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#448 Update dependencies #449

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merged 5 commits into from
Nov 3, 2022
Merged

#448 Update dependencies #449

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0335e03
Issue 448 - Update dependencies
reckart Nov 3, 2022
17fea7a
Issue 448 - Update dependencies
reckart Nov 3, 2022
eb68d1e
Issue 448 - Update dependencies
reckart Nov 3, 2022
b94860b
Issue 448 - Update dependencies
reckart Nov 3, 2022
48d7022
Issue 448 - Update dependencies
reckart Nov 3, 2022
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10 changes: 6 additions & 4 deletions ...ht/src/main/java/org/cleartk/ml/tksvmlight/TkSvmLightBooleanOutcomeClassifierBuilder.java
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Expand Up @@ -53,9 +53,9 @@ public class TkSvmLightBooleanOutcomeClassifierBuilder
extends
TreeKernelSvmBooleanOutcomeClassifierBuilder<TreeKernelSvmBooleanOutcomeClassifier>{

static Logger logger = UIMAFramework.getLogger(TkSvmLightBooleanOutcomeClassifierBuilder.class);
static final Logger logger = UIMAFramework.getLogger(TkSvmLightBooleanOutcomeClassifierBuilder.class);

public static String COMMAND_ARGUMENT = "--executable";
public static final String COMMAND_ARGUMENT = "--executable";

/**
* Train a SVMTK classifier. Assumes the executable name is "tk_svm_learn". Note: this is public
Expand Down Expand Up @@ -90,7 +90,8 @@ public static void train(String filePath, String[] args) throws Exception {
process.waitFor();
}

public File getTrainingDataFile(File dir) {
@Override
public File getTrainingDataFile(File dir) {
return new File(dir, "training-data.svmlight");
}

Expand All @@ -107,7 +108,8 @@ private File getModelFile(File dir) {
* The arguments to be used by the tk_svm_classify command. Note: -t 5 is used to specify
* the use of Tree Kernels.
*/
public void trainClassifier(File dir, String... args) throws Exception {
@Override
public void trainClassifier(File dir, String... args) throws Exception {
File trainingDataFile = (dir.isDirectory() ? getTrainingDataFile(dir) : dir);
train(trainingDataFile.getPath(), args);
}
Expand Down
3 changes: 0 additions & 3 deletions cleartk-ml-tksvmlight/src/test/java/org/cleartk/ml/tksvmlight/RunTkSvmLightTest.java
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Expand Up @@ -50,7 +50,6 @@
import org.cleartk.test.util.DefaultTestBase;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;

import com.google.common.collect.Lists;
Expand Down Expand Up @@ -220,7 +219,6 @@ public void testTreeFeatures() throws Exception {
}
}

@Ignore
@Test
public void testTKSVMlight() throws Exception {
this.assumeTestsEnabled(COMMON_TESTS_PROPERTY_VALUE, TK_SVMLIGHT_TESTS_PROPERTY_VALUE);
Expand Down Expand Up @@ -265,7 +263,6 @@ public void testTKSVMlight() throws Exception {
}
}

@Ignore
@Test
public void testOVATKSVMlight() throws Exception {
this.assumeTestsEnabled(COMMON_TESTS_PROPERTY_VALUE, TK_SVMLIGHT_TESTS_PROPERTY_VALUE);
Expand Down
70 changes: 41 additions & 29 deletions cleartk-ml/pom.xml
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@@ -1,31 +1,43 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<artifactId>cleartk-ml</artifactId>
<packaging>jar</packaging>
<name>ClearTK ML</name>
<description>ClearTK machine learning library and interfaces</description>
<parent>
<artifactId>cleartk</artifactId>
<groupId>org.cleartk</groupId>
<version>2.1.0-SNAPSHOT</version>
<relativePath>..</relativePath>
</parent>
<dependencies>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-util</artifactId>
</dependency>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<artifactId>cleartk-ml</artifactId>
<packaging>jar</packaging>
<name>ClearTK ML</name>
<description>ClearTK machine learning library and interfaces</description>
<parent>
<artifactId>cleartk</artifactId>
<groupId>org.cleartk</groupId>
<version>2.1.0-SNAPSHOT</version>
<relativePath>..</relativePath>
</parent>
<dependencies>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-util</artifactId>
</dependency>

<!-- test only -->
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-test-util</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-document-annotation</artifactId>
<scope>test</scope>
</dependency>

</dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.assertj</groupId>
<artifactId>assertj-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-test-util</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-document-annotation</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
</project>
7 changes: 3 additions & 4 deletions cleartk-ml/src/test/java/org/cleartk/ml/jar/JarDataWriterTest.java
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Expand Up @@ -23,6 +23,7 @@
*/
package org.cleartk.ml.jar;

import static org.assertj.core.api.Assertions.assertThat;
import static org.junit.Assert.assertTrue;

import java.io.File;
Expand All @@ -37,7 +38,6 @@
import org.cleartk.ml.test.DefaultStringTestDataWriterFactory;
import org.cleartk.ml.test.StringTestDataWriter;
import org.cleartk.test.util.DefaultTestBase;
import org.junit.Assert;
import org.junit.Test;

