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import pymupdf4llm
from markdown_it import MarkdownIt
from mdit_plain.renderer import RendererPlain
import os
import re
from typing import Tuple, Optional, List, Dict, Any
import fitz # PyMuPDF
from collections import defaultdict, Counter
import language_tool_python
import json
import traceback
import io
import tempfile
# import os # Already imported
import gradio as gr
# Set JAVA_HOME environment variable (from target script)
os.environ['JAVA_HOME'] = '/usr/lib/jvm/java-11-openjdk-amd64'
# --- Functions for PDF to Markdown to Plain Text ---
def convert_markdown_to_plain_text(markdown_text: str) -> str:
"""
Converts a Markdown string to plain text.
"""
if not markdown_text:
return ""
try:
parser = MarkdownIt(renderer_cls=RendererPlain)
plain_text = parser.render(markdown_text)
return plain_text
except Exception as e:
print(f"Error converting Markdown to plain text: {e}")
return markdown_text
# --- Function for Rectangle Conversion ---
def convert_rect_to_dict(rect: fitz.Rect) -> Optional[Dict[str, float]]:
"""Converts a fitz.Rect object to a dictionary."""
if not rect or not isinstance(rect, fitz.Rect):
print(f"Warning: Invalid rect object received: {rect}")
return None
return {
"x0": rect.x0,
"y0": rect.y0,
"x1": rect.x1,
"y1": rect.y1,
"width": rect.width,
"height": rect.height
}
# --- Helper function for mapping LT issues to PDF rectangles ---
def try_map_issues_to_page_rects(
issues_to_map_for_context: List[Dict[str, Any]],
pdf_rects: List[fitz.Rect],
page_number_for_mapping: int # 1-based page number
) -> int:
mapped_count = 0
num_issues_to_try = len(issues_to_map_for_context)
num_available_rects = len(pdf_rects)
limit = min(num_issues_to_try, num_available_rects)
for i in range(limit):
issue_to_update = issues_to_map_for_context[i]
if issue_to_update['is_mapped_to_pdf']: # Check the correct flag name
continue
pdf_rect = pdf_rects[i]
coord_dict = convert_rect_to_dict(pdf_rect)
if coord_dict:
issue_to_update['pdf_coordinates_list'] = [coord_dict] # Store as list of dicts
issue_to_update['is_mapped_to_pdf'] = True
issue_to_update['mapped_page_number'] = page_number_for_mapping
mapped_count += 1
else:
print(f" Warning: Could not convert rect for context '{issue_to_update['context_text'][:30]}...' on page {page_number_for_mapping}")
return mapped_count
# ------------------------------
# Analysis Functions (from target script, with modifications)
# ------------------------------
def extract_pdf_text(file_input: Any) -> str:
"""Extracts full text from a PDF file using PyMuPDF4LLM (as Markdown)."""
temp_file_path_for_pymupdf4llm = None
actual_path_to_process = None
try:
if isinstance(file_input, str):
actual_path_to_process = file_input
elif hasattr(file_input, 'read') and callable(file_input.read):
temp_file_obj = tempfile.NamedTemporaryFile(suffix=".pdf", delete=False)
temp_file_path_for_pymupdf4llm = temp_file_obj.name
file_input.seek(0)
temp_file_obj.write(file_input.read())
temp_file_obj.close()
actual_path_to_process = temp_file_path_for_pymupdf4llm
else:
raise ValueError("Input 'file_input' must be a file path (str) or a file-like object.")
doc_for_page_count = fitz.open(actual_path_to_process)
page_count = len(doc_for_page_count)
doc_for_page_count.close()
print(f"PDF has {page_count} pages. Extracting Markdown using pymupdf4llm.")
markdown_text = pymupdf4llm.to_markdown(actual_path_to_process)
print(f"Total extracted Markdown text length: {len(markdown_text)} characters.")
