virtool-workflow 7.0.0__tar.gz → 7.1.1__tar.gz

{virtool_workflow-7.0.0 → virtool_workflow-7.1.1}/PKG-INFO

@@ -1,16 +1,14 @@
 Metadata-Version: 2.1
 Name: virtool-workflow
-Version: 7.0.0
+Version: 7.1.1
 Summary: A framework for developing bioinformatics workflows for Virtool.
 Home-page: https://github.com/virtool/virtool-workflow
 License: MIT
 Author: Ian Boyes
 Maintainer: Ian Boyes
-Requires-Python: >=3.10,<3.13
+Requires-Python: >=3.12,<3.13
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Dist: aiofiles (>=0.7.0,<0.8.0)
 Requires-Dist: aiohttp (>=3.8.1,<4.0.0)
@@ -20,7 +18,7 @@ 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 (>=12.0.0,<13.0.0)
+Requires-Dist: virtool-core (>=14.0.0,<15.0.0)
 Project-URL: Repository, https://github.com/virtool/virtool-workflow
 Description-Content-Type: text/markdown
 

{virtool_workflow-7.0.0 → virtool_workflow-7.1.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "virtool-workflow"
-version = "7.0.0"
+version = "7.1.1"
 description = "A framework for developing bioinformatics workflows for Virtool."
 authors = [
     "Ian Boyes",
@@ -29,7 +29,7 @@ packages = [
 ]
 
 [tool.poetry.dependencies]
-python = "^3.10,<3.13"
+python = "~3.12"
 aiofiles = "^0.7.0"
 aiohttp = "^3.8.1"
 biopython = "^1.81"
@@ -38,7 +38,7 @@ orjson = "^3.9.9"
 pydantic-factories = "^1.17.3"
 pyfixtures = "^1.0.0"
 sentry-sdk = "^2.3.1"
-virtool-core = "^12.0.0"
+virtool-core = "^14.0.0"
 
 [tool.poetry.scripts]
 run-workflow = "virtool_workflow.cli:cli_main"
@@ -71,8 +71,14 @@ exclude = [
     ".ruff_cache",
     "__pypackages__",
 ]
+target-version = "py312"
 
 [tool.ruff.lint]
+ignore = [
+    "ANN101",
+    "D203",
+    "D213"
+]
 select = ["ALL"]
 
 [build-system]

{virtool_workflow-7.0.0 → virtool_workflow-7.1.1}/virtool_workflow/api/acquire.py

@@ -4,7 +4,11 @@ from aiohttp import ClientConnectionError, ClientSession, TCPConnector
 from structlog import get_logger
 from virtool_core.models.job import JobAcquired
 
-from virtool_workflow.errors import JobAlreadyAcquired, JobsAPIError, JobsAPIServerError
+from virtool_workflow.errors import (
+    JobAlreadyAcquiredError,
+    JobsAPIError,
+    JobsAPIServerError,
+)
 
 logger = get_logger("api")
 
@@ -39,7 +43,7 @@ async def acquire_job_by_id(
 
                     if resp.status == 400:
                         if "already acquired" in await resp.text():
-                            raise JobAlreadyAcquired(await resp.json())
+                            raise JobAlreadyAcquiredError(await resp.json())
 
                     logger.critical(
                         "unexpected api error during job acquisition",

{virtool_workflow-7.0.0 → virtool_workflow-7.1.1}/virtool_workflow/api/utils.py

@@ -10,10 +10,10 @@ from aiohttp import (
 from structlog import get_logger
 
 from virtool_workflow.errors import (
-    JobsAPIBadRequest,
-    JobsAPIConflict,
-    JobsAPIForbidden,
-    JobsAPINotFound,
+    JobsAPIBadRequestError,
+    JobsAPIConflictError,
+    JobsAPIForbiddenError,
+    JobsAPINotFoundError,
     JobsAPIServerError,
 )
 
