Merge branch 'master' of github.com:VEuPathDB/WDK

Model/lib/rng/wdkModel-config.rng

@@ -13,6 +13,17 @@
             <optional>
                 <attribute name="smtpPassword" />
             </optional>
+            <optional>
+                <attribute name="smtpTlsEnabled">
+                    <data type="boolean" />
+                </attribute>
+            </optional>
+            <optional>
+                <attribute name="smtpPort">
+                    <data type="unsignedShort" />
+                </attribute>
+            </optional>
+
             <optional>
                 <attribute name="webAppUrl" />
             </optional>

Model/src/main/java/org/gusdb/wdk/model/Utilities.java

@@ -217,18 +217,18 @@ public static void sendEmail(String smtpServer, String sendTos, String reply,
     String subject, String content, String ccAddresses, Attachment[] attachments) 
     throws WdkModelException {
       //  call the 8 parameter one
-      sendEmail(smtpServer, null, null, sendTos, reply, subject, content, ccAddresses, null, attachments);
+      sendEmail(smtpServer, null, null, sendTos, reply, subject, content, ccAddresses, null, attachments, 25, false);
   }
 
   public static void sendEmail(String smtpServer, String sendTos, String reply,
                                String subject, String content, String ccAddresses, String bccAddresses,
                                Attachment[] attachments) throws WdkModelException {
-    sendEmail(smtpServer, null, null, sendTos, reply, subject, content, ccAddresses, bccAddresses, attachments);
+    sendEmail(smtpServer, null, null, sendTos, reply, subject, content, ccAddresses, bccAddresses, attachments, 25, false);
   }
 
-  // sendEmail()  all 10 parameters
+  // sendEmail()  all 12 parameters
   public static void sendEmail(String smtpServer, String username, String password, String sendTos, String reply,
-    String subject, String content, String ccAddresses, String bccAddresses, Attachment[] attachments) throws WdkModelException {
+    String subject, String content, String ccAddresses, String bccAddresses, Attachment[] attachments, int smtpPort, boolean tlsEnabled) throws WdkModelException {
 
     LOG.debug("Sending message to: " + sendTos + ", bcc to: " + bccAddresses +
       ",reply: " + reply + ", using SMPT: " + smtpServer);
@@ -237,6 +237,14 @@ public static void sendEmail(String smtpServer, String username, String password
     Properties props = new Properties();
     props.put("mail.smtp.host", smtpServer);
     props.put("mail.debug", "true");
+    props.put("mail.smtp.port", smtpPort);
+
+    if (tlsEnabled) {
+      props.put("mail.smtp.starttls.enable","true");
+      props.put("mail.smtp.ssl.protocols", "TLSv1.2");
+      props.put("mail.smtp.ssl.trust", smtpServer);
+    }
+
     Authenticator auth = null;
 
     if (username != null && password != null) {

Model/src/main/java/org/gusdb/wdk/model/config/ModelConfig.java

@@ -14,7 +14,7 @@
 /**
  * An object representation of the {@code model-config.xml} file. It holds all the configuration information
  * for the WDK system.
- * 
+ *
  * @author Jerric
  */
 public class ModelConfig implements OAuthConfig, KeyStoreConfig {
@@ -53,6 +53,17 @@ public String getName() {
   private final Optional<String> _smtpPassword;
 
 
+  /**
+   * the SMTP port to connect to on SMTP server.
+   */
+  private final int _smtpPort;
+
+  /**
+   * Determines whether to use TLS when connecting to SMTP server.
+   */
+  private final boolean _smtpTlsEnabled;
+
+
   /**
    * the reply of the registration & recover password emails.
    */
@@ -155,8 +166,8 @@ public String getName() {
 
