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1776 lines
59 KiB
Python
1776 lines
59 KiB
Python
#!/usr/bin/env python3
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"""
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report_generator.py — Comprehensive HTML + Markdown Report Generator
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for the Geng Skill Academic Fraud Detection Project.
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Generates professional, self-contained analysis reports from assessment JSON
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produced by the detection pipeline. Supports two output formats:
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- HTML (self-contained with embedded CSS/figures, printable)
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- Markdown (for GitHub/documentation, figures as relative paths)
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Usage:
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python3 report_generator.py --input assessment.json --figures figures/ --output report/
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The input assessment.json is expected to have this structure:
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{
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"metadata": { "source_file", "timestamp", "tool_version", "columns", "rows", ... },
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"overall_risk": { "score": 0-100, "level": "LOW|MEDIUM|HIGH|CRITICAL" },
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"data_overview": { "columns": [...], "preview": [...], "statistics": {...} },
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"modules": [
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{
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"name": "...",
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"description": "...",
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"method": "...",
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"results": { ... },
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"figures": ["fig1.png", ...],
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"risk_level": "LOW|MEDIUM|HIGH|CRITICAL",
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"p_value": ...,
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"test_statistic": ...,
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"evidence_summary": "..."
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}, ...
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],
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"suspicious_points": [
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{ "row": ..., "column": "...", "value": ..., "reason": "...", "module": "..." }, ...
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],
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"confidence": { "overall": ..., "intervals": {...}, "limitations": [...] },
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"recommendations": [ { "priority": 1, "action": "...", "rationale": "..." }, ... ]
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}
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Author: BioMaster / Geng Skill Project
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License: MIT
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"""
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import argparse
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import base64
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import json
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import os
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import sys
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from datetime import datetime, timezone
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from pathlib import Path
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from typing import Any, Dict, List, Optional
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# ---------------------------------------------------------------------------
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# Constants
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# ---------------------------------------------------------------------------
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TOOL_VERSION = "1.0.0"
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TOOL_NAME = "Geng Skill Academic Data Integrity Analyzer"
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RISK_COLORS = {
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"LOW": "#28a745", # green
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"MEDIUM": "#ffc107", # yellow/amber
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"HIGH": "#fd7e14", # orange
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"CRITICAL": "#dc3545", # red
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}
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RISK_EMOJI = {
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"LOW": "🟢",
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"MEDIUM": "🟡",
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"HIGH": "🟠",
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"CRITICAL": "🔴",
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}
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RISK_LABELS = {
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"LOW": "Low Risk",
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"MEDIUM": "Medium Risk",
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"HIGH": "High Risk",
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"CRITICAL": "Critical Risk",
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}
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METHODOLOGY_REFERENCES = {
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"benford": {
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"name": "Benford's Law (First-Digit Test)",
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"description": (
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"Tests whether the distribution of leading digits in the dataset "
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"conforms to the logarithmic distribution predicted by Benford's Law. "
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"Fabricated data often shows uniform or biased digit distributions."
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),
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"references": [
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"Benford, F. (1938). The law of anomalous numbers. Proc. Amer. Phil. Soc., 78(4), 551-572.",
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"Nigrini, M.J. (2012). Benford's Law. Wiley.",
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],
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},
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"terminal_digit": {
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"name": "Terminal Digit Analysis",
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"description": (
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"Examines the distribution of last digits in numeric data. "
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"Authentic measurements typically show uniform terminal digit distribution, "
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"while fabricated data often exhibits preference for certain digits (e.g., 0, 5)."
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),
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"references": [
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"Mosimann, J.E., Wiseman, C.V., & Edelman, R.E. (1995). Data fabrication. "
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"Chance, 8(2), 7-12.",
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],
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},
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"grim": {
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"name": "GRIM Test (Granularity-Related Inconsistency of Means)",
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"description": (
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"Verifies whether reported means are mathematically possible given the "
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"reported sample size and measurement granularity. Impossible means indicate "
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"either reporting errors or data fabrication."
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),
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"references": [
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"Brown, N.J.L., & Heathers, J.A.J. (2017). The GRIM test. "
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"Social Psychological and Personality Science, 8(4), 363-369.",
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],
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},
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"sprite": {
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"name": "SPRITE (Sample Parameter Reconstruction via Iterative TEchniques)",
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"description": (
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"Reconstructs possible raw data distributions consistent with reported "
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"summary statistics. Flags cases where no valid distribution exists."
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),
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"references": [
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"Heathers, J.A.J., & Brown, N.J.L. (2019). SPRITE. PeerJ Preprints.",
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],
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},
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"distribution": {
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"name": "Distribution Shape Analysis",
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"description": (
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"Tests data against expected statistical distributions using "
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"Kolmogorov-Smirnov, Shapiro-Wilk, or Anderson-Darling tests. "
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"Fabricated data often shows abnormal distributional properties."
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),
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"references": [
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"Simonsohn, U. (2013). Just post it. Psychological Science, 24(10), 1875-1888.",
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],
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},
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"duplicates": {
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"name": "Duplicate/Near-Duplicate Detection",
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"description": (
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"Identifies exact and near-duplicate values, rows, or patterns that occur "
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"more frequently than expected by chance."
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),
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"references": [
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"Bik, E.M., Casadevall, A., & Fang, F.C. (2016). The prevalence of "
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"inappropriate image duplication. mBio, 7(3), e00809-16.",
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],
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},
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"variance": {
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"name": "Variance Analysis (ANOVA / Levene's Test)",
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"description": (
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"Examines whether variance patterns are consistent with genuine experimental "
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"data. Fabricated data often shows abnormally low or uniform variance."
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),
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"references": [
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"Carlisle, J.B. (2017). Data fabrication and other reasons for "
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"non-random sampling. Anaesthesia, 72(8), 944-952.",
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],
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},
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"correlation": {
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"name": "Correlation Structure Analysis",
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"description": (
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"Checks whether inter-variable correlations are biologically/experimentally "
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"plausible. Fabricated data may show correlations that are too perfect or "
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"internally inconsistent."
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),
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"references": [
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"Simonsohn, U. (2014). Posterior-Hacking. Available at SSRN.",
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],
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},
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}
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DISCLAIMER_EN = """
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**DISCLAIMER**: This report is generated by an automated statistical analysis tool and is intended
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for preliminary screening purposes ONLY. The results do NOT constitute proof of misconduct.
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Statistical anomalies can arise from legitimate methodological choices, measurement artifacts,
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or natural data properties. Any findings should be interpreted by qualified experts and investigated
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through proper institutional channels before any conclusions about research integrity are drawn.
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This tool should NEVER be used as the sole basis for accusations of fraud or misconduct.
