Merge branch 'main' of github.com:jmzhang1911/snakemake-logger-plugin-flowo into main

Author: jmzhang1911

.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

.vscode/settings.json

@@ -0,0 +1,5 @@
+{
+    "python-envs.defaultEnvManager": "ms-python.python:conda",
+    "python-envs.defaultPackageManager": "ms-python.python:conda",
+    "python-envs.pythonProjects": []
+}

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
 

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"
@@ -23,8 +23,6 @@ classifiers = [
     "Topic :: Software Development :: Libraries :: Python Modules",
 ]
 dependencies = [
-    "numpy==1.26.4",
-    "pandas==1.3.5",
     "psycopg2-binary>=2.9.9",
     "pydantic>=2.11.5",
     "pydantic-settings>=2.9.1",
@@ -41,9 +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"]
@@ -52,6 +50,6 @@ packages = ["snakemake_logger_plugin_flowo"]
 url = "https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple"
 default = true
 
-[[tool.uv.index]]
-url = "https://pypi.org/simple/"
-name = "pypi"
+# [[tool.uv.index]]
+# url = "https://pypi.org/simple/"
+# name = "pypi"

snakemake_logger_plugin_flowo/__init__.py

@@ -6,9 +6,6 @@
 
 from snakemake_interface_logger_plugins.base import LogHandlerBase
 from .log_handler import PostgresqlLogHandler
-from pathlib import Path
-import logging
-from snakemake.logging import DefaultFormatter, DefaultFilter
 
 __version__ = "0.1.0"
 
@@ -29,28 +26,6 @@ def __post_init__(self) -> None:
             )
         self.flowo_path_valid()
 
-        self.log_file_path = Path(self.context.get("logfile"))
-        if not self.log_file_path.parent.exists():
-            self.log_file_path.parent.mkdir(parents=True, exist_ok=True)
-        self.file_handler = logging.FileHandler(self.log_file_path, encoding="utf-8")
-        self.file_handler.setFormatter(
-            DefaultFormatter(
-                self.common_settings.quiet, self.common_settings.show_failed_logs
-            )
-        )
-        self.file_handler.addFilter(
-            DefaultFilter(
-                self.common_settings.quiet,
-                self.common_settings.debug_dag,
-                self.common_settings.dryrun,
-                self.common_settings.printshellcmds,
-            )
-        )
-        self.file_handler.setLevel(
-            logging.DEBUG if self.common_settings.verbose else logging.INFO
-        )
-        self.baseFilename = str(self.log_file_path)
-
     @property
     def writes_to_stream(self) -> bool:
         """Whether this plugin writes to stderr/stdout"""

snakemake_logger_plugin_flowo/log_handler.py

@@ -10,11 +10,14 @@
 import logging
 from .config import settings
 from sqlalchemy import text
+from sqlalchemy import select, exists
 
+from snakemake.logging import DefaultFormatter, DefaultFilter
 
 from snakemake_interface_logger_plugins.common import LogEvent
 from snakemake_interface_logger_plugins.settings import OutputSettingsLoggerInterface
 from .models.workflow import Workflow
+from .models.job import Job
 from .models.enums import Status
 from .event_handlers import (
     EventHandler,
@@ -76,6 +79,36 @@ def __init__(
             **self._workflow_config,
         }
 
+        self.file_handler = self.file_handler_init()
+
+    def file_handler_init(self):
+        self.log_file_path = Path(self.context.get("logfile"))
+
+        if not self.log_file_path.parent.exists():
+            self.log_file_path.parent.mkdir(parents=True, exist_ok=True)
+
+        file_handler = logging.FileHandler(self.log_file_path, encoding="utf-8")
+        file_handler.setFormatter(
+            DefaultFormatter(
+                self.common_settings.quiet, self.common_settings.show_failed_logs
+            )
+        )
+
+        file_handler.addFilter(
+            DefaultFilter(
+                self.common_settings.quiet,
+                self.common_settings.debug_dag,
+                self.common_settings.dryrun,
+                self.common_settings.printshellcmds,
+            )
+        )
+
+        file_handler.setLevel(
+            logging.DEBUG if self.common_settings.verbose else logging.INFO
+        )
+
+        return file_handler
+
     def db_connected(self) -> bool:
 
         try:
@@ -179,16 +212,17 @@ def emit(self, record: LogRecord) -> None:
         self.file_handler.emit(record)
         try:
             event = getattr(record, "event", None)
+
             if not event:
                 return
             event_value = event.value if hasattr(event, "value") else str(event).lower()
             handler = self.event_handlers.get(event_value)
             if not handler or self.context.get("dryrun"):
                 return
-
             with self.session_scope() as session:
                 handler.handle(record, session, self.context)
-        except Exception:
+        except Exception as e:
+            logger.info(e)
             self.handleError(record)
 
     def close(self) -> None:
@@ -200,9 +234,21 @@ def close(self) -> None:
                     workflow = session.query(Workflow).get(
                         self.context["current_workflow_id"]
                     )
-                    if workflow and workflow.status != Status.ERROR:
-                        workflow.status = Status.SUCCESS
-                        workflow.end_time = datetime.now()
+                    if workflow:
+
+                        stmt = select(
+                            exists().where(
+                                Job.workflow_id == workflow.id,
+                                Job.status == Status.ERROR,
+                            )
+                        )
+                        has_error = session.scalar(stmt)
+                        if has_error:
+                            workflow.status = Status.ERROR
+                        else:
+                            workflow.status = Status.SUCCESS
+                            workflow.end_time = datetime.now()
+
             except Exception as e:
                 self.handleError(
                     logging.LogRecord(