src/app.py

import streamlit as st
from transformers import pipeline
import html
from collections import defaultdict

# 设置页面
st.set_page_config(
    page_title="OpenMed NER Demo",
    page_icon="🏥",
    layout="wide"
)

# 模型映射
MODELS = {
    "Pharmacology": "OpenMed/OpenMed-NER-PharmaDetect-SuperClinical-434M",
    "Oncology Genetics": "OpenMed/OpenMed-NER-OncologyDetect-SuperMedical-355M",
    "Species Detection": "OpenMed/OpenMed-NER-SpeciesDetect-PubMed-335M",
    "Chemical Detection": "OpenMed/OpenMed-NER-ChemicalDetect-PubMed-335M",
    "Anatomy Detection": "OpenMed/OpenMed-NER-AnatomyDetect-PubMed-335M",
    "Blood Cancer Detection": "OpenMed/OpenMed-NER-BloodCancerDetect-TinyMed-82M",
    "Disease Detection": "OpenMed/OpenMed-NER-DiseaseDetect-SuperClinical-434M"
}

# 实体类型颜色映射
ENTITY_COLORS = {
    "DRUG": "#FF9999",          # 药物 - 浅红色
    "CHEMICAL": "#FFCC99",      # 化学物质 - 浅橙色
    "DISEASE": "#FF99CC",       # 疾病 - 浅粉色
    "ANATOMY": "#99CCFF",       # 解剖结构 - 浅蓝色
    "SPECIES": "#99FF99",       # 物种 - 浅绿色
    "GENE": "#CC99FF",          # 基因 - 浅紫色
    "PROTEIN": "#FFFF99",       # 蛋白质 - 浅黄色
    "CELL": "#99FFFF",          # 细胞 - 浅青色
    "default": "#DDDDDD"        # 默认 - 浅灰色
}

# 初始化会话状态
if "text_input" not in st.session_state:
    st.session_state.text_input = ""
if "entities" not in st.session_state:
    st.session_state.entities = []
if "model_loaded" not in st.session_state:
    st.session_state.model_loaded = None

# 缓存模型加载
@st.cache_resource
def load_model(model_name):
    try:
        ner_pipeline = pipeline(
            "token-classification",
            model=model_name,
            aggregation_strategy="simple"
        )
        return ner_pipeline
    except Exception as e:
        st.error(f"Error loading model: {str(e)}")
        return None

# 高亮文本中的实体
def highlight_entities(text, entities):
    if not entities:
        return text
    
    # 将文本转换为HTML安全格式
    safe_text = html.escape(text)
    
    # 按起始位置排序实体
    sorted_entities = sorted(entities, key=lambda x: x['start'])
    
    # 构建高亮文本
    highlighted_parts = []
    last_end = 0
    
    for entity in sorted_entities:
        # 添加实体前的文本
        if entity['start'] > last_end:
            highlighted_parts.append(safe_text[last_end:entity['start']])
        
        # 获取实体颜色
        entity_type = entity['entity_group']
        color = ENTITY_COLORS.get(entity_type, ENTITY_COLORS['default'])
        
        # 添加高亮的实体
        entity_text = safe_text[entity['start']:entity['end']]
        highlighted_parts.append(
            f'<mark style="background-color: {color}; padding: 2px 4px; border-radius: 3px;" '
            f'title="{entity_type} (confidence: {entity["score"]:.3f})">'
            f'{entity_text}'
            f'</mark>'
        )
        
        last_end = entity['end']
    
    # 添加剩余文本
    if last_end < len(safe_text):
        highlighted_parts.append(safe_text[last_end:])
    
    return ''.join(highlighted_parts)

# 应用标题
st.title("🏥 OpenMed Named Entity Recognition Demo")
st.markdown("Using domain-specific pre-trained models for medical text analysis")

# 侧边栏 - 模型选择
st.sidebar.header("Model Selection")
selected_domain = st.sidebar.selectbox(
    "Select Domain",
    list(MODELS.keys())
)

# 加载选定模型
model_name = MODELS[selected_domain]

# 如果模型改变，清除之前的实体结果
if st.session_state.model_loaded != model_name:
    st.session_state.entities = []
    st.session_state.model_loaded = model_name

ner_pipeline = load_model(model_name)

