Revert "Merge branch 'main' into main"

This reverts commit 9c53e06, reversing
changes made to a3c38e1.

.fuseki.ttl

@@ -1,46 +1,24 @@
-PREFIX :        <#>
-PREFIX fuseki:  <http://jena.apache.org/fuseki#>
-PREFIX ja:      <http://jena.hpl.hp.com/2005/11/Assembler#>
-PREFIX tdb:     <http://jena.hpl.hp.com/2008/tdb#>
+@prefix fuseki:  <http://jena.apache.org/fuseki#> .
+@prefix rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix tdb:     <http://jena.hpl.hp.com/2008/tdb#> .
+@prefix ja:      <http://jena.hpl.hp.com/2005/11/Assembler#> .
+@prefix :        <#> .
 
-# Service 1: Assertions endpoint
-:service1  a               		  		fuseki:Service ;
-    fuseki:name                   		"tutorial2" ;
-    fuseki:dataset                		:assertions ;
-    fuseki:serviceQuery           		"" , "query", "sparql" ;
-    fuseki:serviceUpdate          		"" , "update" ;
-    fuseki:serviceReadWriteGraphStore 	"data" ;
-	.
+[] rdf:type fuseki:Server .
 
-# Service 2: Inference endpoint
-:service2	  a               		  	fuseki:Service ;
-    fuseki:name                   		"tutorial2-inf" ;
-    fuseki:dataset                		:inferences ;
-    fuseki:serviceQuery           		"" , "query", "sparql" ;
-    fuseki:serviceUpdate          		"" , "update" ;
-    fuseki:serviceReadWriteGraphStore 	"data" ;
-    fuseki:serviceReadGraphStore  		"get" ;
-	.
-
-:inferences a ja:RDFDataset ;
-	ja:defaultGraph :inf_model ;
-	.
+<#service> rdf:type fuseki:Service ;
+    rdfs:label          "Tutorial2" ;												# Human readable label for dataset
+    fuseki:name         "tutorial2" ;												# Name of the dataset in the endpoint url
+    fuseki:serviceReadWriteGraphStore "data" ;											# SPARQL Graph store protocol (read and write)
+    fuseki:endpoint 	[ fuseki:operation fuseki:query ;	fuseki:name "sparql"  ] ;	# SPARQL query service
+    fuseki:endpoint 	[ fuseki:operation fuseki:shacl ;	fuseki:name "shacl" ] ;		# SHACL query service
+    fuseki:dataset      <#dataset> .
 
-:inf_model a ja:InfModel ;
-	ja:baseModel :baseModel ;
-	ja:reasoner [
-		ja:reasonerURL <http://jena.hpl.hp.com/2003/GenericRuleReasoner> ;
-		ja:rulesFrom <build/owl/example.com/tutorial2/vocabulary/bundle.rules> ;
-	] 
-	.
-
-:baseModel a tdb:GraphTDB ;
-	tdb:graphName <urn:x-arq:DefaultGraph> ;
-	tdb:dataset :assertions ;
-	.
-
-:assertions a tdb:DatasetTDB ;
-	# location is relative to the .fuseki folder
-	tdb:location  "assertions" ;
-	tdb:context [ ja:cxtName "arq:queryTimeout" ; ja:cxtValue "1000" ] ;
-	.
+## In memory TDB with union graph.
+<#dataset> rdf:type   tdb:DatasetTDB ;
+  tdb:location "--mem--" ;
+  # Query timeout on this dataset (1s, 1000 milliseconds)
+  ja:context [ ja:cxtName "arq:queryTimeout" ; ja:cxtValue "1000" ] ;
+  # Make the default graph be the union of all named graphs.
+  tdb:unionDefaultGraph true .

.gitpod.yml

@@ -4,17 +4,8 @@
 
 # Learn more from ready-to-use templates: https://www.gitpod.io/docs/introduction/getting-started/quickstart
 
-# Docker image
-image:
-  file: .gitpod.Dockerfile
-
-# Tasks to run 
 tasks:
-  - init: ./gradlew owlLoad
+  - init: sdk install java 17
+  - init: ./gradlew build
+
 
-# VSCode attributes
-vscode:
-    extensions:
-        - https://github.com/microsoft/vscode-gradle/releases/download/3.12.7/vscjava.vscode-gradle-3.12.7.vsix
-        - https://github.com/opencaesar/oml-vision/releases/download/v0.2.0/oml-vision-v0.2.0.vsix
-        - https://github.com/opencaesar/oml-luxor/releases/download/2.4.0/oml-luxor-2.4.0.vsix

build.gradle

@@ -74,8 +74,6 @@ task omlToOwl(type:io.opencaesar.oml2owl.Oml2OwlTask, group:"oml", dependsOn: do
     inputCatalogPath = file('catalog.xml')
     // OWL catalog
     outputCatalogPath = file('build/owl/catalog.xml')
-    // Generate rules
-    generateRules = true
 }
 
