From 2ecde3ecf2bda9b3cb754dd141c9188422278722 Mon Sep 17 00:00:00 2001
From: Maged Elaasar <melaasar@gmail.com>
Date: Tue, 28 May 2024 22:46:08 -0700
Subject: [PATCH] Fixing owl-query error message and fixing owl doc bug

---
 .../java/io/opencaesar/owl/doc/OwlDocApp.java |  4 +--
 .../io/opencaesar/owl/query/OwlQueryTask.java | 32 +++++++++----------
 .../io/opencaesar/owl/query/OwlQueryApp.java  |  2 +-
 3 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/owl-doc/src/main/java/io/opencaesar/owl/doc/OwlDocApp.java b/owl-doc/src/main/java/io/opencaesar/owl/doc/OwlDocApp.java
index 0def690..cd984dc 100755
--- a/owl-doc/src/main/java/io/opencaesar/owl/doc/OwlDocApp.java
+++ b/owl-doc/src/main/java/io/opencaesar/owl/doc/OwlDocApp.java
@@ -580,7 +580,7 @@ private Map<File, String> generateClassesFile(OwlModel owlModel) throws IOExcept
 
 			var image = getClassImage(path1, s);
 			var axioms = getAxioms(path1, s.listProperties());
-			var superClasses = getNodes(path1, "directSuperClassOf", IMG_CLASS, s.listSubClasses(true).toList());
+			var superClasses = getNodes(path1, "directSuperClassOf", IMG_CLASS, s.listSubClasses(true).filterDrop(i -> i.isAnon()).toList());
 			var properties = getNodes("directDomainOf", owlModel.ontModel.listSubjectsWithProperty(RDFS.domain, s).toList(), IMG_PROPERTY, i -> asString(path1, i)+" → "+asString(path1, owlModel.ontModel.getOntProperty(i.asResource().getURI()).listRange().toList()));
 			var restrictedProperties = getNodes("directHasRestrictionOn", s.listSuperClasses(true).filterKeep(i -> i.isRestriction()).mapWith(i -> i.asRestriction()).toList(), IMG_PROPERTY, restrictionFunc);
 			final var content = new StringBuffer(String.format(
@@ -671,7 +671,7 @@ private Map<File, String> generateClassHierarchyFile(OwlModel owlModel) throws I
 				getRelativePath(path, path1), 
 				aClass.getLocalName()));
 
-            List<OntClass> subClasses = aClass.listSubClasses(true).toList();
+            List<OntClass> subClasses = aClass.listSubClasses(true).filterDrop(i -> i.isAnon()).toList();
 
             for (OntClass subClass : subClasses) {
                 levels.put(subClass, indentLevel+1);
diff --git a/owl-query-gradle/src/main/java/io/opencaesar/owl/query/OwlQueryTask.java b/owl-query-gradle/src/main/java/io/opencaesar/owl/query/OwlQueryTask.java
index db7ece1..20fb64d 100644
--- a/owl-query-gradle/src/main/java/io/opencaesar/owl/query/OwlQueryTask.java
+++ b/owl-query-gradle/src/main/java/io/opencaesar/owl/query/OwlQueryTask.java
@@ -39,16 +39,16 @@ public OwlQueryTask() {
 	@Input
 	public abstract Property<String> getEndpointURL();
 
-    /**
-     * The short name of the query service (optional, default is 'sparql').
-     *
-     * @return String Property
-     */
-    @Optional
-    @Input
-    public abstract Property<String> getQueryService();
+	/**
+	 * The short name of the query service (optional, default is 'sparql').
+	 *
+	 * @return String Property
+	 */
+	@Optional
+	@Input
+	public abstract Property<String> getQueryService();
 
-    /**
+	/**
 	 * The required gradle task input query path where to search for *.sparql files.
 	 * 
 	 * @return File Property
@@ -142,17 +142,17 @@ private File replacePathAndExtension(File file, File newPath, String newExt) {
 	/**
 	 * The gradle task action logic.
 	 */
-    @TaskAction
-    public void run() {
+	@TaskAction
+	public void run() {
 		final ArrayList<String> args = new ArrayList<>();
 		if (getEndpointURL().isPresent()) {
 			args.add("-e");
 			args.add(getEndpointURL().get());
 		}
-        if (getQueryService().isPresent()) {
-            args.add("-qs");
-            args.add(getQueryService().get());
-        }
+		if (getQueryService().isPresent()) {
+			args.add("-qs");
+			args.add(getQueryService().get());
+		}
 		if (getQueryPath().isPresent()) {
 			args.add("-q");
 			args.add(getQueryPath().get().getAbsolutePath());
@@ -173,5 +173,5 @@ public void run() {
 		} catch (Exception e) {
 			throw new GradleException(e.getLocalizedMessage(), e);
 		}
-    }
+	}
 }
diff --git a/owl-query/src/main/java/io/opencaesar/owl/query/OwlQueryApp.java b/owl-query/src/main/java/io/opencaesar/owl/query/OwlQueryApp.java
index 7b63511..fa027bb 100644
--- a/owl-query/src/main/java/io/opencaesar/owl/query/OwlQueryApp.java
+++ b/owl-query/src/main/java/io/opencaesar/owl/query/OwlQueryApp.java
@@ -335,7 +335,7 @@ private HashMap<String, Query> collectQueries(final File directory) throws Query
 						try {
 							queries.put(getFileName(file), QueryFactory.read(file.toURI().getPath()));
 						} catch (QueryException e) {
-							throw new QueryException("File: " + file.getName() + " . Error with parsing this file's query: ", e);
+							throw new QueryException("In file '" + file.getName() + "': " + e.getMessage());
 						}
 					}
 				} else if (file.isDirectory()) {