refactor: migrate main app codebase to Jakarta EE 10

IQSS · Jun 28, 2023 · b51d2fc · b51d2fc
1 parent ed75148
commit b51d2fc
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diff --git a/src/main/java/edu/harvard/iq/dataverse/AbstractGlobalIdServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/AbstractGlobalIdServiceBean.java
@@ -3,8 +3,8 @@
 import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
 import edu.harvard.iq.dataverse.util.SystemConfig;
 import java.io.InputStream;
-import javax.ejb.EJB;
-import javax.inject.Inject;
+import jakarta.ejb.EJB;
+import jakarta.inject.Inject;
 import java.util.*;
 import java.util.logging.Level;
 import java.util.logging.Logger;

diff --git a/src/main/java/edu/harvard/iq/dataverse/AlternativePersistentIdentifier.java b/src/main/java/edu/harvard/iq/dataverse/AlternativePersistentIdentifier.java
@@ -3,14 +3,14 @@
 
 import java.io.Serializable;
 import java.util.Date;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
 
 /**
  *

diff --git a/src/main/java/edu/harvard/iq/dataverse/ApiTokenPage.java b/src/main/java/edu/harvard/iq/dataverse/ApiTokenPage.java
@@ -5,14 +5,14 @@
 import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import edu.harvard.iq.dataverse.api.Util;
-import java.sql.Timestamp;
+
 import java.util.ArrayList;
 import java.util.List;
 import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
 
 /**
  * @todo Rename this to ApiTokenFragment? The separate page is being taken out

diff --git a/src/main/java/edu/harvard/iq/dataverse/AuxiliaryFile.java b/src/main/java/edu/harvard/iq/dataverse/AuxiliaryFile.java
@@ -4,16 +4,16 @@
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import java.io.Serializable;
 import java.util.MissingResourceException;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.NamedNativeQueries;
-import javax.persistence.NamedNativeQuery;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.NamedNativeQueries;
+import jakarta.persistence.NamedNativeQuery;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
 
 /**
  *

diff --git a/src/main/java/edu/harvard/iq/dataverse/AuxiliaryFileServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/AuxiliaryFileServiceBean.java
@@ -14,19 +14,19 @@
 import java.util.ArrayList;
 import java.util.List;
 import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
-import javax.persistence.TypedQuery;
-import javax.ws.rs.ClientErrorException;
-import javax.ws.rs.InternalServerErrorException;
-import javax.ws.rs.ServerErrorException;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
+import jakarta.persistence.TypedQuery;
+import jakarta.ws.rs.ClientErrorException;
+import jakarta.ws.rs.InternalServerErrorException;
+import jakarta.ws.rs.ServerErrorException;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
 
 import org.apache.tika.Tika;
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/BannerMessage.java b/src/main/java/edu/harvard/iq/dataverse/BannerMessage.java
@@ -4,13 +4,13 @@
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import java.io.Serializable;
 import java.util.Collection;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.OneToMany;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.OneToMany;
 
 
 /**

diff --git a/src/main/java/edu/harvard/iq/dataverse/BannerMessageServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/BannerMessageServiceBean.java
@@ -10,10 +10,10 @@
 import java.util.Date;
 import java.util.List;
 import java.util.logging.Logger;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
 
 /**
  *

diff --git a/src/main/java/edu/harvard/iq/dataverse/BannerMessageText.java b/src/main/java/edu/harvard/iq/dataverse/BannerMessageText.java
@@ -6,13 +6,13 @@
 package edu.harvard.iq.dataverse;
 
 import java.io.Serializable;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
 
 /**
  *

diff --git a/src/main/java/edu/harvard/iq/dataverse/CitationServlet.java b/src/main/java/edu/harvard/iq/dataverse/CitationServlet.java
@@ -6,14 +6,14 @@
 package edu.harvard.iq.dataverse;
 
 import edu.harvard.iq.dataverse.pidproviders.PidUtil;
-import edu.harvard.iq.dataverse.util.StringUtil;
+
 import java.io.IOException;
-import java.io.PrintWriter;
-import javax.ejb.EJB;
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+
+import jakarta.ejb.EJB;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 
 /**
  *

diff --git a/src/main/java/edu/harvard/iq/dataverse/ConfigureFragmentBean.java b/src/main/java/edu/harvard/iq/dataverse/ConfigureFragmentBean.java
@@ -16,10 +16,10 @@
 
 import java.sql.Timestamp;
 import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
 import java.util.Date;
 
