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RYA-534 Upgrade to RDF4J 3.2 and RYA-496 Upgrading to Accumulo 1.9.3 #315

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RYA-534 Upgrade to RDF4J 3.2 and RYA-496 Upgrading to Accumulo 1.9.3 #315

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1ba1402
RYA-534 Upgrade to RDF4J 3.2 and RYA-496 Upgrading to Accumulo 1.9.3
brushworth Jun 30, 2020
6bdd629
Replacing the old @Immutable annotation with @Contract(threading = Th…
brushworth Jul 14, 2020
dc8896d
RYA-534 Upgrade to RDF4J 3.4.4
brushworth Nov 16, 2020
db14378
Merge branch 'master' of github.com:apache/rya into RYA-534_rdf4j_squ…
brushworth Jan 8, 2021
6a988ac
RYA-534 The geoindexing profile needed some refactoring following its…
brushworth Jan 8, 2021
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1 change: 1 addition & 0 deletions common/rya.provenance/pom.xml
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Expand Up @@ -33,6 +33,7 @@ under the License.
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-runtime</artifactId>
<type>pom</type>
</dependency>

<dependency>
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2 changes: 1 addition & 1 deletion extras/indexing/pom.xml
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Expand Up @@ -70,7 +70,6 @@
<artifactId>httpclient</artifactId>
</dependency>


<!-- PCJ Indexing -->
<dependency>
<groupId>org.apache.rya</groupId>
Expand All @@ -84,6 +83,7 @@
<groupId>org.apache.rya</groupId>
<artifactId>rya.periodic.notification.api</artifactId>
</dependency>

<!-- RDF4J -->
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
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33 changes: 16 additions & 17 deletions extras/indexing/src/main/java/org/apache/rya/indexing/entity/model/Entity.java
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Expand Up @@ -18,7 +18,20 @@
*/
package org.apache.rya.indexing.entity.model;

import static java.util.Objects.requireNonNull;
import com.google.common.collect.ImmutableList;
import com.google.common.collect.ImmutableMap;
import com.google.common.collect.Maps;
import edu.umd.cs.findbugs.annotations.DefaultAnnotation;
import edu.umd.cs.findbugs.annotations.NonNull;
import edu.umd.cs.findbugs.annotations.Nullable;
import org.apache.http.annotation.Contract;
import org.apache.http.annotation.ThreadingBehavior;
import org.apache.log4j.Logger;
import org.apache.rya.api.domain.RyaIRI;
import org.apache.rya.indexing.entity.storage.EntityStorage;
import org.apache.rya.indexing.smarturi.SmartUriAdapter;
import org.apache.rya.indexing.smarturi.SmartUriException;
import org.eclipse.rdf4j.model.IRI;

import java.util.ArrayList;
import java.util.HashMap;
Expand All @@ -28,21 +41,7 @@
import java.util.Objects;
import java.util.Optional;

import org.apache.http.annotation.Immutable;
import org.apache.log4j.Logger;
import org.apache.rya.api.domain.RyaIRI;
import org.apache.rya.indexing.entity.storage.EntityStorage;
import org.apache.rya.indexing.smarturi.SmartUriAdapter;
import org.apache.rya.indexing.smarturi.SmartUriException;
import org.eclipse.rdf4j.model.IRI;

import com.google.common.collect.ImmutableList;
import com.google.common.collect.ImmutableMap;
import com.google.common.collect.Maps;

import edu.umd.cs.findbugs.annotations.DefaultAnnotation;
import edu.umd.cs.findbugs.annotations.NonNull;
import edu.umd.cs.findbugs.annotations.Nullable;
import static java.util.Objects.requireNonNull;