return markdown_text
except Exception as e:
print(f"Error extracting text from PDF: {str(e)}")
traceback.print_exc()
return ""
finally:
if temp_file_path_for_pymupdf4llm and os.path.exists(temp_file_path_for_pymupdf4llm):
os.remove(temp_file_path_for_pymupdf4llm)
def check_text_presence(full_text: str, search_terms: List[str]) -> Dict[str, bool]:
return {term: term.lower() in full_text.lower() for term in search_terms}
def label_authors(full_text: str) -> str:
# This function was in the original script but not directly used by analyze_pdf's output structure.
# Keeping it in case it's called elsewhere or for future use.
author_line_regex = r"^(?:.*\n)(.*?)(?:\n\n)"
match = re.search(author_line_regex, full_text, re.MULTILINE)
if match:
authors = match.group(1).strip()
return full_text.replace(authors, f"Authors: {authors}")
return full_text
def check_metadata(plain_text: str) -> Dict[str, Any]:
return {
"author_email": bool(re.search(r'\b[\w.-]+?@\w+?\.\w+?\b', plain_text)),
"list_of_authors": bool(re.search(r'Authors?:', plain_text, re.IGNORECASE)),
"keywords_list": bool(re.search(r'Keywords?:', plain_text, re.IGNORECASE)),
"word_count": len(plain_text.split()) or "Missing"
}
def check_disclosures(plain_text: str) -> Dict[str, bool]:
search_terms = [
"conflict of interest statement",
"ethics statement",
"funding statement",
"data access statement"
]
results = check_text_presence(plain_text, search_terms)
has_author_contribution = ("author contribution statement" in plain_text.lower() or
"author contributions statement" in plain_text.lower())
results["author contribution statement"] = has_author_contribution
return results
def check_figures_and_tables(plain_text: str) -> Dict[str, bool]:
return {
"figures_with_citations": bool(re.search(r'Figure \d+.*?citation', plain_text, re.IGNORECASE)),
"figures_legends": bool(re.search(r'Figure \d+.*?legend', plain_text, re.IGNORECASE)),
"tables_legends": bool(re.search(r'Table \d+.*?legend', plain_text, re.IGNORECASE))
}
def check_references_summary(plain_text: str) -> Dict[str, Any]: # Renamed from check_references for clarity
abstract_candidate = plain_text[:2000]
return {
"old_references": bool(re.search(r'\b19[0-9]{2}\b', plain_text)),
"citations_in_abstract": bool(re.search(r'\[\d+\]', abstract_candidate, re.IGNORECASE)) or \
bool(re.search(r'\bcit(?:ation|ed)\b', abstract_candidate, re.IGNORECASE)),
"reference_count": len(re.findall(r'\[\d+(?:,\s*\d+)*\]', plain_text)),
"self_citations": bool(re.search(r'Self-citation', plain_text, re.IGNORECASE))
}
def check_structure(plain_text: str) -> Dict[str, bool]:
text_lower = plain_text.lower()
return {
"imrad_structure": all(section.lower() in text_lower for section in ["introduction", "method", "result", "discussion"]),
"abstract_structure": "structured abstract" in text_lower
}
def check_language_issues_and_regex(markdown_text_from_pdf: str) -> Dict[str, Any]:
"""
Performs LanguageTool and specific regex checks on text derived from PDF's Markdown.
Filters issues to only include those between "abstract" and "references/bibliography".
Returns a list of issue dictionaries with fields for mapping.
"""
if not markdown_text_from_pdf.strip():
return {"total_issues": 0, "issues_list": [], "text_used_for_analysis": ""}
plain_text_from_markdown = convert_markdown_to_plain_text(markdown_text_from_pdf)
text_for_analysis = plain_text_from_markdown.replace('\n', ' ')
text_for_analysis = re.sub(r'\s+', ' ', text_for_analysis).strip()
if not text_for_analysis:
return {"total_issues": 0, "issues_list": [], "text_used_for_analysis": ""}
# --- Determine content boundaries ---
text_for_analysis_lower = text_for_analysis.lower()
abstract_match = re.search(r'\babstract\b', text_for_analysis_lower)
# If "abstract" is found, analysis starts from its beginning. Otherwise, from text start.
content_start_index = abstract_match.start() if abstract_match else 0
if abstract_match:
print(f"Found 'abstract' at index {content_start_index}")
else:
print(f"Did not find 'abstract', starting language analysis from index 0")
references_match = re.search(r'\breferences\b', text_for_analysis_lower)
bibliography_match = re.search(r'\bbibliography\b', text_for_analysis_lower)
content_end_index = len(text_for_analysis) # Default to end of text
if references_match and bibliography_match:
content_end_index = min(references_match.start(), bibliography_match.start())
print(f"Found 'references' at {references_match.start()} and 'bibliography' at {bibliography_match.start()}. Using {content_end_index} as end boundary.")
