From 8241e97d6f68cec00b85c72c106849da3d829cc7 Mon Sep 17 00:00:00 2001
From: Joel Weiser <joel.weiser@oicr.on.ca>
Date: Sun, 16 Feb 2025 02:24:21 -0500
Subject: [PATCH 1/3] substitute javax.mail for Simple Java Mail

---
 pom.xml                                       |  9 ++--
 .../server/tools/indexer/util/MailUtil.java   | 48 +++++++++----------
 2 files changed, 27 insertions(+), 30 deletions(-)

diff --git a/pom.xml b/pom.xml
index c4559fa..14785c8 100644
--- a/pom.xml
+++ b/pom.xml
@@ -74,12 +74,9 @@
         </dependency>
         <!-- Mail Service -->
         <dependency>
-            <groupId>javax.mail</groupId>
-            <artifactId>javax.mail-api</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>com.sun.mail</groupId>
-            <artifactId>javax.mail</artifactId>
+            <groupId>org.simplejavamail</groupId>
+            <artifactId>simple-java-mail</artifactId>
+            <version>8.12.4</version>
         </dependency>
 
         <!--Logging: will transitively add logback core and slf4j-api-->
diff --git a/src/main/java/org/reactome/server/tools/indexer/util/MailUtil.java b/src/main/java/org/reactome/server/tools/indexer/util/MailUtil.java
index 998d2d0..e439835 100644
--- a/src/main/java/org/reactome/server/tools/indexer/util/MailUtil.java
+++ b/src/main/java/org/reactome/server/tools/indexer/util/MailUtil.java
@@ -2,29 +2,29 @@
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-
-import javax.mail.Message;
-import javax.mail.MessagingException;
-import javax.mail.Session;
-import javax.mail.Transport;
-import javax.mail.internet.InternetAddress;
-import javax.mail.internet.MimeMessage;
-import java.util.Properties;
+import org.simplejavamail.api.mailer.Mailer;
+import org.simplejavamail.email.Email;
+import org.simplejavamail.email.EmailBuilder;
+import org.simplejavamail.mailer.MailerBuilder;
 
 /**
- * Mail Utility class.
+ * Mail Utility class using Simple Java Mail.
+ *
+ * Note: If your SMTP server requires authentication,
+ * supply the username and password to withSMTPServer(...).
  *
- * @author Guilherme S. Viteri <gviteri@ebi.ac.uk>
  */
 public class MailUtil {
     private static final Logger logger = LoggerFactory.getLogger("importLogger");
     private static MailUtil mailUtil;
-    private Properties properties;
+    private final Mailer mailer;
 
     private MailUtil(String host, Integer port) {
-        properties = new Properties();
-        properties.setProperty("mail.smpt.host", host);
-        properties.setProperty("mail.smtp.port", String.valueOf(port));
+        // Configure the Mailer using the SMTP host and port.
+        // If no authentication is required, pass null for username and password.
+        this.mailer = MailerBuilder
+                .withSMTPServer(host, port, null, null)
+                .buildMailer();
     }
 
     public static MailUtil getInstance(String host, Integer port) {
@@ -35,17 +35,17 @@ public static MailUtil getInstance(String host, Integer port) {
     }
 
     public void send(String from, String to, String subject, String text) {
-        Session session = Session.getDefaultInstance(properties);
         try {
-            MimeMessage message = new MimeMessage(session);
-            message.setFrom(new InternetAddress(from));
-            message.addRecipient(Message.RecipientType.TO, new InternetAddress(to));
-            message.setSubject(subject);
-            message.setText(text);
-            Transport.send(message);
-        } catch (MessagingException e) {
-            logger.error("Error sending notification message");
+            Email email = EmailBuilder.startingBlank()
+                    .from(from)
+                    .to(to)
+                    .withSubject(subject)
+                    .withPlainText(text)
+                    .build();
+
+            mailer.sendMail(email);
+        } catch (Exception e) {
+            logger.error("Error sending notification message", e);
         }
     }
 }
-

From 448f900840b4ff637054f08e5c0c0a9e4f307d23 Mon Sep 17 00:00:00 2001
From: Joel Weiser <joel.weiser@oicr.on.ca>
Date: Sun, 16 Feb 2025 03:28:08 -0500
Subject: [PATCH 2/3] fixes email build

---
 .../reactome/server/tools/indexer/util/MailUtil.java | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/main/java/org/reactome/server/tools/indexer/util/MailUtil.java b/src/main/java/org/reactome/server/tools/indexer/util/MailUtil.java
index e439835..73c8f92 100644
--- a/src/main/java/org/reactome/server/tools/indexer/util/MailUtil.java
+++ b/src/main/java/org/reactome/server/tools/indexer/util/MailUtil.java
@@ -3,7 +3,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.simplejavamail.api.mailer.Mailer;
-import org.simplejavamail.email.Email;
+import org.simplejavamail.api.email.Email;
 import org.simplejavamail.email.EmailBuilder;
 import org.simplejavamail.mailer.MailerBuilder;
 
@@ -37,11 +37,11 @@ public static MailUtil getInstance(String host, Integer port) {
     public void send(String from, String to, String subject, String text) {
         try {
             Email email = EmailBuilder.startingBlank()
-                    .from(from)
-                    .to(to)
-                    .withSubject(subject)
-                    .withPlainText(text)
-                    .build();
+                .from(from)
+                .to(to)
+                .withSubject(subject)
+                .withPlainText(text)
+                .buildEmail();
 
             mailer.sendMail(email);
         } catch (Exception e) {

From 646e3721a0b10cd77501392770d31b5fffa44874 Mon Sep 17 00:00:00 2001
From: Joel Weiser <joel.weiser@oicr.on.ca>
Date: Sun, 16 Feb 2025 03:42:51 -0500
Subject: [PATCH 3/3] adds Jakarta Mail dependency for use by Simple Java Mail

---
 pom.xml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/pom.xml b/pom.xml
index 14785c8..b77705b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -78,6 +78,12 @@
             <artifactId>simple-java-mail</artifactId>
             <version>8.12.4</version>
         </dependency>
+        <dependency>
+            <groupId>com.sun.mail</groupId>
+            <artifactId>jakarta.mail</artifactId>
+            <version>2.0.1</version>
+        </dependency>
+
 
         <!--Logging: will transitively add logback core and slf4j-api-->
         <dependency>