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""".strip()
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DISCLAIMER_ZH = """
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**免责声明**：本报告由自动化统计分析工具生成，仅用于初步筛查目的。分析结果不构成学术不端的证据。
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统计异常可能源于合理的方法学选择、测量误差或数据的自然属性。任何发现都应由具备资质的专家解读，
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并通过正规的机构渠道进行调查，方可得出关于研究诚信的结论。本工具绝不应作为指控欺诈或不端行为的
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唯一依据。
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""".strip()
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# ---------------------------------------------------------------------------
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# HTML Template & CSS
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# ---------------------------------------------------------------------------
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HTML_CSS = """
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:root {
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--primary: #2c3e50;
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--secondary: #34495e;
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--accent: #3498db;
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--bg: #ffffff;
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--bg-alt: #f8f9fa;
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--border: #dee2e6;
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--text: #212529;
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--text-muted: #6c757d;
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--success: #28a745;
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--warning: #ffc107;
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--danger: #dc3545;
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--orange: #fd7e14;
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}
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* { box-sizing: border-box; }
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body {
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font-family: 'Segoe UI', -apple-system, BlinkMacSystemFont, 'Helvetica Neue', Arial, sans-serif;
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line-height: 1.6;
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color: var(--text);
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background: var(--bg);
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margin: 0;
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padding: 0;
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}
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.container {
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max-width: 1100px;
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margin: 0 auto;
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padding: 2rem;
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}
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/* Header */
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.report-header {
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border-bottom: 3px solid var(--primary);
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padding-bottom: 1.5rem;
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margin-bottom: 2rem;
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}
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.report-header h1 {
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font-size: 1.8rem;
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color: var(--primary);
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margin: 0 0 0.5rem 0;
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}
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.report-header .subtitle {
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font-size: 1rem;
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color: var(--text-muted);
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margin: 0;
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}
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/* Risk Badge */
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.risk-badge {
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display: inline-block;
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padding: 0.4rem 1rem;
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border-radius: 4px;
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font-weight: 700;
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font-size: 0.9rem;
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color: #fff;
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text-transform: uppercase;
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letter-spacing: 0.5px;
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}
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.risk-badge.low { background: var(--success); }
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.risk-badge.medium { background: var(--warning); color: #212529; }
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.risk-badge.high { background: var(--orange); }
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.risk-badge.critical { background: var(--danger); }
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/* Score Meter */
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.score-meter {
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width: 100%;
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height: 24px;
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background: #e9ecef;
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border-radius: 12px;
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overflow: hidden;
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margin: 0.5rem 0;
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}
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.score-meter .fill {
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height: 100%;
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border-radius: 12px;
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transition: width 0.5s;
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display: flex;
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align-items: center;
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justify-content: center;
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font-size: 0.75rem;
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font-weight: 700;
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color: #fff;
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}
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/* Sections */
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.section {
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margin-bottom: 2.5rem;
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}
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.section h2 {
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font-size: 1.4rem;
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color: var(--primary);
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border-bottom: 2px solid var(--accent);
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padding-bottom: 0.5rem;
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margin-bottom: 1rem;
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}
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.section h3 {
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font-size: 1.1rem;
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color: var(--secondary);
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margin-top: 1.5rem;
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margin-bottom: 0.5rem;
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}
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/* Cards */
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.card {
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background: var(--bg);
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border: 1px solid var(--border);
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border-radius: 8px;
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padding: 1.2rem;
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margin-bottom: 1rem;
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box-shadow: 0 1px 3px rgba(0,0,0,0.04);
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}
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.card.risk-low { border-left: 4px solid var(--success); }
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.card.risk-medium { border-left: 4px solid var(--warning); }
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.card.risk-high { border-left: 4px solid var(--orange); }
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.card.risk-critical { border-left: 4px solid var(--danger); }
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.card-header {
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display: flex;
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justify-content: space-between;
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align-items: center;
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margin-bottom: 0.8rem;
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}
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.card-header h3 {
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margin: 0;
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font-size: 1.05rem;
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}
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/* Tables */
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table {
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width: 100%;
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border-collapse: collapse;
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margin: 1rem 0;
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font-size: 0.9rem;
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}
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th, td {
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padding: 0.6rem 0.8rem;
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text-align: left;
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border-bottom: 1px solid var(--border);
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}
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th {
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background: var(--primary);
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color: #fff;
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font-weight: 600;
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position: sticky;
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top: 0;
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}
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tr:nth-child(even) {
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background: var(--bg-alt);
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}
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tr:hover {
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background: #e8f4fd;
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}
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/* Figures */
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.figure-container {
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text-align: center;
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margin: 1rem 0;
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}
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.figure-container img {
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max-width: 100%;
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height: auto;
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border: 1px solid var(--border);
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border-radius: 4px;
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}
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.figure-caption {
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font-size: 0.85rem;
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color: var(--text-muted);
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margin-top: 0.4rem;
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font-style: italic;
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}
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/* Stats Grid */
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.stats-grid {
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display: grid;
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grid-template-columns: repeat(auto-fit, minmax(200px, 1fr));
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gap: 1rem;
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margin: 1rem 0;
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}
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.stat-box {
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background: var(--bg-alt);
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border: 1px solid var(--border);
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border-radius: 6px;
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padding: 1rem;
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text-align: center;
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}
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.stat-box .stat-value {
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font-size: 1.6rem;
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font-weight: 700;
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color: var(--primary);
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}
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.stat-box .stat-label {
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font-size: 0.8rem;
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color: var(--text-muted);
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text-transform: uppercase;
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letter-spacing: 0.5px;
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}
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/* Evidence */
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.evidence-list {
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list-style: none;
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padding: 0;
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}
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.evidence-list li {
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padding: 0.4rem 0;
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padding-left: 1.5rem;
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position: relative;
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}
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.evidence-list li::before {
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content: '•';
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position: absolute;
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left: 0.5rem;
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color: var(--accent);
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font-weight: 700;
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}
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/* Suspicious Points Table */
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.suspicious-row {
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background: #fff3cd !important;
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}
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/* Disclaimer */
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.disclaimer {
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background: #f8d7da;
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border: 1px solid #f5c6cb;
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border-radius: 6px;
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padding: 1.2rem;
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margin: 2rem 0;
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font-size: 0.9rem;
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}
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.disclaimer h3 {
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color: var(--danger);
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margin-top: 0;
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}
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/* Footer */
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.report-footer {
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border-top: 2px solid var(--border);
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padding-top: 1rem;
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margin-top: 3rem;
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font-size: 0.8rem;
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color: var(--text-muted);
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display: flex;
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justify-content: space-between;
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flex-wrap: wrap;
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}
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/* Print Styles */
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@media print {
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body { font-size: 10pt; }
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.container { max-width: 100%; padding: 0; }
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.card { break-inside: avoid; }
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.section { break-inside: avoid; }
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table { font-size: 8pt; }
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.report-header { border-bottom-width: 2px; }
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}
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/* Recommendations */
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.recommendation {
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display: flex;
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align-items: flex-start;
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gap: 0.8rem;
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padding: 0.8rem;
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margin-bottom: 0.5rem;
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background: var(--bg-alt);
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border-radius: 6px;
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}
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.recommendation .priority-num {
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background: var(--accent);
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color: #fff;
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width: 28px;
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height: 28px;
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border-radius: 50%;
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display: flex;
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align-items: center;
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justify-content: center;
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font-weight: 700;
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font-size: 0.85rem;
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flex-shrink: 0;
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}
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.recommendation .rec-content {
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flex: 1;
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}
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.recommendation .rec-action {
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font-weight: 600;
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margin-bottom: 0.2rem;
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}
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.recommendation .rec-rationale {
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font-size: 0.85rem;
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color: var(--text-muted);
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}
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/* Methodology */
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.method-entry {
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margin-bottom: 1.2rem;
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padding-left: 1rem;
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border-left: 3px solid var(--accent);
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}
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.method-entry .method-name {
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font-weight: 700;
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margin-bottom: 0.3rem;
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}
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.method-entry .method-desc {
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font-size: 0.9rem;
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margin-bottom: 0.3rem;
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}
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.method-entry .method-ref {
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font-size: 0.8rem;
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color: var(--text-muted);
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font-style: italic;
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}
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"""
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# ---------------------------------------------------------------------------
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# Helper Functions
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# ---------------------------------------------------------------------------
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|
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|
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def load_assessment(path: str) -> Dict[str, Any]:
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"""Load and validate the assessment JSON file.
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Args:
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path: Path to the assessment JSON file.
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Returns:
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Parsed assessment dictionary.
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Raises:
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FileNotFoundError: If the assessment file doesn't exist.
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json.JSONDecodeError: If the file is not valid JSON.
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ValueError: If required fields are missing.
