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Update dependencies #280

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merged 8 commits into from
Oct 1, 2024
Merged

Update dependencies #280

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cc37010
bump some deps
bigerl Sep 16, 2024
12871fc
Replace json simple
nck-mlcnv Sep 18, 2024
a377939
Update jena
nck-mlcnv Sep 18, 2024
ace9fea
Remove trailing zeros from results
nck-mlcnv Sep 18, 2024
a1ea988
Revert changes of test
nck-mlcnv Sep 18, 2024
fea4394
Revert changes of test 2
nck-mlcnv Sep 18, 2024
91d02d8
Fix dependencies
nck-mlcnv Sep 20, 2024
28230b1
Fix dependencies 2
nck-mlcnv Sep 20, 2024
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61 changes: 34 additions & 27 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -41,12 +41,10 @@
<build.version>0</build.version>

<java.version>17</java.version>
<jena.version>4.2.0</jena.version>
<jena.version>5.1.0</jena.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compile.target>17</maven.compile.target>
<maven.compile.source>17</maven.compile.source>

<log4j.version>2.19.0</log4j.version>
</properties>

<distributionManagement>
Expand Down Expand Up @@ -76,38 +74,48 @@
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.4.14</version>
<version>1.5.6</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-jsr310</artifactId>
<version>2.17.2</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-yaml</artifactId>
<version>2.12.5</version>
<version>2.17.2</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-jsr310</artifactId>
<version>2.12.5</version>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
<version>2.17.2</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.17.2</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
<version>2.17.2</version>
</dependency>
<dependency>
<groupId>com.networknt</groupId>
<artifactId>json-schema-validator</artifactId>
<version>1.0.78</version>
</dependency>
<dependency>
<groupId>com.googlecode.json-simple</groupId>
<artifactId>json-simple</artifactId>
<version>1.1.1</version>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
<version>5.9.2</version>
<version>5.10.3</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.opencsv</groupId>
<artifactId>opencsv</artifactId>
<version>5.7.1</version>
<version>5.9</version>
</dependency>
<dependency>
<groupId>org.lz4</groupId>
Expand All @@ -117,7 +125,7 @@
<dependency>
<groupId>org.apache.hbase</groupId>
<artifactId>hbase-common</artifactId>
<version>2.5.5</version>
<version>2.6.0</version>
</dependency>
<dependency>
<groupId>com.beust</groupId>
Expand All @@ -127,13 +135,13 @@
<dependency>
<groupId>com.github.tomakehurst</groupId>
<artifactId>wiremock-jre8-standalone</artifactId>
<version>2.35.1</version>
<version>2.35.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents.client5</groupId>
<artifactId>httpclient5</artifactId>
<version>5.3</version>
<version>5.3.1</version>
</dependency>
</dependencies>

Expand All @@ -142,7 +150,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<version>3.13.0</version>
<configuration>
<source>17</source>
<target>17</target>
Expand All @@ -159,7 +167,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>3.1.2</version>
<version>3.3.1</version>
<configuration>
<argLine>-Xmx16384M</argLine>
</configuration>
Expand All @@ -169,7 +177,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.4.1</version>
<version>3.6.0</version>
<configuration>
<createDependencyReducedPom>false</createDependencyReducedPom>
<finalName>iguana</finalName>
Expand All @@ -195,17 +203,16 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.4.0</version>
<version>3.8.0</version>
<configuration>
<doclint>-html</doclint>
<reportOutputDirectory>javadoc/${revision}/</reportOutputDirectory>
<destDir></destDir>
</configuration>
</plugin>

<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>3.1.0</version>
<version>3.3.1</version>
<executions>
<execution>
<id>copy-resources</id>
Expand Down Expand Up @@ -239,7 +246,7 @@
<!-- needs to be correct version fitting to junit-jupiter -->
<groupId>org.junit.platform</groupId>
<artifactId>junit-platform-launcher</artifactId>
<version>1.9.2</version>
<version>1.10.3</version>
<scope>test</scope>
</dependency>
</dependencies>
Expand All @@ -248,7 +255,7 @@
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>1.6.0</version>
<version>3.4.1</version>
<executions>
<execution>
<id>run-script</id>
Expand Down Expand Up @@ -283,7 +290,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>3.1.2</version>
<version>3.2.5</version>
</plugin>
<plugin>
<groupId>org.graalvm.buildtools</groupId>
Expand Down
58 changes: 20 additions & 38 deletions src/main/java/org/aksw/iguana/cc/lang/impl/SaxSparqlJsonResultCountingParser.java
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Original file line number Diff line number Diff line change
@@ -1,20 +1,14 @@
package org.aksw.iguana.cc.lang.impl;

import com.fasterxml.jackson.core.JsonFactory;
import org.aksw.iguana.cc.lang.LanguageProcessor;
import org.json.simple.parser.ContentHandler;
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
import org.slf4j.Logger;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.List;

import static org.json.simple.parser.ParseException.ERROR_UNEXPECTED_EXCEPTION;

