feat: overhauled ontology imports

build.gradle.kts

@@ -51,6 +51,9 @@ repositories {
 dependencies {
   implementation("org.jetbrains.kotlinx:kotlinx-coroutines-core:1.8.0")
 
+  // Reflections
+  implementation("org.reflections:reflections:0.10.2")
+
   // Guava
   implementation("com.google.guava:guava:33.2.0-jre")
 

src/main/kotlin/parser/Parser.kt

@@ -5,16 +5,22 @@ import kotlinx.coroutines.channels.Channel
 import org.apache.jena.rdf.model.RDFNode
 import technology.idlab.bridge.*
 import technology.idlab.extensions.*
-import technology.idlab.extensions.loadIntoJVM
 import technology.idlab.extensions.query
 import technology.idlab.extensions.readModelRecursively
-import technology.idlab.extensions.validate
 import technology.idlab.logging.Log
 import technology.idlab.runner.Processor
+import technology.idlab.runner.ProcessorDefinition
 
 class Parser(file: File) {
-  /** An RDF model of the configuration file. */
-  private val model = file.readModelRecursively().validate()
+  /** RDF model which imports the base pipeline ontology. */
+  private val model =
+      this::class
+          .java
+          .getResource("/pipeline.ttl")
+          .let { it ?: Log.shared.fatal("Pipeline file not found") }
+          .toURI()
+          .let { File(it) }
+          .readModelRecursively()
 
   /** Class references to the different processors. */
   private val processors: MutableMap<String, Class<*>> = mutableMapOf()
@@ -33,14 +39,20 @@ class Parser(file: File) {
 
   /** Parse the model for processor declarations and save results as a field. */
   init {
-    model.query("/queries/processors.sparql") {
-      val uri = it["processor"].toString()
-      val path = it["file"].toString().drop(7)
-      val sourceFile = File(path)
-      processors[uri] = sourceFile.loadIntoJVM()
+    ProcessorDefinition.scan().forEach {
+      // Save the processor class and URI to the map.
+      processors[it.uri] = it.clazz
+
+      // Load the ontology file into the model.
+      model.read(it.ontology.inputStream(), null, "TTL")
     }
   }
 
+  /** Parse the pipeline. */
+  init {
+    model.read(file.inputStream(), null, "TTL").validate()
+  }
+
   /** Parse the shape for each processor. */
   init {
     processors.forEach { processor ->

src/main/kotlin/runner/ProcessorDefinition.kt

@@ -0,0 +1,34 @@
+package technology.idlab.runner
+
+import java.io.File
+import technology.idlab.logging.Log
+import technology.idlab.util.classesWithAnnotation
+
+@Target(AnnotationTarget.CLASS)
+@Retention(AnnotationRetention.RUNTIME)
+@MustBeDocumented
+annotation class ProcessorDefinition(val resource: String) {
+  data class Config(val clazz: Class<out Processor>, val ontology: File, val uri: String)
+
+  companion object {
+    fun scan(): List<Config> {
+      return classesWithAnnotation(ProcessorDefinition::class.java)
+          .map {
+            try {
+              it.asSubclass(Processor::class.java)
+            } catch (e: ClassCastException) {
+              Log.shared.fatal("Class $it is not a Processor")
+            }
+          }
+          .map {
+            val annotation = it.getAnnotation(ProcessorDefinition::class.java)
+
+            val resource =
+                it.getResource(annotation.resource)
+                    ?: Log.shared.fatal("Resource ${annotation.resource} not found")
+
+            Config(it, File(resource.toURI()), "https://w3id.org/conn/jvm#${it.simpleName}")
+          }
+    }
+  }
+}

src/main/kotlin/std/FileReader.kt

@@ -3,7 +3,9 @@ package technology.idlab.std
 import java.io.File
 import technology.idlab.bridge.Writer
 import technology.idlab.runner.Processor
+import technology.idlab.runner.ProcessorDefinition
 
+@ProcessorDefinition("/std/file_reader.ttl")
 class FileReader(args: Map<String, Any>) : Processor(args) {
   /** Arguments */
   private val path: String = this.getArgument("path")

src/main/kotlin/std/FileWriter.kt

@@ -3,7 +3,9 @@ package technology.idlab.std
 import java.io.File
 import technology.idlab.bridge.Reader
 import technology.idlab.runner.Processor
+import technology.idlab.runner.ProcessorDefinition
 
+@ProcessorDefinition("/std/file_writer.ttl")
 class FileWriter(args: Map<String, Any>) : Processor(args) {
   /** Processor default values. */
   private val overwriteDefault = true

src/main/kotlin/std/HttpFetch.kt

@@ -9,7 +9,9 @@ import io.ktor.http.*
 import kotlinx.coroutines.runBlocking
 import technology.idlab.bridge.Writer
 import technology.idlab.runner.Processor
+import technology.idlab.runner.ProcessorDefinition
 
