feat(server): support jobs without rights field

Author: igboyes

.github/workflows/ci.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-22.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Commitlint
         uses: wagoid/commitlint-github-action@v5
   test:
@@ -34,6 +34,10 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12.3
       - name: Install Poetry
         uses: snok/install-poetry@v1
       - name: Poetry Build

.github/workflows/publish.yml

@@ -14,7 +14,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.12.3'
       - name: Checkout
         uses: actions/checkout@v4
       - name: Install Poetry

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.12-bookworm
+FROM python:3.12.3-bookworm
 WORKDIR /test
 COPY --from=ghcr.io/virtool/workflow-tools:2.0.1 /opt/fastqc /opt/fastqc
 COPY --from=ghcr.io/virtool/workflow-tools:2.0.1 /opt/hmmer /opt/hmmer

poetry.lock

@@ -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]

pyproject.toml

@@ -13,23 +13,21 @@
       'pinged_at': datetime.datetime(2020, 1, 1, 1, 1, 1),
     }),
     'progress': 6380,
-    'rights': dict({
-    }),
     'stage': 'iPhGgaTklZTpXCJkWJYU',
     'state': <JobState.RUNNING: 'running'>,
     'status': list([
       dict({
         'error': dict({
           'details': list([
-            'VCqTDwYzyKtSiEMpnbXp',
+            'vhVGiBXJqoyUfQBjWTjz',
           ]),
           'traceback': list([
-            'WhbIXmchuyDmybzRLozZ',
+            'ACAdPsEbpDIRnZLXrjSy',
           ]),
-          'type': 'ASTUagoKFMbsJQgaCJfJ',
+          'type': 'OqopAJsorWvViTxsrhYk',
         }),
-        'progress': 3132,
-        'stage': 'aOwDKGzVuuSkpRdRKwoO',
+        'progress': 5931,
+        'stage': 'WyJLLiOEIvGOHLbiwHlJ',
         'state': <JobState.ERROR: 'error'>,
         'step_description': None,
         'step_name': None,

tests/data/__snapshots__/test_jobs.ambr

@@ -4,13 +4,12 @@
 from pyfixtures import FixtureScope
 
 from virtool_workflow.data.analyses import WFAnalysis
-from virtool_workflow.errors import JobsAPIConflict, JobsAPINotFound
+from virtool_workflow.errors import JobsAPIConflictError, JobsAPINotFoundError
 from virtool_workflow.pytest_plugin.data import Data
 
 
 async def test_ok(data: Data, scope: FixtureScope):
-    """Test that the analysis fixture returns an Analysis object with the expected values.
-    """
+    """Test that the analysis fixture returns an Analysis object with the expected values."""
     data.job.args["analysis_id"] = data.analysis.id
 
     analysis = await scope.instantiate_by_key("analysis")
@@ -22,12 +21,15 @@ async def test_not_found(data: Data, scope: FixtureScope):
     """Test that JobsAPINotFound is raised if the analysis does not exist."""
     data.job.args["analysis_id"] = "not_found"
 
-    with pytest.raises(JobsAPINotFound) as err:
+    with pytest.raises(JobsAPINotFoundError) as err:
         await scope.instantiate_by_key("analysis")
 
 
 async def test_upload_file(
-    captured_uploads_path: Path, data: Data, scope: FixtureScope, work_path: Path,
+    captured_uploads_path: Path,
+    data: Data,
+    scope: FixtureScope,
+    work_path: Path,
 ):
     """Test that the ``Analysis`` object returned by the fixture can be used to upload an
     analysis file.
@@ -67,7 +69,7 @@ async def test_delete_finalized(data: Data, scope: FixtureScope):
 
     analysis: WFAnalysis = await scope.instantiate_by_key("analysis")
 
-    with pytest.raises(JobsAPIConflict) as err:
+    with pytest.raises(JobsAPIConflictError) as err:
         await analysis.delete()
 
     assert "Analysis is finalized" in str(err)

tests/data/test_analyses.py

@@ -4,9 +4,9 @@
 from pyfixtures import FixtureScope
 from syrupy import SnapshotAssertion
 
-from virtool_workflow.pytest_plugin.data import Data
 from virtool_workflow.data.indexes import WFIndex, WFNewIndex
-from virtool_workflow.errors import JobsAPINotFound, JobsAPIConflict
+from virtool_workflow.errors import JobsAPIConflictError, JobsAPINotFoundError
+from virtool_workflow.pytest_plugin.data import Data
 
 
 class TestIndex:
@@ -18,8 +18,7 @@ async def test_ok(
         snapshot: SnapshotAssertion,
         work_path: Path,
     ):
-        """
-        Test that the index fixture instantiates, contains the expected data, and
+        """Test that the index fixture instantiates, contains the expected data, and
         downloads the index files to the work path.
         """
         data.job.args["analysis_id"] = data.analysis.id
@@ -67,14 +66,12 @@ async def test_ok(
             work_path / "test.fa",
         )
 
-        assert open(work_path / "test.fa", "r").read() == snapshot(name="fasta")
+        assert open(work_path / "test.fa").read() == snapshot(name="fasta")
 
 
 class TestNewIndex:
     async def test_ok(self, data: Data, scope: FixtureScope, work_path: Path):
-        """
-        Test that the ``new_index`` fixture instantiates and contains the expected data.
-        """
+        """Test that the ``new_index`` fixture instantiates and contains the expected data."""
         data.job.args["index_id"] = data.new_index.id
 
         new_index: WFNewIndex = await scope.instantiate_by_key("new_index")
@@ -129,14 +126,17 @@ async def test_upload_and_finalize(
         }
 
     async def test_upload_invalid_filename(
-        self, data: Data, example_path: Path, scope: FixtureScope
+        self,
+        data: Data,
+        example_path: Path,
+        scope: FixtureScope,
     ):
         """Test that an invalid filename raises an error."""
         data.job.args["index_id"] = data.new_index.id
 
         new_index: WFNewIndex = await scope.instantiate_by_key("new_index")
 
-        with pytest.raises(JobsAPINotFound) as err:
+        with pytest.raises(JobsAPINotFoundError) as err:
             await new_index.upload(
                 example_path / "hmms/annotations.json.gz",
                 "unknown",
@@ -164,7 +164,7 @@ async def test_finalize_incomplete(
                 "unknown",
             )
 
-        with pytest.raises(JobsAPIConflict) as err:
+        with pytest.raises(JobsAPIConflictError) as err:
             await new_index.finalize()
 
         assert (