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Merged
josemduarte merged 3 commits into from
Jan 5, 2024
Merged

Updated to Jakarta JAXB and Java 17 (ref: #1075) #1076

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d5ea96c
Updated to Jakarta JAXB and Java 17
hilbertglm Dec 29, 2023
171aef0
Changed the JDK back to Java 11 and reran tests
hilbertglm Jan 1, 2024
f0320f5
Removed explicit versioning for JAX-B API and runtime, except for the…
hilbertglm Jan 4, 2024
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7 changes: 5 additions & 2 deletions biojava-aa-prop/pom.xml
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Expand Up @@ -105,12 +105,15 @@
</dependency>

<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
<version>4.0.0</version>
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@josemduarte josemduarte Jan 3, 2024

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Please remove version here. It should be only in dependencyManagement in top pom.xml

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@hilbertglm hilbertglm Jan 4, 2024

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Removed explicit versions and scope from POM as required.

</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<version>4.0.3</version>
<scope>runtime</scope>
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@josemduarte josemduarte Jan 3, 2024

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Please remove version and scope here. It should be only in dependencyManagement in top pom.xml

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@hilbertglm hilbertglm Jan 4, 2024

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Removed explicit versions and scope from POM as required.

</dependency>
</dependencies>
</project>
2 changes: 1 addition & 1 deletion biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java
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import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;

import javax.xml.bind.JAXBException;
import jakarta.xml.bind.JAXBException;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Map;
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3 changes: 1 addition & 2 deletions biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java
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import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.xml.bind.JAXBException;
import jakarta.xml.bind.JAXBException;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Arrays;
Expand All @@ -37,7 +37,6 @@
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;
import java.util.stream.Stream;

/**
* This is an adaptor class which enable the ease of generating protein properties.
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6 changes: 3 additions & 3 deletions biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java
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import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Unmarshaller;
import jakarta.xml.bind.JAXBContext;
import jakarta.xml.bind.JAXBException;
import jakarta.xml.bind.Unmarshaller;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
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2 changes: 1 addition & 1 deletion biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java
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*/
package org.biojava.nbio.aaproperties.xml;

import javax.xml.bind.annotation.*;
import jakarta.xml.bind.annotation.*;
import java.util.List;

@XmlRootElement(name = "compoundcomposition", namespace ="http://biojava.org")
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8 changes: 4 additions & 4 deletions ...va-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java
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*/
package org.biojava.nbio.aaproperties.xml;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlRootElement;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlElement;
import jakarta.xml.bind.annotation.XmlRootElement;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
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8 changes: 4 additions & 4 deletions biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java
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*/
package org.biojava.nbio.aaproperties.xml;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlElement;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlAttribute;
import jakarta.xml.bind.annotation.XmlElement;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
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2 changes: 1 addition & 1 deletion biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java
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*/
package org.biojava.nbio.aaproperties.xml;

import javax.xml.bind.annotation.XmlRootElement;
import jakarta.xml.bind.annotation.XmlRootElement;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
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8 changes: 4 additions & 4 deletions biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java
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*/
package org.biojava.nbio.aaproperties.xml;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlAttribute;
import jakarta.xml.bind.annotation.XmlType;


@XmlType(name = "Iostope", propOrder = {"name","neutronsNum","mass"})
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6 changes: 3 additions & 3 deletions ...ava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java
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import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.xml.bind.ValidationEvent;
import javax.xml.bind.ValidationEventHandler;
import javax.xml.bind.ValidationEventLocator;
import jakarta.xml.bind.ValidationEvent;
import jakarta.xml.bind.ValidationEventHandler;
import jakarta.xml.bind.ValidationEventLocator;

public class MyValidationEventHandler implements ValidationEventHandler{

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6 changes: 3 additions & 3 deletions biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Name2Count.java
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*/
package org.biojava.nbio.aaproperties.xml;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlAttribute;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlAttribute;

@XmlAccessorType(XmlAccessType.FIELD)
public class Name2Count{
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2 changes: 1 addition & 1 deletion biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java
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*/
package org.biojava.nbio.aaproperties.xml;

import javax.xml.bind.SchemaOutputResolver;
import jakarta.xml.bind.SchemaOutputResolver;
import javax.xml.transform.Result;
import javax.xml.transform.stream.StreamResult;
import java.io.File;
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3 changes: 1 addition & 2 deletions biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java
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*/
package org.biojava.nbio.aaproperties;

import org.biojava.nbio.aaproperties.PeptideProperties;
import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.xml.bind.JAXBException;
import jakarta.xml.bind.JAXBException;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Map;
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4 changes: 1 addition & 3 deletions biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java
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*/
package org.biojava.nbio.aaproperties;

import org.biojava.nbio.aaproperties.PeptideProperties;
import org.biojava.nbio.aaproperties.Utils;
import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.xml.bind.JAXBException;
import jakarta.xml.bind.JAXBException;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Map;
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8 changes: 4 additions & 4 deletions biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/AminoAcidTest.java
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import org.biojava.nbio.aaproperties.PeptideProperties;
import org.junit.Test;

