app.py

#!/usr/bin/env python3
"""
OpenMed NER Model Discovery App
A beautiful Gradio interface for exploring and discovering OpenMed NER models
"""

import gradio as gr
import pandas as pd
from pathlib import Path
import re
from collections import Counter


class OpenMedModelDiscovery:
    def __init__(self):
        self.data_file = Path(__file__).parent / "data" / "openmed_models_database.csv"
        self.df = pd.read_csv(self.data_file)

        # Clean and prepare data
        self._prepare_data()

        # Define entity colors
        self.entity_colors = {
            "Chemical": "#2E8B57",  # SeaGreen
            "DNA": "#4169E1",  # RoyalBlue
            "RNA": "#1E90FF",  # DodgerBlue
            "Protein": "#9932CC",  # DarkOrchid
            "Gene": "#8A2BE2",  # BlueViolet
            "Gene/Protein": "#6A5ACD",  # SlateBlue
            "Disease": "#DC143C",  # Crimson
            "Cell Line": "#FF6347",  # Tomato
            "Cell Type": "#FF4500",  # OrangeRed
            "Cell": "#FF8C00",  # DarkOrange
            "Anatomy": "#32CD32",  # LimeGreen
            "Species": "#228B22",  # ForestGreen
            "Cancer": "#8B0000",  # DarkRed
            "Clinical": "#4682B4",  # SteelBlue
            "Protein Complex": "#9370DB",  # MediumPurple
            "Protein Family": "#8B008B",  # DarkMagenta
            "Protein Variant": "#9400D3",  # Violet
            "Amino Acid": "#BA55D3",  # MediumOrchid
            "Cellular Component": "#20B2AA",  # LightSeaGreen
            "Default": "#696969",  # DimGray
        }

    def _prepare_data(self):
        """Clean and prepare the data for better display"""
        # Fill missing values
        self.df["entities"] = self.df["entities"].fillna("")
        self.df["size_mb"] = pd.to_numeric(self.df["size_mb"], errors="coerce")

        # Create size categories
        self.df["size_category"] = self.df["size_mb"].apply(self._categorize_size)

        # Split entities into lists for easier filtering
        self.df["entity_list"] = self.df["entities"].apply(
            lambda x: [e.strip() for e in x.split(",")] if x else []
        )

    def _categorize_size(self, size_mb):
        """Categorize model size"""
        if pd.isna(size_mb):
            return "Unknown"
        elif size_mb < 100:
            return "Compact (<100M)"
        elif size_mb < 200:
            return "Medium (100-200M)"
        elif size_mb < 400:
            return "Large (200-400M)"
        else:
            return "XLarge (>400M)"

    def create_entity_badge(self, entity):
        """Create a colored badge for an entity type"""
        color = self.entity_colors.get(entity, self.entity_colors["Default"])
        return f'<span style="background-color: {color}; color: white; padding: 3px 8px; border-radius: 12px; font-size: 12px; margin: 3px 4px; display: inline-block; line-height: 1.4;">{entity}</span>'

    def create_model_card(self, row):
        """Create a beautiful model card HTML"""
        entities_html = " ".join(
            [self.create_entity_badge(e) for e in row["entity_list"] if e]
        )

        size_text = f"{row['size_mb']:.0f}M" if pd.notna(row["size_mb"]) else "Unknown"

        card_html = f"""
        <div style="border: 1px solid #ddd; border-radius: 8px; padding: 16px; margin: 8px 0; background: linear-gradient(135deg, #f8f9fa 0%, #e9ecef 100%);">
            <div style="display: flex; justify-content: space-between; align-items: center; margin-bottom: 8px;">
                <h3 style="margin: 0; color: #2c3e50; font-size: 18px;">{row['short_name']}</h3>
                <span style="background-color: #6c757d; color: white; padding: 4px 8px; border-radius: 4px; font-size: 12px;">{row['architecture']}</span>
            </div>

            <div style="margin-bottom: 8px;">
                <strong>Domain:</strong> <span style="color: #495057;">{row['domain']}</span> |
                <strong>Size:</strong> <span style="color: #495057;">{size_text}</span>
            </div>

            <div style="margin-bottom: 12px;">
                <strong>Entities:</strong><br>
                <div style="margin-top: 6px; line-height: 1.6;">
                    {entities_html if entities_html else '<span style="color: #6c757d; margin: 20px;">No entities available</span>'}
                </div>
            </div>

            <div style="margin-bottom: 12px;">
                <strong>Description:</strong><br>
                <span style="color: #6c757d; font-style: italic;">{row['description']}</span>
            </div>