@@ -80,10 +80,10 @@ async def raise_exception_by_status_code(resp: ClientResponse):
     :raise JobsAPIServerError: the response status code is 500
     """
     status_exception_map = {
-        400: JobsAPIBadRequest,
-        403: JobsAPIForbidden,
-        404: JobsAPINotFound,
-        409: JobsAPIConflict,
+        400: JobsAPIBadRequestError,
+        403: JobsAPIForbiddenError,
+        404: JobsAPINotFoundError,
+        409: JobsAPIConflictError,
         500: JobsAPIServerError,
     }
 

{virtool_workflow-7.0.0 → virtool_workflow-7.1.1}/virtool_workflow/data/indexes.py

@@ -13,7 +13,7 @@ from virtool_core.models.reference import ReferenceNested
 from virtool_core.utils import decompress_file
 
 from virtool_workflow.api.client import APIClient
-from virtool_workflow.errors import MissingJobArgument
+from virtool_workflow.errors import MissingJobArgumentError
 from virtool_workflow.files import VirtoolFileFormat
 
 logger = get_logger("api")
@@ -43,9 +43,7 @@ class WFIndex:
 
     @property
     def bowtie_path(self) -> Path:
-        """The path to the Bowtie2 index prefix for the Virtool index.
-
-        """
+        """The path to the Bowtie2 index prefix for the Virtool index."""
         return self.path / "reference"
 
     @property
@@ -151,7 +149,10 @@ class WFNewIndex:
         await self._api.patch_json(f"/indexes/{self.id}", {})
 
     async def upload(
-        self, path: Path, fmt: VirtoolFileFormat = "fasta", name: str | None = None,
+        self,
+        path: Path,
+        fmt: VirtoolFileFormat = "fasta",
+        name: str | None = None,
     ):
         """Upload a file to associate with the index being built.
 
@@ -272,14 +273,16 @@ async def index(
 
 @fixture
 async def new_index(
-    _api: APIClient, job: Job, proc: int, work_path: Path,
+    _api: APIClient,
+    job: Job,
+    proc: int,
+    work_path: Path,
 ) -> WFNewIndex:
-    """The :class:`.WFNewIndex` for an index being created by the current job.
-    """
+    """The :class:`.WFNewIndex` for an index being created by the current job."""
     try:
         id_ = job.args["index_id"]
     except KeyError:
-        raise MissingJobArgument("Missing jobs args key 'index_id'")
+        raise MissingJobArgumentError("Missing jobs args key 'index_id'")
 
     log = logger.bind(resource="new_index", id=id_, job_id=job.id)
     log.info("loading index")

{virtool_workflow-7.0.0 → virtool_workflow-7.1.1}/virtool_workflow/data/samples.py

@@ -12,7 +12,7 @@ from virtool_core.models.samples import Quality, Sample
 from virtool_workflow.analysis.utils import ReadPaths
 from virtool_workflow.api.client import APIClient
 from virtool_workflow.data.uploads import WFUploads
-from virtool_workflow.errors import JobsAPINotFound
+from virtool_workflow.errors import JobsAPINotFoundError
 from virtool_workflow.files import VirtoolFileFormat
 
 logger = get_logger("api")
@@ -83,7 +83,10 @@ class WFNewSample:
 
 @fixture
 async def sample(
-    _api: APIClient, job: Job, uploads: WFUploads, work_path: Path,
+    _api: APIClient,
+    job: Job,
+    uploads: WFUploads,
+    work_path: Path,
 ) -> WFSample:
     """The sample associated with the current job."""
     id_ = job.args["sample_id"]
@@ -92,8 +95,8 @@ async def sample(
 
     try:
         sample_json = await _api.get_json(base_url_path)
-    except JobsAPINotFound:
-        raise JobsAPINotFound("Sample not found")
+    except JobsAPINotFoundError:
+        raise JobsAPINotFoundError("Sample not found")
 
     sample = Sample(**sample_json)
 
