tools.py

"""
tools.py — Core functions for the AI-driven topic modeling pipeline.

This module provides all analytical functions used by the TopicAgent:
  - CSV ingestion and validation
  - Text preprocessing (lowercasing, stopword removal, cleaning)
  - Topic modeling via BERTopic (with fallback to sklearn LDA)
  - Automatic human-readable label generation
  - Cross-source theme comparison (Title vs Abstract)
  - Taxonomy mapping (MAPPED / NOVEL classification)
"""

import re
import json
import logging
from typing import Dict, List, Tuple, Optional, Any

import numpy as np
import pandas as pd
import nltk
from nltk.corpus import stopwords
from nltk.tokenize import word_tokenize

# ---------------------------------------------------------------------------
# Logging
# ---------------------------------------------------------------------------
logger = logging.getLogger(__name__)
logging.basicConfig(level=logging.INFO, format="%(asctime)s [%(levelname)s] %(message)s")

# ---------------------------------------------------------------------------
# NLTK data download (idempotent) with error handling
# ---------------------------------------------------------------------------
for _resource in ("punkt", "punkt_tab", "stopwords"):
    try:
        nltk.data.find(f"tokenizers/{_resource}" if "punkt" in _resource else f"corpora/{_resource}")
    except (LookupError, OSError, Exception):
        try:
            nltk.download(_resource, quiet=True)
        except Exception:
            pass  # Gracefully handle NLTK download failures

# ---------------------------------------------------------------------------
# Reference taxonomy of known AI / business / research themes
# Used by create_taxonomy_map() for MAPPED vs NOVEL classification
# ---------------------------------------------------------------------------
KNOWN_THEMES: List[str] = [
    # AI / ML
    "artificial intelligence", "machine learning", "deep learning", "neural network",
    "natural language processing", "computer vision", "reinforcement learning",
    "generative ai", "large language model", "transformer", "chatbot",
    "recommendation system", "knowledge graph", "robotics", "autonomous",
    "explainable ai", "federated learning", "transfer learning", "ai ethics",
    "adversarial", "gan", "diffusion model", "prompt engineering",
    # Data science
    "data mining", "big data", "analytics", "data science", "data quality",
    "feature engineering", "dimensionality reduction", "clustering", "classification",
    "regression", "time series", "anomaly detection", "sentiment analysis",
    # Business / Management
    "digital transformation", "innovation", "strategy", "supply chain",
    "customer experience", "marketing", "e-commerce", "fintech", "blockchain",
    "sustainability", "corporate social responsibility", "knowledge management",
    "decision support", "business intelligence", "enterprise", "organizational",
    "human resource", "leadership", "entrepreneurship", "business model",
    # Information systems
    "information systems", "technology adoption", "user acceptance", "privacy",
    "security", "trust", "social media", "online community", "platform",
    "crowdsourcing", "cloud computing", "iot", "internet of things",
    "software engineering", "agile", "devops", "digital platform",
    # Healthcare / Society
    "healthcare", "telemedicine", "electronic health", "public health",
    "education", "e-learning", "smart city", "government", "policy",
    "ethics", "fairness", "bias", "misinformation", "content moderation",
    # Research methods
    "survey", "experiment", "case study", "meta-analysis", "bibliometric",
    "systematic review", "structural equation", "grounded theory",
]


# ===================================================================
# 1. load_csv  — Ingest and validate the CSV dataset
# ===================================================================
def load_csv(filepath: str) -> pd.DataFrame:
    """
    Load a CSV file and ensure the required columns (Title, Abstract) exist.

    Parameters
    ----------
    filepath : str
        Path to the CSV file.

    Returns
    -------
    pd.DataFrame
        DataFrame with at least 'Title' and 'Abstract' columns.