   public ModelConfig(String modelName, String projectId, Path gusHome, boolean caching, boolean useWeights,
       String paramRegex, Optional<Path> secretKeyFile, String secretKey, Path wdkTempDir, String webServiceUrl, String assetsUrl,
-      String smtpServer, Optional<String> smtpUser, Optional<String> smtpPassword, String supportEmail, List<String> adminEmails, String emailSubject,
-      String emailContent, ModelConfigUserDB userDB, ModelConfigAppDB appDB,
+      String smtpServer, Optional<String> smtpUser, Optional<String> smtpPassword, Integer smtpPort, boolean smtpTlsEnabled, String supportEmail,
+      List<String> adminEmails, String emailSubject, String emailContent, ModelConfigUserDB userDB, ModelConfigAppDB appDB,
       ModelConfigUserDatasetStore userDatasetStoreConfig, QueryMonitor queryMonitor,
       boolean monitorBlockedThreads, int blockedThreshold, AuthenticationMethod authenticationMethod,
       String oauthUrl, String oauthClientId, String oauthClientSecret, String changePasswordUrl,
@@ -185,6 +196,9 @@ public ModelConfig(String modelName, String projectId, Path gusHome, boolean cac
     _smtpServer = smtpServer;
     _smtpUserName = smtpUser;
     _smtpPassword = smtpPassword;
+    _smtpPort = smtpPort;
+    _smtpTlsEnabled = smtpTlsEnabled;
+
     _supportEmail = supportEmail;
     _adminEmails = adminEmails;
     _emailSubject = emailSubject;
@@ -221,7 +235,7 @@ public ModelConfig(String modelName, String projectId, Path gusHome, boolean cac
 
   /**
    * If it returns true, a monitoring thread will be turned on when webapp is initialized.
-   * 
+   *
    * @return
    */
   public boolean isMonitorBlockedThreads() {
@@ -230,7 +244,7 @@ public boolean isMonitorBlockedThreads() {
 
   /**
    * An report will be fired when the number of blocked threads reaches the threshold.
-   * 
+   *
    * @return
    */
   public int getBlockedThreshold() {
@@ -277,6 +291,14 @@ public Optional<String> getSmtpPassword() {
     return _smtpPassword;
   }
 
+  public int getSmtpPort() {
+    return _smtpPort;
+  }
+
+  public boolean isSmtpTlsEnabled() {
+    return _smtpTlsEnabled;
+  }
+
   /**
    * @return Returns the emailContent.
    */
@@ -317,9 +339,9 @@ public ModelConfigAppDB getAppDB() {
    * Returns a cached secret key, generated by encrypting the value in the
    * configured secret key file.  If the configured filename is null or the contents
    * of the file cannot be read for any reason, null is returned.
-   * 
+   *
    * Note: as of 8/12/24, you can alternatively directly set the secretKey in model-config.xml
-   * 
+   *
    * @return secret key
    */
   public String getSecretKey() {
@@ -444,7 +466,7 @@ public QueryMonitor getQueryMonitor() {
    * own cache behavior. if global caching is disabled, then caching on sqlQuery will always be disabled,
    * regardless of the individual setting on the query. Please note that this flag has no effect on
    * processQueries, which is always cached.
-   * 
+   *
    * @return whether global caching is turned on or not.
    */
   public boolean isCaching() {

Model/src/main/java/org/gusdb/wdk/model/config/ModelConfigBuilder.java

@@ -16,6 +16,7 @@
 public class ModelConfigBuilder {
 
   private static final Logger LOG = Logger.getLogger(ModelConfigBuilder.class);
+  private static final int DEFAULT_SMTP_PORT = 25;
 
   // basic model information
   private String _modelName;
@@ -40,6 +41,8 @@ public class ModelConfigBuilder {
   private String _smtpServer;
   private String _smtpUsername;
   private String _smtpPassword;
+  private Integer _smtpPort;
+  private boolean _smtpTlsEnabled;
   private String _supportEmail;
   private List<String> _adminEmails = Collections.emptyList();
   private String _emailSubject = "";
@@ -98,6 +101,7 @@ public ModelConfig build() throws WdkModelException {
     Optional<String> smtpUsername = Optional.ofNullable(_smtpUsername).filter(s -> !s.isBlank());
     Optional<String> smtpPassword = Optional.ofNullable(_smtpPassword).filter(s -> !s.isBlank());
     String smtpServer = _smtpServer == null ? "localhost" : _smtpServer;
+    int smtpPort = _smtpPort == null ? DEFAULT_SMTP_PORT : _smtpPort;
 
     return new ModelConfig(
 
@@ -124,6 +128,8 @@ public ModelConfig build() throws WdkModelException {
       smtpServer,
       smtpUsername,
       smtpPassword,
+      smtpPort,
+      _smtpTlsEnabled,
       _supportEmail,
       _adminEmails,
       _emailSubject,
@@ -214,6 +220,14 @@ public void setSmtpPassword(String smtpPassword) {
     _smtpPassword = smtpPassword;
   }
 
+  public void setSmtpPort(int smtpPort) {
+    _smtpPort = smtpPort;
+  }
+
+  public void setSmtpTlsEnabled(boolean smtpTlsEnabled) {
+    _smtpTlsEnabled = smtpTlsEnabled;
+  }
+
   /**
    * @param emailContent
    *          The emailContent to set.

