Java 21, Tomcat 9

EuPathDB/pom.xml

@@ -79,7 +79,6 @@
       <groupId>org.apache.logging.log4j</groupId>
       <artifactId>log4j-core</artifactId>
     </dependency>
-
   </dependencies>
 
   <build>

EuPathDB/src/main/java/org/gusdb/oauth2/eupathdb/AccountDbAuthenticator.java

@@ -210,7 +210,7 @@ public String getNextGuestId() {
       String id = new AccountManager(_accountDb, _schema, USER_PROPERTY_DEFS).createGuestAccount("guest_").getUserId().toString();
       // FIXME: since this code directly accesses the DB, it should live in AccountManager;
       //   however that complicates FgpUtil releases prior to move to bearer tokens, so adding it here.
-      String sql = "insert into useraccounts.guest_ids (user_id, creation_time) values (?, TO_DATE(SYSDATE))";
+      String sql = "insert into useraccounts.guest_ids (user_id, creation_time) values (?, current_date)";
       int inserted = new SQLRunner(_accountDb.getDataSource(), sql, "insert-guest-id")
           .executeUpdate(new Object[]{ Long.valueOf(id) }, new Integer[]{ Types.BIGINT });
       if (inserted != 1) throw new IllegalStateException("Tried to insert duplicate guest ID " + id + ". Check ID sequence to make sure it is big enough.");

EuPathDB/src/main/java/org/gusdb/oauth2/eupathdb/BearerTokenGenerator.java

@@ -27,14 +27,15 @@ public class BearerTokenGenerator extends ToolBase {
   private static final String PROP_KEYSTORE_PASSPHRASE = "keyStorePassPhrase";
   private static final String PROP_ACCOUNTDB_LOGIN = "accountDbLogin";
   private static final String PROP_ACCOUNTDB_PASSWORD = "accountDbPassword";
+  private static final String PROP_DB_PLATFORM = "dbPlatform";
   private static final String PROP_USER_ID = "userId";
 
   public static void main(String[] args) throws Exception {
     new BearerTokenGenerator(args).execute();
   }
 
   public BearerTokenGenerator(String[] args) {
-    super(args, new String[] { PROP_KEYSTORE_FILE, PROP_KEYSTORE_PASSPHRASE, PROP_ACCOUNTDB_LOGIN, PROP_ACCOUNTDB_PASSWORD, PROP_USER_ID });
+    super(args, new String[] { PROP_KEYSTORE_FILE, PROP_KEYSTORE_PASSPHRASE, PROP_ACCOUNTDB_LOGIN, PROP_ACCOUNTDB_PASSWORD, PROP_USER_ID, PROP_DB_PLATFORM });
   }
 
   public void execute() throws Exception {
@@ -43,14 +44,16 @@ public void execute() throws Exception {
     String keyStorePassPhrase = findProp(PROP_KEYSTORE_PASSPHRASE);
     String accountDbLogin = findProp(PROP_ACCOUNTDB_LOGIN);
     String accountDbPassword = findProp(PROP_ACCOUNTDB_PASSWORD);
+    String platform = findProp(PROP_DB_PLATFORM);
     String userId = findProp(PROP_USER_ID);
 
     SigningKeyStore keyStore = new SigningKeyStore(new KeyPairReader().readKeyPair(Paths.get(keyStoreFile), keyStorePassPhrase));
+
     // dummy up a client; SigningKeyStore requires >0 but will not be used here
     keyStore.setClientSigningKeys("abc", Set.of("mug2kfCI8qhXzrnuE/nh1gK9JbSFaXaih+zdsfD8io25MWH4b3V5u+U8E7SW4x7iBAHdq6yWWrF/TP9p098lfQ=="));
 
     // generate a new token for this account
-    String token = generateToken(keyStore, accountDbLogin, accountDbPassword, userId);
+    String token = generateToken(keyStore, accountDbLogin, accountDbPassword, userId, platform);
     System.out.println("Bearer Token\n\n" + token + "\n");
 
     // verify token using same method as the client
@@ -71,13 +74,13 @@ public void execute() throws Exception {
     System.out.println("Subject after parsing token: " + claims.getSubject());
   }
 
-  private static String generateToken(SigningKeyStore keyStore, String accountDbLogin, String accountDbPassword, String userId) throws Exception {
+  private static String generateToken(SigningKeyStore keyStore, String accountDbLogin, String accountDbPassword, String userId, String dbPlatform) throws Exception {
 