/**
* An {@link Entity} is a named concept that has at least one defined structure
Expand Down Expand Up @@ -74,7 +73,7 @@
* the {@link Type}, but nothing has explicitly indicated it is of that Type.
* Once something has done so, it is an explicitly typed Entity.
*/
@Immutable
@Contract(threading = ThreadingBehavior.IMMUTABLE)
@DefaultAnnotation(NonNull.class)
public class Entity {
private static final Logger log = Logger.getLogger(Entity.class);
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16 changes: 8 additions & 8 deletions extras/indexing/src/main/java/org/apache/rya/indexing/entity/model/Property.java
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Expand Up @@ -18,21 +18,21 @@
*/
package org.apache.rya.indexing.entity.model;

import static java.util.Objects.requireNonNull;
import edu.umd.cs.findbugs.annotations.DefaultAnnotation;
import edu.umd.cs.findbugs.annotations.NonNull;
import org.apache.http.annotation.Contract;
import org.apache.http.annotation.ThreadingBehavior;
import org.apache.rya.api.domain.RyaIRI;
import org.apache.rya.api.domain.RyaType;

import java.util.Objects;

import org.apache.http.annotation.Immutable;
import org.apache.rya.api.domain.RyaType;
import org.apache.rya.api.domain.RyaIRI;

import edu.umd.cs.findbugs.annotations.DefaultAnnotation;
import edu.umd.cs.findbugs.annotations.NonNull;
import static java.util.Objects.requireNonNull;

/**
* A value that has been set for an {@link TypedEntity}.
*/
@Immutable
@Contract(threading = ThreadingBehavior.IMMUTABLE)
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@DLotts DLotts Nov 11, 2020

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Explainer: https://dev-aux.com/java/org-apache-http-annotation-threadsafe-class-not-found

@DefaultAnnotation(NonNull.class)
public class Property {

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17 changes: 8 additions & 9 deletions extras/indexing/src/main/java/org/apache/rya/indexing/entity/model/Type.java
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Expand Up @@ -18,18 +18,17 @@
*/
package org.apache.rya.indexing.entity.model;

import static java.util.Objects.requireNonNull;

import java.util.Objects;

import org.apache.http.annotation.Immutable;
import com.google.common.collect.ImmutableSet;
import edu.umd.cs.findbugs.annotations.DefaultAnnotation;
import edu.umd.cs.findbugs.annotations.NonNull;
import org.apache.http.annotation.Contract;
import org.apache.http.annotation.ThreadingBehavior;
import org.apache.rya.api.domain.RyaIRI;
import org.apache.rya.indexing.entity.storage.TypeStorage;

import com.google.common.collect.ImmutableSet;
import java.util.Objects;

import edu.umd.cs.findbugs.annotations.DefaultAnnotation;
import edu.umd.cs.findbugs.annotations.NonNull;
import static java.util.Objects.requireNonNull;

/**
* Defines the structure of an {@link TypedEntity}.
Expand All @@ -44,7 +43,7 @@
* &lt;urn:nutritionalInformation>
* </pre>
*/
@Immutable
@Contract(threading = ThreadingBehavior.IMMUTABLE)
@DefaultAnnotation(NonNull.class)
public class Type {

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23 changes: 11 additions & 12 deletions extras/indexing/src/main/java/org/apache/rya/indexing/entity/model/TypedEntity.java
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Expand Up @@ -18,29 +18,28 @@
*/
package org.apache.rya.indexing.entity.model;

import static java.util.Objects.requireNonNull;
import com.google.common.collect.ImmutableCollection;
import com.google.common.collect.ImmutableMap;
import edu.umd.cs.findbugs.annotations.DefaultAnnotation;
import edu.umd.cs.findbugs.annotations.NonNull;
import edu.umd.cs.findbugs.annotations.Nullable;
import org.apache.http.annotation.Contract;
import org.apache.http.annotation.ThreadingBehavior;
import org.apache.rya.api.domain.RyaIRI;
import org.apache.rya.api.domain.RyaType;

import java.util.HashMap;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;

import org.apache.http.annotation.Immutable;
import org.apache.rya.api.domain.RyaType;
import org.apache.rya.api.domain.RyaIRI;

import com.google.common.collect.ImmutableCollection;
import com.google.common.collect.ImmutableMap;

import edu.umd.cs.findbugs.annotations.DefaultAnnotation;
import edu.umd.cs.findbugs.annotations.NonNull;
import edu.umd.cs.findbugs.annotations.Nullable;
import static java.util.Objects.requireNonNull;

