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readme.md

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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.
+
+---