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"""
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filepath = Path(path)
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if not filepath.exists():
|
|
raise FileNotFoundError(f"Assessment file not found: {path}")
|
|
|
|
with open(filepath, "r", encoding="utf-8") as f:
|
|
data = json.load(f)
|
|
|
|
# Validate required top-level keys
|
|
required = ["metadata", "overall_risk", "modules"]
|
|
missing = [k for k in required if k not in data]
|
|
if missing:
|
|
raise ValueError(f"Assessment JSON missing required keys: {missing}")
|
|
|
|
return data
|
|
|
|
|
|
def encode_figure_base64(figure_path: str, figures_dir: str) -> Optional[str]:
|
|
"""Encode a figure file as base64 data URI for HTML embedding.
|
|
|
|
Args:
|
|
figure_path: Filename or relative path of the figure.
|
|
figures_dir: Directory containing figures.
|
|
|
|
Returns:
|
|
Base64 data URI string, or None if file not found.
|
|
"""
|
|
full_path = Path(figures_dir) / figure_path
|
|
if not full_path.exists():
|
|
return None
|
|
|
|
suffix = full_path.suffix.lower()
|
|
mime_map = {
|
|
".png": "image/png",
|
|
".jpg": "image/jpeg",
|
|
".jpeg": "image/jpeg",
|
|
".svg": "image/svg+xml",
|
|
".gif": "image/gif",
|
|
}
|
|
mime_type = mime_map.get(suffix, "image/png")
|
|
|
|
with open(full_path, "rb") as f:
|
|
encoded = base64.b64encode(f.read()).decode("ascii")
|
|
|
|
return f"data:{mime_type};base64,{encoded}"
|
|
|
|
|
|
def risk_level_to_css_class(level: str) -> str:
|
|
"""Convert risk level string to CSS class name.
|
|
|
|
Args:
|
|
level: Risk level (LOW, MEDIUM, HIGH, CRITICAL).
|
|
|
|
Returns:
|
|
CSS class string.
|
|
"""
|
|
return level.lower()
|
|
|
|
|
|
def format_p_value(p: Optional[float]) -> str:
|
|
"""Format a p-value for display with appropriate precision.
|
|
|
|
Args:
|
|
p: The p-value to format, or None.
|
|
|
|
Returns:
|
|
Formatted string representation.
|
|
"""
|
|
if p is None:
|
|
return "N/A"
|
|
if p < 0.001:
|
|
return f"< 0.001 (p = {p:.2e})"
|
|
elif p < 0.01:
|
|
return f"{p:.4f}"
|
|
elif p < 0.05:
|
|
return f"{p:.3f}"
|
|
else:
|
|
return f"{p:.3f}"
|
|
|
|
|
|
def score_to_color(score: float) -> str:
|
|
"""Map a 0-100 risk score to a gradient color.
|
|
|
|
Args:
|
|
score: Risk score (0-100).
|
|
|
|
Returns:
|
|
CSS color string.
|
|
"""
|
|
if score <= 25:
|
|
return RISK_COLORS["LOW"]
|
|
elif score <= 50:
|
|
return RISK_COLORS["MEDIUM"]
|
|
elif score <= 75:
|
|
return RISK_COLORS["HIGH"]
|
|
else:
|
|
return RISK_COLORS["CRITICAL"]
|
|
|
|
|
|
def score_to_level(score: float) -> str:
|
|
"""Map a 0-100 risk score to a risk level string.
|
|
|
|
Args:
|
|
score: Risk score (0-100).
|
|
|
|
Returns:
|
|
Risk level string.
|
|
"""
|
|
if score <= 25:
|
|
return "LOW"
|
|
elif score <= 50:
|
|
return "MEDIUM"
|
|
elif score <= 75:
|
|
return "HIGH"
|
|
else:
|
|
return "CRITICAL"
|
|
|
|
|
|
# ---------------------------------------------------------------------------
|
|
# HTML Report Generator
|
|
# ---------------------------------------------------------------------------
|
|
|
|
|
|
class HTMLReportGenerator:
|
|
"""Generates a self-contained HTML report from assessment data.
|
|
|
|
The report includes embedded CSS, base64-encoded figures, and is
|
|
designed to be printable without external dependencies.
|
|
|
|
Attributes:
|
|
assessment: The assessment data dictionary.
|
|
figures_dir: Path to the directory containing figure files.
|
|
"""
|
|
|
|
def __init__(self, assessment: Dict[str, Any], figures_dir: str):
|
|
"""Initialize the HTML report generator.
|
|
|
|
Args:
|
|
assessment: Parsed assessment dictionary.
|
|
figures_dir: Path to directory containing figure image files.
|
|
"""
|
|
self.assessment = assessment
|
|
self.figures_dir = figures_dir
|
|
|
|
def generate(self) -> str:
|
|
"""Generate the complete HTML report.
|
|
|
|
Returns:
|
|
Complete HTML document as a string.
|
|
"""
|
|
parts = [
|
|
self._html_head(),
|
|
'<body>',
|
|
'<div class="container">',
|
|
self._header(),
|
|
self._executive_summary(),
|
|
self._data_overview(),
|
|
self._module_results(),
|
|
self._suspicious_points(),
|
|
self._confidence_limitations(),
|
|
self._methodology(),
|
|
self._recommendations(),
|
|
self._disclaimer(),
|
|
self._footer(),
|
|
'</div>',
|
|
'</body>',
|
|
'</html>',
|
|
]
|
|
return "\n".join(parts)
|
|
|
|
def _html_head(self) -> str:
|
|
"""Generate HTML head with embedded CSS."""
|
|
title = f"{TOOL_NAME} — Analysis Report"
|
|
return f"""<!DOCTYPE html>
|
|
<html lang="en">
|
|
<head>
|
|
<meta charset="UTF-8">
|
|
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
|
<title>{title}</title>
|
|
<style>{HTML_CSS}</style>
|
|
</head>"""
|
|
|
|
def _header(self) -> str:
|
|
"""Generate report header section."""
|
|
meta = self.assessment.get("metadata", {})
|
|
source = meta.get("source_file", "Unknown")
|
|
timestamp = meta.get("timestamp", datetime.now(timezone.utc).isoformat())
|
|
|
|
return f"""
|
|
<div class="report-header">
|
|
<h1>📊 {TOOL_NAME}</h1>
|
|
<p class="subtitle">Analysis Report — {source}</p>
|
|
<p class="subtitle">Generated: {timestamp}</p>
|
|
</div>"""
|
|
|
|
def _executive_summary(self) -> str:
|
|
"""Generate executive summary section with overall risk score."""
|
|
risk = self.assessment.get("overall_risk", {})
|
|
score = risk.get("score", 0)
|
|
level = risk.get("level", score_to_level(score))
|
|
color = score_to_color(score)
|
|
emoji = RISK_EMOJI.get(level, "⚪")
|
|
label = RISK_LABELS.get(level, "Unknown")
|
|
|
|
# Key findings
|
|
modules = self.assessment.get("modules", [])
|
|
flagged = [m for m in modules if m.get("risk_level", "LOW") in ("HIGH", "CRITICAL")]
|
|
suspicious_count = len(self.assessment.get("suspicious_points", []))
|
|
|
|
findings_html = ""
|
|
if flagged:
|
|
findings_html = "<ul>"
|
|
for m in flagged:
|
|
me = RISK_EMOJI.get(m.get("risk_level", "LOW"), "⚪")
|
|
findings_html += f'<li>{me} <strong>{m.get("name", "Unknown")}</strong>: {m.get("evidence_summary", "Anomaly detected")}</li>'
|
|
findings_html += "</ul>"
|
|
else:
|
|
findings_html = "<p>No high-risk anomalies detected across all modules.</p>"
|
|
|
|
# Conclusion
|
|
if level == "CRITICAL":
|
|
conclusion = (
|
|
"Multiple strong statistical indicators suggest significant anomalies in this dataset. "
|
|
"The patterns observed are highly unlikely to arise from legitimate experimental data. "
|
|
"Further expert review is strongly recommended."
|
|
)
|
|
elif level == "HIGH":
|
|
conclusion = (
|
|
"Several statistical indicators show notable anomalies that warrant further investigation. "
|
|
"While not conclusive evidence of data integrity issues, the patterns deserve scrutiny."
|
|
)
|
|
elif level == "MEDIUM":
|
|
conclusion = (
|
|
"Some mild statistical anomalies were detected. These may reflect legitimate methodological "
|
|
"choices or minor reporting inconsistencies. Routine verification is advisable."
|
|
)
|
|
else:
|
|
conclusion = (
|
|
"The dataset shows no significant statistical anomalies across the tests performed. "
|
|
"The data patterns appear consistent with legitimate experimental measurements."