import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Marshaller;
import javax.xml.bind.Unmarshaller;
import jakarta.xml.bind.JAXBContext;
import jakarta.xml.bind.JAXBException;
import jakarta.xml.bind.Marshaller;
import jakarta.xml.bind.Unmarshaller;
import java.io.*;
import java.util.ArrayList;
import java.util.List;
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12 changes: 4 additions & 8 deletions biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/ElementTest.java
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*/
package org.biojava.nbio.aaproperties.xml;

import org.biojava.nbio.aaproperties.xml.Element;
import org.biojava.nbio.aaproperties.xml.ElementTable;
import org.biojava.nbio.aaproperties.xml.Isotope;
import org.biojava.nbio.aaproperties.xml.SchemaGenerator;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Marshaller;
import javax.xml.bind.Unmarshaller;
import jakarta.xml.bind.JAXBContext;
import jakarta.xml.bind.JAXBException;
import jakarta.xml.bind.Marshaller;
import jakarta.xml.bind.Unmarshaller;
import java.io.*;
import java.util.ArrayList;
import java.util.List;
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7 changes: 5 additions & 2 deletions biojava-core/pom.xml
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<artifactId>log4j-core</artifactId>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
<version>4.0.0</version>
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@josemduarte josemduarte Jan 3, 2024

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Please remove version here. It should be only in dependencyManagement in top pom.xml

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@hilbertglm hilbertglm Jan 4, 2024

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Removed explicit versions and scope from POM as required.

</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<version>4.0.3</version>
<scope>runtime</scope>
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Please remove version and scope here. It should be only in dependencyManagement in top pom.xml

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@hilbertglm hilbertglm Jan 4, 2024

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Removed explicit versions and scope from POM as required.

</dependency>
</dependencies>
</project>
7 changes: 5 additions & 2 deletions biojava-modfinder/pom.xml
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Expand Up @@ -54,12 +54,15 @@
<artifactId>log4j-core</artifactId>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
<version>4.0.0</version>
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Please remove version here. It should be only in dependencyManagement in top pom.xml

</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<version>4.0.3</version>
<scope>runtime</scope>
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Please remove version and scope here. It should be only in dependencyManagement in top pom.xml

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@hilbertglm hilbertglm Jan 4, 2024

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Removed explicit versions and scope from POM as required.

</dependency>
</dependencies>
<build>
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7 changes: 5 additions & 2 deletions biojava-protein-disorder/pom.xml
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Expand Up @@ -85,12 +85,15 @@
<artifactId>log4j-core</artifactId>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
<version>4.0.0</version>
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Please remove version here. It should be only in dependencyManagement in top pom.xml

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@hilbertglm hilbertglm Jan 4, 2024

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Removed explicit versions and scope from POM as required.

</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<version>4.0.3</version>
<scope>runtime</scope>
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Please remove version and scope here. It should be only in dependencyManagement in top pom.xml

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@hilbertglm hilbertglm Jan 4, 2024

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Removed explicit versions and scope from POM as required.

</dependency>
</dependencies>

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4 changes: 2 additions & 2 deletions biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/FastaSequence.java
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package org.biojava.nbio.data.sequence;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

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9 changes: 5 additions & 4 deletions biojava-structure/pom.xml
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<version>1.4.0</version>
</dependency>

<!-- JAXb explicit dependency is needed since Java 9. See https://stackoverflow.com/questions/43574426/how-to-resolve-java-lang-noclassdeffounderror-javax-xml-bind-jaxbexception-in-j
Note versions are set in parent pom in dependency management section -->
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
<version>4.0.0</version>
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Please remove version here. It should be only in dependencyManagement in top pom.xml

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@hilbertglm hilbertglm Jan 4, 2024

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Removed explicit versions and scope from POM as required.

</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<version>4.0.3</version>
<scope>runtime</scope>
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Please remove version and scope here. It should be only in dependencyManagement in top pom.xml

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@hilbertglm hilbertglm Jan 4, 2024

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Removed explicit versions and scope from POM as required.

</dependency>

<!-- Used for json deserialization in PDBStatus -->
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6 changes: 3 additions & 3 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Domain.java
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*/
package org.biojava.nbio.structure.domain.pdp;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlRootElement;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlRootElement;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
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6 changes: 3 additions & 3 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDescription.java
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*/
package org.biojava.nbio.structure.scop;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlRootElement;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlRootElement;
import java.io.Serializable;

/** Contains data from
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6 changes: 3 additions & 3 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java
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import java.util.List;
import java.util.Set;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlRootElement;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlRootElement;

import org.biojava.nbio.structure.PdbId;
import org.biojava.nbio.structure.ResidueRange;
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6 changes: 3 additions & 3 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopNode.java
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package org.biojava.nbio.structure.scop;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlRootElement;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlRootElement;
import java.io.Serializable;
import java.util.List;

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14 changes: 7 additions & 7 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java
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import javax.vecmath.Matrix3d;
import javax.vecmath.Matrix4d;
import javax.vecmath.Vector3d;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Marshaller;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
import jakarta.xml.bind.JAXBContext;
import jakarta.xml.bind.JAXBException;
import jakarta.xml.bind.Marshaller;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlRootElement;
import jakarta.xml.bind.annotation.adapters.XmlJavaTypeAdapter;

import java.io.ByteArrayOutputStream;
import java.io.PrintStream;
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java
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import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.xml.bind.JAXBException;
import jakarta.xml.bind.JAXBException;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
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