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---
# Compound Batch Query Tool
## Project Overview
This project is a compound batch query tool designed to annotating Contaminants of Emerging Concern (CECs）through databases and API interactions. It includes a Dify-based annotating agent, Flask-based SQL query service and a Tkinter-based graphical user interface for batch annotating CECs.
### Key Features
1.**CECs annotating agent**:
- Utilizes Dify's visual workflow orchestration engine and chains together the logic for querying multiple databases (such as PubChem Lite and InVitroDB) to form an automated pipeline.
- Supports CECs annotaing, which includes: `Category`, `EndpointName`, `XLogP, `BioPathway`, `ToxicityInfo`, `KnownUse`, `DisorderDisease`.
2. **SQL Query Service**:
- Provides a RESTful API (via Flask) to execute `SELECT` queries on PubChem Lite and InVitroDB databases.
- Supports dual-database switching with robust security design.
- Ensures safe SQL operations by restricting queries to `SELECT` only.
3. **Batch Compound Classification Tool**:
- A desktop GUI tool (built using Tkinter) that processes compound names from CSV files.
- Uses Dify's API to classify compounds into categories such as main category, subcategories, biological pathways, toxicity information, etc.
- Saves the results as CSV files with detailed logs for reference.
---
## File Structure
```
.
├── step1_pubchemlite_invitro_to_dify_en.py
└── step2_CECs annotating_agent_v1.0.py
```
### File Details
#### 1. `pubchemlite_invitro_to_dify_en.py`
This is a Flask-based SQL query API service with the following key functionalities:
- Allows users to execute SQL queries via HTTP POST requests.
- Provides dual-database support for PubChem Lite and InVitroDB.
- Ensures safety by restricting operations to `SELECT` queries only (disallows `INSERT`, `DELETE`, `UPDATE`, `DROP`, etc.).
- Includes robust error handling with detailed feedback.
**How to Run**:
```bash
python pubchemlite_invitro_to_dify_en.py
```
The service runs on `http://127.0.0.1:5000` by default.
#### 1. `CECs annotating_agent_v1.0.py`
This is a Tkinter-based batch compound classification tool with the following key functionalities:
- Allows users to select a CSV file and configure parameters through a graphical interface.
- Uses Dify's API to classify compounds into predefined categories.
- Supports batch processing and saves results as CSV files.
- Provides detailed logging and error messages for each step.
**How to Run**:
```bash
python CECs annotating_agent_v1.0.py
```
**Key Dependencies**:
- `tkinter`: For the graphical user interface.
- `pandas`: For loading and saving CSV files.
- `requests`: For making RESTful API calls.
- `json`: For parsing and generating JSON data.
---
## Usage Guide
### 1. Environment Setup
Ensure you have the following Python packages installed:
```bash
pip install flask pandas sqlalchemy requests pymysql
```
### 2. SQL Query Service
- Modify the database connection details in `pubchemlite_invitro_to_dify_en.py`:
```python
DB_CONFIGS = {
"pubchemlite": {
"uri": "mysql+pymysql://<username>:<password>@<host>:<port>/<database>"
},
"invitrodb_v4_3": {
"uri": "mysql+pymysql://<username>:<password>@<host>:<port>/<database>"
}
}
```
- Start the service and test the API with the examples provided above.
### 3. Batch Compound Classification Tool
- Update the default configuration in `CECs annotating_agent_v1.0.py`:
```python
self.default_api_key = "<DIFY_API_KEY>"
self.default_base_url = "http://<DIFY_HOST>:<PORT>/v1"
self.default_csv_path = "./path_to_your_data.csv"
```
- Run the program and use the GUI to upload a CSV file and execute batch classification.
---
## Example Data
### Input File Format
The input CSV file should contain a column with compound names. For example:
```csv
IUPAC_name
Methanol
Ethanol
Acetone
```
### Output File Format
The output file will be in CSV format and include the following fields:
- `CompoundName`: The compound name.
- `MainCategory`: The main classification category.
- `AdditionalCategory1`: Subcategory 1.
- `AdditionalCategory2`: Subcategory 2.
- `EndpointName`: Expanded endpoint classification.
- `XLogP`: XLogP value.
- `BioPathway`: Biological pathway information.
- `ToxicityInfo`: Toxicity information.
- `KnownUse`: Known uses of the compound.
- `DisorderDisease`: Associated disorders or diseases.
---
## Contributors
We welcome contributions! If you are interested in improving this project, feel free to submit pull requests or suggestions.
---
## License
This project is licensed under the cc-by-nc-4.0 License.
---
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