Merge main into develop (#4912)

Author: hmottestad

.github/workflows/develop-status.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        jdk: [11, 21]
+        jdk: [11, 17]
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/main-status.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        jdk: [11, 21]
+        jdk: [11, 17]
 
     steps:
     - uses: actions/checkout@v2

core/rio/api/src/main/java/org/eclipse/rdf4j/rio/helpers/RDFaParserSettings.java

@@ -22,11 +22,14 @@
 public class RDFaParserSettings {
 
 	/**
-	 * Boolean setting for parser to determine the RDFa version to use when processing the document.
-	 * <p>
-	 * Defaults to {@link RDFaVersion#RDFA_1_0}.
+	 * Boolean setting for parser to determine the RDFa version to use when processing the document. Note that although
+	 * these settings are not used within RDF4J, they are in use by external plugins.
+	 *
+	 * @see <a href=
+	 *      "https://github.com/eclipse-rdf4j/rdf4j/issues/4779">https://github.com/eclipse-rdf4j/rdf4j/issues/4779</a>
+	 *      <p>
+	 *      Defaults to {@link RDFaVersion#RDFA_1_0}.
 	 */
-	@Deprecated(since = "4.3.0", forRemoval = true)
 	public static final RioSetting<RDFaVersion> RDFA_COMPATIBILITY = new RioSettingImpl<>(
 			"org.eclipse.rdf4j.rio.rdfa.version", "RDFa Version Compatibility", RDFaVersion.RDFA_1_0);
 

core/rio/api/src/main/java/org/eclipse/rdf4j/rio/helpers/RDFaVersion.java

@@ -11,11 +11,14 @@
 package org.eclipse.rdf4j.rio.helpers;
 
 /**
- * Enumeration for tracking versions of the RDFa specification to specify processing capabilities of RDFa modules.
+ * Enumeration for tracking versions of the RDFa specification to specify processing capabilities of RDFa modules. Note
+ * that although these settings are not used within RDF4J, they are in use by external plugins.
+ *
+ * @see <a href=
+ *      "https://github.com/eclipse-rdf4j/rdf4j/issues/4779">https://github.com/eclipse-rdf4j/rdf4j/issues/4779</a>
  *
  * @author Peter Ansell
  */
-@Deprecated(since = "4.3.0", forRemoval = true)
 public enum RDFaVersion {
 
 	/**

core/sail/elasticsearch-store/pom.xml

@@ -193,7 +193,7 @@
 					<httpPort>9200</httpPort>
 					<environmentVariables>
 						<ingest.geoip.downloader.enabled>false</ingest.geoip.downloader.enabled>
-						<ES_JAVA_OPTS>${java.sec.mgr} -Xmx1g</ES_JAVA_OPTS>
+						<ES_JAVA_OPTS>${java.sec.mgr} -Xmx1G -Xms1G</ES_JAVA_OPTS>
 					</environmentVariables>
 					<instanceCount>1</instanceCount>
 					<instanceSettings>

core/sail/shacl/src/main/java/org/eclipse/rdf4j/sail/shacl/ShaclValidator.java

@@ -77,7 +77,7 @@ public static ValidationReport validate(Sail dataRepo, Sail shapesRepo) {
 
 			}
 			shapesConnection.commit();
-		} catch (Exception e) {
+		} catch (Throwable e) {
 			logger.warn("Failed to read shapes", e);
 			throw e;
 		}
@@ -98,7 +98,7 @@ public static ValidationReport validate(Sail dataRepo, Sail shapesRepo) {
 			return performValidation(shapes, new ConnectionsGroup(verySimpleRdfsBackwardsChainingConnection, null,
 					null, null, new Stats(), () -> reasoner,
 					new ShaclSailConnection.Settings(true, true, true, IsolationLevels.NONE), true));
-		} catch (Exception e) {
+		} catch (Throwable e) {
 			logger.warn("Failed to validate shapes", e);
 			throw e;
 		}

core/sail/shacl/src/main/java/org/eclipse/rdf4j/sail/shacl/ShapeValidationContainer.java

@@ -53,7 +53,12 @@ public ShapeValidationContainer(Shape shape, Supplier<PlanNode> planNodeSupplier
 			} else {
 				this.planNode = planNode;
 			}
-		} catch (Exception e) {
+		} catch (Throwable e) {
+			logger.warn("Error processing SHACL Shape {}", shape.getId(), e);
+			logger.warn("Error processing SHACL Shape\n{}", shape, e);
+			if (e instanceof Error) {
+				throw e;
+			}
 			throw new SailException("Error processing SHACL Shape " + shape.getId() + "\n" + shape, e);
 		}
 
