Merge pull request #12 from sdsc-ordes/refactor/template

refactor: template-compliant file hierarchy

Author: rmfranken

.github/workflows/build.yml

@@ -1,12 +1,12 @@
 name: Build ontology assets
 
 on:
-  workflow_dispatch:
-  # workflow_call:
-  #   inputs:
-  #     is_release:
-  #       required: true
-  #       type: boolean
+  workflow_call:
+    inputs:
+      is_release:
+        required: false
+        type: boolean
+        default: false
 
 jobs:
 
@@ -29,8 +29,8 @@ jobs:
 
       - name: build
         run: |
-          bash tools/bash/build/create-combined-turtle.sh
-          python tools/python/build/create-schemas.py src/imaging-ontology/ build/
+          bash ./tools/bash/build/create-combined-turtle.sh src/imaging-ontology/
+          python ./tools/python/build/create-schemas.py --input build/ontology_combined.ttl --output build/locales/en/schema.json
 
       - name: upload assets in artifacts
         uses: actions/upload-artifact@v4

.github/workflows/checks.yml

@@ -0,0 +1,35 @@
+name: SHACL validation
+
+on:
+  workflow_call:
+  pull_request:
+    paths:
+      - 'src/imaging-ontology/**'
+
+jobs:
+  validate:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r tools/python/requirements.txt
+
+      - name: Build ontology bundle
+        run: |
+          bash ./tools/bash/build/create-combined-turtle.sh src/imaging-ontology/
+          python ./tools/python/build/create-schemas.py --input build/ontology_combined.ttl --output build/locales/en/schema.json
+
+      - name: SHACL validation
+        run: |
+          python tools/python/checks/shacl.py build/ontology_combined.ttl src/quality-checks/shacl-shacl.ttl
+

.github/workflows/createCombinedTurtle.yml

@@ -0,0 +1,25 @@
+# name: Build ontology docs
+
+# on:
+#   workflow_call:
+
+# jobs:
+
+#   build:
+#     runs-on: ubuntu-latest
+
+#     steps:
+
+#       - uses: actions/checkout@v4
+
+#       - name: Set up Python
+#         uses: actions/setup-python@v5
+#         with:
+#           python-version: '3.12'
+
+#       - name: Install dependencies
+#         run: |
+#           python -m pip install --upgrade pip
+#           pip install 
+
+# TODO: BUILD DOCUMENTATION USING RESPECTER

.github/workflows/createSchemas.yml

@@ -0,0 +1,22 @@
+name: Main and PR pipeline
+
+on:
+  push:
+    branches:
+      - main
+
+  workflow_call:
+
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  checks:
+    uses: ./.github/workflows/checks.yml
+
+  build:
+    uses: ./.github/workflows/build.yml
+    with:
+      is_release: false
+

.github/workflows/docs.yml

@@ -0,0 +1,38 @@
+name: Include ontology assets in the release
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+
+  build:
+    uses: ./.github/workflows/build.yml
+    with:
+      is_release: true
+
+  checks:
+    uses: ./.github/workflows/checks.yml
+    with:
+      is_release: true
+    needs: build 
+
+  make_release:
+    runs-on: ubuntu-latest
+    needs:
+      - checks
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: get schema assets
+        uses: actions/download-artifact@v4.1.8
+        with:
+          name: schema-bundle
+          path: build/
+
+      - name: create release
+        uses: softprops/action-gh-release@v2
+        with:
+          files: build/*

.github/workflows/main-and-pr.yml

@@ -1 +1,3 @@
 .env
+./build/*
+bin/act

.github/workflows/release.yml

@@ -0,0 +1,9 @@
+v0.1: Initial release, ex: prefixes updated, sh:nodekind sh:IRI replaced with a regex.
+v0.2: Changed shapes, ontology definitions, fairlevel validator.
+v0.3: Changed fair calculation.
+v0.4: Fixed loose nodes for PySHACL.
+v0.5: Updated definitions, cardinality of several shapes.
+v0.6: Added ontology metadata.
+v0.7: Internalize & objectify hasExecutableNotebook, update prefixes from ex: to imag:
+v0.8: Update FAIR levels, contributors+producers become authors. First+Last name becomes schema:name.
+v0.9: Support for runnable examples, dicom dataset properties, spelling mistakes.