@@ -101,7 +104,8 @@ async def sample(
     await asyncio.to_thread(reads_path.mkdir, exist_ok=True, parents=True)
 
     await _api.get_file(
-        f"{base_url_path}/reads/reads_1.fq.gz", reads_path / "reads_1.fq.gz",
+        f"{base_url_path}/reads/reads_1.fq.gz",
+        reads_path / "reads_1.fq.gz",
     )
 
     if sample.paired:
@@ -110,7 +114,8 @@ async def sample(
             reads_path / "reads_2.fq.gz",
         )
         await _api.get_file(
-            f"{base_url_path}/reads/reads_2.fq.gz", reads_path / "reads_2.fq.gz",
+            f"{base_url_path}/reads/reads_2.fq.gz",
+            reads_path / "reads_2.fq.gz",
         )
     else:
         read_paths = (reads_path / "reads_1.fq.gz",)
@@ -127,7 +132,10 @@ async def sample(
 
 @fixture
 async def new_sample(
-    _api: APIClient, job: Job, uploads: WFUploads, work_path: Path,
+    _api: APIClient,
+    job: Job,
+    uploads: WFUploads,
+    work_path: Path,
 ) -> WFNewSample:
     """The sample associated with the current job."""
     id_ = job.args["sample_id"]

{virtool_workflow-7.0.0 → virtool_workflow-7.1.1}/virtool_workflow/data/subtractions.py

@@ -15,7 +15,7 @@ from virtool_core.models.subtraction import (
 from virtool_workflow.api.client import APIClient
 from virtool_workflow.data.analyses import WFAnalysis
 from virtool_workflow.data.uploads import WFUploads
-from virtool_workflow.errors import MissingJobArgument
+from virtool_workflow.errors import MissingJobArgumentError
 
 logger = get_logger("api")
 
@@ -118,7 +118,9 @@ class WFNewSubtraction:
 
 @fixture
 async def subtractions(
-    _api: APIClient, analysis: WFAnalysis, work_path: Path,
+    _api: APIClient,
+    analysis: WFAnalysis,
+    work_path: Path,
 ) -> list[WFSubtraction]:
     """The subtractions to be used for the current analysis job."""
     subtraction_work_path = work_path / "subtractions"
@@ -158,7 +160,10 @@ async def subtractions(
 
 @fixture
 async def new_subtraction(
-    _api: APIClient, job: Job, uploads: WFUploads, work_path: Path,
+    _api: APIClient,
+    job: Job,
+    uploads: WFUploads,
+    work_path: Path,
 ) -> WFNewSubtraction:
     """A new subtraction that will be created during the current job.
 
@@ -167,12 +172,12 @@ async def new_subtraction(
     try:
         id_ = job.args["subtraction_id"]
     except KeyError:
-        raise MissingJobArgument("subtraction_id")
+        raise MissingJobArgumentError("subtraction_id")
 
     try:
         upload_id = job.args["files"][0]["id"]
     except KeyError:
-        raise MissingJobArgument("files")
+        raise MissingJobArgumentError("files")
 
     subtraction_json = await _api.get_json(f"/subtractions/{id_}")
     subtraction_ = Subtraction(**subtraction_json)
@@ -221,7 +226,9 @@ async def new_subtraction(
         log.info("Uploading subtraction file")
 
         await _api.put_file(
-            f"/subtractions/{subtraction_.id}/files/{filename}", path, "unknown",
+            f"/subtractions/{subtraction_.id}/files/{filename}",
+            path,
+            "unknown",
         )
 
         log.info("Finished uploading subtraction file")

{virtool_workflow-7.0.0 → virtool_workflow-7.1.1}/virtool_workflow/decorators.py

@@ -1,11 +1,13 @@
 """Create Workflows by decorating module scope functions."""
+
+from collections.abc import Callable
 from types import ModuleType
-from typing import Callable
 
+from virtool_workflow.errors import WorkflowStepsError
 from virtool_workflow.workflow import Workflow
 
 
-def step(func: Callable = None, *, name: str | None = None) -> Callable:
+def step(func: Callable | None = None, *, name: str | None = None) -> Callable:
     """Mark a function as a workflow step function.
 