@@ -76,8 +81,12 @@ public ValidationResultIterator performValidation() {
 		try (CloseableIteration<? extends ValidationTuple> iterator = planNode.iterator()) {
 			validationResults = new ValidationResultIterator(iterator, effectiveValidationResultsLimitPerConstraint);
 			return validationResults;
-		} catch (Exception e) {
+		} catch (Throwable e) {
 			logger.warn("Error validating SHACL Shape {}", shape.getId(), e);
+			logger.warn("Error validating SHACL Shape\n{}", shape, e);
+			if (e instanceof Error) {
+				throw e;
+			}
 			throw new SailException("Error validating SHACL Shape " + shape.getId() + "\n" + shape, e);
 		} finally {
 			handlePostLogging(before, validationResults);

core/sail/shacl/src/main/java/org/eclipse/rdf4j/sail/shacl/ast/Shape.java

@@ -450,8 +450,9 @@ public PlanNode generatePlans(ConnectionsGroup connectionsGroup, ValidationSetti
 			} else {
 				throw new ShaclUnsupportedException("Unknown validation approach: " + validationApproach);
 			}
-		} catch (RuntimeException e) {
+		} catch (Throwable e) {
 			logger.warn("Error processing SHACL Shape {}", id, e);
+			logger.warn("Error processing SHACL Shape\n{}", this, e);
 			throw new SailException("Error processing SHACL Shape " + id + "\n" + this, e);
 		}
 
@@ -707,7 +708,7 @@ public static List<ContextWithShape> getShapesInContext(ShapeSource shapeSource,
 						.map(r -> {
 							try {
 								return new ShaclProperties(r, shapeSourceWithContext);
-							} catch (Exception e) {
+							} catch (Throwable e) {
 								logger.warn("Error parsing shape {}", r, e);
 								throw new ShaclShapeParsingException(e, r);
 							}
@@ -720,7 +721,7 @@ public static List<ContextWithShape> getShapesInContext(ShapeSource shapeSource,
 									return PropertyShape.getInstance(p, shapeSourceWithContext, parseSettings, cache);
 								}
 								throw new ShaclShapeParsingException("Unknown shape type", p.getId());
-							} catch (Exception e) {
+							} catch (Throwable e) {
 								logger.warn("Error parsing shape {}", p.getId(), e);
 								if (e instanceof ShaclShapeParsingException) {
 									throw e;
@@ -746,6 +747,7 @@ public String toString() {
 		statements.setNamespace(RSX.NS);
 		statements.setNamespace(RDFS.NS);
 		statements.setNamespace(RDF.NS);
+		statements.setNamespace(DASH.NS);
 		WriterConfig writerConfig = new WriterConfig()
 				.set(BasicWriterSettings.PRETTY_PRINT, true)
 				.set(BasicWriterSettings.INLINE_BLANK_NODES, true);

core/sail/shacl/src/main/java/org/eclipse/rdf4j/sail/shacl/results/lazy/LazyValidationReport.java

@@ -81,7 +81,7 @@ private void evaluateLazyAspect() {
 				validationResultIterators = null;
 
 			}
-		} catch (Exception e) {
+		} catch (Throwable e) {
 			logger.warn("Error evaluating lazy validation report", e);
 			throw e;
 		}
@@ -104,7 +104,7 @@ public Model asModel(Model model) {
 			}
 
 			return model;
-		} catch (Exception e) {
+		} catch (Throwable e) {
 			logger.warn("Error converting validation report to model", e);
 			throw e;
 		}

pom.xml

@@ -724,7 +724,7 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-javadoc-plugin</artifactId>
-					<version>3.6.0</version>
+					<version>3.6.3</version>
 					<configuration>
 						<encoding>utf8</encoding>
 						<source>11</source>

site/content/documentation/programming/lmdb-store.md

@@ -125,7 +125,7 @@ Please note that the actual footprint also depends largely on the size of IRIs a
 Some basic information about LMDB database and RAM sizes can be found in the
 [OpenLDAP & LMDB Sizing Guide](https://3bmahv3xwn6030jbn72hlx3j-wpengine.netdna-ssl.com/wp-content/uploads/2018/08/OpenLDAP-LMDB-Sizing-Guide.pdf).
 
-The bottom line is thatt more RAM is better. The best is to have enough RAM to accommodate the
+The bottom line is that more RAM is better. The best is to have enough RAM to accommodate the
 
 entire database or at least the database's working set.