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