Added basic shape expression testing

.github/workflows/GroovyScriptTest.yml

@@ -0,0 +1,21 @@
+name: Update the Open SbD4Nano Cache
+
+on:
+  workflow_dispatch:
+  push:
+
+jobs:
+  fetch-data:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: true
+          fetch-depth: 0
+
+      - name: Install groovy
+        run: sudo apt install groovy
+
+      - name: Generate the Shex validation reports
+        run: |
+          groovy validate.groovy

shapes/InteractionData.shex

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+BASE <http://bigcat-um.github.io/KinRDF/shapes#>
+PREFIX : <http://bigcat-um.github.io/KinRDF/shapes#>
+
+PREFIX dc:    <http://purl.org/dc/elements/1.1/>
+PREFIX dct:   <http://purl.org/dc/terms/>
+PREFIX foaf:  <http://xmlns.com/foaf/0.1/>
+PREFIX rdfs:  <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX sbd:   <https://www.sbd4nano.eu/rdf/#>
+PREFIX xsd:   <http://www.w3.org/2001/XMLSchema#>
+PREFIX wp:    <http://vocabularies.wikipathways.org/wp#>
+
+:InteractionData {
+  a [ wp:InteractionData ]
+}

validate.groovy

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+// MIT, Copyright (c) Egon Willighagen
+@Grab(group='io.github.egonw.bacting', module='managers-rdf', version='0.3.6')
+
+import org.apache.jena.shex.ShexStatus
+
+workspaceRoot = "."
+rdf = new net.bioclipse.managers.RDFManager(workspaceRoot);
+
+file = "/Output/RDF_Kin_Data_2022-Dec.ttl"
+clazz = "InteractionData"
+
+store = rdf.createInMemoryStore(true);
+store = rdf.importFile(store, "${file}", "TURTLE")
+report = rdf.validateAllOfType(
+  store,
+  "/shapes/${clazz}.shex",
+  "http://bigcat-um.github.io/KinRDF/shapes#${clazz}",
+  "http://vocabularies.wikipathways.org/wp#${clazz}"
+)
+
+println "{"
+println "  \"target\": \"${clazz}\","
+println "  \"conformant\": ["
+report.forEachReport { reportEntry ->
+  status = reportEntry.status
+  reason = reportEntry.reason
+  focusNode = reportEntry.focus
+
+  switch (status) {
+    case ShexStatus.conformant :
+      println "    {\n      \"class\":  \"${focusNode}\",\n      \"status\": \"${status}\"\n    },"
+  }
+}
+println "    {}"
+println "  ],"
+nonconformantCounter = 0
+println "  \"nonconformant\": ["
+report.forEachReport { reportEntry ->
+  status = reportEntry.status
+  reason = reportEntry.reason
+  focusNode = reportEntry.focus
+
+  switch (status) {
+    case ShexStatus.nonconformant :
+      nonconformantCounter = nonconformantCounter + 1
+      println "    {\n      \"class\":  \"${focusNode}\",\n      \"status\": \"${status}\",\n      \"reason\": \"${reason}\"\n    },"
+  }
+}
+println "    {}"
+println "  ]"
+println "}"
+
+if (nonconformantCounter > 0) System.exit(1)