     :param func: the workflow step function
@@ -16,7 +18,7 @@ def step(func: Callable = None, *, name: str | None = None) -> Callable:
         return lambda _f: step(_f, name=name)
 
     func.__workflow_marker__ = "step"
-    func.__workflow_step_props__ = dict(name=name)
+    func.__workflow_step_props__ = {"name": name}
 
     return func
 
@@ -39,7 +41,7 @@ def collect(module: ModuleType) -> Workflow:
         if marked.__workflow_marker__ == "step":
             workflow.step(marked, **marked.__workflow_step_props__)
 
-    if len(workflow.steps) == 0:
-        raise ValueError(f"No workflow steps could be found in {module}")
+    if not workflow.steps:
+        raise WorkflowStepsError(str(module))
 
     return workflow

virtool_workflow-7.1.1/virtool_workflow/errors.py

@@ -0,0 +1,62 @@
+"""Custom exceptions for ``virtool_workflow``."""
+
+from subprocess import SubprocessError
+
+
+class JobAlreadyAcquiredError(Exception):
+    """Raised when an attempt is made to reacquire a job."""
+
+    def __init__(self, job_id: str) -> None:
+        """Initialize the exception with a message containing the job ID."""
+        super().__init__(
+            f"Job {job_id} is has already been acquired.",
+        )
+
+
+class JobsAPIError(Exception):
+    """A base exception for errors due to HTTP errors from the jobs API."""
+
+
+class JobsAPIBadRequestError(JobsAPIError):
+    """A ``400 Bad Request`` response was received from the jobs API."""
+
+    status = 400
+
+
+class JobsAPIForbiddenError(JobsAPIError):
+    """A ``403 Forbidden`` response was received from the jobs API."""
+
+    status = 403
+
+
+class JobsAPINotFoundError(JobsAPIError):
+    """A ``404 Not Found`` response was received from the jobs API."""
+
+    status = 404
+
+
+class JobsAPIConflictError(JobsAPIError):
+    """A ``409 Conflict`` response was received from the jobs API."""
+
+    status = 409
+
+
+class JobsAPIServerError(JobsAPIError):
+    """A ``500 Internal Server Error`` response was received from the jobs API."""
+
+    status = 500
+
+
+class MissingJobArgumentError(ValueError):
+    """The `job.args` dict is missing a required key for some funcionality."""
+
+
+class WorkflowStepsError(Exception):
+    """Raised when no workflow steps are found in a module."""
+
+    def __init__(self, module: str) -> None:
+        super().__init__(f"No workflow steps could be found in {module}")
+
+
+class SubprocessFailedError(SubprocessError):
+    """Subprocess exited with non-zero status during a workflow."""

virtool_workflow-7.1.1/virtool_workflow/files.py

@@ -0,0 +1,40 @@
+"""Dataclasses for describing files uploaded to the Virtool server."""
+
+import datetime
+from dataclasses import dataclass
+from typing import Literal
+
+VirtoolFileFormat = Literal[
+    "sam",
+    "bam",
+    "fasta",
+    "fastq",
+    "csv",
+    "tsv",
+    "json",
+    "unknown",
+]
+"""A literal type hint for the format of a :class:`.VirtoolFile`."""
+
+
+@dataclass
+class VirtoolFile:
+    """A description of a file  uploaded to the Virtool server."""
+
+    id: int
+    """The unique ID for the file."""
+
+    name: str
+    """The name of the file."""
+
+    size: int
+    """The size of the file in bytes."""
+
+    format: VirtoolFileFormat
+    """The format of the file."""
+
+    name_on_disk: str | None = None
+    """The actual name of the file on disk."""
+
+    uploaded_at: datetime.datetime | None = None
+    """When the file was uploaded."""