/**
* SAX Parser for SPARQL JSON Results.
Expand All @@ -30,22 +24,31 @@ public class SaxSparqlJsonResultCountingParser extends LanguageProcessor {

@Override
public LanguageProcessingData process(InputStream inputStream, long hash) {
var parser = new JSONParser();
var handler = new SaxSparqlJsonResultContentHandler();
try {
parser.parse(new BufferedReader(new InputStreamReader(inputStream, StandardCharsets.UTF_8)), handler);
if (handler.isAskResult())
return new BooleanResultData(hash, handler.booleanResult(), handler.links(), null);
return new ResultCountData(hash, handler.solutions(), handler.boundValues(), handler.variables(), handler.links(), null);
JsonFactory factory = new JsonFactory();
try (var parser = factory.createParser(inputStream)) {
while (parser.nextToken() != null) {
switch (parser.getCurrentToken()) {
case START_OBJECT -> handler.startObject();
case END_OBJECT -> handler.endObject();
case START_ARRAY -> handler.startArray();
case END_ARRAY -> handler.endArray();
case FIELD_NAME -> handler.startObjectEntry(parser.getCurrentName());
case VALUE_STRING, VALUE_NUMBER_INT, VALUE_NUMBER_FLOAT, VALUE_NULL -> handler.primitive(parser.getValueAsString());
case VALUE_TRUE, VALUE_FALSE -> handler.primitive(parser.getBooleanValue());
}
}
} catch (IOException e) {
throw new RuntimeException(e);
} catch (ParseException e) {
LOGGER.error("Error while parsing SPARQL XML Results.", e);
LOGGER.error("Error while parsing SPARQL JSON Results.", e);
return new ResultCountData(hash, -1, -1, null, null, e);
}

if (handler.isAskResult())
return new BooleanResultData(hash, handler.booleanResult(), handler.links(), null);
return new ResultCountData(hash, handler.solutions(), handler.boundValues(), handler.variables(), handler.links(), null);
}

private static class SaxSparqlJsonResultContentHandler implements ContentHandler {
private static class SaxSparqlJsonResultContentHandler {
// TODO: code is unnecessary complicated

private boolean headFound = false;
Expand All @@ -64,18 +67,6 @@ private static class SaxSparqlJsonResultContentHandler implements ContentHandler
private final List<String> variables = new ArrayList<>();
private final List<String> links = new ArrayList<>();


@Override
public void startJSON() {
}

@Override
public void endJSON() throws ParseException {
if (inResults || inBindings || inBindingsArray || !headFound || objectDepth != 0)
throw new ParseException(ERROR_UNEXPECTED_EXCEPTION, "SPARQL Json Response was malformed.");
}

@Override
public boolean startObject() {
objectDepth += 1;
if (inBindingsArray) {
Expand All @@ -87,7 +78,6 @@ public boolean startObject() {
return true;
}

@Override
public boolean endObject() {
switch (objectDepth) {
case 1:
Expand All @@ -104,15 +94,13 @@ public boolean endObject() {
return true;
}

@Override
public boolean startArray() {
if (objectDepth == 2 && inResults && inBindings && !inBindingsArray) {
inBindingsArray = true;
}
return true;
}

@Override
public boolean endArray() {
if (inVars)
inVars = false;
Expand All @@ -125,7 +113,6 @@ public boolean endArray() {
}


@Override
public boolean startObjectEntry(String key) {
switch (objectDepth) {
case 1 -> {
Expand Down Expand Up @@ -156,11 +143,6 @@ public boolean startObjectEntry(String key) {
return true;
}

@Override
public boolean endObjectEntry() {
return true;
}

public boolean primitive(Object value) {
if (inVars)
variables.add(value.toString());
Expand Down
9 changes: 0 additions & 9 deletions src/main/java/org/aksw/iguana/cc/lang/impl/SaxSparqlXmlResultCountingParser.java
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Original file line number Diff line number Diff line change
@@ -1,13 +1,6 @@
package org.aksw.iguana.cc.lang.impl;

import org.aksw.iguana.cc.lang.LanguageProcessor;
import org.aksw.iguana.cc.storage.Storable;
import org.aksw.iguana.commons.rdf.IPROP;
import org.aksw.iguana.commons.rdf.IRES;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.rdf.model.ResourceFactory;
import org.slf4j.Logger;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
Expand All @@ -22,8 +15,6 @@
import java.util.List;
import java.util.Objects;

import static org.json.simple.parser.ParseException.ERROR_UNEXPECTED_EXCEPTION;

