Merge pull request #118 from ghga-de/refactor

Merge refactor branch into main

Author: lkuchenb

.devcontainer/Dockerfile

@@ -0,0 +1,18 @@
+FROM mcr.microsoft.com/vscode/devcontainers/python:3.9-bullseye
+
+ENV PYTHONUNBUFFERED 1
+
+# Update args in docker-compose.yaml to set the UID/GID of the "vscode" user.
+ARG USER_UID=1000
+ARG USER_GID=$USER_UID
+RUN if [ "$USER_GID" != "1000" ] || [ "$USER_UID" != "1000" ]; then groupmod --gid $USER_GID vscode && usermod --uid $USER_UID --gid $USER_GID vscode; fi
+
+# [Option] Install Node.js
+ARG INSTALL_NODE="true"
+ARG NODE_VERSION="lts/*"
+RUN if [ "${INSTALL_NODE}" = "true" ]; then su vscode -c "umask 0002 && . /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
+
+# Copy install and launcher script to bin:
+COPY ./dev_install /bin
+
+CMD ["sleep", "infinity"]

.devcontainer/dev_build

@@ -0,0 +1,7 @@
+#!/bin/bash
+# build artifacts from the linkml schema
+
+cd /workspace
+
+make all
+make gen-creation-schema-artifacts stage-derived-schemas

.devcontainer/dev_install

@@ -0,0 +1,9 @@
+#!/bin/bash
+# install service in dev container
+
+cd /workspace
+
+# install in edit mode with testing dependencies
+pip install \
+    -r \
+    requirements.txt

.devcontainer/devcontainer.json

@@ -0,0 +1,81 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.177.0/containers/python-3-postgres
+// Update the VARIANT arg in docker-compose.yml to pick a Python version: 3, 3.8, 3.7, 3.6
+{
+	"name": "ghga-metadata-schema",
+	"dockerComposeFile": "docker-compose.yml",
+	"service": "app",
+	"workspaceFolder": "/workspace",
+	// Set *default* container specific settings.json values on container create.
+	"customizations": {
+		"vscode": {
+			// Set *default* container specific settings.json values on container create.
+			"settings": {
+				"terminal.integrated.profiles.linux": {
+					"bash": {
+						"path": "/bin/bash"
+					}
+				},
+				"python.pythonPath": "/usr/local/bin/python",
+				"python.languageServer": "Pylance",
+				"python.linting.enabled": true,
+				"python.linting.pylintEnabled": true,
+				"python.formatting.autopep8Path": "/usr/local/py-utils/bin/autopep8",
+				"python.formatting.blackPath": "/usr/local/py-utils/bin/black",
+				"python.formatting.yapfPath": "/usr/local/py-utils/bin/yapf",
+				"python.formatting.provider": "black",
+				"python.analysis.typeCheckingMode": "basic",
+				"python.linting.banditPath": "/usr/local/py-utils/bin/bandit",
+				"python.linting.mypyPath": "/usr/local/py-utils/bin/mypy",
+				"python.linting.pycodestylePath": "/usr/local/py-utils/bin/pycodestyle",
+				"python.linting.pydocstylePath": "/usr/local/py-utils/bin/pydocstyle",
+				"python.linting.pylintPath": "/usr/local/py-utils/bin/pylint",
+				"python.testing.pytestPath": "/usr/local/py-utils/bin/pytest",
+				"python.testing.unittestEnabled": false,
+				"python.testing.pytestEnabled": true,
+				"editor.formatOnSave": true,
+				"editor.renderWhitespace": "all",
+				"editor.rulers": [
+					88
+				],
+				"licenser.license": "Custom",
+				"licenser.customHeaderFile": "/workspace/.devcontainer/license_header.txt"
+			},
+			// Add the IDs of extensions you want installed when the container is created.
+			"extensions": [
+				"mikestead.dotenv",
+				"ms-azuretools.vscode-docker",
+				"ms-python.python",
+				"ms-python.isort",
+				"ms-python.vscode-pylance",
+				"ms-toolsai.jupyter",
+				"njpwerner.autodocstring",
+				"redhat.vscode-yaml",
+				"42crunch.vscode-openapi",
+				"arjun.swagger-viewer",
+				"eamodio.gitlens",
+				"github.vscode-pull-request-github",
+				"streetsidesoftware.code-spell-checker",
+				"yzhang.markdown-all-in-one",
+				"visualstudioexptteam.vscodeintellicode",
+				"ymotongpoo.licenser",
+				"editorconfig.editorconfig",
+				"bierner.markdown-mermaid"
+			]
+		}
+	},
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [5000, 5432],
+	// Use 'postCreateCommand' to run commands after the container is created.
+	"postCreateCommand": "dev_install",
+	// Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
+	"remoteUser": "vscode",
+	"features": {
+		"ghcr.io/devcontainers/features/docker-in-docker:2": {
+			"version": "latest",
+			"enableNonRootDocker": "true",
+			"moby": true,
+			"azureDnsAutoDetection": false
+		}
+	}
+}

