Merge branch 'main' into main

.devcontainer/devcontainer.json

@@ -0,0 +1,52 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/debian
+{
+	"name": "Kepler16b",
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"image": "mcr.microsoft.com/devcontainers/base:bullseye",
+	"features": {
+		"ghcr.io/devcontainers/features/docker-in-docker:2": {
+			"version": "latest",
+			"enableNonRootDocker": "true",
+			"moby": "true"
+		},
+		"ghcr.io/devcontainers/features/java:1": {
+			"installGradle": true,
+			"version": "17",
+			"jdkDistro": "ms",
+			"gradleVersion": "latest",
+			"mavenVersion": "latest",
+			"antVersion": "latest",
+			"groovyVersion": "latest"
+		}
+	},
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Configure tool-specific properties.
+	"customizations": {
+        "vscode": {
+          "extensions": [
+            // Extensions below are for quality of life improvments
+            "eamodio.gitlens",
+            "esbenp.prettier-vscode",
+            "TabNine.tabnine-vscode",
+            "mhutchie.git-graph",
+            "wayou.vscode-todo-highlight",
+            "vscode-icons-team.vscode-icons",
+            "ms-azuretools.vscode-docker",
+			"firefox-devtools.vscode-firefox-debug",
+			// Extension below is for VSCode Gradle Plugin needed for OML Vision
+			"vscjava.vscode-gradle"
+          ]
+        }
+      }
+
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.fuseki.ttl

@@ -1,24 +1,46 @@
-@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 :        <#> .
+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#>
 
-[] rdf:type fuseki:Server .
+# Service 1: Assertions endpoint
+:service1  a               		  		fuseki:Service ;
+    fuseki:name                   		"tutorial2" ;
+    fuseki:dataset                		:assertions ;
+    fuseki:serviceQuery           		"" , "query", "sparql" ;
+    fuseki:serviceUpdate          		"" , "update" ;
+    fuseki:serviceReadWriteGraphStore 	"data" ;
+	.
 
-<#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> .
+# 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 ;
+	.
 
-## 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 .
+: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" ] ;
+	.

.github/dependabot.yml

@@ -0,0 +1,12 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for more information:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+# https://containers.dev/guide/dependabot
+
+version: 2
+updates:
+ - package-ecosystem: "devcontainers"
+   directory: "/"
+   schedule:
+     interval: weekly

.gitpod.Dockerfile

@@ -0,0 +1,10 @@
+# Grab gitpod image
+FROM gitpod/workspace-full
+
+# Set the user as gitpod
+USER gitpod
+
+# Set the version to Java 17
+RUN bash -c ". /home/gitpod/.sdkman/bin/sdkman-init.sh && \
+    sdk install java 17.0.3-ms && \
+    sdk default java 17.0.3-ms"

.gitpod.yml

@@ -4,8 +4,17 @@
 
 # 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: sdk install java 17
-  - init: ./gradlew build
-
+  - init: ./gradlew owlLoad
 
+# 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

@@ -74,6 +74,8 @@ 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
 }
 
 /*
@@ -117,7 +119,7 @@ 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:"oml") {
+task startFuseki(type: io.opencaesar.owl.fuseki.StartFusekiTask, group:"vision", dependsOn: owlReason) {
     configurationPath = file('.fuseki.ttl')
     outputFolderPath = file('.fuseki')
     webUI = true
@@ -127,24 +129,33 @@ task startFuseki(type: io.opencaesar.owl.fuseki.StartFusekiTask, group:"oml") {
  * 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:"oml") {
+task stopFuseki(type: io.opencaesar.owl.fuseki.StopFusekiTask, group:"vision") {
     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/$dataset".toString()
+    endpointURL = "http://localhost:3030/$dataset-inf".toString()
     fileExtensions = ['owl', 'ttl']
-    iris = [
-        "$rootIri/classes".toString(),
-        "$rootIri/properties".toString(),
-        "$rootIri/individuals".toString()
-    ]
+    iris = ["$rootIri/classes".toString(), "$rootIri/properties".toString()]
+    loadToDefaultGraph = true
 }
 
 /*
@@ -153,7 +164,7 @@ 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/$dataset".toString()
+    endpointURL = "http://localhost:3030/$dataset-inf".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 ?c1_id ?c1_name ?c1_mass ?c2_id ?c2_name
+SELECT DISTINCT ?iri ?c2Iri ?c1_id ?c1_name ?c1_mass ?c2_id ?c2_name
 WHERE {
-	?c1 a mission:Component ;
+	?iri a mission:Component ;
 		base:hasIdentifier ?c1_id ;
 		base:hasCanonicalName ?c1_name .
 	OPTIONAL {
-		?c1	base:isContainedIn ?c2 .
-		?c2 base:hasIdentifier ?c2_id ;
+		?iri	base:isContainedIn ?c2Iri .
+		?c2Iri base:hasIdentifier ?c2_id ;
 			base:hasCanonicalName ?c2_name .
 	}
 	OPTIONAL {
-		?c1_mass_mag vim4:characterizes ?c1 ;
+		?c1_mass_mag vim4:characterizes ?iri ;
 			vim4:hasDoubleNumber ?c1_mass .
 	}
 }

