Merge pull request #26 from mrnolte/playground

Playground

.github/workflows/documentation.yml

@@ -1,13 +1,14 @@
 name: Documentation
 on:
-  push:
-    paths:
-      - 'owl/**'
-      - 'docs/**'
-      - '.github/**'
+  workflow_dispatch:
+  workflow_run:
+    workflows: ["Evaluation"]
+    types: 
+      - completed
 
 jobs:
   vocabulary:
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
     name: SOMA Vocabulary
     runs-on: ubuntu-latest
     defaults:
@@ -36,6 +37,7 @@ jobs:
           path: ./SOMA-vocabulary.pdf
 
   handbook:
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
     name: NEEM Handbook
     runs-on: ubuntu-latest
 

docs/vocab/SOMA-vocabulary.tex

@@ -3,11 +3,11 @@
 \usepackage{pythontex}
 \usepackage{multicol}
 \usepackage{microtype} % Improves spacing
-\usepackage{fancyhdr} 
+\usepackage{fancyhdr}
 \fancyhead[L]{\rightmark}
-\fancyhead[R]{\leftmark} 
+\fancyhead[R]{\leftmark}
 
-\pagestyle{fancy} 
+\pagestyle{fancy}
 \newcommand{\appendixstyle}[2]{\textbf{#1}\markboth{#1}{#1}\ {#2}}
 
 \begin{document}
@@ -18,7 +18,7 @@
 from owl_reader import OWLReader
 
 OWL_FILES=[
-    "https://raw.githubusercontent.com/ease-crc/soma/master/owl/SOMA.owl"
+    "https://ease-crc.github.io/soma/owl/current/SOMA.owl"
 ]
 
 reader = OWLReader(OWL_FILES)

docs/vocab/owl_reader.py

@@ -21,7 +21,7 @@ def __init__(self, iri_list):
 		self.class_objects = []
 
 	def get_classes(self):
-		''' 
+		'''
 		Gets the classes defined in the ontology their corresponding
 		superclass, label and comment
 		'''
@@ -54,6 +54,8 @@ def _create_class_objects(self):
 		return objects
 
 	def set_class_info(self, target_class):
+	    class_obj = getattr(getattr(self.namespace, target_class)
+	    print(f"Class_obj {class_obj}")
 
 		comment = getattr(getattr(self.namespace, target_class), "comment")
 		if(comment):

owl/USD.owl

@@ -10,7 +10,7 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:xformOp="https://ease-crc.org/ont/USD#xformOp:">
     <owl:Ontology rdf:about="https://ease-crc.org/ont/USD.owl">
-        <owl:imports rdf:resource="http://www.ontologydesignpatterns.org/ont/dul/DUL.owl"/>
+        <owl:imports rdf:resource="http://www.ease-crc.org/ont/DUL.owl"/>
         <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The purpose of the USD ontology is to establish a graph model of the USD language, and to support translation from USD to a KG representation of scene graphs. To this end, the core vocabulary of USD is defined in terms of an upper-level ontology. In addition, a set of re-usable built-in schemata that are used in the USD language to describe prims are defined. In order to fasciliate translation, the ontological model attempts to replicate the structure of USD as closely as possible while in addition entailing semantics of USD entities.</rdfs:comment>
         <rdfs:label>USD Ontology</rdfs:label>
         <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0.1</owl:versionInfo>

scripts/java/src/main/java/main/GuardingXmlCatalogIriMapper.java

@@ -0,0 +1,35 @@
+package main;
+
+import org.protege.xmlcatalog.CatalogUtilities;
+import org.protege.xmlcatalog.XMLCatalog;
+import org.protege.xmlcatalog.entry.Entry;
+import org.protege.xmlcatalog.redirect.UriRedirectVisitor;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLOntologyIRIMapper;
+
+import java.io.File;
+import java.io.IOException;
+
+public class GuardingXmlCatalogIriMapper implements OWLOntologyIRIMapper {
+    private final XMLCatalog catalog;
+
+    public GuardingXmlCatalogIriMapper(File f) throws IOException {
+        this(CatalogUtilities.parseDocument(f.toURI().toURL()));
+    }
+
+    public GuardingXmlCatalogIriMapper(XMLCatalog catalog) {
+        this.catalog = catalog;
+    }
+
+    public IRI getDocumentIRI(IRI original) {
+        UriRedirectVisitor visitor = new UriRedirectVisitor(original.toURI());
+
+        for (Entry subEntry : catalog.getEntries()) {
+            subEntry.accept(visitor);
+            if (visitor.getRedirect() != null) {
+                return IRI.create(visitor.getRedirect());
+            }
+        }
+        throw new RuntimeException("You are trying to load an ontology from an online source, but we decided to self-host them, e.g, DUL. The ontology you are trying to load is: " + original);
+    }
+}

scripts/java/src/main/java/main/OntologyManager.java

@@ -44,8 +44,12 @@ public OntologyManager(final OntologyConfig config) throws OWLOntologyCreationEx
 
 	@SuppressWarnings("OverlyBroadThrowsClause")
 	private void loadCatalog(final Path ontologyDirectory) throws IOException {
-		final OWLOntologyIRIMapper xmlCatalogIriMapper = new XMLCatalogIRIMapper(
+		// use this if you want to prohibit ontologies being loaded from online
+		final OWLOntologyIRIMapper xmlCatalogIriMapper = new GuardingXmlCatalogIriMapper(
 				ontologyDirectory.resolve(XML_CATALOG_PATH).toFile());
+		// use this if you want to allow to load ontologies from online
+		// final OWLOntologyIRIMapper xmlCatalogIriMapper = new XMLCatalogIRIMapper(
+		// 		ontologyDirectory.resolve(XML_CATALOG_PATH).toFile());
 		ontologyManager.getIRIMappers().add(xmlCatalogIriMapper);
 	}
 

scripts/java/src/main/java/main/ci_runners/OntologySaver.java

@@ -35,6 +35,7 @@ public void run() throws OWLOntologyStorageException {
 			if (ontologyConfig.format() == null) {
 				ontology.saveOntology();
 			} else {
+				LOGGER.info("Using format {}", ontologyConfig.format());
 				ontology.saveOntology(ontologyConfig.format());
 			}
 		}