/**
* A {@link TypedEntity} is a view of an {@link Entity} that has had a specific
* {@link Type} applied to it.
*/
@Immutable
@Contract(threading = ThreadingBehavior.IMMUTABLE)
@DefaultAnnotation(NonNull.class)
public class TypedEntity {

Expand Down
42 changes: 20 additions & 22 deletions extras/indexing/src/main/java/org/apache/rya/sail/config/RyaAccumuloSailConfig.java
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Expand Up @@ -20,16 +20,16 @@

import org.apache.rya.accumulo.AccumuloRdfConfiguration;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.Literal;
import org.eclipse.rdf4j.model.Model;
import org.eclipse.rdf4j.model.Resource;
import org.eclipse.rdf4j.model.Value;
import org.eclipse.rdf4j.model.ValueFactory;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.eclipse.rdf4j.model.util.GraphUtil;
import org.eclipse.rdf4j.model.util.GraphUtilException;
import org.eclipse.rdf4j.sail.config.AbstractSailImplConfig;
import org.eclipse.rdf4j.sail.config.SailConfigException;

import java.util.Set;

/**
* @deprecated Use {@link AccumuloRdfConfiguration} instead.
*/
Expand Down Expand Up @@ -117,9 +117,7 @@ public void validate() throws SailConfigException {
public Resource export(final Model model) {
final Resource implNode = super.export(model);

@SuppressWarnings("deprecation")
final
ValueFactory v = model.getValueFactory();
final ValueFactory v = SimpleValueFactory.getInstance();

model.add(implNode, USER, v.createLiteral(user));
model.add(implNode, PASSWORD, v.createLiteral(password));
Expand All @@ -136,27 +134,27 @@ public void parse(final Model model, final Resource implNode) throws SailConfigE
System.out.println("parsing");

try {
final Literal userLit = GraphUtil.getOptionalObjectLiteral(model, implNode, USER);
if (userLit != null) {
setUser(userLit.getLabel());
final Set<Value> userLit = model.filter(implNode, USER, null).objects();
if (userLit.size() == 1) {
setUser(userLit.iterator().next().stringValue());
}
final Literal pwdLit = GraphUtil.getOptionalObjectLiteral(model, implNode, PASSWORD);
if (pwdLit != null) {
setPassword(pwdLit.getLabel());
final Set<Value> pwdLit = model.filter(implNode, PASSWORD, null).objects();
if (pwdLit.size() == 1) {
setPassword(pwdLit.iterator().next().stringValue());
}
final Literal instLit = GraphUtil.getOptionalObjectLiteral(model, implNode, INSTANCE);
if (instLit != null) {
setInstance(instLit.getLabel());
final Set<Value> instLit = model.filter(implNode, INSTANCE, null).objects();
if (instLit.size() == 1) {
setInstance(instLit.iterator().next().stringValue());
}
final Literal zooLit = GraphUtil.getOptionalObjectLiteral(model, implNode, ZOOKEEPERS);
if (zooLit != null) {
setZookeepers(zooLit.getLabel());
final Set<Value> zooLit = model.filter(implNode, ZOOKEEPERS, null).objects();
if (zooLit.size() == 1) {
setZookeepers(zooLit.iterator().next().stringValue());
}
final Literal mockLit = GraphUtil.getOptionalObjectLiteral(model, implNode, IS_MOCK);
if (mockLit != null) {
setMock(Boolean.parseBoolean(mockLit.getLabel()));
final Set<Value> mockLit = model.filter(implNode, IS_MOCK, null).objects();
if (mockLit.size() == 1) {
setMock(Boolean.parseBoolean(mockLit.iterator().next().stringValue()));
}
} catch (final GraphUtilException e) {
} catch (final Exception e) {
throw new SailConfigException(e.getMessage(), e);
}
}
Expand Down
1 change: 1 addition & 0 deletions extras/kafka.connect/api/pom.xml
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Expand Up @@ -68,6 +68,7 @@
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-runtime</artifactId>
<type>pom</type>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
Expand Down
2 changes: 1 addition & 1 deletion extras/periodic.notification/twill.yarn/pom.xml
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Expand Up @@ -43,7 +43,7 @@
<dependency>
<groupId>org.apache.twill</groupId>
<artifactId>twill-yarn</artifactId>
<version>0.12.0</version>
<version>${twill.version}</version>
</dependency>
<dependency>
<groupId>org.apache.rya</groupId>
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13 changes: 11 additions & 2 deletions extras/periodic.notification/twill/pom.xml
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Expand Up @@ -77,12 +77,12 @@