# 显示模型信息
st.sidebar.header("Model Information")
st.sidebar.write(f"**Domain**: {selected_domain}")
st.sidebar.write(f"**Model**: {model_name.split('/')[-1]}")

# 示例文本 (英文)
example_texts = {
    "Pharmacology": "The patient was prescribed aspirin and warfarin for anticoagulation therapy.",
    "Oncology Genetics": "BRCA1 gene mutations are associated with increased risk of breast and ovarian cancer.",
    "Species Detection": "Researchers tested the new drug in a mouse model and observed significant effects.",
    "Chemical Detection": "Glucose and oxygen molecules play key roles in cellular respiration processes.",
    "Anatomy Detection": "The patient reported pain in the right knee joint radiating to the thigh.",
    "Blood Cancer Detection": "The patient was diagnosed with chronic lymphocytic leukemia and requires regular monitoring of lymphocyte counts.",
    "Disease Detection": "Patients with diabetes mellitus often have increased risk of hypertension and cardiovascular disease."
}

# 主区域
col1, col2 = st.columns([1, 1])

with col1:
    st.header("Text Input")
    
    # 示例文本按钮
    if st.button("Load Example Text"):
        st.session_state.text_input = example_texts[selected_domain]
        st.session_state.entities = []  # 清除之前的实体结果
    
    # 文本输入区域
    text = st.text_area(
        "Enter text to analyze:",
        value=st.session_state.text_input,
        height=200,
        help="Enter medical text for analysis",
        key="text_input_widget"
    )
    
    # 更新会话状态中的文本
    st.session_state.text_input = text
    
    # 分析按钮
    if st.button("Analyze Text", type="primary"):
        if st.session_state.text_input.strip():
            with st.spinner("Analyzing..."):
                try:
                    entities = ner_pipeline(st.session_state.text_input)
                    st.session_state.entities = entities
                    st.success("Analysis completed!")
                except Exception as e:
                    st.error(f"Error during analysis: {str(e)}")
        else:
            st.warning("Please enter text to analyze")

with col2:
    st.header("NER Results")
    
    if st.session_state.entities and st.session_state.text_input:
        entities = st.session_state.entities
        
        # 显示高亮文本
        st.markdown("### Highlighted Text")
        highlighted_text = highlight_entities(st.session_state.text_input, entities)
        st.markdown(highlighted_text, unsafe_allow_html=True)
        
        # 显示实体统计
        st.markdown("### Entity Statistics")
        entity_counts = defaultdict(int)
        for entity in entities:
            entity_counts[entity['entity_group']] += 1
        
        if entity_counts:
            for entity_type, count in entity_counts.items():
                color = ENTITY_COLORS.get(entity_type, ENTITY_COLORS['default'])
                st.markdown(
                    f'<span style="background-color: {color}; padding: 4px 8px; '
                    f'border-radius: 4px; margin-right: 8px; color: black;">'
                    f'{entity_type}: {count}'
                    f'</span>',
                    unsafe_allow_html=True
                )
        else:
            st.info("No entities detected")
        
        # 显示详细实体列表
        st.markdown("### Entity Details")
        if entities:
            for i, entity in enumerate(entities):
                color = ENTITY_COLORS.get(entity['entity_group'], ENTITY_COLORS['default'])
                st.markdown(
                    f"{i+1}. **{entity['word']}** - "
                    f"<span style='color: {color};'>{entity['entity_group']}</span> "
                    f"(confidence: {entity['score']:.3f})",
                    unsafe_allow_html=True
                )
        else:
            st.info("No entities detected")
    else:
        st.info("Please enter text and click 'Analyze Text'")

# 底部信息
st.markdown("---")
st.markdown(
    "### Instructions\n"
    "1. Select a domain-specific NER model from the left sidebar\n"
    "2. Enter or paste medical text in the input box\n"
    "3. Click the 'Analyze Text' button to run the model\n"
    "4. View the entity recognition results on the right\n\n"
    "Different colored highlights represent different entity types. Hover over entities to see type and confidence."
)

# 隐藏Streamlit默认样式
hide_st_style = """

            <style>

            #MainMenu {visibility: hidden;}

            footer {visibility: hidden;}

            header {visibility: hidden;}

            </style>

            """
st.markdown(hide_st_style, unsafe_allow_html=True)