            <div style="display: flex; gap: 8px; margin-bottom: 8px;">
                <a href="{row['hf_link']}" target="_blank" style="background-color: #007bff; color: white; padding: 6px 12px; border-radius: 4px; text-decoration: none; font-size: 12px;">🤗 View on HF</a>
                <button onclick="copyToClipboard('{row['code_snippet']}')" style="background-color: #28a745; color: white; padding: 6px 12px; border-radius: 4px; border: none; cursor: pointer; font-size: 12px;">📋 Copy Code</button>
            </div>

            <details style="margin-top: 8px;">
                <summary style="cursor: pointer; color: #007bff;">📝 Usage Code</summary>
                <pre style="background-color: #f8f9fa; padding: 8px; border-radius: 4px; margin-top: 4px; font-size: 11px; overflow-x: auto;"><code>from transformers import {row['code_snippet']}</code></pre>
            </details>
        </div>
        """
        return card_html

    def search_models(
        self, text_query, entity_filters, domain_filters, size_filters, limit=20
    ):
        """Search and filter models based on criteria"""
        filtered_df = self.df.copy()

        # Text search
        if text_query.strip():
            text_mask = (
                filtered_df["model_name"].str.contains(text_query, case=False, na=False)
                | filtered_df["short_name"].str.contains(
                    text_query, case=False, na=False
                )
                | filtered_df["domain"].str.contains(text_query, case=False, na=False)
                | filtered_df["description"].str.contains(
                    text_query, case=False, na=False
                )
                | filtered_df["entities"].str.contains(text_query, case=False, na=False)
            )
            filtered_df = filtered_df[text_mask]

        # Entity filters
        if entity_filters:
            entity_mask = filtered_df["entity_list"].apply(
                lambda entities: any(entity in entity_filters for entity in entities)
            )
            filtered_df = filtered_df[entity_mask]

        # Domain filters
        if domain_filters:
            filtered_df = filtered_df[filtered_df["domain"].isin(domain_filters)]

        # Size filters
        if size_filters:
            filtered_df = filtered_df[filtered_df["size_category"].isin(size_filters)]

        # Limit results
        filtered_df = filtered_df.head(limit)

        if filtered_df.empty:
            return "<div style='text-align: center; padding: 40px; color: #6c757d;'><h3>No models found 😞</h3><p>Try adjusting your search criteria</p></div>"

        # Create model cards
        cards_html = f"<div style='margin-bottom: 16px;'><h2>Found {len(filtered_df)} models</h2></div>"

        for _, row in filtered_df.iterrows():
            cards_html += self.create_model_card(row)

        return cards_html

    def get_entity_stats(self):
        """Get entity statistics"""
        all_entities = []
        for entity_list in self.df["entity_list"]:
            all_entities.extend(entity_list)

        entity_counts = Counter(all_entities)
        # Remove empty strings
        entity_counts = {k: v for k, v in entity_counts.items() if k}

        return entity_counts

    def get_filter_options(self):
        """Get all available filter options"""
        # Get unique domains
        domains = sorted(self.df["domain"].unique())

        # Get unique sizes
        sizes = sorted(self.df["size_category"].unique())

        # Get all unique entities
        all_entities = set()
        for entity_list in self.df["entity_list"]:
            all_entities.update(entity_list)
        entities = sorted([e for e in all_entities if e])  # Remove empty strings

        return entities, domains, sizes


# Initialize the app
app = OpenMedModelDiscovery()

# Get filter options
ALL_ENTITIES = [
    "amino_acid",
    "anatomical_system",
    "anatomy",
    "cancer",
    "cell",
    "cell_line",
    "cell_line_name",
    "cell_type",
    "cellular_component",
    "chemical",
    "clinical",
    "developing_anatomical_structure",
    "disease",
    "dna",
    "gene/protein",
    "gene_or_protein",
    "immaterial_anatomical_entity",
    "multi_tissue_structure",
    "organ",
    "organism",
    "organism_subdivision",
    "organism_substance",
    "pathological_formation",
    "protein",
    "protein_complex",
    "protein_family",
    "protein_variant",
    "rna",
    "species",
    "tissue",
]

entities, domains, sizes = app.get_filter_options()

# Use comprehensive entity list instead of dynamic extraction for UI
entities = ALL_ENTITIES

# Custom CSS
custom_css = """
<style>
.gradio-container {
    max-width: 1200px !important;
}

.model-grid {
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(400px, 1fr));
    gap: 16px;
    margin-top: 16px;
}

/* Copy to clipboard functionality */
</style>

<script>
function copyToClipboard(text) {
    navigator.clipboard.writeText(text).then(function() {
        alert('Code copied to clipboard!');
    });
}
</script>
"""

# Create the Gradio interface
with gr.Blocks(
    theme=gr.themes.Soft(
        primary_hue="blue", secondary_hue="green", neutral_hue="slate"
    ),
    css=custom_css,
    title="🔬 OpenMed NER Model Discovery App",
) as demo:

