Merge pull request #6 from NIEHS/develop

Set up main with basic actions, skeleton

.github/workflows/lint-and-test.yml

@@ -0,0 +1,43 @@
+---
+name: CI/CD
+on:
+  push:
+    branches:
+    - main
+    - develop
+    - feature/**
+  pull_request:
+    branches:
+    - main
+    - develop
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: psf/black@stable
+        with:
+          options: "--check --verbose"
+          src: "./accelerator_core"
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ "3.10" ]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      - name: Test with pytest
+        run: |
+          coverage run -m pytest  -v -s
+      - name: Generate Coverage Report
+        run: |
+          coverage report -m

.gitignore

@@ -169,3 +169,6 @@ cython_debug/
 
 # PyPI configuration file
 .pypirc
+
+.idea
+.DS_Store

.pre-commit-config.yaml

@@ -0,0 +1,15 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 25.1.0
+    hooks:
+    -  id: black
+       language_version: python3.11

README.md

@@ -3,13 +3,27 @@ Core libraries and classes for accelerator metadata backbone
 
 ## Description
 
-This project is the base python package and libraries for the core of the Accellerator Project
+This project is the base python package and libraries for the core of the Accelerator Project
 
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![CI/CD](https://github.com/NIEHS/accelerator-core/actions/workflows/lint-and-test.yml/badge.svg)](https://github.com/NIEHS/accelerator-core/actions/workflows/lint-and-test.yml)
 
 ![System Whiteboard](https://github.com/user-attachments/assets/2a2b07fa-bbed-454c-9050-73eccb7cbf6c)
 
 The project implements all of the core components (accession, dissemination) and provides abstract superclasses and supporting code for all of the source and dissemination components. Addtional tools for test development, etc can be placed here but should be incorporated into specific projects as a python import
 
 Each source and disseination target should be developed in a separate accelerator-source-xxx or accelerator-dissemination-xxx repository
 
-
+
+## Developer Notes
+
+This project uses pre-commit hooks to validate code, run tests, and accomplish other tasks.
+
+Loading the requirements.txt into your dev environment will install pre-commit, then you can set up the pre-commit
+hooks by running:
+
+```
+pre-commit install
+```
+
+This should be the first thing you do when cloning this project. More docs on pre-commit are available [here](https://pre-commit.com/)

accelerator_core/accession.py

@@ -0,0 +1,29 @@
+from accelerator_core.crosswalk import Crosswalk
+
+
+class Accession:
+    """Handles validation and CRUD operations for metadata records."""
+
+    def __init__(self, data: dict):
+        """Initialize Accession with validated data."""
+        self.data = data
+
+    def validate(self) -> bool:
+        """Validate JSON output from Crosswalk."""
+        pass
+
+    def create(self) -> str:
+        """Create a new record in the database."""
+        pass
+
+    def read(self, record_id: str) -> dict:
+        """Retrieve a record from the database."""
+        pass
+
+    def update(self, record_id: str, new_data: dict) -> bool:
+        """Update an existing record."""
+        pass
+
+    def delete(self, record_id: str) -> bool:
+        """Delete a record from the database."""
+        pass

accelerator_core/crosswalk.py

@@ -0,0 +1,10 @@
+from abc import ABC, abstractmethod
+
+
+class Crosswalk(ABC):
+    """Abstract superclass for mapping raw data to a structured JSON format."""
+
+    @abstractmethod
+    def transform(self, raw_data: dict) -> dict:
+        """Convert raw data into a standardized format."""
+        pass

accelerator_core/dissemination.py

@@ -0,0 +1,18 @@
+class Dissemination:
+    """Retrieves data from the database and transforms it into a JSON document for endpoint systems."""
+
+    def __init__(self, record_id: str):
+        """Initialize Dissemination with a record ID."""
+        self.record_id = record_id
+
+    def fetch_data(self) -> dict:
+        """Retrieve data from the database."""
+        pass
+
+    def format_for_endpoint(self, system: str) -> dict:
+        """Convert data into a format required by a specific endpoint (CHORDS, Navigator, CEDAR)."""
+        pass
+
+    def export(self, system: str) -> bool:
+        """Send the formatted data to the respective system."""
+        pass

accelerator_core/schema/README.md

@@ -0,0 +1,12 @@
+# Accelerator Data Model
+## Version: 0.0.1-alpha
+
+## Description
+
+This accel.json file, and the accompanying JSON schema, represent the core data model for Accelerator.
+
+
+## Development process
+
+The initial accel.json file is derived from the Excel model of the 1.5 CHORDS model
+found here: https://nih.sharepoint.com/:f:/r/sites/NIH-DataAcceleratorProgram/Shared%20Documents/General/Design/term%20mappings?csf=1&web=1&e=1JTZT1