Merge branch 'main' into feat-initial-waterlog

.flake8

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

.github/workflows/tag_and_publish.yml

@@ -3,9 +3,7 @@ on:
   push:
     branches:
       - main
-# Remove line 61 to enable automated semantic version bumps.
-# Change line 67 from "if: false" to "if: true" to enable PyPI publishing. 
-# Requires that svc-aindscicomp be added as an admin to repo.
+
 jobs:
   update_badges:
     runs-on: ubuntu-latest
@@ -16,10 +14,10 @@ jobs:
         ref: ${{ env.DEFAULT_BRANCH }}
         fetch-depth: 0
         token: ${{ secrets.SERVICE_TOKEN }}
-    - name: Set up Python 3.8
+    - name: Set up Python 3.10
       uses: actions/setup-python@v3
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - name: Install dependencies
       run: | 
         python -m pip install -e .[dev] --no-cache-dir
@@ -62,22 +60,20 @@ jobs:
         add: '["README.md"]'
   tag:
     needs: update_badges
-    if: ${{github.event.repository.name == 'aind-library-template'}}
     uses: AllenNeuralDynamics/aind-github-actions/.github/workflows/tag.yml@main
     secrets:
       SERVICE_TOKEN: ${{ secrets.SERVICE_TOKEN }}
   publish:
     needs: tag
-    if: false
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - name: Pull latest changes
         run: git pull origin main
-      - name: Set up Python 3.8
+      - name: Set up Python 3.10
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: '3.10'
       - name: Install dependencies
         run: |
           pip install --upgrade setuptools wheel twine build

.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 }}

README.md

@@ -5,7 +5,7 @@
 [![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)
 ![Interrogate](https://img.shields.io/badge/interrogate-100.0%25-brightgreen)
 ![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen?logo=codecov)
-![Python](https://img.shields.io/badge/python->=3.7-blue?logo=python)
+![Python](https://img.shields.io/badge/python->=3.10-blue?logo=python)
 
 This library is for pythonic access to data stored in the AIND SLIMS deployment. It is not meant to be a generic way to interact with SLIMS, but rather specific to how data is modeled in AIND's SLIMS instance.
 

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

@@ -1,9 +1,9 @@
 """Init package"""
 
-__version__ = "0.0.0"
+__version__ = "0.0.2"
 
-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

@@ -87,6 +87,7 @@ class MyModel(SlimsBaseModel):
     """
 
     pk: int = None
+    json_entity: dict = None
     _slims_table: SLIMSTABLES
 
     @field_validator("*", mode="before")
@@ -137,7 +138,7 @@ 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,
@@ -191,9 +192,10 @@ 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
 
@@ -220,7 +222,7 @@ 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
@@ -231,9 +233,7 @@ def rest_link(self, table: SLIMSTABLES, **kwargs):
         queries = [f"?{k}={v}" for k, v in kwargs.items()]
         return base_url + "".join(queries)
 
-    def add_model(
-        self, model: SlimsBaseModel, *args, **kwargs
-    ) -> SlimsBaseModel:
+    def add_model(self, model: SlimsBaseModel, *args, **kwargs) -> SlimsBaseModel:
         """Given a SlimsBaseModel object, add it to SLIMS
         Args
             model (SlimsBaseModel): object to add

src/aind_slims_api/mouse.py

@@ -3,9 +3,9 @@
 import logging
 from typing import Annotated
 
-from pydantic import Field, ValidationError
+from pydantic import Field, BeforeValidator, ValidationError
 
-from .core import SlimsBaseModel, SlimsClient, UnitSpec, SLIMSTABLES
+from aind_slims_api.core import SlimsBaseModel, SlimsClient, UnitSpec, SLIMSTABLES
 
 logger = logging.getLogger()
 
@@ -16,10 +16,10 @@ class SlimsMouseContent(SlimsBaseModel):
     baseline_weight_g: Annotated[float | None, UnitSpec("g")] = Field(
         ..., alias="cntn_cf_baselineWeight"
     )
-    point_of_contact: str | None = Field(
-        ..., alias="cntn_cf_scientificPointOfContact"
+    point_of_contact: str | None = Field(..., alias="cntn_cf_scientificPointOfContact")
+    water_restricted: Annotated[bool, BeforeValidator(lambda x: x or False)] = Field(
+        ..., alias="cntn_cf_waterRestricted"
     )
-    water_restricted: bool = Field(..., alias="cntn_cf_waterRestricted")
     barcode: str = Field(..., alias="cntn_barCode")
     pk: int = Field(..., alias="cntn_pk")
 
@@ -45,7 +45,7 @@ class SlimsMouseContent(SlimsBaseModel):
 def fetch_mouse_content(
     client: SlimsClient,
     mouse_name: str,
-) -> SlimsMouseContent:
+) -> SlimsMouseContent | dict | None:
     """Fetches mouse information for a mouse with labtracks id {mouse_name}"""
     mice = client.fetch(
         "Content",
@@ -58,7 +58,7 @@ 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")
@@ -68,6 +68,6 @@ def fetch_mouse_content(
         mouse = SlimsMouseContent.model_validate(mouse_details)
     except ValidationError as e:
         logger.error(f"SLIMS data validation failed, {repr(e)}")
-        return
+        return mouse_details.json_entity
 
     return mouse

src/aind_slims_api/unit.py

@@ -0,0 +1,20 @@
+"""Contains a model for a unit"""
+
+import logging
+from typing import Optional
+
+from pydantic import Field
+
+from aind_slims_api.core import SlimsBaseModel
+
+logger = logging.getLogger()
+
+
+class SlimsUnit(SlimsBaseModel):
+    """Model for unit information in SLIMS"""
+
+    name: str = Field(..., alias="unit_name")
+    abbreviation: Optional[str] = Field("", alias="unit_abbreviation")
+    pk: int = Field(..., alias="unit_pk")
+
+    _slims_table: str = "Unit"

src/aind_slims_api/user.py

@@ -5,7 +5,7 @@
 
 from pydantic import Field, ValidationError
 
-from .core import SlimsBaseModel, SlimsClient
+from aind_slims_api.core import SlimsBaseModel, SlimsClient
 
 logger = logging.getLogger()
 
@@ -27,7 +27,7 @@ class SlimsUser(SlimsBaseModel):
 def fetch_user(
     client: SlimsClient,
     username: str,
-) -> SlimsUser:
+) -> SlimsUser | dict | None:
     """Fetches user information for a user with username {username}"""
     users = client.fetch(
         "User",
@@ -39,16 +39,17 @@ 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 {username}, "
+                f"using pk={user_details.pk()}"
             )
     else:
         logger.warning("Warning, User not in SLIMS")
         return
 
     try:
-        mouse = SlimsUser.model_validate(user_details)
+        user = SlimsUser.model_validate(user_details)
     except ValidationError as e:
         logger.error(f"SLIMS data validation failed, {repr(e)}")
-        return
+        return user_details.json_entity
 
-    return mouse
+    return user