snakemake-logger-plugin-spectio 0.0.0__tar.gz

snakemake_logger_plugin_spectio-0.0.0/PKG-INFO

@@ -0,0 +1,22 @@
+Metadata-Version: 2.4
+Name: snakemake-logger-plugin-spectio
+Version: 0.0.0
+Summary: Snakemake logger plugin that writes run events as JSON lines for Spectio (early release)
+License-Expression: MIT
+Requires-Dist: snakemake-interface-logger-plugins>=2.0,<3
+Requires-Python: >=3.11
+Project-URL: Repository, https://github.com/spectio-org/spectio
+Description-Content-Type: text/markdown
+
+# snakemake-logger-plugin-spectio
+
+A Snakemake logger plugin for [Spectio](https://github.com/spectio-org/spectio), the tool that launches, monitors and steers Nextflow and Snakemake runs.
+
+This early `0.0.0` release writes every Snakemake log event as one JSON line to a file (`--logger-spectio-file`, default `spectio-events.jsonl`, created 0600, never through a symlink), so another program can follow a run:
+
+```bash
+pip install snakemake-logger-plugin-spectio
+snakemake --cores 1 --logger spectio --logger-spectio-file events.jsonl
+```
+
+Each line holds the time, the level, the event name (`job_info`, `job_finished`, `error`…), the message and the event's own fields (rule name, job ID…). The full Spectio bridge comes with Spectio's first release.

snakemake_logger_plugin_spectio-0.0.0/README.md

@@ -0,0 +1,12 @@
+# snakemake-logger-plugin-spectio
+
+A Snakemake logger plugin for [Spectio](https://github.com/spectio-org/spectio), the tool that launches, monitors and steers Nextflow and Snakemake runs.
+
+This early `0.0.0` release writes every Snakemake log event as one JSON line to a file (`--logger-spectio-file`, default `spectio-events.jsonl`, created 0600, never through a symlink), so another program can follow a run:
+
+```bash
+pip install snakemake-logger-plugin-spectio
+snakemake --cores 1 --logger spectio --logger-spectio-file events.jsonl
+```
+
+Each line holds the time, the level, the event name (`job_info`, `job_finished`, `error`…), the message and the event's own fields (rule name, job ID…). The full Spectio bridge comes with Spectio's first release.

snakemake_logger_plugin_spectio-0.0.0/pyproject.toml

@@ -0,0 +1,15 @@
+[project]
+name = "snakemake-logger-plugin-spectio"
+version = "0.0.0"
+description = "Snakemake logger plugin that writes run events as JSON lines for Spectio (early release)"
+readme = "README.md"
+license = "MIT"
+requires-python = ">=3.11"
+dependencies = ["snakemake-interface-logger-plugins>=2.0,<3"]
+
+[project.urls]
+Repository = "https://github.com/spectio-org/spectio"
+
+[build-system]
+requires = ["uv_build==0.11.32"]  # = UV_VERSION in dev/versions.env
+build-backend = "uv_build"

snakemake_logger_plugin_spectio-0.0.0/src/snakemake_logger_plugin_spectio/__init__.py

@@ -0,0 +1,79 @@
+"""Snakemake logger plugin: one JSON line per log event, for Spectio."""
+
+import json
+import logging
+import os
+import stat
+from dataclasses import dataclass, field
+
+from snakemake_interface_logger_plugins.base import LogHandlerBase
+from snakemake_interface_logger_plugins.settings import LogHandlerSettingsBase
+
+# Attributes every LogRecord has; anything else on a record is an event field set by Snakemake.
+_STANDARD = set(vars(logging.makeLogRecord({}))) | {"message", "asctime"}
+
+
+@dataclass
+class LogHandlerSettings(LogHandlerSettingsBase):
+    file: str = field(
+        default="spectio-events.jsonl",
+        metadata={"help": "File the JSON lines are appended to."},
+    )
+
+
+class LogHandler(LogHandlerBase):
+    def __post_init__(self) -> None:
+        # The CLI always passes settings; the interface's type allows None (an API caller).
+        settings = self.settings or LogHandlerSettings()
+        # Snakemake reads baseFilename from file-writing handlers, as on logging.FileHandler.
+        self.baseFilename = os.path.abspath(settings.file)
+        # O_NOFOLLOW: a symlink planted at the path is refused, never followed.
+        # O_NONBLOCK: a FIFO planted at the path fails or is refused below, instead of blocking the run.
+        flags = os.O_WRONLY | os.O_APPEND | os.O_CREAT | os.O_NOFOLLOW | os.O_NONBLOCK
+        fd = os.open(self.baseFilename, flags, 0o600)
+        st = os.fstat(fd)
+        if not stat.S_ISREG(st.st_mode) or st.st_uid != os.getuid() or st.st_nlink != 1:
+            os.close(fd)
+            raise PermissionError(f"refusing {self.baseFilename}: not a regular file of ours with one link")
+        os.fchmod(fd, 0o600)
+        self._out = os.fdopen(fd, "a", encoding="utf-8")
+
+    def emit(self, record: logging.LogRecord) -> None:
+        try:
+            line = {
+                "time": record.created,
+                "level": record.levelname,
+                "event": str(getattr(record, "event", "")) or None,
+                "message": record.getMessage(),
+            }
+            for key, value in vars(record).items():
+                if key not in _STANDARD and key not in line:
+                    line[key] = value
+            self._out.write(json.dumps(line, default=str) + "\n")
+            self._out.flush()
+        except Exception:
+            self.handleError(record)
+
+    def close(self) -> None:
+        self._out.close()
+        super().close()
+
+    @property
+    def writes_to_stream(self) -> bool:
+        return False
+
+    @property
+    def writes_to_file(self) -> bool:
+        return True
+
+    @property
+    def has_filter(self) -> bool:
+        return False
+
+    @property
+    def has_formatter(self) -> bool:
+        return False
+
+    @property
+    def needs_rulegraph(self) -> bool:
+        return False