virtool-workflow 7.1.5__py3-none-any.whl → 7.2.0__py3-none-any.whl

virtool_workflow/runtime/run.py

@@ -38,7 +38,7 @@ from virtool_workflow.runtime.redis import (
     get_next_job_with_timeout,
     wait_for_cancellation,
 )
-from virtool_workflow.runtime.sentry import configure_sentry
+from virtool_workflow.runtime.sentry import configure_sentry, set_workflow_context
 from virtool_workflow.utils import configure_logs, get_virtool_workflow_version
 from virtool_workflow.workflow import Workflow
 
@@ -182,6 +182,9 @@ async def run_workflow(
         scope["proc"] = config.proc
         scope["results"] = {}
 
+        # Set Sentry context with workflow metadata
+        set_workflow_context(job.workflow, job.id)
+
         async with create_work_path(config) as work_path:
             scope["work_path"] = work_path
 

virtool_workflow/runtime/sentry.py

@@ -9,7 +9,7 @@ from virtool_workflow.utils import get_virtool_workflow_version
 logger = get_logger("runtime")
 
 
-def configure_sentry(dsn: str):
+def configure_sentry(dsn: str | None) -> None:
     """Initialize Sentry for log aggregation."""
     if dsn:
         logger.info("initializing sentry", dsn=f"{dsn[:15]}...")
@@ -26,3 +26,25 @@ def configure_sentry(dsn: str):
         )
     else:
         logger.info("sentry disabled because no dsn was provided")
+
+
+def set_workflow_context(
+    workflow_name: str,
+    job_id: str,
+):
+    """Set workflow context for Sentry reporting."""
+    try:
+        with open("VERSION") as f:
+            workflow_version = f.read().strip()
+    except FileNotFoundError:
+        workflow_version = "UNKNOWN"
+
+    sentry_sdk.set_context(
+        "workflow",
+        {
+            "workflow_name": workflow_name,
+            "workflow_version": workflow_version,
+            "virtool_workflow_version": get_virtool_workflow_version(),
+            "job_id": job_id,
+        },
+    )

virtool_workflow/utils.py

@@ -82,7 +82,7 @@ async def make_directory(path: Path):
 
 def untar(path: Path, target_path: Path):
     with tarfile.open(path, "r:gz") as tar:
-        tar.extractall(target_path)
+        tar.extractall(target_path, filter="data")
 
 
 def move_all_model_files(source_path: Path, target_path: Path):

{virtool_workflow-7.1.5.dist-info → virtool_workflow-7.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: virtool-workflow
-Version: 7.1.5
+Version: 7.2.0
 Summary: A framework for developing bioinformatics workflows for Virtool.
 License: MIT
 Author: Ian Boyes

{virtool_workflow-7.1.5.dist-info → virtool_workflow-7.2.0.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=m-Dtdpbho-Qa9W5IYJCeEEZ7vv04hYu5yALsxOJr0FY,1813
-virtool_workflow/runtime/run.py,sha256=l0HguLLdYRVKvYTnIjoUB-9h6oDxffK-xzZYqO9lSIM,7599
+virtool_workflow/runtime/run.py,sha256=pkfNyjaDBsVHrEGqmz5Ah5FkHJN4SkCHKkEmfDO1QRU,7725
 virtool_workflow/runtime/run_subprocess.py,sha256=OFHVQ2ao16X8I9nl6Nm_f3IL7rHnmLH8ixtlAFKlOLk,4790
-virtool_workflow/runtime/sentry.py,sha256=y4mh1sT-hoijRtKr4meE7yn1E-alxRKDylzGxmN6ndU,755
-virtool_workflow/utils.py,sha256=jLsOtwh3RP7BCdgcr_rQr3DqzK1nLP2NILFXxbgAyGk,2530
+virtool_workflow/runtime/sentry.py,sha256=WJ9CI2fshJD5As6s3umUtJrUq4Z-hQRrSxAgbjceXrk,1326
+virtool_workflow/utils.py,sha256=9rHSlcvZsV2qE1Wo-cUDqESIATswr1zR_P8V-wP6jdk,2545
 virtool_workflow/workflow.py,sha256=W8IEFzd28wjdNNlqRrPDKyX9LeQpR6Vxy7zKeYEMQEc,2655
-virtool_workflow-7.1.5.dist-info/LICENSE,sha256=nkoVQw9W4aoQM9zgtNzHDmztap5TuXZ1L2-87vNr3w8,1097
-virtool_workflow-7.1.5.dist-info/METADATA,sha256=2noOApATUCmR9G0i7FCgHWjzATEaC1KkV_90p9Aso_A,1757
-virtool_workflow-7.1.5.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-virtool_workflow-7.1.5.dist-info/entry_points.txt,sha256=d4MA8ZDTJOU0jKZ3ymtHZbfLVoRPgItEIN5U4uIqay8,62
-virtool_workflow-7.1.5.dist-info/RECORD,,
+virtool_workflow-7.2.0.dist-info/LICENSE,sha256=nkoVQw9W4aoQM9zgtNzHDmztap5TuXZ1L2-87vNr3w8,1097
+virtool_workflow-7.2.0.dist-info/METADATA,sha256=vD14kwwt5OFViEIoJuz-fZ870H-hJ0i2i3oNBLPQXmQ,1757
+virtool_workflow-7.2.0.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+virtool_workflow-7.2.0.dist-info/entry_points.txt,sha256=d4MA8ZDTJOU0jKZ3ymtHZbfLVoRPgItEIN5U4uIqay8,62
+virtool_workflow-7.2.0.dist-info/RECORD,,