<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<artifactId>guava</artifactId> <!-- Twill runtime requires 11.0 < guava < 14.0. Rename the package in the maven-shade-plugin -->
</dependency>
<dependency>
<groupId>org.apache.twill</groupId>
<artifactId>twill-api</artifactId>
<version>0.12.0</version>
<version>${twill.version}</version>
</dependency>

<!-- Mark Accumulo Hadoop and Zookeeper as provided dependencies -->
Expand Down Expand Up @@ -165,6 +165,15 @@
<exclude>commons-logging:commons-logging</exclude>
<exclude>org.slf4j:slf4j-log4j12</exclude>
<exclude>log4j:log4j</exclude>

<!-- exclude signed jar that probably isn't needed anyway -->
<!-- Causes: org.codehaus.mojo:animal-sniffer-maven-plugin:1.16:check failed: Invalid signature file digest for Manifest main attributes -->
<exclude>org.locationtech.spatial4j:spatial4j</exclude>

<!-- https://rdf4j.org/release-notes/3.3.0/ -->
<exclude>com.fasterxml.jackson.core:jackson-annotations</exclude>
<exclude>com.fasterxml.jackson.core:jackson-core</exclude>
<exclude>com.fasterxml.jackson.core:jackson-databind</exclude>
</excludes>
</artifactSet>
</configuration>
Expand Down
5 changes: 3 additions & 2 deletions ...ort.accumulo/src/main/java/org/apache/rya/export/api/conf/AccumuloMergeConfiguration.java
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Expand Up @@ -18,14 +18,15 @@
*/
package org.apache.rya.export.api.conf;

import org.apache.http.annotation.Immutable;
import org.apache.http.annotation.Contract;
import org.apache.http.annotation.ThreadingBehavior;
import org.apache.rya.export.InstanceType;

/**
* Immutable configuration object to allow the MergeTool to connect to the parent and child
* databases for data merging.
*/
@Immutable
@Contract(threading = ThreadingBehavior.IMMUTABLE)
public class AccumuloMergeConfiguration extends MergeConfigurationDecorator {
/**
* Information needed to connect to the parent database
Expand Down
9 changes: 5 additions & 4 deletions ...ya.export/export.api/src/main/java/org/apache/rya/export/api/conf/MergeConfiguration.java
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Expand Up @@ -18,17 +18,18 @@
*/
package org.apache.rya.export.api.conf;

import static com.google.common.base.Preconditions.checkNotNull;

import org.apache.http.annotation.Immutable;
import org.apache.http.annotation.Contract;
import org.apache.http.annotation.ThreadingBehavior;
import org.apache.rya.export.DBType;
import org.apache.rya.export.MergePolicy;

import static com.google.common.base.Preconditions.checkNotNull;

/**
* Immutable configuration object to allow the MergeTool to connect to the parent and child
* databases for data merging.
*/
@Immutable
@Contract(threading = ThreadingBehavior.IMMUTABLE)
public class MergeConfiguration {
/**
* Information needed to connect to the parent database
Expand Down
3 changes: 2 additions & 1 deletion extras/rya.forwardchain/pom.xml
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Expand Up @@ -33,7 +33,8 @@ under the License.
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-runtime</artifactId>
</dependency>
<type>pom</type>
</dependency>
<dependency>
<groupId>org.apache.rya</groupId>
<artifactId>rya.api</artifactId>
Expand Down
5 changes: 5 additions & 0 deletions extras/rya.giraph/pom.xml
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Expand Up @@ -105,5 +105,10 @@ under the License.
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
</project>
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