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ANY23-611 -- general upgrades #321

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6c35682
ANY23-611 -- general upgrades
tballison May 24, 2023
615c580
ANY23-611 -- general upgrades - fix javadoc
tballison May 24, 2023
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3 changes: 2 additions & 1 deletion cli/pom.xml
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Expand Up @@ -360,7 +360,8 @@
<bundledSignature>jdk-reflection</bundledSignature>
<bundledSignature>jdk-internal</bundledSignature>
<!--bundledSignature>jdk-system-out</bundledSignature-->
<bundledSignature>commons-io-unsafe-${commons-io.version}</bundledSignature>
<bundledSignature>commons-io-unsafe-2.11.0</bundledSignature>
<!-- revert to this once forbiddenapis includes the latest <bundledSignature>commons-io-unsafe-${commons-io.version}</bundledSignature> -->
</bundledSignatures>
</configuration>
<executions>
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2 changes: 2 additions & 0 deletions cli/src/test/java/org/apache/any23/cli/MimeDetectorTest.java
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Expand Up @@ -17,6 +17,7 @@

package org.apache.any23.cli;

import org.junit.Ignore;
import org.junit.Test;

/**
Expand All @@ -31,6 +32,7 @@ public MimeDetectorTest() {
}

@Test
@Ignore("URL broken")
public void testDetectURL() throws Exception {
assumeOnlineAllowed();
runToolCheckExit0("http://twitter.com#micmos");
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2 changes: 2 additions & 0 deletions cli/src/test/java/org/apache/any23/cli/RoverTest.java
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Expand Up @@ -23,6 +23,7 @@
import org.apache.any23.util.URLUtils;
import org.junit.Assert;
import org.junit.Assume;
import org.junit.Ignore;
import org.junit.Test;
import org.eclipse.rdf4j.model.Statement;
import org.eclipse.rdf4j.rio.RDFFormat;
Expand Down Expand Up @@ -112,6 +113,7 @@ public void testDelegatingWriterFactory() throws Exception {
/* BEGIN: online tests. */

@Test
@Ignore("URLs are broken")
public void testRunMultiURLs() throws Exception {
// Assuming first accessibility to remote resources.
assumeOnlineAllowed();
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3 changes: 2 additions & 1 deletion core/src/main/java/org/apache/any23/extractor/yaml/YAMLExtractor.java
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Expand Up @@ -32,6 +32,7 @@
import org.eclipse.rdf4j.model.vocabulary.RDFS;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.yaml.snakeyaml.LoaderOptions;
import org.yaml.snakeyaml.Yaml;
import org.yaml.snakeyaml.constructor.SafeConstructor;

Expand All @@ -42,7 +43,7 @@ public class YAMLExtractor implements Extractor.ContentExtractor {

private final Logger log = LoggerFactory.getLogger(getClass());

private static final Yaml yml = new Yaml(new SafeConstructor());
private static final Yaml yml = new Yaml(new SafeConstructor(new LoaderOptions()));

private static final YAML vocab = YAML.getInstance();

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17 changes: 17 additions & 0 deletions core/src/main/java/org/apache/any23/rdf/Any23ValueFactoryWrapper.java
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Expand Up @@ -30,6 +30,7 @@
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.Value;
import org.eclipse.rdf4j.model.ValueFactory;
import org.eclipse.rdf4j.model.base.CoreDatatype;
import org.eclipse.rdf4j.model.vocabulary.RDF;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
Expand Down Expand Up @@ -181,6 +182,22 @@ public Literal createLiteral(String pref, IRI value) {
return wrappedFactory.createLiteral(pref, value);
}

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@tballison tballison May 24, 2023

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I don't know what I'm doing here. This needs to be reviewed and fixed by someone who does.