|
|
)
|
|
|
|
return f"""
|
|
<div class="section">
|
|
<h2>Executive Summary</h2>
|
|
<div class="stats-grid">
|
|
<div class="stat-box">
|
|
<div class="stat-value" style="color: {color}">{score}/100</div>
|
|
<div class="stat-label">Overall Risk Score</div>
|
|
</div>
|
|
<div class="stat-box">
|
|
<div class="stat-value">{emoji} {label}</div>
|
|
<div class="stat-label">Risk Level</div>
|
|
</div>
|
|
<div class="stat-box">
|
|
<div class="stat-value">{len(modules)}</div>
|
|
<div class="stat-label">Tests Performed</div>
|
|
</div>
|
|
<div class="stat-box">
|
|
<div class="stat-value" style="color: {'var(--danger)' if suspicious_count > 0 else 'var(--success)'}">{suspicious_count}</div>
|
|
<div class="stat-label">Suspicious Data Points</div>
|
|
</div>
|
|
</div>
|
|
<div class="score-meter">
|
|
<div class="fill" style="width: {score}%; background: {color};">{score}%</div>
|
|
</div>
|
|
<h3>Key Findings</h3>
|
|
{findings_html}
|
|
<h3>Conclusion</h3>
|
|
<p>{conclusion}</p>
|
|
</div>"""
|
|
|
|
def _data_overview(self) -> str:
|
|
"""Generate data overview section with column stats and preview."""
|
|
overview = self.assessment.get("data_overview", {})
|
|
meta = self.assessment.get("metadata", {})
|
|
|
|
# File info
|
|
source = meta.get("source_file", "Unknown")
|
|
rows = meta.get("rows", "N/A")
|
|
cols = meta.get("columns_count", len(meta.get("columns", [])))
|
|
file_size = meta.get("file_size", "N/A")
|
|
|
|
info_html = f"""
|
|
<div class="stats-grid">
|
|
<div class="stat-box">
|
|
<div class="stat-value" style="font-size:1rem">{source}</div>
|
|
<div class="stat-label">Source File</div>
|
|
</div>
|
|
<div class="stat-box">
|
|
<div class="stat-value">{rows}</div>
|
|
<div class="stat-label">Rows</div>
|
|
</div>
|
|
<div class="stat-box">
|
|
<div class="stat-value">{cols}</div>
|
|
<div class="stat-label">Columns</div>
|
|
</div>
|
|
<div class="stat-box">
|
|
<div class="stat-value" style="font-size:1rem">{file_size}</div>
|
|
<div class="stat-label">File Size</div>
|
|
</div>
|
|
</div>"""
|
|
|
|
# Column statistics table
|
|
statistics = overview.get("statistics", {})
|
|
stats_table = ""
|
|
if statistics:
|
|
stats_table = """
|
|
<h3>Column Statistics</h3>
|
|
<table>
|
|
<tr><th>Column</th><th>Type</th><th>Non-Null</th><th>Mean</th><th>Std</th><th>Min</th><th>Max</th></tr>"""
|
|
for col_name, stats in statistics.items():
|
|
dtype = stats.get("dtype", "—")
|
|
non_null = stats.get("non_null", "—")
|
|
mean = stats.get("mean", "—")
|
|
std = stats.get("std", "—")
|
|
min_val = stats.get("min", "—")
|
|
max_val = stats.get("max", "—")
|
|
# Format numeric values
|
|
if isinstance(mean, float):
|
|
mean = f"{mean:.4g}"
|
|
if isinstance(std, float):
|
|
std = f"{std:.4g}"
|
|
if isinstance(min_val, float):
|
|
min_val = f"{min_val:.4g}"
|
|
if isinstance(max_val, float):
|
|
max_val = f"{max_val:.4g}"
|
|
stats_table += f"\n <tr><td>{col_name}</td><td>{dtype}</td><td>{non_null}</td><td>{mean}</td><td>{std}</td><td>{min_val}</td><td>{max_val}</td></tr>"
|
|
stats_table += "\n </table>"
|
|
|
|
# Preview table
|
|
preview = overview.get("preview", [])
|
|
preview_html = ""
|
|
if preview:
|
|
columns = overview.get("columns", list(preview[0].keys()) if preview else [])
|
|
preview_html = "\n <h3>Data Preview (first rows)</h3>\n <table>\n <tr>"
|
|
for col in columns:
|
|
preview_html += f"<th>{col}</th>"
|
|
preview_html += "</tr>"
|
|
for row in preview[:10]:
|
|
preview_html += "\n <tr>"
|
|
for col in columns:
|
|
val = row.get(col, "—")
|
|
preview_html += f"<td>{val}</td>"
|
|
preview_html += "</tr>"
|
|
preview_html += "\n </table>"
|
|
|
|
return f"""
|
|
<div class="section">
|
|
<h2>Data Overview</h2>
|
|
{info_html}
|
|
{stats_table}
|
|
{preview_html}
|
|
</div>"""
|
|
|
|
def _module_results(self) -> str:
|
|
"""Generate module-by-module results section."""
|
|
modules = self.assessment.get("modules", [])
|
|
if not modules:
|
|
return """
|
|
<div class="section">
|
|
<h2>Module-by-Module Results</h2>
|
|
<p>No detection modules were executed.</p>
|
|
</div>"""
|
|
|
|
cards_html = ""
|
|
for i, module in enumerate(modules, 1):
|
|
name = module.get("name", f"Module {i}")
|
|
description = module.get("description", "No description available.")
|
|
method = module.get("method", "Unknown method")
|
|
risk_level = module.get("risk_level", "LOW")
|
|
p_value = module.get("p_value")
|
|
test_stat = module.get("test_statistic")
|
|
evidence = module.get("evidence_summary", "")
|
|
results = module.get("results", {})
|
|
figures = module.get("figures", [])
|
|
|
|
css_class = risk_level_to_css_class(risk_level)
|
|
emoji = RISK_EMOJI.get(risk_level, "⚪")
|
|
label = RISK_LABELS.get(risk_level, "Unknown")
|
|
color = RISK_COLORS.get(risk_level, "#6c757d")
|
|
|
|
# Statistics row
|
|
stats_html = '<div class="stats-grid">'
|
|
if p_value is not None:
|
|
stats_html += f"""
|
|
<div class="stat-box">
|
|
<div class="stat-value" style="font-size:1rem">{format_p_value(p_value)}</div>
|
|
<div class="stat-label">p-value</div>
|
|
</div>"""
|
|
if test_stat is not None:
|
|
ts_display = f"{test_stat:.4g}" if isinstance(test_stat, float) else str(test_stat)
|
|
stats_html += f"""
|
|
<div class="stat-box">
|
|
<div class="stat-value" style="font-size:1rem">{ts_display}</div>
|
|
<div class="stat-label">Test Statistic</div>
|
|
</div>"""
|
|
stats_html += f"""
|
|
<div class="stat-box">
|
|
<div class="stat-value" style="color:{color}">{emoji} {label}</div>
|
|
<div class="stat-label">Risk Assessment</div>
|
|
</div>
|
|
</div>"""
|
|
|
|
# Additional results
|
|
results_html = ""
|
|
if results:
|
|
results_html = "<h4>Detailed Results</h4><ul class='evidence-list'>"
|
|
for key, val in results.items():
|
|
if isinstance(val, float):
|
|
val = f"{val:.4g}"
|
|
results_html += f"<li><strong>{key}</strong>: {val}</li>"
|
|
results_html += "</ul>"
|
|
|
|
# Figures
|
|
figures_html = ""
|
|
for fig in figures:
|
|
b64 = encode_figure_base64(fig, self.figures_dir)
|
|
if b64:
|
|
figures_html += f"""
|
|
<div class="figure-container">
|
|
<img src="{b64}" alt="{name} - {fig}">
|
|
<p class="figure-caption">{fig}</p>
|
|
</div>"""
|
|
|
|
# Evidence summary
|
|
evidence_html = ""
|
|
if evidence:
|
|
evidence_html = f"<p><strong>Evidence:</strong> {evidence}</p>"
|
|
|
|
cards_html += f"""
|
|
<div class="card risk-{css_class}">
|
|
<div class="card-header">
|
|
<h3>{emoji} {name}</h3>
|
|
<span class="risk-badge {css_class}">{label}</span>
|
|
</div>
|
|
<p><em>{description}</em></p>
|
|
<p><strong>Method:</strong> {method}</p>
|
|
{stats_html}
|
|
{evidence_html}
|
|
{results_html}
|
|
{figures_html}
|
|
</div>"""
|
|
|
|
return f"""
|
|
<div class="section">
|
|
<h2>Module-by-Module Results</h2>
|
|
{cards_html}
|
|
</div>"""
|
|
|
|
def _suspicious_points(self) -> str:
|
|
"""Generate suspicious data points section."""