    Raises
    ------
    FileNotFoundError
        If the specified file does not exist.
    ValueError
        If required columns are missing.
    """
    logger.info("Loading CSV from %s", filepath)
    df = pd.read_csv(filepath, encoding="utf-8", on_bad_lines="skip")
    logger.info("Loaded %d rows × %d columns", len(df), len(df.columns))

    # Validate required columns (case-insensitive match)
    col_map = {c.strip().lower(): c for c in df.columns}
    required = {"title", "abstract"}
    missing = required - set(col_map.keys())
    if missing:
        raise ValueError(f"CSV is missing required columns: {missing}. Found: {list(df.columns)}")

    # Rename to canonical form
    df = df.rename(columns={col_map["title"]: "Title", col_map["abstract"]: "Abstract"})

    # Drop rows where both Title and Abstract are empty
    df = df.dropna(subset=["Title", "Abstract"], how="all").reset_index(drop=True)
    df["Title"] = df["Title"].fillna("")
    df["Abstract"] = df["Abstract"].fillna("")

    logger.info("After cleaning: %d usable rows", len(df))
    return df


# ===================================================================
# 2. preprocess_text  — Clean and normalise a list of text documents
# ===================================================================
def preprocess_text(documents: List[str]) -> List[str]:
    """
    Apply professional-grade text preprocessing:
      1. Lowercase
      2. Remove URLs, emails, special characters, digits
      3. Tokenize
      4. Remove stopwords (NLTK English)
      5. Remove very short tokens (length ≤ 2)
      6. Rejoin into cleaned strings

    Parameters
    ----------
    documents : list of str
        Raw text documents.

    Returns
    -------
    list of str
        Cleaned text documents.
    """
    stop_words = set(stopwords.words("english"))
    # Extended stopwords common in academic abstracts
    stop_words.update([
        "©", "elsevier", "rights", "reserved", "doi", "http", "https",
        "vol", "pp", "fig", "table", "journal", "author", "authors",
        "study", "paper", "research", "results", "findings", "however",
        "propose", "proposed", "approach", "using", "based", "also",
        "show", "shows", "shown", "may", "used", "use", "one", "two",
        "three", "new", "well", "within", "among", "across", "toward",
        "towards", "et", "al", "ie", "eg", "cf", "thus", "therefore",
        "moreover", "furthermore", "addition", "conclusion", "conclusions",
    ])

    cleaned: List[str] = []
    for doc in documents:
        if not isinstance(doc, str) or not doc.strip():
            cleaned.append("")
            continue

        text = doc.lower()
        # Remove URLs
        text = re.sub(r"https?://\S+|www\.\S+", " ", text)
        # Remove emails
        text = re.sub(r"\S+@\S+", " ", text)
        # Remove digits and special characters but keep spaces
        text = re.sub(r"[^a-z\s]", " ", text)
        # Collapse whitespace
        text = re.sub(r"\s+", " ", text).strip()

        # Tokenize and filter
        tokens = word_tokenize(text)
        tokens = [t for t in tokens if t not in stop_words and len(t) > 2]

        cleaned.append(" ".join(tokens))

    logger.info("Preprocessed %d documents", len(cleaned))
    return cleaned


# ===================================================================
# 3. run_topic_modeling  — Discover topics via BERTopic (or LDA fallback)
# ===================================================================
def run_topic_modeling(
    documents: List[str],
    source_label: str = "documents",
    min_topics: int = 100,
    use_bertopic: bool = True,
) -> Tuple[pd.DataFrame, Any]:
    """
    Perform topic modeling on a corpus of preprocessed documents.

    Strategy:
      1. Try BERTopic with UMAP + HDBSCAN.  If the result has < min_topics,
         automatically fall back to sklearn LDA.
      2. LDA is configured with n_components = min_topics to guarantee the
         requested topic count.

    Parameters
    ----------
    documents : list of str
        Preprocessed text documents.
    source_label : str
        Label for logging (e.g. "Titles" or "Abstracts").
    min_topics : int
        Minimum number of topics required (default 100).
    use_bertopic : bool
        Whether to attempt BERTopic first.

    Returns
    -------
    topics_df : pd.DataFrame
        Columns: topic_id, keywords (comma-separated), representative_docs
    model : object
        The fitted topic model for downstream inspection.
    """
    # Filter out empty documents
    valid_docs = [d for d in documents if d.strip()]
    if len(valid_docs) < 20:
        raise ValueError(f"Not enough valid documents ({len(valid_docs)}) for topic modeling.")

    logger.info("Running topic modeling on %d %s (target ≥ %d topics)", len(valid_docs), source_label, min_topics)

    topics_df = None
    model = None

    # ------ Attempt BERTopic ------
    if use_bertopic:
        try:
            topics_df, model = _run_bertopic(valid_docs, source_label, min_topics)
        except Exception as exc:
            logger.warning("BERTopic failed (%s). Falling back to LDA.", exc)
            topics_df = None

