Merge pull request #23 from sdsc-ordes/main

Pull main into develop

Author: rmfranken

.github/workflows/build.yml

@@ -7,16 +7,25 @@ on:
         required: false
         type: boolean
         default: false
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+    branches:
+      - main
 
-jobs:
 
+jobs:
   build:
     runs-on: ubuntu-latest
 
     steps:
-
       - uses: actions/checkout@v4
-
+        with:
+          ref: main
+          fetch-depth: 0
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
@@ -27,14 +36,28 @@ jobs:
           python -m pip install --upgrade pip
           pip install -r tools/python/requirements.txt
 
-      - name: build
+      - name: Build combined ontology and schemas
         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: upload assets in artifacts
-        uses: actions/upload-artifact@v4
-        if: ${{ inputs.is_release }}
-        with:
-          name: schema-bundle
-          path: build/*
+      - name: Commit and push built files back to repo
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+
+          git add build/
+
+          if ! git diff --cached --quiet; then
+            git commit -m "Update generated build files"
+
+            # Fetch latest main and rebase
+            git fetch origin main
+            git rebase origin/main
+
+            git push origin main
+          else
+            echo "No changes in build folder, nothing to commit."
+          fi

.github/workflows/docs.yml

@@ -1,25 +1,78 @@
-# name: Build ontology docs
+name: SHACL Documentation Generation
 
-# on:
-#   workflow_call:
+on:
+  push:
+    paths:
+      - 'src/imaging-ontology/**'
+  pull_request:
+    paths:
+      - 'src/imaging-ontology/**'
 
-# jobs:
+jobs:
+  generate-docs:
+    runs-on: ubuntu-latest
 
-#   build:
-#     runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
 
-#     steps:
+      - name: Set up Python and install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install rdflib
 
-#       - uses: actions/checkout@v4
+      - name: Enrich ontology with rdflib
+        id: enrich
+        run: |
+          python tools/python/docs/sparql.py
+          echo "enriched_file=/tmp/enriched.ttl" >> $GITHUB_ENV
+          
 
-#       - name: Set up Python
-#         uses: actions/setup-python@v5
-#         with:
-#           python-version: '3.12'
+      - name: Set up Java 11
+        uses: actions/setup-java@v4
+        with:
+          distribution: 'temurin'
+          java-version: '11'
 
-#       - name: Install dependencies
-#         run: |
-#           python -m pip install --upgrade pip
-#           pip install 
+      - name: Install Graphviz
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y graphviz
 
-# TODO: BUILD DOCUMENTATION USING RESPECTER
+      - name: Set DOT_PATH environment variable
+        run: echo "GRAPHVIZ_DOT=/usr/bin/dot" >> $GITHUB_ENV
+
+      - name: Download SHACL Play CLI
+        run: |
+          wget https://github.com/sparna-git/shacl-play/releases/download/0.10.2/shacl-play-app-0.10.2-onejar.jar -O shacl-play-cli.jar
+
+      - name: Generate Documentation
+        run: |
+          java -jar shacl-play-cli.jar \
+            doc \
+            -d \
+            -i ${{ env.enriched_file }} \
+            -l en \
+            -o docs/index.html
+
+      - name: Generate Ontology Diagram
+        run: |
+          java -jar shacl-play-cli.jar \
+            draw \
+            -i ${{ env.enriched_file }} \
+            -o docs/ontology.svg 
+
+      - name: Commit generated docs
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git add docs/index.html
+          git add docs/ontology.svg
+          git commit -m "Update generated docs" || echo "Nothing to commit"
+          git push
+
+      - name: Upload generated documentation as an artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: shacl-documentation
+          path: docs/index.html

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

@@ -4,9 +4,6 @@ on:
   push:
     branches:
       - main
-
-  workflow_call:
-
   pull_request:
     branches:
       - main
@@ -17,6 +14,3 @@ jobs:
 
   build:
     uses: ./.github/workflows/build.yml
-    with:
-      is_release: false
-