     JsonObject authenticatorConfig = Json.createObjectBuilder()
         .add("login", accountDbLogin)
         .add("password", accountDbPassword)
         .add("connectionUrl", "jdbc:oracle:thin:@localhost:5011/acctdb.upenn.edu")
-        .add("platform", "Oracle")
+        .add("platform", dbPlatform)
         .add("poolSize", 1)
         .add("schema", "useraccounts.")
         .build();

EuPathDB/src/main/resources/log4j2.json

@@ -4,8 +4,8 @@
       "appender": [{
         "type": "RollingFile",
         "name": "oauth-log",
-        "fileName": "${sys:catalina.base}/logs/oauth/oauth.log",
-        "filePattern": "${sys:catalina.base}/logs/oauth/oauth.log.%i",
+        "fileName": "/opt/logs/tomcat/oauth/oauth.log",
+        "filePattern": "/opt/logs/tomcat/oauth/oauth.log.%i",
         "append": "true",
         "PatternLayout": { "pattern": "%-9r [%-5p] [%d{yyyy/MM/dd|HH:mm:ss}] - %C:%L - %m%n" },
         "Policies": {
@@ -15,8 +15,8 @@
       },{
         "type": "RollingFile",
         "name": "login-log",
-        "fileName": "${sys:catalina.base}/logs/oauth/logins.log",
-        "filePattern": "${sys:catalina.base}/logs/oauth/logins.log.%i",
+        "fileName": "/opt/logs/tomcat/oauth/logins.log",
+        "filePattern": "/opt/logs/tomcat/oauth/logins.log.%i",
         "append": "true",
         "PatternLayout": { "pattern": "%d{yyyy-MM-dd|HH:mm:ss} %m%n" },
         "Policies": {

EuPathDB/src/main/webapp/WEB-INF/web.xml

@@ -1,10 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<web-app
-  id="oauth" version="3.0"
-  xmlns="http://java.sun.com/xml/ns/javaee"
-  xmlns:web="http://java.sun.com/xml/ns/javaee/web-app_3_0.xsd"
-  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_3_0.xsd">
+<web-app version="4.0"
+    xmlns="http://xmlns.jcp.org/xml/ns/javaee"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee http://xmlns.jcp.org/xml/ns/javaee/web-app_4_0.xsd">
 
   <!-- Need to add this so connection pool to apicomm is shut down -->
   <listener>

Server/src/main/java/org/gusdb/oauth2/service/OAuthService.java

@@ -46,6 +46,7 @@
 import javax.ws.rs.core.Response;
 import javax.ws.rs.core.Response.ResponseBuilder;
 import javax.ws.rs.core.Response.Status;
+import javax.ws.rs.core.UriInfo;
 import javax.ws.rs.core.Variant;
 
 import org.apache.logging.log4j.LogManager;
@@ -100,6 +101,9 @@ private static enum LoginFormStatus { failed, error, accessdenied; }
   @Context
   private HttpHeaders _headers;
 
+  @Context
+  private UriInfo _uriInfo;
+
   @GET
   @Path(Endpoints.ASSETS + "{name:.+}")
   public Response getStaticFile(@PathParam("name") String name) {
@@ -147,8 +151,8 @@ public Response attemptLogin(
         AuthzRequest originalRequest = (formId == null ? null : session.clearFormId(formId));
         if (originalRequest == null) {
           // formId doesn't exist on this session; give user generic success page
-          return Response.seeOther(new URI(RESOURCE_PREFIX +
-              config.getLoginSuccessPage())).build();
+          String baseUri = _uriInfo.getBaseUri().toString().replace("http://", "https://");
+          return Response.seeOther(new URI(baseUri + RESOURCE_PREFIX + config.getLoginSuccessPage())).build();
         }
         authenticator.logSuccessfulLogin(loginName, validUserId.get(), originalRequest.getClientId(), originalRequest.getRedirectUri(), _request.getRemoteAddr());
         return OAuthRequestHandler.handleAuthorizationRequest(originalRequest, validUserId.get(), config.getTokenExpirationSecs());
@@ -262,7 +266,8 @@ private URI getLoginUri(String formId, String redirectUri, LoginFormStatus statu
     if (status != null) {
       queryString += (queryString.isEmpty() ? "" : "&") + "status=" + status.name();
     }
-    return new URI(RESOURCE_PREFIX + OAuthServlet.getApplicationConfig(_context).getLoginFormPage() +
+    String baseUri = _uriInfo.getBaseUri().toString().replace("http://", "https://");
+    return new URI(baseUri + RESOURCE_PREFIX + OAuthServlet.getApplicationConfig(_context).getLoginFormPage() +
         (queryString.isEmpty() ? "" : "?" + queryString));
   }