    # ------ Fallback to LDA if needed ------
    if topics_df is None or len(topics_df) < min_topics:
        logger.info("Using LDA to guarantee ≥ %d topics for %s", min_topics, source_label)
        topics_df, model = _run_lda(valid_docs, source_label, min_topics)

    logger.info("Topic modeling complete for %s: %d topics discovered", source_label, len(topics_df))
    return topics_df, model


def _run_bertopic(docs: List[str], source_label: str, min_topics: int):
    """Run BERTopic with tuned parameters."""
    from bertopic import BERTopic
    from umap import UMAP
    from hdbscan import HDBSCAN
    from sklearn.feature_extraction.text import CountVectorizer

    umap_model = UMAP(
        n_neighbors=10,
        n_components=5,
        min_dist=0.0,
        metric="cosine",
        random_state=42,
    )
    hdbscan_model = HDBSCAN(
        min_cluster_size=5,
        min_samples=2,
        prediction_data=True,
    )
    vectorizer = CountVectorizer(
        stop_words="english",
        ngram_range=(1, 2),
        max_df=0.90,
        min_df=2,
    )

    topic_model = BERTopic(
        umap_model=umap_model,
        hdbscan_model=hdbscan_model,
        vectorizer_model=vectorizer,
        nr_topics="auto",
        top_n_words=10,
        verbose=False,
    )

    topics, _probs = topic_model.fit_transform(docs)
    info = topic_model.get_topic_info()
    # Exclude outlier topic (-1)
    info = info[info["Topic"] != -1].reset_index(drop=True)

    rows = []
    for _, row in info.iterrows():
        tid = int(row["Topic"])
        topic_words = topic_model.get_topic(tid)
        kw = ", ".join([w for w, _ in topic_words[:10]])
        rows.append({"topic_id": tid, "keywords": kw, "source": source_label})

    df = pd.DataFrame(rows)
    return df, topic_model


def _run_lda(docs: List[str], source_label: str, n_topics: int):
    """Run sklearn LDA to guarantee the requested number of topics."""
    from sklearn.decomposition import LatentDirichletAllocation
    from sklearn.feature_extraction.text import CountVectorizer

    vectorizer = CountVectorizer(
        stop_words="english",
        max_df=0.90,
        min_df=2,
        ngram_range=(1, 2),
        max_features=10000,
    )
    dtm = vectorizer.fit_transform(docs)
    feature_names = vectorizer.get_feature_names_out()

    lda = LatentDirichletAllocation(
        n_components=n_topics,
        max_iter=25,
        learning_method="online",
        random_state=42,
        n_jobs=-1,
    )
    lda.fit(dtm)

    rows = []
    for idx, component in enumerate(lda.components_):
        top_indices = component.argsort()[-10:][::-1]
        kw = ", ".join([feature_names[i] for i in top_indices])
        rows.append({"topic_id": idx, "keywords": kw, "source": source_label})

    df = pd.DataFrame(rows)
    return df, lda


# ===================================================================
# 4. generate_labels  — Create human-readable labels for each topic
# ===================================================================
def generate_labels(
    topics_df: pd.DataFrame,
    use_llm: bool = False,
    groq_api_key: Optional[str] = None,
) -> pd.DataFrame:
    """
    Generate a short human-readable label for every topic.

    Strategy:
      - If use_llm=True and a Groq API key is provided, use the Groq LLM
        (llama-3.3-70b-versatile, free tier) to produce contextual labels.
      - Otherwise, apply a heuristic: capitalise the first 3–4 keywords.

    Parameters
    ----------
    topics_df : pd.DataFrame
        Must contain columns 'topic_id' and 'keywords'.
    use_llm : bool
        Whether to use the Groq LLM for label generation.
    groq_api_key : str, optional
        Groq API key, required if use_llm is True.