 /*
@@ -119,7 +117,7 @@ task generateDocs(type: io.opencaesar.owl.doc.OwlDocTask, dependsOn: owlReason)
  * Start the headless Fuseki server
  * @seeAlso https://github.com/opencaesar/owl-tools/blob/master/owl-doc/README.md
  */
-task startFuseki(type: io.opencaesar.owl.fuseki.StartFusekiTask, group:"vision", dependsOn: owlReason) {
+task startFuseki(type: io.opencaesar.owl.fuseki.StartFusekiTask, group:"oml") {
     configurationPath = file('.fuseki.ttl')
     outputFolderPath = file('.fuseki')
     webUI = true
@@ -129,33 +127,24 @@ task startFuseki(type: io.opencaesar.owl.fuseki.StartFusekiTask, group:"vision",
  * Stop the headless Fuseki server
  * @seeAlso https://github.com/opencaesar/owl-tools/blob/master/owl-fuseki/README.md
  */
-task stopFuseki(type: io.opencaesar.owl.fuseki.StopFusekiTask, group:"vision") {
+task stopFuseki(type: io.opencaesar.owl.fuseki.StopFusekiTask, group:"oml") {
     outputFolderPath = file('.fuseki')
 }
 
-/*
- * A task to load an OWL catalog to a TDB-persisted Fuseki dataset endpoint
- * @seeAlso https://github.com/opencaesar/owl-tools/blob/master/owl-load/README.md
- */
-task owlLoadTdb(type:io.opencaesar.owl.load.OwlLoadTask, group:"oml", dependsOn: startFuseki) {
-    inputs.files(startFuseki.outputFolderPath) // rerun when fuseki restarts
-    catalogPath = file('build/owl/catalog.xml')
-    endpointURL = "http://localhost:3030/$dataset".toString()
-    fileExtensions = ['owl', 'ttl']
-    iris = ["$rootIri".toString()]
-}
-
 /*
  * A task to load an OWL catalog to a Fuseki dataset endpoint
  * @seeAlso https://github.com/opencaesar/owl-tools/blob/master/owl-load/README.md
  */
 task owlLoad(type:io.opencaesar.owl.load.OwlLoadTask, group:"oml", dependsOn: [owlReason, startFuseki]) {
     inputs.files(startFuseki.outputFolderPath) // rerun when fuseki restarts
     catalogPath = file('build/owl/catalog.xml')
-    endpointURL = "http://localhost:3030/$dataset-inf".toString()
+    endpointURL = "http://localhost:3030/$dataset".toString()
     fileExtensions = ['owl', 'ttl']
-    iris = ["$rootIri/classes".toString(), "$rootIri/properties".toString()]
-    loadToDefaultGraph = true
+    iris = [
+        "$rootIri/classes".toString(),
+        "$rootIri/properties".toString(),
+        "$rootIri/individuals".toString()
+    ]
 }
 
 /*
@@ -164,7 +153,7 @@ task owlLoad(type:io.opencaesar.owl.load.OwlLoadTask, group:"oml", dependsOn: [o
  */
 task owlQuery(type:io.opencaesar.owl.query.OwlQueryTask, group:"oml", dependsOn: owlLoad) {
     inputs.files(owlLoad.inputs.files) // rerun when the dataset changes
-    endpointURL = "http://localhost:3030/$dataset-inf".toString()
+    endpointURL = "http://localhost:3030/$dataset".toString()
     queryPath = file('src/sparql')
     resultPath = file('build/results')
     format = 'json'

src/sparql/components.sparql

@@ -2,18 +2,18 @@ PREFIX base:        <http://example.com/tutorial2/vocabulary/base#>
 PREFIX mission:     <http://example.com/tutorial2/vocabulary/mission#>
 PREFIX vim4:		<http://bipm.org/jcgm/vim4#>
 
-SELECT DISTINCT ?iri ?c2Iri ?c1_id ?c1_name ?c1_mass ?c2_id ?c2_name
+SELECT DISTINCT ?c1_id ?c1_name ?c1_mass ?c2_id ?c2_name
 WHERE {
-	?iri a mission:Component ;
+	?c1 a mission:Component ;
 		base:hasIdentifier ?c1_id ;
 		base:hasCanonicalName ?c1_name .
 	OPTIONAL {
-		?iri	base:isContainedIn ?c2Iri .
-		?c2Iri base:hasIdentifier ?c2_id ;
+		?c1	base:isContainedIn ?c2 .
+		?c2 base:hasIdentifier ?c2_id ;
 			base:hasCanonicalName ?c2_name .
 	}
 	OPTIONAL {
-		?c1_mass_mag vim4:characterizes ?iri ;
+		?c1_mass_mag vim4:characterizes ?c1 ;
 			vim4:hasDoubleNumber ?c1_mass .
 	}
 }