pdfs --list-backends
   

   Output: Shows available backends and GPU status.

Alternative Execution Methods

If the extract-pdfs CLI isn't installed, install it first (recommended):

# Install as global UV tool (from repo root); the code ships in the autorun-ai distribution:
cd "${CLAUDE_PLUGIN_ROOT}/../.." && uv tool install --force --editable "./plugins/autorun[pdf]"
extract-pdfs --list-backends  # verify

Or use these fallback methods without installing:

# From a source checkout, without installing (the package lives in plugins/autorun):
uv run --project plugins/autorun --extra pdf python -m pdf_extraction document.pdf

# Module execution, if the console script is not on PATH
python -m pdf_extraction document.pdf

Backend Selection Guide

Custom Backend Ordering

Specify backends in any order with --backends. The system tries each in order, stopping on first success:

# Tables first, then general extraction
extract-pdfs document.pdf --backends pdfplumber markitdown pdfminer

# Scanned documents: vision-based first
extract-pdfs scanned.pdf --backends docling markitdown

# Most permissive fallback order (handles problematic PDFs)
extract-pdfs document.pdf --backends pdfminer pypdf2 markitdown

# Single backend only (no fallback)
extract-pdfs document.pdf --backends markitdown

CPU-Only Systems (Default)

For systems without GPU, the recommended backend order:

• markitdown - Microsoft's lightweight converter (MIT, fast, no models)
• pdfplumber - Excellent for tables (MIT)
• pdfminer - Pure Python, reliable (MIT)
• pypdf2 - Basic extraction through maintained pypdf (BSD-3; pdf extra)

GPU Systems

For systems with CUDA-enabled GPU:

• docling - IBM layout analysis (MIT, downloads models on first use)
• Plus all CPU backends as fallback

The marker backend is recognized only for separately managed installations; it is not selected by a published extra because its dependency graph pins an unpatched Pillow release.

Backend Comparison

Backend	License	Models	Best For	Speed
markitdown	MIT	None	General text, forms	Fast
pdfplumber	MIT	None	Tables, structured data	Fast
pdfminer	MIT	None	Simple text documents	Fast
pypdf2	BSD-3	None	Basic extraction	Fast
docling	MIT	~500MB	Layout analysis	Medium
marker	GPL-3.0	~1GB	Scanned documents	Slow
pymupdf4llm	AGPL-3.0	None	LLM-optimized output	Fast
pdfbox	Apache-2.0	None	Tables (Java-based)	Medium
pdftotext	System	None	Simple text (CLI)	Fast

Backend Decision Matrix

Document Type	Recommended Backend(s)	Why
Digital text PDF (default)	markitdown, pdfplumber	Fast, accurate
PDF with tables/invoices	pdfplumber, pdfbox	Best table structure
Complex layouts/columns	docling (GPU)	Layout analysis
Scanned documents/images	marker, docling (GPU)	OCR/vision required
Insurance policies/forms	markitdown, pdfplumber	Handles form fields
Academic papers	docling	Equations, figures
Maximum compatibility	pdfminer, pypdf2	Fewest dependencies
Commercial use required	markitdown, pdfplumber	MIT license

Programmatic Usage

To use the extraction library directly in Python code:

from pdf_extraction import extract_single_pdf, pdf_to_txt, detect_gpu_availability

# Check available backends
gpu_info = detect_gpu_availability()
print(f"Recommended backends: {gpu_info['recommended_backends']}")

# Extract single file
result = extract_single_pdf(
    input_file='/path/to/document.pdf',
    output_file='/path/to/output.md',
    backends=['markitdown', 'pdfplumber']
)

if result['success']:
    print(f"Extracted with {result['backend_used']}")
    print(f"Quality metrics: {result['quality_metrics']}")

# Batch extract directory
output_files, metadata = pdf_to_txt(
    input_dir='/path/to/pdfs/',
    output_dir='/path/to/output/',
    resume=True,  # Skip already-extracted files
    return_metadata=True
)

Extraction Metadata

Every extraction returns metadata for quality assessment:

{
    'success': True,
    'backend_used': 'markitdown',
    'extraction_time_seconds': 2.5,
    'output_size_bytes': 15234,
    'quality_metrics': {
        'char_count': 15234,
        'line_count': 450,
        'word_count': 2800,
        'table_markers': 12,      # Count of | (tables)
        'has_structure': True     # Has markdown structure
    },
    'encrypted': False,
    'error': None
}

Handling Common Scenarios

Encrypted PDFs

The system detects encrypted PDFs and reports them:

if result['encrypted']:
    print("PDF is password-protected")

Encrypted PDFs cannot be extracted without the password.

Empty or Failed Extractions

When all backends fail:

1. Check if PDF is encrypted
2. Try with --backends pdfminer pypdf2 (most permissive)
3. Check PDF isn't corrupted
4. Consider OCR-based backends for scanned documents

Resume Batch Processing

To continue interrupted batch extraction:

extract-pdfs /path/to/pdfs/ /path/to/output/

The resume=True default skips already-extracted files.