+@ProcessorDefinition("/std/http_fetch.ttl")
 class HttpFetch(args: Map<String, Any>) : Processor(args) {
   /** Meta configuration. */
   private var engine: HttpClientEngine = CIO.create()

src/main/kotlin/std/RDFValidator.kt

@@ -11,7 +11,9 @@ import technology.idlab.bridge.Writer
 import technology.idlab.extensions.readModelRecursively
 import technology.idlab.logging.Log
 import technology.idlab.runner.Processor
+import technology.idlab.runner.ProcessorDefinition
 
+@ProcessorDefinition("/std/rdf_validator.ttl")
 class RDFValidator(args: Map<String, Any>) : Processor(args) {
   /** Default values. */
   private val errorIsFatalDefault = false

src/main/kotlin/util/Reflect.kt

@@ -0,0 +1,19 @@
+package technology.idlab.util
+
+import org.reflections.Reflections
+import org.reflections.scanners.Scanners
+import org.reflections.util.ConfigurationBuilder
+
+internal fun classesWithAnnotation(annotation: Class<out Annotation>): Set<Class<*>> {
+  // Get a list of all classes with type annotations.
+  val config =
+      ConfigurationBuilder()
+          .forPackages("") // Root package, adjust if needed
+          .addScanners(Scanners.TypesAnnotated)
+
+  // Initialize a Reflections client.
+  val reflections = Reflections(config)
+
+  // Filter based on JVMRunnerProcessor
+  return reflections.getTypesAnnotatedWith(annotation)
+}

src/main/resources/pipeline.ttl

@@ -5,28 +5,12 @@
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.
 @prefix owl: <http://www.w3.org/2002/07/owl#>.
 
-# Include the Standard Processor Library
-<> owl:imports
-  <./std/file_reader.ttl>,
-  <./std/file_writer.ttl>,
-  <./std/http_fetch.ttl>,
-  <./std/rdf_validator.ttl>.
-
 # Definition of a Processor.
 []
   a sh:NodeShape;
   sh:targetClass jvm:Processor;
-  sh:property [
-    sh:path jvm:file;
-    sh:minCount 1;
-    sh:maxCount 1;
-  ], [
-    sh:path jvm:language;
-    sh:in( "Java" "Kotlin" );
-    sh:datatype xsd:string;
-    sh:minCount 1;
-    sh:maxCount 1;
-  ].
+  sh:closed true;
+  sh:ignoredProperties ( rdf:type ).
 
 # A bridge takes in a reader and writer.
 []

src/main/resources/std/file_reader.ttl

@@ -4,11 +4,7 @@
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#>.
 @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>.
 
-<> owl:imports <../pipeline.ttl>.
-
-jvm:FileReader a jvm:Processor;
-  jvm:file <../../../classes/kotlin/main/technology/idlab/std/FileReader.class>;
-  jvm:language "Kotlin".
+jvm:FileReader a jvm:Processor.
 
 [] a sh:NodeShape;
   sh:targetClass jvm:FileReader;

src/main/resources/std/file_writer.ttl

@@ -4,11 +4,7 @@
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#>.
 @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>.
 
-<> owl:imports <../pipeline.ttl>.
-
-jvm:FileWriter a jvm:Processor;
-  jvm:file <../../../classes/kotlin/main/technology/idlab/std/FileWriter.class>;
-  jvm:language "Kotlin".
+jvm:FileWriter a jvm:Processor.
 
 [] a sh:NodeShape;
   sh:targetClass jvm:FileWriter;

src/main/resources/std/http_fetch.ttl

@@ -4,11 +4,7 @@
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#>.
 @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>.
 
-<> owl:imports <../pipeline.ttl>.
-
-jvm:HttpFetch a jvm:Processor;
-  jvm:file <../../../classes/kotlin/main/technology/idlab/std//HttpFetch.class>;
-  jvm:language "Kotlin".
+jvm:HttpFetch a jvm:Processor.
 
 [] a sh:NodeShape;
   sh:targetClass jvm:HttpFetch;

src/main/resources/std/rdf_validator.ttl

@@ -4,11 +4,7 @@
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#>.
 @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>.
 
-<> owl:imports <../pipeline.ttl>.
-
-jvm:RDFValidator a jvm:Processor;
-  jvm:file <../../../classes/kotlin/main/technology/idlab/std/RDFValidator.class>;
-  jvm:language "Kotlin".
+jvm:RDFValidator a jvm:Processor.
 
