virtool-workflow 7.1.5__tar.gz → 7.2.0__tar.gz

{virtool_workflow-7.1.5 → virtool_workflow-7.2.0}/PKG-INFO

@@ -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 → virtool_workflow-7.2.0}/pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "virtool-workflow"
 description = "A framework for developing bioinformatics workflows for Virtool."
-version = "7.1.5"
+version = "7.2.0"
 authors = [
     {name = "Ian Boyes"},
     {name = "Reece Hoffman"},
@@ -46,8 +46,10 @@ structlog-sentry = "^2.2.1"
 virtool = "^31.1.3"
 
 [tool.poetry.group.dev.dependencies]
+mypy = "^1.16.0"
 piccolo-theme = "^0.24.0"
 pytest = "^7.4.2"
+pytest-aiohttp = "^1.1.0"
 pytest-asyncio = "^0.21.0"
 pytest-mock = "^3.10.0"
 pytest-structlog = "^1.0"
@@ -57,7 +59,6 @@ sphinx-autobuild = "^2021.3.14"
 sphinx-nameko-theme = "^0.0.3"
 sphinx-toolbox = "^3.5.0"
 syrupy = "^3.0.5"
-pytest-aiohttp = "^1.1.0"
 
 [tool.pytest.ini_options]
 asyncio_mode = "auto"
@@ -82,6 +83,11 @@ ignore = [
 ]
 select = ["ALL"]
 
+[tool.ruff.per-file-ignores]
+"tests/**/test_*.py" = [
+    "S101",
+]
+
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"

{virtool_workflow-7.1.5 → virtool_workflow-7.2.0}/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-7.1.5 → virtool_workflow-7.2.0}/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-7.1.5 → virtool_workflow-7.2.0}/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):