To force re-extraction:

extract-pdfs /path/to/pdfs/ --no-resume

Tables and Structured Data

For PDFs with tables, prioritize:

extract-pdfs document.pdf --backends pdfplumber markitdown

The output will contain markdown tables when detected:

| Column1 | Column2 | Column3 |
|---------|---------|---------|
| Data    | Data    | Data    |

Module Structure Reference

Source Code Layout

Location: plugins/pdf-extractor/src/pdf_extraction/ in a source checkout, and the importable pdf_extraction package once autorun is installed. This plugin directory holds the manifest, command, and this skill; the code ships inside the autorun-ai distribution behind its pdf extra.

File	Purpose
__init__.py	Package exports (extract_single_pdf, pdf_to_txt, etc.)
__main__.py	Support for python -m pdf_extraction
cli.py	CLI entry point with argparse
backends.py	BackendExtractor base class + 9 backend implementations
extractors.py	extract_single_pdf(), pdf_to_txt() functions
utils.py	GPU detection, quality metrics, encryption check

Key Classes and Functions

Component	Location	Purpose
BackendExtractor	backends.py:35-123	Base class with Template Method pattern
DoclingExtractor	backends.py:130-142	IBM Docling backend (MIT, GPU)
MarkerExtractor	backends.py:145-158	Vision-based marker backend (GPL-3.0, GPU)
MarkItDownExtractor	backends.py:161-173	Microsoft MarkItDown (MIT, CPU)
PdfplumberExtractor	backends.py:244-253	Table-focused extraction (MIT)
PdfminerExtractor	backends.py:219-226	Pure Python fallback (MIT)
Pypdf2Extractor	backends.py:229-241	Basic extraction through optional pypdf (BSD-3)
BACKEND_REGISTRY	backends.py:279-292	Dict mapping backend names to factories
detect_gpu_availability()	utils.py:9-40	Auto-detect GPU and recommend backends
extract_single_pdf()	extractors.py:13-80	Extract one PDF with backend fallback
pdf_to_txt()	extractors.py:83-170	Batch extract directory with resume

Key implementation details:

• Backend fallback loop: extractors.py:55-78 - Tries each backend in order, stops on first success
• Lazy initialization: backends.py:77-79 - Converters created only when first used
• Quality metrics: utils.py:43-76 - Calculates char/word/table counts

Additional Resources

Reference Files

For detailed backend documentation and advanced patterns:

• references/backends.md - Detailed backend comparison and selection guide

Example Usage

Working examples in the insurance analysis that prompted this skill:

• Extracted 21 PDFs from mortgage statements and insurance policies
• Used markitdown backend for fast extraction
• Parsed structured data (dates, amounts, policy numbers)

Error Handling

The extraction system handles errors gracefully:

1. Backend failures: Automatically tries next backend
2. Import errors: Skips unavailable backends
3. File errors: Reports specific error message
4. Partial success: Continues with remaining files in batch

All errors are captured in metadata rather than raising exceptions.

Dependencies

The base package has no required Python dependencies. Select extras for the backends you need:

• pdf: markitdown, pdfplumber, pdfminer.six, and maintained pypdf (the CLI backend id stays pypdf2)
• pdf-gpu: docling on Linux/Windows; empty on macOS while docling's model stack selects an advisory-affected transformers 4.x release
• pdf-llm: pymupdf4llm
• pdf-progress: tqdm
• pdf-all: every extra above

Install CPU dependencies:

uv pip install "markitdown>=0.1.0" "pdfplumber>=0.10.0" "pdfminer.six>=20221105" "pypdf>=6.0.0" tqdm

For the supported GPU extra on Linux or Windows:

uv pip install "docling>=2.94.0"

The marker backend remains discoverable for separately managed installs, but marker-pdf is excluded from published extras because its supported-platform dependency graph pins Pillow below the first fully patched release.

Troubleshooting

extract-pdfs: command not found

# Install as global UV tool from repo root:
uv tool install --force --editable "./plugins/autorun[pdf]"
extract-pdfs --list-backends  # verify

ModuleNotFoundError: No module named 'pdf_extraction' (or 'markitdown', 'pdfplumber')

# Re-install with all base dependencies:
uv tool install --force --editable "./plugins/autorun[pdf]"
# Or install explicitly:
uv pip install "markitdown>=0.1.0" "pdfplumber>=0.10.0" "pdfminer.six>=20221105" "pypdf>=6.0.0" tqdm

GPU backend (docling) not available

# Requires PyTorch; install the GPU extra:
uv tool install --force --editable "./plugins/autorun[pdf,pdf-gpu]"
extract-pdfs --list-backends  # verify docling appears
# Note: docling downloads models on first use.

Empty output from scanned PDF (image-only document)

# Scanned PDFs require OCR; docling is in the supported GPU extra:
extract-pdfs scanned.pdf --backends docling
# If GPU unavailable, try pdftotext (system tool):
brew install poppler        # macOS
# apt install poppler-utils  # Ubuntu/Debian
extract-pdfs scanned.pdf --backends pdftotext

pdfminer import error (package name confusion)

# Install correct package (name has .six suffix):
uv pip install "pdfminer.six>=20221105"
# Import is still: from pdfminer.high_level import extract_text  (no .six)

markitdown version conflict

# API changed significantly in 0.1.0; ensure correct version:
uv pip install "markitdown>=0.1.0"