 [] a sh:NodeShape;
   sh:targetClass jvm:RDFValidator;

src/test/resources/sources/Filter.java → src/test/java/processors/Filter.java

@@ -1,8 +1,12 @@
+package processors;
+
 import java.util.List;
 import java.util.Map;
 import technology.idlab.bridge.*;
 import technology.idlab.runner.Processor;
+import technology.idlab.runner.ProcessorDefinition;
 
+@ProcessorDefinition(resource = "/processors/filter.ttl")
 public class Filter extends Processor {
   // Parameters
   private final List<Integer> whitelist;

src/test/resources/sources/Literals.java → src/test/java/processors/Literals.java

@@ -1,8 +1,12 @@
+package processors;
+
 import java.util.Date;
 import java.util.Map;
 import technology.idlab.bridge.*;
 import technology.idlab.runner.Processor;
+import technology.idlab.runner.ProcessorDefinition;
 
+@ProcessorDefinition(resource = "/processors/literals.ttl")
 public class Literals extends Processor {
   // Parameters
   private final boolean _bool;

src/test/resources/sources/Optionals.java → src/test/java/processors/Optionals.java

@@ -1,7 +1,11 @@
+package processors;
+
 import java.util.Map;
 import java.util.Optional;
 import technology.idlab.runner.Processor;
+import technology.idlab.runner.ProcessorDefinition;
 
+@ProcessorDefinition(resource = "/processors/optionals.ttl")
 public class Optionals extends Processor {
   // Parameters
   public final String required;

src/test/resources/sources/Range.java → src/test/java/processors/Range.java

@@ -1,7 +1,11 @@
+package processors;
+
 import java.util.Map;
 import technology.idlab.bridge.Writer;
 import technology.idlab.runner.Processor;
+import technology.idlab.runner.ProcessorDefinition;
 
+@ProcessorDefinition(resource = "/processors/range.ttl")
 public class Range extends Processor {
   // Parameters
   private final int start;

src/test/resources/sources/Reporter.java → src/test/java/processors/Reporter.java

@@ -1,7 +1,11 @@
+package processors;
+
 import java.util.Map;
 import technology.idlab.bridge.Reader;
 import technology.idlab.runner.Processor;
+import technology.idlab.runner.ProcessorDefinition;
 
+@ProcessorDefinition(resource = "/processors/reporter.ttl")
 public class Reporter extends Processor {
   private final Reader reader;
 

src/test/resources/sources/Square.java → src/test/java/processors/Square.java

@@ -1,8 +1,12 @@
+package processors;
+
 import java.util.Map;
 import technology.idlab.bridge.Reader;
 import technology.idlab.bridge.Writer;
 import technology.idlab.runner.Processor;
+import technology.idlab.runner.ProcessorDefinition;
 
+@ProcessorDefinition(resource = "/processors/square.ttl")
 public class Square extends Processor {
   // Channels
   private final Reader reader;

src/test/resources/sources/Negator.kt → src/test/kotlin/processors/Negator.kt

@@ -1,6 +1,10 @@
+package processors
+
 import technology.idlab.bridge.*
 import technology.idlab.runner.Processor
+import technology.idlab.runner.ProcessorDefinition
 
+@ProcessorDefinition("/processors/negator.ttl")
 class Negator(args: Map<String, Any>) : Processor(args) {
   private val input: Reader = this.getArgument("input")
   private val output: Writer = this.getArgument("output")

src/test/kotlin/std/RDFValidatorTest.kt

@@ -15,7 +15,7 @@ import technology.idlab.std.RDFValidator
 
 /** Ontology location. */
 private val ontology =
-    Thread.currentThread().contextClassLoader.getResource("pipeline.ttl")!!.let { File(it.file) }
+    File(Thread.currentThread().contextClassLoader.getResource("pipeline.ttl")!!.file)
 
 /** Textual representation of a valid SHACL file. */
 private const val validShape =
@@ -56,7 +56,7 @@ private const val validInput =
 @prefix ex: <http://example.org#> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 
-ex:ValidPoint 
+ex:ValidPoint
   a ex:Point;
   ex:x "1"^^xsd:int;
   ex:y "2"^^xsd:int.

src/test/resources/pipelines/filter.ttl

@@ -2,11 +2,6 @@
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#>.
 @prefix owl: <http://www.w3.org/2002/07/owl#>.
 
-# Include processor definitions.
-<> owl:imports
-  <../pipeline.ttl>,
-  <../processors/filter.ttl>.
-
 # Range -> Filter
 <reader> a jvm:MemoryChannelReader.
 <writer> a jvm:MemoryChannelWriter.