@Override
public Literal createLiteral(String s, CoreDatatype coreDatatype) {
if (s == null) {
return null;
}
return wrappedFactory.createLiteral(s, coreDatatype);
}

@Override
public Literal createLiteral(String s, IRI iri, CoreDatatype coreDatatype) {
if (s == null) {
return null;
}
return wrappedFactory.createLiteral(s, iri, coreDatatype);
}

@Override
public Literal createLiteral(Date date) {
return wrappedFactory.createLiteral(date);
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2 changes: 1 addition & 1 deletion core/src/main/java/org/apache/any23/rdf/RDFUtils.java
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Expand Up @@ -391,7 +391,7 @@ public static BNode getBNode(String id) {
* @param s
* subject {@link org.eclipse.rdf4j.model.Resource}
* @param p
* predicate {@link org.eclipse.rdf4j.model.URI}
* predicate {@link org.eclipse.rdf4j.model.IRI}
* @param o
* object {@link org.eclipse.rdf4j.model.Value}
*
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2 changes: 2 additions & 0 deletions core/src/test/java/org/apache/any23/Any23Test.java
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Expand Up @@ -51,6 +51,7 @@
import org.apache.any23.writer.TripleHandlerException;
import org.apache.commons.io.IOUtils;
import org.junit.AssumptionViolatedException;
import org.junit.Ignore;
import org.junit.Test;
import org.eclipse.rdf4j.model.Statement;
import org.eclipse.rdf4j.repository.Repository;
Expand Down Expand Up @@ -286,6 +287,7 @@ protected int getSoTimeout() {
* if there is an error defining input URI's
*/
@Test
@Ignore("URL no longer works")
public void testGZippedContent() throws IOException, URISyntaxException, ExtractionException {
assumeOnlineAllowed();
final Any23 runner = new Any23();
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95 changes: 78 additions & 17 deletions pom.xml
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Expand Up @@ -21,7 +21,7 @@
<parent>
<groupId>org.apache</groupId>
<artifactId>apache</artifactId>
<version>26</version>
<version>29</version>
</parent>

<groupId>org.apache.any23</groupId>
Expand Down Expand Up @@ -273,18 +273,18 @@
<implementation.build.tstamp>${maven.build.timestamp}</implementation.build.tstamp>
<project.build.outputTimestamp>1</project.build.outputTimestamp>

<httpclient.version>4.5.13</httpclient.version>
<httpcore.version>4.4.15</httpcore.version>
<owlapi.version>5.1.20</owlapi.version>
<rdf4j.version>3.7.4</rdf4j.version>
<httpclient.version>4.5.14</httpclient.version>
<httpcore.version>4.4.16</httpcore.version>
<owlapi.version>5.5.0</owlapi.version>
<rdf4j.version>4.3.1</rdf4j.version>
<semargl.version>0.7</semargl.version>
<log4j2.version>2.17.2</log4j2.version>
<log4j2.version>2.20.0</log4j2.version>
<slf4j.version>1.7.36</slf4j.version>
<tika.version>2.4.0</tika.version>
<openie_2.11.version>4.2.6</openie_2.11.version>
<openregex.version>1.1.1</openregex.version>
<jackson.version>2.13.1</jackson.version>
<commons-io.version>2.11.0</commons-io.version>
<jackson.version>2.14.3</jackson.version>
<commons-io.version>2.12.0</commons-io.version>
<velocity.version>1.7</velocity.version>

<!-- Overridden in profiles to add JDK specific arguments to surefire -->
Expand Down Expand Up @@ -320,7 +320,7 @@
<maven-gpg-plugin.version>3.0.1</maven-gpg-plugin.version>
<maven-invoker-plugin.version>3.2.2</maven-invoker-plugin.version>
<spotbugs-maven-plugin.version>4.7.0.0</spotbugs-maven-plugin.version>
<forbiddenapis.version>3.3</forbiddenapis.version>
<forbiddenapis.version>3.5.1</forbiddenapis.version>
<formatter-maven-plugin.version>2.18.0</formatter-maven-plugin.version>
<ossindex-maven-plugin.version>3.2.0</ossindex-maven-plugin.version>
<maven-enforcer-plugin.version>3.0.0</maven-enforcer-plugin.version>
Expand All @@ -346,6 +346,21 @@

