virtool-workflow 7.1.0__tar.gz → 7.1.2__tar.gz

{virtool_workflow-7.1.0 → virtool_workflow-7.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: virtool-workflow
-Version: 7.1.0
+Version: 7.1.2
 Summary: A framework for developing bioinformatics workflows for Virtool.
 Home-page: https://github.com/virtool/virtool-workflow
 License: MIT
@@ -18,7 +18,8 @@ Requires-Dist: orjson (>=3.9.9,<4.0.0)
 Requires-Dist: pydantic-factories (>=1.17.3,<2.0.0)
 Requires-Dist: pyfixtures (>=1.0.0,<2.0.0)
 Requires-Dist: sentry-sdk (>=2.3.1,<3.0.0)
-Requires-Dist: virtool-core (>=14.0.0,<15.0.0)
+Requires-Dist: structlog-sentry (>=2.2.1,<3.0.0)
+Requires-Dist: virtool-core (>=14.0.4,<15.0.0)
 Project-URL: Repository, https://github.com/virtool/virtool-workflow
 Description-Content-Type: text/markdown
 

{virtool_workflow-7.1.0 → virtool_workflow-7.1.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "virtool-workflow"
-version = "7.1.0"
+version = "7.1.2"
 description = "A framework for developing bioinformatics workflows for Virtool."
 authors = [
     "Ian Boyes",
@@ -38,7 +38,8 @@ orjson = "^3.9.9"
 pydantic-factories = "^1.17.3"
 pyfixtures = "^1.0.0"
 sentry-sdk = "^2.3.1"
-virtool-core = "^14.0.0"
+virtool-core = "^14.0.4"
+structlog-sentry = "^2.2.1"
 
 [tool.poetry.scripts]
 run-workflow = "virtool_workflow.cli:cli_main"

{virtool_workflow-7.1.0 → virtool_workflow-7.1.2}/virtool_workflow/runtime/run.py

@@ -1,12 +1,10 @@
 import asyncio
-import logging
 import signal
 import sys
 from asyncio import CancelledError
+from collections.abc import Callable
 from pathlib import Path
-from typing import Callable
 
-import structlog
 from pyfixtures import FixtureScope, runs_in_new_fixture_context
 from structlog import get_logger
 from virtool_core.models.job import JobState
@@ -41,7 +39,7 @@ from virtool_workflow.runtime.redis import (
     wait_for_cancellation,
 )
 from virtool_workflow.runtime.sentry import configure_sentry
-from virtool_workflow.utils import get_virtool_workflow_version
+from virtool_workflow.utils import configure_logs, get_virtool_workflow_version
 from virtool_workflow.workflow import Workflow
 
 logger = get_logger("runtime")
@@ -161,11 +159,14 @@ async def run_workflow(
 
     job = await acquire_job_by_id(config.jobs_api_connection_string, job_id)
 
-    async with api_client(
-        config.jobs_api_connection_string,
-        job.id,
-        job.key,
-    ) as api, FixtureScope() as scope:
+    async with (
+        api_client(
+            config.jobs_api_connection_string,
+            job.id,
+            job.key,
+        ) as api,
+        FixtureScope() as scope,
+    ):
         # These fixtures should not be used directly by the workflow. They are used
         # by other built-in fixtures.
         scope["_api"] = api
@@ -209,23 +210,7 @@ async def start_runtime(
 
     When a job ID is received, the runtime acquires the job from the jobs API and
     """
-    # configure_logs(dev)
-
-    logging.basicConfig(level=logging.INFO, format="%(message)s")
-
-    structlog.configure(
-        wrapper_class=structlog.make_filtering_bound_logger(logging.INFO),
-        logger_factory=structlog.stdlib.LoggerFactory(),
-        cache_logger_on_first_use=True,
-        processors=[
-            structlog.stdlib.filter_by_level,
-            structlog.stdlib.add_logger_name,
-            structlog.stdlib.add_log_level,
-            structlog.stdlib.PositionalArgumentsFormatter(),
-            structlog.processors.TimeStamper(fmt="%Y-%m-%d %H:%M.%S"),
-            structlog.dev.ConsoleRenderer(colors=True, sort_keys=True),
-        ],
-    )
+    configure_logs(bool(sentry_dsn))
 