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/ControlledVocabAlternate.java b/src/main/java/edu/harvard/iq/dataverse/ControlledVocabAlternate.java
@@ -7,15 +7,15 @@
 
 import java.io.Serializable;
 import java.util.Objects;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
 
 /**
  *

diff --git a/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValue.java b/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValue.java
@@ -17,16 +17,16 @@
 import java.util.Objects;
 import java.util.logging.Logger;
 import java.util.MissingResourceException;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.Table;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.Table;
 
 /**
  *

diff --git a/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValueConverter.java b/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValueConverter.java
@@ -5,13 +5,13 @@
  */
 package edu.harvard.iq.dataverse;
 
-import javax.ejb.EJB;
-import javax.enterprise.inject.spi.CDI;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.inject.spi.CDI;
 
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.convert.Converter;
-import javax.faces.convert.FacesConverter;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.convert.Converter;
+import jakarta.faces.convert.FacesConverter;
 
 /**
  *

diff --git a/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValueServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValueServiceBean.java
@@ -6,11 +6,11 @@
 package edu.harvard.iq.dataverse;
 
 import java.util.List;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.TypedQuery;
 
 /**
  *

diff --git a/src/main/java/edu/harvard/iq/dataverse/CustomQuestion.java b/src/main/java/edu/harvard/iq/dataverse/CustomQuestion.java
@@ -1,7 +1,7 @@
 package edu.harvard.iq.dataverse;
 import java.io.Serializable;
 import java.util.List;
-import javax.persistence.*;
+import jakarta.persistence.*;
 import org.hibernate.validator.constraints.NotBlank;
 
 /**

diff --git a/src/main/java/edu/harvard/iq/dataverse/CustomQuestionResponse.java b/src/main/java/edu/harvard/iq/dataverse/CustomQuestionResponse.java
@@ -7,8 +7,8 @@
 
 import java.io.Serializable;
 import java.util.List;
-import javax.faces.model.SelectItem;
-import javax.persistence.*;
+import jakarta.faces.model.SelectItem;
+import jakarta.persistence.*;
 
 /**
  *

diff --git a/src/main/java/edu/harvard/iq/dataverse/CustomQuestionValue.java b/src/main/java/edu/harvard/iq/dataverse/CustomQuestionValue.java
@@ -1,7 +1,7 @@
 package edu.harvard.iq.dataverse;
 
 import java.io.Serializable;
-import javax.persistence.*;
+import jakarta.persistence.*;
 import org.hibernate.validator.constraints.NotBlank;
 
 /**

diff --git a/src/main/java/edu/harvard/iq/dataverse/CustomizationFilesServlet.java b/src/main/java/edu/harvard/iq/dataverse/CustomizationFilesServlet.java
@@ -14,13 +14,13 @@
 import java.io.PrintWriter;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import javax.servlet.ServletException;
-import javax.servlet.annotation.WebServlet;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.annotation.WebServlet;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
-import javax.ejb.EJB;
+import jakarta.ejb.EJB;
 import org.apache.commons.io.IOUtils;
 
 /**

diff --git a/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterCache.java b/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterCache.java
@@ -7,14 +7,14 @@
 
 
 import java.io.Serializable;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Lob;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Lob;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
 import org.hibernate.validator.constraints.NotBlank;
 
 /**

diff --git a/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java b/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java
@@ -18,11 +18,11 @@
 import java.util.Map;
 import java.util.logging.Level;
 import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.TypedQuery;
 
 import edu.harvard.iq.dataverse.settings.JvmSettings;
 import org.apache.commons.text.StringEscapeUtils;