Add chebi smiles property to rdfa generation, cache groovy deps

.github/workflows/extract.yml

@@ -19,8 +19,21 @@ jobs:
         with:
           java-version: 17
           distribution: 'temurin'
+      - name: Cache Groovy/Maven dependencies
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.groovy/grapes
+            ~/.groovy/grapeCache
+            ~/.ivy2/cache
+            ~/.m2/repository
+          key: ${{ runner.os }}-grapes-${{ hashFiles('extractOWL.groovy') }}
+          restore-keys: |
+            ${{ runner.os }}-grapes-
       - name: Install dependencies
-        run: sudo apt install groovy
+        run: sudo apt-get update && sudo apt-get install -y groovy pandoc
+      - name: Generate temporary HTML from index.md
+        run: pandoc index.md -s -o index.html
       - name: Extract OWL
         run: groovy extractOWL.groovy | tee glossary.owl
       - name: Commit OWL file

extractOWL.groovy

@@ -6,6 +6,7 @@
 
 import org.apache.any23.Any23
 import org.apache.any23.source.HTTPDocumentSource
+import org.apache.any23.source.FileDocumentSource
 import org.apache.any23.writer.NTriplesWriter
 
 workspaceRoot = "../ws"
@@ -16,7 +17,15 @@ url = "https://vhp4safety.github.io/glossary/"
 Any23 runner = new Any23();
 runner.setHTTPUserAgent("test-user-agent");
 httpClient = runner.getHTTPClient()
-source = new HTTPDocumentSource(runner.getHTTPClient(), url)
+// prefer a local file if provided as an argument or if index.html exists
+source = null
+if (this.args?.length && new File(this.args[0]).exists()) {
+    source = new FileDocumentSource(new File(this.args[0]))
+} else if (new File('index.html').exists()) {
+    source = new FileDocumentSource(new File('index.html'))
+} else {
+    source = new HTTPDocumentSource(runner.getHTTPClient(), url)
+}
 
 out = new ByteArrayOutputStream();
 handler = new NTriplesWriter(out);
@@ -33,6 +42,7 @@ rdf.addPrefix(kb, "skos", "http://www.w3.org/2004/02/skos/core#")
 rdf.addPrefix(kb, "dc", "http://purl.org/dc/elements/1.1/")
 rdf.addPrefix(kb, "dct", "http://purl.org/dc/terms/")
 rdf.addPrefix(kb, "ncit", "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#")
+rdf.addPrefix(kb, "chebi", "http://purl.obolibrary.org/obo/chebi/")
 rdf.addPrefix(kb, "og", "http://ogp.me/ns#")
 rdf.importFromStream(kb, n3Stream, "N3")