src/sparql/update.sparql

@@ -0,0 +1,11 @@
+PREFIX base:        <http://example.com/tutorial2/vocabulary/base#>
+PREFIX mission:     <http://example.com/tutorial2/vocabulary/mission#>
+PREFIX components: <http://example.com/tutorial2/description/components#> 
+PREFIX vim4:		<http://bipm.org/jcgm/vim4#>
+
+INSERT DATA {
+  	components:test a mission:Component ; 
+  		base:hasIdentifier "testID" ;
+  		base:hasCanonicalName "testName" ;
+    	base:contains components:orbiter-launch-system .
+}

src/vision/config/sparqlConfig.json

@@ -0,0 +1,5 @@
+{
+  "queryEndpoint": "http://localhost:3030/tutorial2-inf/sparql",
+  "updateEndpoint": "http://localhost:3030/tutorial2-inf/update",
+  "pingEndpoint": "http://localhost:3030/$/ping"
+}

src/vision/sparql/components.sparql

@@ -0,0 +1,20 @@
+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
+WHERE {
+	?iri a mission:Component ;
+		base:hasIdentifier ?c1_id ;
+		base:hasCanonicalName ?c1_name .
+	OPTIONAL {
+		?iri	base:isContainedIn ?c2Iri .
+		?c2Iri base:hasIdentifier ?c2_id ;
+			base:hasCanonicalName ?c2_name .
+	}
+	OPTIONAL {
+		?c1_mass_mag vim4:characterizes ?iri ;
+			vim4:hasDoubleNumber ?c1_mass .
+	}
+}
+ORDER BY ?c1_id ?c2_id

src/vision/sparql/connections.sparql

@@ -0,0 +1,12 @@
+PREFIX base:        <http://example.com/tutorial2/vocabulary/base#>
+PREFIX mission:     <http://example.com/tutorial2/vocabulary/mission#>
+
+SELECT DISTINCT ?c1_name ?c2_name
+WHERE {
+	?c1 a mission:Component ;
+		base:hasCanonicalName ?c1_name ;
+		mission:connectsTo [
+			base:hasCanonicalName ?c2_name
+		]
+}
+ORDER BY ?c1_name ?c2_name

src/vision/sparql/general-properties.sparql

@@ -0,0 +1,13 @@
+PREFIX xsd:  <http://www.w3.org/2001/XMLSchema#>
+PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl:  <http://www.w3.org/2002/07/owl#>
+PREFIX base: <http://example.com/tutorial2/vocabulary/base#>
+
+select distinct ?anyIri ?id ?name
+WHERE {
+  BIND(<${iri}> AS ?anyIri)
+  ?anyIri a owl:NamedIndividual ;
+      base:hasIdentifier ?id ;
+      base:hasCanonicalName ?name .
+}

src/vision/sparql/missions-diagram.sparql

@@ -0,0 +1,23 @@
+PREFIX base:        <http://example.com/tutorial2/vocabulary/base#>
+PREFIX mission:     <http://example.com/tutorial2/vocabulary/mission#>
+
+SELECT DISTINCT ?m_id ?m_name
+WHERE {
+	?m a mission:Mission ;
+		base:hasIdentifier ?m_id ;
+		base:hasCanonicalName ?m_name ;
+}
+ORDER BY ?m_id
+
+# PREFIX oml:			<http://opencaesar.io/oml#>
+# PREFIX dc: 			<http://purl.org/dc/elements/1.1#> 
+# PREFIX base:        <http://example.com/tutorial2/vocabulary/base#>
+# PREFIX mission:     <http://example.com/tutorial2/vocabulary/mission#>
+
+# CONSTRUCT {
+# 	?mission dc:type oml:Concept ;
+# 		mission:pursues ?objective .
+# }
+# WHERE {
+# 	?mission mission:pursues ?objective ;
+# }

src/vision/sparql/missions.sparql

@@ -0,0 +1,10 @@
+PREFIX base:        <http://example.com/tutorial2/vocabulary/base#>
+PREFIX mission:     <http://example.com/tutorial2/vocabulary/mission#>
+
+SELECT DISTINCT ?iri ?m_id ?m_name
+WHERE {
+	?iri a mission:Mission ;
+		base:hasIdentifier ?m_id ;
+		base:hasCanonicalName ?m_name ;
+}
+ORDER BY ?m_id ?o_id

src/vision/sparql/objectives-edge.sparql

@@ -0,0 +1,15 @@
+PREFIX base:        <http://example.com/tutorial2/vocabulary/base#>
+PREFIX mission:     <http://example.com/tutorial2/vocabulary/mission#>
+
+SELECT DISTINCT ?m_id ?m_name ?o_id ?o_name
+WHERE {
+	?m a mission:Mission ;
+		base:hasIdentifier ?m_id ;
+		base:hasCanonicalName ?m_name ;
+		mission:pursues [
+        a mission:Objective ;
+        base:hasIdentifier ?o_id ;
+    	  base:hasCanonicalName ?o_name
+    ]
+}
+ORDER BY ?o_id

src/vision/sparql/objectives.sparql

@@ -0,0 +1,14 @@
+PREFIX base:        <http://example.com/tutorial2/vocabulary/base#>
+PREFIX mission:     <http://example.com/tutorial2/vocabulary/mission#>
+
+SELECT DISTINCT ?iri ?o1_id ?o1_name ?o2_id ?o2_name
+WHERE {
+    ?iri a mission:Objective ;
+		base:hasIdentifier ?o1_id ;
+		base:hasCanonicalName ?o1_name ;
+		base:aggregates [
+        	base:hasIdentifier ?o2_id ;
+        	base:hasCanonicalName ?o2_name
+      	]
+}
+ORDER BY ?o1_id ?o2_id