Add Cavatica acceptance test

.pre-commit-config.yaml

@@ -62,3 +62,8 @@ repos:
   - id: interrogate
     exclude: ^(docs/conf.py|setup.py|tests)
     args: [--config=pyproject.toml]
+
+- repo: https://github.com/jendrikseipp/vulture
+  rev: 'v2.7'
+  hooks:
+    - id: vulture

pyproject.toml

@@ -29,3 +29,13 @@ verbose = true
 fail-under = 95
 ignore-module = true
 ignore-nested-functions = true
+
+[tool.vulture]
+paths = ["src/orca/"]
+# exclude = ["*file*.py", "dir/"]
+# ignore_decorators = ["@app.route", "@require_*"]
+# ignore_names = ["visit_*", "do_*"]
+# make_whitelist = true
+min_confidence = 80
+# sort_by_size = true
+# verbose = true

setup.cfg

@@ -90,6 +90,7 @@ dev =
     sphinx-autodoc-typehints~=1.21
     interrogate~=1.5
     jupyterlab~=3.6
+    vulture~=2.7
 
 [options.entry_points]
 # Add here console scripts like:
@@ -114,7 +115,7 @@ apache_airflow_provider =
 #          Comment those flags to avoid this pytest issue.
 addopts =
     --cov "orca" --cov-report "term-missing" --cov-report "xml"
-    -m "not slow and not integration"
+    -m "not slow and not integration and not acceptance"
     --verbose
 norecursedirs =
     dist
@@ -130,7 +131,7 @@ testpaths =
 markers =
     slow: mark tests as slow (deselect with '-m "not slow"')
     integration: mark tests that interact with external services
-    # acceptance: mark end-to-end acceptance tests
+    acceptance: mark end-to-end acceptance tests
 
 [devpi:upload]
 # Options for the devpi: PyPI server and packaging tool

src/orca/services/sevenbridges/client_factory.py

@@ -1,15 +1,19 @@
+from __future__ import annotations
+
 import os
 from dataclasses import field
 from functools import cached_property
-from typing import Any, ClassVar, Optional, Type
+from typing import TYPE_CHECKING, Any, ClassVar, Optional, Type
 
-from airflow.models.connection import Connection
 from pydantic.dataclasses import dataclass
 from sevenbridges import Api
 from sevenbridges.http.error_handlers import maintenance_sleeper, rate_limit_sleeper
 
 from orca.errors import ClientArgsError, ClientRequestError
 
+if TYPE_CHECKING:
+    from airflow.models.connection import Connection
+
 
 @dataclass(kw_only=False)
 class SevenBridgesClientFactory:
@@ -62,14 +66,14 @@ def __post_init_post_parse__(self) -> None:
         self.update_client_kwargs()
 
     @staticmethod
-    def map_connection(connection: Connection) -> dict[str, Any]:
-        """Map Airflow connection fields to client arguments.
+    def parse_connection(connection: Connection) -> dict[str, Optional[str]]:
+        """Map Airflow connection fields to keyword arguments.
 
         Args:
             connection: An Airflow connection object.
 
         Returns:
-            A dictionary of client arguments.
+            Keyword arguments relevant to SevenBridges.
         """
         api_endpoint = None
         if connection.host:
@@ -80,9 +84,34 @@ def map_connection(connection: Connection) -> dict[str, Any]:
         kwargs = {
             "api_endpoint": api_endpoint,
             "auth_token": connection.password,
+            "project": connection.extra_dejson.get("project"),
         }
         return kwargs
 
+    @classmethod
+    def connection_from_env(cls) -> Connection:
+        """Generate Airflow connection from environment variable.
+
+        Returns:
+            An Airflow connection
+        """
+        # Following Airflow's lead on this non-standard practice
+        # because this import does introduce a bit of overhead
+        from airflow.models.connection import Connection
+
+        env_connection_uri = os.environ.get(cls.CONNECTION_ENV)
+        return Connection(uri=env_connection_uri)
+
+    @classmethod
+    def kwargs_from_env(cls) -> dict[str, Optional[str]]:
+        """Parse environment variable for keyword arguments.
+
+        Returns:
+            Keyword arguments relevant to SevenBridges.
+        """
+        env_connection = cls.connection_from_env()
+        return cls.parse_connection(env_connection)
+
     def resolve_credentials(self) -> None:
         """Resolve SevenBridges credentials based on priority.
 
@@ -93,9 +122,7 @@ def resolve_credentials(self) -> None:
             return
 
         # Get value from environment, which is confirmed to be available
-        env_connection_uri = os.environ[self.CONNECTION_ENV]
-        env_connection = Connection(uri=env_connection_uri)
-        env_kwargs = self.map_connection(env_connection)
+        env_kwargs = self.kwargs_from_env()
 
         # Resolve single values for each client argument based on priority
         self.api_endpoint = self.api_endpoint or env_kwargs["api_endpoint"]

src/orca/services/sevenbridges/hook.py

@@ -1,11 +1,19 @@
+from __future__ import annotations
+
 from functools import cached_property
+from typing import TYPE_CHECKING
 
+from airflow.exceptions import AirflowNotFoundException
 from airflow.hooks.base import BaseHook
 from sevenbridges import Api
 
+from orca.errors import ClientArgsError
 from orca.services.sevenbridges.client_factory import SevenBridgesClientFactory
 from orca.services.sevenbridges.ops import SevenBridgesOps
 