Model/src/main/java/org/gusdb/wdk/model/user/UserPasswordEmailer.java

@@ -42,6 +42,8 @@ public void emailTemporaryPassword(User user, String password) throws WdkModelEx
     // Unwrap optionals here to maintain consistency with nullable arguments in Utilities.sendEmail method.
     String smtpUser = wdkModelConfig.getSmtpUserName().orElse(null);
     String smtpPass = wdkModelConfig.getSmtpPassword().orElse(null);
+    int smtpPort = wdkModelConfig.getSmtpPort();
+    boolean smtpTlsEnabled = wdkModelConfig.isSmtpTlsEnabled();
 
     // populate email content macros with user data
     String emailContent = wdkModelConfig.getEmailContent()
@@ -52,6 +54,6 @@ public void emailTemporaryPassword(User user, String password) throws WdkModelEx
         .replaceAll("\\$\\$" + EMAIL_MACRO_PASSWORD + "\\$\\$",
             Matcher.quoteReplacement(password));
 
-    Utilities.sendEmail(smtpServer, smtpUser, smtpPass, user.getEmail(), supportEmail, emailSubject, emailContent, null, null, new Attachment[]{});
+    Utilities.sendEmail(smtpServer, smtpUser, smtpPass, user.getEmail(), supportEmail, emailSubject, emailContent, null, null, new Attachment[]{}, smtpPort, smtpTlsEnabled);
   }
 }

Model/src/main/java/org/gusdb/wdk/model/user/UserReferenceFactory.java

@@ -29,9 +29,10 @@ class UserReferenceFactory {
 
   public static final String USER_SCHEMA_MACRO = "$$USER_SCHEMA$$";
   private static final String IS_GUEST_VALUE_MACRO = "$$IS_GUEST$$";
+  private static final String FIRST_ACCESS_MACRO = "$$FIRST_ACCESS$$";
 
   // types used by SQL returned by getInsertUserRefSql() below
-  private static final Integer[] INSERT_USER_REF_PARAM_TYPES = { Types.BIGINT, Types.TIMESTAMP };
+  private static final Integer[] INSERT_USER_REF_PARAM_TYPES = { Types.BIGINT };
 
   // SQL and types to select user ref by ID
   private static final String SELECT_USER_REF_BY_ID_SQL =
@@ -72,12 +73,13 @@ public int addUserReference(User user) throws WdkModelException {
     try {
       long userId = user.getUserId();
       boolean isGuest = user.isGuest();
-      Timestamp insertedOn = new Timestamp(new Date().getTime());
+      Date insertedOn = new Date();
       String sql = getInsertUserRefSql()
           .replace(USER_SCHEMA_MACRO, _userSchema)
-          .replace(IS_GUEST_VALUE_MACRO, _userDb.getPlatform().convertBoolean(isGuest).toString());
+          .replace(IS_GUEST_VALUE_MACRO, _userDb.getPlatform().convertBoolean(isGuest).toString())
+          .replace(FIRST_ACCESS_MACRO, _userDb.getPlatform().toDbDateSqlValue(insertedOn));
       return new SQLRunner(_userDb.getDataSource(), sql, "insert-user-ref")
-        .executeUpdate(new Object[]{ userId, insertedOn }, INSERT_USER_REF_PARAM_TYPES);
+          .executeUpdate(new Object[]{userId}, INSERT_USER_REF_PARAM_TYPES);
     }
     catch (SQLRunnerException e) {
       throw WdkModelException.translateFrom(e);
@@ -86,7 +88,7 @@ public int addUserReference(User user) throws WdkModelException {
 
   private String getInsertUserRefSql() {
     return "MERGE INTO " + USER_SCHEMA_MACRO + TABLE_USERS + " tgt " +
-        "USING (SELECT ? AS user_id, ? AS first_access, " + IS_GUEST_VALUE_MACRO + " AS is_guest" + _userDb.getPlatform().getDummyTable() + ") src " +
+        "USING (SELECT ? AS user_id, " + FIRST_ACCESS_MACRO + " AS first_access, " + IS_GUEST_VALUE_MACRO + " AS is_guest" + _userDb.getPlatform().getDummyTable() + ") src " +
         "ON (tgt." + COL_USER_ID + " = src.user_id) " +
         "WHEN NOT MATCHED THEN " +
         "INSERT (" + COL_USER_ID + ", " + COL_IS_GUEST + ", " + COL_FIRST_ACCESS + ") " +