app.py

import spacy
import gradio as gr
import json
from typing import Dict, List, Tuple, Any

from zshot import PipelineConfig
from zshot.linker import LinkerSMXM
from zshot.utils.data_models import Entity

from spacy.cli import download
download("en_core_web_sm")

# Function to load the NER model
def load_model(entity_data):
    entities = [
        Entity(
            name=entity["name"],
            description=entity["description"],
            vocabulary=entity.get("vocabulary")
        ) for entity in entity_data
    ]
    
    nlp = spacy.blank("en")
    nlp_config = PipelineConfig(
        linker=LinkerSMXM(model_name="disi-unibo-nlp/openbioner-base"),
        entities=entities,
        device='cpu'  # Change to 'cpu' if GPU not available
    )
    nlp.add_pipe("zshot", config=nlp_config, last=True)
    
    return nlp

# Default entities - focusing on BACTERIUM example
default_entities = [
    {
        "name": "BACTERIUM",
        "description": "A bacterium refers to a type of microorganism that can exist as a single cell and may cause infections or play a role in various biological processes. Examples include species like Streptococcus pneumoniae and Streptomyces ahygroscopicus.",
    }
]

# Initialize model with default entities
nlp = load_model(default_entities)

# Function to create HTML visualization of entities
def get_entity_html(doc) -> str:
    colors = {
        "BACTERIUM": "#8dd3c7",
        "CHEMICAL": "#fb8072", 
        "DISEASE": "#80b1d3",
        "GENE": "#fdb462",
        "SPECIES": "#b3de69"
    }
    
    html_parts = []
    last_idx = 0
    
    # Display text with highlighted entities
    for ent in doc.ents:
        # Add text before the entity
        html_parts.append(doc.text[last_idx:ent.start_char])
        
        # Add the highlighted entity
        color = colors.get(ent.label_, "#ddd")
        html_parts.append(
            f'<span style="background-color: {color}; padding: 0.2em 0.3em; '
            f'border-radius: 0.35em; margin: 0 0.1em; font-weight: bold; color: #000;">'
            f'{doc.text[ent.start_char:ent.end_char]}'
            f'<span style="font-size: 0.8em; font-weight: bold; margin-left: 0.5em">{ent.label_}</span>'
            f'</span>'
        )
        
        # Update the last index
        last_idx = ent.end_char
    
    # Add any remaining text
    html_parts.append(doc.text[last_idx:])
    
    # Wrap the result in a div with dark theme styling
    return f'<div style="line-height: 1.5; padding: 10px; background: #222; color: #fff; border-radius: 5px;">{"".join(html_parts)}</div>'

# Function to get entity details including spans
def get_entity_details(doc) -> List[Dict[str, Any]]:
    entity_details = []
    for ent in doc.ents:
        entity_details.append({
            "text": ent.text,
            "type": ent.label_,
            "start": ent.start_char,
            "end": ent.end_char
        })
    return entity_details

# Main processing function
def process_text(text: str, entities_json: str) -> Tuple[str, List[Dict[str, Any]]]:
    global nlp
    
    # Update model if entities have changed
    try:
        entities = json.loads(entities_json)
        nlp = load_model(entities)
    except json.JSONDecodeError:
        return "Error: Invalid JSON in entity configuration", []
    
    # Process the text with the NER model
    doc = nlp(text)
    
    # Generate visualization HTML
    html_output = get_entity_html(doc)
    
    # Get detailed entity information including spans
    entity_details = get_entity_details(doc)
    
    return html_output, entity_details

# Set theme to dark
theme = gr.themes.Soft(
    primary_hue="blue",
    secondary_hue="slate",
    neutral_hue="slate",
    text_size=gr.themes.sizes.text_md,
).set(
    body_background_fill="#1a1a1a",
    background_fill_primary="#222",
    background_fill_secondary="#333",
    border_color_primary="#444",
    block_background_fill="#222",
    block_label_background_fill="#333",
    block_label_text_color="#fff",
    block_title_text_color="#fff",
    body_text_color="#fff",
    button_primary_background_fill="#2563eb",
    button_primary_text_color="#fff",
    input_background_fill="#333",
    input_border_color="#555",
    input_placeholder_color="#888",
    panel_background_fill="#222",
    slider_color="#2563eb",
)

# Create Gradio interface with dark theme
with gr.Blocks(title="Named Entity Recognition", theme=theme) as demo:
    gr.Markdown("# OpenBioNER - Demo")
    
    # First row: Entity Definitions
    with gr.Row():
        entities_input = gr.Code(
            label="Entity Definitions (JSON)",
            language="json", 
            value=json.dumps(default_entities, indent=2),
            lines=6
        )
    
    # Second row: Input text and examples side by side
    with gr.Row():
        # Left side - Input text
        with gr.Column():
            text_input = gr.Textbox(
                label="Text to analyze",
                placeholder="Enter text to analyze...",
                value="Impact of cofactor - binding loop mutations on thermotolerance and activity of E. coli transketolase",
                lines=3
            )
            
            analyze_btn = gr.Button("Analyze Text", variant="primary")
        
        # Right side - Example texts
        with gr.Column():
            gr.Markdown("### Quick Examples")
            example1_btn = gr.Button("E. coli research")
            example2_btn = gr.Button("Bacterial infection case")
            example3_btn = gr.Button("Multiple bacterial species")
    
    # Third row: Output visualization and spans side by side
    with gr.Row():
        # Left side - Highlighted text output
        with gr.Column():
            gr.Markdown("### Recognized Entities")
            result_html = gr.HTML()
        
        # Right side - Entity spans details
        with gr.Column():
            gr.Markdown("### Entity Details with Spans")
            entity_details = gr.JSON()
    
    # Set up event handlers for the analyze button
    analyze_btn.click(
        fn=process_text,
        inputs=[text_input, entities_input],
        outputs=[result_html, entity_details]
    )
    
    # Set up event handlers for example buttons
    example1_btn.click(
        fn=lambda: "Impact of cofactor - binding loop mutations on thermotolerance and activity of E. coli transketolase",
        inputs=None,
        outputs=text_input
    )
    
    example2_btn.click(
        fn=lambda: "The patient was diagnosed with pneumonia caused by Streptococcus pneumoniae and treated with antibiotics for 7 days.",
        inputs=None,
        outputs=text_input
    )
    
    example3_btn.click(
        fn=lambda: "We compared growth rates of E. coli, B. subtilis and S. aureus in various media containing different carbon sources.",
        inputs=None,
        outputs=text_input
    )

if __name__ == "__main__":
    demo.launch()