|
|
points = self.assessment.get("suspicious_points", [])
|
|
|
|
if not points:
|
|
return """
|
|
<div class="section">
|
|
<h2>Suspicious Data Points</h2>
|
|
<p>🟢 No individual data points were flagged as suspicious.</p>
|
|
</div>"""
|
|
|
|
table_html = """
|
|
<table>
|
|
<tr><th>#</th><th>Row</th><th>Column</th><th>Value</th><th>Reason</th><th>Module</th></tr>"""
|
|
|
|
for i, point in enumerate(points, 1):
|
|
row = point.get("row", "—")
|
|
col = point.get("column", "—")
|
|
value = point.get("value", "—")
|
|
reason = point.get("reason", "—")
|
|
module = point.get("module", "—")
|
|
if isinstance(value, float):
|
|
value = f"{value:.6g}"
|
|
table_html += f"""
|
|
<tr class="suspicious-row">
|
|
<td>{i}</td><td>{row}</td><td>{col}</td><td>{value}</td><td>{reason}</td><td>{module}</td>
|
|
</tr>"""
|
|
|
|
table_html += "\n </table>"
|
|
|
|
return f"""
|
|
<div class="section">
|
|
<h2>🔍 Suspicious Data Points</h2>
|
|
<p>The following <strong>{len(points)}</strong> data point(s) triggered alerts. Each entry shows the
|
|
exact row/column reference, the observed value, and the reason for flagging.</p>
|
|
{table_html}
|
|
</div>"""
|
|
|
|
def _confidence_limitations(self) -> str:
|
|
"""Generate confidence and limitations section."""
|
|
confidence = self.assessment.get("confidence", {})
|
|
overall_conf = confidence.get("overall", "Not calculated")
|
|
intervals = confidence.get("intervals", {})
|
|
limitations = confidence.get("limitations", [])
|
|
|
|
# Confidence intervals
|
|
intervals_html = ""
|
|
if intervals:
|
|
intervals_html = """
|
|
<h3>Confidence Intervals</h3>
|
|
<table>
|
|
<tr><th>Measure</th><th>Estimate</th><th>95% CI Lower</th><th>95% CI Upper</th></tr>"""
|
|
for measure, data in intervals.items():
|
|
est = data.get("estimate", "—")
|
|
lower = data.get("ci_lower", "—")
|
|
upper = data.get("ci_upper", "—")
|
|
if isinstance(est, float):
|
|
est = f"{est:.4g}"
|
|
if isinstance(lower, float):
|
|
lower = f"{lower:.4g}"
|
|
if isinstance(upper, float):
|
|
upper = f"{upper:.4g}"
|
|
intervals_html += f"\n <tr><td>{measure}</td><td>{est}</td><td>{lower}</td><td>{upper}</td></tr>"
|
|
intervals_html += "\n </table>"
|
|
|
|
# Limitations
|
|
limitations_html = ""
|
|
if limitations:
|
|
limitations_html = "\n <h3>Limitations — What This Tool Cannot Detect</h3>\n <ul>"
|
|
for lim in limitations:
|
|
limitations_html += f"\n <li>{lim}</li>"
|
|
limitations_html += "\n </ul>"
|
|
else:
|
|
# Default limitations
|
|
limitations_html = """
|
|
<h3>Limitations — What This Tool Cannot Detect</h3>
|
|
<ul>
|
|
<li>Selective reporting or HARKing (Hypothesizing After Results are Known)</li>
|
|
<li>Subtle p-hacking through flexible analysis choices</li>
|
|
<li>Data fabrication that perfectly mimics expected statistical properties</li>
|
|
<li>Image manipulation or duplication (requires specialized image forensics)</li>
|
|
<li>Plagiarism or text recycling</li>
|
|
<li>Errors in experimental design or methodology</li>
|
|
<li>Conflicts of interest or undisclosed funding</li>
|
|
<li>Small-scale selective data exclusion that preserves distributional properties</li>
|
|
</ul>"""
|
|
|
|
# Overall confidence display
|
|
if isinstance(overall_conf, (int, float)):
|
|
conf_display = f"{overall_conf:.1%}" if overall_conf <= 1 else f"{overall_conf:.1f}%"
|
|
else:
|
|
conf_display = str(overall_conf)
|
|
|
|
return f"""
|
|
<div class="section">
|
|
<h2>Confidence & Limitations</h2>
|
|
<div class="stat-box" style="max-width:300px; margin: 1rem 0;">
|
|
<div class="stat-value">{conf_display}</div>
|
|
<div class="stat-label">Overall Assessment Confidence</div>
|
|
</div>
|
|
<p>Confidence reflects the reliability of the statistical tests given the data size,
|
|
quality, and number of applicable tests. Higher confidence means the results are
|
|
more likely to be meaningful rather than artifacts of small samples or noise.</p>
|
|
{intervals_html}
|
|
{limitations_html}
|
|
</div>"""
|
|
|
|
def _methodology(self) -> str:
|
|
"""Generate methodology section with academic references."""
|
|
modules = self.assessment.get("modules", [])
|
|
methods_used = set()
|
|
for m in modules:
|
|
method_key = m.get("method_key", m.get("name", "").lower().replace(" ", "_"))
|
|
methods_used.add(method_key)
|
|
|
|
entries_html = ""
|
|
for key in sorted(methods_used):
|
|
info = METHODOLOGY_REFERENCES.get(key)
|
|
if info:
|
|
refs_html = "<br>".join(info["references"])
|
|
entries_html += f"""
|
|
<div class="method-entry">
|
|
<div class="method-name">{info['name']}</div>
|
|
<div class="method-desc">{info['description']}</div>
|
|
<div class="method-ref">{refs_html}</div>
|
|
</div>"""
|
|
|
|
# If no known methods matched, list from module descriptions
|
|
if not entries_html:
|
|
for m in modules:
|
|
name = m.get("name", "Unknown")
|
|
method = m.get("method", "Not specified")
|
|
entries_html += f"""
|
|
<div class="method-entry">
|
|
<div class="method-name">{name}</div>
|
|
<div class="method-desc">Method: {method}</div>
|
|
</div>"""
|
|
|
|
return f"""
|
|
<div class="section">
|
|
<h2>Methodology</h2>
|
|
<p>The following statistical methods were applied during this analysis.
|
|
Each method targets a specific class of data integrity anomalies.</p>
|
|
{entries_html}
|
|
</div>"""
|
|
|
|
def _recommendations(self) -> str:
|
|
"""Generate prioritized recommendations section."""
|
|
recs = self.assessment.get("recommendations", [])
|
|
|
|
if not recs:
|
|
# Generate default recommendations based on risk level
|
|
risk = self.assessment.get("overall_risk", {})
|
|
level = risk.get("level", "LOW")
|
|
if level in ("HIGH", "CRITICAL"):
|
|
recs = [
|
|
{"priority": 1, "action": "Request raw data and analysis scripts from authors",
|
|
"rationale": "Direct verification of data provenance is the most reliable method."},
|
|
{"priority": 2, "action": "Have an independent statistician review the flagged anomalies",
|
|
"rationale": "Expert review can distinguish genuine anomalies from methodological artifacts."},
|
|
{"priority": 3, "action": "Check for corroborating evidence in supplementary materials",
|
|
"rationale": "Supplementary data may provide context that explains apparent anomalies."},
|
|
{"priority": 4, "action": "Consider contacting the journal or institution",
|
|
"rationale": "If anomalies persist after review, formal investigation may be warranted."},
|
|
]
|
|
else:
|
|
recs = [
|
|
{"priority": 1, "action": "Archive this report for reference",
|
|
"rationale": "Maintaining records supports longitudinal monitoring."},
|
|
{"priority": 2, "action": "No immediate action required",
|
|
"rationale": "Current findings do not indicate significant integrity concerns."},
|
|
]
|
|
|
|
recs_html = ""
|
|
for rec in sorted(recs, key=lambda r: r.get("priority", 99)):
|
|
priority = rec.get("priority", "—")
|
|
action = rec.get("action", "—")
|
|
rationale = rec.get("rationale", "")
|
|
recs_html += f"""
|
|
<div class="recommendation">
|
|
<div class="priority-num">{priority}</div>
|
|
<div class="rec-content">
|
|
<div class="rec-action">{action}</div>
|
|
<div class="rec-rationale">{rationale}</div>
|
|
</div>
|
|
</div>"""
|
|
|
|
return f"""
|
|
<div class="section">
|
|
<h2>Recommendations</h2>
|
|
{recs_html}
|
|
</div>"""
|
|
|
|
def _disclaimer(self) -> str:
|
|
"""Generate bilingual disclaimer section."""