elif references_match:
content_end_index = references_match.start()
print(f"Found 'references' at {content_end_index}. Using it as end boundary.")
elif bibliography_match:
content_end_index = bibliography_match.start()
print(f"Found 'bibliography' at {content_end_index}. Using it as end boundary.")
else:
print(f"Did not find 'references' or 'bibliography'. Language analysis up to end of text (index {content_end_index}).")
# If "abstract" is found after "references/bibliography", the range is invalid for filtering.
# In such a case, or if no abstract is found, we might effectively process a very small or no region.
# This logic correctly makes the valid region empty if abstract_start >= content_end.
if content_start_index >= content_end_index:
print(f"Warning: Content start index ({content_start_index}) is not before content end index ({content_end_index}). No language issues will be reported from this range.")
# Effectively, no issues will pass the filter below.
tool = None
processed_issues: List[Dict[str, Any]] = []
try:
tool = language_tool_python.LanguageTool('en-US')
raw_lt_matches = tool.check(text_for_analysis)
lt_issues_in_range = 0
for idx, match in enumerate(raw_lt_matches):
if match.ruleId == "EN_SPLIT_WORDS_HYPHEN": continue
# Filter by content boundaries
if not (content_start_index <= match.offset < content_end_index):
continue
lt_issues_in_range +=1
context_str = text_for_analysis[match.offset : match.offset + match.errorLength]
processed_issues.append({
'_internal_id': f"lt_{idx}",
'ruleId': match.ruleId,
'message': match.message,
'context_text': context_str,
'offset_in_text': match.offset,
'error_length': match.errorLength,
'replacements_suggestion': match.replacements[:3] if match.replacements else [],
'category_name': match.category,
'is_mapped_to_pdf': False,
'pdf_coordinates_list': [],
'mapped_page_number': -1
})
print(f"LanguageTool found {len(raw_lt_matches)} raw issues, {lt_issues_in_range} issues within defined content range.")
regex_pattern = r'\b(\w+)\[(\d+)\]'
regex_matches = list(re.finditer(regex_pattern, text_for_analysis))
regex_issues_in_range = 0
for reg_idx, match in enumerate(regex_matches):
# Filter by content boundaries
if not (content_start_index <= match.start() < content_end_index):
continue
regex_issues_in_range += 1
word = match.group(1)
number = match.group(2)
processed_issues.append({
'_internal_id': f"regex_{reg_idx}",
'ruleId': "SPACE_BEFORE_BRACKET",
'message': f"Missing space before '[' in '{word}[{number}]'. Should be '{word} [{number}]'.",
'context_text': text_for_analysis[match.start():match.end()],
'offset_in_text': match.start(),
'error_length': match.end() - match.start(),
'replacements_suggestion': [f"{word} [{number}]"],
'category_name': "Formatting",
'is_mapped_to_pdf': False,
'pdf_coordinates_list': [],
'mapped_page_number': -1
})
print(f"Regex check found {len(regex_matches)} raw matches, {regex_issues_in_range} issues within defined content range.")