<dependencyManagement>
<dependencies>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
Expand Down Expand Up @@ -379,7 +394,17 @@
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
<version>1.21</version>
<version>1.23.0</version>
</dependency>
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-model-api</artifactId>
<version>4.3.1</version>
</dependency>
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-model-vocabulary</artifactId>
<version>4.3.1</version>
</dependency>
<dependency>
<groupId>xerces</groupId>
Expand All @@ -389,12 +414,12 @@
<dependency>
<groupId>org.jsoup</groupId>
<artifactId>jsoup</artifactId>
<version>1.15.1</version>
<version>1.16.1</version>
</dependency>
<dependency>
<groupId>net.sf.biweekly</groupId>
<artifactId>biweekly</artifactId>
<version>0.6.6</version>
<version>0.6.7</version>
</dependency>

<!-- BEGIN: Tika -->
Expand Down Expand Up @@ -609,7 +634,7 @@
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-csv</artifactId>
<version>1.9.0</version>
<version>1.10.0</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
Expand Down Expand Up @@ -659,7 +684,7 @@
<dependency>
<groupId>org.yaml</groupId>
<artifactId>snakeyaml</artifactId>
<version>1.30</version>
<version>2.0</version>
</dependency>

<!-- BEGIN: Test Dependencies -->
Expand All @@ -672,7 +697,7 @@
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>4.5.1</version>
<version>5.3.1</version>
<scope>test</scope>
</dependency>
<!-- END: Test Dependencies -->
Expand Down Expand Up @@ -735,7 +760,18 @@
<tarLongFileMode>posix</tarLongFileMode>
</configuration>
</plugin>

<!--
mvn versions:display-plugin-updates
mvn versions:display-dependency-updates
-->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>versions-maven-plugin</artifactId>
<version>2.15.0</version>
<configuration>
<generateBackupPoms>false</generateBackupPoms>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>appassembler-maven-plugin</artifactId>
Expand Down Expand Up @@ -837,6 +873,30 @@
<!-- Remove once we upgrade to org.apache.tika:tika-parsers-standard-package:jar:2.3.0 -->
<exclude>af5f9c26-c09d-401f-a7fc-0785eeabeab3</exclude>
</excludeVulnerabilityIds>
<excludeCoordinates>
<!-- https://ossindex.sonatype.org/component/pkg:maven/com.google.guava/guava@30.1.1-jre?utm_source=ossindex-client&utm_medium=integration&utm_content=1.8.1 -->
<exclude>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>30.1.1-jre</version>
</exclude>
<exclude>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
<version>2.12.2</version>
</exclude>
<!-- remove these two when upgrading to Tika 2.8.0 -->
<exclude>
<groupId>org.apache.tika</groupId>
<artifactId>tika-core</artifactId>
<version>2.4.0</version>
</exclude>
<exclude>
<groupId>com.drewnoakes</groupId>
<artifactId>metadata-extractor</artifactId>
<version>2.17.0</version>
</exclude>
</excludeCoordinates>
</configuration>
<executions>
<execution>
Expand All @@ -863,7 +923,8 @@
<bundledSignature>jdk-reflection</bundledSignature>
<bundledSignature>jdk-internal-${javac.src.version}</bundledSignature>
<bundledSignature>jdk-system-out</bundledSignature>
<bundledSignature>commons-io-unsafe-${commons-io.version}</bundledSignature>
<bundledSignature>commons-io-unsafe-2.11.0</bundledSignature>
<!-- revert to this once forbiddenapis includes the latest <bundledSignature>commons-io-unsafe-${commons-io.version}</bundledSignature> -->
</bundledSignatures>
</configuration>
<executions>
Expand Down