|
|
return f"""
|
|
<div class="disclaimer">
|
|
<h3>⚠️ Disclaimer / 免责声明</h3>
|
|
<p>{DISCLAIMER_EN}</p>
|
|
<hr style="border-color:#f5c6cb; margin: 1rem 0;">
|
|
<p>{DISCLAIMER_ZH}</p>
|
|
</div>"""
|
|
|
|
def _footer(self) -> str:
|
|
"""Generate report footer with metadata."""
|
|
meta = self.assessment.get("metadata", {})
|
|
source = meta.get("source_file", "Unknown")
|
|
version = meta.get("tool_version", TOOL_VERSION)
|
|
now = datetime.now(timezone.utc).strftime("%Y-%m-%d %H:%M:%S UTC")
|
|
|
|
return f"""
|
|
<div class="report-footer">
|
|
<span>Generated by {TOOL_NAME} v{version}</span>
|
|
<span>Input: {source}</span>
|
|
<span>Report timestamp: {now}</span>
|
|
</div>"""
|
|
|
|
|
|
# ---------------------------------------------------------------------------
|
|
# Markdown Report Generator
|
|
# ---------------------------------------------------------------------------
|
|
|
|
|
|
class MarkdownReportGenerator:
|
|
"""Generates a Markdown report from assessment data.
|
|
|
|
Figures are referenced as relative paths (suitable for GitHub rendering).
|
|
|
|
Attributes:
|
|
assessment: The assessment data dictionary.
|
|
figures_dir: Relative path to figures directory for Markdown links.
|
|
"""
|
|
|
|
def __init__(self, assessment: Dict[str, Any], figures_dir: str):
|
|
"""Initialize the Markdown report generator.
|
|
|
|
Args:
|
|
assessment: Parsed assessment dictionary.
|
|
figures_dir: Relative path to figures directory for image links.
|
|
"""
|
|
self.assessment = assessment
|
|
self.figures_dir = figures_dir
|
|
|
|
def generate(self) -> str:
|
|
"""Generate the complete Markdown report.
|
|
|
|
Returns:
|
|
Complete Markdown document as a string.
|
|
"""
|
|
parts = [
|
|
self._header(),
|
|
self._executive_summary(),
|
|
self._data_overview(),
|
|
self._module_results(),
|
|
self._suspicious_points(),
|
|
self._confidence_limitations(),
|
|
self._methodology(),
|
|
self._recommendations(),
|
|
self._disclaimer(),
|
|
self._footer(),
|
|
]
|
|
return "\n\n".join(parts)
|
|
|
|
def _header(self) -> str:
|
|
"""Generate Markdown header."""
|
|
meta = self.assessment.get("metadata", {})
|
|
source = meta.get("source_file", "Unknown")
|
|
timestamp = meta.get("timestamp", datetime.now(timezone.utc).isoformat())
|
|
|
|
return f"""# 📊 {TOOL_NAME}
|
|
|
|
## Analysis Report
|
|
|
|
- **Source File:** {source}
|
|
- **Generated:** {timestamp}
|
|
- **Tool Version:** {meta.get('tool_version', TOOL_VERSION)}
|
|
|
|
---"""
|
|
|
|
def _executive_summary(self) -> str:
|
|
"""Generate executive summary in Markdown."""
|
|
risk = self.assessment.get("overall_risk", {})
|
|
score = risk.get("score", 0)
|
|
level = risk.get("level", score_to_level(score))
|
|
emoji = RISK_EMOJI.get(level, "⚪")
|
|
label = RISK_LABELS.get(level, "Unknown")
|
|
|
|
modules = self.assessment.get("modules", [])
|
|
flagged = [m for m in modules if m.get("risk_level", "LOW") in ("HIGH", "CRITICAL")]
|
|
suspicious_count = len(self.assessment.get("suspicious_points", []))
|
|
|
|
findings = ""
|
|
if flagged:
|
|
for m in flagged:
|
|
me = RISK_EMOJI.get(m.get("risk_level", "LOW"), "⚪")
|
|
findings += f"- {me} **{m.get('name', 'Unknown')}**: {m.get('evidence_summary', 'Anomaly detected')}\n"
|
|
else:
|
|
findings = "- No high-risk anomalies detected across all modules.\n"
|
|
|
|
# Conclusion
|
|
if level == "CRITICAL":
|
|
conclusion = (
|
|
"Multiple strong statistical indicators suggest significant anomalies in this dataset. "
|
|
"The patterns observed are highly unlikely to arise from legitimate experimental data. "
|
|
"Further expert review is strongly recommended."
|
|
)
|
|
elif level == "HIGH":
|
|
conclusion = (
|
|
"Several statistical indicators show notable anomalies that warrant further investigation. "
|
|
"While not conclusive evidence of data integrity issues, the patterns deserve scrutiny."
|
|
)
|
|
elif level == "MEDIUM":
|
|
conclusion = (
|
|
"Some mild statistical anomalies were detected. These may reflect legitimate methodological "
|
|
"choices or minor reporting inconsistencies. Routine verification is advisable."
|
|
)
|
|
else:
|
|
conclusion = (
|
|
"The dataset shows no significant statistical anomalies across the tests performed. "
|
|
"The data patterns appear consistent with legitimate experimental measurements."
|
|
)
|
|
|
|
return f"""## Executive Summary
|
|
|
|
| Metric | Value |
|
|
|--------|-------|
|
|
| **Overall Risk Score** | {score}/100 |
|
|
| **Risk Level** | {emoji} {label} |
|
|
| **Tests Performed** | {len(modules)} |
|
|
| **Suspicious Data Points** | {suspicious_count} |
|
|
|
|
### Key Findings
|
|
|
|
{findings}
|
|
### Conclusion
|
|
|
|
{conclusion}"""
|
|
|
|
def _data_overview(self) -> str:
|
|
"""Generate data overview in Markdown."""
|
|
overview = self.assessment.get("data_overview", {})
|
|
meta = self.assessment.get("metadata", {})
|
|
|
|
source = meta.get("source_file", "Unknown")
|
|
rows = meta.get("rows", "N/A")
|
|
cols = meta.get("columns_count", len(meta.get("columns", [])))
|
|
file_size = meta.get("file_size", "N/A")
|
|
|
|
md = f"""## Data Overview
|
|
|
|
| Property | Value |
|
|
|----------|-------|
|
|
| Source File | {source} |
|
|
| Rows | {rows} |
|
|
| Columns | {cols} |
|
|
| File Size | {file_size} |
|
|
"""
|
|
|
|
# Column statistics
|
|
statistics = overview.get("statistics", {})
|
|
if statistics:
|
|
md += "\n### Column Statistics\n\n"
|
|
md += "| Column | Type | Non-Null | Mean | Std | Min | Max |\n"
|
|
md += "|--------|------|----------|------|-----|-----|-----|\n"
|
|
for col_name, stats in statistics.items():
|
|
dtype = stats.get("dtype", "—")
|
|
non_null = stats.get("non_null", "—")
|
|
mean = stats.get("mean", "—")
|
|
std = stats.get("std", "—")
|
|
min_val = stats.get("min", "—")
|
|
max_val = stats.get("max", "—")
|
|
if isinstance(mean, float):
|
|
mean = f"{mean:.4g}"
|
|
if isinstance(std, float):
|
|
std = f"{std:.4g}"
|
|
if isinstance(min_val, float):
|
|
min_val = f"{min_val:.4g}"
|
|
if isinstance(max_val, float):
|
|
max_val = f"{max_val:.4g}"
|
|
md += f"| {col_name} | {dtype} | {non_null} | {mean} | {std} | {min_val} | {max_val} |\n"
|
|
|
|
# Preview
|
|
preview = overview.get("preview", [])
|
|
if preview:
|
|
columns = overview.get("columns", list(preview[0].keys()) if preview else [])
|
|
md += "\n### Data Preview\n\n"
|
|
md += "| " + " | ".join(str(c) for c in columns) + " |\n"
|
|
md += "| " + " | ".join("---" for _ in columns) + " |\n"
|
|
for row in preview[:10]:
|
|
vals = [str(row.get(c, "—")) for c in columns]
|
|
md += "| " + " | ".join(vals) + " |\n"
|
|
|
|
return md
|
|
|
|
def _module_results(self) -> str:
|
|
"""Generate module results in Markdown."""