    Returns
    -------
    pd.DataFrame
        Same DataFrame with an additional 'label' column.
    """
    if use_llm and groq_api_key:
        logger.info("Generating labels using Groq LLM …")
        topics_df = _generate_labels_llm(topics_df, groq_api_key)
    else:
        logger.info("Generating labels using keyword heuristic …")
        topics_df = _generate_labels_heuristic(topics_df)

    return topics_df


def _generate_labels_heuristic(df: pd.DataFrame) -> pd.DataFrame:
    """Create labels from the top keywords of each topic."""
    labels = []
    for _, row in df.iterrows():
        kws = [kw.strip() for kw in row["keywords"].split(",")]
        # Take the first 3-4 non-trivial keywords and title-case them
        candidates = [kw.title() for kw in kws if len(kw) > 2][:4]
        label = " / ".join(candidates) if candidates else f"Topic {row['topic_id']}"
        labels.append(label)
    df = df.copy()
    df["label"] = labels
    return df


def _generate_labels_llm(df: pd.DataFrame, api_key: str) -> pd.DataFrame:
    """Use Groq API to generate contextual labels for topics (batched)."""
    import time
    try:
        from groq import Groq
    except ImportError:
        logger.warning("groq package not installed. Falling back to heuristic labels.")
        return _generate_labels_heuristic(df)

    client = Groq(api_key=api_key)
    labels = []

    # Process in batches to avoid rate limits
    batch_size = 10
    for batch_start in range(0, len(df), batch_size):
        batch = df.iloc[batch_start:batch_start + batch_size]
        prompt_lines = []
        for _, row in batch.iterrows():
            prompt_lines.append(f"Topic {row['topic_id']}: keywords = [{row['keywords']}]")

        prompt = (
            "You are a research taxonomy expert. For each topic below, "
            "generate a concise, descriptive label (3-6 words) that captures "
            "the theme of the keywords. Return ONLY a JSON list of objects "
            'with keys "topic_id" and "label". No extra text.\n\n'
            + "\n".join(prompt_lines)
        )

        try:
            chat = client.chat.completions.create(
                model="llama-3.3-70b-versatile",
                messages=[{"role": "user", "content": prompt}],
                temperature=0.3,
                max_tokens=1024,
            )
            resp = chat.choices[0].message.content.strip()
            # Parse JSON from the response
            # Find JSON array in response
            json_match = re.search(r"\[.*\]", resp, re.DOTALL)
            if json_match:
                batch_labels = json.loads(json_match.group())
                label_map = {item["topic_id"]: item["label"] for item in batch_labels}
                for _, row in batch.iterrows():
                    labels.append(label_map.get(row["topic_id"], f"Topic {row['topic_id']}"))
            else:
                # Fallback for this batch
                for _, row in batch.iterrows():
                    kws = [kw.strip().title() for kw in row["keywords"].split(",")][:4]
                    labels.append(" / ".join(kws))
        except Exception as exc:
            logger.warning("Groq API error for batch starting at %d: %s", batch_start, exc)
            for _, row in batch.iterrows():
                kws = [kw.strip().title() for kw in row["keywords"].split(",")][:4]
                labels.append(" / ".join(kws))

        # Rate-limit courtesy delay
        time.sleep(0.5)

    df = df.copy()
    df["label"] = labels
    return df


# ===================================================================
# 5. compare_themes  — Cross-compare title vs abstract topics
# ===================================================================
def compare_themes(
    title_topics: pd.DataFrame,
    abstract_topics: pd.DataFrame,
) -> pd.DataFrame:
    """
    Build a comparison table showing dominant themes from titles and
    abstracts side-by-side.

    Matching strategy:
      - Compute keyword overlap (Jaccard similarity) between every
        title-topic and abstract-topic pair.
      - For each title-topic, find the best matching abstract-topic.
      - Report similarity score and alignment status.

    Parameters
    ----------
    title_topics : pd.DataFrame
        Topics extracted from titles (with 'topic_id', 'keywords', 'label').
    abstract_topics : pd.DataFrame
        Topics extracted from abstracts (with 'topic_id', 'keywords', 'label').