     logger.info(
         "found virtool-workflow",
@@ -242,7 +227,7 @@ async def start_runtime(
     async with Redis(redis_connection_string) as redis:
         try:
             job_id = await get_next_job_with_timeout(redis_list_name, redis, timeout)
-        except asyncio.TimeoutError:
+        except TimeoutError:
             # This happens due to Kubernetes scheduling issues or job cancellations. It
             # is not an error.
             logger.warning("timed out while waiting for job id")

virtool_workflow-7.1.2/virtool_workflow/utils.py

@@ -0,0 +1,83 @@
+import asyncio
+import logging
+import sys
+import tarfile
+from collections.abc import Callable
+from functools import wraps
+from importlib import metadata
+from inspect import iscoroutinefunction
+from pathlib import Path
+
+import structlog
+from structlog.processors import LogfmtRenderer
+from structlog_sentry import SentryProcessor
+
+
+def coerce_to_coroutine_function(func: Callable):
+    """Wrap a non-async function in an async function."""
+    if iscoroutinefunction(func):
+        return func
+
+    @wraps(func)
+    async def _func(*args, **kwargs):
+        return func(*args, **kwargs)
+
+    return _func
+
+
+def configure_logs(use_sentry: bool):
+    logging.basicConfig(
+        format="%(message)s",
+        stream=sys.stdout,
+        level=logging.INFO,
+    )
+
+    processors = [
+        structlog.stdlib.filter_by_level,
+        structlog.stdlib.add_logger_name,
+        structlog.stdlib.add_log_level,
+        structlog.stdlib.PositionalArgumentsFormatter(),
+        structlog.processors.TimeStamper(fmt="%Y-%m-%dT%H:%M:%SZ"),
+        structlog.processors.StackInfoRenderer(),
+        structlog.processors.UnicodeDecoder(),
+    ]
+
+    if use_sentry:
+        processors.append(
+            SentryProcessor(event_level=logging.WARNING, level=logging.INFO),
+        )
+
+    processors.append(
+        LogfmtRenderer(
+            key_order=["timestamp", "level", "logger", "event"],
+        ),
+    )
+
+    structlog.configure(
+        cache_logger_on_first_use=True,
+        logger_factory=structlog.stdlib.LoggerFactory(),
+        processors=processors,
+        wrapper_class=structlog.stdlib.BoundLogger,
+    )
+
+
+def get_virtool_workflow_version() -> str:
+    """Get the version of the installed virtool-workflow package."""
+    try:
+        return metadata.version("virtool-workflow")
+    except metadata.PackageNotFoundError:
+        return "0.0.0"
+
+
+async def make_directory(path: Path):
+    await asyncio.to_thread(path.mkdir, exist_ok=True, parents=True)
+
+
+def untar(path: Path, target_path: Path):
+    with tarfile.open(path, "r:gz") as tar:
+        tar.extractall(target_path)
+
+
+def move_all_model_files(source_path: Path, target_path: Path):
+    for file in source_path.iterdir():
+        file.rename(target_path / file.name)

virtool_workflow-7.1.0/virtool_workflow/utils.py

@@ -1,41 +0,0 @@
-import asyncio
-import tarfile
-from collections.abc import Callable
-from functools import wraps
-from importlib import metadata
-from inspect import iscoroutinefunction
-from pathlib import Path
-
-
-def coerce_to_coroutine_function(func: Callable):
-    """Wrap a non-async function in an async function."""
-    if iscoroutinefunction(func):
-        return func
-
-    @wraps(func)
-    async def _func(*args, **kwargs):
-        return func(*args, **kwargs)
-
-    return _func
-
-
-def get_virtool_workflow_version() -> str:
-    """Get the version of the installed virtool-workflow package."""
-    try:
-        return metadata.version("virtool-workflow")
-    except metadata.PackageNotFoundError:
-        return "0.0.0"
-
-
-async def make_directory(path: Path):
-    await asyncio.to_thread(path.mkdir, exist_ok=True, parents=True)
-
-
-def untar(path: Path, target_path: Path):
-    with tarfile.open(path, "r:gz") as tar:
-        tar.extractall(target_path)
-
-
-def move_all_model_files(source_path: Path, target_path: Path):
-    for file in source_path.iterdir():
-        file.rename(target_path / file.name)