Feat 2 slims ephys (#3)

* wip

* models for SLIMS tables

* wip restart

* unit tests (wip)

* unit tests

* renames workflows dir

* moves workflows dir into .github

* code cleanup (wip)

* adds missing docstrings

* models cleanup

* moves alias, fixes

* flake8 linter

* fixing tests (wip)

* finish up tests, flake8

* add missing docstrings

* test fix

* cleanup

* updates service readme

* reverts models

* staticmethods

* adds missing changes from last commit

* table handler class methods

* AwareDatetime

Author: mekhlakapoor

workflow_templates/tag_and_publish.yml .github/workflows/tag_and_publish.ymlworkflow_templates/tag_and_publish.yml renamed to .github/workflows/tag_and_publish.yml

@@ -1,21 +1,17 @@
-# aind-service-template
-A template repo that can be used for rapid development of FastAPI services.
+# aind-slims-service
+REST service to connect to SLIMS and return information.
 
 ## Usage
 
-### Initialize a repo
+### Create the server.
 
-- Click the green "Use This Template" button
-- Once the repo is created, please wait several seconds for the github action to initialize the files. You can check the status in the "Actions" tab.
-- Update the main README and *-server/README files if desired
-- It's recommended to update the repo settings to require Pull Requests and Reviews.
+- The server code is developed in the aind-slims-service-server package.
+- On a push to main, a docker image will be built and published to GitHub's container registry.
+- You can then run the server in a docker container or k8s pod.
+- More details can be found in the [service README](aind-slims-service-server/README.md) file
 
-### Auto-run tests, publish docker image, and create client code
+### Auto-generated client code.
 
-- In the repo settings, add `svc-aindscicomp` as an admin to the list of Collaborators.
-- Move the yaml files from `workflow_templates` to `.github/workflows/`
-- When a PR is opened, the server code will be tested.
-- When a PR is merged into main:
-  - The tag will be incremented
-  - The server code will be published as a docker image
-  - The client code will be autogenerated from the openapi specification and published to PyPI
+- The client code is autogenerated using an openapi generator.
+- On a push to main, a python library will be built and published to PyPI.
+- The client can then be pip installed as `pip install aind-slims-service-client`

workflow_templates/test_server.yml .github/workflows/test_server.ymlworkflow_templates/test_server.yml renamed to .github/workflows/test_server.yml

@@ -1,4 +1,4 @@
-# aind-service-template-server
+# aind-slims-service-server
 
 [![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
 ![Code Style](https://img.shields.io/badge/code%20style-black-black)
@@ -7,5 +7,74 @@
 ![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen?logo=codecov)
 ![Python](https://img.shields.io/badge/python->=3.10-blue?logo=python)
 
-REST service to retrieve data from an backend.
+REST service to retrieve data from SLIMS.
+
+## Local Development
+
+Requires docker to build and run package locally.
+
+- Create a file called env/webapp.env with appropriate env variables.
+- Run `docker build -t aind-slims-service-server-local:latest .`
+- Run `docker run -p 58350:58350 -p 5000:80 --env-file=env/webapp.env aind-slims-service-server-local:latest`
+- Service will be available at `http://localhost:5000`
+- Check docs at `http://localhost:5000/docs`
+
+### Linters and testing
+
+There are several libraries used to run linters, check documentation, and run
+ tests.
+
+- Please test your changes using the **coverage** library, which will run the
+ tests and log a coverage report:
+
+```
+coverage run -m pytest && coverage report
+```
+
+- Use **interrogate** to check that modules, methods, etc. have been documented
+ thoroughly:
+
+```
+interrogate .
+```
+
+- Use **flake8** to check that code is up to standards
+ (no unused imports, etc.):
+```
+flake8 .
+```
+
+- Use **black** to automatically format the code into PEP standards:
+```
+black .
+```
+
+- Use **isort** to automatically sort import statements:
+```
+isort .
+```
+
+### Pull requests
+
+For internal members, please create a branch. For external members, please fork
+ the repo and open a pull request from the fork. We'll primarily use
+ [Angular](https://github.com/angular/angular/blob/main/CONTRIBUTING.md#commit)
+  style for commit messages. Roughly, they should follow the pattern:
+```
+<type>(<scope>): <short summary>
+```
+
+where scope (optional) describes the packages affected by the code changes and
+type (mandatory) is one of:
+
+- **build**: Changes that affect the build system or external dependencies
+ (example scopes: pyproject.toml, setup.py)
+- **ci**: Changes to our CI configuration files and scripts
+ (examples: .github/workflows/ci.yml)
+- **docs**: Documentation only changes
+- **feat**: A new feature
+- **fix**: A bug fix
+- **perf**: A code change that improves performance
+- **refactor**: A code change that neither fixes a bug nor adds a feature
+- **test**: Adding missing tests or correcting existing tests
 

README.md

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "aind-slims-service-server"
-description = "Package to serve data from backend."
+description = "Package to serve data from SLIMS."
 license = {text = "MIT"}
 requires-python = ">=3.10"
 authors = [
@@ -17,10 +17,12 @@ readme = "README.md"
 dynamic = ["version"]
 
 dependencies = [
-    'requests-toolbelt',  # Used for example. Remove if not needed.
     'pydantic>=2.0',
     'pydantic-settings>=2.0',
     'fastapi[standard]>=0.114.0',
+    'slims-python-api',
+    'networkx',
+    'aind-settings-utils>=0.0.3',
 ]
 
 [project.optional-dependencies]
@@ -90,5 +92,8 @@ fail-under = 100
 asyncio_mode="auto"
 asyncio_default_fixture_loop_scope="function"
 env = [
-    "MYENV_HOST=example"
+    "SLIMS_USERNAME=slims_user",
+    "SLIMS_PASSWORD=slims_password",
+    "SLIMS_HOST=slims_host",
+    "SLIMS_DB=slims_db"
 ]

aind-slims-service-server/README.md

@@ -1,18 +1,20 @@
-"""Module for settings to connect to backend"""
+"""Module for settings to connect to SLIMS backend"""
 
-from pydantic import Field
-from pydantic_settings import BaseSettings, SettingsConfigDict
+from aind_settings_utils.aws import (
+    ParameterStoreAppBaseSettings,
+)
+from pydantic import Field, SecretStr
+from pydantic_settings import SettingsConfigDict
 
 
-class Settings(BaseSettings):
-    """
-    ### Settings needed to connect to a database or website.
-    We will just connect to an example website.
-    """
+class Settings(ParameterStoreAppBaseSettings):
+    """Settings for connecting to SLIMS Database."""
 
-    model_config = SettingsConfigDict(env_prefix="MYENV_")
-    host: str = Field(
-        ...,
-        title="Host",
-        description="Host address of example.com",
+    username: str = Field(..., description="User name")
+    password: SecretStr = Field(..., description="Password")
+    host: str = Field(..., description="host")
+    db: str = Field(default="slims", description="Database")
+    model_config = SettingsConfigDict(
+        env_prefix="SLIMS_",
+        case_sensitive=False,
     )

aind-slims-service-server/pyproject.toml

@@ -0,0 +1 @@
+"""Handlers for the AIND SLIMS Service Server."""