PDF Text Extraction with Progressive Tool Fallback

This skill provides a robust workflow for extracting text from PDF documents using a sequenced approach with agent tools, with explicit fallback mechanisms based on observed tool behavior.

Critical Insight from Execution Data

read_file often returns binary/image data for PDFs, not extracted text. When this occurs, immediately escalate to run_shell with pdftotext before attempting Python-based extraction.

Entry Point: Determine Your Starting Point

Before beginning, identify your scenario:

Scenario	Start Here	Skip
PDF already on local disk	Step 1 (read_file attempt)	Download steps
PDF at a web URL	Download first, then Step 1	None
PDF content already extracted	Step 4 (Quality verification)	Steps 1-3

Overview

PDF extraction failures cascade when tool sequencing is unclear. This workflow ensures maximum success rate through explicit tool progression:

1. read_file - Quick attempt, but may return binary data
2. run_shell + pdftotext - Reliable extraction when read_file fails
3. execute_code_sandbox + PyMuPDF - Final fallback for complex PDFs

Step-by-Step Instructions

Step 1: Attempt read_file First

Always try the simplest approach first:

Tool: read_file
Path: document.pdf

Expected outcome: Extracted text content

Critical check: Examine the returned content:

• ✅ Text visible: Proceed to Step 4 (Quality verification)
• ⚠️ Binary/image data detected: Immediately proceed to Step 2
• ❌ File not found: Verify path or download first

Binary data indicators:

• Content starts with %PDF- header without text extraction
• Content appears as garbled characters or base64
• Content contains PNG/JPEG markers within PDF wrapper
• File size seems reasonable but no readable text

Step 2: Escalate to run_shell with pdftotext

When read_file returns binary data, do NOT attempt execute_code_sandbox yet. Use run_shell immediately:

Tool: run_shell
Command: pdftotext document.pdf document.txt

If pdftotext is not available:

Tool: run_shell
Command: apt-get update && apt-get install -y poppler-utils && pdftotext document.pdf document.txt

Then read the extracted text:

Tool: read_file
Path: document.txt

Expected outcome: Clean text extraction

If this fails:

• Check if file is password-protected
• Check if file is corrupted (run file document.pdf)
• Proceed to Step 3

Step 3: Final Fallback to execute_code_sandbox with PyMuPDF

Only attempt this if Steps 1-2 fail:

Tool: execute_code_sandbox
Language: python
Code: |
  import fitz  # PyMuPDF
  
  try:
      doc = fitz.open("document.pdf")
      text = ""
      for page in doc:
          text += page.get_text()
      doc.close()
      
      with open("document_pymupdf.txt", "w") as f:
          f.write(text)
      
      print("SUCCESS: Extracted {} characters".format(len(text)))
  except Exception as e:
      print(f"FAILED: {e}")

Then read the result:

Tool: read_file
Path: document_pymupdf.txt

Step 4: Quality Verification

Regardless of which method succeeded, verify extraction quality:

1. Check text length: Should be proportional to PDF pages (~500-2000 chars per page)
2. Check readability: Text should form coherent sentences
3. Check for truncation: Look for cut-off words or missing sections
4. Compare methods: If multiple methods worked, compare outputs

If quality is poor:

• Try alternative extraction tools (pdfplumber, camelot-py for tables)
• Consider OCR for scanned documents
• Document limitations clearly

Step 5: Graceful Degradation to Domain Knowledge

If all extraction methods fail:

1. Document the specific failure mode for each tool attempted
2. Extract any partial content that was successfully retrieved
3. Supplement missing content from established domain knowledge
4. Clearly mark which portions are from source vs. generated from knowledge
5. Provide citations for any claimed requirements or specifications

Example degradation note:

NOTE: Source document [path/URL] was inaccessible due to [specific tool failures].
Content below combines partial extraction with established domain knowledge 
for [topic]. All claims verified against [alternative sources] where possible.

Tool Failure Log:
- read_file: Returned binary data (no text extraction)
- run_shell/pdftotext: Command not available in environment
- execute_code_sandbox/PyMuPDF: Sandbox execution failed with [error]

Complete Tool Orchestration Script

# pdf-extract-orchestrator.py
# Implements the progressive tool fallback pattern

def extract_pdf_text(pdf_path):
    """
    Progressive PDF extraction following tool precedence:
    1. read_file (quick check)
    2. run_shell + pdftotext (primary extraction)
    3. execute_code_sandbox + PyMuPDF (final fallback)
    """
    extraction_log = []
    
    # Step 1: Try read_file
    print("Step 1: Attempting read_file...")
    try:
        content = read_file(pdf_path)
        if is_binary_or_image_data(content):
            extraction_log.append("read_file: Returned binary data")
            # Proceed to Step 2
        else:
            extraction_log.append("read_file: Success")
            return content, extraction_log
    except Exception as e:
        extraction_log.append(f"read_file: Failed - {e}")
    