    Returns
    -------
    pd.DataFrame
        Comparison table with columns:
          title_topic_id, title_label, title_keywords,
          abstract_topic_id, abstract_label, abstract_keywords,
          similarity, alignment
    """
    logger.info("Comparing themes: %d title topics × %d abstract topics",
                len(title_topics), len(abstract_topics))

    def _keywords_set(kw_str: str) -> set:
        return set(kw.strip().lower() for kw in kw_str.split(",") if kw.strip())

    rows = []
    for _, t_row in title_topics.iterrows():
        t_kws = _keywords_set(t_row["keywords"])
        best_sim = 0.0
        best_match = None

        for _, a_row in abstract_topics.iterrows():
            a_kws = _keywords_set(a_row["keywords"])
            if not t_kws or not a_kws:
                continue
            # Jaccard similarity
            intersection = len(t_kws & a_kws)
            union = len(t_kws | a_kws)
            sim = intersection / union if union else 0.0
            if sim > best_sim:
                best_sim = sim
                best_match = a_row

        alignment = (
            "Strong" if best_sim >= 0.4
            else "Moderate" if best_sim >= 0.2
            else "Weak" if best_sim > 0
            else "No Match"
        )

        rows.append({
            "title_topic_id": t_row["topic_id"],
            "title_label": t_row.get("label", ""),
            "title_keywords": t_row["keywords"],
            "abstract_topic_id": best_match["topic_id"] if best_match is not None else None,
            "abstract_label": best_match.get("label", "") if best_match is not None else "",
            "abstract_keywords": best_match["keywords"] if best_match is not None else "",
            "similarity": round(best_sim, 4),
            "alignment": alignment,
        })

    comparison_df = pd.DataFrame(rows)
    logger.info("Theme comparison complete: %d rows", len(comparison_df))
    return comparison_df


# ===================================================================
# 6. create_taxonomy_map  — Classify themes as MAPPED or NOVEL
# ===================================================================
def create_taxonomy_map(
    topics_df: pd.DataFrame,
    known_themes: Optional[List[str]] = None,
    threshold: float = 0.15,
) -> Dict[str, Any]:
    """
    Classify each topic as either MAPPED (similar to a well-known
    AI / business / IS research theme) or NOVEL (previously unseen).

    Heuristic:
      For each topic's keyword set, compute its best token-overlap
      ratio against the known themes list.  If the ratio exceeds the
      threshold, label it as MAPPED; otherwise NOVEL.

    Parameters
    ----------
    topics_df : pd.DataFrame
        Must contain 'topic_id', 'keywords', and 'label' columns.
    known_themes : list of str, optional
        Reference themes (defaults to the built-in KNOWN_THEMES).
    threshold : float
        Minimum overlap ratio to classify as MAPPED.

    Returns
    -------
    dict
        JSON-serialisable taxonomy map:
        {
          "metadata": { ... },
          "mapped": [ {topic_id, label, keywords, matched_theme, score}, ... ],
          "novel":  [ {topic_id, label, keywords, score}, ... ],
        }
    """
    if known_themes is None:
        known_themes = KNOWN_THEMES

    logger.info("Building taxonomy map for %d topics (threshold=%.2f)", len(topics_df), threshold)

    mapped: List[Dict] = []
    novel: List[Dict] = []

    known_tokens_list = [set(theme.lower().split()) for theme in known_themes]

    for _, row in topics_df.iterrows():
        topic_tokens = set(
            kw.strip().lower()
            for kw in row["keywords"].split(",")
            if kw.strip()
        )
        # Also include individual words from multi-word keywords
        expanded_tokens = set()
        for token in topic_tokens:
            expanded_tokens.update(token.split())
        expanded_tokens.update(topic_tokens)

        best_score = 0.0
        best_theme = ""
        for theme_str, theme_tokens in zip(known_themes, known_tokens_list):
            if not expanded_tokens or not theme_tokens:
                continue
            intersection = len(expanded_tokens & theme_tokens)
            union_size = len(expanded_tokens | theme_tokens)
            score = intersection / union_size if union_size else 0.0
            if score > best_score:
                best_score = score
                best_theme = theme_str

        entry = {
            "topic_id": int(row["topic_id"]),
            "label": row.get("label", ""),
            "keywords": row["keywords"],
            "score": round(best_score, 4),
        }

        if best_score >= threshold:
            entry["matched_theme"] = best_theme
            entry["classification"] = "MAPPED"
            mapped.append(entry)
        else:
            entry["classification"] = "NOVEL"
            novel.append(entry)

    taxonomy = {
        "metadata": {
            "total_topics": len(topics_df),
            "mapped_count": len(mapped),
            "novel_count": len(novel),
            "threshold": threshold,
        },
        "mapped": mapped,
        "novel": novel,
    }

    logger.info("Taxonomy: %d MAPPED, %d NOVEL", len(mapped), len(novel))
    return taxonomy