|
|
modules = self.assessment.get("modules", [])
|
|
if not modules:
|
|
return "## Module-by-Module Results\n\nNo detection modules were executed."
|
|
|
|
md = "## Module-by-Module Results\n"
|
|
|
|
for i, module in enumerate(modules, 1):
|
|
name = module.get("name", f"Module {i}")
|
|
description = module.get("description", "No description available.")
|
|
method = module.get("method", "Unknown method")
|
|
risk_level = module.get("risk_level", "LOW")
|
|
p_value = module.get("p_value")
|
|
test_stat = module.get("test_statistic")
|
|
evidence = module.get("evidence_summary", "")
|
|
results = module.get("results", {})
|
|
figures = module.get("figures", [])
|
|
|
|
emoji = RISK_EMOJI.get(risk_level, "⚪")
|
|
label = RISK_LABELS.get(risk_level, "Unknown")
|
|
|
|
md += f"\n### {emoji} {name}\n\n"
|
|
md += f"**Description:** {description}\n\n"
|
|
md += f"**Method:** {method}\n\n"
|
|
|
|
# Statistics table
|
|
md += "| Metric | Value |\n|--------|-------|\n"
|
|
if p_value is not None:
|
|
md += f"| p-value | {format_p_value(p_value)} |\n"
|
|
if test_stat is not None:
|
|
ts = f"{test_stat:.4g}" if isinstance(test_stat, float) else str(test_stat)
|
|
md += f"| Test Statistic | {ts} |\n"
|
|
md += f"| Risk Assessment | {emoji} {label} |\n"
|
|
|
|
if evidence:
|
|
md += f"\n**Evidence:** {evidence}\n"
|
|
|
|
# Detailed results
|
|
if results:
|
|
md += "\n**Detailed Results:**\n\n"
|
|
for key, val in results.items():
|
|
if isinstance(val, float):
|
|
val = f"{val:.4g}"
|
|
md += f"- **{key}**: {val}\n"
|
|
|
|
# Figures
|
|
for fig in figures:
|
|
fig_path = f"{self.figures_dir}/{fig}" if self.figures_dir else fig
|
|
md += f"\n\n"
|
|
md += f"*Figure: {fig}*\n"
|
|
|
|
md += "\n---\n"
|
|
|
|
return md
|
|
|
|
def _suspicious_points(self) -> str:
|
|
"""Generate suspicious points section in Markdown."""
|
|
points = self.assessment.get("suspicious_points", [])
|
|
|
|
if not points:
|
|
return "## 🔍 Suspicious Data Points\n\n🟢 No individual data points were flagged as suspicious."
|
|
|
|
md = f"## 🔍 Suspicious Data Points\n\n"
|
|
md += f"The following **{len(points)}** data point(s) triggered alerts:\n\n"
|
|
md += "| # | Row | Column | Value | Reason | Module |\n"
|
|
md += "|---|-----|--------|-------|--------|--------|\n"
|
|
|
|
for i, point in enumerate(points, 1):
|
|
row = point.get("row", "—")
|
|
col = point.get("column", "—")
|
|
value = point.get("value", "—")
|
|
reason = point.get("reason", "—")
|
|
module = point.get("module", "—")
|
|
if isinstance(value, float):
|
|
value = f"{value:.6g}"
|
|
md += f"| {i} | {row} | {col} | {value} | {reason} | {module} |\n"
|
|
|
|
return md
|
|
|
|
def _confidence_limitations(self) -> str:
|
|
"""Generate confidence and limitations section in Markdown."""
|
|
confidence = self.assessment.get("confidence", {})
|
|
overall_conf = confidence.get("overall", "Not calculated")
|
|
intervals = confidence.get("intervals", {})
|
|
limitations = confidence.get("limitations", [])
|
|
|
|
if isinstance(overall_conf, (int, float)):
|
|
conf_display = f"{overall_conf:.1%}" if overall_conf <= 1 else f"{overall_conf:.1f}%"
|
|
else:
|
|
conf_display = str(overall_conf)
|
|
|
|
md = f"## Confidence & Limitations\n\n"
|
|
md += f"**Overall Assessment Confidence:** {conf_display}\n\n"
|
|
md += (
|
|
"Confidence reflects the reliability of the statistical tests given the data size, "
|
|
"quality, and number of applicable tests.\n"
|
|
)
|
|
|
|
if intervals:
|
|
md += "\n### Confidence Intervals\n\n"
|
|
md += "| Measure | Estimate | 95% CI Lower | 95% CI Upper |\n"
|
|
md += "|---------|----------|--------------|-------------|\n"
|
|
for measure, data in intervals.items():
|
|
est = data.get("estimate", "—")
|
|
lower = data.get("ci_lower", "—")
|
|
upper = data.get("ci_upper", "—")
|
|
if isinstance(est, float):
|
|
est = f"{est:.4g}"
|
|
if isinstance(lower, float):
|
|
lower = f"{lower:.4g}"
|
|
if isinstance(upper, float):
|
|
upper = f"{upper:.4g}"
|
|
md += f"| {measure} | {est} | {lower} | {upper} |\n"
|
|
|
|
md += "\n### Limitations — What This Tool Cannot Detect\n\n"
|
|
if limitations:
|
|
for lim in limitations:
|
|
md += f"- {lim}\n"
|
|
else:
|
|
md += """- Selective reporting or HARKing (Hypothesizing After Results are Known)
|
|
- Subtle p-hacking through flexible analysis choices
|
|
- Data fabrication that perfectly mimics expected statistical properties
|
|
- Image manipulation or duplication (requires specialized image forensics)
|
|
- Plagiarism or text recycling
|
|
- Errors in experimental design or methodology
|
|
- Conflicts of interest or undisclosed funding
|
|
- Small-scale selective data exclusion that preserves distributional properties
|
|
"""
|
|
|
|
return md
|
|
|
|
def _methodology(self) -> str:
|
|
"""Generate methodology section in Markdown."""
|
|
modules = self.assessment.get("modules", [])
|
|
methods_used = set()
|
|
for m in modules:
|
|
method_key = m.get("method_key", m.get("name", "").lower().replace(" ", "_"))
|
|
methods_used.add(method_key)
|
|
|
|
md = "## Methodology\n\n"
|
|
md += "The following statistical methods were applied during this analysis:\n\n"
|
|
|
|
has_entries = False
|
|
for key in sorted(methods_used):
|
|
info = METHODOLOGY_REFERENCES.get(key)
|
|
if info:
|
|
has_entries = True
|
|
md += f"### {info['name']}\n\n"
|
|
md += f"{info['description']}\n\n"
|
|
md += "**References:**\n\n"
|
|
for ref in info["references"]:
|
|
md += f"- {ref}\n"
|
|
md += "\n"
|
|
|
|
if not has_entries:
|
|
for m in modules:
|
|
name = m.get("name", "Unknown")
|
|
method = m.get("method", "Not specified")
|
|
md += f"### {name}\n\n"
|
|
md += f"Method: {method}\n\n"
|
|
|
|
return md
|
|
|
|
def _recommendations(self) -> str:
|
|
"""Generate recommendations section in Markdown."""