    # Header
    gr.HTML(
        """
    <div style="text-align: center; padding: 20px; background: linear-gradient(135deg, #667eea 0%, #764ba2 100%); border-radius: 10px; margin-bottom: 20px;">
        <h1 style="color: white; margin: 0; font-size: 36px;">🔬 OpenMed NER Model Discovery</h1>
        <p style="color: white; margin: 10px 0 0 0; font-size: 18px;">Discover the perfect NER model for your biomedical text analysis from 380+ free OpenMed models</p>
    </div>
    """
    )

    with gr.Tabs():
        # Search Tab
        with gr.Tab("🔍 Search Models", elem_id="search-tab"):
            with gr.Row():
                with gr.Column(scale=1):
                    gr.Markdown("### 🎯 Search & Filter")

                    text_search = gr.Textbox(
                        label="Search Models",
                        placeholder="e.g., chemical detection, cancer genomics, DNA...",
                        lines=1,
                    )

                    entity_filter = gr.Dropdown(
                        choices=entities,
                        label="Entities",
                        info="Search and select entities (e.g., Chemical, DNA, Disease)...",
                        multiselect=True,
                        value=[],
                        interactive=True,
                    )

                    with gr.Row():
                        domain_filter = gr.CheckboxGroup(
                            choices=domains, label="Domains", value=[]
                        )

                        size_filter = gr.CheckboxGroup(
                            choices=sizes, label="Model Size", value=[]
                        )

                    result_limit = gr.Slider(
                        minimum=5, maximum=50, value=20, step=5, label="Max Results"
                    )

                    clear_btn = gr.Button("🗑️ Clear Filters", variant="secondary")

                with gr.Column(scale=2):
                    gr.Markdown("### 📋 Search Results")
                    results_display = gr.HTML()

            # Auto-search on any input change
            def auto_search(*args):
                return app.search_models(*args)

            # Connect auto-search to all inputs
            for component in [
                text_search,
                entity_filter,
                domain_filter,
                size_filter,
                result_limit,
            ]:
                component.change(
                    fn=auto_search,
                    inputs=[
                        text_search,
                        entity_filter,
                        domain_filter,
                        size_filter,
                        result_limit,
                    ],
                    outputs=results_display,
                )

            # Clear filters
            def clear_filters():
                return "", [], [], [], 20

            clear_btn.click(
                fn=clear_filters,
                outputs=[
                    text_search,
                    entity_filter,
                    domain_filter,
                    size_filter,
                    result_limit,
                ],
            )

        # About Tab
        with gr.Tab("ℹ️ About", elem_id="about-tab"):
            gr.Markdown(
                """
            # 🔬 About OpenMed NER Model Discovery

            ## What is OpenMed?

            OpenMed is a collection of **380+ state-of-the-art Named Entity Recognition (NER) models** for biomedical and clinical text analysis. All models are:

            - ✅ **Completely Free** - Apache 2.0 license
            - ✅ **High Performance** - F1 scores up to 99.8%
            - ✅ **Ready to Use** - Compatible with Hugging Face Transformers
            - ✅ **Diverse** - Covers 8+ medical domains and 20+ entity types

            ## 🎯 Use Cases

            - **Drug Discovery** - Identify chemicals and compounds
            - **Clinical Research** - Extract diseases and symptoms
            - **Genomics** - Detect genes, proteins, and DNA/RNA
            - **Medical Records** - Parse anatomical terms and clinical notes
            - **Pharmacovigilance** - Monitor drug safety and adverse events

            ## 🏗️ Model Architectures

            - **BERT** - Bidirectional transformers for robust performance
            - **DeBERTa** - Enhanced attention mechanisms
            - **RoBERTa** - Optimized training for biomedical text
            - **ModernBERT** - Latest advances in transformer architecture

            ## 📊 Coverage

            - **8 Medical Domains** - Pharmacology, Genomics, Oncology, Pathology, etc.
            - **20+ Entity Types** - Chemical, DNA, RNA, Protein, Disease, Anatomy, etc.
            - **Multiple Sizes** - From 33M to 568M parameters
            - **380+ Models** - Comprehensive coverage for any biomedical NLP task

            ## 🚀 Getting Started

            1. **Search** - Use the search tab to find models by domain, entity type, or keywords
            2. **Compare** - View model cards with performance metrics and descriptions
            3. **Copy Code** - Get ready-to-use code snippets
            4. **Deploy** - Download and use with Hugging Face Transformers

            ## 📧 Contact & Support

            - **Models** - [OpenMed on Hugging Face](https://huggingface.co/OpenMed)
            - **Paper** - Coming soon on arXiv
            - **Community** - Join discussions on Hugging Face

            ---

            Built with ❤️ for the biomedical research community
            """
            )

    # Load initial results
    demo.load(fn=lambda: app.search_models("", [], [], [], 20), outputs=results_display)

if __name__ == "__main__":
    demo.launch(server_name="0.0.0.0", server_port=7860, share=False, show_error=True)