Address PR comments

.pre-commit-config.yaml

@@ -49,6 +49,7 @@ repos:
   rev: 'v0.991'
   hooks:
   - id: mypy
+    additional_dependencies: [pydantic~=1.10]
 
 - repo: https://github.com/kynan/nbstripout
   rev: '0.6.1'

CONTRIBUTING.md

@@ -101,15 +101,15 @@ This often provides additional considerations and avoids unnecessary work.
    cd orca
    ```
 
-4. You should run:
+4. Install `pipx` to easily run Python CLI tools like `tox` and `pipenv`.
+
+4. Create an isolated virtual environment containing package dependencies,
+   including those needed for development (*e.g.* testing, documentation) by running:
 
    ```console
-   pipenv install --dev
+   pipx run tox -e pipenv
    ```
 
-   to create an isolated virtual environment containing package dependencies,
-   including those needed for development (*e.g.* testing, documentation).
-
 5. Install [pre-commit] hooks:
 
    ```

docs/requirements.txt

@@ -4,7 +4,9 @@
 
 apache-airflow~=2.4
 myst-parser[linkify]
+pydantic~=1.10
 sevenbridges-python~=2.9
 sphinx>=3.2.1
 sphinx-autodoc-typehints~=1.21
 sphinx-rtd-theme~=1.0
+sqlalchemy<2.0

pyproject.toml

@@ -9,7 +9,13 @@ build-backend = "setuptools.build_meta"
 version_scheme = "no-guess-dev"
 
 [tool.mypy]
-disable_error_code = "type-abstract"
+plugins = [
+  "pydantic.mypy"
+]
+disable_error_code = [
+	"type-abstract",
+	"import"
+]
 
 [[tool.mypy.overrides]]
 module = "orca"

setup.cfg

@@ -47,9 +47,11 @@ python_requires = >=3.8
 # For more information, check out https://semver.org/.
 
 # Updates here should be reflected in `docs/requirements.txt`
+# Also, run `tox -e pipenv` to update your virtual environment
 install_requires =
     apache-airflow~=2.4
-    sqlalchemy<2.0
+    pydantic~=1.10
+    sqlalchemy<2.0  # To address SQLAlchemy warning (https://sqlalche.me/e/b8d9)
 
 [options.packages.find]
 where = src

src/orca/services/__init__.py

@@ -21,5 +21,11 @@
     class from `tasks.py` using the credentials defined by an Airflow
     connection. These hook classes are deliberately thin wrappers around
     the tasks classes. The aim here is to minimize Airflow-specific
-    code, which is harder to test.
+    code, which is harder to test. This hook also takes advantage of
+    extra field associated with connection objects to configure the
+    underlying client and/or tasks objects. Whether to include a value
+    as the extra connection field probably depends on whether that
+    value is useful to change the overall state of the underlying
+    client and/or tasks objects (e.g., `project` for SevenBridgesTasks)
+    and whether the value is invariable for a given DAG.
 """

src/orca/services/sevenbridges/client_factory.py

@@ -1,16 +1,17 @@
 import os
-from dataclasses import dataclass, field
+from dataclasses import field
 from functools import cached_property
 from typing import Any, Optional
 
 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
 
 
-@dataclass
+@dataclass(kw_only=False)
 class SevenBridgesClientFactory:
     """Factory for constructing SevenBridges clients.
 
@@ -49,7 +50,8 @@ class SevenBridgesClientFactory:
         "https://cavatica-api.sbgenomics.com/v2",
     }
 
-    def __post_init__(self):
+    # Using `__post_init_post_parse__()` to perform steps after validation
+    def __post_init_post_parse__(self) -> None:
         """Resolve and validate credentials."""
         self.resolve_credentials()
         self.update_credentials()
@@ -78,7 +80,7 @@ def map_connection(connection: Connection) -> dict[str, Any]:
         }
         return kwargs
 
-    def resolve_credentials(self):
+    def resolve_credentials(self) -> None:
         """Resolve SevenBridges credentials based on priority.
 
         This method will update the attribute values (if applicable).
@@ -87,21 +89,21 @@ def resolve_credentials(self):
         if os.environ.get(self.CONNECTION_ENV) is None:
             return
 
-        # Retrieve information from environment (if available)
-        env_connection_uri = os.environ.get(self.CONNECTION_ENV, "")
+        # 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)
 
         # Resolve single values for each client argument based on priority
         self.api_endpoint = self.api_endpoint or env_kwargs["api_endpoint"]
         self.auth_token = self.auth_token or env_kwargs["auth_token"]
 
-    def update_credentials(self):
+    def update_credentials(self) -> None:
         """Update credentials for consistency."""
         if isinstance(self.api_endpoint, str):
             self.api_endpoint = self.api_endpoint.rstrip("/")
 
-    def validate_credentials(self):
+    def validate_credentials(self) -> None:
         """Validate the currently available credential attributes.
 
         Raises:
@@ -132,7 +134,7 @@ def validate_credentials(self):
             addendum = f"Auth auth_token ({self.auth_token}) should be a string."
             raise ClientArgsError(common_message + addendum)
 
-    def update_client_kwargs(self):
+    def update_client_kwargs(self) -> None:
         """Update client keyword arguments with default values."""
         default_handlers = [rate_limit_sleeper, maintenance_sleeper]
         self.client_kwargs.setdefault("error_handlers", default_handlers)
@@ -161,7 +163,7 @@ def get_and_test_client(self) -> Api:
         return client
 
     @staticmethod
-    def test_client(client: Api):
+    def test_client(client: Api) -> None:
         """Test the client with an authenticated request.
 
         Raises:

src/orca/services/sevenbridges/tasks.py

@@ -1,14 +1,15 @@
 from __future__ import annotations
 
-from dataclasses import dataclass
 from typing import Any, Optional
 
+from pydantic import ConfigDict
+from pydantic.dataclasses import dataclass
 from sevenbridges import Api
 
 from orca.services.sevenbridges.client_factory import SevenBridgesClientFactory
 
 
-@dataclass
+@dataclass(config=ConfigDict(arbitrary_types_allowed=True), kw_only=False)
 class SevenBridgesTasks:
     """Common tasks for SevenBridges platforms.