    # Step 2: Try run_shell with pdftotext
    print("Step 2: Attempting run_shell + pdftotext...")
    try:
        run_shell(f"pdftotext {pdf_path} output.txt")
        content = read_file("output.txt")
        if content and len(content) > 100:
            extraction_log.append("run_shell/pdftotext: Success")
            return content, extraction_log
        else:
            extraction_log.append("run_shell/pdftotext: Empty extraction")
    except Exception as e:
        extraction_log.append(f"run_shell/pdftotext: Failed - {e}")
    
    # Step 3: Try execute_code_sandbox with PyMuPDF
    print("Step 3: Attempting execute_code_sandbox + PyMuPDF...")
    try:
        code = """
import fitz
doc = fitz.open("""" + pdf_path + """")
text = ""
for page in doc:
    text += page.get_text()
doc.close()
print(text[:1000])  # Preview
"""
        result = execute_code_sandbox(language="python", code=code)
        extraction_log.append("execute_code_sandbox/PyMuPDF: Success")
        return result, extraction_log
    except Exception as e:
        extraction_log.append(f"execute_code_sandbox/PyMuPDF: Failed - {e}")
    
    # Step 4: All methods failed
    extraction_log.append("ALL METHODS FAILED - Escalate to domain knowledge")
    return None, extraction_log

def is_binary_or_image_data(content):
    """Detect if content is binary/image data rather than extracted text"""
    if not content:
        return True
    # Check for PDF header without text extraction
    if content.startswith("%PDF-"):
        return True
    # Check for high ratio of non-printable characters
    non_printable = sum(1 for c in content if ord(c) < 32 and c not in '\n\r\t')
    if len(content) > 0 and non_printable / len(content) > 0.1:
        return True
    return False

Tool Precedence Decision Tree

                    ┌─────────────────┐
                    │  Start: PDF     │
                    │  Available?     │
                    └────────┬────────┘
                             │
                    ┌────────▼────────┐
                    │   Step 1:       │
                    │   read_file     │
                    └────────┬────────┘
                             │
              ┌──────────────┼──────────────┐
              │              │              │
        ┌─────▼─────┐  ┌─────▼─────┐  ┌─────▼─────┐
        │  Text     │  │  Binary   │  │  Error/   │
        │  Returned │  │  Data     │  │  Not Found│
        └─────┬─────┘  └─────┬─────┘  └─────┬─────┘
              │              │              │
              │         ┌────▼─────┐  ┌────▼─────┐
              │         │ Step 2:  │  │ Download │
              │         │ run_shell│  │ or Fix   │
              │         │ pdftotext│  │ Path     │
              │         └────┬─────┘  └──────────┘
              │              │
              │         ┌────▼─────┐
              │         │ Success? │
              │         └────┬─────┘
              │              │
        ┌─────▼─────┐  ┌─────▼─────┐
        │  Yes      │  │  No       │
        └─────┬─────┘  └─────┬─────┘
              │              │
              │         ┌────▼─────────┐
              │         │ Step 3:      │
              │         │ execute_     │
              │         │ code_sandbox │
              │         │ PyMuPDF      │
              │         └──────────────┘
              │
        ┌─────▼──────────────────┐
        │  Step 4: Quality Check │
        │  Step 5: Document      │
        │  Limitations           │
        └────────────────────────┘

Best Practices

1. Check read_file output immediately: Don't assume it extracted text - verify before proceeding
2. Escalate quickly on binary data: Don't waste iterations trying read_file multiple times
3. Prefer run_shell over execute_code_sandbox: Shell tools are more reliable for PDF extraction when available
4. Log each tool attempt: Document which method succeeded for future reference
5. Preserve extraction artifacts: Keep intermediate files for debugging
6. Verify extraction quality: Check text length and readability before accepting results
7. Document tool failures: When falling back to domain knowledge, specify which tools failed and why

Common Failure Modes by Tool

Tool	Symptom	Cause	Solution
read_file	Binary PDF data	Tool doesn't extract PDF text	Escalate to run_shell immediately
read_file	PNG/JPEG data	PDF contains embedded images	Use OCR tools or request text version
run_shell	pdftotext not found	Tool not installed	Install poppler-utils first
run_shell	Empty output	Password-protected PDF	Request accessible version
execute_code_sandbox	Unknown error	Sandbox execution issue	Try run_shell alternative or document limitation
execute_code_sandbox	Import error	PyMuPDF not installed	Include pip install in script

When to Use This Skill

• PDFs from web downloads: After downloading, apply this extraction workflow
• PDFs already local: Start at Step 1 with existing file path
• Automated document processing: Where reliability matters more than speed
• Regulatory/compliance documents: Where source verification is critical
• Situations with tool uncertainty: When environment capabilities are unknown

Migration from Parent Skill

This skill enhances pdf-download-extract-fallback by:

1. Explicit tool sequencing: Parent described shell commands; this specifies agent tool order
2. Binary detection: Parent assumed download success; this checks read_file output quality
3. Faster escalation: Parent tried pdftotext then PyMuPDF; this escalates immediately on binary data
4. Agent-focused: Parent was shell-script focused; this is optimized for agent tool calls
5. Execution insights: Incorporates learnings from failed task 0353ee0c showing read_file limitations