/**
Expand All @@ -61,7 +61,8 @@ public void testManifest() throws Throwable {
dataWriter.finish();
File manifestFile = new File(outputDirectory, "MANIFEST.MF");
String actualManifest = FileUtils.file2String(manifestFile);
Assert.assertEquals(expectedManifest, actualManifest.replaceAll("\r", "").trim());

assertThat(actualManifest).isEqualToIgnoringWhitespace(expectedManifest);
}

@Test
Expand All @@ -75,7 +76,5 @@ public void testFinish() throws Throwable {
DataWriter<String> dataWriter = factory.createDataWriter();
dataWriter.finish();
assertTrue(new File(outputDirectory, FeaturesEncoder_ImplBase.ENCODERS_FILE_NAME).exists());

}

}
10 changes: 5 additions & 5 deletions cleartk-ml/src/test/java/org/cleartk/ml/viterbi/ViterbiDataWriterTest.java
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Expand Up @@ -24,6 +24,9 @@

package org.cleartk.ml.viterbi;

import static java.nio.charset.StandardCharsets.UTF_8;
import static org.assertj.core.api.Assertions.assertThat;
import static org.assertj.core.api.Assertions.contentOf;
import static org.junit.Assert.assertTrue;

import java.io.File;
Expand All @@ -33,7 +36,6 @@
import java.util.List;
import java.util.Set;

import org.apache.commons.io.FileUtils;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
Expand All @@ -52,7 +54,6 @@
import org.cleartk.test.util.DefaultTestBase;
import org.cleartk.test.util.type.Sentence;
import org.cleartk.test.util.type.Token;
import org.junit.Assert;
import org.junit.Test;

/**
Expand Down Expand Up @@ -118,8 +119,8 @@ public void testConsumeAll() throws Exception {
+ "classifierBuilderClass: org.cleartk.ml.viterbi.ViterbiClassifierBuilde\n" + " r";

File manifestFile = new File(outputDirectoryName, "MANIFEST.MF");
String actualManifest = FileUtils.readFileToString(manifestFile);
Assert.assertEquals(expectedManifest, actualManifest.replaceAll("\r", "").trim());
String actualManifest = contentOf(manifestFile, UTF_8);
assertThat(actualManifest).isEqualToIgnoringWhitespace(expectedManifest);

ViterbiClassifierBuilder<String> builder = new ViterbiClassifierBuilder<String>();
File delegatedOutputDirectory = builder.getDelegatedModelDirectory(outputDirectory);
Expand Down Expand Up @@ -166,5 +167,4 @@ private void testFeatures(String trainingDataLine, String... expectedFeatures) {
assertTrue(features.contains(expectedFeature));
}
}

}
180 changes: 94 additions & 86 deletions cleartk-timeml/pom.xml
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Original file line number Diff line number Diff line change
@@ -1,89 +1,97 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<artifactId>cleartk-timeml</artifactId>
<packaging>jar</packaging>
<name>ClearTK TimeML</name>
<description>ClearTK annotators for temporal information extraction</description>
<parent>
<artifactId>cleartk</artifactId>
<groupId>org.cleartk</groupId>
<version>2.1.0-SNAPSHOT</version>
<relativePath>..</relativePath>
</parent>
<dependencies>
<dependency>
<groupId>com.lexicalscope.jewelcli</groupId>
<artifactId>jewelcli</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-util</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-eval</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-ml</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-ml-liblinear</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-type-system</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-feature</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-corpus</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-token</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-snowball</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-opennlp-tools</artifactId>
</dependency>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<artifactId>cleartk-timeml</artifactId>
<packaging>jar</packaging>
<name>ClearTK TimeML</name>
<description>ClearTK annotators for temporal information extraction</description>
<parent>
<artifactId>cleartk</artifactId>
<groupId>org.cleartk</groupId>
<version>2.1.0-SNAPSHOT</version>
<relativePath>..</relativePath>
</parent>
<dependencies>
<dependency>
<groupId>com.lexicalscope.jewelcli</groupId>
<artifactId>jewelcli</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-util</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-eval</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-ml</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-ml-liblinear</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-type-system</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-feature</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-corpus</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-token</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-snowball</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-opennlp-tools</artifactId>
</dependency>

<!-- test only -->
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-test-util</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<plugins>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-test-util</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.xmlunit</groupId>
<artifactId>xmlunit-assertj3</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<plugins>
<!-- increase max memory for tests since models must be loaded -->
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<argLine>-Xmx512m</argLine>
</configuration>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>org.cleartk.timeml.TimeMLAnnotate</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<argLine>-Xmx512m</argLine>
</configuration>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>org.cleartk.timeml.TimeMLAnnotate</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
</project>
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