.devcontainer/docker-compose.yml

@@ -0,0 +1,30 @@
+version: '3'
+
+services:
+  app:
+    build:
+      context: .
+      dockerfile: ./Dockerfile
+      args:
+        # [Choice] Python version: 3, 3.8, 3.7, 3.6
+        VARIANT: 3.9
+        # [Choice] Install Node.js
+        INSTALL_NODE: "true"
+        NODE_VERSION: "lts/*"
+        # Please adapt to package name:
+        PACKAGE_NAME: "my_microservice"
+        # On Linux, you may need to update USER_UID and USER_GID below if not your local UID is not 1000.
+        USER_UID: 1000
+        USER_GID: 1000
+
+    init: true
+    privileged: true
+
+    volumes:
+      - ..:/workspace:cached
+
+    # Overrides default command so things don't shut down after the process ends.
+    command: sleep infinity
+
+    # Uncomment the next line to use a non-root user for all processes.
+    user: vscode

.erdiagrams.yaml

@@ -0,0 +1,42 @@
+# Configuration parameters used by ./scripts/update_entity_relations.py
+- title: Global Overview
+  description: An overview of the entire submission schema.
+  model: submission.yaml
+  tree_root: true
+  include_attributes: false
+- title: Sample, Biospecimen, & Individual
+  description: Focusses on the relation between Sample, Biospecimen, and Individual.
+  model: submission.yaml
+  classes: ["Sample", "Biospecimen", "Individual"]
+  tree_root: false
+  include_attributes: false
+- title: Experiment, Sample, & File
+  description: Focusses on the relation between Experiment, Sample, and File.
+  model: submission.yaml
+  classes: ["SequencingExperiment", "Sample", "File", "SequencingProcess"]
+  tree_root: false
+  include_attributes: false
+- title: Study, Condition, & Sample
+  description: Focusses on the relation between Study, Condition, and Sample.
+  model: submission.yaml
+  classes: ["Study", "Condition", "Sample"]
+  tree_root: false
+  include_attributes: false
+- title: Sample, Biospecimen, & Individual (with attributes)
+  description: Focusses on the details of the relation between Sample, Biospecimen, and Individual.
+  model: submission.yaml
+  classes: ["Sample", "Biospecimen", "Individual"]
+  tree_root: false
+  include_attributes: true
+- title: Experiment, Sample, & File (with attributes)
+  description: Focusses on the relation between Experiment, Sample, and File.
+  model: submission.yaml
+  classes: ["SequencingExperiment", "Sample", "File", "SequencingProcess"]
+  tree_root: false
+  include_attributes: true
+- title: Study, Condition, & Sample (with attributes)
+  description: Focusses on the relation between Study, Condition, and Sample.
+  model: submission.yaml
+  classes: ["Study", "Condition", "Sample"]
+  tree_root: false
+  include_attributes: true

.github/workflows/build-artifacts.yml

@@ -1,49 +1,23 @@
-# This is a basic workflow to help you get started with Actions
-
 name: Build Documentation
 
-# Controls when the workflow will run
-on:
-  workflow_run:
-    workflows: ["Build and update artifacts"]
-    branches: [main]
-    types: 
-      - completed
-  push:
-    branches: [ main ]
-    paths:
-    - docs/*
-
-  # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
-
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+on: push
+ 
 jobs:
-  # This workflow contains a single job called "build"
-  build:
-    # The type of runner that the job will run on
+  build-docs:
+    name: Build documentation
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.9]
-
-    # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: 3.9
 
       - name: Install dependencies
-        run: |
+        run: >-
           pip install -r requirements.txt
-      
-      - name: Build docs and push to gh-pages
-        run: |
-          git pull
-          git config --local user.email "action@github.com"
-          git config --local user.name "GitHub Action"
-          make gh-deploy
+
+      - name: Build docs
+        run: >-
+          ./scripts/generate_linkml_docs.py --check

.github/workflows/build-documentation.yml

@@ -0,0 +1,23 @@
+name: Check entity relationship diagrams
+
+on: push
+
+jobs:
+  check-erdiagrams:
+    name: check entity relationship diagrams
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.9
+
+      - name: Install dependencies
+        run: >-
+          pip install -r requirements.txt
+
+      - name: check entity relationship diagrams
+        run: >-
+          ./scripts/update_entity_relations.py --check