Merge main into develop (#4912)

hmottestad · web-flow · commit 5300320fc83f · 2024-02-19T21:46:27.000+01:00
diff --git a/.github/workflows/develop-status.yml b/.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
diff --git a/.github/workflows/main-status.yml b/.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
diff --git a/core/rio/api/src/main/java/org/eclipse/rdf4j/rio/helpers/RDFaParserSettings.java b/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);
 
diff --git a/core/rio/api/src/main/java/org/eclipse/rdf4j/rio/helpers/RDFaVersion.java b/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 {
 
 	/**
diff --git a/core/sail/elasticsearch-store/pom.xml b/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>
diff --git a/core/sail/shacl/src/main/java/org/eclipse/rdf4j/sail/shacl/ShaclValidator.java b/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;
 		}
diff --git a/core/sail/shacl/src/main/java/org/eclipse/rdf4j/sail/shacl/ShapeValidationContainer.java b/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);
diff --git a/core/sail/shacl/src/main/java/org/eclipse/rdf4j/sail/shacl/ast/Shape.java b/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);
diff --git a/core/sail/shacl/src/main/java/org/eclipse/rdf4j/sail/shacl/results/lazy/LazyValidationReport.java b/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;
 		}
diff --git a/pom.xml b/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>
diff --git a/site/content/documentation/programming/lmdb-store.md b/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.
 

Original file line number	Diff line number	Diff line change
`@@ -77,7 +77,7 @@ public static ValidationReport validate(Sail dataRepo, Sail shapesRepo) {`
`77`	`77`
`78`	`78`	`}`
`79`	`79`	`shapesConnection.commit();`
`80`		`- } catch (Exception e) {`
	`80`	`+ } catch (Throwable e) {`
`81`	`81`	`logger.warn("Failed to read shapes", e);`
`82`	`82`	`throw e;`
`83`	`83`	`}`
`@@ -98,7 +98,7 @@ public static ValidationReport validate(Sail dataRepo, Sail shapesRepo) {`
`98`	`98`	`return performValidation(shapes, new ConnectionsGroup(verySimpleRdfsBackwardsChainingConnection, null,`
`99`	`99`	`null, null, new Stats(), () -> reasoner,`
`100`	`100`	`new ShaclSailConnection.Settings(true, true, true, IsolationLevels.NONE), true));`
`101`		`- } catch (Exception e) {`
	`101`	`+ } catch (Throwable e) {`
`102`	`102`	`logger.warn("Failed to validate shapes", e);`
`103`	`103`	`throw e;`
`104`	`104`	`}`
Original file line number	Diff line number	Diff line change
`@@ -81,7 +81,7 @@ private void evaluateLazyAspect() {`
`81`	`81`	`validationResultIterators = null;`
`82`	`82`
`83`	`83`	`}`
`84`		`- } catch (Exception e) {`
	`84`	`+ } catch (Throwable e) {`
`85`	`85`	`logger.warn("Error evaluating lazy validation report", e);`
`86`	`86`	`throw e;`
`87`	`87`	`}`
`@@ -104,7 +104,7 @@ public Model asModel(Model model) {`
`104`	`104`	`}`
`105`	`105`
`106`	`106`	`return model;`
`107`		`- } catch (Exception e) {`
	`107`	`+ } catch (Throwable e) {`
`108`	`108`	`logger.warn("Error converting validation report to model", e);`
`109`	`109`	`throw e;`
`110`	`110`	`}`