return {
"total_issues": len(processed_issues),
"issues_list": processed_issues,
"text_used_for_analysis": text_for_analysis
}
except Exception as e:
print(f"Error in check_language_issues_and_regex: {e}")
traceback.print_exc()
return {"error": str(e), "total_issues": 0, "issues_list": [], "text_used_for_analysis": text_for_analysis}
finally:
if tool: tool.close()
def check_figure_order(plain_text: str) -> Dict[str, Any]:
figure_pattern = r'(?:Fig(?:ure)?\.?|Figure)\s*(\d+)'
figure_references_str = re.findall(figure_pattern, plain_text, re.IGNORECASE)
valid_figure_numbers_int = []
for num_str in figure_references_str:
if num_str.isdigit():
valid_figure_numbers_int.append(int(num_str))
unique_sorted_figures = sorted(list(set(valid_figure_numbers_int)))
is_sequential = all(unique_sorted_figures[i] + 1 == unique_sorted_figures[i+1] for i in range(len(unique_sorted_figures)-1))
missing_figures = []
if unique_sorted_figures:
expected_figures = set(range(1, max(unique_sorted_figures) + 1))
missing_figures = sorted(list(expected_figures - set(unique_sorted_figures)))
counts = Counter(valid_figure_numbers_int)
duplicate_refs = [num for num, count in counts.items() if count > 1]
return {
"sequential_order_of_unique_figures": is_sequential,
"figure_count_unique": len(unique_sorted_figures),
"missing_figures_in_sequence_to_max": missing_figures,
"figure_order_as_encountered": valid_figure_numbers_int,
"duplicate_references_to_same_figure_number": duplicate_refs
}
def check_reference_order(plain_text: str) -> Dict[str, Any]:
reference_pattern = r'\[(\d+)\]'
references_str = re.findall(reference_pattern, plain_text)
ref_numbers_int = [int(ref) for ref in references_str if ref.isdigit()]
max_ref_val = 0
out_of_order_details = []
if ref_numbers_int:
max_ref_val = max(ref_numbers_int)
current_max_seen_in_text = 0
for i, ref in enumerate(ref_numbers_int):
if ref < current_max_seen_in_text :
out_of_order_details.append({
"position_in_text_occurrences": i + 1,
"value": ref,
"previous_max_value_seen": current_max_seen_in_text,
"message": f"Reference [{ref}] appeared after a higher reference [{current_max_seen_in_text}] was already cited."
})
current_max_seen_in_text = max(current_max_seen_in_text, ref)
all_expected_refs_up_to_max = set(range(1, max_ref_val + 1)) if max_ref_val > 0 else set()
used_refs_set = set(ref_numbers_int)
missing_refs_in_sequence_to_max = sorted(list(all_expected_refs_up_to_max - used_refs_set))
is_ordered_in_text = all(ref_numbers_int[i] <= ref_numbers_int[i+1] for i in range(len(ref_numbers_int)-1))
return {
"max_reference_number_cited": max_ref_val,
"out_of_order_citations_details": out_of_order_details,
"missing_references_up_to_max_cited": missing_refs_in_sequence_to_max,
"is_citation_order_non_decreasing_in_text": is_ordered_in_text
}
# ------------------------------
# Main Analysis Function
# ------------------------------
def analyze_pdf(filepath_or_stream: Any) -> Tuple[Dict[str, Any], None]:
doc_for_mapping = None
temp_fitz_file_path = None
try:
markdown_text = extract_pdf_text(filepath_or_stream)
if not markdown_text:
return {"error": "Failed to extract text (Markdown) from PDF."}, None
plain_text_for_general_checks = convert_markdown_to_plain_text(markdown_text)
cleaned_plain_text_for_regex = re.sub(r'\s+', ' ', plain_text_for_general_checks.replace('\n', ' ')).strip()
# This will now use the modified function with boundary filtering
language_and_regex_issue_report = check_language_issues_and_regex(markdown_text)
if "error" in language_and_regex_issue_report:
return {"error": f"Language/Regex check error: {language_and_regex_issue_report['error']}"}, None
detailed_issues_for_mapping = language_and_regex_issue_report.get("issues_list", [])
if detailed_issues_for_mapping:
