Feat client unit tests (#11)

* docs: set line length to 88

* tests: adds test coverage

.flake8

@@ -4,3 +4,4 @@ exclude =
     __pycache__,
     build
 max-complexity = 10
+max-line-length = 88

.github/workflows/test_and_lint.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.8', '3.9', '3.10' ]
+        python-version: [ '3.10', '3.11', '3.12' ]
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}

doc_template/source/conf.py

@@ -1,12 +1,15 @@
 """Configuration file for the Sphinx documentation builder."""
+
 #
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
+from datetime import date
+
 # -- Path Setup --------------------------------------------------------------
-from os.path import dirname, abspath
+from os.path import abspath, dirname
 from pathlib import Path
-from datetime import date
+
 from aind_slims_api import __version__ as package_version
 
 INSTITUTE_NAME = "Allen Institute for Neural Dynamics"

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "aind-slims-api"
 description = "Generated from aind-library-template"
 license = {text = "MIT"}
-requires-python = ">=3.7"
+requires-python = ">=3.10"
 authors = [
     {name = "Allen Institute for Neural Dynamics"}
 ]
@@ -40,8 +40,8 @@ where = ["src"]
 version = {attr = "aind_slims_api.__version__"}
 
 [tool.black]
-line-length = 79
-target_version = ['py36']
+line-length = 88
+target_version = ['py310']
 exclude = '''
 
 (
@@ -74,7 +74,7 @@ exclude_lines = [
 fail_under = 100
 
 [tool.isort]
-line_length = 79
+line_length = 88
 profile = "black"
 
 [tool.interrogate]

src/aind_slims_api/__init__.py

@@ -2,8 +2,8 @@
 
 __version__ = "0.0.0"
 
-from .configuration import AindSlimsApiSettings
+from aind_slims_api.configuration import AindSlimsApiSettings
 
 config = AindSlimsApiSettings()
 
-from .core import SlimsClient  # noqa
+from aind_slims_api.core import SlimsClient  # noqa

src/aind_slims_api/core.py

@@ -8,15 +8,13 @@
     methods and integration with SlimsBaseModel subtypes
 """
 
-from functools import lru_cache
 import logging
+from functools import lru_cache
 from typing import Literal, Optional
 
-from slims.slims import Slims, _SlimsApiException
-from slims.internal import (
-    Record as SlimsRecord,
-)
 from slims.criteria import Criterion, conjunction, equals
+from slims.internal import Record as SlimsRecord
+from slims.slims import Slims, _SlimsApiException
 
 from aind_slims_api import config
 
@@ -41,7 +39,7 @@ class SlimsClient:
     def __init__(self, url=None, username=None, password=None):
         """Create object and try to connect to database"""
         self.url = url or config.slims_url
-        self.db: Slims = None
+        self.db: Optional[Slims] = None
 
         self.connect(
             self.url,
@@ -95,9 +93,10 @@ def fetch(
                 start=start,
                 end=end,
             )
-        except _SlimsApiException:
-            raise
-            return None  # TODO: Raise or return empty list?
+        except _SlimsApiException as e:
+            # TODO: Add better error handling
+            #  Let's just raise error for the time being
+            raise e
 
         return records
 
@@ -124,7 +123,7 @@ def update(self, table: SLIMSTABLES, pk: int, data: dict):
         """Update a SLIMS record"""
         record = self.db.fetch_by_pk(table, pk)
         if record is None:
-            raise ValueError('No data in SLIMS "{table}" table for pk "{pk}"')
+            raise ValueError(f'No data in SLIMS "{table}" table for pk "{pk}"')
         new_record = record.update(data)
         logger.info(f"SLIMS Update: {table}/{pk}")
         return new_record

src/aind_slims_api/mouse.py

@@ -1,16 +1,17 @@
 """Contains a model for the mouse content, and a method for fetching it"""
 
 import logging
+from typing import Optional
 
-from .core import SlimsClient
+from aind_slims_api.core import SlimsClient
 
 logger = logging.getLogger()
 
 
 def fetch_mouse_content(
     client: SlimsClient,
     mouse_name: str,
-) -> dict:
+) -> Optional[dict]:
     """Fetches mouse information for a mouse with labtracks id {mouse_name}"""
     mice = client.fetch(
         "Content",
@@ -23,10 +24,10 @@ def fetch_mouse_content(
         if len(mice) > 1:
             logger.warning(
                 f"Warning, Multiple mice in SLIMS with barcode "
-                f"{mouse_name}, using pk={mouse_details.cntn_pk}"
+                f"{mouse_name}, using pk={mouse_details.cntn_pk.value}"
             )
     else:
         logger.warning("Warning, Mouse not in SLIMS")
-        return
+        mouse_details = None
 
-    return mouse_details
+    return None if mouse_details is None else mouse_details.json_entity

src/aind_slims_api/user.py

@@ -1,16 +1,17 @@
 """Contains a model for a user, and a method for fetching it"""
 
 import logging
+from typing import Optional
 
-from .core import SlimsClient
+from aind_slims_api.core import SlimsClient
 
 logger = logging.getLogger()
 
 
 def fetch_user(
     client: SlimsClient,
     username: str,
-) -> dict:
+) -> Optional[dict]:
     """Fetches user information for a user with username {username}"""
     users = client.fetch(
         "User",
@@ -22,10 +23,11 @@ def fetch_user(
         if len(users) > 1:
             logger.warning(
                 f"Warning, Multiple users in SLIMS with "
-                f"username {users}, using pk={user_details.pk}"
+                f"username {[u.json_entity for u in users]}, "
+                f"using pk={user_details.pk()}"
             )
     else:
         logger.warning("Warning, User not in SLIMS")
-        return
+        user_details = None
 
-    return user_details
+    return None if user_details is None else user_details.json_entity