/**
* SAX Parser for SPARQL XML Results.
* For correct SPARQL XML Results it returns the number of solutions, bound values, the names of the variables and links.
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/org/aksw/iguana/cc/metrics/impl/AvgQPS.java
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Expand Up @@ -22,7 +22,7 @@ public Number calculateTaskMetric(List<HttpWorker> workers, List<HttpWorker.Exec
.reduce(BigDecimal.ZERO, BigDecimal::add);

try {
return sum.divide(BigDecimal.valueOf(data.length), 10, RoundingMode.HALF_UP);
return sum.divide(BigDecimal.valueOf(data.length), 10, RoundingMode.HALF_UP).stripTrailingZeros();
} catch (ArithmeticException e) {
return BigDecimal.ZERO;
}
Expand All @@ -37,7 +37,7 @@ public Number calculateWorkerMetric(HttpWorker.Config worker, List<HttpWorker.Ex
}

try {
return sum.divide(BigDecimal.valueOf(data.length), 10, RoundingMode.HALF_UP);
return sum.divide(BigDecimal.valueOf(data.length), 10, RoundingMode.HALF_UP).stripTrailingZeros();
} catch (ArithmeticException e) {
return BigDecimal.ZERO;
}
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/org/aksw/iguana/cc/metrics/impl/NoQPH.java
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Expand Up @@ -21,7 +21,7 @@ public Number calculateTaskMetric(List<HttpWorker> workers, List<HttpWorker.Exec
final var sum = workers.stream()
.map(worker -> (BigDecimal) this.calculateWorkerMetric(worker.config(), data[(int) worker.getWorkerID()]))
.reduce(BigDecimal.ZERO, BigDecimal::add);
return sum;
return sum.stripTrailingZeros();
}

@Override
Expand All @@ -39,7 +39,7 @@ public Number calculateWorkerMetric(HttpWorker.Config worker, List<HttpWorker.Ex
BigDecimal tt = (new BigDecimal(BigInteger.valueOf(totalTime.toNanos()), 9)).divide(BigDecimal.valueOf(3600), 20, RoundingMode.HALF_UP);

try {
return successes.divide(tt, 10, RoundingMode.HALF_UP);
return successes.divide(tt, 10, RoundingMode.HALF_UP).stripTrailingZeros();
} catch (ArithmeticException e) {
return BigDecimal.ZERO;
}
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/org/aksw/iguana/cc/metrics/impl/PAvgQPS.java
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Expand Up @@ -26,7 +26,7 @@ public Number calculateTaskMetric(List<HttpWorker> workers, List<HttpWorker.Exec
.reduce(BigDecimal.ZERO, BigDecimal::add);

try {
return sum.divide(BigDecimal.valueOf(data.length), 10, RoundingMode.HALF_UP);
return sum.divide(BigDecimal.valueOf(data.length), 10, RoundingMode.HALF_UP).stripTrailingZeros();
} catch (ArithmeticException e) {
return BigDecimal.ZERO;
}
Expand All @@ -44,7 +44,7 @@ public Number calculateWorkerMetric(HttpWorker.Config worker, List<HttpWorker.Ex
}

try {
return sum.divide(BigDecimal.valueOf(data.length), 10, RoundingMode.HALF_UP);
return sum.divide(BigDecimal.valueOf(data.length), 10, RoundingMode.HALF_UP).stripTrailingZeros();
} catch (ArithmeticException e) {
return BigDecimal.ZERO;
}
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/aksw/iguana/cc/metrics/impl/PQPS.java
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Expand Up @@ -35,7 +35,7 @@ public Number calculateQueryMetric(List<HttpWorker.ExecutionStats> data) {
BigDecimal tt = (new BigDecimal(BigInteger.valueOf(totalTime.toNanos()), 9));

try {
return numberOfExecutions.divide(tt, 10, RoundingMode.HALF_UP);
return numberOfExecutions.divide(tt, 10, RoundingMode.HALF_UP).stripTrailingZeros();
} catch (ArithmeticException e) {
return BigDecimal.ZERO;
}
Expand Down
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