# The rest of the mapping logic remains the same, operating on the filtered issues.
if isinstance(filepath_or_stream, str):
pdf_path_for_fitz = filepath_or_stream
elif hasattr(filepath_or_stream, 'read') and callable(filepath_or_stream.read):
filepath_or_stream.seek(0)
temp_fitz_file = tempfile.NamedTemporaryFile(suffix=".pdf", delete=False)
temp_fitz_file_path = temp_fitz_file.name
temp_fitz_file.write(filepath_or_stream.read())
temp_fitz_file.close()
pdf_path_for_fitz = temp_fitz_file_path
else:
# This case should ideally be caught by extract_pdf_text, but good to have a fallback
return {"error": "Invalid PDF input for coordinate mapping."}, None
try:
doc_for_mapping = fitz.open(pdf_path_for_fitz)
if doc_for_mapping.page_count > 0:
print(f"\n--- Mapping {len(detailed_issues_for_mapping)} Issues (filtered) to PDF Coordinates ---")
# Only attempt to map issues if there are any after filtering
if detailed_issues_for_mapping:
for page_idx in range(doc_for_mapping.page_count):
page = doc_for_mapping[page_idx]
current_page_num_1_based = page_idx + 1
unmapped_issues_on_this_page_by_context = defaultdict(list)
for issue_dict in detailed_issues_for_mapping:
if not issue_dict['is_mapped_to_pdf']:
unmapped_issues_on_this_page_by_context[issue_dict['context_text']].append(issue_dict)
if not unmapped_issues_on_this_page_by_context:
if all(iss['is_mapped_to_pdf'] for iss in detailed_issues_for_mapping): break
continue
for ctx_str, issues_for_ctx in unmapped_issues_on_this_page_by_context.items():
if not ctx_str.strip(): continue
try:
# Use TEXT_PRESERVE_LIGATURES and TEXT_PRESERVE_WHITESPACE for better matching
# with text derived from pymupdf4llm which tries to preserve structure.
pdf_rects = page.search_for(ctx_str, flags=fitz.TEXT_PRESERVE_LIGATURES | fitz.TEXT_PRESERVE_WHITESPACE)
if pdf_rects:
try_map_issues_to_page_rects(issues_for_ctx, pdf_rects, current_page_num_1_based)
except Exception as search_exc:
print(f"Warning: Error searching for context '{ctx_str[:30]}' on page {current_page_num_1_based}: {search_exc}")
total_mapped = sum(1 for iss in detailed_issues_for_mapping if iss['is_mapped_to_pdf'])
print(f"Finished coordinate mapping. Mapped issues: {total_mapped}/{len(detailed_issues_for_mapping)}.")
else:
print("No language/regex issues found within the defined content boundaries to map.")
except Exception as e_map:
print(f"Error during PDF coordinate mapping: {e_map}")
traceback.print_exc()
finally:
if doc_for_mapping: doc_for_mapping.close()
if temp_fitz_file_path and os.path.exists(temp_fitz_file_path):
os.unlink(temp_fitz_file_path)
final_formatted_issues_list = []
for issue_data in detailed_issues_for_mapping: # This list is already filtered
page_num_for_json = 0
coords_for_json = []
if issue_data['is_mapped_to_pdf'] and issue_data['pdf_coordinates_list']:
# Assuming pdf_coordinates_list stores a list of dicts, take the first one
coord_dict = issue_data['pdf_coordinates_list'][0]
coords_for_json = [coord_dict['x0'], coord_dict['y0'], coord_dict['x1'], coord_dict['y1']]
page_num_for_json = issue_data['mapped_page_number']
final_formatted_issues_list.append({
"message": issue_data['message'],
"context": issue_data['context_text'],
"suggestions": issue_data['replacements_suggestion'],
"category": issue_data['category_name'],
"rule_id": issue_data['ruleId'],
"offset": issue_data['offset_in_text'],
"length": issue_data['error_length'],
"coordinates": coords_for_json,
"page": page_num_for_json
})
results = {
"issues": final_formatted_issues_list, # This will now contain only filtered issues
"document_checks": {
"metadata": check_metadata(cleaned_plain_text_for_regex),
"disclosures": check_disclosures(cleaned_plain_text_for_regex),
"figures_and_tables": check_figures_and_tables(cleaned_plain_text_for_regex),
"references_summary": check_references_summary(cleaned_plain_text_for_regex),
"structure": check_structure(cleaned_plain_text_for_regex),
