app.py

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'

global_constants = {
    "CONTEXT_LENGTH" : 3
}


# --- 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')
        print(text_for_analysis)
        raw_lt_matches = tool.check(text_for_analysis)

        # Define a set of rule IDs to ignore
        rules_to_ignore = {
            "EN_SPLIT_WORDS_HYPHEN",      # Existing rule to ignore
            "MORFOLOGIK_RULE_EN_US"       # New rule to ignore for spelling mistakes
        }

        lt_issues_in_range = 0
        for idx, match in enumerate(raw_lt_matches):
            # Skip if the ruleId is in our set of ignored rules
            if match.ruleId in rules_to_ignore:
                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 - global_constants["CONTEXT_LENGTH"] : match.offset + match.errorLength + global_constants["CONTEXT_LENGTH"]]
            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+)'
    # Find all matches; re.IGNORECASE ensures "figure", "Figure", "FIGURE" are caught
    figure_references_raw = re.findall(figure_pattern, plain_text, re.IGNORECASE)

    # Convert captured numbers (group 1 of the regex) to integers
    # Only include if the captured string is indeed a digit.
    valid_figure_numbers_int: List[int] = []
    for num_str in figure_references_raw:
        if num_str.isdigit():
            valid_figure_numbers_int.append(int(num_str))
        # else:
            # Optional: log or handle non-digit captures if the regex could allow them
            # print(f"Warning: Figure regex captured non-digit '{num_str}'")

    if not valid_figure_numbers_int:
        # No valid figure references found in the text
        return {
            "sequential_order_of_unique_figures": True,  # Vacuously true as no figures to be out of order
            "figure_count_unique": 0,
            "missing_figures_in_sequence_to_max": [],
            "figure_order_as_encountered": [],
            "duplicate_references_to_same_figure_number": [],
            "figures_mentioned_only_once": [] # New: No figures, so none are mentioned only once
        }

    # Get unique figure numbers, sorted
    unique_sorted_figures: List[int] = sorted(list(set(valid_figure_numbers_int)))

    # Check 1: Are the unique, sorted figures consecutive?
    # e.g., [1, 2, 3] is sequential. [1, 3] is not. [2, 3, 4] is sequential by this definition.
    is_sequential = True # Assume true initially
    if len(unique_sorted_figures) > 1: # Only check if there's more than one unique figure
        is_sequential = all(unique_sorted_figures[i] + 1 == unique_sorted_figures[i+1]
                            for i in range(len(unique_sorted_figures) - 1))

    # Check 2: Missing figures in the sequence from 1 up to the highest figure number mentioned.
    # This assumes figures should ideally start from 1 and be continuous up to the max.
    missing_figures: List[int] = []
    # max_found_figure will not error as unique_sorted_figures is non-empty at this point
    max_found_figure = unique_sorted_figures[-1] # Since it's sorted and non-empty
    expected_figures_up_to_max = set(range(1, max_found_figure + 1))
    actual_figures_found_set = set(unique_sorted_figures)
    missing_figures = sorted(list(expected_figures_up_to_max - actual_figures_found_set))

    # Check 3: Count occurrences of each figure reference for duplicates and single mentions
    counts = Counter(valid_figure_numbers_int)

    # Figures mentioned more than once (duplicates in terms of referencing the same figure number)
    duplicate_refs: List[int] = sorted([num for num, count in counts.items() if count > 1])

    # New Check: Figures mentioned exactly once.
    # The requirement is "each figure should have atleast more than 1 mention".
    # So, if a figure's mention count is 1, it fails this condition.
    figures_mentioned_only_once: List[int] = sorted([
        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, # Original list of all found figure numbers in order of appearance
        "duplicate_references_to_same_figure_number": duplicate_refs,
        "figures_mentioned_only_once": figures_mentioned_only_once # NEWLY ADDED
    }

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
    )