fixed

Author: jmzhang

README.md

@@ -1,65 +1,46 @@
 # Snakemake Logger Plugin - Flowo
 
-A Snakemake logger plugin that stores workflow execution data in PostgreSQL.
+A Snakemake logger plugin that stores workflow execution data in PostgreSQL, making your workflow management more efficient and fun! 🎉
 
-## Features
+## 🎈 Features
 
-- Stores Snakemake workflow execution data in PostgreSQL database
-- Tracks jobs, rules, files, and errors
-- Provides comprehensive logging and monitoring capabilities
-- Easy integration with existing Snakemake workflows
+- Stores Snakemake workflow execution data in PostgreSQL database 🚀
+- Tracks jobs, rules, files, and errors 🔍
+- Provides comprehensive logging and monitoring capabilities 🚨
+- Easy integration with existing Snakemake workflows 🔄
 
-## Installation
+## 💻 Installation
 
 ```bash
 pip install snakemake-logger-plugin-flowo
 ```
-
-## Usage
-
-### 1. Configure Database
-
-Set up your PostgreSQL database and configure the connection:
+## 🔧 Configuration
 
 ```bash
-export POSTGRES_USER=snakemake
-export POSTGRES_PASSWORD=snakemake_password
-export POSTGRES_DB=snakemake_logs
-```
+# To generate the default configuration file, run the following command:
+# This will create the default .env configuration file in your $HOME/.config/flowo/ directory.
+flowo --generate-config
 
-### 2. Use with Snakemake
-
-Run your Snakemake workflow with the logger plugin:
-
-```bash
-snakemake --logger flowo
+# After generating the .env file, open it with your preferred text editor to adjust the settings:
+vim $HOME/.config/flowo/.env
 ```
+The following environment variables are available for configuration in the `.env` file:
 
-## Configuration
+- `POSTGRES_USER`: PostgreSQL username (default: flowo)
+- `POSTGRES_PASSWORD`: PostgreSQL password (default: flowo_password)
+- `POSTGRES_DB`: PostgreSQL database name (default: flowo_logs)
+- `POSTGRES_HOST`: PostgreSQL host (default: localhost)
+- `POSTGRES_PORT`: PostgreSQL port (default: localhost: 5432)
+- `FLOWO_USER`: 
+- `FLOWO_WORKING_PATH`:
 
-The plugin can be configured using environment variables:
-
-- `POSTGRES_USER`: PostgreSQL username (default: snakemake)
-- `POSTGRES_PASSWORD`: PostgreSQL password (default: snakemake_password)
-- `POSTGRES_DB`: PostgreSQL database name (default: snakemake_logs)
-- `SQL_ECHO`: Enable SQL query logging (default: False)
-
-## Development
-
-### Setup
+## 🚀 Usage
 
 ```bash
-git clone <repository-url>
-cd snakemake-logger-plugin-flowo
-uv sync
+snakemake --logger flowo 
 ```
 
-### Build
-
-```bash
-uv build
-```
 
-## License
+## 📜 License
 
 MIT License

snakemake_logger_plugin_flowo/__main__.py

@@ -12,7 +12,7 @@ def generate_config():
 POSTGRES_USER=flowo
 POSTGRES_PASSWORD=flowo_password
 POSTGRES_DB=flowo_logs
-POSTGRES_HOST=172.16.3.223
+POSTGRES_HOST=localhost
 POSTGRES_PORT=5432
 
 ### APP setting
@@ -31,11 +31,7 @@ def main():
         action="store_true",
         help="Generate default config at ~/.config/flowo/.env",
     )
-    parser.add_argument(
-        "--health-check",
-        action="store_true",
-        help="Run the new function",
-    )
+
     args = parser.parse_args()
     if args.generate_config:
         generate_config()

snakemake_logger_plugin_flowo/config.py

@@ -36,9 +36,9 @@ def format(self, record):
 
 
 class Settings(BaseSettings):
-    POSTGRES_USER: str = "snakemake"
-    POSTGRES_PASSWORD: str = "snakemake_password"
-    POSTGRES_DB: str = "snakemake_logs"
+    POSTGRES_USER: str = "flowo"
+    POSTGRES_PASSWORD: str = "flowo_password"
+    POSTGRES_DB: str = "flowo_logs"
     POSTGRES_HOST: str | None = None
     POSTGRES_PORT: str | None = None
     SQL_ECHO: bool = False