virtool-workflow 7.1.1__py3-none-any.whl → 7.1.2__py3-none-any.whl

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/utils.py

@@ -1,4 +1,6 @@
 import asyncio
+import logging
+import sys
 import tarfile
 from collections.abc import Callable
 from functools import wraps
@@ -6,6 +8,10 @@ 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."""
@@ -19,6 +25,42 @@ def coerce_to_coroutine_function(func: Callable):
     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:

{virtool_workflow-7.1.1.dist-info → virtool_workflow-7.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: virtool-workflow
-Version: 7.1.1
+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-7.1.1.dist-info → virtool_workflow-7.1.2.dist-info}/RECORD

@@ -33,13 +33,13 @@ virtool_workflow/runtime/hook.py,sha256=ZfmvDHoSE7Qwk4Rpcjyd-pYuwP55mzEddec2ngRZ
 virtool_workflow/runtime/path.py,sha256=J8CsNMTg4XgDtib0gVSsLNvv17q793M-ydsxN6pkHrI,562
 virtool_workflow/runtime/ping.py,sha256=Xm4udRCcldHfSV1Rjpiqr-6vE7G6kaVaZgDlzNSxdao,1434
 virtool_workflow/runtime/redis.py,sha256=RK1u7IZCjgtc9jXiq4Va4Vde9v1_6NWPQ0tUdthSf5E,1806
-virtool_workflow/runtime/run.py,sha256=dJ1u2dzwAsDKG8uomEcJwHPqx5bZbNj849stoCVoc7c,8214
+virtool_workflow/runtime/run.py,sha256=rN8dzojKmDZK7Y5uKcO81Ka8H_uG_3tckmQLQQYFA7w,7608
 virtool_workflow/runtime/run_subprocess.py,sha256=hUeziLbDn3yenmVPlywAn_9FsRpYXgCIVPB1dJQzKfI,4768
 virtool_workflow/runtime/sentry.py,sha256=y4mh1sT-hoijRtKr4meE7yn1E-alxRKDylzGxmN6ndU,755
-virtool_workflow/utils.py,sha256=mc3i8whQC-2zU07v8gaR9GeumKSUic0OpFrv4X63r8o,1089
+virtool_workflow/utils.py,sha256=l3C8XE7DjcEVeTZqlelmAHo3GWG1lQZFzGHvOV9QUSE,2231
 virtool_workflow/workflow.py,sha256=W8IEFzd28wjdNNlqRrPDKyX9LeQpR6Vxy7zKeYEMQEc,2655
-virtool_workflow-7.1.1.dist-info/LICENSE,sha256=nkoVQw9W4aoQM9zgtNzHDmztap5TuXZ1L2-87vNr3w8,1097
-virtool_workflow-7.1.1.dist-info/METADATA,sha256=auGjhsbUFyYurv0ClJN5w1egnfxHjogoHRkDwdvvhsQ,1884
-virtool_workflow-7.1.1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-virtool_workflow-7.1.1.dist-info/entry_points.txt,sha256=d4MA8ZDTJOU0jKZ3ymtHZbfLVoRPgItEIN5U4uIqay8,62
-virtool_workflow-7.1.1.dist-info/RECORD,,
+virtool_workflow-7.1.2.dist-info/LICENSE,sha256=nkoVQw9W4aoQM9zgtNzHDmztap5TuXZ1L2-87vNr3w8,1097
+virtool_workflow-7.1.2.dist-info/METADATA,sha256=SGEUgsFrLqlun0RR1If7gEGVt2hTKlbDGO_rFaT6aCQ,1933
+virtool_workflow-7.1.2.dist-info/WHEEL,sha256=Nq82e9rUAnEjt98J6MlVmMCZb-t9cYE2Ir1kpBmnWfs,88
+virtool_workflow-7.1.2.dist-info/entry_points.txt,sha256=d4MA8ZDTJOU0jKZ3ymtHZbfLVoRPgItEIN5U4uIqay8,62
+virtool_workflow-7.1.2.dist-info/RECORD,,

{virtool_workflow-7.1.1.dist-info → virtool_workflow-7.1.2.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.9.0
+Generator: poetry-core 1.9.1
 Root-Is-Purelib: true
 Tag: py3-none-any