{virtool_workflow-7.0.0 → virtool_workflow-7.1.1}/virtool_workflow/hooks.py

@@ -1,5 +1,4 @@
-"""Hooks provide a way to do things when events happen during the workflow lifecycle.
-"""
+"""Hooks do things when events happen during the workflow lifecycle."""
 
 from virtool_workflow.runtime.hook import Hook
 
@@ -124,7 +123,7 @@ __all__ = [
 ]
 
 
-def cleanup_builtin_status_hooks():
+def cleanup_builtin_status_hooks() -> None:
     """Clear callbacks for built-in status hooks.
 
     This prevents carryover of hooks between tests. Carryover won't be encountered in

{virtool_workflow-7.0.0 → virtool_workflow-7.1.1}/virtool_workflow/pytest_plugin/data.py

@@ -116,7 +116,6 @@ def data(
         "test": True,
     }
     job.ping = JobPing(pinged_at=static_datetime)
-    job.rights = {}
 
     """A finalized sample to be used for testing analyses."""
     sample = SampleFactory.build()

{virtool_workflow-7.0.0 → virtool_workflow-7.1.1}/virtool_workflow/runtime/run_subprocess.py

@@ -1,4 +1,5 @@
 """Code for running and managing subprocesses."""
+
 import asyncio
 from asyncio.subprocess import Process
 from pathlib import Path
@@ -8,7 +9,7 @@ from pyfixtures import fixture
 from structlog import get_logger
 from virtool_core.utils import timestamp
 
-from virtool_workflow.errors import SubprocessFailed
+from virtool_workflow.errors import SubprocessFailedError
 
 logger = get_logger("subprocess")
 
@@ -146,7 +147,7 @@ async def _run_subprocess(
     # Exit code 15 indicates that the process was terminated. This is expected
     # when the workflow fails for some other reason, hence not an exception
     if process.returncode not in [0, 15, -15]:
-        raise SubprocessFailed(
+        raise SubprocessFailedError(
             f"{command[0]} failed with exit code {process.returncode}\n"
             f"arguments: {command}\n",
         )

virtool_workflow-7.0.0/virtool_workflow/errors.py

@@ -1,61 +0,0 @@
-from subprocess import SubprocessError
-
-
-class IllegalJobArguments(ValueError):
-    """The `job.args` dict is in an illegal state."""
-
-
-
-class InsufficientJobRights(Exception):
-    ...
-
-
-class JobAlreadyAcquired(Exception):
-    def __init__(self, job_id: str):
-        super(JobAlreadyAcquired, self).__init__(
-            f"Job {job_id} is has already been acquired.",
-        )
-
-
-class JobAlreadyFinalized(Exception):
-    ...
-
-
-class JobsAPIError(Exception):
-    """A base exception for errors due to HTTP errors from the jobs API."""
-
-
-
-class JobsAPIBadRequest(JobsAPIError):
-    """A ``400 Bad Request`` response from the jobs API."""
-
-    status = 400
-
-
-class JobsAPIForbidden(JobsAPIError):
-    status = 403
-
-
-class JobsAPINotFound(JobsAPIError):
-    status = 404
-
-
-class JobsAPIConflict(JobsAPIError):
-    status = 409
-
-
-class JobsAPIServerError(JobsAPIError):
-    status = 500
-
-
-class MissingJobArgument(ValueError):
-    """The `job.args` dict is missing a required key for some funcionality."""
-
-
-
-class NotFound(KeyError):
-    ...
-
-
-class SubprocessFailed(SubprocessError):
-    """Subprocess exited with non-zero status during a workflow."""

virtool_workflow-7.0.0/virtool_workflow/files.py

@@ -1,24 +0,0 @@
-from dataclasses import dataclass
-from datetime import datetime
-from typing import Literal
-
-VirtoolFileFormat = Literal[
-    "sam",
-    "bam",
-    "fasta",
-    "fastq",
-    "csv",
-    "tsv",
-    "json",
-    "unknown",
-]
-
-
-@dataclass
-class VirtoolFile:
-    id: int
-    name: str
-    size: int
-    format: VirtoolFileFormat
-    name_on_disk: str = None
-    uploaded_at: datetime = None