readme.md

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:

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:

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:

pip install flask pandas sqlalchemy requests pymysql

2. SQL Query Service

• Modify the database connection details in pubchemlite_invitro_to_dify_en.py:

  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:

  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:

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.

---