"figure_order_analysis": check_figure_order(cleaned_plain_text_for_regex),
"reference_order_analysis": check_reference_order(cleaned_plain_text_for_regex),
"plain_language_summary_present": bool(re.search(r'plain language summary', cleaned_plain_text_for_regex, re.IGNORECASE)),
"readability_issues_detected": False, # Placeholder, not implemented
}
}
return results, None
except Exception as e:
print(f"Overall analysis error in analyze_pdf: {e}")
traceback.print_exc()
# Ensure cleanup even if an early error occurs
if doc_for_mapping: doc_for_mapping.close()
if temp_fitz_file_path and os.path.exists(temp_fitz_file_path):
os.unlink(temp_fitz_file_path)
return {"error": str(e)}, None
# ------------------------------
# Gradio Interface
# ------------------------------
def process_upload(file_data_binary: bytes) -> Tuple[str, Optional[str]]:
if file_data_binary is None:
return json.dumps({"error": "No file uploaded"}, indent=2), None
temp_input_path = None
try:
# Create a temporary file with .pdf extension from the binary data
with tempfile.NamedTemporaryFile(delete=False, suffix='.pdf') as temp_input_file:
temp_input_file.write(file_data_binary)
temp_input_path = temp_input_file.name
print(f"Temporary PDF for analysis: {temp_input_path}")
results_dict, _ = analyze_pdf(temp_input_path) # Pass the path to the temp file
results_json = json.dumps(results_dict, indent=2, ensure_ascii=False)
return results_json, None # No annotated PDF path to return for now
except Exception as e:
print(f"Error in process_upload: {e}")
error_message = json.dumps({"error": str(e), "traceback": traceback.format_exc()}, indent=2)
return error_message, None
finally:
if temp_input_path and os.path.exists(temp_input_path):
os.unlink(temp_input_path)
print(f"Cleaned up temporary file: {temp_input_path}")
def create_interface():
with gr.Blocks(title="PDF Analyzer") as interface:
gr.Markdown("# PDF Analyzer")
gr.Markdown("Upload a PDF document to analyze its structure, references, language, and more. Language issues will include PDF coordinates if found, and are filtered to appear between 'Abstract' and 'References/Bibliography'.")
with gr.Row():
file_input = gr.File(
label="Upload PDF",
file_types=[".pdf"],
type="binary" # Changed to binary to handle uploads directly
)
with gr.Row():
analyze_btn = gr.Button("Analyze PDF")
with gr.Row():
results_output = gr.JSON(
label="Analysis Results (Coordinates for issues in 'issues' list)",
show_label=True
)
with gr.Row():
# Keeping the placeholder for PDF output, but it's not functional for annotation
pdf_output = gr.File(
label="Annotated PDF (Functionality Removed - View Coordinates in JSON)",
show_label=True,
# value=None # Ensure it's empty initially
)
analyze_btn.click(
fn=process_upload,
inputs=[file_input],
outputs=[results_output, pdf_output] # pdf_output will receive None
)
return interface
if __name__ == "__main__":
print("\n--- Launching Gradio Interface ---")
# Ensure JAVA_HOME is set if not globally configured
if 'JAVA_HOME' not in os.environ:
# Attempt to set a common default if necessary, or ensure the user sets it.
# For this script, it's set at the top.
print("JAVA_HOME is set to:", os.environ.get('JAVA_HOME'))
else:
print("JAVA_HOME is set to:", os.environ.get('JAVA_HOME'))
# Check if LanguageTool can be initialized (optional check)
try:
lt_test = language_tool_python.LanguageTool('en-US')
lt_test.close()
print("LanguageTool initialized successfully.")
except Exception as lt_e:
print(f"Warning: Could not initialize LanguageTool. Language checks might fail: {lt_e}")
print("Please ensure Java is installed and JAVA_HOME is correctly set.")
print("For example, on Ubuntu with OpenJDK 11: export JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64")
interface = create_interface()
interface.launch(
share=False, # Set to True for public link if ngrok is installed
server_port=None # Gradio will pick an available port
) |