+if TYPE_CHECKING:
+    from airflow.models.connection import Connection
+
 
 class SevenBridgesHook(BaseHook):
     """Wrapper around SevenBridges client and ops classes.
@@ -31,18 +39,45 @@ def __init__(self, conn_id: str = default_conn_name, *args, **kwargs):
         extras = self.connection.extra_dejson
         self.project = extras.get("project")
 
-    def get_conn(self) -> Api:
-        """Retrieve authenticated SevenBridges client."""
-        return self.client
+    @classmethod
+    def get_connection(cls, conn_id: str) -> Connection:
+        """
+        Retrieve Airflow connection
+
+        Args:
+            conn_id: Airflow connection ID.
+
+        Returns:
+            An Airflow connection.
+        """
+        try:
+            connection = super().get_connection(conn_id)
+        except AirflowNotFoundException:
+            connection = SevenBridgesClientFactory.connection_from_env()
+        return connection
+
+    def get_conn(self) -> SevenBridgesOps:
+        """Retrieve the authenticated SevenBridgesOps object.
+
+        This object contains an authenticated SevenBridges client.
+
+        Returns:
+            An authenticated SevenBridgesOps instance.
+        """
+        return self.ops
 
     @cached_property
     def client(self) -> Api:
         """Retrieve authenticated SevenBridges client."""
-        client_args = SevenBridgesClientFactory.map_connection(self.connection)
-        factory = SevenBridgesClientFactory(**client_args)
-        return factory.get_client()
+        return self.ops.client
 
     @cached_property
     def ops(self) -> SevenBridgesOps:
-        """Retrieve authenticated SevenBridgesOps instance."""
-        return SevenBridgesOps(self.client, self.project)
+        """An authenticated SevenBridgesOps instance."""
+        kwargs = SevenBridgesClientFactory.parse_connection(self.connection)
+        endpoint = kwargs.pop("api_endpoint")
+        token = kwargs.pop("auth_token")
+        if endpoint is None or token is None:
+            message = f"Unset 'api_endpoint' ({endpoint}) or 'auth_token' ({token})"
+            raise ClientArgsError(message)
+        return SevenBridgesOps.from_args(endpoint, token, **kwargs)

src/orca/services/sevenbridges/ops.py

@@ -47,14 +47,13 @@ class SevenBridgesOps:
     project: Optional[str] = None
 
     @classmethod
-    def from_creds(
+    def from_args(
         cls,
         api_endpoint: str,
         auth_token: str,
         project: Optional[str] = None,
-        **client_kwargs: Any,
     ) -> SevenBridgesOps:
-        """Construct SevenBridgesOps from credentials.
+        """Construct SevenBridgesOps from individual arguments.
 
         Args:
             api_endpoint: API base endpoint.
@@ -63,13 +62,11 @@ def from_creds(
             project: An owner-prefixed SevenBridges project.
                 For example: <username>/<project-name>.
                 Defaults to None.
-            **client_kwargs: Additional keyword arguments that are passed
-                to the SevenBridges client during its construction.
 
         Returns:
             An authenticated SevenBridgesOps instance.
         """
-        factory = SevenBridgesClientFactory(api_endpoint, auth_token, client_kwargs)
+        factory = SevenBridgesClientFactory(api_endpoint, auth_token)
         client = factory.get_client()
         return SevenBridgesOps(client, project)
 

tests/acceptance/test_cavatica.py

@@ -0,0 +1,32 @@
+import pytest
+from sevenbridges.models.enums import TaskStatus
+
+from orca.services.sevenbridges import SevenBridgesHook
+
+
+@pytest.mark.acceptance
+def test_cavatica_launch_poc_v2(run_id):
+    def create_task():
+        hook = SevenBridgesHook()
+        task_inputs = {
+            "input_type": "FASTQ",
+            "reads1": hook.client.files.get("63e569217a0654635c558c84"),
+            "reads2": hook.client.files.get("63e5694ebfc712185ac37a27"),
+            "runThreadN": 36,
+            "wf_strand_param": "default",
+            "sample_name": "HCC1187_1M",
+            "rmats_read_length": 101,
+            "outSAMattrRGline": "ID:HCC1187_1M\tLB:NA\tPL:Illumina\tSM:HCC1187_1M",
+            "output_basename": run_id,
+        }
+        app_id = "orca-service/test-project/kfdrc-rnaseq-workflow"
+        task_id = hook.ops.create_task(run_id, app_id, task_inputs)
+        return task_id
+
+    def monitor_task(task_name):
+        hook = SevenBridgesHook()
+        return hook.ops.get_task_status(task_name)
+
+    task_id = create_task()
+    task_status, _ = monitor_task(task_id)
+    assert hasattr(TaskStatus, str(task_status))

tests/conftest.py

@@ -1,5 +1,19 @@
+from datetime import datetime
+from getpass import getuser
+from uuid import uuid4
+
 import pytest
 
+UUID = str(uuid4())
+USER = getuser()
+UTCTIME = datetime.now().isoformat("T", "seconds").replace(":", ".")
+RUN_ID = f"{USER}--{UTCTIME}--{UUID}"  # Valid characters: [A-Za-z0-9._-]
+
+
+@pytest.fixture
+def run_id():
+    return RUN_ID
+
 
 @pytest.fixture
 def patch_os_environ(mocker):

tests/services/sevenbridges/conftest.py

@@ -96,7 +96,7 @@ def ops_args(client_args):
 
 @pytest.fixture
 def mock_ops(ops_args, mock_api):
-    yield SevenBridgesOps.from_creds(**ops_args)
+    yield SevenBridgesOps.from_args(**ops_args)
 
 
 # Note that this refers to a SevenBridges task (or workflow run)