.github/workflows/release.yml

@@ -1,4 +1,4 @@
-name: Include ontology assets in the release
+name: Release workflow
 
 on:
   push:
@@ -8,30 +8,9 @@ on:
 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 -r tools/python/requirements.txt
-
-      - name: Build ontology assets
-        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: Upload schema bundle
-        uses: actions/upload-artifact@v4
-        with:
-          name: schema-bundle
-          path: build/*
+    uses: ./.github/workflows/build.yml
+    with:
+      is_release: true  # optional, now unused
 
   checks:
     uses: ./.github/workflows/checks.yml
@@ -44,13 +23,13 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Get schema assets
-        uses: actions/download-artifact@v4.1.8
+      - name: Download built assets
+        uses: actions/download-artifact@v4
         with:
           name: schema-bundle
           path: build/
 
-      - name: Create release
+      - name: Create GitHub release
         uses: softprops/action-gh-release@v2
         with:
           files: build/*

build/locales/en/schema.json

@@ -21,6 +21,7 @@
     "ExecutableNotebook_label": "Executable Notebook",
     "FeatureEnum_label": "Feature Enumeration",
     "HostTypeEnumeration_label": "Host Type Enumeration",
+    "ImageObject_label": "Image object",
     "ImageObjectTagEnum_label": "Image Object Tag Enumeration",
     "ImagingModalityEnum_label": "Imaging Modality Enumeration",
     "IsPluginModuleOfEnum_label": "Plugin Module Enumeration",
@@ -32,7 +33,6 @@
     "DatasetSpecification_label": "Dataset Specification",
     "FundingInformation_label": "Funding Information",
     "SoftwareImage_label": "Software Image",
-    "contentURL_label": "Content URL",
     "distribution_label": "Distribution",
     "AMD64_label": "AMD64",
     "ARM64_label": "ARM64",
@@ -162,6 +162,7 @@
     "author_label": "Author",
     "codeRepository_label": "Code repository",
     "conditionsOfAccess_label": "Conditions of access",
+    "contentUrl_label": "Content URL",
     "defaultValue_label": "Default value",
     "encodingFormat_label": "Encoding format",
     "familyName_label": "Family name",
@@ -243,6 +244,7 @@
     "ExecutableNotebook_placeholder": "An object representing an executable notebook such as Jupyter Notebook",
     "FeatureEnum_placeholder": "Enumeration class for software features",
     "HostTypeEnumeration_placeholder": "Enumeration class for host type",
+    "ImageObject_placeholder": "An image of the software, typically a screenshot, before/after or a logo.",
     "ImageObjectTagEnum_placeholder": "Enumeration class for image object tag",
     "ImagingModalityEnum_placeholder": "Enumeration class for imaging modality",
     "IsPluginModuleOfEnum_placeholder": "Enumeration class for plugin module",
@@ -254,7 +256,6 @@
     "DatasetSpecification_placeholder": "Class designed to describe a type of input or output used or produced by a model. For example, Topoflow has several inputs. One of them is a text file with precipitation values. The representation of this input is an instance of a dataset specification.",
     "FundingInformation_placeholder": "A class to represent the funding information of a software project",
     "SoftwareImage_placeholder": "An image that virtualizes the functionality of a given software. For example, a Docker container.",
-    "contentURL_placeholder": "Actual bytes of the media object, for example the image file or video file.",
     "distribution_placeholder": "A downloadable form of this dataset, at a specific location, in a specific format.",
     "hasInput_placeholder": "Property that links a model configuration to the input types expected by it.",
     "hasOutput_placeholder": "Property that expresses what the outputs of a model are",
@@ -263,6 +264,7 @@
     "author_placeholder": "The author of the software, this can be organizations or people that are maintainers and/or producers of the software.",
     "codeRepository_placeholder": "Primary link to the repository where the un-compiled, human readable code and related code is located (GitLab, GitHub, CodePlex etc.).",
     "conditionsOfAccess_placeholder": "Conditions that affect the availability of, or method(s) of access to, an item. e.g. log-in required ",
+    "contentUrl_placeholder": "Actual bytes of the media object, for example the image file or video file.",
     "defaultValue_placeholder": "The default value of the input. For properties that expect a literal, the default is a literal value, for properties that expect an object, it's an ID reference to one of the current values.",
     "encodingFormat_placeholder": "Expressed using a MIME format (http://www.iana.org/assignments/media-types/media-types.xhtml).",
     "familyName_placeholder": "Family name. In the U.S., the last name of a Person.",