Release

.github/workflows/publish.yml

@@ -28,7 +28,7 @@ jobs:
 
     - name: Build the package with uv
       run: |
-        uv pip install -e .
+        uv sync
         uv build
 
     - name: Publish the package to PyPI

.gitignore

@@ -3,4 +3,4 @@
 *$py.class
 *.so
 .venv/
-dist/
+dist/

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 jmzhang
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,6 +1,8 @@
 # Snakemake Logger Plugin - Flowo
 
-A Snakemake logger plugin that stores workflow execution data in PostgreSQL, making your workflow management more efficient and fun! 🎉
+A Snakemake logger plugin designed to be used with **[FlowO](https://github.com/zhanghaomiao/flowo)** for real-time task monitoring, making workflow management simple, interactive, and fun! 🎉
+
+**Demo page: [flowo online](https://zhanghaomiao.github.io/flowo)**
 
 ## 🎈 Features
 
@@ -31,16 +33,27 @@ The following environment variables are available for configuration in the `.env
 - `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`:
+- `FLOWO_USER`: User displayed in Flowo
+- `FLOWO_WORKING_PATH`: Snakemake execution project path
 
 ## 🚀 Usage
-
+Basic usage
 ```bash
-snakemake --logger flowo 
+snakemake --logger flowo
+```
+config `flowo_project_name` or `flowo_tags`
+```
+snakemake \
+    --config flowo_project_name=your_project_name flowo_tags="tagA,tagB,tagC" \
+    --logger flowo
+```
+or config in --configfile
+```
+flowo_project_name: your_project_name
+flowo_tags: "tagA,tagB,tagC"
 ```
 
+## 🙏 Acknowledgement
 
-## 📜 License
-
-MIT License
+This project is developed based on the excellent work of [cademirch/snakemake-logger-plugin-snkmt](https://github.com/cademirch/snakemake-logger-plugin-snkmt).
+Special thanks to the original author for providing a solid foundation under the MIT License.

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "snakemake-logger-plugin-flowo"
-version = "0.1.2"
+version = "0.1.8"
 description = "A Snakemake logger plugin that stores workflow execution data in PostgreSQL"
 readme = "README.md"
 requires-python = ">=3.12"
@@ -26,6 +26,7 @@ dependencies = [
     "psycopg2-binary>=2.9.9",
     "pydantic>=2.11.5",
     "pydantic-settings>=2.9.1",
+    "pygments>=2.19.2",
     "snakemake>=9.6.2",
     "snakemake-interface-logger-plugins>=1.2.3",
     "sqlalchemy>=2.0.41",
@@ -38,9 +39,9 @@ flowo = "snakemake_logger_plugin_flowo:LogHandler"
 flowo = "snakemake_logger_plugin_flowo.__main__:main"
 
 [project.urls]
-Homepage = "https://github.com/your-org/snakemake-logger-plugin-flowo"
-Repository = "https://github.com/your-org/snakemake-logger-plugin-flowo"
-Issues = "https://github.com/your-org/snakemake-logger-plugin-flowo/issues"
+Homepage = "https://github.com/jmzhang1911/snakemake-logger-plugin-flowo"
+Repository = "https://github.com/jmzhang1911/snakemake-logger-plugin-flowo"
+Issues = "https://github.com/jmzhang1911/snakemake-logger-plugin-flowo/issues"
 
 [tool.hatch.build.targets.wheel]
 packages = ["snakemake_logger_plugin_flowo"]

snakemake_logger_plugin_flowo/__init__.py

@@ -24,7 +24,9 @@ def __post_init__(self) -> None:
             self.emit = lambda _: None
             self.close = lambda: None
         else:
-            logger.info("Plugin is successfully initialized and running. Monitoring ...")
+            logger.info(
+                "Plugin is successfully initialized and running. Monitoring ..."
+            )
         self.flowo_path_valid()
 
         self.log_file_path = Path(self.context.get("logfile"))

snakemake_logger_plugin_flowo/event_handlers.py

@@ -8,7 +8,7 @@
 from . import parsers
 from .models.enums import FileType, Status
 from .models import File, Job, Rule, Error, Workflow
-from .config import settings
+from .config import logger, settings
 
 """
 Context Dictionary Structure:
@@ -84,6 +84,7 @@ def handle(
         workflow = session.query(Workflow).filter(Workflow.id == workflow_id).first()
         if workflow and workflow.status == Status.RUNNING:
             workflow.status = Status.ERROR
+            workflow.end_time = datetime.now()
 
 
 class WorkflowStartedHandler(EventHandler):
@@ -182,6 +183,10 @@ def handle(
         # session.add(job)
         # session.flush()
 
+        # benchmark = job_data.benchmark
+        # if not isinstance(benchmark, list):
+        #     benchmark = [benchmark]
+        # logger.info(benchmark)
         self._add_files(job, job_data.input, FileType.INPUT, session)
         self._add_files(job, job_data.output, FileType.OUTPUT, session)
         self._add_files(job, job_data.log, FileType.LOG, session)

snakemake_logger_plugin_flowo/parsers.py

@@ -4,6 +4,7 @@
 from typing import Any, Dict, List, Optional
 
 from pydantic import BaseModel, Field, field_validator
+from .config import logger
 
 
 class Error(BaseModel):
@@ -72,7 +73,9 @@ def from_record(cls, record: LogRecord) -> "JobInfo":
                 for name, value in zip(record.resources._names, record.resources)  # type: ignore
                 if name not in {"_cores", "_nodes"}
             }
-
+        benchmark = getattr(record, "benchmark", None)
+        if benchmark and not isinstance(benchmark, list):
+            benchmark = [benchmark]
         return cls(
             jobid=getattr(record, "jobid", 0),
             rule_name=getattr(record, "rule_name", ""),
@@ -85,7 +88,7 @@ def from_record(cls, record: LogRecord) -> "JobInfo":
             input=getattr(record, "input", None),
             log=getattr(record, "log", None),
             output=getattr(record, "output", None),
-            benchmark=getattr(record, "benchmark", None),
+            benchmark=benchmark,
             resources=resources,
         )