|
|
recs = self.assessment.get("recommendations", [])
|
|
|
|
if not recs:
|
|
risk = self.assessment.get("overall_risk", {})
|
|
level = risk.get("level", "LOW")
|
|
if level in ("HIGH", "CRITICAL"):
|
|
recs = [
|
|
{"priority": 1, "action": "Request raw data and analysis scripts from authors",
|
|
"rationale": "Direct verification of data provenance is the most reliable method."},
|
|
{"priority": 2, "action": "Have an independent statistician review the flagged anomalies",
|
|
"rationale": "Expert review can distinguish genuine anomalies from methodological artifacts."},
|
|
{"priority": 3, "action": "Check for corroborating evidence in supplementary materials",
|
|
"rationale": "Supplementary data may provide context that explains apparent anomalies."},
|
|
{"priority": 4, "action": "Consider contacting the journal or institution",
|
|
"rationale": "If anomalies persist after review, formal investigation may be warranted."},
|
|
]
|
|
else:
|
|
recs = [
|
|
{"priority": 1, "action": "Archive this report for reference",
|
|
"rationale": "Maintaining records supports longitudinal monitoring."},
|
|
{"priority": 2, "action": "No immediate action required",
|
|
"rationale": "Current findings do not indicate significant integrity concerns."},
|
|
]
|
|
|
|
md = "## Recommendations\n\n"
|
|
for rec in sorted(recs, key=lambda r: r.get("priority", 99)):
|
|
priority = rec.get("priority", "—")
|
|
action = rec.get("action", "—")
|
|
rationale = rec.get("rationale", "")
|
|
md += f"**{priority}.** {action}\n"
|
|
if rationale:
|
|
md += f" > {rationale}\n"
|
|
md += "\n"
|
|
|
|
return md
|
|
|
|
def _disclaimer(self) -> str:
|
|
"""Generate bilingual disclaimer in Markdown."""
|
|
return f"""## ⚠️ Disclaimer / 免责声明
|
|
|
|
{DISCLAIMER_EN}
|
|
|
|
---
|
|
|
|
{DISCLAIMER_ZH}"""
|
|
|
|
def _footer(self) -> str:
|
|
"""Generate footer in Markdown."""
|
|
meta = self.assessment.get("metadata", {})
|
|
source = meta.get("source_file", "Unknown")
|
|
version = meta.get("tool_version", TOOL_VERSION)
|
|
now = datetime.now(timezone.utc).strftime("%Y-%m-%d %H:%M:%S UTC")
|
|
|
|
return f"""---
|
|
|
|
*Generated by {TOOL_NAME} v{version} | Input: {source} | Timestamp: {now}*"""
|
|
|
|
|
|
# ---------------------------------------------------------------------------
|
|
# Main / CLI
|
|
# ---------------------------------------------------------------------------
|
|
|
|
|
|
def generate_reports(
|
|
assessment_path: str,
|
|
figures_dir: str,
|
|
output_dir: str,
|
|
formats: Optional[List[str]] = None,
|
|
) -> Dict[str, str]:
|
|
"""Generate reports in specified formats from an assessment JSON file.
|
|
|
|
Args:
|
|
assessment_path: Path to the assessment JSON file.
|
|
figures_dir: Path to the directory containing figure files.
|
|
output_dir: Directory where output reports will be written.
|
|
formats: List of formats to generate ('html', 'markdown'). Defaults to both.
|
|
|
|
Returns:
|
|
Dictionary mapping format names to output file paths.
|
|
|
|
Raises:
|
|
FileNotFoundError: If assessment file doesn't exist.
|
|
ValueError: If assessment JSON is invalid.
|
|
"""
|
|
if formats is None:
|
|
formats = ["html", "markdown"]
|
|
|
|
# Load assessment
|
|
assessment = load_assessment(assessment_path)
|
|
|
|
# Ensure output directory exists
|
|
output_path = Path(output_dir)
|
|
output_path.mkdir(parents=True, exist_ok=True)
|
|
|
|
# Determine base filename from source
|
|
meta = assessment.get("metadata", {})
|
|
source = meta.get("source_file", "analysis")
|
|
base_name = Path(source).stem if source else "analysis"
|
|
|
|
results = {}
|
|
|
|
if "html" in formats:
|
|
html_gen = HTMLReportGenerator(assessment, figures_dir)
|
|
html_content = html_gen.generate()
|
|
html_path = output_path / f"{base_name}_report.html"
|
|
with open(html_path, "w", encoding="utf-8") as f:
|
|
f.write(html_content)
|
|
results["html"] = str(html_path)
|
|
print(f"✅ HTML report generated: {html_path}")
|
|
|
|
if "markdown" in formats:
|
|
# For markdown, use relative path to figures
|
|
try:
|
|
rel_figures = os.path.relpath(figures_dir, output_dir)
|
|
except ValueError:
|
|
rel_figures = figures_dir
|
|
md_gen = MarkdownReportGenerator(assessment, rel_figures)
|
|
md_content = md_gen.generate()
|
|
md_path = output_path / f"{base_name}_report.md"
|
|
with open(md_path, "w", encoding="utf-8") as f:
|
|
f.write(md_content)
|
|
results["markdown"] = str(md_path)
|
|
print(f"✅ Markdown report generated: {md_path}")
|
|
|
|
return results
|
|
|
|
|
|
def main():
|
|
"""CLI entry point for the report generator.
|
|
|
|
Parses arguments and generates reports in the specified formats.
|
|
"""
|
|
parser = argparse.ArgumentParser(
|
|
description=f"{TOOL_NAME} — Report Generator",
|
|
formatter_class=argparse.RawDescriptionHelpFormatter,
|
|
epilog="""
|
|
Examples:
|
|
# Generate both HTML and Markdown reports
|
|
python3 report_generator.py --input assessment.json --figures figures/ --output report/
|
|
|
|
# Generate only HTML
|
|
python3 report_generator.py --input assessment.json --figures figures/ --output report/ --format html
|
|
|
|
# Generate only Markdown
|
|
python3 report_generator.py --input assessment.json --output report/ --format markdown
|
|
""",
|
|
)
|
|
|
|
parser.add_argument(
|
|
"--input", "-i",
|
|
required=True,
|
|
help="Path to the assessment JSON file produced by the detection pipeline.",
|
|
)
|
|
parser.add_argument(
|
|
"--figures", "-f",
|
|
default="figures/",
|
|
help="Directory containing figure image files (default: figures/).",
|
|
)
|
|
parser.add_argument(
|
|
"--output", "-o",
|
|
default="report/",
|
|
help="Output directory for generated reports (default: report/).",
|
|
)
|
|
parser.add_argument(
|
|
"--format",
|
|
choices=["html", "markdown", "both"],
|
|
default="both",
|
|
help="Output format: html, markdown, or both (default: both).",
|
|
)
|
|
parser.add_argument(
|
|
"--version", "-v",
|
|
action="version",
|
|
version=f"%(prog)s {TOOL_VERSION}",
|
|
)
|
|
|
|
args = parser.parse_args()
|
|
|
|
# Determine formats
|
|
if args.format == "both":
|
|
formats = ["html", "markdown"]
|
|
else:
|
|
formats = [args.format]
|
|
|
|
try:
|
|
results = generate_reports(
|
|
assessment_path=args.input,
|
|
figures_dir=args.figures,
|
|
output_dir=args.output,
|
|
formats=formats,
|
|
)
|
|
print(f"\n{'='*60}")
|
|
print(f"Report generation complete!")
|
|
print(f"{'='*60}")
|
|
for fmt, path in results.items():
|
|
print(f" {fmt.upper():>10}: {path}")
|
|
print()
|
|
|
|
except FileNotFoundError as e:
|
|
print(f"❌ Error: {e}", file=sys.stderr)
|
|
sys.exit(1)
|
|
except json.JSONDecodeError as e:
|
|
print(f"❌ Error: Invalid JSON in assessment file: {e}", file=sys.stderr)
|
|
sys.exit(1)
|
|
except ValueError as e:
|
|
print(f"❌ Error: {e}", file=sys.stderr)
|
|
sys.exit(1)
|
|
except Exception as e:
|
|
print(f"❌ Unexpected error: {e}", file=sys.stderr)
|
|
sys.exit(2)
|
|
|
|
|
|
if __name__ == "__main__":
|
|
main()
|